Theory in Biosciences最新文献_第8页

Geometry and phenomenology of the living: Limits and possibilities of mathematization, complexity and individuation in biological sciences 生命的几何与现象学:生物科学中数学化、复杂性与个性化的限制与可能性

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2022-03-04 DOI: 10.1007/s12064-022-00365-x

Luciano Boi, C. Lobo

引用次数: 0

Delay induced interaction of humoral- and cell-mediated immune responses with cancer. 延迟诱导的体液和细胞介导的免疫反应与癌症的相互作用。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2022-02-01 Epub Date: 2022-02-14 DOI: 10.1007/s12064-022-00364-y

Sumana Ghosh, Sandip Banerjee

引用次数: 1

A mathematical model for viscoelastic properties of biological soft tissue. 生物软组织粘弹性特性的数学模型。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2022-02-01 Epub Date: 2022-02-03 DOI: 10.1007/s12064-021-00361-7

Man Xi, Guohong Yun, B Narsu

引用次数: 0

Is DNA repair controlled by a biological logic circuit? DNA修复是由生物逻辑电路控制的吗?

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2022-02-01 Epub Date: 2022-01-01 DOI: 10.1007/s12064-021-00360-8

Philip G Penketh

{"title":"Is DNA repair controlled by a biological logic circuit?","authors":"Philip G Penketh","doi":"10.1007/s12064-021-00360-8","DOIUrl":"https://doi.org/10.1007/s12064-021-00360-8","url":null,"abstract":"The possible utilization of biological logic circuit(s) in the integration and regulation of DNA repair is discussed. The author believes this mode of regulation likely applies to many other areas of cell biology; however, there are currently more experimental data to support its involvement in the control of DNA repair. Sequential logic processes always require a clock to orchestrate the orderly processing of events. In the proposed hypothesis, the pulses in the expression of p53 serve this function. Given the many advantages of logic type control, one would expect that in the course of ~ 3 billion years of evolution, where single cell life forms were likely the only forms of life, a biological logic type control system would have evolved to control at least some biological processes. Several other required components in addition to the 'clock' have been identified, such as; a method to temporarily inactivate repair processes when they are not required (e.g. the reversible inactivation of MGMT, a suicide repair protein, by phosphorylation); this prevents complex DNA repair systems with potentially overlapping repair functions from interfering with each other.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8894308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39777324","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

Pattern formation features might explain homoplasy: fertile surfaces in higher fungi as an example. 模式形成特征可以解释同质性:高等真菌的可育表面就是一个例子。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2022-02-01 Epub Date: 2022-02-16 DOI: 10.1007/s12064-022-00363-z

Francisco Kuhar, Leticia Terzzoli, Eduardo Nouhra, Gerardo Robledo, Moritz Mercker

{"title":"Pattern formation features might explain homoplasy: fertile surfaces in higher fungi as an example.","authors":"Francisco Kuhar, Leticia Terzzoli, Eduardo Nouhra, Gerardo Robledo, Moritz Mercker","doi":"10.1007/s12064-022-00363-z","DOIUrl":"https://doi.org/10.1007/s12064-022-00363-z","url":null,"abstract":"Fungi show a high degree of morphological convergence. Regarded for a long time as an obstacle for phylogenetic studies, homoplasy has also been proposed as a source of information about underlying morphogenetic patterning mechanisms. The \"local-activation and long-range inhibition principle\" (LALIP), underlying the famous reaction-diffusion model proposed by Alan Turing in 1952, appears to be one of the universal phenomena that can explain the ontogenetic origin of seriate patterns in living organisms. Reproductive structures of fungi in the class Agaricomycetes show a highly periodic structure resulting in, for example, poroid, odontoid, lamellate or labyrinthic hymenophores. In this paper, we claim that self-organized patterns might underlie the basic ontogenetic processes of these structures. Simulations based on LALIP-driven models and covering a wide range of parameters show an absolute mutual correspondence with the morphospace explored by extant agaricomycetes. This could not only explain geometric particularities but could also account for the limited possibilities displayed by hymenial configurations, thus making homoplasy a direct consequence of the limited morphospace resulting from the proposed patterning dynamics.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39930117","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: 1

Searching for structure in collective systems. 在集体系统中寻找结构。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-11-01 Epub Date: 2020-03-23 DOI: 10.1007/s12064-020-00311-9

Colin R Twomey, Andrew T Hartnett, Matthew M G Sosna, Pawel Romanczuk

引用次数: 3

Informational architecture across non-living and living collectives. 跨越非生命和生命集体的信息架构。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-11-01 Epub Date: 2021-02-02 DOI: 10.1007/s12064-020-00331-5

