毛细管电泳芯片信号分析系统的UML建模研究

集成毛细管电泳芯片(Integrate Cpillary Electrophoresis Chip,ICEC)属于分析型生物芯片,近年来发展迅速。ICEC过程复杂,实现困难,有必要前期通过建模等方式,进行必要的系统设计。统一建模语言(Unified Modeling Language,UML)是一种用来描述系统、构造系统模型的面向对象建模语言,运用UML语言对ICEC信号分析系统进行建模研究,可使ICEC的设计逐步优化,从而最终实现混合物高效分析和分离的目的。本文系统描述UML语言和毛细管电泳芯片工作原理,并介绍运用UML语言对ICEC信号分析系统建模方法。     

面向对象的冲压件特征建模研究

应用面向对象的表达策略,对冲压零件的特征及其联系进行了描述,并建立了在语义、结构上有统一形式的冲压件模型.这种冲压件的定义方法不仅有利于设计,而且便于进行冲压件的可制造性评价,更重要的是为后续的冲压工艺设计提供了较为完备的工艺信息.     

基于Agisoft PhotoScan的石器三维建模与应用

打制石器是了解古人类认知、技术、行为等信息的重要物质载体之一,如何能够更加方便地观察绘制、测量以及展示石器是旧石器时代考古学中基础的研究内容。目前多视角影像三维重建技术在中国考古界应用越来越广泛,尤其是Agisoft PhotoScan软件的应用。相比其他类型遗物,石器的形制及片疤样式具有独特性,在建模过程难度较大。我们经过反复尝试,总结出了一套基于Agisoft PhotoScan软件,专门针对打制石器且易于掌握的建模方式,并从观察绘图、数字化、展示三个方面探讨了石器三维模型的应用。     

生物建模和模拟实验

构造模型和模拟实验是进行生命科学研究的最常用的一种方法。其本质是对生物结构及生命现象进行模拟。开设生物建模和模拟实验课程,是高中生命科学课程改革的一个大胆尝试,是培养创造型人才的一项有力措施,这项措施必将推动高中生命科学教学改革,有力地促进青少年科技活动的深入开展。     

数学建模在生物化感及其赫米西斯(Hormesis)现象中的应用

简述了国内外对生物化感数学建模的研究近况,包括通过数学模型描述化感物质的赫米西斯(Hormesis)现象,化感作用在受体植物不同密度条件下的表达,植物残茬中化感物质的分解动态及受体植物的动态响应,环境中化感物质的动态变化规律及在植物-昆虫-天敌系统中的应用等。并对化感数学建模领域的先驱机理模型An-Hormesis模型,An-Liu-Johnson-Lovett模型,和An_Residue模型做了简介。     

关于灌木生物量建模方法的改进

关于灌木生物量建模方法的改进张峰,上官铁梁李素珍（山西大学生物系,太原０３０００６）（太原治金工业学校,０３０００２）ＩｍｐｒｏｖｅｍｅｎｔｏｎｔｈｅＭｏｄｅｌｌｉｎｇＭｅｔｈｏｄｏｆＢｉｏｌｍａｓｓｏｆＢｒｕｓｈ￥ＺｈａｎｇＦｅｎｇ;ＳｈａｎｇｇｕａｎＴｉｅｌｉａｎｇ（Ｄｅｐａｒｔ－ｍｅｎｔｏｆＢｉｏｌｏｇｙ,ＳｈａｎｘｉＵｎｉｖｅｒｓｉｔｙ,Ｔａｉｙｕａｎ０３０００６）,ＬｉＳｕｚｈｅｎ（ＴａｉｙｉｉａｎＭｅｔａｌｌｉｔｒｇｉｃａｌＳｃｈｏｏｌ,Ｔａｉｙｕａｎ０３０００２）．ＣｈｉｎｅｓｅＪｏｕｒｎａｌｏｆＶＥｃｏｌｏｇｙ,１９９３,１２（６）：６７－６９．ＤｕｒｉｎｇｍａｋｉｎｇｒｅｓｅａｒｃｈｏｎｔｈｅｂｉｏｍａｓｓｏｆＥｌａｅａｇｎｕｓｍｏｌｌｉｓ,ｔｈｅｒｅｇｒｅｓｓｉｏｎｍｏｄｅｌｏｆｔｈｅｂｉｏｍａｓｓｉｓｂｕｉｌｔｂｙｒｅｐｌａｃｉｎｇＤ￣２ＨｗｉｔｈＣＨ,Ｔｈｅｒｅｓｕｌｔｓｈｏｗｓｔｈａｔｎｏｔｏｎｌｙｉｔｉｓｃｏｎｖｉｎｉｅｎｔｉｎｔｈｅｆｉｅｌｄｗｏｒｋ,ｂｕｔａｌｓｏｔｈｅｆｏｒｅｃａｓｔｍｏｄｅｌｈａｓｍｏｒｅＤｒｅｃｉｓｉｏｎｗｈｅｎＣＨｉｓｕｓｅｄａｓｔｈｅｉｎｄｅｐｅｎｄ     

