computer simulations

计算机模拟
  • 文章类型: Journal Article
    背景:经导管主动脉瓣膜植入(TAVI)后,需要永久起搏器植入(PPI)的瓣周漏(PVL)和传导障碍仍然是临床相关的挑战。基于计算机断层扫描的模拟可以预测显著的PVL和PPI的风险。
    目的:评估使用FEopsHEARTguide™进行术前计算机模拟的可行性和准确性,以预测使用自膨式超环形ACURATENeo2经导管心脏瓣膜的TAVI后的PVL和PPI。
    方法:前瞻性多中心观察性研究,包括接受ACURATENeo2瓣膜TAVI的连续患者。在TAVI程序之前进行计算机模拟,作为程序前计划的一部分。PPI和PVL的随访期为30天。
    结果:纳入65例患者(中位年龄81岁(第25-75百分位数77-84.5))。5例患者(7.7%)发生新的左束支传导阻滞,2例患者(3%)发生PPI。与没有新的传导障碍的患者相比,接触压力指数(CPI)相似。PPI患者的CPI数值高于无PPI患者(CPI中位数20.0%(第25-75百分位数15.0-25.0)与13.0%(第25-75百分位数5.5-18),p=0.27)。30%以上的微量PVL发生。无微量PVL患者的中位PVL显著降低(3.2mL/s[第25-75百分位数2.2-5.0]),与轻度PVL(5.2mL/s[第25-75百分位数3.2-10.3])和中度PVL(12.6mL/s[第25-75百分位数3.9-21.3])相比(p=0.036)。9.65mL/s的模拟PVL截止值确定了>痕量PVL的患者(AUC0.70(95%CI0.55-0.85),灵敏度42%,特异性95%)。
    结论:在我们的研究中,FEopsHEARTguide™模拟确定了患有ACURATENeo2TAVI而非PPI的>痕量PVL的患者。
    BACKGROUND: Paravalvular leakage (PVL) and conduction disorders that require permanent pacemaker implantation (PPI) remain clinically relevant challenges after transcatheter aortic valve implantation (TAVI). Computed tomography-based simulations may predict the risk of significant PVL and PPI.
    OBJECTIVE: To evaluate the feasibility and accuracy of preprocedural computer simulation with FEops HEARTguide™ to predict >trace PVL and PPI after TAVI with the self-expanding supra-annular ACURATE Neo2 transcatheter heart valve.
    METHODS: Prospective multicenter observational study that included consecutive patients undergoing TAVI with an ACURATE Neo2 valve. Computer simulations were performed before the TAVI procedure as part of the preprocedural planning. Follow-up period for PPI and PVL was 30 days.
    RESULTS: Sixty-five patients were included (median age 81 years (25th-75th percentile 77-84.5)). New left bundle branch block occurred in five patients (7.7%) and PPI in two patients (3%). Contact pressure index (CPI) was similar for patients with vs without new conduction disorders. Patients with PPI had numerically higher CPI than those without PPI (median CPI 20.0% (25th-75th percentile 15.0-25.0) vs. 13.0% (25th-75th percentile 5.5-18), p = 0.27). More than trace PVL occurred in 30%. Median PVL was significantly lower in patients with none-trace PVL (3.2 mL/s [25th-75th percentile 2.2-5.0]), compared to mild PVL (5.2 mL/s [25th-75th percentile 3.2-10.3]) and moderate PVL (12.6 mL/s [25th-75th percentile 3.9-21.3])(p = 0.036). A simulated PVL-cutoff of 9.65 mL/s identified patients with >trace PVL (AUC 0.70 (95% CI 0.55-0.85), sensitivity 42%, specificity 95%).
    CONCLUSIONS: In our study FEops HEARTguide™ simulations identified patients at risk for >trace PVL with ACURATE Neo2 TAVI but not for PPI.
