Unnamed: 0 int64 0 41k | title stringlengths 4 274 | category stringlengths 5 18 | summary stringlengths 22 3.66k | theme stringclasses 8
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4,900 | Probing subtle fluorescence dynamics in cellular proteins by streak camera based Fluorescence Lifetime Imaging Microscopy | q-bio.CB | We report the cell biological applications of a recently developed
multiphoton fluorescence lifetime imaging microscopy system using a streak
camera (StreakFLIM). The system was calibrated with standard fluorophore
specimens and was shown to have high accuracy and reproducibility. We
demonstrate the applicability of th... | biology |
4,901 | Auto-reverse nuclear migration in bipolar mammalian cells on micropatterned surfaces | q-bio.CB | A novel assay based on micropatterning and time-lapse microscopy has been
developed for the study of nuclear migration dynamics in cultured mammalian
cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6
glioma and primary mouse fibroblast cells is diminished. Nevertheless, nuclei
perform an unexpe... | biology |
4,902 | Cytokinesis: the initial linear phase crosses over to a multiplicity of non-linear endings | q-bio.CB | We investigate the final stage of cytokinesis in two types of amoeba,
pointing out the existence of biphasic furrow contraction. The first phase is
characterized by a constant contraction rate, is better studied, and seems
universal to a large extent. The second phase is more diverse. In Dictyostelium
discoideum the tr... | biology |
4,903 | A graph model for the evolution of specificity in humoral immunity | q-bio.CB | The immune system protects the body against health-threatening entities,
known as antigens, through very complex interactions involving the antigens and
the system's own entities. One remarkable feature resulting from such
interactions is the immune system's ability to improve its capability to fight
antigens commonly ... | biology |
4,904 | Mathematical model of solid tumor formation | q-bio.CB | The problem of the onset and growth of solid tumour in homogeneous tissue is
regarded using an approach based on local interaction between the tumoral and
the sane tissue cells. The characteristic sizes and growth rates of spherical
tumours, the points of the beginning and the end of spherical growth, and the
further d... | biology |
4,905 | Aggregation of foraging swarms | q-bio.CB | In this paper we consider a continuous-time anisotropic swarm model with an
attraction/repulsion function and study its aggregation properties. It is shown
that the swarm members will aggregate and eventually form a cohesive cluster of
finite size around the swarm center. We also study the swarm cohesiveness when
the m... | biology |
4,906 | Simulating the Impact of a Molecular 'Decision-Process' on Cellular Phenotype and Multicellular Patterns in Brain Tumors | q-bio.CB | Experimental evidence indicates that human brain cancer cells proliferate or
migrate, yet do not display both phenotypes at the same time. Here, we present
a novel computational model simulating this cellular decision-process leading
up to either phenotype based on a molecular interaction network of genes and
proteins.... | biology |
4,907 | Physical Schemata Underlying Biological Pattern Formation - Examples, Issues and Strategies | q-bio.CB | Biological systems excel at building spatial structures on scales ranging
from nanometers to kilometers and exhibit temporal patterning from milliseconds
to years. One approach that nature has taken to accomplish this relies on the
harnessing of pattern-forming processes of non-equilibrium physics and
chemistry. For th... | biology |
4,908 | Model for the robust establishment of precise proportions in the early Drosophila embryo | q-bio.CB | During embryonic development, a spatial pattern is formed in which
proportions are established precisely. As an early pattern formation step in
Drosophila embryos, an anterior-posterior gradient of Bicoid (Bcd) induces
hunchback (hb) expression (Driever et al. 1989; Tautz et al. 1988). In contrast
to the Bcd gradient, ... | biology |
4,909 | Pattern formation in a stochastic model of cancer growth | q-bio.CB | We investigate noise-induced pattern formation in a model of cancer growth
based on Michaelis-Menten kinetics, subject to additive and multiplicative
noises. We analyse stability properties of the system and discuss the role of
diffusion and noises in the system's dynamics. We find that random dichotomous
fluctuations ... | biology |
4,910 | The reaction-diffusion approach to morphogenesis | q-bio.CB | Morphogenesis is the ensemble of processes that determines form, shape and
patterns in organisms. Based on a reaction-diffusion theoretical setting and
some prototype reaction schemes, we make a review of the models and experiments
that support possible mechanisms of morphogenesis. We present specific case
studies from... | biology |
4,911 | Simulation of stem cell survival in small crypts | q-bio.CB | Monte Carlo simulations of the number of stem cells in human colon crypts
allow for fluctuations which kill the population after sufficiently long times. | biology |
4,912 | Turing Pattern with Proportion Preservation | q-bio.CB | Although Turing pattern is one of the most universal mechanisms for pattern
