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5,300 | Results and Limitations of the Soliton Theory of DNA Transcription | q-bio.OT | It has been suggested by several authors that nonlinear excitations, in
particular solitary waves, could play a fundamental functional role in the
process of DNA transcription, effecting the opening of the double chain needed
for RNA Polymerase to be able to copy the genetic code. Some models have been
proposed to mode... | biology |
5,301 | Galilean Satellites as Sites for Incipient Life, and the Earth as its Shelter | q-bio.OT | Numerous problems connected with an assumption of the life origin on the
Earth do not arise on Galilean satellites. Here, in presence of a practically
non-salt water and of a great deal (~5-10%) of abiogenic organics, a great
diversity of conditions, which are unthinkable for the Earth, were realized
more than once. Th... | biology |
5,302 | Phase synchronization in cerebral hemodynamics | q-bio.OT | A healthy human brain is perfused with blood flowing laminarly through
cerebral vessels, providing brain tissue with substrates such as oxygen and
glucose. Under normal conditions, cerebral blood flow is controlled by
autoregulation as well as metabolic, chemical and neurogenic regulation.
Physiological complexity of t... | biology |
5,303 | Complex Systems Analysis of Cell Cycling Models in Carcinogenesis | q-bio.OT | Carcinogenesis is a complex process that involves dynamically inter-connected
modular sub-networks that evolve under the influence of micro-environmentally
induced perturbations, in non-random, pseudo-Markov chain processes. An
appropriate n-stage model of carcinogenesis involves therefore n-valued Logic
treatments of ... | biology |
5,304 | Applications of Novel Techniques to Health Foods, Medical and Agricultural Biotechnology | q-bio.OT | Selected applications of novel techniques in Agricultural Biotechnology,
Health Food formulations and Medical Biotechnology are being reviewed with the
aim of unraveling future developments and policy changes that are likely to
open new niches for Biotechnology and prevent the shrinking or closing the
existing ones. Am... | biology |
5,305 | Vaccination pattern affects immunological response | q-bio.OT | The response of the immune system to different vaccination patterns is
studied with a simple model. It is argued that the history and characteristics
of the pattern defines very different secondary immune responses in the case of
infection. The memory function of the immune response can be set to work in
very different... | biology |
5,306 | Mathematics, Biology, and Physics: Interactions and Interdependence | q-bio.OT | This paper traces the seminal roles that physicists and mathematicians have
played in the conceptual development of the biological sciences in the past,
and especially in the 19th and 20th centuries. | biology |
5,307 | 1/f Scaling in Heart Rate Requires Antagonistic Autonomic Control | q-bio.OT | We present the first systematic evidence for the origins of 1/f-type temporal
scaling in human heart rate. The heart rate is regulated by the activity of two
branches of the autonomic nervous system: the parasympathetic (PNS) and the
sympathetic (SNS) nervous systems. We examine alterations in the scaling
property when... | biology |
5,308 | SARS oubreaks in Ontario, Hong Kong and Singapore: the role of diagnosis and isolation as a control mechanism | q-bio.OT | In this article we use global and regional data from the SARS epidemic in
conjunction with a model of susceptible, exposed, infective, diagnosed, and
recovered classes of people (``SEIJR'') to extract average properties and rate
constants for those populations. The model is fitted to data from the Ontario
(Toronto) in ... | biology |
5,309 | The Basic Reproductive Number of Ebola and the Effects of Public Health Measures: The Cases of Congo and Uganda | q-bio.OT | Despite improved control measures, Ebola remains a serious public health risk
in African regions where recurrent outbreaks have been observed since the
initial epidemic in 1976. Using epidemic modeling and data from two
well-documented Ebola outbreaks (Congo 1995 and Uganda 2000), we estimate the
number of secondary ca... | biology |
5,310 | Discretization of Time Series Data | q-bio.OT | Data discretization, also known as binning, is a frequently used technique in
computer science, statistics, and their applications to biological data
analysis. We present a new method for the discretization of real-valued data
into a finite number of discrete values. Novel aspects of the method are the
incorporation of... | biology |
5,311 | Towards a Quantitative, Metabolic Theory for Mammalian Sleep | q-bio.OT | Sleep is one of the most noticeable and widespread phenomena occurring in
multicellular animals. Nevertheless, no consensus for a theory of its origins
has emerged. In particular, no explicit, quantitative theory exists that
elucidates or distinguishes between the myriad hypotheses proposed for sleep.