大语言模型在古生物学中的应用初探——以基于RAG的知识问答系统为例*

面向科学的人工智能正推动科学研究的范式变革。大语言模型在科研领域的潜力远不止于文献阅读等基础应用, 众多学科已开始构建领域研究的人工智能系统。商业模型存在使用门槛高、数据安全性难以保障等制约因素, 而开源大模型的本地部署为解决这些问题提供了新思路。本文以教学过程中涉及的构建腕足动物知识问答系统为例, 探索了基于基础检索增强生成(Naive RAG)的开源大语言模型在专业知识获取中的应用价值。该系统通过交互式问答能促进学生对专业知识的掌握, 但仍存在明显优化空间。针对现有局限, 本文提出了基于图检索增强生成(Graph RAG)和代理检索增强生成(Agent RAG)等的改进方案设想。结合当前技术发展趋势,探讨了检索增强生成的自适应推理系统在古生物学跨学科发展势态下的前景、困难与策略。     

心肌细胞电生理建模进展

心脏兴奋收缩的微观基础是心肌细胞的电生理活动,心肌细胞的电生理模型在解剖实验基础上提供了更为全面有力的数据.是研究心肌细胞最有效的方法之一.近年来单细胞意义上的电生理模型越来越精细,使得心肌细胞的工作原理以不同角度在微观领域得以进一步阐述.本文就不同时期有代表性的模型进行了研究和比较,总结了这一领域的发展,并对发展趋势作了进一步的展望.     

COVID-19急症与重症宿主内动力学建模研究

为了研究COVID-19的宿主内动力学、分析急症患者与重症患者之间的差异,本文提出了一个TCL-IR模型。首先,基于靶细胞限制模型和免疫应答模型构建TCL-IR模型,并获得宿主内再生数的表达式;其次,结合已有研究确定模型中的部分参数,再采用自适应Metropolis算法进行未知参数的估计;最后,根据所得结果对急症、重症患者之间的差异进行分析。结果显示,急症和重症患者在免疫反应和病毒载量上均有一定差别。急症患者的T细胞增殖系数为0.652,免疫凋亡速率为4.137×10^-6;重症患者的T细胞增殖系数为0.266,免疫凋亡速率为3.283×10^-6。急症患者的病毒载量在35 d左右达到峰值,约为7.20×10⁴copies/mL;重症患者的病毒载量在28 d左右达到峰值且峰值更高,约为1.38×10⁵copies/mL。根据结果分析和文献印证,研究发现部分急症患者的病情加重并不是因为体内过高的病毒载量,而是因为自身过度的免疫反应。因此,急症患者的治疗需要考虑免疫调节方案。     

