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At least 37 records · Page 2Linked to original sources
arXiv2007

Controlling spatiotemporal chaos and spiral turbulence in excitable media: A review

Excitable media are a generic class of models used to simulate a wide variety of natural systems including cardiac tissue. Propagation of excitation waves in this medium results in the formation of characteristic patterns such as rotating spiral waves. Instabilities in these structures may lead to spatiotemporal chaos through spiral turbulence, which has been linked to clinically diagnosed conditions such as cardiac fibrillation. Usual methods for controlling such phenomena involve very large amplitude perturbations and have several drawbacks. There have been several recent attempts to develop low-amplitude control procedures for spatiotemporal chaos in excitable media which are reviewed in this paper. The control schemes have been broadly classified by us into three types: (i) global, (ii) non-global spatially-extended and (iii) local, depending on the way the control signal is applied, and we discuss the merits and drawbacks for each.

nlin.CD↗
arXiv2008

Modeling the variability of shapes of a human placenta

While it is well-understood what a normal human placenta should look like, a deviation from the norm can take many possible shapes. In this paper we propose a mechanism for this variability based on the change in the structure of the vascular tree.

q-bio.TO↗
arXiv2007

Cyclooxygenase Inhibition Limits Blood-Brain Barrier Disruption following Intracerebral Injection of Tumor Necrosis Factor-alpha in the Rat

Increased permeability of the blood-brain barrier (BBB) is important in neurological disorders. Neuroinflammation is associated with increased BBB breakdown and brain injury. Tumor necrosis factor-a (TNF-a) is involved in BBB injury and edema formation through a mechanism involving matrix metalloproteinase (MMP) upregulation. There is emerging evidence indicating that cyclooxygenase (COX) inhibition limits BBB disruption following ischemic stroke and bacterial meningitis, but the mechanisms involved are not known. We used intracerebral injection of TNF-a to study the effect of COX inhibition on TNF-a-induced BBB breakdown, MMP expression/activity and oxidative stress. BBB disruption was evaluated by the uptake of 14C-sucrose into the brain and by magnetic resonance imaging (MRI) utilizing Gd-DTPA as a paramagnetic contrast agent. Using selective inhibitors of each COX isoform, we found that COX-1 activity is more important than COX-2 in BBB opening. TNF-a induced a significant upregulation of gelatinase B (MMP-9), stromelysin-1 (MMP-3) and COX-2. In addition, TNF-a significantly depleted glutathione as compared to saline. Indomethacin (10 mg/kg; i.p.), an inhibitor of COX-1 and COX-2, reduced BBB damage at 24 h. Indomethacin significantly attenuated MMP-9 and MMP-3 expression and activation, and prevented the loss of endogenous radical scavenging capacity following intracerebral injection of TNF-a. Our results show for the first time that BBB disruption during neuroinflammation can be significantly reduced by administration of COX inhibitors. Modulation of COX in brain injury by COX inhibitors or agents modulating prostaglandin E2 formation/signaling may be useful in clinical settings associated with BBB disruption.

q-bio.TO↗
arXiv2009

Flow-correlated dilution of a regular network leads to a percolating network during tumor induced angiogenesis

We study a simplified stochastic model for the vascularization of a growing tumor, incorporating the formation of new blood vessels at the tumor periphery as well as their regression in the tumor center. The resulting morphology of the tumor vasculature differs drastically from the original one. We demonstrate that the probabilistic vessel collapse has to be correlated with the blood shear force in order to yield percolating network structures. The resulting tumor vasculature displays fractal properties. Fractal dimension, microvascular density (MVD), blood flow and shear force has been computed for a wide range of parameters.

q-bio.CB↗
arXiv2007

A ptototype compartmental model of blood pressure distribution

We consider a system of differential equations the behavior of which solutions possesses several properties characteristic of the blood pressure distribution. The system can be used for a compartmental modeling of the cardiovascular system. It admits a unique bounded solution such that all coordinates of the solution are separated from zero by positive numbers, and which is periodic, eventually periodic or almost periodic depending on the moments of heart contraction. Appropriate numerical simulations are provided.