Here, we develop ... | biology |
5,312 | Reading Sequences of Interspike Intervals in Biological Neural Circuits | q-bio.OT | Sensory systems pass information about an animal's environment to higher
nervous system units through sequences of action potentials. When these action
potentials have essentially equivalent waveforms, all information is contained
in the interspike intervals (ISIs) of the spike sequence. We address the
question: How do... | biology |
5,313 | Impact of Climate Change on Forests in India | q-bio.OT | Global assessments have shown that future climate change is likely to
significantly impact forest ecosystems. The present study makes an assessment
of the impact of projected climate change on forest ecosystems in India. This
assessment is based on climate projections of Regional Climate Model of the
Hadley Centre (Had... | biology |
5,314 | Modeling stochastic gene expression under repression | q-bio.OT | Intrinsic transcriptional noise induced by operator fluctuations is
investigated with a simple spin like stochastic model. The effects of
transcriptional fluctuations in protein synthesis is probed by coupling
transcription and translation by an amplificative interaction. In the presence
of repression a new term contri... | biology |
5,315 | Pure multiplicative stochastic resonance of anti-tumor model with seasonal modulability | q-bio.OT | The effects of pure multiplicative noise on stochastic resonance in an
anti-tumor system modulated by a seasonal external field are investigated by
using theoretical analyses of the generalized potential and numerical
simulations. For optimally selected values of the multiplicative noise
intensity quasi-symmetry of two... | biology |
5,316 | Mechanochemical coupling of kinesin studied with the neck linker swing model | q-bio.OT | We have proposed the neck linker swing model to investigate the mechanism of
mechanochemical coupling of kinesin. The Michaelis-Menten-like curve for
velocity vs ATP concentration at different loads has been obtained, which is in
agreement with experiments. We have predicted that Michaelis constant doesn't
increase mon... | biology |
5,317 | Straub tail, the deprivation effect and addiction to aggression | q-bio.OT | It has been observed that male mice who are consistently winning fights with
conspecifics can raise their tail, which is very similar to a morphine-induced
Straub tail response. Since this response is a typical index of opiate
activation, it has been proposed that the opioidergic systems of such mice are
chronically ac... | biology |
5,318 | Thriving at high hydrostatic pressure: the example of ammonoids (extinct cephalopods) | q-bio.OT | Ammonoids are a group of extinct mollusks belonging to the same class of the
living genus Nautilus (Cephalopoda). In both Nautili and ammonoids, the
(usually planospiral) shell is divided into chambers separated by septa that
during the lifetime were filled with gas at atmospheric pressure. The
intersection of septa wi... | biology |
5,319 | Bistable equilibrium points of mercury body burden | q-bio.OT | In the last century mercury levels in the global environment have tripled as
a result of increased pollution from industrial, occupational, medicinal and
domestic uses \cite{BaMe03}. Glutathione is known to be the main agent
responsible for the excretion of mercury (we refer to \cite{Thim05},
\cite{ZalBar99} and \cite{... | biology |
5,320 | Use of the Metropolis algorithm to simulate the dynamics of protein chains | q-bio.OT | The Metropolis implementation of the Monte Carlo algorithm has been developed
to study the equilibrium thermodynamics of many-body systems. Choosing small
trial moves, the trajectories obtained applying this algorithm agree with those
obtained by Langevin's dynamics. Applying this procedure to a simplified
protein mode... | biology |
5,321 | Cicada's wings as determinant factor for the sound emission: The case of \textit{Quesada gigas} | q-bio.OT | Cicadas (Homoptera:Cicadidae) are insects able to produce loudly songs and it
is known that the mechanism to produce sound of tymballing cicadas works as a
Helmholtz resonator. In this work we offer evidence on the participation of the
wings in a high quality resonating process which defines the details of the
acoustic... | biology |
5,322 | Genetic Code as a Harmonic System | q-bio.OT | In a certain way, this paper presents the continuation of the previous one
which discussed the harmonic structure of the genetic code (Rakocevic, 2004).
Several new harmonic structures presented in this paper, through specific unity
and coherence, together with the previously presented (Rakocevic, 2004), show
that it m... | biology |
5,323 | Quantum Effects and Genetics Code: Dynamics and Information Transfer in DNA Replication | q-bio.OT | The possible role of quantum effects in transfer of genetic information is
studied. It's argued that the nucleotides selection during DNA replication is
performed by means of proton tunneling between nucleotide and DNA-polimerase
bound by hydrogen bonds. Such mechanism is sensitive to the structure of
nucleotide hydrog... | biology |
5,324 | Compression stress in opposite wood of angiosperms: observations in chestnut, mani and poplar | q-bio.OT | In order to face environmental constraints, trees are able to re-orient their
axes by controlling the stress level in the newly formed wood layers.
