Theory in Biosciences最新文献_第10页

Equivalence classes of circular codes induced by permutation groups. 由置换群诱导的圆码的等价类。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-02-01 DOI: 10.1007/s12064-020-00337-z

Fariba Fayazi, Elena Fimmel, Lutz Strüngmann

{"title":"Equivalence classes of circular codes induced by permutation groups.","authors":"Fariba Fayazi, Elena Fimmel, Lutz Strüngmann","doi":"10.1007/s12064-020-00337-z","DOIUrl":"https://doi.org/10.1007/s12064-020-00337-z","url":null,"abstract":"In the 1950s, Crick proposed the concept of so-called comma-free codes as an answer to the frame-shift problem that biologists have encountered when studying the process of translating a sequence of nucleotide bases into a protein. A little later it turned out that this proposal unfortunately does not correspond to biological reality. However, in the mid-90s, a weaker version of comma-free codes, so-called circular codes, was discovered in nature in J Theor Biol 182:45-58, 1996. Circular codes allow to retrieve the reading frame during the translational process in the ribosome and surprisingly the circular code discovered in nature is even circular in all three possible reading-frames ([Formula: see text]-property). Moreover, it is maximal in the sense that it contains 20 codons and is self-complementary which means that it consists of pairs of codons and corresponding anticodons. In further investigations, it was found that there are exactly 216 codes that have the same strong properties as the originally found code from J Theor Biol 182:45-58. Using an algebraic approach, it was shown in J Math Biol, 2004 that the class of 216 maximal self-complementary [Formula: see text]-codes can be partitioned into 27 equally sized equivalence classes by the action of a transformation group [Formula: see text] which is isomorphic to the dihedral group. Here, we extend the above findings to circular codes over a finite alphabet of even cardinality [Formula: see text] for [Formula: see text]. We describe the corresponding group [Formula: see text] using matrices and we investigate what classes of circular codes are split into equally sized equivalence classes under the natural equivalence relation induced by [Formula: see text]. Surprisingly, this is not always the case. All results and constructions are illustrated by examples.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 1","pages":"107-121"},"PeriodicalIF":1.1,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00337-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25318410","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: 2

Mathematical modeling and analysis of anemia during pregnancy and postpartum. 妊娠及产后贫血的数学建模与分析。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-02-01 Epub Date: 2021-02-15 DOI: 10.1007/s12064-020-00334-2

Auni Aslah Mat Daud, Cher Qing Toh, Salilah Saidun

引用次数: 2

Scientific traditions in conflict: the Rusconi-von Baer controversy on the embryology of frogs and the development of the cell theory. 冲突中的科学传统:Rusconi-von Baer关于青蛙胚胎学的争论和细胞理论的发展。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-02-01 Epub Date: 2020-11-03 DOI: 10.1007/s12064-020-00325-3

Margherita Raineri, Erki Tammiksaar

{"title":"Scientific traditions in conflict: the Rusconi-von Baer controversy on the embryology of frogs and the development of the cell theory.","authors":"Margherita Raineri, Erki Tammiksaar","doi":"10.1007/s12064-020-00325-3","DOIUrl":"https://doi.org/10.1007/s12064-020-00325-3","url":null,"abstract":"In 1835, the meaning of the cleavage furrows in the division of frog eggs was the cause of a heated argument between the Italian naturalist Mauro Rusconi and Karl Ernst von Baer. These furrows were first described by Prévost and Dumas (Ann Sci Nat 2:100-121, 129-149, 1824b) who did not realize they cut the egg into separate masses. Rusconi (Développement de la grenouille comune depuis le moment de sa naissance jusque a son état parfait, Giusti, Milano, 1826) hypothesized a connection between the furrows and a peculiar crystallization of the content of the egg which eventually produced elementary molecules as the building blocks of the embryo. von Baer (Arch Anat Phys Wiss Med 6:481-509, 1834) was the first to establish a link between the furrows and an active process of dichotomous division he considered to be the basis for all further development and differentiation. The present paper analyses the theoretical reasons behind these divergent interpretations and focuses attention on their implications for the development of the cell theory and the conceptions of life. Prévost, Dumas and Rusconi interpreted cleavage and the whole embryonic development in the light of eighteenth-century scientific theories and the French materialism of the early nineteenth century, which explained life in terms of ordered molecular movement. Starting from other premises partly rooted in German philosophy von Baer (1834) gave a totally different picture which anticipated the cell theory and modern embryology.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 1","pages":"45-75"},"PeriodicalIF":1.1,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00325-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38668585","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

Are topological explanations really free of mechanisms? 拓扑学解释真的不受机制的影响吗?

