Quantitative Biology

Previous months:
2007 - 0702(1)
2010 - 1003(1) - 1004(1) - 1005(1) - 1008(1)
2011 - 1103(1) - 1106(1) - 1110(1) - 1112(1)
2012 - 1202(1) - 1204(2) - 1205(1) - 1210(1) - 1212(1)
2013 - 1302(3) - 1303(1) - 1304(3) - 1306(1) - 1308(1) - 1311(1)
2014 - 1403(3) - 1405(1) - 1408(1) - 1411(3) - 1412(1)
2015 - 1501(4) - 1502(5) - 1504(1) - 1505(1) - 1506(1) - 1508(1) - 1510(1) - 1511(1) - 1512(3)
2016 - 1601(1) - 1602(1) - 1604(1) - 1606(1) - 1607(3) - 1609(1) - 1610(1) - 1612(5)
2017 - 1701(2) - 1703(2) - 1704(6) - 1705(2) - 1706(1) - 1708(3) - 1709(4) - 1710(1) - 1711(3) - 1712(1)
2018 - 1801(2) - 1802(2) - 1803(1) - 1804(1) - 1808(2) - 1811(2) - 1812(2)
2019 - 1905(1) - 1906(1) - 1907(34) - 1911(2) - 1912(16)

Recent submissions

Any replacements are listed farther down

[156] viXra:1912.0058 [pdf] submitted on 2019-12-03 05:42:16

Population Structure, Fecundity and Morphological Characteristics of M. Vollenhovenii (Herklots, 1857) on Lower Volta River Basin Channel, Ghana

Authors: Eniade Abiodun Adeyemi, Odedeyi Dominic Olabode, Bello-Olusoji A Oluayo, Adebayo Olabode Thomas, Agyakwah Seth Koranteng
Comments: 11 Pages.

Population structure, fecundity and morphological characteristics of M. vollenhovenii were studied around Lower Volta River, Ghana subject to dirt of information on this prawn species around the study location. The most prominent morphological characteristics already documented for identification of this species was rostrum bearing 13-15 continuous teeth dorsally and 4-5 teeth on its ventral part. These morphological traits formed the principal components for identification in this study. Results showed that morphological traits on second pereiopods such as presence of spines, spinules, teeth borne within the fingers, and dense projections of setae-like features on telson and uropod were observed relevant for identification purposes. Other results revealed that maximum total length recorded in this study (150-155mm) was higher than total length ranges (≤125mm) documented for this species in earlier studies. Consequently, two adult’s classes of prawns were identified (old adult class 81-120mm; and young adults 31-80mm) and older class was observed to be more in catches than the younger prawns. Absolute fecundity revealed that oocytes estimation varied with respect to seasons, ages of prawns and body sizes of specimens examined. In conclusion, this study observed that M. vollenhovenii fishery is operating in a sustainable manner at the time of this study around the study location.
Category: Quantitative Biology

[155] viXra:1912.0056 [pdf] submitted on 2019-12-03 05:47:18

Bacteriological Quality of Kunu-Zaki Sold on the Streets of Owerri Metropolis, Nigeria

Authors: Anumudu I. C., Anumudu C. K.
Comments: 5 Pages.

Kunu-zaki is a nourishing non-alcoholic beverage widely consumed in Nigeria. There is no standardized method for its preparation thus production practices differ amongst retailers. This study was undertaken to evaluate the bacteriological quality of kunu drink retailed in major markets of Owerri metropolis, Nigeria. Triplicate samples were obtained from four markets in Owerri and a control sample prepared in the laboratory. Kunu drink was analysed using the standard pour plate procedure. The results obtained showed that total heterotrophic bacteria count, total coliform count and total Salmonella Shigella count ranged from 1.4 x 103 – 4.5 x 104 cfu/ml, 1.2 x 103 – 3.8 x 104 cfu/ml to 0.6 x 103 – 3.1 x 104 respectively. A total of 9 bacteria genera including Staphylococcus specie, E. coli, Enterobacter specie, Proteus specie, Citrobacter specie, Serratia specie, Lactobacillus specie, Salmonella specie and Streptococcus specie were isolated with the highest percentage frequency of occurrence recorded for Staphylococcus sp. (16.66%) indicating possible low hygiene of the kunu zaki producers. The bacteria genera isolated from kunu zaki sold in Owerri and their number constitute main concerns for public health as these can cause a variety of infections or food intoxications. Thus, there is a need to establish a system of monitoring of street vended kunu zaki to make sure that it is safe for consumption.
Category: Quantitative Biology

[154] viXra:1912.0053 [pdf] submitted on 2019-12-03 05:55:36

Quantum Entanglement in Theoretical Physics as a New Insight Into Cancer Biology

Authors: Sorush Niknamian, Spmayeh Zaminpira, Sprephanie Seneff
Comments: 12 Pages.

Quantum entanglement is a phenomenon in theoretical physics that happens when pairs or groups of particles are generated in such a way that the quantum state of each particle cannot be described independently of the others, even when the particles are separated by a large distance. Instead, a quantum state must be described for the system as a whole. Based on the theory of cancer as an evolutionary metabolic disease (Evolutionary Metabolic Hypothesis of Cancer or EMHC), the cancerous cells are eukaryotic cells with different metabolic rate from healthy cells due to the damaged or shut down mitochondria in them. Assuming each human eukaryotic cell as a particle and the whole body as a Quantum Entangled System (QES), is a new perspective on the description of cancer disease, and this link between theoretical physics and biological sciences in the field of cancer therapies can be a new insight into the cause, prevention and treatment of cancer. Additionally, this perspective admits the Lamarckian evolution in the understanding of the mentioned disease. We have presented each human eukaryotic cell containing mitochondria as a QES, and the whole body containing healthy and normal cells as a QES as well. The difference between the entropy of the healthy cells and cancer cells has also been mentioned in this research.
Category: Quantitative Biology

[153] viXra:1912.0052 [pdf] submitted on 2019-12-03 05:56:45

Variations of Biomass and Carbon Contents in Different Traits and Components of Herbaceous Species from Tropical Grassland

Authors: Preeti Verma, R. Sagar, Hariom Verma, Abhishek Rai, Pratibha Chaturvedi, Prem Pratap Singh, Kuldeep Kumar, Sandeep Kumar Singh
Comments: 32 Pages.

Grasslands play a critical role in the global storage of atmospheric carbon (C). Precise estimation of C contents in different plant components is essential to formulate a strategy for mitigating the atmospheric C. Biomass (B) and C of different herbaceous plant components at species, functional group and site levels from tropical grassland locating on the campus of Banaras Hindu University, Varanasi, India were estimated. For this; 117 herbaceous species just-before flowering were harvested. B and C contents for each species and component were measured and statistically analyzed. The measured C (g plant-1) across the components varied from 0.08 to 31.12. On gm-2 basis; it varied between 29 (leaf) and 49 (root). Plant components, species and functional groups in isolation caused significant differences in the measured C. In the present study; the C content of stem was greater than the leaf and root. The perennial, erect, leguminous and native traits had greater C than the others. Therefore, this observation revealed that the perennial, erect, leguminous and native plants could be a better option for reducing the atmospheric CO2 by capturing it and then converting into B through photosynthesis. Further, the fitted regression equation between the root and shoot for B and C could be used for the extrapolation of B and C of the root component based on the shoot component. The conservative field measurement methods may give precise data on B and C but are destructive to grassland, difficult, time-consuming, and costly to cover at large scale. Hence, the present work could be substantial for the estimation of root C based on shoot component.
Category: Quantitative Biology

[152] viXra:1912.0051 [pdf] submitted on 2019-12-03 05:57:47

Explaining the Benefits of Human Genome Patent

Authors: Shahima Akter Topu
Comments: 5 Pages.

Gene patenting has been facing backlash for decades now. Even Michael Crichton, science fiction novelist, as joined the bandwagon speaking against gene patent.1 Such hostility towards patents, the professional interests of academics, researchers and inventors are under the threat of losing their rights over the work they have done. The biotech industry can never be out of discoveries. With constant biological changes, new diseases are appearing and they have to dig deeper. However, not all progress is free. Rewarding the inventors is not at all unfair. This paper will demonstrate that (i) patents are a foundation of the industry. They need to innovate further progress. The reason patent law exists to protect the inventions for a limited period of time. The paper will also demonstrate that (ii) the social myths about gene patent are not really manifested in reality. It will discuss the argument against gene patenting and then will present counter arguments with empirical evidence whether the myths are really true.
Category: Quantitative Biology

[151] viXra:1912.0050 [pdf] submitted on 2019-12-03 05:58:46

Genetic and Environmental Factors in Skin Color Determination

Authors: Callixte Yadufashije, Rebero Samuel
Comments: 4 Pages.

The origin of skin color has been significantly a discussion of importance among human biology scientists, anthropologists and others interested in evolution of human skin color. Experience was done to chimpanzee and other primates shared almost the same characters with mankind, and this impressed scientists to know what makes difference in skin color among people. Different researches conducted to know the real cause of dark skin and light skin among people of the same origin. There are no other results found out of permanent variation happened to our ancestors based on geographical location. Environmental factors played a huge role in skin color determination. High UVR has been led to dark skin color and low production of UVR led to lightly skin. By natural selection genes responded to environmental conditions for a human to survive in his own environment. Melanin production came as a response to UVR to protect against consequence of UVR in low latitude regions. Depigmentation happened due migration from low latitude to high latitude regions and led lightly skinned color for our ancestors. Everyone has skin color due to ancestry antique geographical location.
Category: Quantitative Biology

[150] viXra:1912.0049 [pdf] submitted on 2019-12-03 05:59:43

Dormancy and Germination in Two Australian Native Species (Acacia Aneura and Rhodanthe Floribunda)

Authors: Paul Theophile Epee Misse
Comments: 5 Pages.

In the laboratory of plant physiology of the University of Queensland (Gatton Campus), a seed germination experiment was undertaken on seeds of two Australian native plant species – Rhodanthe floribundato and Acacia aneura. Most Acacia, including A. aneura exhibit a physical dormancy due to the waxy coat covering the seed. Comparably, just a few species of Rhodanthe are studied as to their dormancy. However, they are also known to present different forms of dormancy. To understand and describe these dormancy mechanisms, a seed germination experiment was conducted on Acacia aneura and Rhodanthe floribunda. This experiment will either add to the existing knowledge regarding these species’ dormancy or corroborate them. It is expected that both species display some form(s) of dormancy.
Category: Quantitative Biology

[149] viXra:1912.0044 [pdf] submitted on 2019-12-03 06:07:48

Study of Chorioamnionitis Among Women with Preterm Birth at Ruhengeri Referral Hospital

Authors: Callixte Yadufashije, Jasmine Umugwaneza, Cedrick Izere, Emmanuel Munyeshyaka, Thierry Habyarimana
Comments: 8 Pages.

Background: Chorioamnionitis is the association of microorganisms infection in fetal membrane, placental membrane and amniotic fluid. About 2 to 4% of chorioamnionitis occurs in full-term deliveries, but higher than this prevalence in preterm birth. Objectives: The objective of this study was to detect the most dominant bacteria of chorioamnionitis and evaluate correlation of the presence of microorganisms infection in placental membrane, fetal membrane and amniotic fluids in women with preterm birth. Methods: It was cross section study where 20 women with preterm premature rupture of membrane, premature rupture of membrane or preterm birth. By caesarean section or without caesarean section with a group of control of 10 women with term delivery. After delivery immediately the samples swab of amniotic fluid, fetal membrane and placenta membrane sample were placed in separate sterile container (swabs Stuart plastic) in the hospital, where it was stored at temperatures ranging between 8oC-20oC. Culture technique, gram staining and biochemical test were used to identify the microorganisms in this study at INES-Ruhengeri Microbiology laboratory. At the Ruhengeri Referral Hospital and analyzed according to INES Microbiology Laboratory standard operating procedures. Results: in 20 women with preterm birth, the most dominant mircoroganism was yeast 28.4% and mould 28.4%, other infections were caused by Escherichia coli, with 9.3%, Klebsiella species with 3.7%, Streptococcus species with 9.3%, Staphylococcus species with 9.3%, Candida albican with 11.7%. Those microorganisms show the association in fetal membrane, placenta membrane and amniotic fluid, of all women suspected to have chorioamnionitis. In 10 samples of control group, for women with term birth, same microorganisms were found like in fetal membrane were (Staphylococcus species 11%, mould 33%, and Yeast 56%), in placenta membrane were (Staphylococcus species 20%, mould 30%, Yeast 50%) and Amniotic fluid were (Staphylococcus species 0%, mould 33%, Yeast 67%). Conclusion: Chorioamnionitis can be in women with preterm birth or with term birth, untreated microorganism infections will cause a big problem of chorioamnionitis in pregnant women this will conduct to preterm morbidity and mortality.
Category: Quantitative Biology

[148] viXra:1912.0043 [pdf] submitted on 2019-12-03 06:09:43

Artificial Neural Network (Ann) and Regression Model for Predicting the Albumin to Globulin (A/g) Ratio in a Serum Protein Electrophoresis Test

Authors: Akshansh Mishra
Comments: 10 Pages.

Multiple myeloma affects the several parts of bodies such as the spine, skull, pelvis and ribs. The cause of multiple myeloma is not known properly. The poor prognoses is associated with most cancers creates a sense of urgency for the brains behind healthcare Artificial Intelligence (AI) research. AI is able to detect cancer and other diseases earlier than possible through standard diagnostic methods, which could be lifesaving for future patients. The main objective of the research paper is to predict the Albumin to Globulin (A/G) ratio obtained by the electrophoresis test by developing regression model and Artificial Neural Network (ANN) model. The results obtained showed that the Mean Square Error (MSE) obtained by ANN model is less than the MSE obtained by the regression model.
Category: Quantitative Biology

[147] viXra:1912.0042 [pdf] submitted on 2019-12-03 06:11:26

Susceptibility of Common Weeds and Cultivated Crops in Major Maize Growing Agroecological Zones of Uganda to Viruses Causing Maize Lethal Necrosis Disease

Authors: Mudde, B., Miano D. W., Olubayo, F. M., Asea, G., Kilalo, D.c., Kwemoi, D. B., Adriko, J., Ssekiwoko, F., Male, A., Kiggundu, A.
Comments: 14 Pages.

Maize lethal necrosis (MLN) disease is caused when maize plants become coinfected with Maize chlorotic mottle virus (MCMV) and potyviruses notably Sugarcane Mosaic Virus (SCMV). Apart from maize, little is known about susceptibility of weed species and cultivated crop species usually growing in proximity with maize to MLN viruses in Uganda. The common weeds and crop plants were mechanically inoculated with combined sap from MCMV and SCMV infected maize plants. Samples were tested for MLN causing viruses by Double Antibody Sandwich Enzyme-Linked Immunosorbent Assay (DAS-ELISA) and Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR). The weeds that were susceptibility to MCMV were Digitaria abyssinica, Eleusine africana and Roetboellia cochinchinensis; while those susceptible to SCMV were Pennisetum purpureum, Panicum maximum and Roetboellia cochinchinensis. The cultivated crops were susceptible only to MCMV and included cassava (Manihot esculenta), groundnut (Arachis hypogaea) and bean (Phaseolus vulgaris). Common weeds and cultivated crops growing close to maize in Uganda have differential susceptibility to MLN causing viruses and can act as reservoirs of MLN causing viruses. It is critical to identify non MLN hosts in cultivated crops for crop rotation and early weeding to reduce on MLN virus inoculum in cropping systems.
Category: Quantitative Biology

[146] viXra:1912.0041 [pdf] submitted on 2019-12-03 06:13:08

Effect of Dietary Substitution of Maize Meal with Finger Millet Meal on Fat Deposition on Broiler Meat

Authors: Ndlovu, N., Usai, T., Usai, E., Manhokwe, S.
Comments: 9 Pages.

The aim of this study was to investigate the effect of a finger millet-based broiler feed on the meat quality of chicken. Proximate nutrient composition was analyzed on the finger millet meal and a feed formulated with finger millet as the main energy source. The feed was formulated on percent crude protein (CP) basis using Pearson square method. An experiment was designed and conducted on Ross Hybrid chickens to determine the effect of the feed on lean tissue development. A two-tailed t-test statistical analysis was conducted at a significance level of 5% to determine the effect of the feed on fat deposition and lean tissue development in broiler muscle. The finger millet feed increased mean lean tissue mass by 3.47%. This study showed that use of finger millet feed reduced the fat deposition and favored protein deposition in broiler muscle (increased leanness). This study also showed that finger millet feed significantly enhanced broiler growth performance. We concluded that finger millet has the potential to replace maize meal in broiler feed formulation in order to produce lean and healthier meat for consumers.
Category: Quantitative Biology

[145] viXra:1912.0040 [pdf] submitted on 2019-12-03 06:14:57

Phylogenetic and Morphological Diversity of Culturable Cyanobacteria from Lake Magadi in Kenya

Authors: Ngetha Edwin, Julia Khayeli Akhwale, Romano Mwirichia
Comments: 8 Pages.

Lake Magadi is an alkaline saline Lake in Kenya, which lies on the Great Eastern Rift valley. Although the lake is characterized by extremes of salt, pH and temperature, it supports diverse groups of cyanobacteria. In this study, we used different media to isolate novel groups of cyanobacteria. We recovered 11 isolates affiliated to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. Isolates affiliated to Chroococcidiopsis species had similarity values below 90% to currently characterized taxa indicating that these could be completely new phylotypes. This taxon has not been isolated before from the soda lake indicating the power of molecular techniques in identifying novel cyanobacterial taxa. Only two of the recovered isolates had 99% similarity to known organisms. Previous studies have mainly relied on microscopic examination and identification, which can lead to misidentification and subsequent assignment of an organism to the wrong taxon. The recovered isolates are a useful resource of more studies on taxonomy and secondary metabolite production.
Category: Quantitative Biology

[144] viXra:1912.0039 [pdf] submitted on 2019-12-03 06:16:46

Comparative Growth and Survival Performance of Sea Cucumber (Holothuria Scabra) in co-Cultured Pen System with Commercial Macroalgae

Authors: Muumin I. Hamad, Augustine W. Mwandya, Renalda S. Munubi, Sebastian Chenyambuga, Heiromin A. Lamtane.
Comments: 10 Pages.

Mariculture has recently been adopted in many parts of coastal East Africa as a source of income and employment to many women and heartbroken fishermen who are the main victim of dwindling wild stock of aquatic resources. The sea cucumber (Holothuria scabra) has for long time been collected and sold as export marine product. Macroalgae (Eucheuma denticulatum and Kappaphycus alvarezii) are the common cultured seaweed species that provide hope for future increase in mariculture production. An experiment was conducted along the intertidal lagoon of Unguja Ukuu village in Zanzibar to assess the survival and growth performance of sea cucumber (H. scabra) in two separate pens under co-cultured systems with E. denticulatum and K. alvarezii. Juvenile sea cucumber H. scabra with mean weight (± se) of 67.18 ± 2.06 were integrated with the two common commercial seaweed in pen system for 10 weeks. The results revealed that the growth rate and survival of H. scabra, E. denticulatum and K. alvarezii were better under integration system. The growth of H. scabra was higher (1.038 gd-1) in pen systems co-cultured with K. alvarezii compared to 0.898 gd-1 in pen systems co-culture with E. denticulatum. Survival rate of H. scabra was higher (76%) in the pen systems co-cultured with E. denticulatum compared to that (70%) observed in pen systems co-cultured with K. alvarezii. The results suggest that the best integration of sea cucumber and macroalgae is between H. scabra and K. alvarezii. However, reliable source of H. scabra juvenile is essential for the future expansion of pen co-culture system.
Category: Quantitative Biology

[143] viXra:1912.0038 [pdf] submitted on 2019-12-03 06:17:52

Influence of Mangrove Deforestation and Land Use Change on Trophic Organization of Fish Assemblages in Creek Systems

Authors: Augustine W. Mwandya
Comments: 15 Pages.

The impacts of human related activities on trophic structure of mangrove associated fish species, was investigated by sampling fish in mangrove creeks. Trophic organization and stable isotope signatures (δ13C and δ15N) of fish in undisturbed mangrove creeks were compared with clear-cut areas of mangrove and reservoirs for saltworks and fish farms constructed after mangrove clearing. Results showed significantly higher densities, species numbers, diversity (H’) and numbers of trophic groups in undisturbed sites compared to disturbed sites. Overall, omnivorous fish comprised the most abundant feeding guild, which dominated in the cleared sites followed in order by the uncleared sites and reservoirs. The zoobenthivores/piscivores was the most diverse group, with the highest species richness in the undisturbed areas. Multivariate analysis showed that assemblage structure of omnivores in the reservoirs was separated from those in uncleared and cleared sites, while zoobenthivores/piscivores differed between uncleared sites and disturbed areas. Stable isotope ratios of δ13C and δ15N values in fish muscles indicated significant diet shifts between undisturbed and disturbed mangrove creek systems, although the effects were species-specific. The findings suggest that mangrove deforestation combined with land-use changes, has a greater impact on the trophic structure of fish in mangrove creeks than mangrove deforestation only.
Category: Quantitative Biology

[142] viXra:1912.0037 [pdf] submitted on 2019-12-03 06:19:20

Determination Prevalence of Cymothoid Parasite Fish Families in Iwofe (Port Harcourt) Rivers State

Authors: Gloria Wonodi, Ugbomeh A.P., Gabriel U.U.
Comments: 10 Pages.

The aim of this study is to provide information on the morphology of the Cymothoid parasites of Haemulidae and Elopidae from Iwofe in Port Harcourt determine physico chemical parameter of study area. To determine the percentage prevalence of Cymothoid parasite of both fish families in the study area. To determine the species of the Cymothoid parasite in the study area. To compare the structure and morphology of the different life stages of the Cymothoids. A total of seventy six (76) fishes from Iwofe landing site were examined, forty six (46) fishes were infected with a prevalence of 68%, Pomadasys perotetei had (96.7%), Pomadasys jubelini had (57.1%), Clarias arius had (50%) and none was also isolated from Mugil curema. During the period of study no Elopidae was found in this station, samples were obtained only from Haemulidae. The fishermen said they do not always have that catch because of the kind of net they use in fishing the morphology of the Cymothoid parasites of Haemulidae and Elopidae and the sampling sites was Iwofe water side . The isolated parasite that was collected was Cymothoid parasites and they Cymothoid sodwana, Cymothoid pleibeia, Cymothoid spp1, Cymothoid spp2, Nerocila acuminata, Nerocila lomatia and Nerocila orbignyi. The physical chemical parameters of the water was analyzed and the result showed that there was a significant difference in salinity, Dissolved Oxygen (DO) and Electrical Conductivity (EC) across the sampling stations. Pomadasyidae had a higher prevalence of isopods than the other fish hosts and more than one type of parasite was found in the mouth while Elopidae had the parasite on their fins and body wall and none was recorded in the mouth. The cephalon, pereomeres, pleomeres, pleotelson, eyes and marsupium was different in the Cymothoids studied. The parasite also affected the condition of the fish.
Category: Quantitative Biology

[141] viXra:1912.0036 [pdf] submitted on 2019-12-03 06:20:24

Detection of Helicobacter Pylori Among Gastritis Patients Attending Nemba District Hospital

Authors: Callixte Yadufashije, Ange Yvette Uwitonze, Yvonne Manizabayo, Thierry Habyarimana
Comments: 8 Pages.