Angiosperms and gymnosperms evolved into two distinct mechanisms: the former
produce a wood with large tension pre-stress on the upper side of the tilted
axis, while the la... | biology |
5,325 | Nucleotide Frequencies in Human Genome and Fibonacci Numbers | q-bio.OT | This work presents a mathematical model that establishes an interesting
connection between nucleotide frequencies in human single-stranded DNA and the
famous Fibonacci's numbers. The model relies on two assumptions. First,
Chargaff's second parity rule should be valid, and, second, the nucleotide
frequencies should app... | biology |
5,326 | Gene expression from polynomial dynamics in the 2-adic information space | q-bio.OT | We perform geometrization of genetics by representing genetic information by
points of the 4-adic {\it information space.} By well known theorem of number
theory this space can also be represented as the 2-adic space. The process of
DNA-reproduction is described by the action of a 4-adic (or equivalently
2-adic) dynami... | biology |
5,327 | A number theoretical observation about the degeneracy of the genetic code | q-bio.OT | We discuss the similarity of the degeneration structure of the genetic code
with a pure number theoretic -- ``divisors code.'' The most interesting thing
about our observation is not that there is a connection between number theory
and the genetic code, but the simplicity of the rule. We hope that the
observation and t... | biology |
5,328 | Short-time dynamics of polypeptides | q-bio.OT | The authors study the short-time dynamics of helix-forming polypeptide chains
using an all-atom representation of the molecules and an implicit solvation
model to approximate the interaction with the surrounding solvent. The results
confirm earlier observations that the helix-coil transition in proteins can be
describe... | biology |
5,329 | Noise Correlation Induced Synchronization in a Mutualism Ecosystem | q-bio.OT | Understanding the cause of the synchronization of population evolution is an
important issue for ecological improvement. Here we present a
Lotka-Volterra-type model driven by two correlated environmental noises and
show, via theoretical analysis and direct simulation, that noise correlation
can induce a synchronization... | biology |
5,330 | The G-Ball, a New Icon for Codon Symmetry and the Genetic Code | q-bio.OT | A codon table is a useful tool for mapping codons to amino acids as they have
been assigned by nature. It has become a scientific icon because of the way it
embodies our understanding of this natural process and the way it immediately
communicates this understanding. However, advancements in molecular biology
over the ... | biology |
5,331 | Complexities of Human Promoter Sequences | q-bio.OT | By means of the diffusion entropy approach, we detect the scale-invariance
characteristics embedded in the 4737 human promoter sequences. The exponent for
the scale-invariance is in a wide range of $[ {0.3,0.9} ]$, which centered at
$\delta_c = 0.66$. The distribution of the exponent can be separated into left
and righ... | biology |
5,332 | Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs | q-bio.OT | This letter reports complete sets of two-fold symmetries between partitions
of the universal genetic code. By substituting bases at each position of the
codons according to a fixed rule, it happens that properties of the degeneracy
pattern or of tRNA aminoacylation specificity are exchanged. | biology |
5,333 | Dimensionality and dynamics in the behavior of C. elegans | q-bio.OT | A major challenge in analyzing animal behavior is to discover some underlying
simplicity in complex motor actions. Here we show that the space of shapes
adopted by the nematode C. elegans is surprisingly low dimensional, with just
four dimensions accounting for 95% of the shape variance, and we partially
reconstruct "e... | biology |
5,334 | The Light Quanta Modulated Physiological Response of Brassica Juncea Seedlings Subjected to Ni(II) Stress | q-bio.OT | This work is a study of the inter-relationship between parameters that
principally affect metal up-take in the plant. The relationships between the
concentration of metal in the growth medium, Cs, the concentration of metal
absorbed by the plant, Cp, and the total biomass achieved, M, all of which are
factors relevant ... | biology |
5,335 | Infected surfaces of vehicles as possible way of people's infection by bird flu pathogenic culture | q-bio.OT | Possible variant of people's infection by bird flu pathogenic culture in
passing of everyday infection is presented in the work: through the contact of
open parts of the skin with infected surfaces of the vehicle, that is the
sequent of the reused water, which contains all species spectrum of pathogen
accumulated on th... | biology |
5,336 | The genetic code multiplet structure, in one number | q-bio.OT | The standard genetic code multiplet structure as well as the correct
degeneracies, class by class, are all extracted from the (unique) number 23,
the order of the permutation group of 23 objects. | biology |
5,337 | Partition test and sexual motivation in male mice | q-bio.OT | Theoretical analysis of own and literature investigations of sexual
motivation with the use of the partition test [Kudryavtseva, 1987, 1994] in
male mice was carried out. It has been shown that appearance of a receptive
female in the neighboring compartment of common cage separated by perforated
transparent partition p... | biology |
5,338 | A model for exploring bird morphology | q-bio.OT | A simplified model of the bird skeleton along with elongation parameters for
the flight feathers is used to explore the diversity of bird shapes. Varying a
small number of parameters simulates a wide range of observed bird silhouettes.