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  • 文章类型: Journal Article
    解开结构性景观因素和动物运动行为的作用可能会给管理景观的从业者带来挑战,以保持功能连通性并实现保护目标。我们使用了景观遗传学方法来结合强大的人口统计学,具有空间显式模拟的行为和遗传数据集,以评估人为障碍的影响(水坝,涵洞)和自然景观阻力(梯度,海拔)影响扩散行为,西坡割喉鳟鱼(Oncorhynchusclarkiilewisi)常住人口的遗传连通性和遗传结构。基于10年的抽样努力的分析揭示了一种受限扩散的模式,种群遗传学确定了远端支流和主干流之间的离散种群簇,而主干流中没有结构。退化模拟表明,对于这个人口来说,现有的人为障碍对人口结构的影响是多余的,而与潜在的环境阻力相关的限制扩散的影响是多余的。我们的方法提供了一个示例,说明如何将广泛的野外采样与景观遗传学相结合,可以将其纳入空间显式模拟建模中,以探索如何,一起,运动生态学和景观阻力可用于指导有关恢复和连通性的决策。
    Disentangling the roles of structural landscape factors and animal movement behaviour can present challenges for practitioners managing landscapes to maintain functional connectivity and achieve conservation goals. We used a landscape genetics approach to combine robust demographic, behavioural and genetic datasets with spatially explicit simulations to evaluate the effects of anthropogenic barriers (dams, culverts) and natural landscape resistance (gradient, elevation) affecting dispersal behaviour, genetic connectivity and genetic structure in a resident population of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi). Analyses based on 10 years of sampling effort revealed a pattern of restricted dispersal, and population genetics identified discrete population clusters between distal tributaries and the mainstem stream and no structure within the mainstem stream. Demogenetic simulations demonstrated that, for this population, the effects of existing anthropogenic barriers on population structure are redundant with effects of restricted dispersal associated with the underlying environmental resistance. Our approach provides an example of how extensive field sampling combined with landscape genetics can be incorporated into spatially explicit simulation modelling to explore how, together, movement ecology and landscape resistance can be used to inform decisions around restoration and connectivity.
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  • 文章类型: Journal Article
    细胞在脂滴(LD)内储存三酰甘油(TAG)。尚不存在描述内质网(ER)膜上完全LD形成的动态模型。提出了LD合成的生化-生物物理模型。它描述了TAG在ER膜中的时间依赖性积累,即形成了由膜的内部和外部单层的球形帽界定的潜在LD(pLD)。pLD的膨胀率取决于TAG供应,ER膜的弹性特性,以及磷脂(PL)向覆盖帽的单层募集。模型模拟提供了以下见解:(a)盖单层的表面张力的边际差异足以完全驱动pLD向细胞溶胶或内腔的扩展。(b)选择性减少向管腔单层供应的PL确保稳定形成胞质LD。无论ER膜的弹性机械性能如何变化。(c)向胞质单层供应TAG的速率对LD的大小和成熟时间具有主要影响,但对每个单独LD的TAG输出没有显著影响。在pLD的上限单层中招募额外的PLs至关重要地控制了萌芽方向,尺寸,和LD的成熟时间。细胞获得额外LD起始位点的能力似乎是应对急剧高水平的潜在毒性游离脂肪酸的关键。
    Cells store triacylglycerol (TAG) within lipid droplets (LDs). A dynamic model describing complete LD formation at the endoplasmic reticulum (ER) membrane does not yet exist. A biochemical-biophysical model of LD synthesis is proposed. It describes the time-dependent accumulation of TAG in the ER membrane as the formation of a potential LD (pLD) bounded by spherical caps of the inner and outer monolayers of the membrane. The expansion rate of the pLD depends on the TAG supply, the elastic properties of the ER membrane, and the recruitment of phospholipids (PLs) to the cap-covering monolayers. Model simulations provided the following insights: (a) Marginal differences in the surface tension of the cap monolayers are sufficient to fully drive the expansion of the pLD towards the cytosol or lumen. (b) Selective reduction of PL supply to the luminal monolayer ensures stable formation of cytosolic LDs, irrespective of variations in the elasto-mechanical properties of the ER membrane. (c) The rate of TAG supply to the cytosolic monolayer has a major effect on the size and maturation time of LDs but has no significant effect on the TAG export per individual LD. The recruitment of additional PLs to the cap monolayers of pLDs critically controls the budding direction, size, and maturation time of LDs. The ability of cells to acquire additional LD initiation sites appears to be key to coping with acutely high levels of potentially toxic free fatty acids.
