Biomechanical rationale of coronary artery bypass grafting of multivessel disease

The biomechanical model of human coronary arteries was modified for improving the quality of diagnosis and surgical treatment for coronary heart disease. The problem of hemodynamics in the left coronary artery with multivessel bed disease – 45% stenosis of the anterior descending branch and 75% stenosis of the circumflex branch – was particularly considered. Numerical simulation of the coronary arterial bypass of the main trunk was carried out to estimate the functional condition of the coronary arteries after restoring myocardial blood supply by surgery.     

How good are comparative models in the understanding of protein dynamics?

The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.     

Graphical modeling for gene set analysis: A critical appraisal

Current demand for understanding the behavior of groups of related genes, combined with the greater availability of data, has led to an increased focus on statistical methods in gene set analysis. In this paper, we aim to perform a critical appraisal of the methodology based on graphical models developed in Massa et al. ( 2010 ) that uses pathway signaling networks as a starting point to develop statistically sound procedures for gene set analysis. We pay attention to the potential of the methodology with respect to the organizational aspects of dealing with such complex but highly informative starting structures, that is pathways. We focus on three themes: the translation of a biological pathway into a graph suitable for modeling, the role of shrinkage when more genes than samples are obtained, the evaluation of respondence of the statistical models to the biological expectations. To study the impact of shrinkage, two simulation studies will be run. To evaluate the biological expectation we will use data from a network with known behavior that offer the possibility of carrying out a realistic check of respondence of the model to changes in the experimental conditions.     

基于长时间序列landsat数据的科尔沁沙地土地利用演变分析

以科尔沁沙地沙丘-草甸过渡带区域主要土地覆被类型为研究对象，以1987-2017年多时相Landsat TM/OLI遥感影像解译分类为基础，参考生态学植被演替研究方法，系统分析研究区30年来的土地利用/覆被动态演变规律，研究结果表明：（1）决策树法在复杂下垫面不同覆被类型的同步识别效果较好，所有影像分类精度均达到88%以上，分类效果较好，其中2017年分类精度最高为95.24%，达到了分类研究的要求；（2）研究区存在着"半灌丛-草甸地-灌丛"的植被结构特征，且整体表现为"南进北退"的变化趋势。结合土地利用动态度分析结果表明人类活动干涉下，研究区整体上遵循了半干旱区植被条件改善的一般规律，侧面反映该研究区域生态环境的持续不稳定性和脆弱性；（3）研究区覆被类型发生变化的总面积达到2623.59 hm²，总变化强度为63.76%。其中正向演替的比例为52.61%，以半灌丛面积的持续减小与沙地草甸面积的持续扩张为主要变化特征。但同时，半灌丛转为沙地的面积为184.95 hm²，表明以放牧为主的研究区同时发生着局部的逆行演变；（4）质心迁移结果反映了1987-2017年间，除人为影响较大的林地、草地以及耕地向北迁移外，其他植被类型的质心都有很明显的南迁，主要植被类型重心迁移距离依次由大到小为耕地 > 半灌丛 > 灌丛 > 沙地草甸 > 湿地草甸 > 林地。研究通过记录科尔沁沙地连续扩展的时空模式，展示了遥感-生态和时间序列影像在30 m分辨率下跟踪土地利用/覆被变化的潜力，为提高干旱半干旱区土地利用情况的动态监测效率，开展土地利用/覆被动态演变研究提供参考。     

Costs for switching partners reduce network dynamics but not cooperative behaviour

Social networks represent the structuring of interactions between group members. Above all, many interactions are profoundly cooperative in humans and other animals. In accordance with this natural observation, theoretical work demonstrates that certain network structures favour the evolution of cooperation. Yet, recent experimental evidence suggests that static networks do not enhance cooperative behaviour in humans. By contrast, dynamic networks do foster cooperation. However, costs associated with dynamism such as time or resource investments in finding and establishing new partnerships have been neglected so far. Here, we show that human participants are much less likely to break links when costs arise for building new links. Especially, when costs were high, the network was nearly static. Surprisingly, cooperation levels in Prisoner''s Dilemma games were not affected by reduced dynamism in social networks. We conclude that the mere potential to quit collaborations is sufficient in humans to reach high levels of cooperative behaviour. Effects of self-structuring processes or assortment on the network played a minor role: participants simply adjusted their cooperative behaviour in response to the threats of losing a partner or of being expelled.     

Substrate-enzyme interactions and catalytic mechanism in phospholipase C: a molecular modeling study using the GRID program.

Based on the high-resolution X-ray crystallographic structure of phospholipase C from Bacillus cereus, the orientation of the phosphatidylcholine substrate in the active site of the enzyme is proposed. The proposal is based on extensive calculations using the GRID program and molecular mechanics geometry relaxations. The substrate model has been constructed by successively placing phosphate, choline and diacylglycerol moieties in the positions indicated from GRID calculations. On the basis of the resulting orientation of a complete phosphatidylcholine molecule, we propose a mechanism for the hydrolysis of the substrate.     

Effect of the anisotropic permeability in the frequency dependent properties of the superficial layer of articular cartilage

Abstract

Articular cartilage is a tissue of fundamental importance for the mechanics of joints, since it provides a smooth and lubricated surface for the proper transfer of loads. From a mechanical point of view, this tissue is an anisotropic poroviscoelastic material: its characteristics at the macroscopic level depend on the complex microscopic architecture. With the ability to probe the local microscopic features, dynamic nanoindentation test is a powerful tool to investigate cartilage mechanics. In this work we focus on a length scale where the time dependent behaviour is regulated by poroelasticity more than viscoelasticity and we aim to understand the effect of the anisotropic permeability on the mechanics of the superficial layer of the articular cartilage. In a previous work, a finite element model for the dynamic nanoindentation test has been presented. In this work, we improve the model by considering the presence of an anisotropic permeability tensor that depends on the collagen fibers distribution. Our sensitivity analysis highlights that the permeability decreases with increasing indentation, thus making the tissue stiffer than the case of isotropic permeability, when solicited at the same frequency. With this improved model, a revised identification of the mechanical and physical parameters for articular cartilage is provided. To this purpose the model was used to simulate experimental data from tests performed on bovine tissue, giving a better estimation of the anisotropy in the elastic properties. A relation between the identified macroscopic anisotropic permeability properties and the microscopic rearrangement of the fiber/matrix structure during indentation is also provided.     

Three-dimensional chromatin ensemble reconstruction via stochastic embedding

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