formation, in its standard model the number of stripes changes with the system
size, since the wavelength of the pattern is invariant: It fails to preserve
the proportionality of the pattern, i.e., the ratio of the wavelength to the
size, that ... | biology |
4,913 | Power laws of complex systems from Extreme physical information | q-bio.CB | Many complex systems obey allometric, or power, laws y=Yx^{a}. Here y is the
measured value of some system attribute a, Y is a constant, and x is a
stochastic variable. Remarkably, for many living systems the exponent a is
limited to values +or- n/4, n=0,1,2... Here x is the mass of a randomly
selected creature in the ... | biology |
4,914 | Spontaneous polarization in eukaryotic gradient sensing: A mathematical model based on mutual inhibition of frontness and backness pathways | q-bio.CB | A key problem of eukaryotic cell motility is the signaling mechanism of
chemoattractant gradient sensing. Recent experiments have revealed the
molecular correlate of gradient sensing: Frontness molecules, such as PI3P and
Rac, localize at the front end of the cell, and backness molecules, such as Rho
and myosin II, acc... | biology |
4,915 | Dynamics and pattern formation in invasive tumor growth | q-bio.CB | In this work, we study the in-vitro dynamics of the most malignant form of
the primary brain tumor: Glioblastoma Multiforme. Typically, the growing tumor
consists of the inner dense proliferating zone and the outer less dense
invasive region. Experiments with different types of cells show qualitatively
different behavi... | biology |
4,916 | A stochastic model for wound healing | q-bio.CB | We present a discrete stochastic model which represents many of the salient
features of the biological process of wound healing. The model describes fronts
of cells invading a wound. We have numerical results in one and two dimensions.
In one dimension we can give analytic results for the front speed as a power
series ... | biology |
4,917 | How to formulate membrane potential in a spatially homogeneous myocyte model? | q-bio.CB | Membrane potential in a mathematical model of a cardiac myocyte can be
formulated in different ways. Assuming a spatially homogeneous myocyte that is
strictly charge-conservative and electroneutral as a whole, two methods will be
compared: (1) the differential formulation dV/dt=-I/C_m of membrane potential
used traditi... | biology |
4,918 | Genetically engineered cardiac pacemaker: stem cells transfected with HCN2 gene and myocytes - a model | q-bio.CB | Artificial biological pacemakers were developed and tested in canine
ventricles. Next steps will require obtaining oscillations sensitive to
external regulations, and robust with respect to long term drifts of expression
levels of pacemaker currents and gap junctions. We introduce mathematical
models intended to be use... | biology |
4,919 | Bacterial self-organisation and computation | q-bio.CB | In this article we highlight chemotaxis (cellular movement) as a rich source
of potential engineering applications and computational models, highlighting
current research and possible future work. We first give a brief description of
the biological mechanism, before describing recent work on modelling it in
silico. We ... | biology |
4,920 | A model for regulated fatty acid metabolism in liver; equilibria and their changes | q-bio.CB | We build a model for the hepatic fatty acid metabolism and its metabolic and
genetic regulations. The model has two functioning modes: synthesis and
oxidation of fatty acids. We provide a sufficient condition (the strong
lipolytic condition) for the uniqueness of its equilibrium. Under this
condition, modifications of ... | biology |
4,921 | Different Strategies for Cancer Treatment: Mathematical Modeling | q-bio.CB | We formulate and analyze a mathematical model describing immune response to
avascular tumor under the influence of immunotherapy and chemotherapy and their
combinations as well as vaccine treatments. The effect of vaccine therapy is
considered as a parametric perturbation of the model. In the case of a weak
immune resp... | biology |
4,922 | Synthetic Turing protocells: vesicle self-reproduction through symmetry-breaking instabilities | q-bio.CB | The reproduction of a living cell requires a repeatable set of chemical
events to be properly coordinated. Such events define a replication cycle,
coupling the growth and shape change of the cell membrane with internal
metabolic reactions. Although the logic of such process is determined by
potentially simple physico-c... | biology |
4,923 | Hysteresis and bi-stability by an interplay of calcium oscillations and action potential firing | q-bio.CB | Many cell types exhibit oscillatory activity, such as repetitive action
potential firing due to the Hodgkin-Huxley dynamics of ion channels in the cell
membrane or reveal intracellular inositol triphosphate (IP$_3$) mediated
calcium oscillations (CaOs) by calcium-induced calcium release channels
(IP$_3$-receptor) in th... | biology |
4,924 | A mass conserved reaction-diffusion system captures properties of cell polarity | q-bio.CB | Various molecules exclusively accumulate at the front or back of migrating
eukaryotic cells in response to a shallow gradient of extracellular signals.