Background: Helicobacter pylori (H. pylori) is a small, spiral-shaped bacterium that lives in the surface of the stomach and duodenum. More than half of the world’s population is colonized with H. pylori in the gastric mucosa which is the major cause of chronic gastritis, peptic ulcer and also the most important etiological factor responsible for the duodenal and gastric ulcer and has an important role in the pathogenesis leading to gastric cancer. Objectives: The objectives of this study was to determine the prevalence of H. pylori among gastritis patients at Nemba district hospital, to compare sex prevalence level of H. pylori among gastritis patients and determine the prevalence of H. pylori among gastritis patients according to the age of gastritis patients. Methods: This study involved 140 patients with gastritis who attended Nemba district hospital from August to October 2018. The samples were collected and H. pylori rapid test strip was performed for all patients to diagnose H. pylori among gastritis patients. Results: Findings of the study showed that the prevalence of H. pylori infection was found to be significantly high among female participants than male participants. Despite high prevalence in females, the findings showed that there was no statistical significance of sex with H. pylori infection (χ2 = 0.6 and p > 0.05, p = 0.1). On basis of age, the prevalence of H. pylori infection was found to be high among participants and the prevalence increase between young age and old age. Results show that there was statistical significance between age and H. pylori infection with χ2 = 1.2 and p > 0.05, p = 0.04. the group of individuals with that ≥ 45 years old were more affected compared to other age groups and the prevalence of H. pylori infection was increased in older patients than younger patients. Our study showed an overall prevalence of H. pylori among gastritis patients was (45.7% n = 140). Conclusion: H. pylori infection is terrible burden of public health and affect people of all age and sex. H. pylori infection was significantly high in females and significance was found in age group of patients. Number of people are carrier of this terrible bacterium, thus hospitals are recommended to carry out early diagnosis to avoid later complication of infection.
Category: Quantitative Biology

[140] viXra:1911.0516 [pdf] submitted on 2019-11-29 21:13:33

Integrating Induction and Deduction in Order to Complement Experiments and Priors for the Understanding, Forecast, Control and Foresight of Apparently Complex Processes in Internet of Beings.

Authors: Diego Liberati
Comments: 12 Pages.

integrating inference and deductions
Category: Quantitative Biology

[139] viXra:1911.0088 [pdf] submitted on 2019-11-05 02:45:02

(Asea in DMD Conferinta Ramnicu Sarat 2.11.2019) Efectele Remarcabile Ale Suplimentului Redox "Asea"® în 2 Cazuri de Distrofie Musculară Duchenne la Copil și Potențialul Terapeutic al Asea în Bolile Acute și Cronice cu O Importantă Componentă de Stres

Authors: Andrei Lucian Dragoi
Comments: 45 Pages. https://www.researchgate.net/publication/336990483

TITLE IN ENGLISH: The remarkable effects of " >® redox supplement" (ARS) in 2 cases of Duchenne muscular dystrophy in children and the therapeutic potential of Asea / ARS in acute and chronic diseases with a significant component of cellular oxidative stress) ABSTRACT IN ENGLISH: This research aims at discovering dietary supplements which may show comparable or even stronger beneficial effects (with less or none adverse effects) than corticosteroids in children with Duchenne Muscular Dystrophy (DMD). This paper presents a case report on the effects of an ionized “saline water” called “ASEA redox Supplement®” (ARS) oral solution in a ~2-year-old boy with DMD from Bucharest, Romania. In vitro studies showed that ARS is a very potent selective NRF2 activator, thus a very potent (indirect) antioxidant: the studies conducted in vivo also support this main pharmacological mechanism of ARS, with no toxicity up to high doses, in contrast with the much more toxic corticosteroids. From the first months of ARS treatment all the rhabdomyolysis markers (with very high initial serum levels) dropped significantly, with no found toxicity. The main conclusions of this paper are: (1) ARS has remarkable antioxidant and immunomodulatory effects and should be studied on larger groups of children with DMD under the age of 4 years old (but also on other age groups of children and even young adults), as an alternative to early corticosteroids; (2) Given its immunomodulatory effect (NRF2 selective activation and NF-kB inhibition), ARS deserves future cohort studies on its potential to replace corticosteroids and other non-steroidal immunosuppressants (at least partially) in many types of pulmonary/renal/hepatic/ articular/skin autoimmune and even malignant diseases of both children and adults; (3) Given its very strong antioxidant effects (by highly selective NRF2 potent activation), ARS deserves future cohort studies on acute/chronic diseases that imply high levels of tissular oxidative stress, especially some acute/chronic cardiovascular and respiratory diseases like acute myocardial infarction with acute/chronic heart failure, stroke, Chronic Obstructive Pulmonary Disease (COPD), asthma etc. of both children and adults (so that ARS may help millions and even billions worldwide). Keywords: ASEA redox supplement (ARS) oral solution, 3-year-old boy, Duchenne muscular dystrophy (DMD), NRF2 selective activation, corticosteroids --------------------------------- REZUMATUL LUCRARII/PREZENTARII (Rezumatul lucrării/prezentării) Această cercetare își propune să descopere suplimente alimentare care pot demonstra efecte benefice comparabile sau chiar mai puternice (cu efecte adverse mai mici sau deloc) decât corticosteroizii la copiii cu distrofie musculară Duchenne (DMD). Această prezentare conține 2 raporturi de caz (în premieră mondială) asupra efectelor unei soluții saline ionizate (de uz intern oral) numite "supliment redox < >”® (SRA) la doi băieței cu DMD de 4 respectiv 5 ani, ambii din București. Studiile in vitro au arătat că Asea este un foarte potent activator selectiv al factorului de transcripție nucleară NRF2 (ce guvernează răspunsul anti-stress celular de fază B), deci un antioxidant foarte puternic (indirect): studiile efectuate in vivo până în prezent susțin și ele acest principal mecanism farmacologic de acțiune al Asea, fără toxicitate demonstrată in vivo chiar până la doze relativ mari, în contrast cu toate tipurile de corticosteroizi, care au toxicitate demonstrată pe multe aparate și sisteme. Încă din primele luni de tratament cu Asea, toți markerii de rabdomioliză (cu niveluri serice inițiale foarte mari, tipice pentru DMD) au scăzut semnificativ, fără nici un semn clinic și/sau paraclinic de toxicitate. PRINCIPALELE CONCLUZII ALE ACESTUI ARTICOL (Principalele concluzii ale acestei lucrări) sunt: (1) Asea are efecte antioxidante și imunomodulatoare remarcabile și merită studiată pe grupuri mai mari de copii cu DMD cu vârsta sub 4 ani (dar și pe alte grupe de vârstă de copii și chiar adulți tineri), ca alternativă la corticosteroizii administrați precoce încă de la vârsta de 2-3 ani (cu cel puțin 1 an înainte de vârsta standard de 4 ani actualmente unanim acceptată ca moment de inițiere corticoizi în DMD); (2) Având în vedere efectul său imunomodulator (activarea selectivă a NRF2 și inhibarea factorului de transcripție NF-kB, ce guvernează răspunsul anti-stress celular de fază A), Asea merită studii viitoare de cohortă asupra potențialului său de a înlocui (cel puțin parțial!) corticosteroizii și alte imunosupresoare nesteroidiene în multe tipuri de boli pulmonare / renale / hepatice / boli autoimune articulare / cutanate și chiar maligne ale copiilor și adulților; (3) Având în vedere efectele antioxidante foarte puternice (prin hiper-activare înalt selectivă a NRF2), Asea merită studii viitoare de cohortă în bolile acute / cronice care implică niveluri ridicate de stres oxidativ tisular/celular, în special unele boli cardiovasculare și respiratorii acute / cronice precum infarctul miocardic acut cu insuficiență cardiacă acută / cronică, accident vascular cerebral, boală pulmonară obstructivă cronică (BPOC), astm bronșic etc. atât la copii cât și la adulți (astfel încât Asea poate ajuta milioane și chiar miliarde de bolnavi la nivel mondial). Cuvinte-cheie: supliment redox Asea (SRA) soluție orală, distrofie musculară Duchenne (DMD), factorii de transcripție nucleară NRF2 și NF-kB, activare selectivă de NRF2, corticosteroizi More Info: www.dragoii.com
Category: Quantitative Biology

[138] viXra:1908.0282 [pdf] submitted on 2019-08-13 14:33:35

Possible Traces of Resonance Signaling in the Genome

Authors: Ivan Savelyev, Max Myakishev-Rempel
Comments: 11 Pages.

Although theories regarding the role of sequence-specific DNA resonance in biology have abounded for over 40 years, the published evidence for it is lacking. Here, the authors reasoned that for sustained resonance signaling, the number of oscillating DNA sequences per genome should be exceptionally high and that, therefore, genomic repeats of various sizes are good candidates for serving as resonators. Moreover, it was suggested that for the two DNA sequences to resonate, they do not necessarily have to be identical. Therefore, the existence of sequences differing in the primary sequence but having similar resonating sub-structures was proposed. It was hypothesized that such sequences, named HIDERs, would be enriched in the genomes of multicellular species. Specifically, it was hypothesized that delocalized electron clouds of purine-pyrimidine sequences could serve as the basis of HIDERs. The consequent genomic analysis confirmed the enrichment of purine-pyrimidine HIDERs in a few selected genomes of mammals, an insect, and a plant, compared to randomized sequence controls. Similarly, it was suggested that hypothetical delocalized proton clouds of the hydrogen bonds of multiple stacked bases could serve as sequence-dependent hydrogen-bond-based HIDERs. Similarly, the enrichment of such HIDERs was observed. It is suggested that these enrichments are the first evidence in support of sequence-specific resonance signaling in the genome.
Category: Quantitative Biology

[137] viXra:1907.0319 [pdf] submitted on 2019-07-16 16:42:09

Estudo Taxonômico da Tribo Cassieae (Leguminosae – Caesalpinioideae) no Parque Ecológico Engenheiro Ávidos, Cajazeiras–PB

Authors: Flávio Sousa Souto, Aclébia Alves Quaresma, Rubens Teixeira de Queiroz, Maria do Socorro Pereira
Comments: 21 Pages.

This work consists in a taxonomic study of the Tribe Cassieae in the Engenheiro Ávidos Ecological Park, Cajazeiras - Paraíba, carried out between February/2017 an April/2018. Twelve species were recorded in the area, distributed in two genera: Chamaecrista (6) and Senna (6). Among the species found, we highlight Chamaecrista pilosa, here cited as a new registry for the state of Paraíba and the occurrences of C. amiciella and C. duckeana, endemic species of the Caatinga. Analytical key for species identification, morphological descriptions and complementary information are presented. In this context, the relevant contribution of this study to the knowledge of the flora in the region is evidenced.
Category: Quantitative Biology

[136] viXra:1907.0318 [pdf] submitted on 2019-07-16 16:44:47

Lista Atualizada da Flora Vascular do Parque Nacional (Parna) Serra de Itabaiana, Sergipe, Brasil

Authors: Ana Cecília da Cruz Silva, Eduardo Vinícius da Silva Oliveira, Marccus Alves, Marta Cristina Vieira Farias, Aline da Costa Mota, Christopher Anderson Santos Souza, Ana Paula do Nascimento Prata
Comments: 28 Pages.

The Serra de Itabaiana National Park is located in an ecotone between Atlantic Rainforest and Caatinga biomes. It is one of the main areas of scientific studies in Sergipe. There are works approaching botanical families and listings of vascular flora. However, there is a need to update and compile the lists to better knowledge of the diversity of local flora. Therefore, a checklist was prepared from previous publications and Herbarium database of the Federal University of Sergipe (ASE). In total 124 families and 830 species of vascular plants were recorded distributed between Angiosperm (803 species), Ferns and Lycophytes (26) and Gymnosperms (1). The families of greater richness were: Fabaceae (73 species), Poaceae (65), Cyperaceae (59), Rubiaceae (40) and Asteraceae (36). The most representative habits were herbs (41.2%), shrubs (24.7%) and tree (17.6%). One hundred and seventy species are new occurrences for Sergipe, there is a new species for science, six rare species, three endangered species, nine almost endangered and three vulnerable, in addition there are 80 endemic species of the Atlantic Forest and 13 endemic to the Caatinga.
Category: Quantitative Biology

[135] viXra:1907.0317 [pdf] submitted on 2019-07-16 16:46:52

Estudo Taxonômico Das Subfamílias Cercidoideae e Detarioideae (Leguminosae) no Parque Ecológico Engenheiro Ávidos, Sertão Paraibano

Authors: Flávio Sousa Souto, Aclébia Alves Quaresma, Anaine Batista Araruna, Rubens Teixeira de Queiroz, Maria do Socorro Pereira
Comments: 7 Pages.

The subfamilies Cercidoideae and Detarioideae represent the basal lineages among the Leguminosae. In this work it is reported the occurrence of three species in the Engenheiro Ávidos Ecological Park, being two members of Cercidoideae, Bauhinia cheilantha (Bong.) Steud. and B. pentandra (Bong.) D. Dietr. and one of Detarioideae, Tamarindus indica L. It is worth mentioning that B. pentandra occurs in Paraíba only in the municipalities that comprise the Sertão mesoregion, while B. cheilantha is distributed in all geographic regions of the state. Tamarindus indica is an exotic species, widely cultivated, due to its food potential. These floristic data are relevant because they contribute to the increase of the knowledge of the vegetal cover in the semiarid.
Category: Quantitative Biology

[134] viXra:1907.0299 [pdf] submitted on 2019-07-15 07:45:04

Fragmentação Florestal na Área de Proteção Ambiental de Tambaba, Paraíba, Brasil

Authors: Saara Souza Rodrigues, Cleber Salimon, Saulo Roberto de Oliveira Vital
Comments: 8 Pages.

One of the most fragmented ecosystems in Brazil is the Atlantic Rain Forest, due to centuries of deforestation along the coast which holds one of the world’s greatest biodiversity. Landscape metrics and shape can impact on border effect on patterns and processes of a forested ecosystem. In this paper, we map and characterize the forest fragmentation of the Tambaba Environmental Protection Area (APA), on the coast of Paraíba State, Brazil, using landscape metrics to verify the effectiveness of this protected area. We conducted a land cover classification (supervised classification by maximum likelyhood, RapidEye imagery) into two categories (1) forest and (2) non forest. Landscape metrics (number of fragments, total core area, proportion of core area, among others) were calculated using ArcGis extension Patch Analyst. From the APA’s total 11.550 ha, 2.200 ha were classified as forest (19%), distributed in 1.364 fragments of different sizes. Total core area varied from 1.470 (10 m border effect) to 370 ha (50 m border effect), dependending on edge effect distance, which provides a true conservation of only 13 to 3% of the total APA. These results point to the necessity of an intense and rigorous surveillance of the compliance with laws, as well as a rational and participatory management, through the APA’s management council and public agencies, in order to protect the remnant fragments.
Category: Quantitative Biology

[133] viXra:1907.0298 [pdf] submitted on 2019-07-15 07:48:04

Predation of Dermatonotus Muelleri (Anura, Microhylidae) by Guira Guira (Cuculiformes, Cuculidae) in the Coastline of the Sergipe State, Northeastern Brazil

Authors: Francis Luiz Santos Caldas, Bruno Jackson Melo de Almeida, Rafael Alves dos Santos
Comments: 4 Pages.

Predation can drive significant effect upon the community structure. However, the observation and documentation of this ecological interaction is occasional and yet scarce for many groups. Our goal here is to report the predation of Dermatonotus muelleri (Boettger, 1885) by Guira guira (Gmelin, JF, 1788). Because G. guira diet frequently includes small vertebrates we believe that this species may act as an important regulator of D. muelleri population. This predation report can input insights about the knowledge of interactions of Microhylidae Günther, 1858 (1843) members and others species.
Category: Quantitative Biology

[132] viXra:1907.0296 [pdf] submitted on 2019-07-15 07:52:04

Occurrence of Amblyomma Sp. (Acari: Ixodidae) in Tropidurus Hispidus (Spix, 1825) (Squamata: Tropiduridae) in Parque Nacional Serra de Itabaiana, Sergipe, Brazil

Authors: Daniel Oliveira Santana, Francis Luiz Santos Caldas, Lucas Barbosa de Queiroga Cavalcanti, Fabíola Fonseca Almeida Gomes, Bruno Duarte da Silva, Rafael Alves dos Santos, Renato Gomes Faria
Comments: 5 Pages.

Lizards are often parasitized by Acari species (mites and ticks). In this study we report the occurrence of a specimen of tick (Amblyomma sp.) parasitizing a juvenile individual of Tropidurus hispidus (Spix, 1825) in Parque Nacional Serra de Itabaiana (PNSI) in the state of Sergipe, northeastern Brazil.
Category: Quantitative Biology

[131] viXra:1907.0295 [pdf] submitted on 2019-07-15 07:53:59

Aranhas Epígeas de um Fragmento de Mata em área Urbana em Fortaleza, Ceará, Brasil

Authors: Raul Azevedo, Kamilla Gonçalves Menezes, Raissa Aguiar Barbosa, Joaquin Deusdedit Rocha Matos Neto, José Onofre Nascimento Monteiro, Alysson Guedes Coutinho, Luis Gonzaga Sales Júnior
Comments: 10 Pages.

Spiders are indicators of environment quality due fact of been sensible to environment changes. Their adaptions among the environment and their relations between vegetal communities make them have a special role in forest ecosystems. However, this relation makes spiders susceptible to effects of urban process and to defloration and ecosystem fragmentation process. A spider fauna survey was developed using 50 “pitfall traps”, annual sample process begun in 2010 and finished in 2011 (total samples = 600) in an urbanized patch. A total of 1238 individuals were collected, constituting 51 species belonged to 18 families which Zodariidae and Lycosidae were most abundant, and Salticidae and Theridiidae were the richest families. It´s also observed many rare species (Singletons and Doubletons). The richness estimators didn´t exhibit a trend do exhibit an asymptote and the relation between collected species and estimated species, suggesting more samples process also suggests a necessity of develop politics to preserve the local biodiversity.
Category: Quantitative Biology

[130] viXra:1907.0294 [pdf] submitted on 2019-07-15 07:55:39

Críticas ao “Tree Thinking”: Elucidando O Significado Das Relações Filogenéticas

Authors: Rafael Gomes de Souza
Comments: 15 Pages.

The “Tree Thinking” is regarded as the dominant methodology in current Systematic Biology. However, criticisms of the procedures carried out by it are diverse. Here the criticisms made by Fitzhugh regarding its philosophical basis and the consequences of such modifications are presented and defended. Thus, the present work aims to demonstrate that “Tree Thinking”, as it has been used, is incomplete because it does not recognize that phylogenetic relationships are of the causal type previously summarized in an explanatory sketch (cladogram). In addition, to support such an argument, a discussion on the definition and objectives of Systematic Biology and “Tree Thinking” is provided. As a result, it is possible to observe confusion between classifying and systematizing the knowledge by those who follow "Tree Thinking". In addition, “Tree Thinking” fails to provide causal explanations regarding the origin and fixation of the characteristics studied. In this way, “Tree Thinking” can be considered an incomplete practice within Systematic Biology and, therefore, the application of the proposals of Fitzhugh are recommended.
Category: Quantitative Biology

[129] viXra:1907.0293 [pdf] submitted on 2019-07-15 07:57:45

New Records and Geographic Distribution Map of Pseudopaludicola Pocoto (Anura: Leptodactylidae: Leiuperinae) in Northeastern Brazil

Authors: Charles de Sousa Silva, Igor Joventino Roberto, Robson Waldemar Ávila, Drausio Honorio Morais
Comments: 5 Pages.

We provide new records and an updated geographic distribution map of Pseudopaludicola pocoto Magalhães, Loebmann, Kokubum, Haddad & Garda, 2014 for the Brazilian states of Ceará, Rio Grande do Norte and Pernambuco. The present work helps to fill gaps in distribution of this recently described species in Caatinga Biome, which can be useful in future conservation plans.
Category: Quantitative Biology

[128] viXra:1907.0292 [pdf] submitted on 2019-07-15 07:59:27

O Status Ecológico Das Comunidades de Fungos Coprófilos

Authors: Francisco J. Simões Calaça, Jéssica Conceição Araújo, Solange Xavier-Santos
Comments: 7 Pages.

We discuss the ecological status of coprophilous fungi communities lato sensu, presenting key points to the definition of scientific hypothesis and future studies aiming to understand the ecological factors that modulate the coprophilous lifestyle’s choice by these fungi. We present a new scientific term (copromycodiversity) that better describes the magnitude of this group, considering the comprehensiveness of this fungal group, including the morphological, physiological and ecological diversities to a coprophilous fungi population recorded to a specific geographical region. Furthermore, we raised some questions related to the life cycle of these fungi, taking into account recent studies as well as the traditionally accepted assumption that supports the spore passage through animals’s gut to its growth and development on dung. We expect that future research would best define these communities, avoiding uncertainties about the definition of the coprophilous lifestyle, even that some species would growth on others substrates (fimicolous fungi), but still displaying some connection with its animal host (coprophilia). While we are waiting for future directions, new hypothesis must be planned and tested aiming the predictors that truly modulates the occurrence of coprophilous fungi in different environments.
Category: Quantitative Biology

[127] viXra:1907.0291 [pdf] submitted on 2019-07-15 08:01:27

Acidentes Causados Por Aranhas e Escorpiões no Estado do Ceará, Nordeste do Brasil: Casos Subnotificados e Superestimados Baseados na Distribuição Geográfica Das Espécies

Authors: Raul Azevedo, Francisco Roberto de Azevedo, Relrison Dias Ramalho, Paulo André Margonari Goldoni, Antonio Domingos Brescovit
Comments: 14 Pages.

The accidents caused by arachnids have increased its frequency along the years and the majority of accidents reports do not contain species identification, contributing to underreporting of data. In Ceará state, specific information about accidents with full notifications or accident description are scarce. In this present study, data about accidents involving spiders and scorpions in Ceará state from 2010 to 2015 period were correlated with geographic distribution based on data from main Brazilian scientific collections of arachnids. An increased number of accidents caused by spiders and scorpions was observed, mainly in 2013 for scorpions, and a constant number of municipalities reported scorpionic accidents to this period. According to Sistema de Informação de Agravos de Notificação - SINAN, in Ceará state, many cases were credited to Phoneutria sp., Loxosceles sp., and Latrodectus sp., whoever this occurrence is not correlated with their geographic distribution supported on arachnid collections data. Therefore, knowledge on species geographic distribution with public health significance combined with properly notified records can contribute to reduction of accidents numbers and development of politics aimed to public health.
Category: Quantitative Biology

[126] viXra:1907.0285 [pdf] submitted on 2019-07-15 13:29:00

Bats (Mammalia, Chiroptera) from an Area of Caatinga in Southwestern Bahia, Brazil

Authors: Fábio Soares, Patrício Adriano da Rocha, Stephen Ferrari, Thiago Acioli, James Prado Pinto-Sobrinho
Comments: 9 Pages.