q-bio.TO↗
arXiv2007

Global dynamical model of the cardiovascular system

Blood system functions are very diverse and important for most processes in human organism. One of its primary functions is matter transport among different parts of the organism including tissue supplying with oxygen, carbon dioxide excretion, drug propagation etc. Forecasting of these processes under normal conditions and in the presence of different pathologies like atherosclerosis, loss of blood, anatomical abnormalities, pathological changing in chemical transformations and others is significant issue for many physiologists. In this connection should be pointed out that global processes are of special interest as they include feedbacks and interdependences among different regions of the organism. Thus the main goal of this work is to develop the model allowing to describe effectively blood flow in the whole organism. As we interested in global processes the models of the four vascular trees (arterial and venous parts of systemic and pulmonary circulation) must be closed with heart and peripheral circulation models. As one of the model applications the processes of the blood loss is considered in the end of the paper.

physics.bio-ph↗
arXiv2007

Numerical simulations of cardiovascular diseases and global matter transport

Numerical model of the peripheral circulation and dynamical model of the large vessels and the heart are discussed in this paper. They combined together into the global model of blood circulation. Some results of numerical simulations concerning matter transport through the human organism and heart diseases are represented in the end.

physics.bio-ph↗
arXiv2008

Hot spot formation in tumor vasculature during tumor growth in an arterio-venous-network environment

Hot spots in tumors are regions of high vascular density in the center of the tumor and their analysis is an important diagnostic tool in cancer treatment. We present a model for vascular remodeling in tumors predicting that the formation of hot spots correlates with local inhomogeneities of the original arterio-venous vasculature of the healthy tissue. Probable locations for hot spots in the late stages of the tumor are locations of increased blood pressure gradients. The developing tumor vasculature is non-hierarchical but still complex displaying algebraically decaying density distributions.

q-bio.TO↗
arXiv2008

Hepatocyte Aggregates: Methods of Preparation in the Microgravity Simulating Bioreactor Use in Tissue Engineering

Tissue Engineering concerns the three-dimensional cell growth so that bio-artificial tissues could be created and used for transplantation. The recently expressed concerns from the Tissue Engineering research community for a re-direction of the research activities necessitate the proposition of new methodologies. We propose a methodology that has to do with the simulation in bioreactor systems of liver structures as are described in liver anatomy. I this way the hepatocyte microenvironments that determine their function could be re-created in vitro. The approach needs the use of hepatocyte aggregates as entities to load the bioreactor systems. A new bioreactor, the microgravity simulating rotation bioreactor, has been used for the preparation of cell aggregates. Microcontact printing has been used to produce a patterned surfaces. They were tested adsorbing BSA proteins, and will be used in future for the mmobilization of cell aggregates in order to gain further understanding of the role of cell heterogeneity in the cooperative behaviour of cells in vitro.

q-bio.TO↗
arXiv2008

Epidermal corneocytes: dead guards of the hidden treasure

Gradual transformation of the epidermal stem cells to corneocytes involves a chain of chronologically well-arranged events that mostly stimulated locally by their neighbors. Cell diversity that observed during the differentiation through the different epidermal cell layers included the consisted changes of cell shape, intercellular contacts and proliferation. However, the most dramatically these changes appeared at the molecular level through gene expression, catalysis and intraprotein interactions. The proposed review explains these changes by switching systemic transcription factors that unlike their counterparts those role is limited to a contribution to gene expression also prepare cells to the next step of differentiation via modification of the chromatin pattern . Since primary epidermal keratinocytes are one of the most easy available type of the stem cells, a better understanding of the epidermal differentiation will benefit the research in the other areas by a discovery of basic coordinating mechanisms that stand behind such distinct molecular events as cell signaling and gene expression, and formulate basic principles for a smart therapeutic correction of the metabolism.