The model may serve to examine developmental factors involved, help museum
curators ... | biology |
5,339 | Effect of THz-radiation on Behavior of Male Mice | q-bio.OT | Effect of terahertz radiation (3.6 THz, 81.5 mkm,15 mV) on some behavioral
patterns of intact mice has been investigated. In home cage mice demonstrated
avoidance of laser ray and enhanced replacement activity in free behavior.
Animals irradiated during 30 minutes manifested an increased level of anxiety,
which was eva... | biology |
5,340 | Top-Down Causation by Information Control: From a Philosophical Problem to a Scientific Research Program | q-bio.OT | It has been claimed that different types of causes must be considered in
biological systems, including top-down as well as same-level and bottom-up
causation, thus enabling the top levels to be causally efficacious in their own
right. To clarify this issue, important distinctions between information and
signs are intro... | biology |
5,341 | The immune system: look who's talking | q-bio.OT | Human language and its governing rules present a number of analogies with the
organization and structure of communication and information management in
living organisms. This chapter will provide a short general introduction about
grammar, as well as a brief explanation on how linguistic approaches
effectively contamin... | biology |
5,342 | Imposition of Different Optimizing Object with Non-Linear Constraints on Flux Sampling and Elimination of Free Futile Pathways | q-bio.OT | Constraint-based modeling has been widely used on metabolic networks
analysis, such as biosynthetic prediction and flux optimization. The linear
constraints, like mass conservation constraint, reversibility constraint,
biological capacity constraint, can be imposed on linear algorithms. However,
recently a non-linear c... | biology |
5,343 | Nucleosome shape dictates chromatin-fiber structure | q-bio.OT | Apart from being the gateway for all access to the eukaryotic genome,
chromatin has in recent years been identified as carrying an epigenetic code
regulating transcriptional activity. The detailed knowledge of this code
contrasts the ignorance of the fiber structure which it regulates, and none of
the suggested fiber m... | biology |
5,344 | Induction level determines signature of gene expression noise in cellular systems | q-bio.OT | Noise in gene expression, either due to inherent stochasticity or to varying
inter- and intracellular environment, can generate significant cell-to-cell
variability of protein levels in clonal populations. We present a theoretical
framework, based on stochastic processes, to quantify the different sources of
gene expre... | biology |
5,345 | Biological Organization and Negative Entropy: Based on Schroedinger's reflections | q-bio.OT | This paper proposes a systemic perspective for some aspects of both
phylogenesis and ontogenesis, in the light of the notion of biological
organization as negative entropy, following some hints by Schroedinger. To this
purpose, we introduce two extra principles to the thermodynamic ones, which are
(mathematically) comp... | biology |
5,346 | Predictability and epidemic pathways in global outbreaks of infectious diseases: the SARS case study | q-bio.OT | Background: The global spread of the severe acute respiratory syndrome (SARS)
epidemic has clearly shown the importance of considering the long-range
transportation networks in the understanding of emerging diseases outbreaks.