Hyunju Kim, Gabriele Valentini, Jake Hanson, Sara Imari Walker

{"title":"Informational architecture across non-living and living collectives.","authors":"Hyunju Kim, Gabriele Valentini, Jake Hanson, Sara Imari Walker","doi":"10.1007/s12064-020-00331-5","DOIUrl":"https://doi.org/10.1007/s12064-020-00331-5","url":null,"abstract":"Collective behavior is widely regarded as a hallmark property of living and intelligent systems. Yet, many examples are known of simple physical systems that are not alive, which nonetheless display collective behavior too, prompting simple physical models to often be adopted to explain living collective behaviors. To understand collective behavior as it occurs in living examples, it is important to determine whether or not there exist fundamental differences in how non-living and living systems act collectively, as well as the limits of the intuition that can be built from simpler, physical examples in explaining biological phenomenon. Here, we propose a framework for comparing non-living and living collectives as a continuum based on their information architecture: that is, how information is stored and processed across different degrees of freedom. We review diverse examples of collective phenomena, characterized from an information-theoretic perspective, and offer views on future directions for quantifying living collective behaviors based on their informational structure.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00331-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25325481","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: 5

Quantifying the impact of network structure on speed and accuracy in collective decision-making. 量化网络结构对集体决策速度和准确性的影响。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-11-01 Epub Date: 2021-02-26 DOI: 10.1007/s12064-020-00335-1

Bryan C Daniels, Pawel Romanczuk

{"title":"Quantifying the impact of network structure on speed and accuracy in collective decision-making.","authors":"Bryan C Daniels, Pawel Romanczuk","doi":"10.1007/s12064-020-00335-1","DOIUrl":"https://doi.org/10.1007/s12064-020-00335-1","url":null,"abstract":"Found in varied contexts from neurons to ants to fish, binary decision-making is one of the simplest forms of collective computation. In this process, information collected by individuals about an uncertain environment is accumulated to guide behavior at the aggregate scale. We study binary decision-making dynamics in networks responding to inputs with small signal-to-noise ratios, looking for quantitative measures of collectivity that control performance in this task. We find that decision accuracy is directly correlated with the speed of collective dynamics, which is in turn controlled by three factors: the leading eigenvalue of the network adjacency matrix, the corresponding eigenvector's participation ratio, and distance from the corresponding symmetry-breaking bifurcation. A novel approximation of the maximal attainable timescale near such a bifurcation allows us to predict how decision-making performance scales in large networks based solely on their spectral properties. Specifically, we explore the effects of localization caused by the hierarchical assortative structure of a \"rich club\" topology. This gives insight into the trade-offs involved in the higher-order structure found in living networks performing collective computations.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00335-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25407824","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: 7

Innovations are disproportionately likely in the periphery of a scientific network. 创新不成比例地出现在科学网络的外围。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-11-01 Epub Date: 2021-11-12 DOI: 10.1007/s12064-021-00359-1

Deryc T Painter, Bryan C Daniels, Manfred D Laubichler

{"title":"Innovations are disproportionately likely in the periphery of a scientific network.","authors":"Deryc T Painter, Bryan C Daniels, Manfred D Laubichler","doi":"10.1007/s12064-021-00359-1","DOIUrl":"https://doi.org/10.1007/s12064-021-00359-1","url":null,"abstract":"The origins of innovation in science are typically understood using historical narratives that tend to be focused on small sets of influential authors, an approach that is rigorous but limited in scope. Here, we develop a framework for rigorously identifying innovation across an entire scientific field through automated analysis of a corpus of over 6000 documents that includes every paper published in the field of evolutionary medicine. This comprehensive approach allows us to explore statistical properties of innovation, asking where innovative ideas tend to originate within a field's pre-existing conceptual framework. First, we develop a measure of innovation based on novelty and persistence, quantifying the collective acceptance of novel language and ideas. Second, we study the field's conceptual landscape through a bibliographic coupling network. We find that innovations are disproportionately more likely in the periphery of the bibliographic coupling network, suggesting that the relative freedom allowed by remaining unconnected with well-established lines of research could be beneficial to creating novel and lasting change. In this way, the emergence of collective computation in scientific disciplines may have robustness-adaptability trade-offs that are similar to those found in other biosocial complex systems.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39708645","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: 8

Introduction to the special issue: quantifying collectivity. 专题导论:量化集体。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-11-01 Epub Date: 2021-11-17 DOI: 10.1007/s12064-021-00358-2

Bryan C Daniels, Manfred D Laubichler, Jessica C Flack

引用次数: 1