Directional sensing and signal amplification highlight the essential properties
in the migrating cells, known as cell polarity. In addition to these, such
properties of... | biology |
4,925 | Force balance and membrane shedding at the Red Blood Cell surface | q-bio.CB | During the aging of the red-blood cell, or under conditions of extreme
echinocytosis, membrane is shed from the cell plasma membrane in the form of
nano-vesicles. We propose that this process is the result of the
self-adaptation of the membrane surface area to the elastic stress imposed by
the spectrin cytoskeleton, vi... | biology |
4,926 | A Multiscale Model of Biofilm as a Senescence-Structured Fluid | q-bio.CB | We derive a physiologically structured multiscale model for biofilm
development. The model has components on two spatial scales, which induce
different time scales into the problem. The macroscopic behavior of the system
is modeled using growth-induced flow in a domain with a moving boundary.
Cell-level processes are i... | biology |
4,927 | Efficiency, selectivity and robustness of the nuclear pore complex transport | q-bio.CB | All materials enter or exit the cell nucleus through nuclear pore complexes
(NPCs), efficient transport devices that combine high selectivity and
throughput. A central feature of this transport is the binding of
cargo-carrying soluble transport factors to flexible, unstructured
proteinaceous filaments called FG-nups th... | biology |
4,928 | Modulation of the reaction rate of regulating protein induces large morphological and motional change of amoebic cell | q-bio.CB | Morphologies of moving amoebae are categorized into two types. One is the
``neutrophil'' type in which the long axis of cell roughly coincides with its
moving direction. This type of cell extends a leading edge at the front and
retracts a narrow tail at the rear, whose shape has been often drawn as a
typical amoeba in ... | biology |
4,929 | The role of cell-cell adhesion in wound healing | q-bio.CB | We present a stochastic model which describes fronts of cells invading a
wound. In the model cells can move, proliferate, and experience cell-cell
adhesion. We find several qualitatively different regimes of front motion and
analyze the transitions between them. Above a critical value of adhesion and
for small prolifer... | biology |
4,930 | Senescence Can Explain Microbial Persistence | q-bio.CB | It has been known for many years that small fractions of persister cells
resist killing in many bacterial colony-antimicrobial confrontations. These
persisters are not believed to be mutants. Rather it has been hypothesized that
they are phenotypic variants. Current models allow cells to switch in and out
of the persis... | biology |
4,931 | Directionality of glioblastoma invasion in a 3d in vitro experiment | q-bio.CB | Glioblastoma is the most malignant form of brain cancer. It is extremely
invasive; the mechanisms that govern invasion are not well understood. To
better understand the process of invasion, we conducted an in vitro experiment
in which a 3d tumour spheroid is implanted into a collagen gel. The paths of
individual invasi... | biology |
4,932 | Network formation of tissue cells via preferential attraction to elongated structures | q-bio.CB | Vascular and non-vascular cells often form an interconnected network in
vitro, similar to the early vascular bed of warm blooded embryos. Our
time-lapse recordings show that the network forms by extending sprouts, i.e.,
multicellular linear segments. To explain the emergence of such structures, we
propose a simple mode... | biology |
4,933 | Velocity oscillations in actin-based motility | q-bio.CB | We present a simple and generic theoretical description of actin-based
motility, where polymerization of filaments maintains propulsion. The dynamics
is driven by polymerization kinetics at the filaments' free ends, crosslinking
of the actin network, attachment and detachment of filaments to the obstacle
interfaces and... | biology |
4,934 | Inverse Geometric Approach to the Simulation of the Circular Growth. The Case of Multicellular Tumor Spheroids | q-bio.CB | We demonstrate the power of the genetic algorithms to construct the cellular
automata model simulating the growth of 2-dimensional close-to-circular
clusters revealing the desired properties, such as the growth rate and, at the
same time, the fractal behavior of their contours. The possible application of
the approach ... | biology |
4,935 | Simulating non-small cell lung cancer with a multiscale agent-based model | q-bio.CB | Background The epidermal growth factor receptor (EGFR) is frequently
overexpressed in many cancers, including non-small cell lung cancer (NSCLC). In
silcio modeling is considered to be an increasingly promising tool to add
useful insights into the dynamics of the EGFR signal transduction pathway.
