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At least 235 records · Page 13Linked to original sources

arXiv2013

Determination, Calculation and Representation of the Upper and Lower Sealing Zones During Virtual Stenting of Aneurysms

In this contribution, a novel method for stent simulation in preoperative computed tomography angiography (CTA) acquisitions of patients is presented where the sealing zones are automatically calculated and visualized. The method is eligible for non-bifurcated and bifurcated stents (Y-stents). Results of the proposed stent simulation with an automatic calculation of the sealing zones for specific diseases (abdominal aortic aneurysms (AAA), thoracic aortic aneurysms (TAA), iliac aneurysms) are presented. The contribution is organized as follows. Section 2 presents the proposed approach. In Section 3, experimental results are discussed. Section 4 concludes the contribution and outlines areas for future work.

cs.CV↗

arXiv2022

Overt and covert paths for sound in the auditory system of mammals

The consensus, according to which the transmission of sound from the tympanum to the Outer Hair Cells is solely mechanical, is problematic, especially with respect to high pitched sounds. We demonstrate that the collagenous fibers of the tympanum produce electric potentials synchronous to acoustic vibrations and that, contrary to expectations, their amplitude increases as the frequency of the vibration increases. These electrical potentials cannot be reduced to the cochlear microphonic. Moreover, the alteration of collagen as well as that of the gap junctions (electric synapses) necessary for the transmission of the electric potentials to the complex formed by the Deiters Cells and Outer Hair Cells, results in hypoacousis or deafness. The discovery of an electronic pathway, complementary to air and bone conduction has the potential for elucidating certain important as yet unexplained aspects of hearing with respect to cochlear amplification, otoacoustic emissions, and hypoacusis related to the deterioration of collagen or of gap-junctions. Thus, our findings have important implications for both theory and practice.

q-bio.TO↗

arXiv2013

Manipulate the coiling and uncoiling movements of Lepidoptera proboscis by its conformation optimizing

Many kinds of adult Lepidoptera insects possess a long proboscis which is used to suck liquids and has the coiling and uncoiling movements. Although experiments revealed qualitatively that the coiling movement is governed by the hydraulic mechanism and the uncoiling movement is due to the musculature and the elasticity, it needs a quantitative investigation to reveal how insects achieve these behaviors accurately. Here a quasi-one-dimensional (Q1D) curvature elastica model is proposed to reveal the mechanism of these behaviors. We find that the functions of internal stipes muscle and basal galeal muscle which locate at the bottom of proboscis are to adjust the initial states in the coiling and uncoiling processes, respectively. The function of internal galeal muscle which exists along proboscis is to adjust the line tension. The knee bend shape is due to the local maximal spontaneous curvature and is an advantage for nectar-feeding butterfly. When there is no knee bend, the proboscis of fruit-piercing butterfly is easy to achieve the piercing movement which induced by the increase of internal hydraulic pressure. All of the results are in good agreement with experiential observation. Our study provides a revelatory method to investigate the mechanical behaviors of other 1D biologic structures, such as proboscis of marine snail and elephant. Our method and results are also significant in designing the bionic devices.

q-bio.TO↗

arXiv2013

Modèle théorique de la contraction musculaire squelettique : ressorts entropiques, processus stochastiques et mécanique classique (A theoretical model of skeletal muscular contraction : entropic springs, stochastic processes and classical mechanics)

The model analyzes the muscle fiber as a deformable system for which experimental data are determinated with the help of the laws of Newtonian mechanic. The model predicts the four transient phases for the shortening of a muscle fiber according to a force or length step. The model shows, on the one hand, the importance of the viscosity during the first phase of these two types of step and, secondly, the interdependence of the six other phases towards a bimodal state after disappearance of actions due to viscosity. The model provides an interpretation for the behavior of a fiber with shortening staircase. The model is consistent with experimental data during temperature changes or various structural alterations.

