The intravascular contribution to fmri signal change: monte carlo modeling and diffusion-weighted studies in vivo

Understanding the relationship between fMRI signal changes and activated cortex is paramount to successful mapping of neuronal activity. To this end, the relative extravascular and intravascular contribution to fMRI signal change from capillaries (localized), venules (less localized) and macrovessels (remote, draining veins) must be determined. In this work, the authors assessed both the extravascular and intravascular contribution to blood oxygenation level-dependent gradient echo signal change at 1.5 T by using a Monte Carlo model for susceptibility-based contrast in conjunction with a physiological model for neuronal activation-induced changes in oxygenation and vascular volume fraction. The authors compared our Model results with experimental fMRI signal changes with and without velocity sensitization via bipolar gradients to null the intravascular signal. The model and experimental results are in agreement and suggest that the intravascular spins account for the majority of fMRI signal change on T₂^*-weighted images at 1.5 T.     

基于OBE理念的“医用数学建模”教学设计与实践

目的 基于成果导向教育（outcomes-based education,OBE）理念,以提升学员医用数学建模能力为目标,围绕《医用高等数学》课程中医用数学建模模块进行教学设计与实践并明确改进方向。方法 以“传染病模型”为例,进行教学实践;随后利用问卷方式收集44位学员反馈意见。综合运用统计描述、Mann-Whitney U检验、单因素方差分析和Scheffe法,以及卡方检验和z-检验对数据进行分析。结果 90.91%的学员对课程主题感兴趣,65.91%的学员认为该模式明显提升了学习效果。本次课程中学员学习主动性在对课程主题有、无兴趣这两个水平上无显著差异,而对知识点掌握程度和继续开展翻转课堂的意愿却有显著影响。结论 教学模式总体有效,但需在“突出建模,淡化计算”、提升学员参与度和强化课堂学习效果3个方面进一步改进。     

A framework for automatic analysis of the dynamic behaviour of coronary angiograms

A framework for coronary vessels analysis in digital subtracted angiograms is described. This method combines the motion estimation with the frame-to-frame structure detection in a natural way such that they act interactively. The first step consists of the extraction of the vessel centrelines in one image and their organization into meaningful constituents or branches of the coronary arterial tree. The motion is then estimated along the centrelines through a gradient based method. These motion estimates supply an initial positioning of an active contour model (or snake) in the next image. This model adapts itself by changing its shape to accurately fit onto the new centrelines. This process is then reiterated on the subsequent images to depict the dynamic behaviour of all the relevant branches. The main interests of this scheme are: (1) the active models operate locally so a fast detection of the vessels can be performed; (2) the centrelines extraction is fully guided by the confluence of the motion estimation and the contour model; (3) both morphological and kinetic features are provided on a quantitative basis.     

Evolution of Vertebroplasty: A Biomechanical Perspective

This paper is a collection of computational, finite element studies on vertebroplasty performed in our laboratory, which attempts to provide new biomechanical evidence and a fresh perspective into how the procedure can be implemented more effectively toward the goal of preventing osteoporosis-related fractures. The percutaneous application of a bone cement to vertebral defects associated with osteoporotic vertebral compression fracture has proven clinical successful in alleviating back pain. When the biomechanical efficacy of the procedure was examined, however, vertebroplasty was found to be limited in its ability to provide sufficient augmentation to prevent further fractures without risking complications arising from cement extravasations. The procedure may instead be more efficient biomechanically as a prophylactic treatment, to mechanically reinforce osteoporotic vertebrae at risk for fracture. Patient selection for such intervention may be reliably achieved with the more accurate fracture risk assessments based on vertebral strength, predicted using geometrically detailed, specimen-specific finite element models, rather than on bone density alone. Optimal cement volume, placement, and material properties were also recommended. The future of vertebroplasty involving biodegradable augmentation material laced with osteogenic agents that upon release will stimulate new bone growth and increase bone mass was proposed.     

儿童退缩和同伴关系的相关

目的：用元分析方法对近20年关于儿童退缩和同伴关系相关的研究结果进行总结。方法：用多水平分析技术对儿童退缩和同伴接受的相关、退缩和同伴拒绝相关的研究结果进行总结分析。结果：儿童退缩和同伴接受之间有显著的负相关关系，退缩和同伴拒绝之间有低度的非负相关关系，各研究结果之间的变异显著。结论：退缩导致儿童不良的同伴关系。     

Computer Simulations of the “Hairy Rod” Model

Summary: Using extensive Molecular Dynamics simulations we study the behavior of very rigid polyelectrolytes with hydrophobic side chains that are known to form cylindrical micelles in aqueous solution. We investigate the stability of such micelles with respect to hydrophobicity, Coulomb interaction, and micellar size. We show that for the parameter range relevant for poly(p‐phenylene sulfonate)s (PPP) one finds a stable finite micellar size close to the experimental parameter region. We also point out that our model has some similarities to DNA solutions with added condensing agents, hinting to the possibility that the size of DNA aggregates is under certain circumstances thermodynamically limited.

DNA‐like morphologies of the polyelectrolytes.     