The introduction of extensive transportation data sets is therefore an
important step in orde... | biology |
5,347 | Towards an unifying perspective of the fundamental properties and structural principles governing the immune system | q-bio.OT | In the study of the basic properties observed in the immune system and, in a
broader view, in biological systems, several concepts have already been
mathematically formulated or treated in an analytical perspective, such as
degeneracy, robustness, noise, and bow tie architecture. These properties,
among others, seem to... | biology |
5,348 | Within-host HIV models with periodic antiretroviral therapy | q-bio.OT | This paper investigates the effect of drug treatment on the standard
within-host HIV model, assuming that therapy occurs periodically. It is shown
that eradication is possible under these periodic regimes, and we
quantitatively characterize successful drugs or drug combinations, both
theoretically and numerically. We a... | biology |
5,349 | The degeneracy of the genetic code and Hadamard matrices | q-bio.OT | The matrix form of the presentation of the genetic code is described as the
cognitive form to analyze structures of the genetic code. A similar matrix form
is utilized in the theory of signal processing. The Kronecker family of the
genetic matrices is investigated, which is based on the genetic matrix [C A; U
G], where... | biology |
5,350 | Matrix genetics, part 1: permutations of positions in triplets and symmetries of genetic matrices | q-bio.OT | The Kronecker family of the genetic matrices is investigated, which is based
on the genetic matrix [C T; A G], where C, T, A, G are the letters of the
genetic alphabet. The matrix [C T; A G] in the second Kronecker power is the
(4*4)-matrix of 16 duplets. The matrix [C T; A G] in the third Kronecker power
is the (8*8)-... | biology |
5,351 | Maximum Power Efficiency and Criticality in Random Boolean Networks | q-bio.OT | Random Boolean networks are models of disordered causal systems that can
occur in cells and the biosphere. These are open thermodynamic systems
exhibiting a flow of energy that is dissipated at a finite rate. Life does work
to acquire more energy, then uses the available energy it has gained to perform
more work. It is... | biology |
5,352 | Analytical Equations to the Chromaticity Cone: Algebraic Methods for Describing Color | q-bio.OT | We describe an affine transformation on the (CIE) color matching functions
and map the spectral locus as a circle. We then homogenize the right circular
cylinder erected by the circle, with respect to a normalizing plane and develop
an analytical equation to the chromaticity cone, for the spectral colors. In
the interi... | biology |
5,353 | The genetic code Via Godel encoding | q-bio.OT | The genetic code structure into distinct multiplet-classes as well as the
numeric degeneracies of the latter are revealed by a two-step process. First,
an empirical inventory of the degeneracies (of the shuffled multiplets) in two
specific equal moieties of the experimental genetic code table is made and
transcribed in... | biology |
5,354 | Drug absorption through a cell monolayer: a theoretical work on a non-linear three-compartment model | q-bio.OT | The subject of analysis is a non-linear three-compartment model, widely used
in pharmacological absorption studies. It has been transformed into a general
form, thus leading automatically to an appropriate approximation. This made the
absorption profile accessible and expressions for absorption times, apparent
permeabi... | biology |
5,355 | Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases | q-bio.OT | The production of peroxide and superoxide is an inevitable consequence of
aerobic metabolism, and while these particular "reactive oxygen species" (ROSs)
can exhibit a number of biological effects, they are not of themselves
excessively reactive and thus they are not especially damaging at physiological
concentrations.... | biology |
5,356 | A (possible) mathematical model to describe biological "context-dependence" : case study with protein structure | q-bio.OT | Context-dependent nature of biological phenomena are well documented in every
branch of biology. While there have been few previous attempts to (implicitly)
model various facets of biological context-dependence, a formal and general
mathematical construct to model the wide spectrum of context-dependence, eludes
the stu... | biology |
5,357 | The genetic code degeneracy and the amino acids chemical composition are connected | q-bio.OT | We show that our recently published Arithmetic Model of the genetic code
based on Godel Encoding is robust against symmetry transformations, specially
Rumer s one U > G, A > C, and constitutes a link between the degeneracy
structure and the chemical composition of the 20 canonical amino acids. As a
result, several rema... | biology |
5,358 | A new simulation-based model for calculating post-mortem intervals using developmental data for Lucilia sericata (Dipt.: Calliphoridae) | q-bio.OT | Homicide investigations often depend on the determination of a minimum
post-mortem interval (PMI$_{min}$) by forensic entomologists. The age of the
most developed insect larvae (mostly blow fly larvae) gives reasonably reliable
information about the minimum time a person has been dead. Methods such as
isomegalen diagra... | biology |
5,359 | Leaf litter decomposition -- Estimates of global variability based on Yasso07 model | q-bio.OT | Litter decomposition is an important process in the global carbon cycle. It
accounts for most of the heterotrophic soil respiration and results in
formation of more stable soil organic carbon (SOC) which is the largest
terrestrial carbon stock. Litter decomposition may induce remarkable feedbacks
to climate change beca... | biology |
5,360 | A taylor-made arithmetic model of the genetic code and applications | q-bio.OT | We present a completely new version of our arithmetic model of the standard
genetic code and compute in a straightforward manner the exact numeric
degeneracies of the five multiplets without any trick for the doublets and the
sextets, as we have done previously. We give also some interesting
applications. | biology |
5,361 | Multiple positive steady states in subnetworks defined by stoichiometric generators | q-bio.OT | In Systems Biology there is a growing interest in the question, whether or
not a given mathematical model can admit more than one steady state. As
parameter values are often unknown or subject to a very high uncertainty, one
is often interested in the question, whether or not a given mathematical model
can, for some co... | biology |
5,362 | On (Schröedinger's) quest for new physics for life | q-bio.OT | Two recent investigations are reviewed: quantum effects for DNA aggregates
and scars formation on virus capsids. The possibility that scars could explain
certain data recently obtained by Sundquist's group in electron cryotomography
of immature HIV-1 virions is also briefly addressed. Furthermore, a bottom-up
reflectio... | biology |
5,363 | A Hybrid Agent Based and Differential Equation Model of Body Size Effects on Pathogen Replication and Immune System Response | q-bio.OT | Many emerging pathogens infect multiple host species, and multi-host
pathogens may have very different dynamics in different host species. This
research addresses how pathogen replication rates and Immune System (IS)
response times are constrained by host body size. An Ordinary Differential
Equation (ODE) model is used... | biology |
5,364 | Genetic Code and Number Theory | q-bio.OT | Living organisms are the most complex, interesting and significant objects
regarding all substructures of the universe. Life science is regarded as a
science of the 21st century and one can expect great new discoveries in the
near futures. This article contains an introductory brief review of genetic
information, its c... | biology |
5,365 | Optimization of Production Protocol of Alkaline Protease by Streptomyces pulvereceus | q-bio.OT | Extra cellular alkaline protease producing species is an isolate from soil
which was characterized and identified as Streptomyces pulvereceus MTCC 8374.