The present study provides an inventory of the bat species recorded in the municipality of Caetité, in southwestern Bahia, Brazil. Sixty-eight individuals were captured, belonging to nine species and three families. The Jackknife 1 procedure estimated a species richness of 9.9. The phyllostomid bats were the most abundant, and Carollia perspicillata (Linnaeus, 1758) was captured most frequently. Our results are consistent with previous studies conducted in Bahia and the Caatinga, providing data on the local bat community structure. It also highlights the importance of rapid inventories for the understanding of the diversity and distribution of the bat fauna.
Category: Quantitative Biology

[125] viXra:1907.0284 [pdf] submitted on 2019-07-15 13:30:51

Note on bats (Mammalia, Chiroptera) in a Restinga area of Rio Grande do Norte, Brazil

Authors: Fábio Soares, Marcela Daher, Raul Perrelli, José Armando Torres Moreno, Stephen Ferrari
Comments: 5 Pages.

Currently, forty-one species of bats are known to occur in the restingas of Brazil. However, most studies on restingas’ bats are limited to the south and southeastern regions of Brazil, leaving the northeastern region with a gap of knowledge. The present article presents data on bats captured in three areas of restinga of the municipality of Tibau do Sul, Rio Grande do Norte, collected from a short-term sampling. Mist nets were used to capture bats near the ground and the water bodies. Were captured 38 individuals of six species and two families: five Phyllostomidae and one Molossidae. The bat Carollia perspicillata (Linnaeus, 1758) was the most abundant species. We present here the first list of bats captured in the restinga area for the Rio Grande do Norte State.
Category: Quantitative Biology

[124] viXra:1907.0283 [pdf] submitted on 2019-07-15 13:32:22

New Records of Albardia Furcata Van Der Weele, 1903 (Neuroptera, Ascalaphidae, Albardiinae) from Paraíba, with Notes on a Predator Species

Authors: Alessandre Pereira-Colavite, Izabela Souza Braga, Wellington Emanuel dos Santos
Comments: 5 Pages.

New records of the rare owlfly Albardia furcata van der Weele, 1903 are provided from the state of Paraiba, in the Caatinga and Atlantic Forest, including four new localities. A referential map is included to the recorded specimens. The first report of the predator fly Peckia (Sarcodexia) lambens (Wiedemann, 1830) on dead body of A. furcata is registered.
Category: Quantitative Biology

[123] viXra:1907.0282 [pdf] submitted on 2019-07-15 13:33:40

Papel Das Moscas (Insecta, Diptera) na Entomologia Forense

Authors: Wellington Emanuel dos Santos
Comments: 8 Pages.

This paper presents a brief review of the role of flies (Insecta, Diptera) in Forensic Entomology. Discussions on presence in human cadavers and vertebrate carcasses, Postmortem Interval (PMI) estimations, studies carried out in Brazil and other countries, families of forensic importance and biological, ecological and distribution aspects of the main species are presented.
Category: Quantitative Biology

[122] viXra:1907.0281 [pdf] submitted on 2019-07-15 13:36:23

Invasão Biológica Por Cryptostegia Madagascariensis: Uma Abordagem Voltada Para Estresses Abióticos

Authors: Jailma dos Santos de Medeiros, Francisco de Oliveira Mesquita, Leonaldo Alves de Andrade, Cleiton José de Oliveira, Edlânia Maria de Souza, Jânio Kleiber Camelo de Souza
Comments: 11 Pages.

The introduction, accidental or deliberate, of exotic species by different vectors is currently a major global changes, resulting in a number of local and global problems. Although not all introductions of non-native species have negative effects, many of the non-native species can have undesirable effects on biodiversity from the genetic level to the landscape. This work aimed to present the current knowledge on biological invasions by species and particularly on invasive Cryptostegia madagascariensis Bojer ex Decne. New introductions are made every year around the world and only a small part of these taxa become invasive, yet cause serious damage to ecosystems invaded. The success of weed plants is due to the intrinsic characteristics of these species that ensures the same competitive advantages with native species and the level of disruption in new niches which makes them totally supportive environments to establish new species and the emergence of monodominadas areas. In this context is C. madagascariensis, origin of climbing on the island of Madagascar in Africa, which was introduced in Brazil with ornamental purposes, becoming invasive in natural ecosystems, especially in riparian environments and humid lowlands, in the field of savanna and associated ecosystems.
Category: Quantitative Biology

[121] viXra:1907.0280 [pdf] submitted on 2019-07-15 13:38:03

Diversity and Community Composition of Marine Mollusks Fauna on a Mainland Island of the Coast of Paraná, Southern Brazil

Authors: Marcos de Vasconcellos Gernet, Eduardo Colley, Elizângela da Veiga Santos, Carlos João Birckolz
Comments: 11 Pages.

Farol Island is a continental island in the state of Paraná, southern Brazil. Due to its position in relation to the continent, three distinct environmental areas are observed: rocky shore area with open exposure to the sea (A); estuarine area (B); sandy beach area (C). Considering that the continental islands are excellent study models that reproduce the environmental conditions of the coastal zone in a smaller scale, the study aimed at surveying and researching the marine malacofauna on the Farol Island and comparing the diversity and shellfish composition. The sampling method was based on a monthly collection in three locations for two years (2011-2012). The survey found 91 species: 47 Gastropoda, 41 Bivalvia and three Scaphopoda. The highest abundance and species richness prevailed in environmental area A. The greatest equitability was observed in B and the highest dominance in C. There was a predominance of Gastropoda and Bivalvia in A, while the frequency of Scaphopoda did not vary among environments. The species composition of the three classes varied among the three areas. The variation of diversity and species composition in the three environments may be related to the natural characteristics of each side of the island, as salinity and wave action.
Category: Quantitative Biology

[120] viXra:1907.0279 [pdf] submitted on 2019-07-15 13:39:33

New Records of Two Species of Acanthocarpus Stimpson, 1871 (Crustacea: Decapoda: Calappidae) in Northeastern Brazil

Authors: Flavio de Almeida Alves-Jr., Ângela Ferreira Pereira, Marina de Sá Leitão Câmara de Araújo
Comments: 7 Pages.

The gladiator box crab of the genus Acanthocarpus Stimpson, 1871 has benthonic habits, occurring in continental shelf on gravel or muddy substrates with occurrence in all oceans, especially between 20-522 m depth. In this paper we report the occurrence of Acanthocarpus alexandri Stimpson, 1871 and A. bispinosus A. Milne-Edwards, 1880 from the Potiguar Basin (Rio Grande do Norte), located in the Brazilian northeast and increase the knowledge about the distributional aspects of this species from Brazilian coast.
Category: Quantitative Biology

[119] viXra:1907.0278 [pdf] submitted on 2019-07-15 13:42:16

Predation of Hemidactylus Mabouia (Sauria: Gekkonidae) by a Vine Snake Oxybelis Aeneus (Serpentes: Colubridae) in an Atlantic Forest Fragment, Northeastern Brazil

Authors: Lissa Dellefrate Franzini, Carmem Karime Bacalháo Pedro, Lucas Barbosa de Queiroga Cavalcanti, Daniel Oliveira Mesquita
Comments: 4 Pages.

Oxybelis aeneus (Wagler, 1824) is an arboreal snake species that is widely distributed in the American continent whose diet is composed mainly by vertebrates, such as lizards. Several lizard species have already been reported as prey of this snake, including the alien species Hemidactylus mabouia (Moreau de Jonnès, 1818). Herein we describe in details a predation event of H. mabouia by O. aeneus, widening our knowledge regarding the natural history of both species to scientific literature.
Category: Quantitative Biology

[118] viXra:1907.0275 [pdf] submitted on 2019-07-15 19:29:24

Efeito de Técnicas de Enriquecimento Ambiental no Comportamento de Leontopithecus Chrysomelas (Kuhl, 1820) (Primates: Callitrichidae)

Authors: Denise Costa Rebouças Lauton, Antônio de Oliveira Costa Neto
Comments: 8 Pages.

Environmental enrichment consists in techniques that modify the captive environment, in order to make it more dynamic. The adoption of the method, often, results in the reduction of abnormal behavior (stereotypies) and expression of a more typical behavioral repertoire. Believing in the effectiveness of environmental enrichment techniques and that it is possible to improve the condition of captives individuals, this work was proposed. There were applied techniques of Physical and Feed enrichment to groups and solitary individuals captives of Leontopithecus chrysomelas (Kuhl, 1820) kept in Tropical Laboratory of Primatology (TLP), of the Universidade Federal da Paraíba (UFPB). The observations were made in three phases: Control; Enrichment of the Physical; and Nutritional. Individuals presented frequent abnormal behaviors during Control phase, such as pacing and excessive watching, especially the lonely individuals. During the experimental phase, only the act to guard presented significant difference for the family groups (Fr2 = 7.58; gl = 2; p = 0.023). The results show that L. chrysomelas of the TLP seem to be more resistant to change, possibly due to the long period of exposition of these to a conditioned environment to a routine and without stimuli. Aimed to modify this scenario, it is suggested to adopt methods of “routine break” concomitant to the techniques of environmental enrichment.
Category: Quantitative Biology

[117] viXra:1907.0274 [pdf] submitted on 2019-07-15 19:31:38

Population Structure and Fecundity of Upogebia Omissa (Decapoda: Gebiidea: Upogebiidae) in an Estuarine Region in Sergipe, Northeastern Brazil

Authors: Rafael de Carvalho Santos, Luiz Filipe Santos Silva, Bruna dos Santos, Juliana Menezes Motta, Douglas Fernandes Rodrigues Alves
Comments: 9 Pages.

Upogebiidae mud shrimps are important organisms in soft-bottom communities, where they dig burrows acting as ecosystem engineers. The present study describes some parameters of the population structure and the reproductive biology of the mud shrimp Upogebia omissa. The mud shrimps were sampled in the Vaza-Barris estuarine river, Sergipe State, northeastern Brazil. In laboratory, specimens were sexed and measured for carapace length (CL). Ovigerous females had their total eggs counted. The body size ranged between 3.0 and 12.9 mm CL. Males were significantly smaller than females. The overall sex ratio was 0.34, female-biased (binomial test, P = 0.001). Fecundity ranged from 240 to 2339 eggs per female, and it was significantly affected by the bodysize. The sexual dimorphism evidenced by the mean size of each sex is a common pattern in decapods that incubate eggs, and in that case, fecundity normally varies in function of body size. Finally, we suggest that additional studies are needed, given the ecological importance of these mud shrimps and the scarcity of studies about them.
Category: Quantitative Biology

[116] viXra:1907.0273 [pdf] submitted on 2019-07-15 19:33:27

Some Pycnogonida (Arthropoda: Chelicerata) from the “Paulo Young” Invertebrate Collection (CIPY) of the Federal University of Paraíba (UFPB), Brazil

Authors: Rudá Amorim Lucena, Martin Lindsey Christoffersen
Comments: 13 Pages.

Biodiversity studies are increasingly urgent, due mainly to the speed with which anthropic degredation is affecting the environment, marine localities in particular. Due to these human impacts, part of the marine biota is becoming increasingly unavailable in natural environments. Biological collections thus are of key importance, functioning as data bases for studies in Taxonomy, Systematics and Biogeography, as well as for several applied areas of research. Biological collections in Brazil suffer from lack of financial support, lack of human resources (both technical and scientific) and are difficult to access by the scientific cummunity. The Invertebrate Collection “Paulo Young” (CIPY) contains more than 18.000 identified and numbered samples of several marine invertebrates, from sponges to tunicates. The pycnogonid section, although less numerous than many other animal groups, has been the focus of attention in recent years. Several new species and new records have been reported from Brazil. The aim of the present paper is to disclose the CIPY reference collection, recording the Pycnogonida collection that was not the subject of previous publications.
Category: Quantitative Biology

[115] viXra:1907.0272 [pdf] submitted on 2019-07-15 19:35:41

Relação Entre Massa Corporal e Taxa Respiratória em Arthropoda de Floresta Atlântica (Paraíba, Brasil)

Authors: Idalio Amaranto, Cleber Ibraim Salimon, Douglas Zeppelini
Comments: 10 Pages.

Respiratory rate studies in arthropods refer to important physiological data, since these animals perform important ecosystem functions and because they are the greatest diversity and abundance of animals present on Earth. This study measures and describes respiratory rates through the emission of CO2, and relates them to the body mass of arthropods. The study was carried out in remnant fragments of coastal Atlantic Forest of Paraíba, Brazil. The research encompasses all living subphyla of arthropods (Crustacea, Chelicerata, Myriapoda and Hexapoda) represented by 705 specimens actively collected and tested through respirometry and measured by Infrared Gas Analyzer (IRGA). As a result, we observed that among the studied arthropods, Hexapoda and Chelicerata showed higher rates of carbon dioxide emission, while Crustacea and Myriapoda had the lowest rates. Regarding its relationship with body mass, Hexapoda and Crustacea showed higher respiration by specific mass and, in general, all Arthropoda corroborated the pattern described by animal physiology, where body mass and animal respiratory rate are inversely correlated.
Category: Quantitative Biology

[114] viXra:1907.0271 [pdf] submitted on 2019-07-15 19:37:35

Breve História da Sistemática de Agaricaceae (Fungi) e Distribuição no Brasil

Authors: Felipe Wartchow
Comments: 17 Pages.

The family Agaricaceae belongs to order Agaricales. In general the agaricoid species of this group are characterized by having squamulose pileus. This revision presents a brief history of the systematic of this group and distribution of their agaricoid species in Brazil since from early 19th Century to present days.
Category: Quantitative Biology

[113] viXra:1907.0270 [pdf] submitted on 2019-07-15 19:39:19

Registro de Olivancillaria Vesica (Gastropoda, Olividae) Sinistrógira no Litoral do Estado do Paraná, Brasil

Authors: Marcos de Vasconcellos Gernet, Carlos Eduardo Belz, Carlos João Birckolz, Elizângela da Veiga Santos
Comments: 4 Pages.

Olivancillaria vesica (Gmelin, 1791) commonly inhabitant beaches in southern and southeastern Brazil, living semi-buried in sandy substrates from the intertidal zone to deeper areas in the sub-littoral. In this work, we report the meeting of a sinistral shell of O. vesica, characteristic that is rare for this species. Its main measurements are: 10.6 mm in height, 5.1 mm in width, 8.1 mm in height of the aperture and 2.1 mm in width of the aperture. It was collected in the municipality of Matinhos, coast of Paraná state, southernern Brazil, in biodetritic gravel.
Category: Quantitative Biology

[112] viXra:1907.0269 [pdf] submitted on 2019-07-15 19:41:56

First Record of Calycuoniscus Goeldii (Lemos de Castro, 1967) (Oniscidea: Dubioniscidae) for the State of Piauí, Northeastern Brazil

Authors: Vanderley Ferreira Silva Costa, Daniela Correia Grangeiro, Carlos Anderson Soares Bezerra Pereira
Comments: 6 Pages.

The present work provides the first record of Calycuoniscus goeldii (Lemos de Castro, 1967) from the municipality of Picos, state of Piauí, northeastern Brazil. In addition, this paper contributes to increase the knowledge about the biodiversity of terrestrial isopods of the state of Piauí and distribution of the family Dubioniscidae in northeastern Brazil.
Category: Quantitative Biology

[111] viXra:1907.0268 [pdf] submitted on 2019-07-15 19:44:04

Exploração e Utilização do Potencial Madeireiro da Caatinga no Município de Aurora – Estado do Ceará

Authors: Amanda Pereira de Souza, Francisco Carlos Pinheiro da Costa, Rosana Ferreira de Alencar, Silvio Felipe Barbosa Lima
Comments: 10 Pages.

Plant species of the Caatinga have considerable logging and economic potential. This paper addresses the extraction and use of Caatinga wood in the municipality of Aurora (state of Ceará, Brazil) as well as residents’ conceptions regarding the origins and environmental impacts of the exploitation of this resource. A semi-structured questionnaire was used to obtain information on the origin and the forms of wood used. The data showed that, even when recognizing the risks of these actions, the interviewees extract wood from the Caatinga in a destructive manner, which is used for making furniture, doors, sculptures, instruments and fences as well as for fuel in cooking activities in homes, bakeries and pizzerias. The following species were more cited: Mimosa tenuiflora (jurema-preta), Croton sonderianus (marmeleiro), Mimosa caesalpiniifolia (sabiá), Amburana cearensis (cumaru), Combretum leprosum (mufumbo), Myracrodruon urundeuva (aroeira) and Handroanthus impetiginosus (pau-d’arco). The results point to the need for implementation of actions for the supervision and control of the exploitation of the Caatinga vegetation as well as adequate management guidelines for this important natural resource.
Category: Quantitative Biology

[110] viXra:1907.0267 [pdf] submitted on 2019-07-15 19:46:27

Guia Ilustrado Dos Echinodermata da Porção Sul do Embaiamento Sul Brasileiro

Authors: Maristela de Lima Bueno, Renata Aparecida dos Santos Alitto, Pablo Damian Borges Guilherme, Maikon Di Domenico, Michela Borges
Comments: 68 Pages.

The present guide describes 57 species of Echinodermata Bruguière, 1791 [ex Klein, 1734] from the southern portion of the Brazilian South Estuary (BSE), which includes the following coasts: the Southern of the State of São Paulo, entire of the State of Paraná and Northern of the State of Santa Catarina. We designed this guide for students and researchers providing a valuable resource for the identification and appreciation of shallow-water echinoderms. The guide describes the general features of the phylum Echinodermata, has a brief presentation of the study area and the techniques of collection and preservation of the specimens. For each class, the main morphological structures are illustrated, followed by the diagnoses of the species recorded in the BSE. Within each class, the species are organized by family, then alphabetically according to genus and species. For each species, we provide diagnoses, photos, geographic distribution and habitat when available in the literature. This work is the first illustrated guide of echinoderms in Brazil and complements the knowledge of biodiversity this group and provide support for future interventions, management and maintenance of the diversity of this wonderful group of marine animals.
Category: Quantitative Biology

[109] viXra:1907.0266 [pdf] submitted on 2019-07-15 19:52:39

Ocorrência de Dentes Fossilizados de Tubarões em Cascalhos Biodetríticos na Praia Dos Amores, Matinhos, Paraná, Brasil

Authors: Marcos de Vasconcellos Gernet, Elizângela da Veiga Santos, Esther Valentina da Veiga de V. Gernet
Comments: 4 Pages.

The coastal plain of Paraná originated in the Quaternary Period from cyclical movements of transgression and marine regression from the Holocene climatic oscillations. The sediments of the coastal plain present dates that vary from Pleistocene to Holocene. Along the coast of Paraná, several points are found that present deposits of biodetritic gravel, with great accumulation of fossiliferous material coming from this geologic period, among them shark teeth. The site chosen for collecting the fossilized teeth was in the gravel bank located in front of the Farol Island, located in the Amores Beach, in the municipality of Matinhos, Paraná. In total, 563 fossilized shark teeth were found, from six different species of two families. These data are very important to better understand this past biodiversity.
Category: Quantitative Biology

[108] viXra:1907.0243 [pdf] submitted on 2019-07-14 09:30:12

O Gênero Amanita (Fungi): Sistemática e Distribuição no Brasil

Authors: Felipe Wartchow
Comments: 16 Pages.

This revision presents topic related to the iconic mushrooms belonging to fungal genus Amanita. A brief story regarding to the Systematic and Taxonomy and the distribution of the species in Brazil are also presented.
Category: Quantitative Biology

[107] viXra:1907.0242 [pdf] submitted on 2019-07-14 09:31:50

Checklist of the Holothuroidea (Echinodermata) from the State of Paraíba, Brazil

Authors: Jéssica Prata, Martin Lindsey Christoffersen
Comments: 14 Pages.

The study presents the first species list for holothurians from the coast of the State of Paraíba, northeastern Brazil. The list was made based on the study of specimens deposited in the Invertebrate Collection Paulo Young, Federal University of Paraíba. A total of 16 species from seven families of Holothuroidea were recorded. This paper contributes to the biodiversity studies from the northeast coast of Brazil.
Category: Quantitative Biology

[106] viXra:1907.0241 [pdf] submitted on 2019-07-14 09:33:30

Lizard Predation Tropidurus Hispidus (Squamata, Tropiduridae) by False Coral Snake Oxyrhopus Trigeminus (Squamata, Dipsadidae) in the Caatinga, in Northeastern Brazil

Authors: Jefferson Simanas Mikalauskas, Daniel Oliveira Santana, Stephen Francis Ferrari
Comments: 8 Pages.

The predation of lizards is rarely observed in the wild, and events involving snakes are scarcer still. Here we document in detail the predation of a lizard (Tropidurus hispidus (Spix, 1825)) by a snake (Oxyrhopus trigeminus Duméril, Bibron & Duméril, 1854). Many studies have identified Tropidurus Wied-Neuwied, 1825 lizards as prey for Brazilian snakes. Thus, this record provides important insights into the natural history of both species, especially O. trigeminus, which are essential for the understanding of their ecology.
Category: Quantitative Biology

[105] viXra:1907.0240 [pdf] submitted on 2019-07-14 09:35:07

Physical, Biological and Human-Induced Effects on the Reef Fishes of Fernando de Noronha Archipelago, Brazil

Authors: Paulo Roberto de Medeiros, Ana Maria Alves de Medeiros
Comments: 15 Pages.

Several factors have the potential to influence the distribution and composition of reef fish communities. Amongst the most important are rugosity, wave exposure, substrate cover and human activities. The present study evaluated the influence of these factors on reef fishes from sites following a gradient of human-induced effects on the Fernando de Noronha archipelago, northeast Brazil and determined their relative importance to reef fish ecology. Rugosity did not influence fish richness, but had a positive influence on number of individuals, juveniles and endemic species, whereas benthic cover did not seem to be an important determinant for any fish variable evaluated. These results suggest that availability of shelter (physical protection) is more limiting than availability of food (i.e. benthic cover). Furthermore, water flow showed somewhat low values, but even so, had negative effects on fish numbers. Recreational activities, albeit seemingly non-impacting, had a negative effect on fish abundance with the partially protected site (Atalaia) showing a similar community structure to the unrestricted site (Porto). These results suggest that human presence, even when supervised, may interfere on reef fish structure. Low-impact tourism practices are required especially in partially protected and unprotected areas.
Category: Quantitative Biology

[104] viXra:1907.0090 [pdf] submitted on 2019-07-05 15:22:57

Thresholding for Population-Level Polygenic Scores to Maximize Predictive Accuracy: iq and Educational Abilities.

Authors: Davide Piffer
Comments: 16 Pages.

Polygenic scores (PGS) are being used to predict group-level traits across time and space, hence proving useful to detect recent selection. The aim of this study is to investigate the impact of different p value thresholds on signal to noise ratio and predictive validity of polygenic scores, using the largest GWAS of educational attainment and cognition to date. Signal to noise ratio linearly decreases with p value, but this phenomenon is limited to Eurasians. There is a linear degradation of validity and population differentiation in allele frequencies with higher p values. However, compounded polygenic scores have a quadratic relationship with p value. A thresholding at or below the conventional GWAS significance (p<5*10-8) seems to maximize validity, corroborating earlier results. The highest correlation with population IQ is achieved by the Highest Math Class completed and the EDU MTAG PGS (r= 0.90 and 0.89, respectively). Using random SNPs, it is shown that correlations of this magnitude occur only once out of 46k trials. A table provides an empirical estimate of the rarity of the correlation coefficients and it is shown that they are a function of PGS size. Finally, an analogy between the noise contained in polygenic scores and physical instruments is put forward.
Category: Quantitative Biology

[103] viXra:1906.0245 [pdf] submitted on 2019-06-13 09:07:41

The Contributions of the Gallo Team and the Montagnier Team to the Discovery of the AIDS Virus

Authors: Rainer W. Kühne
Comments: 4 Pages.