However, most of the p... | biology |
4,936 | Immune response to a malaria infection: properties of a mathematical model | q-bio.CB | We establish some properties of a within host mathematical model of malaria
proposed by Recker et al which includes the role of the immune system during
the infection. The model accounts for the antigenic variation exhibited by the
malaria parasite (P. falciparum). We show that the model can exhibit a wide
variety of d... | biology |
4,937 | Multi-strain virus dynamics with mutations: A global analysis | q-bio.CB | We consider within-host virus models with more than one strain and allow
mutation between the strains. If there is no mutation, a Lyapunov function
establishes global stability of the steady state corresponding to the fittest
strain. For small perturbations this steady state persists, perhaps with small
concentrations ... | biology |
4,938 | A Map-Based Model of the Cardiac Action Potential | q-bio.CB | A discrete time model that is capable of replicating the basic features of
cardiac cell action potentials is suggested. The paper shows how the map-based
approaches can be used to design highly efficient computational models
(algorithms) that enable large-scale simulations and analysis of discrete
network models of car... | biology |
4,939 | Intermittent dynamics and 1/f^beta noise in single cardiac muscle cells | q-bio.CB | Fluctuations in the spontaneous beating activity of isolated cardiac cells
were studied over a timescale of six decades. The beat dynamics of single
cardiac cells were heterogeneous and intermittent. The interbeat intervals
(IBIs) were power-law distributed in a long-time regime. Furthermore, for long
timescales up to ... | biology |
4,940 | Regulative Differentiation as Bifurcation of Interacting Cell Population | q-bio.CB | In multicellular organisms, several cell states coexist. For determining each
cell type, cell-cell interactions are often essential, in addition to
intracellular gene expression dynamics. Based on dynamical systems theory, we
propose a mechanism for cell differentiation with regulation of populations of
each cell type ... | biology |
4,941 | Entropy Production in a Cell and Reversal of Entropy Flow as an Anticancer Therapy | q-bio.CB | The entropy production rate of cancer cell is always higher than healthy cell
under the case of no external field applied. Different entropy production
between two kinds of cells determines the direction of entropy flow among
cells. The entropy flow is the carrier of information flow. The entropy flow
from cancer to he... | biology |
4,942 | The motility of normal and cancer cells in response to the combined influence of substrate rigidity and anisotropic microstructure | q-bio.CB | Cell adhesion and migration are strongly influenced by extracellular matrix
(ECM) architecture and rigidity, but little is known about the concomitant
influence of such environmental signals to cell responses, especially when
considering cells of similar origin and morphology, but exhibiting a normal or
cancerous pheno... | biology |
4,943 | Shoot regeneration seedlings from transverse thin cell layer explants excised from cotyledon, petiole, hypocotyl of [{Brassica juncea} L. Czern.] in the presence of CdCl$_2$ | q-bio.CB | The present work describes a novel neoformation process of \textit{Brassica
juncea} (L.) Czern. seedlings from transverse thin cell layers in the presence
of CdCl$_2$. In order to investigate the regeneration ability of this crop, the
effect of CdCl$_2$ on shoot regeneration (frequency of regeneration and bud
number pe... | biology |
4,944 | Pattern Formation of Glioma Cells: Effects of Adhesion | q-bio.CB | We investigate clustering of malignant glioma cells. \emph{In vitro}
experiments in collagen gels identified a cell line that formed clusters in a
region of low cell density, whereas a very similar cell line (which lacks an
important mutation) did not cluster significantly. We hypothesize that the
mutation affects the ... | biology |
4,945 | Force and length-dependent catastrophe activities explain interphase microtubule organization in fission yeast | q-bio.CB | The cytoskeleton is essential for the maintenance of cell morphology in
eukaryotes. In fission yeast for example, polarized growth sites are organized
by actin whereas microtubules (MT) acting upstream control where growth occurs
(La Carbona et al, 2006). Growth is limited to the cell poles when MTs undergo
catastrophe... | biology |
4,946 | VE-cadherin and claudin-5: it takes two to tango | q-bio.CB | Endothelial barrier function requires the adhesive activity of VE-cadherin
and claudin-5, which are key components of adherens and tight endothelial
junctions, respectively. Emerging evidence suggests that VE-cadherin controls
claudin-5 expression by preventing the nuclear accumulation of FoxO1 and
-catenin, which repr... | biology |
4,947 | Protein Kinase C-related Kinase and ROCK Are Required for Thrombin-induced Endothelial Cell Permeability Downstream from G{alpha}12/13 and G{alpha}11/q | q-bio.CB | Increase in vascular permeability occurs under many physiological conditions
and is central in diverse human pathologies. Thrombin is a pro-coagulant serine
protease, which causes the local loss of endothelial barrier integrity thereby
enabling the rapid extravasation of plasma proteins and the local formation of
fibri... | biology |
4,948 | Breaking the VE-cadherin bonds | q-bio.CB | Exchanges between the blood compartment and the surrounding tissues require a
tight regulation by the endothelial barrier. Recent reports inferred that
VE-cadherin, an endothelial specific cell-cell adhesion molecule, plays a
pivotal role in the formation, maturation and remodeling of the vascular wall.
Indeed, a growi... | biology |
4,949 | Modeling tumor cell migration: from microscopic to macroscopic | q-bio.CB | It has been shown experimentally that contact interactions may influence the
migration of cancer cells. Previous works have modelized this thanks to
stochastic, discrete models (cellular automata) at the cell level. However, for
the study of the growth of real-size tumors with several millions of cells, it
is best to u... | biology |
4,950 | Oscillatory Notch pathway activity in a delay model of neuronal differentiation | q-bio.CB | Lateral inhibition resulting from a double-negative feedback loop underlies
the assignment of different fates to cells in many developmental processes.