Studies on submerged fermentation revealed that maximum level of enzyme
production was during early stationary phase. Optimum pH, inoculum and
temperature were 9.0, 3 ... | biology |
5,366 | Complete Human Mitochondrial Genome Construction Using L-systems | q-bio.OT | Recently, scientists from The Craig J. Venter Institute reported construction
of very long DNA molecules using a variety of experimental procedures adopting
a number of working hypotheses. Finding a mathematical rule for generation of
such a long sequence would revolutionize our thinking on various advanced areas
of bi... | biology |
5,367 | The genome is software and evolution is a software developer | q-bio.OT | The genome is software because it a set of verbal instructions for a
programmable computer, the ribosome. The theory of evolution now reads:
evolution is the software developer responsible for the existence of the
genome. We claim that this setting, whose official name is genetic programming,
is necessary and sufficien... | biology |
5,368 | A heuristic view about the evolution and species | q-bio.OT | The controversy concerning both the definition of the species and methods for
inferring the boundaries and numbers of species has occupied biologists for
centuries, and the debate itself has become known as the species problem. The
modern theory of evolution depends on a fundamental redefinition of "species".
Here we s... | biology |
5,369 | A 2-dimensional Geometry for Biological Time | q-bio.OT | This paper proposes an abstract mathematical frame for describing some
features of biological time. The key point is that usual physical (linear)
representation of time is insufficient, in our view, for the understanding key
phenomena of life, such as rhythms, both physical (circadian, seasonal ...) and
properly biolog... | biology |
5,370 | Protention and retention in biological systems | q-bio.OT | This paper proposes an abstract mathematical frame for describing some
features of cognitive and biological time. We focus here on the so called
"extended present" as a result of protentional and retentional activities
(memory and anticipation). Memory, as retention, is treated in some physical
theories (relaxation phe... | biology |
5,371 | Matrix genetics, part 5: genetic projection operators and direct sums | q-bio.OT | The article is devoted to phenomena of symmetries and algebras in matrix
presentations of the genetic code. The Kronecker family of the genetic matrices
is investigated, which is based on the alphabetical matrix [C A; U G], where C,
A, U, G are the letters of the genetic alphabet. The matrix P=[C A; U G] in the
third K... | biology |
5,372 | Technical performance and interpretation of physical experiment in problems of cell biology | q-bio.OT | The lecture summarises main results of my team over last five years in the
field of technical experiment design and interpretation of results of
experiments for cell bi-ology. I introduce the theoretical concept of the
experiment, based mainly on ideqas of stochastic systems theory, and confront
it with general ideas o... | biology |
5,373 | Identificación de nuevos medicamentos a través de métodos computacionales | q-bio.OT | Resumen: El desarrollo de nuevos medicamentos es un problema complejo que
carece de una soluci\'on \'unica y autom\'atica desde un punto de vista
computacional, debido a la carencia de programas que permitan manejar grandes
vol\'umenes de informaci\'on que est\'an distribuidos a lo largo de todo el
mundo entre m\'ultip... | biology |
5,374 | A Network-Based Meta-Population Approach to Model Rift Valley Fever Epidemics | q-bio.OT | Rift Valley fever virus (RVFV) has been expanding its geographical
distribution with important implications for both human and animal health. The
emergence of Rift Valley fever (RVF) in the Middle East, and its continuing
presence in many areas of Africa, has negatively impacted both medical and
veterinary infrastructu... | biology |
5,375 | Characterization of the norepinephrine-activation of adenylate cyclase suggests a role in memory affirmation pathways. Overexposure to epinephrine inactivates adenylate-cyclase,a causal pathway for stress-pathologies | q-bio.OT | Incubation with noradrenaline (norepinephrine) of isolated membranes of rat's
brain corpus striatum and cortex, showed that ionic-magnesium (Mg2+) is
required for the neurotransmitter activatory response of Adenylate Cyclase [ATP
pyrophosphate-lyase (cyclizing), (EC 4.6.1.1)], AC.An Mg2+-dependent response
to the activ... | biology |
5,376 | The Virtual Institute for Integrative Biology (VIIB) | q-bio.OT | The Virtual Institute for Integrative Biology (VIIB) is a Latin American
initiative for achieving global collaborative e-Science in the areas of
bioinformatics, genome biology, systems biology, metagenomics, medical
applications and nanobiotechnolgy. The scientific agenda of VIIB includes:
