Theory in Biosciences最新文献_第3页

Mathematical analysis of a modified Volterra-Leslie chemostat Model 修正的 Volterra-Leslie 化合模型的数学分析

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-04-09 DOI: 10.1007/s12064-024-00415-6

Mohammed Amine Hamra

引用次数: 0

Normalizing need not be the norm: count-based math for analyzing single-cell data. 规范化不一定是常态：用于分析单单元格数据的基于计数的数学。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2023-11-10 DOI: 10.1007/s12064-023-00408-x

Samuel H Church, Jasmine L Mah, Günter Wagner, Casey W Dunn

{"title":"Normalizing need not be the norm: count-based math for analyzing single-cell data.","authors":"Samuel H Church, Jasmine L Mah, Günter Wagner, Casey W Dunn","doi":"10.1007/s12064-023-00408-x","DOIUrl":"10.1007/s12064-023-00408-x","url":null,"abstract":"Counting transcripts of mRNA are a key method of observation in modern biology. With advances in counting transcripts in single cells (single-cell RNA sequencing or scRNA-seq), these data are routinely used to identify cells by their transcriptional profile, and to identify genes with differential cellular expression. Because the total number of transcripts counted per cell can vary for technical reasons, the first step of many commonly used scRNA-seq workflows is to normalize by sequencing depth, transforming counts into proportional abundances. The primary objective of this step is to reshape the data such that cells with similar biological proportions of transcripts end up with similar transformed measurements. But there is growing concern that normalization and other transformations result in unintended distortions that hinder both analyses and the interpretation of results. This has led to an intense focus on optimizing methods for normalization and transformation of scRNA-seq data. Here, we take an alternative approach, by avoiding normalization and transformation altogether. We abandon the use of distances to compare cells, and instead use a restricted algebra, motivated by measurement theory and abstract algebra, that preserves the count nature of the data. We demonstrate that this restricted algebra is sufficient to draw meaningful and practical comparisons of gene expression through the use of the dot product and other elementary operations. This approach sidesteps many of the problems with common transformations, and has the added benefit of being simpler and more intuitive. We implement our approach in the package countland, available in python and R.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":" ","pages":"45-62"},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72016176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimal dispersal and diffusion-enhanced robustness in two-patch metapopulations: origin's saddle-source nature matters. 双补丁元种群中的最佳扩散和扩散增强的稳健性：起源的鞍源性质很重要。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2024-02-21 DOI: 10.1007/s12064-023-00411-2

Marc Jorba-Cuscó, Ruth I Oliva-Zúniga, Josep Sardanyés, Daniel Pérez-Palau

{"title":"Optimal dispersal and diffusion-enhanced robustness in two-patch metapopulations: origin's saddle-source nature matters.","authors":"Marc Jorba-Cuscó, Ruth I Oliva-Zúniga, Josep Sardanyés, Daniel Pérez-Palau","doi":"10.1007/s12064-023-00411-2","DOIUrl":"10.1007/s12064-023-00411-2","url":null,"abstract":"A two-patch logistic metapopulation model is investigated both analytically and numerically focusing on the impact of dispersal on population dynamics. First, the dependence of the global dynamics on the stability type of the full extinction equilibrium point is tackled. Then, the behaviour of the total population with respect to the dispersal is studied analytically. Our findings demonstrate that diffusion plays a crucial role in the preservation of both subpopulations and the full metapopulation under the presence of stochastic perturbations. At low diffusion, the origin is a repulsor, causing the orbits to flow nearly parallel to the axes, risking stochastic extinctions. Higher diffusion turns the repeller into a saddle point. Orbits then quickly converge to the saddle's unstable manifold, reducing extinction chances. This change in the vector field enhances metapopulation robustness. On the other hand, the well-known fact that asymmetric conditions on the patches is beneficial for the total population is further investigated. This phenomenon has been studied in previous works for large enough or small enough values of the dispersal. In this work, we complete the theory for all values of the dispersal. In particular, we derive analytically a formula for the optimal value of the dispersal that maximizes the total population.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":" ","pages":"79-95"},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10904506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139934268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Speciation, natural selection, and networks: three historians versus theoretical population geneticists. 物种、自然选择和网络：三位历史学家与理论人口遗传学家的比较。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2024-01-29 DOI: 10.1007/s12064-024-00412-9