In this paper I review the main works of the teams headed by Robert Gallo and Luc Montagnier which led to the discovery of the HIV retrovirus and to the blood test with which one can prove HIV infection. I show that this discovery which saved millions of human lifes (and perhaps the survival of mankind) was made possible only (i) because Gallo's team discovered the T-cell lymphocyte growth factor with which they were able to discover the first retrovirus that infects humans (HTLV-I) and their hypothesis that AIDS is caused by a retrovirus, and (ii) because Montagnier's team detected an antibody against alpha interferon in order to enhance retrovirus production with which they were able to discover the HIV retrovirus and their examination and blood test that gave evidence that HIV causes AIDS. Their examination was improved by the Gallo team who proved without doubt that HIV is the cause of AIDS. I leave the question open whether Gallo deserved the Nobel Prize or whether the Nobel committee's decision to award the prize only to Montagnier and Barre-Sinoussi was correct.
Category: Quantitative Biology

[102] viXra:1905.0006 [pdf] submitted on 2019-05-02 05:37:15

Arguments that Prehistorical and Modern Humans Belong to the Same Species

Authors: Rainer W. Kühne
Comments: 3 Pages.

I argue that the evidence of the Out-of-Africa hypothesis and the evidence of multiregional evolution of prehistorical humans can be understood if there has been interbreeding between Homo erectus, Homo neanderthalensis, and Homo sapiens at least during the preceding 700,000 years. These interbreedings require descendants who are capable of reproduction and therefore parents who belong to the same species. I suggest that a number of prehistorical humans who are at present regarded as belonging to different species belong in fact to one single species.
Category: Quantitative Biology

[101] viXra:1812.0278 [pdf] submitted on 2018-12-16 21:44:40

Computer Models of Brain Tumor Metastasis

Authors: James Bonnar
Comments: 13 Pages.

A computer model of brain tumor metastasis is developed and simulated using the language Mathematica. Diffusion of cancer cells through regions of gray and white matter is differentiated resulting in realistic asymmetric tumor growth. Applications include the precise treatment of a patient’s “future tumor” with focused radiation, and modelling the effects of chemotherapy.
Category: Quantitative Biology

[100] viXra:1812.0166 [pdf] submitted on 2018-12-09 13:37:14

Why Recessive Lethal Alleles Have not Disappeared?

Authors: Jorma Jormakka
Comments: 11 Pages. I have several times tried to submit this paper, please delete the earlier versions.

The article derives the probability for lethal recessive alleles in the case of recessive disadvantage or advantage and discusses why lethal recessive alleles have not disappeared. It is shown that recessive advantage of a lethal gene can be detected by the ratio of heterozygotes and homozygotes. This demonstrates that higher IQ of certain ethnic groups cannot be explained by recessive advantage of lethal genes.
Category: Quantitative Biology

[99] viXra:1811.0352 [pdf] submitted on 2018-11-23 03:03:51

Failure of Complex Systems, Cascading Disasters, and the Onset of Disease

Authors: Anthony J Webster
Comments: 18 Pages.

Complex systems can fail through different routes, often progressing through a series of (rate-limiting) steps and modified by environmental exposures. The onset of disease, cancer in particular, is no different. A simple but very general mathematical framework is described for studying the failure of complex systems, or equivalently, the onset of disease. It includes the Armitage-Doll multi-stage cancer model as a particular case, and has potential to provide new insights into how diseases arise and progress. A method described by E.T. Jaynes is developed to provide an analytical solution for the models, and highlights connections between the convolution of Laplace transforms, sums of random samples, and Schwinger/Feynmann parameterisations. Examples include: exact solutions to the Armitage-Doll model, the sum of Gamma-distributed variables with integer-valued shape parameters, a clonal-growth cancer model, and a model for cascading disasters. The approach is sufficiently general to be used in many contexts, such as engineering, project management, disease progression, and disaster risk for example, allowing the estimation of failure rates in complex systems and projects. The intended result is a mathematical toolkit for the study of failure rates in complex systems and the onset of disease, cancer in particular.
Category: Quantitative Biology

[98] viXra:1811.0095 [pdf] submitted on 2018-11-06 17:35:13

A Geometric Pattern that Distinguishes the “Iron Sulfur” Group of Cytochrome P450 Enzymes

Authors: James A Studier
Comments: 4 Pages.

Given a phylogenetic tree of the P450 enzymes we describe a geometric pattern that distinguishes a major subtree.
Category: Quantitative Biology

[97] viXra:1808.0466 [pdf] submitted on 2018-08-22 03:30:10

Introgression from Gorilla Caused the Human-Chimpanzee Split

Authors: Johan Nygren
Comments: 4 Pages.

ABSTRACT: The Gorilla Genome Project (Scally, 2012) showed that 30% of the gorilla genome introgressed into the ancestor of humans and chimpanzees, and that the two species diverged through lineage sorting with 15% ending up in Pan and another 15% in Homo. That introgression is the Pan-Homo split, hybridization, which led to speciation as the new hybrid lineages became reproductively isolated from one another.

The NUMT on chromosome 5 fits perfectly with the introgression speciation model, it was formed from mtDNA that had diverged as much as ~4.5 Myr at the time of introgression, perfect fit with the Gorilla/Pan-Homo split, and the mtDNA fragments that formed it were inserted at the time of the Homo/Pan split, and ended up in both the Gorilla, Pan and Homo lineages around the same time period, 6 million years ago. (Popadin, 2017)


Category: Quantitative Biology

[96] viXra:1808.0250 [pdf] submitted on 2018-08-18 14:17:28

The Speciation of Australopithecus and Paranthropus Was Caused by Introgression from the Gorilla Lineage

Authors: Johan Nygren
Comments: 6 Pages.

ABSTRACT: The discovery of Paranthropus deyiremeda in 3.3–3.5 million year old fossil sites in Afar (Haile-Selassie, 2015), together with 30% of the gorilla genome showing lineage sorting between humans and chimpanzees (Scally, 2012), and a NUMT (“nuclear mitochondrial DNA segment”) that is shared by both gorillas, humans and chimpanzees, and that dates back to 6 million years ago (Popadin, 2017), is conclusive evidence that introgression from the gorilla lineage caused the speciation of both the Australopithecus lineage and the Paranthropus lineage, providing a lens into the gorilla-like features within Paranthropus, as well as traits within Homo that originate from the gorilla branch, such as a high opposable thumb index (Almécija, 2015), an adducted great toe (Tocheri, 2011; McHenry, 2006), and large deposits of subcutaneous fat.
Category: Quantitative Biology

[95] viXra:1804.0010 [pdf] submitted on 2018-04-02 11:16:43

Data Integration at Single-Cell

Authors: George Rajna
Comments: 28 Pages.

A team of computational biologists has developed an algorithm that can 'align' multiple sequencing datasets with single-cell resolution. [17] Chemist Ivan Huc finds the inspiration for his work in the molecular principles that underlie biological systems. [16] What makes particles self-assemble into complex biological structures? [15] Scientists from Moscow State University (MSU) working with an international team of researchers have identified the structure of one of the key regions of telomerase—a so-called "cellular immortality" ribonucleoprotein. [14] Researchers from Tokyo Metropolitan University used a light-sensitive iridium-palladium catalyst to make "sequential" polymers, using visible light to change how building blocks are combined into polymer chains. [13] Researchers have fused living and non-living cells for the first time in a way that allows them to work together, paving the way for new applications. [12] UZH researchers have discovered a previously unknown way in which proteins interact with one another and cells organize themselves. [11] Dr Martin Sweatman from the University of Edinburgh's School of Engineering has discovered a simple physical principle that might explain how life started on Earth. [10] Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology. A recent finding by Northwestern University's Prem Kumar adds further evidence that the answer might be yes. [9] A UNSW Australia-led team of researchers has discovered how algae that survive in very low levels of light are able to switch on and off a weird quantum phenomenon that occurs during photosynthesis. [8] This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modeled photoactive prebiotic kernel systems. [7] The human body is a constant flux of thousands of chemical/biological interactions and processes connecting molecules, cells, organs, and fluids, throughout the brain, body, and nervous system. Up until recently it was thought that all these interactions operated in a linear sequence, passing on information much like a runner passing the baton to the next runner. However, the latest findings in quantum biology and biophysics have discovered that there is in fact a tremendous degree of coherence within all living systems. The accelerating electrons explain not only the Maxwell Equations and the Special Relativity, but the Heisenberg Uncertainty Relation, the Wave-Particle Duality and the electron's spin also, building the Bridge between the Classical and Quantum Theories. The Planck Distribution Law of the electromagnetic oscillators explains the electron/proton mass rate and the Weak and Strong Interactions by the diffraction patterns. The Weak Interaction changes the diffraction patterns by moving the electric charge from one side to the other side of the diffraction pattern, which violates the CP and Time reversal symmetry. The diffraction patterns and the locality of the self-maintaining electromagnetic potential explains also the Quantum Entanglement, giving it as a natural part of the Relativistic Quantum Theory and making possible to understand the Quantum Biology.
Category: Quantitative Biology

[94] viXra:1803.0631 [pdf] submitted on 2018-03-24 03:07:17

Could Answer to Russian Poison Novichok Come from Holistic Medicine?

Authors: Edgars Alksnis
Comments: 1 Page.

Some experiments show, that replacement of fragments of neural system could in principle be possible. This requires deep rethinking of what we know about human body.
Category: Quantitative Biology

[93] viXra:1802.0057 [pdf] submitted on 2018-02-05 14:52:22

Estimating Genetic Parameters in a Dominance Model that Includes Inbreeding

Authors: Stephen P. Smith, Asko Mäki-Tanila
Comments: 21 Pages.

A dominance model is described coming with inbreeding, and five genetic parameter plus the environmental variance. The linear model is specified by the phenotypic equations and the mid-parent equations. They are placed in an indefinite system that is highly sparse, not the mixed model equations. From this system the augmented matrix K is built that is symmetric and indefinite, leading to restricted maximum likelihood. Likelihood evaluation follows from the factorization of K, and various sparse matrix tools are described for maximizing the likelihood. The method is used to estimate the six parameters for 2706 egg-laying hens that were part of a selection experiment.
Category: Quantitative Biology

[92] viXra:1801.0185 [pdf] submitted on 2018-01-16 20:14:48

Inverting the Extended Genomic Table: a Case Study

Authors: Stephen P. Smith, Asko Mäki-Tanila
Comments: 12 Pages.

A series of programs are described which calculate the inverse of the extended genomic table. These programs are demonstrated using a pedigree taken from a selection experiment involving egg-laying hens. The calculations are feasible and the inverse matrix was found to be sparse.
Category: Quantitative Biology

[91] viXra:1801.0129 [pdf] submitted on 2018-01-11 10:14:43

Six Fractal Codes of Biological Life: Perspectives in Astrobiology and Emergence of Binary Logics

Authors: Jean claude Perez
Comments: 50 Pages. none

The discovery of a simple numerical formula for the projection of all the atomic mass of life-sustaining CONHSP bioatoms leads to the emergence of a set of Nested CODES unifying all the biological, genetic and genomic components by unifying them from bioatoms up to whole genomes. In particular, we demonstrate the existence of a digital meta-code common to the three languages ​​of biology that are RNA, DNA and amino acid sequences. Through this meta-code, genomic and proteomic images appear almost analogous and correlated. The analysis of the textures of these images then reveals a binary code as well as an undulatory code whose analysis on the human genome makes it possible to predict the alternating bands constituting the karyotypes of the chromosomes. The application of these codes to perspectives in astrobiology and the emergence of binary codes and regions of local stability (voting process), whose fractal nature we demonstrate is illustrated.
Category: Quantitative Biology

[90] viXra:1712.0493 [pdf] submitted on 2017-12-18 09:21:04

The Brain is Processing Information, not Data: Does Anybody Knows About That?

Authors: Emanuel Diamant
Comments: 10 Pages. A preliminary version presented at The ISIS Summit “The Information Society at the Crossroads”, Vienna, Austria, 3–7 June 2015

Discriminating and opposing “data” and “information” (as it is emphasized in the paper’s title) for most of the scientific community sounds like something odd and unnatural. Raised in the spirit of Shannon’s Information Theory, most of the scientific community is convinced that data and information are inseparable. Nevertheless, over the last decade we witness a growing recognition that Shannon’s Information Theory is wrong, or speaking more politely, is limited only to data communication issues. Today, distinguishing data and information processing is gradually becoming a popular and widespread trend. However, because this trend is missing a firm theoretical underpinning, it looks a bit messy and inconsistent. Despite of this, the paradigm shift in contemporary science is clearly evident – from a data processing (computational) approach we are firstly moving to an information processing (cognitive) approach. (“Cognitive” here implies “capable of information processing”). Undeniably, Computational biology, Computational neuroscience, Computational linguistics (and so on) are being replaced today by Cognitive biology, Cognitive neuroscience, Cognitive linguistics, and so on. However, this tendency is hampered by a lack of understanding about what is “information processing”. Subsequently, a question “what is information?” immediately rise up. A consensus answer to it does not exist. I believe I have the answer. But instead of repetitive explanations about what is information, I prefer to bring an informational perspective to the everyday practice of scientific exploration, especially biological and neuroscience explorations. Maybe this will be more advantageous.
Category: Quantitative Biology

[89] viXra:1711.0456 [pdf] submitted on 2017-11-27 09:00:14

On the Importance of the Dynamic Measurement of the Pupil Size

Authors: Vicent Sanchis-Jurado, Álvaro Pons, Santiago García-Lázaro
Comments: 8 Pages.

In this pilot study we analyse the pupil fluctuations of the right eye of two subjects during forty-five seconds while keeping constant the viewing distance and the room illumination. Measurements were taken with an infrared eye-tracker working at 250 Hz. The results were for subject A a median diameter of 2.913 mm with a maximum diameter of 3.313 mm and a minimum diameter of 2.66 mm, for subject B the median diameter was 4.39 mm with a maximum of 5.23 mm and a minimum of 3.26 mm. For both subjects the distribution of the pupil diameter did not follow a normal distribution, this was determined with the Lilliefors test, the p-values were 0.0251 for subject A and 0.001 for subject B. In conclusion, even in constant conditions of illumination and viewing distance the pupil cannot be considered to remain constant and its diameter varies not following a normal distribution.
Category: Quantitative Biology

[88] viXra:1711.0444 [pdf] submitted on 2017-11-28 07:34:24

Effect of Fixation Target on the Contrast Sensitivity in the Foveal and Parafoveal Area

Authors: Vicent Sanchis-Jurado, Sophie Triantaphillidou, Edward Fry, Álvaro Pons
Comments: 12 pages, 4 figures, 1 table

Purpose To determine the influence on the contrast sensitivity when the stimulus contains a fixation target in two retinal locations, foveal and parafoveal. Methods Four young adults with 0.0 logMar acuity participated in this study. The stimulus was based on vertical sinusoidal gratings masked by a circular (for foveal area) or a ring (for parafoveal area). To increase the luminance resolution of the display a bit-stealing technique was used. Four different sets of stimuli were generated, two for exploring the foveal sensitivity and two for the parafoveal area. The difference between the sets designed for the same area was the presence, or absence, of a fixation target (a white cross) in the centre of the stimulus. A modified staircase method was implemented. Results The results show a drop in the contrast sensitivity when the fixation target was present on the stimulus for frequencies smaller than 4 cycles per degree. Conclusions The presence of fixation targets diminishes the contrast sensitivity for low to mid frequencies over different concentric areas of the retina. This could be due to the fixational eye movements, different patterns of eye movements were found using an eyetracker. The relationship between the sensitivity in the foveal area and the parafoveal agrees with those reported by other authors using different designs confirming that the new stimulus design is suitable to measure the contrast sensitivity outside the foveal area.
Category: Quantitative Biology

[87] viXra:1711.0300 [pdf] submitted on 2017-11-13 11:25:35

Rotationally Symmetric Structures of the C-ring of Escherichia Coli

Authors: Herbert Weidner
Comments: 5 Pages.

The C-ring of a motor contains either 34 or 44 copies of FliM but only about 26 copies of FliG. In addition, the amount of FliMs is influenced both by the direction of rotation and by the number of CheY-P signal molecules in the cytoplasm. The rotationally symmetrical model described here combines all known properties.
Category: Quantitative Biology

[86] viXra:1710.0304 [pdf] submitted on 2017-10-29 05:14:23

Color Perception: Controlled Excitation of Opponent Channels

Authors: Prashanth Alluvada
Comments: 15 Pages. Describes monochromatic spectra that cause controlled opponent channel excitation

We describe controlled excitation of opponent color channels. For monochromatic impingement of spectral energy, the wavelength sequences we develop cause a channel to attain a preset excitation level, causing thereby a controlled excitation of color channels.
Category: Quantitative Biology

[85] viXra:1709.0307 [pdf] submitted on 2017-09-20 19:35:33

The Existence of God: An Application of the Poisson Distribution

Authors: Charles M. Byrne
Comments: 13 pages, Keywords: God, evolution, mutation, recombination, genetics, molecular biology, naturalism, Poisson distribution

In his theory of evolution by natural selection, Charles Darwin provided a plausible alternative to Christianity's creation account of human origins. In response, the Christian botanist Asa Gray suggested to Darwin that the variation that drives evolution might be generated by God. Darwin rejected Gray’s hypothesis, invoking philosophical naturalism, a hallmark scientific paradigm. Darwin's conclusion was reached on ideological grounds rather than empirical ones. Biological evidence that emerged subsequent to Darwin’s time yields a different conclusion. A means to assess the question of the source of genetic variation is provided by fitting the Poisson distribution to counts of mutation and chromosome crossover events at the DNA sites where they occur. A general failure of fit between observational data and the Poisson distribution confirms an exception to the naturalistic paradigm, and thereby provides epistemic access to the existence of God.
Category: Quantitative Biology

[84] viXra:1709.0292 [pdf] submitted on 2017-09-19 07:21:06

On Richard III's Y-DNA and Time-Asymmetric Mutation Rates

Authors: John Smith
Comments: 20 Pages.

A skeleton excavated in 2012 is almost certainly that of the English king, Richard III (1452 -1485), and mtDNA (which is passed from mother to child) extracted from the skeleton matches mtDNA taken from descendants of Richard's sister Anne of York. However Y-DNA (which is passed from father to son) extracted from the skeleton apparently doesn't match Y-DNA taken from descendants of Henry Somerset the 5th Duke of Beaufort, who according to history descended from Richard's 2nd great grand father Edward III (1312 - 1377). The implication according to geneticists, and the media, is that there is a "false paternity event" somewhere between Edward and the Somersets. In this note, a formula for calculating the time of the most recent common ancestor is introduced, and some of its consequences outlined. This formula is attached to a mathematical framework within which it is possible that the traditional genealogy is correct. If this framework is the right framework for understanding of genetic inheritance, then it has been wrongly assumed that Y-DNA mutation rates are like-line, constant and smooth - in reality they are wave-like and decrease erratically in the direction of the future, and the contrary impression is is an illusion created by an over-focus on the relatively constant and smooth nature of genetic change in the present and the near-present.
Category: Quantitative Biology

[83] viXra:1709.0286 [pdf] submitted on 2017-09-19 06:50:53

Principal Directon Divising Partitioning Initialisation of K-Means Clustering Allows to Identify the Most Salient Genes in Discriminating Among Leukemias

Authors: Diego Liberati
Comments: 35 Pages.

This paper attempts to cluster leukemia patients described by gene expression data, and to discover the most discriminating genes that are responsible for the clustering. A combined approach of Principal Direction Divisive Partitioning and bisect K-means algorithms is applied to the clustering of the investigated leukemia dataset. Both unsupervised and supervised methods are considered in order to get optimal result. The combination of PDDP and bisect K-means successfully clusters leukemia patients, and efficiently discovers salient genes able to the discriminate the clusters. The combined approach works well on the automatic clustering of leukemia patients depending merely on the gene expression information, and it has great potential on solving similar problems, like classifying pancreatic tumors. The salient identified genes may thus enhance relevant information for discriminating among leukemias.
Category: Quantitative Biology

[82] viXra:1709.0248 [pdf] submitted on 2017-09-16 10:26:26

Simulating the Idling Behavior of Escherichia Coli

Authors: Herbert Weidner
Comments: 10 Pages.

Until now, it is not known how the motors of E. coli reverse the direction of rotation, mostly simultaneously. If the C-ring is bistable and if the number of bound CheY-P depends on the direction of rotation, there is a strong variation in the concentration of CheY-P in the cytoplasm. Then, the synchronous changeover can be explained without further additional assumptions.
Category: Quantitative Biology

[81] viXra:1708.0370 [pdf] submitted on 2017-08-25 14:38:23

Nylonase Genes and Proteins - Distribution, Conservation, and Possible Origins

Authors: S.T. Cordova, J.C. Sanford
Comments: 78 Pages.

Nylon comprises a family of man-made substances that were first manufactured in 1935. Nylonases are biological enzymes that can break down nylon oligomers. Although the most prominent nylonases are within the family of enzymes classified as 6-aminohexanoate hydrolases, some enzymes not formally classified as 6-aminohexanoate hydrolases also have the ability to breakdown nylons, and so can also be classified as nylonases. Organisms that encode a nylonase enzyme do not necessarily have the ability to actually survive on a nylon substrate as their sole carbon source. Among the first documented organisms that did have this ability was the soil bacterium Arthrobacter KI72. It has long been thought that nylonase genes and proteins were essentially absent from the biosphere prior to 1935. This belief led to the widespread assumption that any nylonase gene observed in the present must have emerged since 1935. Several authors developed hypothetical models of how a specific nylonase gene (the nylB gene found within Arthrobacter KI72), might have arisen very recently as a de novo gene. In this paper we show that the widely-held assumption that all nylonase genes must have evolved very recently is no longer credible. This is in light of the wide-spread distribution of diverse nylonases throughout the biosphere. Likewise, we show that the early speculations regarding the possible de novo origin of the nylB nylonase gene are no longer credible. Our review of the literature shows that a variety of nylonase-digesting bacteria have been found in extremely diverse natural environments – far removed from any synthetic nylon sources. In addition, we show there are over 1800 organisms with computationally predicted (provisional) 6-aminohexanoate hydrolase/nylonase genes in the NIH-funded UNIPROT database. These 1800 predicted nylonases are not yet experimentally confirmed to cleave nylons, but have significant homology to the experimentally confirmed nylonases. In addition to 6-aminohexanoate hydrolases, proteases like trypsin and certain lipases have been experimentally demonstrated to have nylonase activity. If we include all proteases and lipases that may have nylonase activity, the number of organisms with nylonase activity may exceed ten thousand. The widespread distribution of nylonases and their homologs strongly suggests that nylonases were already widespread prior to 1935. Lastly, we have carefully examined the claims that the nylB gene arose as a de novo gene very recently. The theories of Ohno (the frame shift hypothesis) and Okada (the gene duplication hypothesis), were speculative in nature, and yet were uncritically accepted. In light of new data, these early speculations no longer appear tenable.
Category: Quantitative Biology

[80] viXra:1708.0243 [pdf] submitted on 2017-08-20 23:59:45

Brain Stimulation with Neutrinos

Authors: Evgeny A Novikov
Comments: 2 Pages.