construction of databases for... | biology |
5,377 | Biological Concepts Instrument (BCI): A diagnostic tool for revealing student thinking | q-bio.OT | A key to effective teaching is an awareness and accurate understanding of the
thinking and implicit assumptions that students bring to the subject to be
learned. In the absence of extensive Socratic interactions with students, one
strategy to assess student thinking involves the use of concept inventories
(CIs). CIs ar... | biology |
5,378 | The multiplet structure of the genetic code, in one and small number | q-bio.OT | In this short paper, it is shown that the multiplet structure of the standard
genetic code is derivable from the total number of nucleotides contained in 64
codons, 192, a small number. The degeneracy class-number is derived as the
number of numbers coprime to the number of Family-Boxes involved for the
quartets, the d... | biology |
5,379 | Rate distortion coevolutionary dynamics and the flow nature of cognitive epigenetic systems | q-bio.OT | We outline a model for a cognitive epigenetic system based on elements of the
Shannon theory of information and the statistical physics of the generalized
Onsager relations. Particular attention is paid to the concept of the rate
distortion function and from another direction as motivated by the
thermodynamics of compu... | biology |
5,380 | The genetic code, 8-dimensional hypercomplex numbers and dyadic shifts | q-bio.OT | Matrix forms of the representation of the multi-level system of
molecular-genetic alphabets have revealed algebraic properties of this system.
Families of genetic (4*4)- and (8*8)-matrices show unexpected connections of
the genetic system with Walsh functions and Hadamard matrices, which are known
in theory of noise-im... | biology |
5,381 | Length, Weight, and Yield in Channel Catfish, Lake Diane, MI | q-bio.OT | Background: Channel catfish (Ictalurus punctatus) are important to both
commercial aquaculture and recreational fisheries. Little published data is
available on length-weight relationships of channel catfish in Michigan. Though
there is no record of public or private stocking, channel catfish appeared in
Lake Diane bet... | biology |
5,382 | From Physics to Biology by Extending Criticality and Symmetry Breakings | q-bio.OT | Symmetries play a major role in physics, in particular since the work by E.
Noether and H. Weyl in the first half of last century. Herein, we briefly
review their role by recalling how symmetry changes allow to conceptually move
from classical to relativistic and quantum physics. We then introduce our
ongoing theoretic... | biology |
5,383 | Randomness and Multi-level Interactions in Biology | q-bio.OT | The dynamic instability of the living systems and the "superposition" of
different forms of randomness are viewed as a component of the contingently
increasing organization of life along evolution. We briefly survey how
classical and quantum physics define randomness differently. We then discuss
why this requires, in o... | biology |
5,384 | Genetic Code: Four Diversity Types of Protein Amino Acids | q-bio.OT | This paper presents, for the first time, four diversity types of protein
amino acids. The first type includes two amino acids (G, P), both without
standard hydrocarbon side chains; the second one four amino acids, as two pairs
[(A, L), (V, I)], all with standard hydrocarbon side chains; the third type
comprises the six... | biology |
5,385 | Experimental Researches of Cutaneous Melanoma Immunotherapy by Antitumor Cell-Whole GM-CSF-Producing Vaccines | q-bio.OT | Various approaches to increase efficiency of antitumor therapy by a
combination of vaccinotherapy, chemotherapy and surgical excision of primary
tumor nodes, and also the comparative analyses of therapeutic and preventive
application of antitumoral vaccines were carried out in melanoma experimental
model. It was postul... | biology |
5,386 | A pulse fishery model with closures as function of the catch: Conditions for sustainability | q-bio.OT | We present a model of single species fishery which alternates closed seasons
with pulse captures. The novelty is that the length of a closed season is
determined by the stock size of the last capture. The process is described by a
new type of impulsive differential equations recently introduced. The main
result is a fi... | biology |
5,387 | Systematic Approach on Differences in Avian Viral Proteins Based on Carbon Composition | q-bio.OT | The distribution of amino acid along the protein sequences plays an
imperative role in facilitating different biological functions. Currently,
there is insufficient scientific data, which represents the arrangement of
amino acid in the proteins based on atomic composition. Our deep observational
and analytical studies ... | biology |
5,388 | Three-stage Origin of Life as a Result of Directional Darwinian Evolution | q-bio.OT | The original hypothesis about Three-stage origin of life (TOL) on the Earth
