Quantitative Biology

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Recent submissions

Any replacements are listed further down

[33] 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

[32] 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

[31] 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

[30] 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

[29] 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

[28] viXra:1311.0062 [pdf] submitted on 2013-11-10 01:54:06

Flexibility in Food Extraction Techniques in Urban Free-Ranging Bonnet Macaques, Macaca Radiata

Authors: Madhur Mangalam, Mewa Singh
Comments: 26 Pages.

Non-human primate populations, other than responding appropriately to naturally occurring challenges, also need to cope with anthropogenic factors such as environmental pollution, resource depletion, and habitat destruction. Populations and individuals are likely to show considerable variations in food extraction abilities, with some populations and individuals more efficient than others at exploiting a set of resources. In this study, we examined among urban free-ranging bonnet macaques, Macaca radiata (a) local differences in food extraction abilities, (b) between-individual variation and within-individual consistency in problem-solving success and the underlying problem-solving characteristics, and (c) behavioral patterns associated with higher efficiency in food extraction. When presented with novel food extraction tasks, the urban macaques having more frequent exposure to novel physical objects in their surroundings, extracted food material from PET bottles and also solved another food extraction task (i.e., extracting an orange from a wire mesh box), more often than those living under more natural conditions. Adults solved the tasks more frequently than juveniles, and females more frequently than males. Both solution-technique and problem-solving characteristics varied across individuals but remained consistent within each individual across the successive presentations of PET bottles. The macaques that solved the tasks showed lesser within-individual variation in their food extraction behavior as compared to those that failed to solve the tasks. A few macaques appropriately modified their problem-solving behavior in accordance with the task requirements and solved the modified versions of the tasks without trial-and-error learning. These observations are ecologically relevant – they demonstrate considerable local differences in food extraction abilities, between-individual variation and within-individual consistency in food extraction techniques among free-ranging bonnet macaques, possibly affecting the species’ local adaptability and resilience to environmental changes.
Category: Quantitative Biology

[27] viXra:1311.0061 [pdf] submitted on 2013-11-10 01:56:18

Division of Labor in Hand Usage in Free-Ranging Bonnet Macaques, Macaca Radiata

Authors: Madhur Mangalam, Nisarg Desai, Mewa Singh
Comments: 31 Pages.

Primates exhibit laterality in hand usage either in terms of (a) hand with which an individual solves a task or while solving a task that requires both hands, executes the most complex action, i.e., ‘hand preference’, or (b) hand with which an individual executes actions most efficiently, i.e., ‘hand performance’. Observations from previous studies indicate that laterality in hand usage might reflect specialization of the two hands for accomplishing tasks that require maneuvering dexterity or physical strength. However, no existing study has investigated handedness with regard to this possibility.In this study, we examined laterality in hand usage in urban free-ranging bonnet macaques, Macaca radiata with regard to the above possibility. While solving four distinct food extraction tasks which varied in the number of steps involved in the food extraction process and the dexterity required in executing the individual steps, the macaques consistently used one hand for extracting food (i.e., task requiring maneuvering dexterity) – the ‘maneuvering’ hand, and the other hand for supporting the body (i.e., task requiring physical strength) – the ‘supporting’ hand. Analogously, the macaques used the maneuvering hand for the spontaneous routine activities that involved maneuvering in three-dimensional space, such as grooming, and hitting an opponent during an agonistic interaction, and the supporting hand for those that required physical strength, such as pulling the body up while climbing. Moreover, while solving a task that ergonomically forced the usage of a particular hand, the macaques extracted food faster with the maneuvering hand as compared to the supporting hand, demonstrating the higher maneuvering dexterity of the maneuvering hand. As opposed to the conventional ideas of handedness in non-human primates, these observations demonstrate division of labor between the two hands marked by their consistent usage across spontaneous and experimental tasks requiring maneuvering in three-dimensional space or those requiring physical strength.
Category: Quantitative Biology

[26] 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

[25] 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

[24] viXra:1307.0091 [pdf] submitted on 2013-07-18 07:58:19

The Noise and the Kiss in the Cancer Stem Cells Niche

Authors: Renato Vieira dos Santos, Linaena Méricy da Silva
Comments: 9 Pages.