Previous studies have shown that the presence of time delays in models of
lateral inhibition can result in significant oscillatory transients before
patterned steady st... | biology |
4,951 | Cortical Factor Feedback Model for Cellular Locomotion and Cytofission | q-bio.CB | Eukaryotic cells can move spontaneously without being guided by external
cues. For such spontaneous movements, a variety of different modes have been
observed, including the amoeboid-like locomotion with protrusion of multiple
pseudopods, the keratocyte-like locomotion with a widely spread lamellipodium,
cell division ... | biology |
4,952 | Microscale adhesion patterns for the precise localization of amoeba | q-bio.CB | In order to get a better understanding of amoeba-substrate interactions in
the processes of cellular adhesion and directional movement, we engineered
glass surfaces with defined local adhesion characteristics at a micrometric
scale. Amoeba (Dictyostelium dicoideum) is capable to adhere to various
surfaces independently... | biology |
4,953 | PAKing up to the endothelium | q-bio.CB | Angiogenesis recapitulates the growth of blood vessels that progressively
expand and remodel into a highly organized and stereotyped vascular network.
During adulthood, endothelial cells that formed the vascular wall retain their
plasticity and can be engaged in neo-vascularization in response to
physiological stimuli,... | biology |
4,954 | A mathematical model of intercellular signaling during epithelial wound healing | q-bio.CB | Recent experiments in epithelial wound healing have demonstrated the
necessity of Mitogen-activated protein kinase (MAPK) for coordinated cell
movement after damage. This MAPK activity is characterized by two wave-like
phenomena. One MAPK "wave" that originates immediately after injury, propagates
deep into the cell la... | biology |
4,955 | Rebuilding cytoskeleton roads: Active-transport-induced polarization of cells | q-bio.CB | Many cellular processes require a polarization axis which generally initially
emerges as an inhomogeneous distribution of molecular markers in the cell. We
present a simple analytical model of a general mechanism of cell polarization
taking into account the positive feedback due to the coupled dynamics of
molecular mar... | biology |
4,956 | Human cell recovery after microwave irradiation | q-bio.CB | Cells of human buccal epithelium of 6 male donors were exposed to microwave
radiation (frequency f=36,64 GHz, power density E = 10, 100, and 400 mcW/cm^2).
Exposure time in all experiments was 10 seconds. Heterochromatin was stained by
2% orcein in 45 % acetic acid. The stainability of cells with trypan blue (0,5
%) an... | biology |
4,957 | In silico estimates of the free energy rates in growing tumor spheroids | q-bio.CB | The physics of solid tumor growth can be considered at three distinct size
scales: the tumor scale, the cell-extracellular matrix (ECM) scale and the
sub-cellular scale. In this paper we consider the tumor scale in the interest
of eventually developing a system-level understanding of the progression of
cancer. At this ... | biology |
4,958 | A symmetry breaking mechanism for epithelial cell polarization | q-bio.CB | In multicellular organisms, epithelial cells form layers separating
compartments responsible for different physiological functions. At the early
stage of epithelial layer formation, each cell of an aggregate defines an inner
and an outer side by breaking the symmetry of its initial state, in a process
known as epitheli... | biology |
4,959 | Chemotactic response and adaptation dynamics in Escherichia coli | q-bio.CB | Adaptation of the chemotaxis sensory pathway of the bacterium Escherichia
coli is integral for detecting chemicals over a wide range of background
concentrations, ultimately allowing cells to swim towards sources of attractant
and away from repellents. Its biochemical mechanism based on methylation and
demethylation of... | biology |
4,960 | A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies | q-bio.CB | A promising direction in drug development is to exploit the ability of
natural killer cells to kill antibody-labeled target cells. Monoclonal
antibodies and drugs designed to elicit this effect typically bind cell-surface
epitopes that are overexpressed on target cells but also present on other
cells. Thus it is import... | biology |
4,961 | Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch | q-bio.CB | Cellular transformations which involve a significant phenotypical change of
the cell's state use bistable biochemical switches as underlying decision
systems. In this work, we aim at linking cellular decisions taking place on a
time scale of years to decades with the biochemical dynamics in signal
transduction and gene... | biology |
4,962 | Analysis of a mathematical model for interactions between T cells and macrophages | q-bio.CB | The aim of this paper is to carry out a mathematical analysis of a system of
ordinary differential equations introduced by R. Lev Bar-Or to model the
interactions between T cells and macrophages. Under certain restrictions on the
parameters of the model, theorems are proved about the number of stationary
solutions and ... | biology |
4,963 | Implications of 3-step swimming patterns in bacterial chemotaxis | q-bio.CB | We recently found that marine bacteria Vibrio alginolyticus execute a cyclic