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  • 文章类型: Journal Article
    通过分子动力学计算机模拟,研究了沿链具有各种带电基团分布的聚两性电解质大分子的构象空间。考虑了粗粒模型,其中链的每个单体单元在与带电侧基连接的大分子主链中作为不带电基团呈现。研究了等电点完全带电链的极限情况。带相反电荷的单体单元以各种模式分布:规则交替,多块,或随机序列。发现具有随机单位分布的链比具有规则分布且具有可比的嵌段长度的链采用更紧凑的构象。计算链条大小及其波动以及空间密度分布,线圈,和球形构象根据链长在图上进行区分和排列,块长度,和Bjerrum长度。
    By means of molecular dynamics computer simulation, the conformational space of polyampholyte macromolecules with various distributions of the charged groups along the chain is studied. A coarse-grained model where each monomer unit of the chain is presented as a non-charged group in the backbone of the macromolecule connected with a charged side pendant is considered. A limiting case of fully charged chains in the isoelectric point is investigated. The oppositely charged monomer units are distributed in various patterns: regular alternating, multiblock, or random sequences. It is found that the chains with random unit distribution adopt much more compacted conformations than the chains with regular distributions with comparable block lengths. Calculating the chain size and its fluctuation along with the spatial density distribution, coil, and globular conformations are distinguished and arranged on the diagrams in terms of chain length, block length, and Bjerrum length.
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  • 文章类型: Journal Article
    关于急性高钠血症的心脏影响的临床和实验数据很少且不一致。我们旨在确定和了解不同程度的急性高钠血症对人心室动作电位的影响。
    我们使用两种不同的计算机模拟,单个人心室心肌细胞的电活动的非常全面的模型,即,Tomek-Rodriguez模型遵循O\'Hara-Rudy动态(ORd)模型和2020年发布的Bartolucci-Passini-Severi模型(称为ToR-ORd和BPS2020模型,分别)。根据高钠血症对细胞体积和个体离子电流的影响的实验数据,将轻度至极端水平的高钠血症引入每个模型。
    在两种型号中,我们观察到细胞内钠和钾浓度增加,细胞内钙浓度的峰值幅度增加,静息膜电位的超极化,动作电位的延长,最大上冲程速度的增加,以及在所有高钠血症水平和所有测试的刺激速率下阈值刺激电流的增加。在轻度至重度高钠血症的情况下,所有这些影响的幅度相对较小,但在极端高钠血症的情况下,这些影响的幅度很大。对动作电位的影响与钠钾泵电流的增加有关,钠钙交换电流的增加,快速和慢速延迟整流钾电流的降低,以及快速和晚期钠电流的增加。
    轻度至重度高钠血症对人心室心肌细胞电活动的影响相对较小。在极端高钠血症的情况下,效果更明显,特别是关于阈值刺激电流的增加。
    UNASSIGNED: Clinical and experimental data on the cardiac effects of acute hypernatremia are scarce and inconsistent. We aimed to determine and understand the effects of different levels of acute hypernatremia on the human ventricular action potential.
    UNASSIGNED: We performed computer simulations using two different, very comprehensive models of the electrical activity of a single human ventricular cardiomyocyte, i.e., the Tomek-Rodriguez model following the O\'Hara-Rudy dynamic (ORd) model and the Bartolucci-Passini-Severi model as published in 2020 (known as the ToR-ORd and BPS2020 models, respectively). Mild to extreme levels of hypernatremia were introduced into each model based on experimental data on the effects of hypernatremia on cell volume and individual ion currents.
    UNASSIGNED: In both models, we observed an increase in the intracellular sodium and potassium concentrations, an increase in the peak amplitude of the intracellular calcium concentration, a hyperpolarization of the resting membrane potential, a prolongation of the action potential, an increase in the maximum upstroke velocity, and an increase in the threshold stimulus current at all levels of hypernatremia and all stimulus rates tested. The magnitude of all of these effects was relatively small in the case of mild to severe hypernatremia but substantial in the case of extreme hypernatremia. The effects on the action potential were related to an increase in the sodium-potassium pump current, an increase in the sodium-calcium exchange current, a decrease in the rapid and slow delayed rectifier potassium currents, and an increase in the fast and late sodium currents.
    UNASSIGNED: The effects of mild to severe hypernatremia on the electrical activity of human ventricular cardiomyocytes are relatively small. In the case of extreme hypernatremia, the effects are more pronounced, especially regarding the increase in threshold stimulus current.