There is a persistent controversy regarding the frequency of cancer stem cells (CSCs) in solid tumors. Initial studies indicated that these cells had a frequency ranging from 0.0001% to 0.1% of total cells. Recent studies have shown that this does not seem to be always the case. Some of these studies have indicated a frequency of 40%. Through a simple population dynamics model, we studied the effects of stochastic noise and cellular plasticity in the minimal path size of a cancer stem cells population, similar to what is done in what is sometimes called the Kierstead–Skellam–Slobodkin (KISS) Size analysis. We show that the possibility of large variations in the results obtained in the experiments may be a consequence of the different conditions under which the different experiments are submitted, specifically regarding the effective cell niche size where stem cells are transplanted. We also show the possibility of a noise induced transition where the stationary probability distribution of the CSC population can present bimodality.
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

[9] viXra:1112.0095 [pdf] submitted on 2011-12-31 15:35:48

Chaotic Attractor in Tumor Growth and Decay

Authors: Wen-sau Yim, Michael Harney
Comments: 14 Pages.

Cancer growth and decay can be modeled as a system of chaotic nonlinear differential equations. The system is based on a reaction-diffusion cancer growth model, expressed by a mathematical model that is simplified by Ivancevicet. al. This allows useful parameters to be applied for simulation and then recreated in C and Java, to directly compare with its predecessor project. A variation in a set of the parameters is found to decrease tumor growth in the early stages of tumor development.
Category: Quantitative Biology

[8] viXra:1110.0001 [pdf] submitted on 1 Oct 2011

Heart Dipole Tracking Algorithm

Authors: Michael Harney
Comments: 6 pages

This paper describes a method of tracking the electromagnetic dipole, with a three-dimensional representation of the dipole being graphically displayed in real-time so as to provide diagnostic information about a patient's heart. By knowing the coordinates and orientation of the heart dipole and comparing this data with a healthy heart, cardio-specialists may be able to determine where damaged tissue is located or other diseases in progress.
Category: Quantitative Biology

[7] viXra:1106.0003 [pdf] submitted on 5 Jun 2011

Klein Bottle Logophysics, Topological Chemistry, The Genetic Code, Universal Rewrite System, Bauplans and the Surmountal of the Cartesian Cut.

Authors: Diego Lucio Rapoport
Comments: 16 pages

We reintroduce logophysics based on self-referential torsion fields and the Klein bottle (KB) logic, which unifies the objective and subjective realms. We apply it to biology, particularly allosterics and the genetic code. We reveal several topologies of the genetic code and its bioinformatics codification, in particular the hyper Klein bottle (HKB) surface. We relate it to the Universal Rewrite System, the Code of Nature, and Dirac algebra.We find that the double helix is unnecessary in this setting, and elaborate the ontology of 3D with regards to time, multistable perception, and a topological (lawless) form of Newton's Third Law. We present the key ideas for a logophysical theory for contextual evolution.
Category: Quantitative Biology

[6] viXra:1103.0085 [pdf] submitted on 22 Mar 2011

Logistic Equation of Population Growth or Exhaustion of Main Resources: Generalization to the Case of Reactive Environment, Reduction to Abel Ode, Asymptotic Solution for Final Human Population Prognosis.

Authors: Sergey V. Ershkov
Comments: 6 pages.

Here are presented a key points of new universal model for population evolution in reactive environment: 1) generalization of the Logistic equation in the case of reactive environment for population dynamics model in biology (also, for the model of exhaustion of main resources in geology, or for filling of an ecological niches in ecology, or for modeling of capacities of a proper markets in economics), 2) new type of asymptotic solution for such an equation (which is tested on human population growth), 3) reduction of such an equation to Abel ordinary differential equation in general case.
Category: Quantitative Biology

[5] viXra:1008.0004 [pdf] submitted on 3 Aug 2010

Methods in Environmental Biotechnology for Environmentalists

Authors: W. B. Vasantha Kandasamy, Florentin Smarandache, S. R. Kannan, S. Ramathilagam
Comments: 144 Pages.