A possibility of brain stimulation with neutrinos is discussed.
Category: Quantitative Biology

[79] viXra:1708.0051 [pdf] submitted on 2017-08-06 05:04:28

Crispr Technology Challenge Facing the Numerical Integrity of Whole Human Genome DNA

Authors: Jean Claude Perez
Comments: 10 Pages.

Background : Global analysis of 3 human genomes of increasing levels of evolution (Neanderthal / Sapiens Build34 / Sapiens hg38) reveals 2 levels of numerical constraints controlling, structuring and optimizing these genome's DNA sequences. A global constraint - called "HGO" for "Human Genome Optimum" - optimizes the genome at its global scale. The same operator applied to each of the 24 individual chromosomes reveals a hierarchical structure of these 24 chromosomes. Results : Then analysing the single strand DNA CG / TA proportions at whole chromosomes and genome scale reveals strong fine-tuned numerical ratios evidencing the "closure" nature (Varela's autopoiesis theory) of whole human genome.
Category: Quantitative Biology

[78] viXra:1706.0297 [pdf] submitted on 2017-06-16 04:26:24

Programa Analizador de Retrovirus

Authors: Roberto Reinosa
Comments: 3 Pages. Spanish

En el presente artículo se va a mostrar un programa, que sirve para realizar una serie de análisis a partir de secuencias provirales de retrovirus.
Category: Quantitative Biology

[77] viXra:1705.0295 [pdf] submitted on 2017-05-19 14:06:52

Combining Genetic Similarities Among Known Relatives that Connect to an Unknown Relative

Authors: Stephen P. Smith, Cambrian Lopez, Nicole Lam
Comments: 15 Pages.

Various DNA testing companies promise their customers a collection of genetic matches to facilitate finding family members. The matches are in centimorgans (cM), where the higher the cM value the closer the relationship to a customer (R). Unless the relationship is close, such as parent-offspring or among 1st cousins, a single cM value is not that informative if the goal is to locate family. This paper describes a statistical method that combines a collection cM values from a cluster of unknown relatives of R, but where the cluster members are known among themselves being for example 2rd and 3th cousins. A presumed envoy is attached to the cluster, where R is a descendant of the envoy, and the various cM values are combined to provide an overall cM value between R and the envoy. The envoy’s cM comes with a statistical error to judge significance. Unlike a single cM value on a typical unknown relative, the envoy’s cM can be quite large and indicative of a real genetic path to R that has previously been undiscovered. This paper describes the method for two sisters, where the path from the envoy led to their lost father, a father that was later discovered.
Category: Quantitative Biology

[76] viXra:1704.0237 [pdf] submitted on 2017-04-19 09:29:00

Tracking the Diffusion of Signal Proteins in Escherichia Coli

Authors: Herbert Weidner
Comments: 6 Pages.

We describe a fast computational model to study the signal transduction in E. coli chemo­taxis. It allows to trace the places and chemical reactions of individual molecules in a cell as a function of time. From the spatial resolution of the model and the known diffusion constant of the proteins, a time step of 3 µs is calculated for the simulation.
Category: Quantitative Biology

[75] viXra:1704.0220 [pdf] submitted on 2017-04-18 03:24:39

Reproductive Cloning

Authors: Ian von Hegner
Comments: 20 Pages.

Progressiv forkortelse af telomere ved DNA replikation er blevet sat i forbindelse med cellulær ældning. Hvad vil der ske med dyr, fremkommet ved somatisk kerneoverførsel, hvis differentierede celler fra voksne dyr med forkortede teleomerelængde benyttes til at starte embryo udvikling? Vil de forkortede telomere påvirke deres livslængde eller udvikling, eller er de forkortede telomere fra donerceller blevet rekonstrueret til fuld længde i klonede dyr?
Category: Quantitative Biology

[74] viXra:1704.0195 [pdf] submitted on 2017-04-14 13:41:27

Recognition from Description Through Synthesis and Reduction to Theory and Model

Authors: Andrzej Gecow
Comments: 9 Pages. in Polish

The half a century attempts to transmit the results of the theoretical work on the biological issues which used the methodology of physics, gave an insight into the methodological limitations resulting from the stereotypes of thinking in biology. It is primarily a lack of interest in the pursuit to deductive theory. Abstraction and deduction - the basis of physics, is despised and omitted as speculation, which creates a blockade in the development of theory in biology. The process of this development stops at an analysis that should (and does not do) reduce the sufficient conditions noted in the description to the necessary and sufficient conditions, ie. to determine the reasons for the phenomena being considered. Determination of the necessary conditions is the basis of reduction, which in the applied reductionism is not noticed. This chapter is not a recognized knowledge imparted authoritatively to use, nor fight against the official position of biology, but a collection of arguments against conservative stereotypes, to compare with other more elaborate sources on the reader's own responsibility to work out his own view rather than uncontrolled take over of the defective tradition.
Category: Quantitative Biology

[73] viXra:1704.0176 [pdf] submitted on 2017-04-13 11:49:24

Materials for Discussion of Methodological Limitations Resulting from the Stereotypes of Biologists Thinking

Authors: Andrzej Gecow
Comments: 18 Pages. in Polish

Attempts to communicate the results of theoretical works on the evolutionary biology using the methodology of physics have not yielded results for half a century, but have led to the recognition of methodological limitations stemming from the stereotypes of thinking in biology. It is primarily a lack of interest in the pursuit of deductive theory. Abstraction and deduction - the basis of physics, are despised and omitted as speculation, which creates a blockade in the development of theory in biology. As a basis for this diagnosis, five reviews of the text addressed to “KOSMOS” have been analyzed, which led to the conclusion that the text, because of the thesis contained therein, is unreadable to biologists. This study is the basis for a wider discussion in a separate publication.
Category: Quantitative Biology

[72] viXra:1704.0151 [pdf] submitted on 2017-04-12 04:55:54

Current Return to Lamarck in Agreement with Darwin

Authors: Andrzej Gecow
Comments: 11 Pages. in Polish

The terms ‘Darwinism’ and ‘Lamarckism’ mean different things to different people. Nowadays, they are rarely used in a historically correct way – clime Jablonka and Lamb, the scientists that mainly contribute to proving than not only genes can curry hereditary information and new hereditary channels show characteristic of Lamarckian mechanisms. Especially Lamarckism was seen in false and superficial way in lot of aspects. The inheritance of acquired characters was connected to Lamarck. It was rejected too radically. Today it revives but mainly not basing on epigenetic inheritance. Generally Lamarckian mechanisms increase in the complex and diverse ways the chances of accurate adaptive changes, so they no longer look like a random, appear as ‘effects of instructions’ or ‘directed variations’ but these ‘instructions’ have been previously acquired through Darwinian natural selection. The richness of these phenomena causes great difficulty of their brief describtion. Lamarckian dimension of evolution is now known better. This phenomena cannot be explained in the range of Modern Synthesis assumptions. It does not mean, that MS is false and should be rejected. Lamarckian mechanisms are created by Darwinian natural selection, but their explanations need wider assumptions, than are a basis of MS, means Extended Evolutionary Synthesis is necessary. This theme is one of the main in current discussion.
Category: Quantitative Biology

[71] viXra:1704.0072 [pdf] submitted on 2017-04-05 19:41:10

Programa Para Análisis de Secuencias Biológicas

Authors: Roberto Reinosa
Comments: 2 Pages. Spanish

Programa para el análisis de secuencias de ADN, ARN y proteínas.
Category: Quantitative Biology

[70] viXra:1703.0230 [pdf] submitted on 2017-03-23 11:15:34

Information as the Evolution Driving Force

Authors: Igor Krichtafovitch
Comments: 17 Pages.

The article presents third alternative for the biological evolution, first two being Darwinism and Intelligent Design (ID). The main hypothesis postulates that Biosphere is a single living organism with all parts and cells interconnected. As such it acts as a gigantic bio-computer capable to generate new life forms. The evolution is driven by recursive growth of total biological memory volume and accelerated complexity of living organisms. Intelligent Design is a natural phenomenon inherent into living matter from pre-biotic RNA to modern complex organisms.
Category: Quantitative Biology

[69] viXra:1703.0172 [pdf] submitted on 2017-03-17 13:49:00

On Richard III, the Livingstons of Callendar, and the Conflict Between Genealogy and Genetics 1.0.0

Authors: John Smith
Comments: 31 Pages.

A skeleton excavated at the presumed site of the Grey Friars friary in Leicester in 2012 is almost certainly that of the English king, Richard III (1452 -1485), and mtDNA (which is passed from mother to child) extracted from the skeleton matches mtDNA taken from descendants of Richard's sister Anne of York. However Y-DNA (which is passed from father to son) extracted from the skeleton apparently doesn't match Y-DNA taken from descendants of Henry Somerset the 5th Duke Of Beaufort, who according to history descended from Richard's 2nd great grand father Edward III (1312 - 1377). The implication according to geneticists, and the media, is that there is a 'false paternity event' somewhere between Edward and the Somersets. Also, the false paternity events don't end there, for only 4 of these 5 Somerset descendants match each other. And it may be worse even than this: the patrilineal line of a Frenchman named Patrice de Warren apparently traces back to Richard III through the illegitimate son of Edward III's 4th great grandfather, Geoffrey Plantagenet, Count of Anjou (1113 - 1151). But de Warren's Y-DNA doesn't match that of either Richard III or any of the Somersets. In this note, a formula for calculating the time of the most recent common ancestor is introduced, and some of its consequences outlined. This formula arises from a mathematical framework within which it is possible that the traditional genealogy is correct, and that Geoffrey Plantaganet was the father of a male line incorporating Richard III, all 5 Somersets, and Patrice de Warren.
Category: Quantitative Biology

[68] viXra:1701.0300 [pdf] submitted on 2017-01-06 07:09:48

Golden and Harmonic Mean in the Genetic Code

Authors: Miloje M. Rakocevic
Comments: 6 Pages. From Proceedings of the 2nd International Conference “Theoretical Approaches to BioInformation Systems” (TABIS.2013), September 17 – 22, 2013, Belgrade, Serbia.

In previous two works [1], [2] we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table (GCT), i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table (DT) and triplets Table (TT), over polarity of amino acids, measured by Cloister energy. (Miloje M. Rakočević) (Belgrade, 6.01.2017) (www.rakocevcode.rs) (mirkovmiloje@gmail.com)
Category: Quantitative Biology

[67] viXra:1701.0294 [pdf] submitted on 2017-01-05 11:15:03

Harmony of Genetic Code (Volume 1)

Authors: Miloje M. Rakocevic
Comments: 255 Pages.

This book contains my works published in the period 2005-2013 on my website (also in arXiv). The concept of "harmony" in the title refers to the determination of the genetic code by golden mean, generalized golden mean and harmonic mean. Some parts of the contents, in the meantime are published in some of the official journals, but most are not, and this was the reason for my decision to publish all papers here in their entirety. Miloje M. Rakočević) (Belgrade, 31.12.2016) (www.rakocevcode.rs) (mirkovmiloje@gmail.com)
Category: Quantitative Biology

[66] viXra:1612.0169 [pdf] submitted on 2016-12-09 08:36:25

Enigmas of the Genetic Code, Enigma 3: a Third Hidden Arithmetical Algorithm

Authors: Miloje M. Rakocevic
Comments: 6 Pages.

This third enigma is standing in relation to enigmas 1 & 2, given in our previous two communications. It is relating to total number of atoms (239) in side chains of 23 protein amino acids, within standard genetic code. By this three amino acids (L, S, R) are included twice each.
Category: Quantitative Biology

[65] viXra:1612.0159 [pdf] submitted on 2016-12-09 05:09:28

Enigmas of the Genetic Code, Enigma 2: a Second Hidden Arithmetical Algorithm

Authors: Miloje M. Rakocevic
Comments: 7 Pages.

This second Enigma is standing in relation to Enigma 1 in our previous communication. It is relating to total number of atoms (204) in side chains of 20 protein amino acids, within standard genetic code.
Category: Quantitative Biology

[64] viXra:1612.0141 [pdf] submitted on 2016-12-09 02:57:30

Enigmas of the Genetic Code, Enigma 1: a Hidden Arithmetical Algorithm

Authors: Miloje M. Rakocevic
Comments: 3 Pages.

In a certain way, this enigma is standing in relation to so-called Gaussian arithmetical algorithm, valid for the genetic code (Rakocevic, 2006). However, the difference is, among other things, that there (in the article on the Gaussian algorithm), I said and showed all openly - what is the enigma [classes of AAs (2 x 2), or (4 x 5), or (2 x 4) with 11, 21, 31, 41, – , 61, 71, 81, 91 of atoms within their side chains, respectively]; and here the hidden algorithm is hidden twice: once by the very Nature, the other way from myself. I make here, namely, only a hint of the solution. Certainly, in coming a few weeks (or months), I will present the solution, if someone else, in meantime, offers (or doesn’t offer) the solution.
Category: Quantitative Biology

[63] viXra:1612.0133 [pdf] submitted on 2016-12-08 11:51:54

Notes About Genetic Code, Note 2: the Relations Between Four Diversity Types of Protein Amino Acids

Authors: Miloje M. Rakocevic
Comments: 5 Pages.

This Note follows from Note 1(viXra:1612.0127, submitted on 2016-12-08 07:01:10) and it shows further distinctions and splittings within four diversity types of protein amino acids (AAs). First type as in Note 1 (G, P) and second one, also as in Note 1 (A, L; V, I). Within third type there is a chemicaly directed splitting into 4 + 2 AAs [(F, Y, H, W) + (C, M)]. Forth type consists of two halves in form of 4 + 4 AAs; four AAs with nitrogen, and four without: [(N, Q; K, R) + ( S, T, D, E)]. All these distinctions are followed through specific arithmetical regularities.
Category: Quantitative Biology

[62] viXra:1612.0127 [pdf] submitted on 2016-12-08 07:01:10

Notes about Genetic Code, Note 1: Four Diversity Types of Protein Amino Acids

Authors: Miloje M. Rakocevic
Comments: 7 Pages.

In this Note is presented the existence of four diversity types of protein amino acids (AAs). Fist type with two AAs (G; P); second with four AAs (A, L; V, I); third with six AAs (F, Y, H, W; C, M); and fourth type with eight AAs (S, T, D, E; N, Q; K, R).
Category: Quantitative Biology

[61] viXra:1610.0125 [pdf] submitted on 2016-10-12 06:41:57

Atomic-Scale MRI

Authors: George Rajna
Comments: 22 Pages.

Researchers at the University of Melbourne have developed a way to radically miniaturise a Magnetic Resonance Imaging (MRI) machine using atomic-scale quantum computer technology. [12] With one in two Australian children reported to have tooth decay in their permanent teeth by age 12, researchers from the University of Sydney believe they have identified some nanoscale elements that govern the behaviour of our teeth. [11] When cryoEM images are obtained from protein nanocrystals the images themselves can appear to be devoid of any contrast. A group of scientists from the Netherlands have now demonstrated that lattice information can be revealed and enhanced by a specialized filter. [10] There is also connection between statistical physics and evolutionary biology, since the arrow of time is working in the biological evolution also. From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. [8] This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modeled photoactive prebiotic kernel systems. [7] The human body is a constant flux of thousands of chemical/biological interactions and processes connecting molecules, cells, organs, and fluids, throughout the brain, body, and nervous system. Up until recently it was thought that all these interactions operated in a linear sequence, passing on information much like a runner passing the baton to the next runner. However, the latest findings in quantum biology and biophysics have discovered that there is in fact a tremendous degree of coherence within all living systems. The accelerating electrons explain not only the Maxwell Equations and the Special Relativity, but the Heisenberg Uncertainty Relation, the Wave-Particle Duality and the electron's spin also, building the Bridge between the Classical and Quantum Theories. The Planck Distribution Law of the electromagnetic oscillators explains the electron/proton mass rate and the Weak and Strong Interactions by the diffraction patterns. The Weak Interaction changes the diffraction patterns by moving the electric charge from one side to the other side of the diffraction pattern, which violates the CP and Time reversal symmetry. The diffraction patterns and the locality of the self-maintaining electromagnetic potential explains also the Quantum Entanglement, giving it as a natural part of the Relativistic Quantum Theory and making possible to understand the Quantum Biology.
Category: Quantitative Biology

[60] viXra:1609.0390 [pdf] submitted on 2016-09-27 09:47:13

A Surgical Simulator for Training Surgeons in a Few Tasks Related to Minimally Invasive Surgery

Authors: Kirana Kumara P
Comments: 8 Pages. This is the complete specification for the application filed for Indian patent (the patent application filed on September 17, 2016; application number: 201641031739).

The present invention relates to a surgical simulator that may be used to train surgeons for minimally invasive surgery. The simulator makes use of the Boundary Element Method together with a simulation approach that was proposed in an academic paper authored by this inventor. Moreover, the simulator makes use of the boundary element codes developed by this inventor. The simulator consists of a computer screen, a keyboard, a mouse, a haptic device, and a multicore CPU. The simulator would include the geometry of representative human kidney and human liver. The simulator has provisions for moving and changing the orientation of the liver and the kidney, and detecting the collision between the liver or the kidney and the mouse pointer. The simulator also has provisions for interactively displaying the deformed shape of the liver or the kidney, depending on the position of the mouse pointer (mouse cursor (pointer) represents the tip of surgical tools). The simulator can be used to train surgeons in the following tasks: eye-hand coordination, manipulating 3D objects while deformation of the objects is observed on 2D screens.
Category: Quantitative Biology

[59] viXra:1607.0062 [pdf] submitted on 2016-07-05 23:14:58

Phenotypic and Biotypic Characterization of Klebsiella Oxytoca: an Impact of Biofield Treatment

Authors: Mahendra Kumar Trivedi
Comments: 4 Pages.

Klebsiella oxytoca (K. oxytoca) is a Gram-negative microbe generally associated with community and hospitalacquired infections. Due to its clinical significance, we evaluated the effect of biofield treatment on phenotype and biotype characteristics of K. oxytoca (ATCC 43165). The study was performed into three groups i.e. C (control), T1 (treatment, revived); and T2 (treatment, lyophilized). Subsequently, groups T1 and T2 were received biofield treatment and control group was remained as untreated. The antimicrobial sensitivity results showed 3.33% and 6.67% alteration in antimicrobials susceptibility in group T1 cells on day 5 and 10, respectively, and 3.33% alteration in antimicrobials susceptibility was observed in group T2 cells on day 10 as compared to control. The sensitivity patterns of cefazolin were changed from resistant (R) to intermediate (I) on day 5, and resistance (R) to susceptible (S) on day 10, in T1 cells of K. oxytoca. The MIC value of cefazolin was decreased by 2-fold in group T1 on day 10 as compared to control. The biofield treated K. oxytoca exhibited the changes in biochemical reactions about 3.03% and 15.15% of total tested biochemicals in group T1 cells on day 5 and 10, respectively as compared to control. The biotype number of K. oxytoca was altered in biofield treated group and organism identified as Raoultella ornithinolytica in T1 on day 10 as compared to control, which is the prominent finding of this study. These changes were found in treated bacteria that might be due to some alteration happened in metabolic/enzymatic pathway and/ or at genetic level of K. oxytoca. Based on these data, it is speculated that biofiled treatment could be an alternative approach that can improve the effectiveness of the existing antimicrobials against the resistant pathogens.
Category: Quantitative Biology

[58] viXra:1607.0061 [pdf] submitted on 2016-07-05 23:17:54

Antibiogram Typing and Biochemical Characterization of Klebsiella Pneumoniae After Biofield Treatment

Authors: Mahendra Kumar Trivedi
Comments: 6 Pages.

Klebsiella pneumoniae (K. pneumoniae) is a common nosocomial pathogen causing respiratory tract (pneumoniae) and blood stream infections. Multidrug-resistant (MDR) isolates of K. pneumoniae infections are difficult to treat in patients in health care settings. Aim of the present study was to determine the impact of Mr. Trivedi’s biofield treatment on four MDR clinical lab isolates (LS) of K. pneumoniae (LS 2, LS 6, LS 7, and LS 14). Samples were divided into two groups i.e. control and biofield treated. Control and treated groups were analyzed for antimicrobial susceptibility pattern, minimum inhibitory concentration (MIC), biochemical study and biotype number using MicroScan Walk-Away® system. The analysis was done on day 10 after biofield treatment as compared with control group. Antimicrobial sensitivity assay showed that there was 46.42% alteration in sensitivity of tested antimicrobials in treated group of MDR K. pneumonia isolates. MIC results showed an alteration in 30% of tested antimicrobials out of thirty after biofield treatment in clinical isolates of K. pneumoniae. An increase in antimicrobial sensitivity and decrease in MIC value was reported (in LS 6) in case of piperacillin/tazobactam and piperacillin. Biochemical study showed a 15.15% change in biochemical reactions as compared to control. A significant change in biotype numbers were reported in all four clinical isolates of MDR K. pneumoniae after biofield treatment as compared to control group. On the basis of changed biotype number after biofield treatment, new organism was identified as Enterobacter aerogenes in LS 2 and LS 14. These results suggest that biofield treatment has a significant effect on altering the antimicrobial sensitivity, MIC values, biochemical reactions and biotype number of multidrug-resistant isolates of K. pneumoniae.
Category: Quantitative Biology

[57] viXra:1607.0045 [pdf] submitted on 2016-07-04 23:24:38

Spectroscopic Characterization of Disodium Hydrogen Orthophosphate and Sodium Nitrate After Biofield Treatment

Authors: Mahendra Kumar Trivedi, Alice Branton, Dahryn Trivedi, Gopal Nayak
Comments: 5 Pages.

Disodium hydrogen orthophosphate is a water soluble white powder widely used as pH regulator and saline laxative. The sodium nitrate is a highly water soluble white solid, used in high blood pressure, dentinal hypersensitivity, and production of fertilizers. The present study was aimed to investigate the impact of biofield treatment on spectral properties of disodium hydrogen orthophosphate and sodium nitrate. The study was performed in two groups i.e., control and treatment of each compound. The treatment groups were subjected to Mr. Trivedi’s biofield treatment. The spectral properties of control and treated groups of both compounds were studied using Fourier transform infrared (FT-IR) and Ultraviolet-Visible (UV-Vis) spectroscopic techniques. FT-IR spectrum of biofield treated disodium hydrogen orthophosphate showed the shifting in wavenumber of vibrational peaks (with respect to control) corresponding to O-H stretching from 2975 to 3357 cm-1, PO-H symmetrical stretching from 2359 to 2350 cm-1, O=P-OH deformation from 1717-1796 cm-1 to 1701-1735 cm-1, P=O asymmetric stretching from 1356 to 1260 cm-1 and P=O symmetric stretching from 1159 to 1132 cm-1, etc. Likewise, the FT-IR spectrum of sodium nitrate exhibited the shifting of vibrational frequency of N=O stretching from 1788 to 1648 cm-1 and NO3 asymmetric and symmetric stretchings from 1369 to 1381 cm-1 and 1340 to 1267 cm-1. UV spectrum of treated disodium hydrogen orthophosphate revealed a negative absorbance; it may be due to decrease in UV absorbance as compared to control. UV spectrum of control sodium nitrate exhibited two absorbance maxima (λmax) at 239.4 nm and 341.4 nm, which were altered to one absorbance maxima (λmax) at 209.2 nm after biofield treatment. Overall, the FT-IR and UV spectroscopic data of both compounds suggest an impact of biofield treatment on spectral properties with respect to force constant, bond strength, dipole moments and transition energy between two orbitals (ground state and excited state) as compared to respective control.
Category: Quantitative Biology

[56] viXra:1606.0288 [pdf] submitted on 2016-06-26 23:21:09

An Evaluation of Biofield Treatment on Susceptibility Pattern of Multidrug Resistant Stenotrophomonas Maltophilia: an Emerging Global Opportunistic Pathogen

Authors: Mahendra Kumar Trivedi, Mayank Gangwar, Snehasis Jana
Comments: 5 Pages.