q-bio.TO↗

arXiv2013

Acute Respiratory Distress Syndrome is a TH17-like and Treg immune disease

Acute Respiratory Distress Syndrome (ARDS) is a very severe syndrome leading to respiratory failure and subsequent mortality. Sepsis is one of the leading causes of ARDS. Thus, extracellular bacteria play an important role in the pathophysiology of ARDS. Overactivated neutrophils are the major effector cells in ARDS. Thus, extracellular bacteria triggered TH17-like innate immunity with neutrophil activation might accounts for the etiology of ARDS. Here, microarray analysis was employed to describe TH17-like innate immunity-related cytokine including TGF-β and IL-6 up-regulation in whole blood of ARDS patients. It was found that the innate TH17-related TLR1,2,4,5,8, HSP70, G-CSF, GM-CSF, complements, defensin, PMN chemokines, cathepsins, Fc receptors, NCFs, FOS, JunB, CEBPs, NFkB, and leukotriene B4 are all up-regulated. TGF-β secreting Treg cells play important roles in lung fibrosis. Up-regulation of Treg associated STAT5B and TGF-β with down-regulation of MHC genes, TCR genes, and co-stimulation molecule CD86 are noted. Key TH17 transcription factors, STAT3 and RORα, are down-regulated. Thus, the full adaptive TH17 helper CD4 T cells may not be successfully triggered. Many fibrosis promoting genes are also up-regulated including MMP8, MMP9, FGF13, TIMP1, TIMP2, PLOD1, P4HB, P4HA1, PDGFC, HMMR, HS2ST1, CHSY1, and CSGALNACT. Failure to induce successful adaptive immunity could also attribute to ARDS pathogenesis. Thus, ARDS is actually a TH17-like and Treg immune disorder.

q-bio.TO↗

arXiv2013

Experimental investigation of the trachea oscillation and its role in the pitch production

Several experiments have been performed to investigate the mechanical vibrations associated with trachea and larynx when Italian vowels are emitted. The mechanical measurements have been made by using two laser Doppler vibrometers (based on the well-known not-invasive optical measurement technique) coupled with the acoustic field measured by high-quality certified microphones. The recorded signals are analyzed by using well-established methods in time and frequency domains. The signals of the mechanical vibrations along the trachea and the larynx are compared with those of the acoustic ones. Focusing the attention of the signals' onsets, we can observe an upward propagation of the mechanical vibrations for which it is possible to estimate a delay between the traces. We observe that the mechanical oscillations at the trachea start before the larynx and acoustic oscillations. Moreover these tracheal oscillations are self-oscillations in time and are associated with the pitch production, indicating a further hydrodynamic instability at trachea. This leads to new insights in the mechanism controlling the pitch in the speech.

q-bio.TO↗

arXiv2013

Model for tumour growth with treatment by continuous and pulsed chemotherapy

In this work we investigate a mathematical model describing tumour growth under a treatment by chemotherapy that incorporates time-delay related to the conversion from resting to hunting cells. We study the model using values for the parameters according to experimental results and vary some parameters relevant to the treatment of cancer. We find that our model exhibits a dynamical behaviour associated with the suppression of cancer cells, when either continuous or pulsed chemotherapy is applied according to clinical protocols, for a large range of relevant parameters. When the chemotherapy is successful, the predation coefficient of the chemotherapic agent acting on cancer cells varies with the infusion rate of chemotherapy according to an inverse relation. Finally, our model was able to reproduce the experimental results obtained by Michor and collaborators [Nature, 435, 1267 (2005)] about the exponential decline of cancer cells when patients are treated with the drug glivec.

q-bio.TO↗

arXiv2013

A Bayesian approach to accounting for variability in mechanical properties in biomaterials

In this paper, we present an approach for modeling bio-tissues that incorporates the variability in properties as part of their characteristics. This is achieved by considering the parameters of the model of a biomaterial to themselves be random variables and represented by a probability distribution over the space of parameters. This probability distribution is obtained by the systematic use of Bayesian inference together with a continuum mechanics based solution of a boundary value problem. We illustrate this approach by characterizing sheep arteries by using a combination of experimental data and different hyperelastic models. Furthermore, we also develop a model based Bayesian classification of new data into different classes based on the computed model parameter probability distribution.

q-bio.TO↗

arXiv2013

Liquid-Solid Phase Transition Alloy as Reversible and Rapid Molding Bone Cement

Bone cement has been demonstrated as an essential restorative material in the orthopedic surgery. However current materials often imply unavoidable drawbacks, such as tissue-cement reaction induced thermal injuries and troublesome revision procedure. Here we proposed an injectable alloy cement to address such problems through its liquid-solid phase transition mechanism. The cement is made of a unique alloy BiInSnZn with a specifically designed low melting point 57.5°C. This property enables its rapid molding into various shapes with high plasticity. Some fundamental characteristics including mechanical strength behaviors and phase transition-induced thermal features have been measured to demonstrate the competence of alloy as unconventional cement with favorable merits. Further biocompatible tests showed that this material could be safely employed in vivo. In addition, experiments also found the alloy cement capability as an excellent contrast agent for radiation imaging. Particularly, the proposed alloy cement with reversible phase transition feature significantly simplifies the revision of cement and prosthesis. This study opens the way to implement alloy material as bone cement to fulfill diverse clinical needs.

cond-mat.mtrl-sci↗

arXiv2013

Effects of space structure and combination therapies on phenotypic heterogeneity and drug resistance in solid tumors