A mathematical model of thrombin production in blood coagulation,Part I: The sparsely covered membrane case

This paper presents the first attempt to model the blood coagulation reactions in flowing blood. The model focuses on the common pathway and includes activation of factor X and prothrombin, including feedback activation of cofactors VIII and V by thrombin, and plasma inhibition of factor Xa and thrombin. In this paper, the first of two, the sparsely covered membrane (SCM) case is presented. This considers the limiting situation where platelet membrane binding sites are in excess, such that no membrane saturation or binding competition occurs. Under these conditions, the model predicts that the two positive feedback loops lead to multiple steady-state behavior in the range of intermediate mass transfer rates. It will be shown that this results in three parameter regions exhibiting very different thrombin production patterns. The model predicts the effect of flow on steady-state and dynamic thrombin production and attempts to explain the difference between venous and arterial thrombi. The reliance of thrombin production on precursor procoagulant protein concentrations is also assessed.     

Computational biology insights into genotype-clinical phenotype-protein phenotype relationships between novel SLC26A2 variants identified in inherited skeletal dysplasias

BackgroundPathogenic variants in the transmembrane sulfate transporter protein SLC26A2 are associated with different phenotypes of inherited chondrodysplasias. As limited data is published from India, in this study we sought to elucidate the molecular basis of inherited chondrodysplasias in an Indian cohort.MethodsMolecular screening of 32 fetuses with antenatally diagnosed lethal skeletal dysplasia was performed by next generation sequencing and Sanger sequencing. The genotype-protein phenotype characterization was done using computational biology techniques like homology modelling, stability and pathogenicity predictions.ResultsWe identified five rare autosomal recessive SLC26A2 [NM_000112.4] variants, including three homozygous c.796dupA(p.Thr266Asnfs*12), c.1724delA(p.Lys575Serfs*10), and c.1375_1377dup(p.Val459dup) and two heterozygous variants (c.532C > T(p.Arg178*)) and (c.1382C > T(p.Ala461Val)) in compound heterozygous form in a total of four foetuses. Genotype-protein phenotype annotations highlighted that the clinically severe achondrogenesis 1B causative c.796dupA(p.Thr266Asnfs*12) and c.1724delA(p.Lys575Serfs*10)variants impact SLC26A2 protein structure by deletion of the protein core and transmembrane STAS domains, respectively. In clinically moderate atelosteogenesis type 2 phenotype, the c.1382C > T(p.Ala461Val) variant is predicted to distort alpha helix conformation and alter the bonding properties and free energy dynamics of transmembrane domains and the c.532C > T(p.Arg178*) variant results in loss of both core transmembrane and STAS domains of the SLC26A2 protein. The c.1375_1377dup(p.Val459dup) variant identified in clinically milder atelosteogenesis type II-diastrophic dysplasia spectrum lethal phenotype is predicted to decrease the Qualitative Model Energy Analysis (QMean), which affects major geometrical aspects of the SLC26A2 protein structure.ConclusionWe expand the spectrum of SLC26A2 related lethal chondrodysplasia and report three novel variants correlating clinical severity and protein phenotype within the lethal spectrum of this rare dysplasia. We demonstrate the relevance of structural characterization to aid novel variant reclassification to provide better prenatal management and reproductive options to families with lethal antenatal skeletal disorder.     

Integration from proteins to organs: the IUPS Physiome Project

The IUPS Physiome Project is an internationally collaborative open source project intended to provide a public domain framework for computational physiology, including the development of modeling standards, computational tools and web-accessible databases of models of structure and function at all spatial scales and across all organ systems. Here, we illustrate the application of this multi-scale modeling approach to three organ systems: the heart, the lungs and the musculo-skeletal system, and in each case we show how the organ level models incorporate tissue and cell-level physiology. Although the computational physiology framework presented here does not yet incorporate models of ageing processes, the model-based approach is certainly capable of describing ageing and disease-related processes both via parameter changes within the models of normal physiological processes and via models of additional processes added to the framework.     

Novel missense mutations in the human lysosomal sialidase gene in sialidosis patients and prediction of structural alterations of mutant enzymes

Three novel missense mutations in the human lysosomal sialidase gene causing amino acid substitutions (P80L, W240R, and P316S) in the coding region were identified in two Japanese sialidosis patients. One patient with a severe, congenital form of type 2 sialidosis was a compound heterozygote for 239C-to-T (P80L) and 718T-to-C (W240R). The other patient with a mild juvenile-onset phenotype (type 1) was a homozygote for the base substitution of 946C-to-T (P316S). None of these mutant cDNA products showed enzymatic activity toward an artificial substrate when coexpressed in galactosialidosis fibroblastic cells together with protective protein/cathepsin A (PPCA). All mutants showed a reticular immunofluorescence distribution when coexpressed with the PPCA gene in COS-1 cells, suggesting that the gene products were retained in the endoplasmic reticulum/Golgi area or rapidly degraded in the lysosomes. Homology modeling of the structural changes introduced by the mutations predicted that the P80L and P316S transversions cause large conformational changes including the active site residues responsible for binding the sialic acid carboxylate group. The W240R substitution was deduced to influence the molecular surface structure of a limited region of the constructed models, which was also influenced by previously identified V217M and G243R transversions. Received: Stptember 21, 2001 / Accepted: November 2, 2001