Stenotrophomonas maltophilia (S. maltophilia) is a Gram-negative bacillus, an opportunistic pathogen, particularly among nosocomial infections. Multi-drug resistant strains are associated with very high rate of morbidity and mortality in severely immunocompromised patients. Present study was designed to evaluate the effect of biofield treatment against multidrug resistant S. maltophilia. Clinical sample of S. maltophilia was collected and divided into two groups i.e. control and biofield treated which were analyzed after 10 days with respect to control. The following parameters viz. susceptibility pattern, minimum inhibitory concentration (MIC), biochemical studies and biotype number of both control and treated samples were measured by MicroScan Walk-Away® system. The results showed an overall change of 37.5% in susceptibility pattern and 39.4% in biochemical study while 33.3% changes in MIC values of tested antimicrobials after biofield treatment. Further, the treated group of S. maltophilia has also shown a significant change in biochemical reactions followed by its biotype number as compared to control group. Biochemical reactions of treated group showed negative reaction to acetamide and positive reactions to colistin, glucose, adonitol, melibiose, arabinose, nitrate, oxidation-fermentation, raffinose, rhaminose, sorbitol, sucrose, and Voges-Proskauer as compared with control. The biofield treatment showed an alteration in MIC values of amikacin, amoxicillin/K-clavulanate, chloramphenicol, gatifloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotetan, ticarcillin/K-clavulanate, trimethoprim/sulfamethoxazole. Altogether, data suggest that biofield treatment has significant effect to alter the sensitivity pattern of antimicrobials and biotype number against multidrug resistant strain of S. maltophilia.
Category: Quantitative Biology

[55] viXra:1604.0390 [pdf] submitted on 2016-04-30 19:19:34

Biopsy-Implantable Chemical Sensor for Monitoring and Adjusting Cancer Treatments

Authors: Ahmed El Demerdash - Hassan Sameh
Comments: 20 Pages.

“In the battle against cancer, which kills nearly 8 million people worldwide each year, doctors have in their arsenal myriads of powerful weapons, including various forms of Chemotherapy and Radiation. What they lack, however, is good reconnaissance — a reliable way to obtain realtime data about how well a particular therapy is working for any given patient. That’s why, a tiny biochemical sensor that is implanted in the cancerous tissue will be made; the sensor then wirelessly sends chemical measurements to an external “reader” device, allowing doctors to better monitor a patient’s progress and switch therapies accordingly. This device boosts treatments’ efficacy while reducing patients’ exposure to serious side effects. “ Design requirements are critical for the success of any project. And so, accuracy and cost are considered the main design requirements of our project. A simple prototype has been crafted in order to test the mechanism of our idea. Dissolved Oxygen (DO) and pH levels are measured, and a simulation has been made in order to mimic the environment of the tumor. In conclusion, our smart device offers an opportunity to accurately monitor the state of the cancerous tissues with a quite low cost.
Category: Quantitative Biology

[54] viXra:1602.0102 [pdf] submitted on 2016-02-08 17:56:09

Efficient Breeding by Genomic Mating

Authors: Deniz Akdemir, Julio Isidro Sanchez
Comments: 15 Pages.

Many breeders use selection as a first step for improvement of complex traits. The theory of selection is well studied in the genetics literature. In this article, we propose a new approach to breeding which focuses on mating instead of selection, we refer it to as genomic mating. We believe breeding by genomic mating uses the genomic information better than a recently proposed method of breeding methodologies like genomic selection. We used concepts of risk and diversification from the economics for formulating the optimum mating theory. The results from our simulations point to the efficiency of our method to selection based breeding.
Category: Quantitative Biology

[53] viXra:1601.0046 [pdf] submitted on 2016-01-06 08:54:14

Patterned Vegetation Created by Ants and Observed in Satellite Images of Arizona

Authors: Amelia Carolina Sparavigna
Comments: 5 Pages. Keywords: Patterned Vegetation, Ecosystems, Satellite images, Google Earth.

Large-scale patterns can arise in the vegetation of homogeneous areas due to biotic interactions of animals and plants. If the satellite imagery has a high enough resolution, such patterns can be easily observed. Here we show some large polka-dot arrangements, probably created by the red harvester ants, in Arizona, near the Grand Canyon.
Category: Quantitative Biology

[52] viXra:1512.0413 [pdf] submitted on 2015-12-23 21:05:27

A Quantitative Numerical Model for TNF-α Mediated Cellular Apoptosis

Authors: Davide Mezza, Marco Pappalettera, Diego Liberati
Comments: 2141 Pages. submitted

Experimental evidence indicates that cells under irradiation induce in the neighbour non- irradiated cells the same biological effects affecting the irradiated ones. This is the so called bystander effect. Up to now in the scientific literature this kind of effect does not appear to be fully understood, even if several experiments show evidence of its existence. It would be reasonable that bystander effect takes place by means of paracrine chemical transmission mediators that would be broadcasted by the damaged cells to the surrounding cells. Furthermore a subset of a special class of signaling proteins, namely the cytokines, are probably the very ones involved in such signaling phenomenon. Among them, Tumor Necrosis Factor (TNF) is a particularly relevant protein belonging to the class of cytokines, because it is known to contribute to mediate various relevant cell functions, like apoptosis, the programmed cell death. As a molecule, TNF is quite interesting, because it can issue two opposite signals through different intracellular molecular signaling chains. One signal induces apoptosis, while the other is opposite, inducing the cell resistance to apoptic signals. The crucial point is thus to understand what makes each of such two signals masking the other. Thus a mathematical model related to the TNF signaling pathway is of interest, paying special attention to the study of the TNF reception mechanisms by cells that are not passed through by the radiation beam. In this work we present a new mathematical model of cellular apoptosis - mediated by TNF - and its validation based on data existent in literature. The model that we present will result to be a stable model with respect to large variation of the parameters and simplified with respect to other models already existent.
Category: Quantitative Biology

[51] viXra:1512.0411 [pdf] submitted on 2015-12-23 21:12:17

Clustering of Pancreatic Endocrine Tumors Via Microarray Gene Expression Analysis

Authors: Silvia Strada, Diego Liberati
Comments: 17 Pages. submitted

A simple, multivariable and linearly initial- ized clustering is shown to be able to deal with unsu- pervised classification of the data originating from pan- creatic endocrine tumors (PET). Results are discussed almost only on the data science side, leaving a more biological discussion to future work, even in the quest of possible hidden pathways.
Category: Quantitative Biology

[50] viXra:1512.0337 [pdf] submitted on 2015-12-16 09:16:24

Logical Modeling of the Mammalian Cell Cycle

Authors: Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry
Comments: 14 Pages.

Proper understanding of the behavior of complex biological regulatory networks requires the integration of heterogeneous data into predictive mathematical models. Logical modeling focuses on qualitative data and offers a flexible framework to delineate the main dynamical properties of such networks. However, formal analysis faces a combinatorial explosion as the number of regulatory components and interactions increases. Here, we show how model-checking techniques can be used to verify sophisticated dynamical properties resulting from model regulatory structure. We demonstrate the power of this approach through the updating of a model of the molecular network controlling mammalian cell cycle. We use model-checking to progressively refine this model in order to fit recent experimental observations. The resulting model accounts for the sequential activation of cyclins, the role of Skp2, and emphasizes a multifunctional role for the cell cycle inhibitor Rb.
Category: Quantitative Biology

[49] viXra:1511.0162 [pdf] submitted on 2015-11-19 01:08:22

What is Love? The Physical Cosmology of Spiritual Union

Authors: Richard L. Amoroso
Comments: 20 Pages.

Until now descriptions of the nature of love have been left to the muse of poets and inspiration of philosophers. Psychologists usually refer to love as an emotion and biologists as a biochemical condition. Proponents of Artificial Intelligence (AI) suggest love can be described by a computer program even with current computer technology if we only knew the correct algorithm. Cognitive psychologists would profess that love reduces to configurational states in neural networks, microtubules or synapses. These aspects are not denied only that they are the wrapping and not the essence of love itself. Now that the physical cosmology of the mind-body interaction (awareness) has been discovered, it is possible to describe the fundamental basis of love. What is the soul, what is life, what is intelligence, and especially what is love and why it takes a whole cosmology to be adequately described are questions that noetic science begins to formally answer. It will take volumes to completely describe the physical cosmology of love; thus in this work we give basic descriptions as a way of introducing what comes in the near future as new noetic technologies become available to explore Self-Organized Living Systems (SOLS). A unique form of meditation to subjectively experience the soul of another person as if one were them is also introduced
Category: Quantitative Biology

[48] viXra:1508.0110 [pdf] submitted on 2015-08-14 10:06:14

A Simple Approach to Verifying the Estimates of the PML Risk During Natalizumab Therapy

Authors: Julian Borchardt
Comments: 7 Pages.

In this short note, we show how to quickly verify the correctness of the estimates of the PML risk on natalizumab established in [Borchardt 2015]. Our approach is simple and elementary in that it requires virtually no knowledge of either statistics or probability theory. For a Kaplan-Meier curve of the PML incidence may be found in [O'Connor et al 2014], based on postmarketing data as of early August 2013, and just using the information from that chart, it is possible to directly derive estimates of the risk of PML in JCV-seropositive natalizumab-treated patients according to prior or no prior immunosuppression. Actually, the resulting figures are almost identical to the ones in [Borchardt 2015], even though the latter were obtained in a very different fashion.
Category: Quantitative Biology

[47] viXra:1506.0122 [pdf] submitted on 2015-06-16 02:19:04

A Literature Survey on the Real-Time Computational Simulation of Biological Organs

Authors: Kirana Kumara P
Comments: 59 Pages. Preprint (draft), list of references

This paper lists some references that could in some way be relevant in the context of the real-time computational simulation of biological organs, the research area being defined in a very broad sense. This paper contains 198 references.
Category: Quantitative Biology

[46] viXra:1505.0226 [pdf] submitted on 2015-05-30 06:37:16

Whywhere2.0: an R Package for Modeling Species Distributions on Big Environmental Data

Authors: David R.B. Stockwell
Comments: 13 Pages.

Previous studies have indicated that multi-interval discretization (segmentation) of continuous-valued attributes for classification learning might provide a robust machine learning approach to modelling species distributions. Here we apply a segmentation model to the $Bradypus~variegatus$ -- the brown-throated three-toed sloth -- using the species occurrence and climatic data sets provided in the niche modelling R package \texttt{dismo} and a set of 940 global data sets of mixed type on the Global Ecosystems Database. The primary measure of performance was the area under the curve of the receiver operating characteristic (AUC) on a k-fold validation of predictions of the segmented model and a third order generalized linear model (GLM). This paper also presents further advances in the \texttt{WhyWhere} algorithm available as an R package from the development site at http://github.com/davids99us/whywhere.
Category: Quantitative Biology

[45] viXra:1504.0148 [pdf] submitted on 2015-04-19 10:31:57

Carefully Estimating the Incidence of Natalizumab-Associated PML

Authors: Julian Borchardt
Comments: 45 Pages.

We show that the quarterly updates about the risk of PML during natalizumab therapy, while in principle helpful, underestimate the real incidences systematically and significantly. Calculating the PML incidences using an appropriate method and on realistic assumptions, we obtain estimates that are up to 80% higher. In fact, with the recent paper [Plavina et al 2014], our approximate incidences are up to ten times as high. The present article describes the shortcomings of the methods used in [Bloomgren et al 2012] and by Plavina et al for computing incidences, and demonstrates how to properly estimate the true (prospective) risk of developing PML during natalizumab treatment. One application is that the newest data concerning the advances in risk-mitigation through the extension of dosing intervals, although characterised as not quite statistically significant, are in fact significant. Lastly, we discuss why the established risk-stratification algorithms, even on assessing the PML incidences correctly, are no longer state-of-the-art; in the light of all the progress that has been made so far, already today it is possible to reliably identify over 95% of patients in whom (a personalised regimen of) natalizumab should be very safe.
Category: Quantitative Biology

[44] viXra:1502.0252 [pdf] submitted on 2015-02-28 12:29:28

Thioredoxin Reductase: Selenotetrapeptide Sequences with Specificity for Thioredoxin and Glutathione Systems

Authors: Mark R. Brenneman
Comments: 4 Pages.

substrate specificities for the thioredoxin (Trx) system which consists of native Trx and the respective cytosolic mitochondrial thioredoxin reductase (TrxR) enzymes
Category: Quantitative Biology

[43] viXra:1502.0211 [pdf] submitted on 2015-02-22 15:35:54

On the Completeness of Genetic Code: Part Vii

Authors: Miloje M. Rakocevic
Comments: 13 Pages. This is seventh Part of the work

In this seventh part of the work on the completeness of the genetic code, we present further relationships of different variants of Genetic Code Table and modified Rumer Table of nucleotide doublets within genetic code.
Category: Quantitative Biology

[42] viXra:1502.0123 [pdf] submitted on 2015-02-15 14:54:48

Another Attack on Evolution, Rationality and Civilization. a Review of Nowak and Highfield ‘SuperCooperators’(2012)

Authors: Michael Starks
Comments: 5 Pages.

Nowak is (or was) a respected Harvard professor of mathematical biology with numerous well regarded publications. Sadly, he has chosen to launch an arrogant attack on science motivated by religious fervor. His recent actions show the evil consequences when universities accept money from religious groups, science journals are so awed by big names that they avoid proper peer review, and egos are permitted to get out of control. Most of this book is good, but it repeats the utterly misconceived attacks on inclusive fitness in favor of group selection which he and his much more famous Harvard colleague E.O.Wilson have been making the last 5 years, so it is on that chapter of the book that I will concentrate. This takes us into the nature of evolution, the basics of scientific methodology, how math relates to science, what constitutes a law or a theory, and what attitudes to religion and generosity are appropriate as we inexorably approach the collapse of industrial civilization.
Category: Quantitative Biology

[41] viXra:1502.0063 [pdf] submitted on 2015-02-08 23:09:13

Altruism, Jesus and the End of the World—how the Templeton Foundation Bought a Harvard Professorship and Attacked Evolution, Rationality and Civilization. a Review of E.o. Wilson 'the Social Conquest of Earth' (2012) and Nowak ‘SuperCooperators'(2012)

Authors: Michael Starks
Comments: 5 Pages.

Famous ant-man E.O. Wilson has always been one of my heros--not only an outstanding biologist, but one of the tiny and vanishing minority of intellectuals who at least dares to hint at the truth about our nature that others fail to grasp, or insofar as they do grasp, studiously avoid for of political expedience. Sadly, he is ending his long career in a most sordid fashion as a party to an ignorant and arrogant attack on science motivated at least in part by religious fervor. It shows the vile consequences when universities accept money from religious groups, science journals are so awed by big names that they avoid proper peer review, and when egos are permitted to get out of control. It takes us into the nature of evolution, the basics of scientific methodology, how math relates to science, what constitutes a theory, and even what attitudes to religion and generosity are appropriate as we inexorably approach the collapse of industrial civilization.
Category: Quantitative Biology

[40] viXra:1502.0041 [pdf] submitted on 2015-02-04 15:36:39

On the Completeness of Genetic Code: Part vi

Authors: Miloje M. Rakocevic
Comments: 4 Pages. The sixth Part of the work

In this sixth part of the work on the completeness of the genetic code, we present further relationships within Rumer Table and modified Rumer Table of nucleotide doublets within genetic code.
Category: Quantitative Biology

[39] viXra:1501.0253 [pdf] submitted on 2015-01-31 15:05:19

On the Completeness of Genetic Code: Part V

Authors: Miloje M. Rakocevic
Comments: 9 Pages. This is fifth part of the work

In this fifth part of the work on the completeness of the genetic code, we present further connections and relations between nucleotide doublets and triplets within Genetic Code Table; in all cases through balances of atom number, nucleon number and isotope number.
Category: Quantitative Biology

[38] viXra:1501.0230 [pdf] submitted on 2015-01-26 15:15:47

On the Completeness of Genetic Code: Part IV

Authors: Miloje M. Rakocevic
Comments: 2 Pages. Part IV of the work

In this fourth part of the work about the completeness of the genetic code, we present further connections and relations between nucleotide doublets and triplets within Genetic Code Table.
Category: Quantitative Biology

[37] viXra:1501.0159 [pdf] submitted on 2015-01-14 17:11:17

On the Completeness of Genetic Code: Part III

Authors: Miloje M. Rakocevic
Comments: 2 Pages. Part III of the work; Part II in viXra:1501.0117

In this third part of the work about the completeness of the genetic code, we present new examples that show that the codon splitting after pyrimidine and purine nucleotides distinctions are followed by specific arithmetical balances of the number of atoms in the amino acid molecules side chains.
Category: Quantitative Biology

[36] viXra:1501.0117 [pdf] submitted on 2015-01-11 08:10:31

On the Completeness of Genetic Code: Part II

Authors: Miloje M. Rakocevic
Comments: 4 Pages. This is Part II of the work; Part I in viXra:1412.0274

As in first part of this work, in this second part we present the chemically meaningful splitting of codons after pyrimidine and purine distinctions; the splitting which is also in relation to Rumer nucleotide doublet Table.
Category: Quantitative Biology

[35] viXra:1412.0274 [pdf] submitted on 2014-12-30 15:56:02

On the Completeness of Genetic Code: Some New Examples

Authors: Miloje M. Rakocevic
Comments: 8 Pages. New facts in connection to the paper, published in JTB, Volume 229 (2004) 221-234

In the paper is presented the chemically meaningful splitting of codons after pyrimidine and purine distinctions; such a splitting that is accompanied by the balance of number of atoms in the set of 61 amino acid molecules. In doing so, the increase or decrease of number of atoms occurs in the quantities of decimal units, what can be understood as analogous filling of the orbitals within atoms.
Category: Quantitative Biology

[34] viXra:1411.0578 [pdf] submitted on 2014-11-27 07:38:16

Division of Labor in Hand Usage is Associated with Higher Hand Performance in Free-Ranging Bonnet Macaques, Macaca Radiata

Authors: Madhur Mangalam, Nisarg Desai, Mew Singh
Comments: 19 Pages.

A practical approach to understanding lateral asymmetries in body, brain, and cognition would be to examine the performance advantages/disadvantages associated with the corresponding functions and behavior. In the present study, we examined whether the division of labor in hand usage, marked by the preferential usage of the two hands across manual operations requiring maneuvering in three-dimensional space (e.g., reaching for food, grooming, and hitting an opponent) and those requiring physical strength (e.g., climbing), as described by Mangalam et al. [1], is associated with higher hand performance in free-ranging bonnet macaques, Macaca radiata. We determined the extent to which (a) the macaques exhibit laterality in hand usage in an experimental unimanual and a bimanual food-reaching task, and (b) manual laterality is associated with hand performance in an experimental hand-performance-differentiation task. We found strong negative relationships between (a) the performance of the preferred hand in the hand-performance-differentiation task (measured as the latency in food extraction; lower latency = higher performance), the preferred hand determined using the bimanual food-reaching task, and the normalized difference in the performance between the two hands (measured as the difference in the latency in food extraction between them normalized by the latency in food extraction using the preferred hand), and (b) the normalized difference in the performance between the two hands and the manual specialization (measured as the absolute difference in the laterality in hand usage between the unimanual and the bimanual food-reaching tasks; lesser difference = higher manual specialization). These observations demonstrate that the division of labor between the two hands is associated with higher hand performance.
Category: Quantitative Biology

[33] viXra:1411.0577 [pdf] submitted on 2014-11-27 07:41:38

Division of Labor: A Democratic Approach to Understanding Manual Asymmetries in Non-Human Primates

Authors: Madhur Mangalam, Nisarg Desai, Mewa Singh
Comments: 37 Pages.

A consequence of the ‘gold rush’ like hunch for human-like handedness in non-human primates has been that researchers have been continually analyzing observations at the level of the population, ignoring the analysis at the level of an individual and, consequently, have potentially missed revelations on the forms and functions of manual asymmetries. Recently, consecutive studies on manual asymmetries in bonnet macaques, Macaca radiata [Mangalam et al., 2014a; Mangalam et al., 2014b] revealed both the functional and the adaptive significance of manual asymmetries respectively, and pointed towards the division of labor as being the general principle underlying the observed hand-usage patterns. We review the studies on manual asymmetries in capuchin monkeys, Cebus spp. and argue that the observed hand-usage patterns might reflect specialization of the two hands for accomplishing tasks that require different dexterity types (i.e., maneuvering in three dimensional space or physical strength). To this end, we do a step-by-step analysis of the various tasks used in the studies on manual asymmetries in capuchin monkeys, wherein we: (a) analyze the different manual tasks that have been used to study manual asymmetries in non-human primates on the basis of the attributes such as the number of hands required to solve a given task (i.e., unimanual, pseudo unimanual, or bimanual) and the spatiotemporal progression of manual actions (i.e., sequential or concurrent). (b) Determine the forms and functions of manual asymmetries that these tasks can potentially elicit within the broader scope of the behavioral repertoire of an individual, a population, or a species. (c) Qualify the scope of the inter-individual, -population, or -species comparisons. We then describe the division of labor as a general principle underlying manual asymmetries in non-human primates, and propose experimental designs that would elaborate the forms and functions of manual asymmetries in non-human primates, and the associated adaptive value.
Category: Quantitative Biology

[32] viXra:1411.0036 [pdf] submitted on 2014-11-05 00:03:43

The Enigma of Darwin Diagram

Authors: Miloje M. Rakocevic
Comments: 80 Pages. This is a pre-print form for a booklet with the same title; the suggestions are welcome!

According to my best knowledge, for the first time here is presented a hypothesis, that the one and only accompanying diagram in Darwin famous book On the Origin of Species contains, may be, a hidden code. Direct inspection reveals that the Diagram, viewed as built of four parts [(two upper and two lower / two left and two right); (two with more and two with less branches / two with multiple and two with single branches)], corresponds to the logical square of the genetic code. When, however, viewed as built of two parts (upper and lower), then it corresponds with Shcherbak diagram (Shcherbak, 1993, 1994) of four-codon and non-four-codon amino acids; not only by the form but also by the number of elementary quantities. The number of nucleons in the upper part of Shcherbak diagram (four-codon amino acids) is determined by the Pythagorean law, meaning that the total number of nucleons makes the product of the number 25 and Prime quantum 037 (925); and the number of branches in the lower part of Darwin diagram is determined by the law of Plato, meaning that the total number of branches makes the product of the number 216 and First quantum 01 (216). On the other hand, in the lower part of the Shcherbak diagram there are 60 of Prime quantum 037 (2220), while in the upper part of the Darwin diagram there are 60 of First quantum 01 (60). There are 216 + 60 = 276 branches (in total), and this number is also the number taken from a specific and unique arithmetical system. Furthermore, it is shown that Darwin, starting from the basic structure of the Diagram, formed a sophisticated structure which strictly corresponds to the arithmetical and /or algebraic structures that also appear to be the key determinants of the genetic code.
Category: Quantitative Biology

[31] viXra:1408.0104 [pdf] submitted on 2014-08-17 11:42:09

A Mathematical Treatise on Polychronous Wavefront Computation and its Application into Modeling Neurosensory Systems

Authors: Joseph I. Thomas
Comments: 194 Pages. Under Review since 12 March 2014

Polychronous Wavefront Computation is the name given to a recently proposed geometric approach on how the brain can be modeled to perform computations. It departs from the conventional use of artificial neural networks involving synapses for systems modeling. This paper, written as a mathematical sequel to the original work on the subject, builds two closely related Neurocomputational Models that together furnishes a plausible mechanism grounded in geometry, for sensory representation of motion, shape and time in the brain.
Category: Quantitative Biology

[30] viXra:1405.0016 [pdf] submitted on 2014-05-03 07:38:55

A Simple Way to Determine the Sex of One-Day Poultry Chickens (Basic Principles)

Authors: Yakov Gershman
Comments: 11 Pages.