Donald R Forsdyke

{"title":"Speciation, natural selection, and networks: three historians versus theoretical population geneticists.","authors":"Donald R Forsdyke","doi":"10.1007/s12064-024-00412-9","DOIUrl":"10.1007/s12064-024-00412-9","url":null,"abstract":"In 1913, the geneticist William Bateson called for a halt in studies of genetic phenomena until evolutionary fundamentals had been sufficiently addressed at the molecular level. Nevertheless, in the 1960s, the theoretical population geneticists celebrated a \"modern synthesis\" of the teachings of Mendel and Darwin, with an exclusive role for natural selection in speciation. This was supported, albeit with minor reservations, by historians Mark Adams and William Provine, who taught it to generations of students. In subsequent decades, doubts were raised by molecular biologists and, despite the deep influence of various mentors, Adams and Provine noted serious anomalies and began to question traditional \"just-so-stories.\" They were joined in challenging the genetic orthodoxy by a scientist-historian, Donald Forsdyke, who suggested that a \"collective variation\" postulated by Darwin's young research associate, George Romanes, and a mysterious \"residue\" postulated by Bateson, might relate to differences in short runs of DNA bases (oligonucleotides). The dispute between a small network of historians and a large network of geneticists can be understood in the context of national politics. Contrasts are drawn between democracies, where capturing the narrative makes reversal difficult, and dictatorships, where overthrow of a supportive dictator can result in rapid reversal.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":" ","pages":"1-26"},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139572208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Modeling stress-induced responses: plasticity in continuous state space and gradual clonal evolution. 压力诱导反应建模：连续状态空间中的可塑性和渐进克隆进化

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2024-01-30 DOI: 10.1007/s12064-023-00410-3

Anuraag Bukkuri

引用次数: 0

Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis. 托马斯·库恩:更好地理解扩展进化综合的关键。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2024-02-01 Epub Date: 2023-11-17 DOI: 10.1007/s12064-023-00409-w

Koen B Tanghe

{"title":"Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis.","authors":"Koen B Tanghe","doi":"10.1007/s12064-023-00409-w","DOIUrl":"10.1007/s12064-023-00409-w","url":null,"abstract":"In recent years, some scholars have explicitly questioned the desirability or utility of applying the classical and \"old-fashioned\" theories of scientific change by the likes of Karl Popper and Thomas S. Kuhn to the question of the precise nature and significance of the extended evolutionary synthesis (EES). Supposedly, these twentieth-century philosophers are completely irrelevant for a better understanding of this new theoretical framework for the study of evolution. Here, it will be argued that the EES can be fruitfully interpreted in terms of, as yet, insufficiently considered or even overlooked elements from Kuhn's theory. First, in his original, historical philosophy of science, Kuhn not only distinguished between small and big scientific revolutions, he also pointed out that paradigms can be extended and reformulated. In contrast with what its name suggests, the mainstream EES can be interpreted as a Kuhnian reformulation of modern evolutionary theory. Second, it has, as yet, also been overlooked that the EES can be interpreted in terms of Kuhn's later, tentative evolutionary philosophy of science. With the EES, an old dichotomy in evolutionary biology is maybe being formalized and institutionalized.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":" ","pages":"27-44"},"PeriodicalIF":1.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136400311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A biosemiotic interpretation of certain genital morphological structures in the spiders Dysdera erythrina and Dysdera crocata (Araneae: Dysderidae). 红蜘蛛和番红花蜘蛛某些生殖器官形态结构的生物计量学解释（蜘蛛目：番红花蜘蛛科）。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2023-11-01 Epub Date: 2023-09-13 DOI: 10.1007/s12064-023-00404-1