Modeling Metal Flow Systems

Substance flow analysis (SFA) is a frequently used industrial ecology technique for studying societal metal flows, but it is limited in its ability to inform us about future developments in metal flow patterns and how we can affect them. Equation‐based simulation modeling techniques, such as dynamic SFA and system dynamics, can usefully complement static SFA studies in this respect, but they are also restricted in several ways. The objective of this article is to demonstrate the ability of agent‐based modeling to overcome these limitations and its usefulness as a tool for studying societal metal flow systems. The body of the article summarizes the parallel implementation of two models—an agent‐based model and a system dynamics model—both addressing the following research question: What conditions foster the development of a closed‐loop flow network for metals in mobile phones? The results from in silico experimentation with these models highlight three important differences between agent‐based modeling (ABM) and equation‐based modeling (EBM) techniques. An analysis of how these differences affected the insights that could be extracted from the constructed models points to several key advantages of ABM in the study of metal flow systems. In particular, this analysis suggests that a key advantage of the ABM technique is its flexibility to enable the representation of societal metal flow systems in a more native manner. This added flexibility endows modelers with enhanced leverage to identify options for steering metal flows and opens new opportunities for using the metaphor of an ecosystem to understand metal flow systems more fully.     

基于统一过程方法的膜片钳系统软件设计

新一代膜片钳系统控制软件使用敏捷UP(统一过程)、可复用面向对象方法,多线程内存共享、事件同步和内存映射文件技术,具有响应速度快、内存消耗小、易移植、维护性能好等特点。实验结果表明,新系统显著提高了电压门控模式的系统响应速度,增加了配体门控模式的记录时间等。     

Modeling resistance to genetic control of insects

The sterile insect technique is an area-wide pest control method that reduces pest populations by releasing mass-reared sterile insects which compete for mates with wild insects. Modern molecular tools have created possibilities for improving and extending the sterile insect technique. As with any new insect control method, questions arise about potential resistance. Genetic RIDL^®1 (Release of Insects carrying a Dominant Lethal) technology is a proposed modification of the technique, releasing insects that are homozygous for a repressible dominant lethal genetic construct rather than being sterilized by irradiation. Hypothetical resistance to the lethal mechanism is a potential threat to RIDL strategies' effectiveness. Using population genetic and population dynamic models, we assess the circumstances under which monogenic biochemically based resistance could have a significant impact on the effectiveness of releases for population control. We assume that released insects would be homozygous susceptible to the lethal genetic construct and therefore releases would have a built-in element of resistance dilution. We find that this effect could prevent or limit the spread of resistance to RIDL constructs; the outcomes are subject to competing selective forces deriving from the fitness properties of resistance and the release ratio. Resistance that is spreading and capable of having a significant detrimental impact on population reduction is identifiable, signaling in advance a need for mitigating action.     

Redefining the Ojibwe Classroom: Indigenous Language Programs within Large Research Universities

Indigenous languages are powerful symbols of self-determination and sovereignty for tribal communities in the United States, and many community-based programs have been developed to support and maintain them. The successes of these programs, however, have been difficult to replicate at large research institutions. This article examines the issues of incorporating Indigenous languages into the university system by focusing on a series of language events developed as part of the Ojibwe language program at Michigan State University. These language events demonstrate a way for communities to participate in and maintain control of Indigenous language programs despite their location in nontribal educational institutions.     

Modeling and experimental study on the anaerobic/aerobic/anoxic process for simultaneous nitrogen and phosphorus removal: The effect of acetate addition

A mathematical model based on the simulation software AQUASIM was developed to validate an anaerobic/aerobic/anoxic (AOA) process that enables simultaneous nitrogen and phosphorus removal in a single reactor by adding external organic carbon to preclude excess aerobic phosphate uptake by polyphosphate-accumulating organisms (PAOs) and provide phosphate for denitrifying PAOs (DNPAOs). Aerobic batch tests after anaerobic phosphate release with different chemical oxygen demand (COD) concentrations indicated that the effect of COD concentration on the phosphate uptake preclusion could be expressed by a simple formula. The reduction factor reflecting the formula, which retards the aerobic phosphate uptake in the presence of COD, was added to the process rates of aerobic polyphosphate storage and PAOs growth in the model. The improved model, which included the reduction factor, reasonably matched the experimental result regarding aerobic phosphate uptake behavior whereas the model without it did not; thus, the former precisely predicts the AOA process behavior.     