q-bio.TO↗
arXiv2008

Characterizing the Diversity of Dynamics in Complex Networks Without Border Effects

The importance of structured, complex connectivity patterns found in several real-world systems is to a great extent related to their respective effects in constraining and even defining the respective dynamics. Yet, while complex networks have been comprehensively investigated along the last decade in terms of their topological measurements, relatively less attention has been focused on the characterization of the respective dynamics. Introduced recently, the diversity entropy of complex systems can provide valuable information about the respective possible unfolding of dynamics. In the case of self-avoiding random walks, the situation assumed here, the diversity measurement allows one to quantify in how many different places an agent may effectively arrive after a given number of steps from its initial activity. Because this measurement is highly affected by border effects frequently found as a consequence of network sampling, it becomes critical to devise means for sound estimation of the diversity without being affected by this type of artifacts. We describe such an algorithm and illustrate its potential with respect to the characterization of the self-avoiding random walk dynamics in two real-world networks, namely bone canals and air transportation.

q-bio.TO↗
arXiv2008

New Mechanics of Traumatic Brain Injury

The prediction and prevention of traumatic brain injury is a very important aspect of preventive medical science. This paper proposes a new coupled loading-rate hypothesis for the traumatic brain injury (TBI), which states that the main cause of the TBI is an external Euclidean jolt, or SE(3)-jolt, an impulsive loading that strikes the head in several coupled degrees-of-freedom simultaneously. To show this, based on the previously defined covariant force law, we formulate the coupled Newton-Euler dynamics of brain's micro-motions within the cerebrospinal fluid and derive from it the coupled SE(3)-jolt dynamics. The SE(3)-jolt is a cause of the TBI in two forms of brain's rapid discontinuous deformations: translational dislocations and rotational disclinations. Brain's dislocations and disclinations, caused by the SE(3)-jolt, are described using the Cosserat multipolar viscoelastic continuum brain model. Keywords: Traumatic brain injuries, coupled loading-rate hypothesis, Euclidean jolt, coupled Newton-Euler dynamics, brain's dislocations and disclinations

q-bio.TO↗
arXiv2009

Allometric metabolic scaling and fetal and placental weight

We tested the hypothesis that the fetal-placental relationship scales allometrically and identified modifying factors. Among women delivering after 34 weeks but prior to 43 weeks gestation, 24,601 participants in the Collaborative Perinatal Project (CPP) had complete data for placental gross proportion measures, specifically, disk shape, larger and smaller disk diameters and thickness, and umbilical cord length. The allometric metabolic equation was solved for alpha and beta by rewriting PW= alpha(BW)^beta as Log (PW) = Log(alpha) + beta*Log(BW). Mean beta was 0.78+ 0.02 (range 0.66, 0.89), 104% of that predicted by a supply-limited fractal system (0.75). Gestational age, maternal age, maternal BMI, parity, smoking, socioeconomic status, infant sex, and changes in placental proportions each had independent and significant effects on alpha. Conclusions: In the CPP cohort, the placental - birth weight relationship scales to approximately 3/4 power.

q-bio.TO↗
arXiv2008

Observation of Cholesterol Dissolved in Microscopic Deposits of Free Fatty Acids in the Lumen of an Aorta of a Mouse Model for Human Atherosclerosis

The Raman spectrum of microscopic droplets of lipid material on the lumen of the aorta of an apolipoprotein E knock-out mouse were reported in the proceedings of an SPIE conference. Based on the absence of the carbonyl band in the spectrum, at that time it was determined that the spectrum represents free fatty acids rather than triglycerides. More recent examination of the spectrum indicates that these droplets contain dissolved cholesterol, and thus can be used as an early indicator of the atherosclerosis process in animal models during drug development.