Joachim Schult, Onno Preik, Stefan Kirschner, Frank Friedrich

{"title":"A biosemiotic interpretation of certain genital morphological structures in the spiders Dysdera erythrina and Dysdera crocata (Araneae: Dysderidae).","authors":"Joachim Schult, Onno Preik, Stefan Kirschner, Frank Friedrich","doi":"10.1007/s12064-023-00404-1","DOIUrl":"10.1007/s12064-023-00404-1","url":null,"abstract":"A biosemiotic approach to the interpretation of morphological data is apt to highlight morphological traits that have hitherto gone unnoticed for their crucial roles in intraspecific sign interpretation and communication processes. Examples of such traits include specific genital structures found in the haplogyne spiders Dysdera erythrina (Walckenaer 1802) and Dysdera crocata (Koch 1838). In both D. erythrina and D. crocata, the distal sclerite of the male bulb and the anterior diverticulum of the female endogyne exhibit a striking, previously unreported correspondence in size and shape, allowing for a precise match between these structures during copulation. In D. erythrina, the sclerite at the tip of the bulb and the anterior diverticulum are semi-circular in shape, whereas in D. crocata they are rectangular. From the perspective of biosemiotics, which studies the production and interpretation of signs and codes in living systems, these structures are considered the morphological zones of an intraspecific sign interpretation process. This process constitutes one of the necessary prerequisites for sperm transfer and the achievement of fertilization. Therefore, these morphological elements deserve particular attention as they hold higher taxonomic value compared to morphological traits of the bulb for which a relevant role in mating and fertilization has not been proven. Thus, an approach to species delimitation based on biosemiotics, with its specific evaluation of morphological structures, provides new insights for the multidisciplinary endeavour of modern integrative taxonomy.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":" ","pages":"371-382"},"PeriodicalIF":1.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10564669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10222373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolution by habit: Peirce, Lamarck, and teleology in biology. 习惯进化论：皮尔斯、拉马克和生物学中的目的论。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2023-11-01 Epub Date: 2023-09-25 DOI: 10.1007/s12064-023-00406-z

Jana Švorcová, Ľudmila Lacková, Eliška Fulínová

引用次数: 0

Myths of past biases and progress in biology. 过去的偏见和生物学进步的神话。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2023-11-01 Epub Date: 2023-09-23 DOI: 10.1007/s12064-023-00403-2

Jani Raerinne

引用次数: 0

Clustering systems of phylogenetic networks. 系统发育网络的聚类系统。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2023-11-01 Epub Date: 2023-08-12 DOI: 10.1007/s12064-023-00398-w

Marc Hellmuth, David Schaller, Peter F Stadler

{"title":"Clustering systems of phylogenetic networks.","authors":"Marc Hellmuth, David Schaller, Peter F Stadler","doi":"10.1007/s12064-023-00398-w","DOIUrl":"10.1007/s12064-023-00398-w","url":null,"abstract":"Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set X of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization that cannot be captured by trees. A variety of classes of such networks have been discussed in the literature, including phylogenetic, level-1, tree-child, tree-based, galled tree, regular, or normal networks as models of different types of evolutionary processes. Clusters arise in models of phylogeny as the sets [Formula: see text] of descendant taxa of a vertex v. The clustering system [Formula: see text] comprising the clusters of a network N conveys key information on N itself. In the special case of rooted phylogenetic trees, T is uniquely determined by its clustering system [Formula: see text]. Although this is no longer true for networks in general, it is of interest to relate properties of N and [Formula: see text]. Here, we systematically investigate the relationships of several well-studied classes of networks and their clustering systems. The main results are correspondences of classes of networks and clustering systems of the following form: If N is a network of type [Formula: see text], then [Formula: see text] satisfies [Formula: see text], and conversely if [Formula: see text] is a clustering system satisfying [Formula: see text] then there is network N of type [Formula: see text] such that [Formula: see text].This, in turn, allows us to investigate the mutual dependencies between the distinct types of networks in much detail.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":" ","pages":"301-358"},"PeriodicalIF":1.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10564800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9984945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1