用于生理组学协同研究的跨层次建模标记语言(M3L)

根据生理组学多领域多层次协同研究的需求,针对中国生理组学研究的特点,设计了一种跨层次建模标记语言(Mul-tiscale Modeling Markup Language,简称M3L),规范研究过程中的信息描述方法,实现了数学模型和计算数据的开放式共享和重用。M3L包含结构化模型机制、数据存档机制、信息交互与重用机制、数学描述机制、可视化模型及附件描述机制。M3L中针对人体和小动物解剖结构数据的特殊设计实现了结构与功能信息的关联,促进了中国生理组学研究中模型和数据的标准化描述;M3L以跨层次结构化的方式描述模型,符合生理组学研究模型的特点,满足了协同开发的需求。     

Modeling the Tertiary Structure of the Patatin Domain of Neuropathy Target Esterase

Neuropathy target esterase (NTE) is a transmembrane protein of unknown function whose specific chemical modification by certain organophosphorus (OP) compounds leads to distal axonopathy. Therefore, solving the 3D structure of NTE would advance the understanding of its pathogenic and physiologic roles. In this study, the tertiary structures of the patatin (catalytic) domain and the N-terminal transmembrane domain of NTE were modeled using the crystal structures of patatin (PDB ID 1oxw) and moricin (PDB ID 1kv4) as templates. Sequence alignments and secondary structure predictions were obtained from the INUB server (Buffalo, NY). O and PyMol were used to build the PNTE and NTE TMD chains from these sequence alignments. The PNTE model was refined in the presence of water using the crystallography and NMR system, while the NTE TMD model was refined in vacuo using the GROMOS implementation in the Swiss PDB viewer. The modeled active site of NTE was found to consist of a Ser966-Asp1086 catalytic dyad, which is characteristic of phospholipase A2 enzymes. The Ser966 Ogamma was located 2.93 A from the Odelta2 of Asp1086. In addition, our NTE model was found to contain a single N-terminal transmembrane domain. This modeling effort provided structural and mechanistic predictions about the catalytic domain of NTE that are being verified via experimental techniques.     

Modeling Epistasis in Genomic Selection

Modeling epistasis in genomic selection is impeded by a high computational load. The extended genomic best linear unbiased prediction (EG-BLUP) with an epistatic relationship matrix and the reproducing kernel Hilbert space regression (RKHS) are two attractive approaches that reduce the computational load. In this study, we proved the equivalence of EG-BLUP and genomic selection approaches, explicitly modeling epistatic effects. Moreover, we have shown why the RKHS model based on a Gaussian kernel captures epistatic effects among markers. Using experimental data sets in wheat and maize, we compared different genomic selection approaches and concluded that prediction accuracy can be improved by modeling epistasis for selfing species but may not for outcrossing species.     

嗜酸热原体菌的超氧化物歧化酶的结构模建和进化踪迹分析

为考察来源于极端高温酸性环境中的超氧化物歧化酶,建立了一个由嗜酸热原体茵的sod基因编码的蛋白质的可靠三维分子结构,并对这个蛋白质进行进化踪迹分析识别出了11个踪迹残基?其中,残基Asn39,Gly105和Glu162的位置随机遍布整个结构,其余的残基却全部都明显地聚于一个靠近铁原子的子类当中?由此从在三维结构确认sod基因编码含铁的超氧化物歧化酶.此外,那些被识别的靠近铁原子的踪迹残基可能跟铁的绑定和催化功能直接相关?     

Sweet Science for ALL! Supporting Inquiry-Based Learning Through M&Ms Investigation for English Language Learners

This article describes a series of inquiry-based lessons that provide English language learners (ELLs) with opportunities to experience science and engineering practices with conceptual understanding as well as to develop their language proficiency in elementary classrooms. The four-lesson sequence models how various types of instructional strategies for ELLs can be embedded through science lessons with thoughtful consideration of ELLs’ diverse cultural backgrounds. The cross-curricular science lessons provide ELLs with opportunities to apply and enhance their mathematics, reading, writing, and communicating skills while investigating the properties of M&Ms.