3-step (run- reverse-flick) motility pattern that is distinctively different
from the 2-step (run-tumble) pattern of Escherichia coli. How this novel
swimming pattern is regulated by cells of V. alginolyticus is not currently
known, but its si... | biology |
4,964 | A computational model of cell polarization and motility coupling mechanics and biochemistry | q-bio.CB | The motion of a eukaryotic cell presents a variety of interesting and
challenging problems from both a modeling and a computational perspective. The
processes span many spatial scales (from molecular to tissue) as well as
disparate time scales, with reaction kinetics on the order of seconds, and the
deformation and mot... | biology |
4,965 | Deterministic and stochastic aspects of VEGF-A production and the cooperative behavior of tumoral cell colony | q-bio.CB | A model is proposed to study the process of hypoxia-induced angiogenesis in
cancer cells. The model accounts for the role played by the vascular
endothelial growth factor (VEGF)-A in regulating the oxygen intake. VEGF-A is
dynamically controlled by the HIF-1alpha concentration. If not degraded,
HIF-1alpha can bind to t... | biology |
4,966 | The in silico macrophage: toward a better understanding of inflammatory disease | q-bio.CB | Macrophages function as sentinel, cell-regulatory hubs capable of initiating,
perpetuating and contributing to the resolution of an inflammatory response,
following their activation from a resting state. Highly complex and varied gene
expression programs within the macrophage enable such functional diversity. To
invest... | biology |
4,967 | Noise characteristics of the Escherichia coli rotary motor | q-bio.CB | The chemotaxis pathway in the bacterium Escherichia coli allows cells to
detect changes in external ligand concentration (e.g. nutrients). The pathway
regulates the flagellated rotary motors and hence the cells' swimming
behaviour, steering them towards more favourable environments. While the
molecular components are w... | biology |
4,968 | Slow dynamics of neuronal excitability under pulse stimulation | q-bio.CB | Neurons fire irregularly on multiple timescales when stimulated with a
periodic pulse train. This raises two questions: Does this irregularity imply
significant intrinsic stochasticity? Can existing neuron models be readily
extended to describe behavior at long timescales? We show here that for
commonly studied neurona... | biology |
4,969 | Modeling the dynamics of Hepatitis C Virus with combined antiviral drug therapy: Interferon and Ribavirin | q-bio.CB | A mathematical modeling of Hepatitis C Virus (HCV) dynamics has been
presented in this paper. The proposed model, which involves four coupled
ordinary differential equations, describes the interaction of target cells
(hepatocytes), infected cells, infectious virions and non-infectious virions.
The model takes into cons... | biology |
4,970 | Resistance to TB drugs in KwaZulu-Natal: causes and prospects for control | q-bio.CB | In 2005 there was an outbreak of XDR (extensively drug resistant) TB in
Tugela Ferry, which is served by the Church of Scotland Hospital (COSH), in the
uMzinyathi District, KwaZulu-Natal, South Africa. An investigation was carried
out to determine if XDR TB was occurring elsewhere in the province, and to
develop hypoth... | biology |
4,971 | Monte Carlo study of gating and selection in potassium channels | q-bio.CB | The study of selection and gating in potassium channels is a very important
issue in modern biology. Indeed such structures are known in all types of cells
in all organisms where they play many important functional roles. The mechanism
of gating and selection of ionic species is not clearly understood. In this
paper we... | biology |
4,972 | Dependence of MAPK mediated signaling on Erk isoforms and differences in nuclear shuttling | q-bio.CB | The mitogen activated protein kinase (MAPK) family of proteins is involved in
regulating cellular fate activities such as proliferation, differentiation and
apoptosis. Their fundamental importance has attracted considerable attention on
different aspects of the MAPK signaling dynamics; this is particularly true for
the... | biology |
4,973 | Contractile network models for adherent cells | q-bio.CB | Cells sense the geometry and stiffness of their adhesive environment by
active contractility. For strong adhesion to flat substrates, two-dimensional
contractile network models can be used to understand how force is distributed
throughout the cell. Here we compare the shape and force distribution for
different variants... | biology |
4,974 | Modeling Regulation of Zinc Uptake via ZIP Transporters in Yeast and Plant Roots | q-bio.CB | In yeast (Saccharomyces cerevisiae) and plant roots (Arabidopsis thaliana)
zinc enters the cells via influx transporters of the ZIP family. Since zinc is
both essential for cell function and toxic at high concentrations, tight
regulation is essential for cell viability. We provide new insight into the
underlying mechan... | biology |
4,975 | Plasmodium knowlesi H strain pregnancy malaria immune responses in olive baboons (Papio anubis) | q-bio.CB | Approximately 24 million pregnant women in Sub-Saharan Africa are at risk of
suffering from pregnancy malaria complications. Mechanisms responsible for
increased susceptibility to malaria in pregnant women are not fully understood.