q-bio.TO↗
arXiv2008

Multi-Scale, Multi-Resolution Brain Cancer Modeling

In advancing discrete-based computational cancer models towards clinical applications, one faces the dilemma of how to deal with an ever growing amount of biomedical data that ought to be incorporated eventually in one form or another. Model scalability becomes of paramount interest. In an effort to start addressing this critical issue, here, we present a novel multi-scale and multi-resolution agent-based in silico glioma model. While "multi-scale" refers to employing an epidermal growth factor receptor (EGFR)-driven molecular network to process cellular phenotypic decisions within the micro-macroscopic environment, "multi-resolution" is achieved through algorithms that classify cells to either active or inactive spatial clusters, which determine the resolution they are simulated at. The aim is to assign computational resources where and when they matter most for maintaining or improving the predictive power of the algorithm, onto specific tumor areas and at particular times. Using a previously described 2D brain tumor model, we have developed four different computational methods for achieving the multi-resolution scheme, three of which are designed to dynamically train on the high-resolution simulation that serves as control. To quantify the algorithms' performance, we rank them by weighing the distinct computational time savings of the simulation runs versus the methods' ability to accurately reproduce the high-resolution results of the control. Finally, to demonstrate the flexibility of the underlying concept, we show the added value of combining the two highest-ranked methods.

q-bio.CB↗
arXiv2008

Cancer Cell Motility: Optimizing Spatial Search Strategies

Aberrantly regulated cell motility is a hallmark of cancer cells. A hybrid agent-based model has been developed to investigate the synergistic and antagonistic cell motility-impacting effects of three microenvironment variables simultaneously: chemoattraction, haptotactic permission, and biomechanical constraint or resistance. Reflecting distinct cell-specific intracellular machinery, the cancer cells are modelled as processing a variety of spatial search strategies that respond to these three influencing factors with differential weights attached to each. While responding exclusively to chemoattraction optimizes cell displacement effectiveness, incorporating permission and resistance components becomes increasingly important with greater distance to the chemoattractant source and/or after reducing the ligand's effective diffusion coefficient. Extending this to a heterogeneous population of cells shows that displacement effectiveness increases with clonal diversity as characterized by the Shannon index. However, the resulting data can be fit best to an exponential function, suggesting that there is a level of population heterogeneity beyond which its added value to the cancer system becomes minimal as directionality ceases to increase. Possible experimental extensions and potential clinical implications are discussed.

q-bio.CB↗
arXiv2008

Potential Phytoextraction with in-vitro regenerated plantlets of Brassica juncea (L.) Czern. in presence of CdCl$_2$: Cadmium accumulation and physiological parameter measurement

Heavy metal contamination of agricultural land is partly responsible for limiting crop productivity. Cd$^{2+}$ is known as a non-essentiel HM that can be harmful to plants even at low concentrations. Brassica juncea (L.) is able to accumulate more than 400 $μ$g.g$^{-1}$ D.W. in the shoot, a physiological trait which may be exploited for the phytoremediation of contaminated soils and waters. . The application of 75 $μ$M CdCl$_2$ for three days does not show any effect in the B. juncea growth parameters (F.W. and D.W.) whatever the type of plantlets. This application decreases also the contents of chlorophyll a, carotenoids and Chl a/b ratio (2.26) for plantlets regenerated in the absence of CdCl$_2$ but not those of plantlets regenerated in its presence. Roots have the highest contents (3071; 1544 $μ$g.g$^{-1}$ D.W.) followed by stems (850; 687$μ$g.g$^{-1}$ D.W.) and leaves (463; 264$μ$g.g$^{-1}$ D.W.) respectively. In our conditions, we suggest that the low accumulation in the plantlets regenerated in the presence of CdCl$_2$ by the means of in-vitro regeneration technology is still benefical, to some extent, for the phytoextraction process and seems to be an interesting technology that allows the cultivation of these plantlets in contaminated soils with low accumulation of metal in their shoots and probably in their seeds used in many food technologies.

q-bio.TO↗