is developed and discussed. The role of the temperature factor in life origin
is considered. It is supposed, that three stages of abiogenesis (DNA world, RNA
world and the Protein world) consistently followed each other during Darwinian
evoluti... | biology |
5,389 | New Osmosis Law and Theory: the New Formula that Replaces van't Hoff Osmotic Pressure Equation | q-bio.OT | This article derived a new abstract concept from the osmotic process and
concluded it via "osmotic force" with a new law -- "osmotic law". The "osmotic
law" describes that, in an osmotic system, osmolyte moves osmotically from the
side with higher "osmotic force" to the side with lower "osmotic force". In
addition, it ... | biology |
5,390 | Individual rules for trail pattern formation in Argentine ants (Linepithema humile) | q-bio.OT | We studied the formation of trail patterns by Argentine ants exploring an
empty arena. Using a novel imaging and analysis technique we estimated
pheromone concentrations at all spatial positions in the experimental arena and
at different times. Then we derived the response function of individual ants to
pheromone conce... | biology |
5,391 | p-Adic Structure of the Genetic Code | q-bio.OT | The genetic code is connection between 64 codons, which are building blocks
of the genes, and 20 amino acids, which are building blocks of the proteins. In
addition to coding amino acids, a few codons code stop signal, which is at the
end of genes, i.e. it terminates process of protein synthesis. This article is
a revi... | biology |
5,392 | Health Matters: Human Organ Donations, Sales, and the Black Market | q-bio.OT | In this paper I explore the human organ procurement system. Which is better
for saving lives and limiting black market use, the present altruistic system
of donations or a free and open sales market? I explain that there is a risk
with maintaining the present system, the altruistic vision, and that people may
die who m... | biology |
5,393 | Dyadic groups, dyadic trees and symmetries in long nucleotide sequences | q-bio.OT | The conception of multi-alphabetical genetics is represented. Matrix forms of
the representation of the multi-level system of molecular-genetic alphabets
have revealed algebraic properties of this system. These properties are
connected with well-known notions of dyadic groups and dyadic-shift matrices.
Matrix genetics ... | biology |
5,394 | Parent-offspring Conflict in feral dogs: A Bioassay | q-bio.OT | The parent-offspring conflict theory is an interesting premise for
understanding the dynamics of parental care. However, this theory is not easy
to test empirically, as exact measures of parental investment in an
experimental set-up are difficult to obtain. We have used the Indian feral dog
as a model system to test th... | biology |
5,395 | Photonic Communications and Information Encoding in Biological Systems | q-bio.OT | The structure of optical radiation emitted by the samples of loach fish eggs
is studied. It was found earlier that such radiation perform the communications
between distant samples, which result in the synchronization of their
development. The photon radiation in form of short quasi-periodic bursts was
observed for fis... | biology |
5,396 | Influenza Virus Vaccine Efficacy Based On Conserved Sequence Alignment | q-bio.OT | The rapid outbreak of bird flu challenges the outcome of effective vaccine
for the upcoming years. The recent research established different norms to
eliminate flu pandemics. This can be made possible with skilled experimental
analyses and by tracking the recent virulent strain and can be broadly
applicable with effect... | biology |
5,397 | Entromics -- thermodynamics of sequence dependent base incorporation into DNA reveals novel long-distance genome organization | q-bio.OT | Zero mode waveguide technology of next generation sequencing demonstrated
sequence-dependence of the enzymatic reaction, incorporating a base into the
genomic DNA. We show that these experimental results indicate existence of a
previously uncharacterized physical property of DNA, the incorporation reaction
chemical pot... | biology |
5,398 | The irregular (integer) tetrahedron as a warehouse of biological information | q-bio.OT | This paper is devoted to a new classification of the twenty amino acids based
on the heronian (integer) tetrahedron. | biology |
5,399 | Potential of Traditional Medicinal Plants for Treating Obesity: A Review | q-bio.OT | Obesity is a global health concern associated with high morbidity and
mortality. Therapeutic strategies include synthetic drugs and surgery, which
may entail high costs and serious complications. Plant-based medicinal agents
offer an alternative approach. A review of the studies on accessible botanical
sources for the ... | biology |
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