Baboons are susceptible to Plasmodium knowlesi and their reproductive
physiology and hos... | biology |
4,976 | Characterisation of placental malaria in olive baboons (Papio anubis) infected with Plasmodium knowlesi H strain | q-bio.CB | Pregnant women have increased susceptibility to malaria infection. In these
women, malaria parasites are frequently found sequestered in the placental
intervillous spaces, a condition referred to as placental malaria (PM).
Placental malaria threatens the health of the mother and the child's life by
causing still births... | biology |
4,977 | The receptor-toxin-antibody interaction: Mathematical model and numerical simulation | q-bio.CB | A reaction-diffusion model of receptor-toxin-antibody (RTA) interaction is
studied numerically. The protective properties of an antibody against a given
toxin are evaluated for a spherical cell placed into a toxin-antibody solution.
The selection of parameters for numerical simulation approximately corresponds
to the p... | biology |
4,978 | Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire | q-bio.CB | Idiosyncratic adverse drug reactions are unpredictable, dose independent and
potentially life threatening; this makes them a major factor contributing to
the cost and uncertainty of drug development. Clinical data suggest that many
such reactions involve immune mechanisms, and genetic association studies have
identifie... | biology |
4,979 | Screening of antibacterial activity of lactic acid bacteria isolated from fermented vegetables against food borne pathogens | q-bio.CB | This study aims to screen the antibacterial activity of lactic acid bacteria
(LAB) isolated from home-made fermented vegetables against common food borne
pathogens. The antagonistic properties of these isolates against Escherichia
coli, Staphylococcus aureus, Yersinia enterocolitica and Bacillus cereus were
examined us... | biology |
4,980 | Quorum sensing contributes to activated B cell homeostasis and to prevent autoimmunity | q-bio.CB | Maintenance of plasma IgM levels is critical for immune system function and
homeostasis in humans and mice. However, the mechanisms that control
homeostasis of the activated IgM-secreting B cells are unknown. After adoptive
transfer into immune-deficient hosts, B-lymphocytes expand poorly but fully
reconstitute the poo... | biology |
4,981 | Tessellations and Pattern Formation in Plant Growth and Development | q-bio.CB | The shoot apical meristem (SAM) is a dome-shaped collection of cells at the
apex of growing plants from which all above-ground tissue ultimately derives.
In Arabidopsis thaliana (thale cress), a small flowering weed of the
Brassicaceae family (related to mustard and cabbage), the SAM typically
contains some three to fi... | biology |
4,982 | Thick collagen-based 3D matrices including growth factors to induce neurite outgrowth | q-bio.CB | Designing synthetic microenvironments for cellular investigations is a very
active area of research at the crossroads of cell biology and materials
science. The present work describes the design and functionalization of a
three-dimensional (3D) culture support dedicated to the study of neurite
outgrowth from neural cel... | biology |
4,983 | Biomembranes report | q-bio.CB | In this report, we analyse and simulate a chemotaxis model given by a system
of stochastic reaction-diffusion equations posed on an evolving surface. | biology |
4,984 | A pathway-based mean-field model for E. coli chemotaxis: Mathematical derivation and Keller-Segel limit | q-bio.CB | A pathway-based mean-field theory (PBMFT) was recently proposed for E. coli
chemotaxis in [G. Si, T. Wu, Q. Quyang and Y. Tu, Phys. Rev. Lett., 109 (2012),
048101]. In this paper, we derived a new moment system of PBMFT by using the
moment closure technique in kinetic theory under the assumption that the
methylation le... | biology |
4,985 | The Myogenic Response in Isolated Rat Cerebrovascular Arteries: Smooth Muscle Cell Model | q-bio.CB | Previous models of the cerebrovascular smooth muscle cell have not addressed
the interaction between the electrical, chemical and mechanical components of
cell function during the development of active tension. These models are
primarily electrical, biochemical or mechanical in their orientation, and do
not permit a fu... | biology |
4,986 | Cell Growth and Size Homeostasis in Silico | q-bio.CB | Cell growth in size is a complex process coordinated by intrinsic and
environmental signals. In a recent work [Tzur et al., Science, 2009,
325:167-171], size distributions in an exponentially growing population of
mammalian cells were used to infer the growth rate in size. The results suggest
that cell growth is neithe... | biology |
4,987 | Distinct cell shapes determine accurate chemotaxis | q-bio.CB | The behaviour of an organism often reflects a strategy for coping with its
environment. Such behaviour in higher organisms can often be reduced to a few
stereotyped modes of movement due to physiological limitations, but finding
such modes in amoeboid cells is more difficult as they lack these constraints.
