Quantitative Biology

1304 Submissions

[3] 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

[2] 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

[1] 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