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  • 文章类型: Journal Article
    表面活性剂对流体界面的吸附发生在许多技术和日常生活环境中。所形成的吸附层在界面处的覆盖率和其它性质决定了表面活性剂在所需应用方面的性能。鉴于这些应用的重要性,对表面活性剂吸附层的全面表征和理解有很大的需求。在这次审查中,我们提供了合适的实验和基于模拟的技术的概述,并回顾了用于研究表面活性剂吸附层的文献。我们得出的结论是,虽然这些技术已成功应用于研究水不溶性表面活性剂的Langmuir单层,它们在水溶性表面活性剂吉布斯吸附层研究中的应用尚未得到充分开发。最后,我们强调这些方法的巨大潜力,提供了一个更深入的了解可溶性表面活性剂在界面的行为,这对于优化它们在各种应用中的性能至关重要。
    Adsorption of surfactants to fluid interfaces occurs in numerous technological and daily-life contexts. The coverage at the interface and other properties of the formed adsorption layers determine the performance of a surfactant with regard to the desired application. Given the importance of these applications, there is a great demand for the comprehensive characterization and understanding of surfactant adsorption layers. In this review, we provide an overview of suitable experimental and simulation-based techniques and review the literature in which they were used for the investigation of surfactant adsorption layers. We come to the conclusion that, while these techniques have been successfully applied to investigate Langmuir monolayers of water-insoluble surfactants, their application to the study of Gibbs adsorption layers of water-soluble surfactants has not been fully exploited. Finally, we emphasize the great potential of these methods in providing a deeper understanding of the behavior of soluble surfactants at interfaces, which is crucial for optimizing their performance in various applications.
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  • 文章类型: Journal Article
    这项研究的目的是评估生成预训练变压器-4(GPT-4)生成的放电指令在预设阅读水平下的完整性和可读性,以用于常见的儿科急诊室投诉。
    按阅读水平(五年级或八年级)和语言(英语,西班牙语)使用GPT-4产生五倍。具体来说,制作并分析了120份出院说明(6种情况:60份英文,西班牙语60;五年级阅读水平60,八年级阅读水平为60),并比较了完整性和可读性(在语言之间,在阅读水平之间,并按小组和阅读水平分层)。完整性定义为出院说明中包含的文献衍生关键点的比例。可读性使用Flesch-Kincaid(英语)和Fernandez-Huerta(西班牙语)可读性评分进行量化。
    英语GPT生成的放电指令包含的必须包括放电指令的比例明显高于西班牙语(英语:平均值(平均值的标准误差)=62%(3%),西班牙语:53%(3%),P=.02)。在五年级和八年级的条件下,英语和西班牙语输出的完整性没有显着差异。不同语言的可读性没有差异。
    GPT-4在调节文档阅读水平的同时,用英语和西班牙语制作了可读的放电说明。英语的放电指令往往比西班牙语的指令具有更高的完整性。
    在快速工程和GPT-4性能方面的未来研究,一般和多种语言,需要通过语言和阅读水平来减少健康差异的可能性。
    UNASSIGNED: The aim of this study was to assess the completeness and readability of generative pre-trained transformer-4 (GPT-4)-generated discharge instructions at prespecified reading levels for common pediatric emergency room complaints.
    UNASSIGNED: The outputs for 6 discharge scenarios stratified by reading level (fifth or eighth grade) and language (English, Spanish) were generated fivefold using GPT-4. Specifically, 120 discharge instructions were produced and analyzed (6 scenarios: 60 in English, 60 in Spanish; 60 at a fifth-grade reading level, 60 at an eighth-grade reading level) and compared for completeness and readability (between language, between reading level, and stratified by group and reading level). Completeness was defined as the proportion of literature-derived key points included in discharge instructions. Readability was quantified using Flesch-Kincaid (English) and Fernandez-Huerta (Spanish) readability scores.
    UNASSIGNED: English-language GPT-generated discharge instructions contained a significantly higher proportion of must-include discharge instructions than those in Spanish (English: mean (standard error of the mean) = 62% (3%), Spanish: 53% (3%), P = .02). In the fifth-grade and eighth-grade level conditions, there was no significant difference between English and Spanish outputs in completeness. Readability did not differ across languages.
    UNASSIGNED: GPT-4 produced readable discharge instructions in English and Spanish while modulating document reading level. Discharge instructions in English tended to have higher completeness than those in Spanish.
    UNASSIGNED: Future research in prompt engineering and GPT-4 performance, both generally and in multiple languages, is needed to reduce potential for health disparities by language and reading level.