Here, we exa... | biology |
4,988 | Self tolerance in a minimal model of the idiotypic network | q-bio.CB | We consider the problem of self tolerance in the frame of a minimalistic
model of the idiotypic network. A node of this network represents a population
of B lymphocytes of the same idiotype which is encoded by a bit string. The
links of the network connect nodes with (nearly) complementary strings. The
population of a ... | biology |
4,989 | Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells | q-bio.CB | Eukaryotic adaptation pathways operate within wide-ranging environmental
conditions without stimulus saturation. Despite numerous differences in the
adaptation mechanisms employed by bacteria and eukaryotes, all require energy
consumption. Here, we present two minimal models showing that expenditure of
energy by the ce... | biology |
4,990 | Signal transduction and directional sensing in eukaryotes | q-bio.CB | Control of the cytoskeleton and mechanical contacts with the extracellular
environment are essential component of motility in eukaryotic cells. In the
absence of signals, cells continuously rebuild the cytoskeleton and
periodically extend pseudopods or other protrusions at random membrane
locations. Extracellular signa... | biology |
4,991 | Spatial anisotropy and heterogeneity in contractility and adhesion distribution may contribute to cell steering during migration | q-bio.CB | Transition from random to persistent cell motility requires spatiotemporal
organization of the cytoskeleton and focal adhesions. The influence of these
two structures on cell steering can also be gleaned from trypsin de-adhesion
experiments, wherein cells exposed to trypsin round up, exhibiting a
combination of rotatio... | biology |
4,992 | Protrusion fluctuations direct cell motion | q-bio.CB | Many physiological phenomena involve directional cell migration. It is
usually attributed to chemical gradients in vivo. Recently, other cues have
been shown to guide cells in vitro, including stiffness/adhesion gradients or
micro-patterned adhesive motifs. However, the cellular mechanism leading to
these biased migrat... | biology |
4,993 | Stable and flexible system for glucose homeostasis | q-bio.CB | Pancreatic islets, controlling glucose homeostasis, consist of \alpha, \beta,
and \delta\ cells. It has been observed that \alpha\ and \beta\ cells generate
out-of-phase synchronization in the release of glucagon and insulin,
counter-regulatory hormones for increasing and decreasing glucose levels, while
\beta\ and \de... | biology |
4,994 | Oscillations in a neurite growth model with extracellular feedback | q-bio.CB | We take into account the influence of extracellular signalling on neurite
elongation in a model of neurite growth mediated by building proteins (e.g.
tubulin). Tubulin production dynamics was supplied by a function describing the
influence of the extracellular signalling that can promote or depress the
elongation. We f... | biology |
4,995 | Mathematical Model of Colorectal Cancer with Monoclonal Antibody Treatments | q-bio.CB | We present a new mathematical model of colorectal cancer growth and its
response to monoclonal-antibody (mAb) therapy. Although promising, most mAb
drugs are still in trial phases, and the possible variations in the dosing
schedules of those currently approved for use have not yet been thoroughly
explored. To investiga... | biology |
4,996 | Comment on Masanari Asano et al. A model of epigenetic evolution based on theory of open quantum systems. Syst Synth Biol, 2013 | q-bio.CB | The comment mostly concerns mis-representation of my position on Quantum
Biology, by stating that I am 'reducing cell's behavior to quantum particles
inside the cell'. I contrast my position with that of McFadden-Al-Khalili, as
well as with the position of Asano et al. I also advertise an idea, described
in our latest ... | biology |
4,997 | A Comparison and Catalog of Intrinsic Tumor Growth Models | q-bio.CB | Determining the mathematical dynamics and associated parameter values that
should be used to accurately reflect tumor growth continues to be of interest
to mathematical modelers, experimentalists and practitioners. However, while
there are several competing canonical tumor growth models that are often
implemented, how ... | biology |
4,998 | MHC Restriction of V-V Interactions in Serum IgG | q-bio.CB | According to Jerne's idiotypic network hypothesis, the adaptive immune system
is regulated by interactions between the variable regions of antibodies, B
cells, and T cells.1 The symmetrical immune network theory2,3 is based on
Jerne's hypothesis, and provides a basis for understanding many of the
phenomena of adaptive ... | biology |
4,999 | Transient Leadership and Collective Cell Movement in Early Diverged Multicellular Animals | q-bio.CB | Collective motion of cells is critical to some of the most vital tasks
including wound healing, development, and immune response [Friedl and Gilmour
2009; Tokarski et al. 2012; Lee et al. 2012; Beltman et al. 2009], and is
common to many pathological processes including cancer cell invasion and
teratogenesis [Khalil an... | biology |
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