The study of environmental pollution by chemicals used in agriculture as pesticide or as fertilizers or pollution caused by industries and chemical plants which use chemicals have not been analysed systematically. This book has five chapters. First chapter is introductory in nature. Here we just study chemical pollution caused by garment industries in chapter two of this book using fuzzy associative memories.
Category: Quantitative Biology

[4] viXra:1005.0022 [pdf] submitted on 11 Mar 2010

Analysis of Social Aspects of Migrant Labourers Living with Hiv/aids Using Fuzzy Theory and Neutrosophic Cognitive Maps

Authors: W. B. Vasantha Kandasamy, Florentin Smarandache
Comments: 472 pages

Neutrosophic logic grew as an alternative to the existing topics and it represents a mathematical model of uncertainty, vagueness, ambiguity, imprecision, undefined-ness, unknown, incompleteness, inconsistency, redundancy and contradiction. Despite various attempts to reorient logic, there has remained an essential need for an alternative system that could infuse into itself a representation of the real world. Out of this need arose the system of neutrosophy and its connected logic, neutrosophic logic. This new logic, which allows also the concept of indeterminacy to play a role in any real-world problem, was introduced first by one of the authors Florentin Smarandache.
Category: Quantitative Biology

[3] viXra:1004.0021 [pdf] submitted on 8 Mar 2010

Statistical Modelling of Primary Ewing Tumours of the Bone

Authors: Sreepurna Malakar, Florentin Smarandache, Sukanto Bhattacharya
Comments: 12 pages

This short technical paper advocates a bootstrapping algorithm from which we can form a statistically reliable opinion based on limited clinically observed data, regarding whether an osteo-hyperplasia could actually be a case of Ewing's osteosarcoma. The basic premise underlying our methodology is that a primary bone tumour, if it is indeed Ewing's osteosarcoma, cannot increase in volume beyond some critical limit without showing metastasis. We propose a statistical method to extrapolate such critical limit to primary tumour volume. Our model does not involve any physiological variables but rather is entirely based on time series observations of increase in primary tumour volume from the point of initial detection to the actual detection of metastases.
Category: Quantitative Biology

[2] viXra:1003.0132 [pdf] submitted on 6 Mar 2010

A Proposed Artificial Neural Network Classifier to Identify Tumor Metastases Part I

Authors: M. Khoshnevisan, Sukanto Bhattacharya, Florentin Smarandache
Comments: 14 pages

In this paper we propose a classification scheme to isolate truly benign tumors from those that initially start off as benign but subsequently show metastases. A non-parametric artificial neural network methodology has been chosen because of the analytical difficulties associated with extraction of closed-form stochastic-likelihood parameters given the extremely complicated and possibly non-linear behavior of the state variables. This is intended as the first of a three-part research output. In this paper, we have proposed and justified the computational schema. In the second part we shall set up a working model of our schema and pilot-test it with clinical data while in the concluding part we shall give an in-depth analysis of the numerical output and model findings and compare it to existing methods of tumor growth modeling and malignancy prediction.
Category: Quantitative Biology

[1] viXra:0702.0027 [pdf] submitted on 25 Feb 2007

Distant Solvent-Mediated Interaction Between Different Proteins and Between Proteins and Cells. Virtual Replicas of Drugs and Homeopathic Memory.

Authors: Alex Kaivarainen
Comments: recovered from sciprint.org

During many years our Laboratory of molecular biophysics was involved in study of solvent dependent large-scale dynamics of proteins determined by relative thermal mobility of their domains and subunits. The role of large-scale dynamics in the mechanism of protein function, the signal transmission, allosteric effects and other water dependent effects in protein solutions have been investigated.
Category: Quantitative Biology

Replacements of recent Submissions

[11] 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

[10] 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

[9] 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

[8] 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

[7] 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

[6] 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

[5] 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

[4] 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

[3] 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

[2] 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

[1] viXra:1103.0085 [pdf] replaced on 2012-05-19 03:51:43

Logistic Equation of Population Growth or Exhaustion of Main Resources: Generalization to the Case of Reactive Environment, Reduction to Abel Ode, Asymptotic Solution for Final Human Population Prognosis

Authors: Sergey V. Ershkov
Comments: 7 Pages. Keywords: Logistic equation; evolution of population; prognosis of Human population; reactive environment; catastrophes theory; Abel ODE

Here are presented a key points of new universal model for evolution of population in reactive environment: 1) generalization of the Logistic equation to the case of reactive environment for models of population dynamics in biology (also, for the model of exhaustion of main resources in geology, or for filling of an ecological niches in ecology, or for modeling of the capacities of a proper markets in economics), 2) new type of asymptotic solution for such equation (which is tested on human population growth), 3) reduction of such an equation to Abel ODE in general case.
Category: Quantitative Biology