Histopathological evidence supports the idea that the emergence of phenotypic heterogeneity and resistance to cytotoxic drugs can be considered as a process of adaptation, or evolution, in tumor cell populations. In this framework, can we explain intra-tumor heterogeneity in terms of cell adaptation to local conditions? How do anti-cancer therapies affect the outcome of cell competition for nutrients within solid tumors? Can we overcome the emergence of resistance and favor the eradication of cancer cells by using combination therapies? Bearing these questions in mind, we develop a model describing cell dynamics inside a tumor spheroid under the effects of cytotoxic and cytostatic drugs. Cancer cells are assumed to be structured as a population by two real variables standing for space position and the expression level of a cytotoxic resistant phenotype. The model takes explicitly into account the dynamics of resources and anti-cancer drugs as well as their interactions with the cell population under treatment. We analyze the effects of space structure and combination therapies on phenotypic heterogeneity and chemotherapeutic resistance. Furthermore, we study the efficacy of combined therapy protocols based on constant infusion and/or bang-bang delivery of cytotoxic and cytostatic drugs.

q-bio.TO↗

arXiv2014

Raman spectroscopic detection of rapid, reversible, early-stage inflammatory cytokine-induced apoptosis of adult hippocampal progenitors/stem cells

The role of neuro-inflammation in diverse, acute and chronic brain pathologies is being increasingly recognized. Neuro-inflammation is accompanied by increased levels of both pro- and anti-inflammatory cytokines; these have deleterious as well as protective/reparative effects. Inflammation has varying effects on neurogenesis and is a subject of intense contemporary interest. We show that TNF-alpha and IFN-gamma, used concomitantly, cause apoptosis of adult rat hippocampal progenitor/stem cells in vitro as detected by the TUNEL and MTT assays on time scales of several hours. We have coupled Raman spectroscopy to an optical trap to probe early changes of apoptosis in single, live neural stem cells that have been treated with pro-inflammatory cytokines, TNF-alpha and IFN-gamma. Changes caused by inflammation-induced denaturation of DNA are observed in the Raman spectra that correspond to very early stages of apoptosis, occurring on very fast time scales: as short as 10 minutes. Addition of the anti-inflammatory cytokine IL-10 either 10-30 min before or 10-30 min after treatment with TNF-alpha and IFN-gamma reverses the changes substantially. Our findings imply that inflammation can induce very rapid changes leading to cell death but that these are reversible, in the early stages at least.

physics.bio-ph↗

arXiv2014

How do digits emerge? - Mathematical Models of Limb Development

The mechanism that controls digit formation has long intrigued developmental and theoretical biologists, and many different models and mechanisms have been proposed. Here we review models of limb development with a specific focus on digit and long bone formation. Decades of experiments have revealed the basic signalling circuits that control limb development, and recent advances in imaging and molecular technologies provide us with unprecedented spatial detail and a broader view on the regulatory networks. Computational approaches are important to integrate the available information into a consistent framework that will allow us to achieve a deeper level of understanding and that will help with the future planning and interpretation of complex experiments, paving the way to in silico genetics. Previous models of development had to be focused on very few, simple regulatory interactions. Algorithmic developments and increasing computing power now enable the generation and validation of increasingly realistic models that can be used to test old theories and uncover new mechanisms.

q-bio.TO↗

arXiv2014

Determination of personalized diabetes treatment plans using a two-delay model

Diabetes cases worldwide have risen steadily over the past decades, lending urgency to the search for more efficient, effective, and personalized ways to treat the disease. Current treatment strategies, however, may fail to maintain ultradian oscillations in blood glucose concentration, an important element of a healthy alimentary system. Building upon recent successes in mathematical modeling of the human glucose-insulin system, we show that both food intake and insulin therapy likely demand increasingly precise control over insulin sensitivity if oscillations at a healthy average glucose concentration are to be maintained. We then suggest guidelines and personalized treatment options for diabetic patients that maintain these oscillations. We show that for a type II diabetic, both blood glucose levels can be controlled and healthy oscillations maintained when the patient gets an hour of daily exercise and is placed on a combination of Metformin and sulfonylurea drugs. We note that insulin therapy and an additional hour of exercise will reduce the patient's need for sulfonylureas. Results of a modeling analysis suggest that a typical type I diabetic's blood glucose levels can be properly controlled with a constant insulin infusion between 0.45 and 0.7 microU/(ml*min). Lastly, we note that all suggested strategies rely on existing clinical techniques and established treatment measures, and so could potentially be of immediate use in the design of an artificial pancreas.