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  • 文章类型: Journal Article
    这项研究调查了不同的细胞大小如何影响光聚合物三重周期性最小表面(TPMS)在不同变形速率下的机械性能。钻石,甲状腺,和原始TPMS结构与空间分级的细胞大小进行了测试。准静态实验测量边界力,代表材料行为,惯性,和变形机制。单独的研究探讨了基础材料的行为及其对应变率的响应,显示强度随应变率的增加而增加。十次压缩试验确定了“灰色专业”材料的临界应变率为0.7s-1,表明失败易感性的转变。X射线断层扫描,摄像机录音,和图像相关技术观察到TPMS结构中的细胞连通性和非均匀变形。超过临界速率的区域较早断裂。在原始结构中,刚度差异导致较小的细胞以较低的速率致密化后塌陷。研究发现塌陷起始应力增加,高原胁迫,致密化应变,和比能量吸收,变形率低于所有TPMS结构的临界率。然而,细胞大小分级的原始结构在500mm/min的速率下显示出平台和比能量吸收的显着降低。
    This study investigates how varying cell size affects the mechanical behaviour of photopolymer Triply Periodic Minimal Surfaces (TPMS) under different deformation rates. Diamond, Gyroid, and Primitive TPMS structures with spatially graded cell sizes were tested. Quasi-static experiments measured boundary forces, representing material behaviour, inertia, and deformation mechanisms. Separate studies explored the base material\'s behaviour and its response to strain rate, revealing a strength increase with rising strain rate. Ten compression tests identified a critical strain rate of 0.7 s-1 for \"Grey Pro\" material, indicating a shift in failure susceptibility. X-ray tomography, camera recording, and image correlation techniques observed cell connectivity and non-uniform deformation in TPMS structures. Regions exceeding the critical rate fractured earlier. In Primitive structures, stiffness differences caused collapse after densification of smaller cells at lower rates. The study found increasing collapse initiation stress, plateau stress, densification strain, and specific energy absorption with higher deformation rates below the critical rate for all TPMS structures. However, cell-size graded Primitive structures showed a significant reduction in plateau and specific energy absorption at a 500 mm/min rate.
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  • 文章类型: Journal Article
    这项工作介绍了X射线计算(XRC),一个开源软件包,旨在模拟X射线反射率(XRR),并根据测得的XRR曲线解决重建膜结构的反问题。XRC具有用户友好的图形界面,便于交互式模拟和重建。该软件采用基于菲涅耳方程的递归方法来计算XRR,并结合了用于对周期性多层结构进行建模的专用工具。本文介绍了最新版本的X-RayCalc软件(XRC3),有显著的改进。这些增强包括利用改进的飞行粒子群优化算法对XRR曲线的自动拟合能力。还开发了一种新颖的成本函数,专门用于拟合周期性结构的XRR曲线。此外,通过开发新的单窗口界面,整体用户体验得到了增强。
    This work introduces X-Ray Calc (XRC), an open-source software package designed to simulate X-ray reflectivity (XRR) and address the inverse problem of reconstructing film structures on the basis of measured XRR curves. XRC features a user-friendly graphical interface that facilitates interactive simulation and reconstruction. The software employs a recursive approach based on the Fresnel equations to calculate XRR and incorporates specialized tools for modeling periodic multilayer structures. This article presents the latest version of the X-Ray Calc software (XRC3), with notable improvements. These enhancements encompass an automatic fitting capability for XRR curves utilizing a modified flight particle swarm optimization algorithm. A novel cost function was also developed specifically for fitting XRR curves of periodic structures. Furthermore, the overall user experience has been enhanced by developing a new single-window interface.
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  • 文章类型: Journal Article
    环二核苷酸(CDN)是由两个磷酸二酯键连接的两个核苷单磷酸组成的环状分子,作为第二信使,与干扰素基因刺激因子(STING)结合,激活下游信号通路,最终诱导干扰素分泌,启动抗感染免疫反应.环二核苷酸及其类似物是传染病和肿瘤免疫治疗的先导化合物,以及具有良好应用的免疫佐剂。已经开发了许多病原体识别受体的激动剂作为优化疫苗免疫原性和功效的有效佐剂。在这项工作中,利用计算机模拟并结合实验结果,从理论上研究了人源干扰素基因刺激蛋白及其同工型与环二核苷酸及其类似物的结合机制,希望为后续环二核苷酸类似物的合成提供指导。
    Cyclic dinucleotides (CDNs) are cyclic molecules consisting of two nucleoside monophosphates linked by two phosphodiester bonds, which act as a second messenger and bind to the interferon gene stimulating factor (STING) to activate the downstream signaling pathway and ultimately induce interferon secretion, initiating an anti-infective immune response. Cyclic dinucleotides and their analogs are lead compounds in the immunotherapy of infectious diseases and tumors, as well as immune adjuvants with promising applications. Many agonists of pathogen recognition receptors have been developed as effective adjuvants to optimize vaccine immunogenicity and efficacy. In this work, the binding mechanism of human-derived interferon gene-stimulating protein and its isoforms with cyclic dinucleotides and their analogs was theoretically investigated using computer simulations and combined with experimental results in the hope of providing guidance for the subsequent synthesis of cyclic dinucleotide analogs.
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