In this work describe the experiments, which shows the principal possibility to develop cheap computerized optical separator for determining the sex of one-day chickens. This can help to improve the income of poultry industry.
Category: Quantitative Biology

[29] viXra:1403.0117 [pdf] submitted on 2014-03-13 00:43:56

Son Birth and Female Lifespan Are Positively Related in Humans

Authors: Madhukar Shivajirao Dama
Comments: 20 Pages.

Sexual dimorphism of human body size starts as early as first trimester of fetal development [1]. Compared to daughters, sons develop faster [2] and weigh 2-3% higher at birth [3]. This dimorphism is believed to create an investment dimorphism for mothers, such that, women bearing sons tend to incur higher physiological investment costs. Further, analysis of human populations has shown that mothers bearing more sons require longer time to reproduce again [4]. These observations lead to the prediction that mothers bearing more sons may need to trade the physiological investments with lifespan [5].
Category: Quantitative Biology

[28] viXra:1403.0115 [pdf] submitted on 2014-03-13 01:10:34

Offspring Sex-Ratio in Humans – Does it Depend on Population Size?

Authors: Madhukar Shivajirao Dama
Comments: 18 Pages.

Balanced sex ratio evolves by a process known as frequency-dependent selection of the minority sex. Efforts to test this theory have focused mainly on experimental populations. Heterogametic sex has greater influence over the sex of the offspring. We tested the prediction that a smaller human population should favor male offspring. Our findings reveal that size of the population has significant inverse correlation with male proportion. We also present evidence for frequency-dependent selection of the minority sex and evolution of balanced sex ratio in isolated human population.
Category: Quantitative Biology

[27] viXra:1403.0003 [pdf] submitted on 2014-03-01 03:35:45

Increasing Quality of Separation of Shelled Peanuts by X-Rays and ir Technologies

Authors: Yakov Gershman
Comments: 4 Pages.

One of the important requirements of the market to peanuts in shell is the lack of incompletely filled with fruit. Traditional mechanical sorting methods cannot solve the problem completely. In this work experimentally proved the possibility of the complete removal of immature fruits ("singles") by using image processing of x-ray and infrared.
Category: Quantitative Biology

[26] viXra:1311.0105 [pdf] submitted on 2013-11-15 12:11:45

On the Evolution of the Tree Form with the Fractal Parameter

Authors: Valerii V. Galitskii
Comments: 13 pages. Russian. Materials of the Third National scientific conference Mathematical modelling in ecology, October, 21-25st, 2013, Pushchino, Russia

Modeling peculiarities of evolution of the tree's branches system on allometric (fractal) parameter µ which connects a green biomass of a tree with its height, are considered, basing on the sectional model of a branches system presented earlier. It is shown that the initial stage of the (endo)symbiotic growth of the first dot "plants" (µ<1) must be characterized by a group placement of photosynthesizing points and growth of µ with the increasing the number of points in group, i.e. with increasing the efficiency of the use of light. Value µ not depends on type of a groups' allocation, but depends on a kind of the points' distribution in group. Thus, in an early ontogenesis of such "protoplants" there should be a stage of gradual growth μ from 0 which may be manifested in the form (usually observable) initial slowdown of growth and in the recapitulation phenomenon. Key words: sectional model of system of tree's branches; green biomass vs. height; fractal parameter; group dot pattern at line segment; endosymbiose of cyanobacteria and protists; origin of "protoplant"; initial slowdown of growth; recapitulation;
Category: Quantitative Biology

[25] viXra:1308.0135 [pdf] submitted on 2013-08-26 23:13:28

The Simulation of Th1-Th2 Cell Differentiation by System Dynamic Model and Stochastic Processes

Authors: Peisheng Shi, Hai Zhang, Zhiguo Zhu
Comments: 17 Pages.

In this article, we use system dynamical model (base on a set of nonlinear differential equations) and stochastic process model (Master equations of elementary reaction) to simulate the T helper cell differentiation (including Th1-Th2-Th17-Treg), especially the Th1-Th2 differentiations signaling network. We draw a conclusion that the critical trigger factor of naive T helper cells differentiation is the concentration of differentiation induced cytokines. We also compare the result of these two models as well as discussed the advantage and disadvantage of them.
Category: Quantitative Biology

[24] viXra:1308.0019 [pdf] submitted on 2013-08-04 19:37:33

The Utilization of Exercise Tests in Evaluating Patients with Pulmonary Vascular Disease

Authors: Abdullah AlShimemeri, Itani M, Alghadeer H, Al-Jahdali H, Al-Moamary M, A. AlDuhaim, A. Mobeireek, Andrew Nassif
Comments: 24 Pages.

It is known that patients with pulmonary hypertension show an augmented ventilatory response to exercise defined as the slope of minute ventilation over carbon dioxide production (VE/VCO2). We suggested that the degree of ventilatory augmentation may be used to differentiate between patients with primary pulmonary hypertension (PPH), Eisenmenger (E.) and chronic thromboembolic (CH.TH.EM.) disease.
Category: Quantitative Biology

[23] viXra:1306.0055 [pdf] submitted on 2013-06-08 17:34:24

A DNA-Binding Protein Gata1 with a Biological Unit Fog1 Zinc Finger Protein Molecule is Synergistic to the Region of the X Chromosome Which Occurred at a 'exome' Splice Site X-Linked Involving the Gata-Type Zinc Finger Domain.

Authors: Mark R. Brenneman
Comments: 3 Pages.

The human ERYF1 gene (summary) NF-E1 DNA-binding protein GATA1, locus Xp11.23
Category: Quantitative Biology

[22] viXra:1304.0162 [pdf] submitted on 2013-04-29 17:19:16

Theoretical Basis of in Vivo Tomographic Tracer Kinetics

Authors: Fabrice Pautot
Comments: 24 Pages.

In vivo tracer kinetics, as probed by current tomographic techniques, is revisited from the point of view of fluid kinematics. Proofs of the standard intravascular advective perfusion model from first premises reveal underlying assumptions and demonstrate that all single input models apply at best to undefined tube-like systems, not to the ones defined by tomography, \textit{i.e.} the voxels. In particular, they do not and cannot account for the circulation across them. More generally, it is simply not possible to define a single non-zero steady volumetric flow rate per voxel. Restarting from the fact that kinematics requires the definition of six volumetric flow rates per voxel, one for each face, minimalist, 4D spatiotemporal analytic models of the advective transport of intravascular tracers in the whole organ of interest are obtained. Their many parameters, plasmatic volumetric flow rates and volumes, can be readily estimated at least in some specific cases. Estimates should be quasi-absolute in homogeneous tissue regions, regardless of the tomographic technique. Potential applications such as dynamic angio-tractography are presented. By contrast, the transport of mixed intra/extravascular tracers cannot be described by conservation of the mass alone and requires further investigation. Should this theory eventually supersede the current one(s), it shall have a deep impact on our understanding of the circulatory system, hemodynamics, perfusion, permeation and metabolic processes and on the clinical applications of tracer tracking tomography to numerous pathologies.
Category: Quantitative Biology

[21] viXra:1304.0056 [pdf] submitted on 2013-04-11 17:09:55

Discovering Taxon Specific Oligomer Repeats in Microbial Genomes

Authors: Li Xia
Comments: 30 Pages.

Using the computational approach, we studied the oligonucleotides repeats in current available bacterial whole genomes. Though, repeats only count for a small portion in bacterial genomes, they still prevail. Our study shows, some of these oligonucleotides have a large copy number in genomes while maintain its taxon specificity. Generally, a length larger than 12 is enough to make a oligonucleotides repeats genus specific. Longer oligonucleotides will become more specific and be the species or strain marker sequences. We show here some examples in archaea and bacteria with different specific taxon levels. As we have a large volume of computational results, we make it available online by our TSOR server.It deals with user’s query and in this thesis we give examples on how to use this server. Moreover as these TSOR sequences are both specific and highly repeated, they would become possible nice candidate for biased microbial community genomes amplification
Category: Quantitative Biology

[20] viXra:1304.0028 [pdf] submitted on 2013-04-05 07:25:31

Thymos I

Authors: Stan Bumble
Comments: 36 Pages.

The following is a power point presentation on Systems Biology including aspects of Self-Organization and Emergence.
Category: Quantitative Biology

[19] viXra:1303.0027 [pdf] submitted on 2013-03-05 11:50:58

The World of Microbes

Authors: Andrew Nassif
Comments: 18 Pages.

Andrew Nassif's guide on the world of microbes and the rise of its cellular growth as a colony.
Category: Quantitative Biology

[18] viXra:1302.0092 [pdf] submitted on 2013-02-13 17:20:12

A Theoretical Solution for Ventricular Septal Defects And Pulmonary Vein Stenosis

Authors: Alan Williams
Comments: 5 Pages.

Ventricular Septal Defects (VSD) and Pulmonary Vein Stenosis (PVS) are both normally non- life- threatening problems for survivors of early childhood. However, it can be a large hindrance to many patients who want a normal life. With this proposed solution, patients should be able to achieve a life mostly free of problems. Hopefully, only regular check-ups will be required after the initial treatment.
Category: Quantitative Biology

[17] viXra:1302.0078 [pdf] submitted on 2013-02-12 22:32:18

Spnb2 Protein Family Architecture Perspective and Differences in Complex Form of Exon/intron Usage

Authors: Mark R. Brenneman
Comments: 1 Page. emissrto@yahoo.com

Spectrin isoforms are found in erythroid and nonerythroid cells. Spectrin is a component (known as the postsynaptic density (PSD)) for the maintenance of cell cytoskeleton shape the main fibrous component of which is spectrin of the erythrocyte membrane controlling Smad3/4 subcellular localization in TGFβ/Smad signalling resulting in nuclear translocation of activated Smad4. beta subunit-fodrin, spectrin-like protein, is a nonerythroid spectrin analogue alpha Spna-1 related to human erythrocytic 1 (hSPTBN1) Nonerythroid brain spectrin (Spnb-2 Beta-II spectrin). Three isoforms of brain spectrin contains three structural domains. A nonerythroid 9 Kb mRNA which encodes neuronal beta SpIIa occurs also in neonatal cardiomyocytes with ankyrin-B and ELF (Spnb-2), a new isoform of beta-G-spectrin. Spnb2 js found to cross-react with human erythrocyte beta subunit spectrin-ankyrin scaffold in restoring similarity of structure to lateral membrane biogenesis, cross-linking protein alpha-chain, and the Actin binding N-terminal domain of beta-chain, a form of exon/intron usage of two antiparallel dimers usage Complementary DNA synthesized from a messenger mRNA a stem cell adaptor protein is found in two to four cells per 30,000-50,000 cells.
Category: Quantitative Biology

[16] viXra:1302.0027 [pdf] submitted on 2013-02-04 16:39:12

On the K-Mer Frequency Spectra of Organism Genome and Proteome Sequences with a Preliminary Machine Learning Assessment of Prime Predictability

Authors: Nathan O. Schmidt
Comments: 130 pages and 18 figures

A regular expression and region-specific filtering system for biological records at the National Center for Biotechnology database is integrated into an object-oriented sequence counting application, and a statistical software suite is designed and deployed to interpret the resulting k-mer frequencies---with a priority focus on nullomers. The proteome k-mer frequency spectra of ten model organisms and the genome k-mer frequency spectra of two bacteria and virus strains for the coding and non-coding regions are comparatively scrutinized. We observe that the naturally-evolved (NCBI/organism) and the artificially-biased (randomly-generated) sequences exhibit a clear deviation from the artificially-unbiased (randomly-generated) histogram distributions. Furthermore, a preliminary assessment of prime predictability is conducted on chronologically ordered NCBI genome snapshots over an 18-month period using an artificial neural network; three distinct supervised machine learning algorithms are used to train and test the system on customized NCBI data sets to forecast future prime states---revealing that, to a modest degree, it is feasible to make such predictions.
Category: Quantitative Biology

[15] viXra:1212.0041 [pdf] submitted on 2012-12-06 09:38:20

Automatic Discovery of Case-Specific Relevant Subgraphs in Large Scale Signaling Networks Using Random Walks

Authors: Aristotelis Kittas, Carito Guziolowski, Niels Grabe
Comments: 20 Pages.

We present a method to discover signaling pathways, quantify the relationship of preselected source/target nodes, and extract relevant subgraphs in large scale biological networks. This is demonstrated over the hepatocyte growth factor (HGF) stimulated cell migration and proliferation in a keratinocyte-fibroblast co-culture. The algorithm (MCWalk) is implemented with random walks using Monte Carlo simulations. We extract a master network by overlaying case specific microarray data from the NCI Pathway Interaction Database (PID) using a fully automatic pipeline without any manual network construction, and uncover the association of HGF receptor c-Met nodes, differentially expressed (DE) protein nodes and cellular states. We show that the network has a scale-free structure and identify key regulator nodes based on their random walk traversal frequency. This property is shown to be very weakly correlated to node degree, contrary to what is expected from similar centrality measures. The differences with standard methods, such as shortest-path, commonly used in the analysis of such networks are discussed and compared with this approach, highlighting important pathways which are exclusively obtained with our random walks algorithm.
Category: Quantitative Biology

[14] viXra:1210.0170 [pdf] submitted on 2012-10-28 21:00:28

Unstable Angina is a Mixed Th17 and Th1 Immune Disorder

Authors: Wan-Jiung Hu
Comments: 34 Pages.

Unstable angina is common clinical manifestation of atherosclerosis. However, the detailed pathogenesis of unstable angina is still not known. Here, I propose that unstable angina is a mixed TH17 and TH1 immune disorder. By using microarray analysis, I find out that TH1 and TH17 related cytokine, cytokine receptor, chemokines, complement, immune-related transcription factors, anti-bacterial genes, Toll-like receptors, and heat shock proteins are all up-regulated in peripheral leukocytes of unstable angina. In addition, H-ATPase, glycolytic genes, platelet and RBC related genes are also up-regulated in peripheral leukocytes of during unstable angina. It also implies that atherosclerosis is a mixed TH17 and TH1 autoimmune disease. If we know the etiology of unstable angina as well as atherosclerosis better, we can have better methods to control and prevent this detrimental illness.
Category: Quantitative Biology

[13] viXra:1205.0090 [pdf] submitted on 2012-05-23 02:08:11

Sepsis is a Syndrome with Hyperactivity of TH17-Like Innate Immunity and Hypoactivity of Adaptive Immunity

Authors: Wan-Jiung Hu
Comments: 44 Pages.

Currently, there are two major theories for the pathogenesis of sepsis: hyperimmune and hypoimmune. Hyperimmune theory suggests that cytokine storm causes the symptoms of sepsis. On the contrary, hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By using microarray study, this study implies that hyperactivity of TH17-like innate immunity and failure of adaptive immunity are noted in sepsis patients. Thus, both hyperimmune and hypoimmune play important roles in the pathophysiology of sepsis.
Category: Quantitative Biology

[12] viXra:1204.0090 [pdf] submitted on 2012-04-24 06:10:46

Acute Respiratory Distress Syndrome is a TH17 and Treg Immune Disease

Authors: Wan-Jiung Hu
Comments: 18 Pages.

Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading to respiratory failure and subsequent mortality. Sepsis is the leading cause of acute respiratory distress syndrome. Thus, extracellular bacteria play an important role in the pathophysiology of ARDS. Overactivated neutrophils are the major effector cells in ARDS. Thus, extracellular bacteria triggered TH17 host immunity with neutrophil activation counts for the etiology of ARDS. Here, I use microarray analysis to describe TH17 related cytokine up-regulation in whole blood of ARDS patients. In addition, TGF-β secreting Treg cells play important roles in lung fibrosis. Thus, ARDS is actually a TH17 and Treg immune disorder.
Category: Quantitative Biology

[11] viXra:1204.0070 [pdf] submitted on 2012-04-16 20:55:43

Schizophrenia is a TH2 Dominant Autoimmune Disease Possibly Against Acetylcholine Receptors of CNS

Authors: Wan-Jiung Hu
Comments: 19 Pages.

Schizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519 significantly expressed genes are immune-related genes. Among them, TH2 related genes are significantly up-regulated including IL-4, histidine decarboxylase, aldehyde dehydrogenase, CCR9, IgE Fc receptor, GATA2, serotonin receptor, phospholipase A2, and prostaglandin D2 synthase. Besides, TH1 and TH17 related genes are down-regulated including CXCL5, cathepsin C, and neutrophil related S100 binding proteins. The new theory sheds a light to better control this detrimental illness. Anti-inflammatory agents could be used to manage schizophrenia in the near future.
Category: Quantitative Biology

[10] viXra:1202.0076 [pdf] submitted on 2012-02-24 14:46:48

Life as Evolving Software

Authors: Gregory Chaitin
Comments: 23 Pages.

In this paper we present an information-theoretic analysis of Darwin's theory of evolution, modeled as a hill-climbing algorithm on a fitness landscape. Our space of possible organisms consists of computer programs, which are subjected to random mutations. We study the random walk of increasing fitness made by a single mutating organism. In two different models we are able to show that evolution will occur and to characterize the rate of evolutionary progress, i.e., the rate of biological creativity.
Category: Quantitative Biology

Replacements of recent Submissions

[27] viXra:1802.0341 [pdf] replaced on 2018-02-25 23:43:58

Genetic Groups and the Feasibility of Reference Sire Schemes

Authors: Stephen P. Smith, Robert D. Scarth, Bruce Tier
Comments: 8 Pages.

A method of measuring linkage in sire reference schemes is described. The method consists of determining estimability and prediction error variance for linear contrasts when the assumed animal model includes genetic groups. Base animals in a herd are assigned a common genetic group and different herds correspond to different genetic groups. The set of linear contrasts used to determine linkage is the set of group differences. Groups differences can be scrutinized using a simplified lease-squares analysis.
Category: Quantitative Biology

[26] viXra:1709.0307 [pdf] replaced on 2017-09-29 10:13:08

The Existence of God: An Application of the Poisson Distribution

Authors: Charles M. Byrne
Comments: 14 pages, Keywords: God, evolution, mutation, recombination, genetics, molecular biology, naturalism, Poisson distribution

In his theory of evolution by natural selection, Charles Darwin provided a plausible alternative to Christianity's creation account of human origins. In response, the Christian botanist Asa Gray suggested to Darwin that the variation that drives evolution might be generated by God. Darwin rejected Gray’s hypothesis, invoking philosophical naturalism, a hallmark scientific paradigm. Darwin's conclusion was reached on ideological grounds rather than empirical ones. Biological evidence that emerged subsequent to Darwin’s time yields a different conclusion. A means to assess the question of the source of genetic variation is provided by fitting the Poisson distribution to counts of point mutation and chromosome crossover events at the DNA sites where they occur. A general failure of fit between observational data and the Poisson distribution constitutes an exception to the naturalistic paradigm, and thereby provides epistemic access to the existence of God.
Category: Quantitative Biology

[25] viXra:1708.0051 [pdf] replaced on 2017-08-11 01:26:45

Crispr Technology Challenge Facing the Numerical Integrity of Whole Human Genome DNA

Authors: Jean Claude Perez
Comments: 10 Pages. updated release

Background : Global analysis of 3 human genomes of increasing levels of evolution (Neanderthal / Sapiens Build34 / Sapiens hg38) reveals 2 levels of numerical constraints controlling, structuring and optimizing these genome's DNA sequences. A global constraint - called "HGO" for "Human Genome Optimum" - optimizes the genome at its global scale. The same operator applied to each of the 24 individual chromosomes reveals a hierarchical structure of these 24 chromosomes. Results : Then analysing the single strand DNA CG / TA proportions at whole chromosomes and genome scale reveals strong fine-tuned numerical ratios evidencing the "closure" nature (Varela's autopoiesis theory) of whole human genome.
Category: Quantitative Biology

[24] viXra:1705.0467 [pdf] replaced on 2017-06-01 23:38:49

Combining Genetic Similarities Among Known Relatives that Connect to a Pair of Unknown Relatives

Authors: Stephen P. Smith, Cambrian Lopez, Nicole Lam
Comments: 12 Pages.

Smith, Lopez and Lam described how to combine genetic similarities, measured in centimorgans (cM), among declared relatives in an outside pedigree, and to concentrate those cM values into a single cM measurement for an envoy that is a representative of the outside pedigree. An unknown relative is presumed to be a descendant of the envoy, but has the cM values with relatives in the outside pedigree. That prior effort was a univariate analysis, where there is only one unknown relative with matches with others in the outside pedigree. The present paper presents a bivariate analysis, where there are two sisters that have matches with others in the outside pedigree. The cM values are now paired, where any DNA tested member of the pedigree has two cM values that match to both sisters. The bivariate analysis offers more efficient use of information, compared to two univariate analyses done for each sister in turn. This advantage comes with an increase in model complexity, in that a model is developed for treating three mutually exclusive categories representing genes found in the sisters: for genes in the first sister but not in the second sister; genes common to both sisters; or genes in the second sister but not in the first. The model is applied to the inheritance of the cM values in the pedigree. Even though the number of random effects is increased by a factor of three, the number of fixed effects that actually spend two degrees of freedom is unchanged from the univariate analysis. This is on top of the doubling of the number of observations for the bivariate analysis compared to one univariate analysis.
Category: Quantitative Biology

[23] viXra:1704.0151 [pdf] replaced on 2017-04-19 12:54:03

Current Return to Lamarck in Agreement with Darwin

Authors: Andrzej Gecow
Comments: 12 Pages. in Polish

The terms ‘Darwinism’ and ‘Lamarckism’ mean different things to different people. Nowadays, they are rarely used in a historically correct way – clime Jablonka and Lamb, the scientists that mainly contribute to proving than not only genes can curry hereditary information and new hereditary channels show characteristic of Lamarckian mechanisms. Especially Lamarckism was seen in false and superficial way in lot of aspects. The inheritance of acquired characters was connected to Lamarck. It was rejected too radically. Today it revives but mainly not basing on epigenetic inheritance. Generally Lamarckian mechanisms increase in the complex and diverse ways the chances of accurate adaptive changes, so they no longer look like a random, appear as ‘effects of instructions’ or ‘directed variations’ but these ‘instructions’ have been previously acquired through Darwinian natural selection. The richness of these phenomena causes great difficulty of their brief describtion. Lamarckian dimension of evolution is now known better. This phenomena cannot be explained in the range of Modern Synthesis assumptions. It does not mean, that MS is false and should be rejected. Lamarckian mechanisms are created by Darwinian natural selection, but their explanations need wider assumptions, than are a basis of MS, means Extended Evolutionary Synthesis is necessary. This theme is one of the main in current discussion.
Category: Quantitative Biology

[22] viXra:1703.0172 [pdf] replaced on 2017-03-17 16:15:01

On Richard III, The Livingstons of Callendar, and the Conflict Between Genealogy and Genetics

Authors: John Smith
Comments: 31 Pages.