q-bio.TO↗

arXiv2014

Collective motion of cells: from experiments to models

Swarming or collective motion of living entities is one of the most common and spectacular manifestations of living systems having been extensively studied in recent years. A number of general principles have been established. The interactions at the level of cells are quite different from those among individual animals therefore the study of collective motion of cells is likely to reveal some specific important features which are overviewed in this paper. In addition to presenting the most appealing results from the quickly growing related literature we also deliver a critical discussion of the emerging picture and summarize our present understanding of collective motion at the cellular level. Collective motion of cells plays an essential role in a number of experimental and real-life situations. In most cases the coordinated motion is a helpful aspect of the given phenomenon and results in making a related process more efficient (e.g., embryogenesis or wound healing), while in the case of tumor cell invasion it appears to speed up the progression of the disease. In these mechanisms cells both have to be motile and adhere to one another, the adherence feature being the most specific to this sort of collective behavior. One of the central aims of this review is both presenting the related experimental observations and treating them in the light of a few basic computational models so as to make an interpretation of the phenomena at a quantitative level as well.

q-bio.CB↗

arXiv2014

Capillary Network, Cancer and Kleiber Law

We develop a heuristic model embedding Kleiber and Murray laws to describe mass growth, metastasis and vascularization in cancer. We analyze the relevant dynamics using different evolution equations (Verhulst, Gompertz and others). Their extension to reaction diffusion equation of the Fisher type is then used to describe the relevant metastatic spreading in space. Regarding this last point, we suggest that cancer diffusion may be regulated by Levy flights mechanisms and discuss the possibility that the associated reaction diffusion equations are of the fractional type, with the fractional coefficient being determined by the fractal nature of the capillary evolution.

physics.bio-ph↗

arXiv2014

Contractile and mechanical properties in epithelia with perturbed actomyosin dynamics

Mechanics has an important role during morphogenesis, both in the generation of forces driving cell shape changes and in determining the effective material properties of cells and tissues. Drosophila dorsal closure (DC) has emerged as a model system for studying the interplay between tissue mechanics and cellular activity. Thereby, the amnioserosa (AS) generates one of the major forces that drive DC through the apical contraction of its constituent cells. We combined quantitation of live data, genetic and mechanical perturbation and cell biology, to investigate how mechanical properties and contraction rate emerge from cytoskeletal activity. We found that a decrease in Myosin phosphorylation induces a fluidization of AS cells which become more compliant. Conversely, an increase in Myosin phosphorylation and an increase in actin linear polymerization induce a solidification of cells. Contrary to expectation, these two perturbations have an opposite effect on the strain rate of cells during DC. While an increase in actin polymerization increases the contraction rate of AS cells, an increase in Myosin phosphorylation gives rise to cells that contract very slowly. The quantification of how the perturbation induced by laser ablation decays throughout the tissue revealed that the tissue in these two mutant backgrounds reacts very differently. We suggest that the differences in the strain rate of cells in situations where Myosin activity or actin polymerization is increased arise from changes in how the contractile forces are transmitted and coordinated across the tissue through ECadherin mediated adhesion. Our results show that there is an optimal level of Myosin activity to generate efficient contraction and suggest that the architecture of the actin cytoskeleton and the dynamics of adhesion complexes are important parameters for the emergence of coordinated activity throughout the tissue.

q-bio.CB↗

arXiv2014

Propagation of Uncertainty and Analysis of Signal-to-Noise in Nonlinear Compliance Estimations of an Arterial System Model

The arterial system dynamically loads the heart through changes in arterial compliance. The pressure-volume relation of arteries is known to be nonlinear, but arterial compliance is often modeled as a constant value, due to ease of estimation and interpretation. Incorporating nonlinear arterial compliance affords insight into the continuous variations of arterial compliance in a cardiac cycle and its effects on the heart, as the arterial system is coupled with the left ventricle. We recently proposed a method for estimating nonlinear compliance parameters that yielded good results under various vasoactive states. This study examines the performance of the proposed method by quantifying the uncertainty of the method in the presence of noise and propagating the uncertainty through the system model to analyze its effects on model predictions. Kernel density estimation used within a bootstrap Monte Carlo simulation showed the method to be stable for various vasoactive states.

q-bio.QM↗

arXiv2016

Simulated annealing approach to vascular structure with application to the coronary arteries

Does the complex processes of angiogenesis during organism development ultimately lead to a near optimal coronary vasculature in the organs of adult mammals? We examine this hypothesis using a powerful and universal method, built on physical and physiological principles, for the determination of globally energetically optimal arterial trees. The method is based on simulated annealing, and can be used to examine arteries in hollow organs with arbitrary tissue geometries. We demonstrate that the approach can generate in-silico vasculatures which closely match porcine anatomical data for the coronary arteries on all length scales, and that the optimised arterial trees improve systematically as computational time increases. The method presented here is general, and could in principle be used to examine the arteries of other organs. Potential applications include improvement of medical imaging analysis and the design of vascular trees for artificial organs.

physics.bio-ph↗