A skeleton excavated at the presumed site of the Grey Friars friary in Leicester in 2012 is almost certainly that of the English king, Richard III (1452 -1485), and mtDNA (which is passed from mother to child) extracted from the skeleton matches mtDNA taken from descendants of Richard's sister Anne of York. However Y-DNA (which is passed from father to son) extracted from the skeleton apparently doesn't match Y-DNA taken from descendants of Henry Somerset the 5th Duke of Beaufort, who according to history descended from Richard's 2nd great grand father Edward III (1312 - 1377). The implication according to geneticists, and the media, is that there is a 'false paternity event' somewhere between Edward and the Somersets. Also, the false paternity events don't end there, for only 4 of these 5 Somerset descendants match each other. And it may be worse even than this: the patrilineal line of a Frenchman named Patrice de Warren apparently traces back to Richard III through the illegitimate son of Edward III's 4th great grandfather, Geoffrey Plantagenet, Count of Anjou (1113 - 1151), but de Warren's Y-DNA doesn't match that of either Richard III or any of the Somersets. In this note, a formula for calculating the time of the most recent common ancestor is introduced, and some of its consequences outlined. This formula arises from a mathematical framework within which it is possible that the traditional genealogy is correct, and that Geoffrey Plantaganet was the father of a male line incorporating Richard III, all 5 Somersets, and Patrice de Warren.
Category: Quantitative Biology

[21] viXra:1701.0300 [pdf] replaced on 2017-10-21 07:02:14

Golden and Harmonic Mean in the Genetic Code

Authors: Miloje M. Rakočević
Comments: 8 Pages. From Proceedings of the 2nd International Conference “Theoretical Approaches to BioInformation Systems” (TABIS.2013), September 17 – 22, 2013, pp. 205-2014, Belgrade, Serbia.

In previous two works [1], [2] we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table (GCT), i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table (DT) and triplets Table (TT), over polarity of amino acids, measured by Cloister energy. (Miloje M. Rakočević) (Belgrade, 6.01.2017) (www.rakocevcode.rs) (mirkovmiloje@gmail.com)
Category: Quantitative Biology

[20] viXra:1512.0411 [pdf] replaced on 2015-12-27 09:48:34

Clustering of Pancreatic Endocrine Tumors Via Microarray Gene Expression Analysis

Authors: Silvia Strada, Diego Liberati
Comments: 10 Pages. submitted

A simple, multivariable and linearly initial- ized clustering is shown to be able to deal with unsu- pervised classification of the data originating from pan- creatic endocrine tumors (PET). Results are discussed almost only on the data science side, leaving a more biological discussion to future work, even in the quest of possible hidden pathways.
Category: Quantitative Biology

[19] viXra:1510.0509 [pdf] replaced on 2015-11-18 21:00:17

Non-Phosphorylating And Phosphorylating Oxidoreductase Glyceraldehyde-3-Phosphate Dehydrogenase As Part Of A Structure-Based Design In Glycolysis As The Glycolytic Protein G3PD.

Authors: Mark R. Brenneman
Comments: 13 Pages.

This enzyme is an example of moonlighting protein which is validated and replaced by alternative reference genes that link (in their nuclear forms) on the multifunctional properties of the enzyme GAPDH known as a key enzyme in glycolysis that contributes to a number of diverse cellular functions unrelated to glycolysis depending upon its subcellular location. GAPDH is a key enzyme in glycolysis the most commonly used expression is as a housekeeping gene.
Category: Quantitative Biology

[18] viXra:1508.0110 [pdf] replaced on 2015-08-16 08:50:17

Estimating the PML Risk on Natalizumab: a Simple Approach

Authors: Julian Borchardt
Comments: 7 Pages. The results from this paper have been published in Multiple Sclerosis and Related Disorders (Vol. 8, pp. 145-150, 2016, doi:10.1016/j.msard.2016.03.005). The complete PDF can be downloaded for free from http://authors.elsevier.com/a/1TQWn7skoepyJK

In this short note, we show how to quickly verify the correctness of the estimates of the PML risk on natalizumab established in [Borchardt 2015]. Our approach is simple and elementary in that it requires virtually no knowledge of either statistics or probability theory. For a Kaplan-Meier curve of the PML incidence may be found in [O'Connor et al 2014], based on postmarketing data as of early August 2013, and just using the information from that chart, it is possible to directly derive estimates of the risk of PML in JCV-seropositive natalizumab-treated patients according to prior or no prior immunosuppression. Actually, the resulting figures are almost identical to the ones in [Borchardt 2015], even though the latter were obtained in a very different fashion.
Category: Quantitative Biology

[17] viXra:1504.0148 [pdf] replaced on 2015-04-19 14:13:15

Carefully Estimating the Incidence of Natalizumab-Associated PML

Authors: Julian Borchardt
Comments: 45 Pages. Parts of this manuscript have been published in Multiple Sclerosis and Related Disorders (Vol. 8, pp. 145-150, 2016, doi:10.1016/j.msard.2016.03.005). The complete PDF can be downloaded for free from http://authors.elsevier.com/a/1TQWn7skoepyJK

We show that the quarterly updates about the risk of PML during natalizumab therapy, while in principle helpful, underestimate the real incidences systematically and significantly. Calculating the PML incidences using an appropriate method and on realistic assumptions, we obtain estimates that are up to 80% higher. In fact, with the recent paper [Plavina et al 2014], our approximate incidences are up to ten times as high. The present article describes the shortcomings of the methods used in [Bloomgren et al 2012] and by Plavina et al for computing incidences, and demonstrates how to properly estimate the true (prospective) risk of developing PML during natalizumab treatment. One application is that the newest data concerning the advances in risk-mitigation through the extension of dosing intervals, although characterised as not quite statistically significant, are in fact significant. Lastly, we discuss why the established risk-stratification algorithms, even on assessing the PML incidences correctly, are no longer state-of-the-art; in the light of all the progress that has been made so far, already today it is possible to reliably identify over 95% of patients in whom (a personalised regimen of) natalizumab should be very safe.
Category: Quantitative Biology

[16] viXra:1501.0230 [pdf] replaced on 2015-01-27 15:12:12

On the Completeness of Genetic Code: Part IV

Authors: Miloje M. Rakocevic
Comments: 4 Pages. In relation to V1, three Surveys and Table 3 are added

In this fourth part of the work about the completeness of the genetic code, we present further connections and relations between nucleotide doublets and triplets within Genetic Code Table.
Category: Quantitative Biology

[15] viXra:1411.0036 [pdf] replaced on 2014-12-16 03:49:17

The Enigma of Darwin Diagram

Authors: Miloje M. Rakocevic
Comments: 96 Pages. This is a pre-print form for a booklet with the same title; the suggestions are welcome! As new, in relation to V3, here are Appendices H & K, and Remark 4.2.

According to my best knowledge, for the first time here is presented a hypothesis, that the one and only accompanying diagram in Darwin famous book On the Origin of Species contains, may be, a hidden code. Direct inspection reveals that the Diagram, viewed as built of four parts [(two upper and two lower / two left and two right); (two with more and two with less branches / two with multiple and two with single branches)], corresponds to the logical square of the genetic code. When, however, viewed as built of two parts (upper and lower), then it corresponds with Shcherbak diagram (Shcherbak, 1993, 1994) of four-codon and non-four-codon amino acids; not only by the form but also by the number of elementary quantities. The number of nucleons in the upper part of Shcherbak diagram (four-codon amino acids) is determined by the Pythagorean law, meaning that the total number of nucleons makes the product of the number 25 and Prime quantum 037 (925); and the number of branches in the lower part of Darwin diagram is determined by the law of Plato, meaning that the total number of branches makes the product of the number 216 and First quantum 01 (216). On the other hand, in the lower part of the Shcherbak diagram there are 60 of Prime quantum 037 (2220), while in the upper part of the Darwin diagram there are 60 of First quantum 01 (60). There are 216 + 60 = 276 branches (in total), and this number is also the number taken from a specific and unique arithmetical system. Furthermore, it is shown that Darwin, starting from the basic structure of the Diagram, formed a sophisticated structure which strictly corresponds to the arithmetical and /or algebraic structures that also appear to be the key determinants of the genetic code.
Category: Quantitative Biology

[14] viXra:1411.0036 [pdf] replaced on 2014-11-18 06:03:22

The Enigma of Darwin Diagram

Authors: Miloje M. Rakocevic
Comments: 86 Pages. This is a pre-print form for a booklet with the same title; the suggestions are welcome!

According to my best knowledge, for the first time here is presented a hypothesis, that the one and only accompanying diagram in Darwin famous book On the Origin of Species contains, may be, a hidden code. Direct inspection reveals that the Diagram, viewed as built of four parts [(two upper and two lower / two left and two right); (two with more and two with less branches / two with multiple and two with single branches)], corresponds to the logical square of the genetic code. When, however, viewed as built of two parts (upper and lower), then it corresponds with Shcherbak diagram (Shcherbak, 1993, 1994) of four-codon and non-four-codon amino acids; not only by the form but also by the number of elementary quantities. The number of nucleons in the upper part of Shcherbak diagram (four-codon amino acids) is determined by the Pythagorean law, meaning that the total number of nucleons makes the product of the number 25 and Prime quantum 037 (925); and the number of branches in the lower part of Darwin diagram is determined by the law of Plato, meaning that the total number of branches makes the product of the number 216 and First quantum 01 (216). On the other hand, in the lower part of the Shcherbak diagram there are 60 of Prime quantum 037 (2220), while in the upper part of the Darwin diagram there are 60 of First quantum 01 (60). There are 216 + 60 = 276 branches (in total), and this number is also the number taken from a specific and unique arithmetical system. Furthermore, it is shown that Darwin, starting from the basic structure of the Diagram, formed a sophisticated structure which strictly corresponds to the arithmetical and /or algebraic structures that also appear to be the key determinants of the genetic code.
Category: Quantitative Biology

[13] viXra:1411.0036 [pdf] replaced on 2014-11-11 03:24:08

The Enigma of Darwin Diagram

Authors: Miloje M. Rakocevic
Comments: 83 Pages. This is a pre-print form for a booklet with the same title; the suggestions are welcome!

According to my best knowledge, for the first time here is presented a hypothesis, that the one and only accompanying diagram in Darwin famous book On the Origin of Species contains, may be, a hidden code. Direct inspection reveals that the Diagram, viewed as built of four parts [(two upper and two lower / two left and two right); (two with more and two with less branches / two with multiple and two with single branches)], corresponds to the logical square of the genetic code. When, however, viewed as built of two parts (upper and lower), then it corresponds with Shcherbak diagram (Shcherbak, 1993, 1994) of four-codon and non-four-codon amino acids; not only by the form but also by the number of elementary quantities. The number of nucleons in the upper part of Shcherbak diagram (four-codon amino acids) is determined by the Pythagorean law, meaning that the total number of nucleons makes the product of the number 25 and Prime quantum 037 (925); and the number of branches in the lower part of Darwin diagram is determined by the law of Plato, meaning that the total number of branches makes the product of the number 216 and First quantum 01 (216). On the other hand, in the lower part of the Shcherbak diagram there are 60 of Prime quantum 037 (2220), while in the upper part of the Darwin diagram there are 60 of First quantum 01 (60). There are 216 + 60 = 276 branches (in total), and this number is also the number taken from a specific and unique arithmetical system. Furthermore, it is shown that Darwin, starting from the basic structure of the Diagram, formed a sophisticated structure which strictly corresponds to the arithmetical and /or algebraic structures that also appear to be the key determinants of the genetic code
Category: Quantitative Biology

[12] viXra:1308.0135 [pdf] replaced on 2013-10-07 00:48:19

The Simulation of Th1 the Simulation of Th1 the Simulation of Th1 the Simulation of Th1 the Simulation of Th1 the Simulation of Th1-Th2 Cell Differentiation by Th2 Cell Differentiation by Th2 Cell Differentiation by Th2 Cell Differentiation by Th2 Cell di

Authors: Peisheng Shi, Hai Zhang, Zhiguo Zhu
Comments: 17 Pages.

In this article, we use system dynamical model (base on a set of nonlinear differential equations) and stochastic process model (Master equations of elementary reaction) to simulate the T helper cell differentiation (including Th1-Th2-Th17-Treg), especially the Th1-Th2 differentiations signaling network. We draw a conclusion that the critical trigger factor of naive T helper cells differentiation is the concentration of differentiation induced cytokines. We also compare the result of these two models as well as discussed the advantage and disadvantage of them.
Category: Quantitative Biology

[11] viXra:1308.0135 [pdf] replaced on 2013-08-31 14:45:28

The Simulation of Th1-Th2 Cell Differentiation by System Dynamic Model and Stochastic Processes

Authors: Peisheng Shi, Hai Zhang, Zhiguo Zhu
Comments: 17 Pages.

In this article, we use system dynamical model (base on a set of nonlinear differential equations) and stochastic process model (Master equations of elementary reaction) to simulate the T helper cell differentiation (including Th1-Th2-Th17-Treg), especially the Th1-Th2 differentiations signaling network. We draw a conclusion that the critical trigger factor of naive T helper cells differentiation is the concentration of differentiation induced cytokines. We also compare the result of these two models as well as discussed the advantage and disadvantage of them.
Category: Quantitative Biology

[10] viXra:1205.0090 [pdf] replaced on 2012-06-12 09:22:14

Sepsis is a Syndrome with Hyperactivity of TH17-Like Innate Immunity and Hypoactivity of Adaptive Immunity

Authors: Wan-Jiung Hu
Comments: 66 Pages.

Currently, there are two major theories for the pathogenesis of sepsis: hyperimmune and hypoimmune. Hyperimmune theory suggests that cytokine storm causes the symptoms of sepsis. On the contrary, hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By using microarray study, this study implies that hyperactivity of TH17-like innate immunity and failure of adaptive immunity are noted in sepsis patients. I find out that innate immunity related genes are significantly up-regulated including CD14, TLR1,2,4,5,8, HSP70, CEBP proteins, AP1(JUNB, FOSL2), TGF-β, IL-6, TGF-α, CSF2 receptor, TNFRSF1A, S100A binding proteins, CCR2, formyl peptide receptor2, amyloid proteins, pentraxin, defensins, CLEC5A, whole complement machinery, CPD, NCF, MMP, neutrophil elastase, caspases, IgG and IgA Fc receptors(CD64, CD32), ALOX5, PTGS, LTB4R, LTA4H, and ICAM1. Majority of adaptive immunity genes are down-regulated including MHC related genes, TCR genes, granzymes/perforin, CD40, CD8, CD3, TCR signaling, BCR signaling, T & B cell specific transcription factors, NK killer receptors, and TH17 helper specific transcription factors(STAT3, RORA, REL). In addition, Treg related genes are up-regulated including TGFβ, IL-15, STAT5B, SMAD2/4, CD36, and thrombospondin. Thus, both hyperimmune and hypoimmune play important roles in the pathophysiology of sepsis.
Category: Quantitative Biology

[9] viXra:1205.0090 [pdf] replaced on 2012-06-10 20:13:06

Sepsis is a Syndrome with Hyperactivity of TH17-Like Innate Immunity and Hypoactivity of Adaptive Immunity

Authors: Wan-Jiung Hu
Comments: 64 Pages.

Currently, there are two major theories for the pathogenesis of sepsis: hyperimmune and hypoimmune. Hyperimmune theory suggests that cytokine storm causes the symptoms of sepsis. On the contrary, hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By using microarray study, this study implies that hyperactivity of TH17-like innate immunity and failure of adaptive immunity are noted in sepsis patients. I find out that innate immunity related genes are significantly up-regulated including CD14, TLR1,2,4,5,8, HSP70, CEBP proteins, AP1(JUNB, FOSL2), TGF-β, IL-6, TGF-α, CSF2 receptor, TNFRSF1A, S100A binding proteins, CCR2, formyl peptide receptor2, amyloid proteins, pentraxin, defensins, CLEC5A, whole complement machinery, CPD, NCF, MMP, neutrophil elastase, caspases, IgG and IgA Fc receptors(CD64, CD32), ALOX5, PTGS, LTB4R, LTA4H, and ICAM1. Majority of adaptive immunity genes are down-regulated including MHC related genes, TCR genes, granzymes/perforin, CD40, CD8, CD3, TCR signaling, BCR signaling, T & B cell specific transcription factors, NK killer receptors, and TH17 helper specific transcription factors(STAT3, RORA, REL). In addition, Treg related genes are up-regulated including TGFβ, IL-15, STAT5B, SMAD2/4, CD36, and thrombospondin. Thus, both hyperimmune and hypoimmune play important roles in the pathophysiology of sepsis.
Category: Quantitative Biology

[8] viXra:1205.0090 [pdf] replaced on 2012-06-03 09:52:38

Sepsis is a Syndrome with Hyperactivity of TH17-Like Innate Immunity and Hypoactivity of Adaptive Immunity

Authors: Wan-Jiung Hu
Comments: 58 Pages.

Currently, there are two major theories for the pathogenesis of sepsis: hyperimmune and hypoimmune. Hyperimmune theory suggests that cytokine storm causes the symptoms of sepsis. On the contrary, hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By using microarray study, this study implies that hyperactivity of TH17-like innate immunity and failure of adaptive immunity are noted in sepsis patients. Thus, both hyperimmune and hypoimmune play important roles in the pathophysiology of sepsis.
Category: Quantitative Biology

[7] viXra:1205.0090 [pdf] replaced on 2012-05-29 02:10:59

Sepsis is a Syndrome with Hyperactivity of TH17-Like Innate Immunity and Hypoactivity of Adaptive Immunity

Authors: Wan-Jiung Hu
Comments: 57 Pages.

Currently, there are two major theories for the pathogenesis of sepsis: hyperimmune and hypoimmune. Hyperimmune theory suggests that cytokine storm causes the symptoms of sepsis. On the contrary, hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By using microarray study, this study implies that hyperactivity of TH17-like innate immunity and failure of adaptive immunity are noted in sepsis patients. Thus, both hyperimmune and hypoimmune play important roles in the pathophysiology of sepsis.
Category: Quantitative Biology

[6] viXra:1204.0090 [pdf] replaced on 2012-05-10 03:03:16

Acute Respiratory Distress Syndrome is a TH17-Like and Treg Immune Disease

Authors: Wan-Jiung Hu
Comments: 44 Pages.

Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading to respiratory failure and subsequent mortality. Sepsis is the leading cause of acute respiratory distress syndrome. Thus, extracellular bacteria play an important role in the pathophysiology of ARDS. Overactivated neutrophils are the major effector cells in ARDS. Thus, extracellular bacteria triggered TH17-like innate immunity with neutrophil activation counts for the etiology of ARDS. Here, I use microarray analysis to describe TH17-like innate immunity related cytokine including TGF-β and IL-6 up-regulation in whole blood of ARDS patients. Innate TH17 related TLR1,2,4,5,8, HSP70, G-CSF, GM-CSF, complements, defensin, PMN chemokines, cathepsins, Fc receptors, NCFs, FOS, JunB, CEBPs, NFkB, and leukotriene B4 are all up-regulated. TGF-β secreting Treg cells play important roles in lung fibrosis. Up-regulation of Treg associated STAT5B and TGF-β with down-regulation of MHC genes, TCR genes, and costimulation molecule CD86 are noted. Key TH17 transcription factors, STAT3 and RORα, are down-regulated. Thus, the full adaptive TH17 helper CD4 T cells may not be successfully triggered. Many fibrosis promoting genes are also up-regulated including MMP8, MMP9, FGF13, TIMP1, TIMP2, PLOD1, P4HB, P4HA1, PDGFC, HMMR, HS2ST1, CHSY1, and CSGALNACT. Failure to induce successful adaptive immunity could also attribute to ARDS pathogenesis. Thus, ARDS is actually a TH17-like and Treg immune disorder.
Category: Quantitative Biology

[5] viXra:1204.0090 [pdf] replaced on 2012-05-09 05:14:56

Acute Respiratory Distress Syndrome is a TH17 and Treg Immune Disease

Authors: Wan-Jiung Hu
Comments: 44 Pages.

Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading to respiratory failure and subsequent mortality. Sepsis is the leading cause of acute respiratory distress syndrome. Thus, extracellular bacteria play an important role in the pathophysiology of ARDS. Overactivated neutrophils are the major effector cells in ARDS. Thus, extracellular bacteria triggered TH17 host immunity with neutrophil activation counts for the etiology of ARDS. Here, I use microarray analysis to describe TH17 innate immunity related cytokine including TGF-β and IL-6 up-regulation in whole blood of ARDS patients. Innate TH17 related TLR1,2,4,5,8, HSP70, G-CSF, GM-CSF, complements, defensin, PMN chemokines, cathepsins, Fc receptors, NCFs, STAT5B, FOS, JunB, CEBPs, NFkB, and leukotriene B4 are all up-regulated. TGF-β secreting Treg cells play important roles in lung fibrosis. Up-regulation of STAT5B and TGF-β with down-regulation of MHC genes, TCR genes, and costimulation molecule CD86 are noted. Many fibrosis promoting genes are also up-regulated including MMP8, MMP9, FGF13, TIMP1, TIMP2, PLOD1, P4HB, P4HA1, PDGFC, HMMR, HS2ST1, CHSY1, and CSGALNACT. Failure to induce successful adaptive immunity could also attribute to ARDS pathogenesis. Thus, ARDS is actually a TH17 and Treg immune disorder.
Category: Quantitative Biology

[4] viXra:1204.0090 [pdf] replaced on 2012-05-04 07:52:09

Acute Respiratory Distress Syndrome is a TH17 and Treg Immune Disease

Authors: Wan-Jiung Hu
Comments: 39 Pages.

Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading to respiratory failure and subsequent mortality. Sepsis is the leading cause of acute respiratory distress syndrome. Thus, extracellular bacteria play an important role in the pathophysiology of ARDS. Overactivated neutrophils are the major effector cells in ARDS. Thus, extracellular bacteria triggered TH17 host immunity with neutrophil activation counts for the etiology of ARDS. Here, I use microarray analysis to describe TH17 related cytokine up-regulation in whole blood of ARDS patients. In addition, TGF-β secreting Treg cells play important roles in lung fibrosis. Thus, ARDS is actually a TH17 and Treg immune disorder.
Category: Quantitative Biology

[3] viXra:1204.0090 [pdf] replaced on 2012-05-03 08:23:33

Acute Respiratory Distress Syndrome is a TH17 and Treg Immune Disease

Authors: Wan-Jiung Hu
Comments: 34 Pages.

Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading to respiratory failure and subsequent mortality. Sepsis is the leading cause of acute respiratory distress syndrome. Thus, extracellular bacteria play an important role in the pathophysiology of ARDS. Overactivated neutrophils are the major effector cells in ARDS. Thus, extracellular bacteria triggered TH17 host immunity with neutrophil activation counts for the etiology of ARDS. Here, I use microarray analysis to describe TH17 related cytokine up-regulation in whole blood of ARDS patients. In addition, TGF-β secreting Treg cells play important roles in lung fibrosis. Thus, ARDS is actually a TH17 and Treg immune disorder.
Category: Quantitative Biology