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-02-01 Epub Date: 2021-01-11 DOI: 10.1007/s12064-020-00336-0

Xin Zhang

引用次数: 0

Aristotle's lobster: the image in the text. 亚里士多德的龙虾:文本中的形象。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-02-01 Epub Date: 2020-10-13 DOI: 10.1007/s12064-020-00322-6

Alexander Fürst von Lieven, Marcel Humar, Gerhard Scholtz

{"title":"Aristotle's lobster: the image in the text.","authors":"Alexander Fürst von Lieven, Marcel Humar, Gerhard Scholtz","doi":"10.1007/s12064-020-00322-6","DOIUrl":"https://doi.org/10.1007/s12064-020-00322-6","url":null,"abstract":"The Anatomai, a lost work written by Aristotle, must have contained a collection of various drawings and figures of species as well as their organs. In his texts (mainly the Historia animalium), Aristotle is often referring to the drawings after the description of species. Our study applies the method of the comparative view ('Vergleichendes Sehen') to provide an access to and reconstruction of Aristotle's lost illustrations based on his textual descriptions. As an example, we chose the treatment of the European lobster (Homarus gammarus L., 1758) in the Aristotelian corpus as a case study. First, we analyse the etymology of the Greek term astakós referring to the lobster and provide an overview on the putative synonyms. Second, we confront the textual basis of the description with several questions concerning the degree of abstraction, the relation between text and image, and the spatial orientation of the image. Finally, we present a step-by-step reconstruction of Aristotle's illustrations of the lobster based on the various passages dealing with its anatomy in the text of the Historia animalium. The problems which arise by a confrontation of the textual basis with hypothetical images are discussed at a more general level. We conclude that this kind of a text-based image reconstruction is only possible if the object described by Aristotle is unambiguously identifiable and still visually accessible.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 1","pages":"1-15"},"PeriodicalIF":1.1,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00322-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38481662","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

The Power of Peptides: The Precision Molecules of Life 肽的力量:生命的精确分子

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2021-01-01 DOI: 10.25163/biosciences.312000

John A Catanazaro, Gregor Mendel, Albrecht Kossel, Walter Sutton, Theodor Boveri. Phoebus Levene, Erwin Chargaff, John Catanzaro

引用次数: 0

Ingredients for robustness. 坚固性的成分。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2020-12-01 Epub Date: 2020-12-02 DOI: 10.1007/s12064-020-00332-4

Nihat Ay

引用次数: 3

Quantifying simultaneous innovations in evolutionary medicine. 量化进化医学中的同步创新。

IF 1.3 4区生物学

Theory in Biosciences Pub Date : 2020-12-01 Epub Date: 2020-11-25 DOI: 10.1007/s12064-020-00333-3

Deryc T Painter, Frank van der Wouden, Manfred D Laubichler, Hyejin Youn

{"title":"Quantifying simultaneous innovations in evolutionary medicine.","authors":"Deryc T Painter, Frank van der Wouden, Manfred D Laubichler, Hyejin Youn","doi":"10.1007/s12064-020-00333-3","DOIUrl":"10.1007/s12064-020-00333-3","url":null,"abstract":"To what extent do simultaneous innovations occur and are independently from each other? In this paper we use a novel persistent keyword framework to systematically identify innovations in a large corpus containing academic papers in evolutionary medicine between 2007 and 2011. We examine whether innovative papers occurring simultaneously are independent from each other by evaluating the citation and co-authorship information gathered from the corpus metadata. We find that 19 out of 22 simultaneous innovative papers do, in fact, occur independently from each other. In particular, co-authors of simultaneous innovative papers are no more geographically concentrated than the co-authors of similar non-innovative papers in the field. Our result suggests producing innovative work draws from a collective knowledge pool, rather than from knowledge circulating in distinct localized collaboration networks. Therefore, new ideas can appear at multiple locations and with geographically dispersed co-authorship networks. Our findings support the perspective that simultaneous innovations are the outcome of collective behavior.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"139 4","pages":"319-335"},"PeriodicalIF":1.3,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7719117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38304463","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

Biological information. 生物信息。

IF 1.1 4区生物学

Theory in Biosciences Pub Date : 2020-12-01 Epub Date: 2020-11-19 DOI: 10.1007/s12064-020-00327-1

Jürgen Jost

引用次数: 7

Are spliced ncRNA host genes distinct classes of lncRNAs? 剪接的 ncRNA 宿主基因是不同类别的 lncRNA 吗？

IF 1.3 4区生物学

Theory in Biosciences Pub Date : 2020-12-01 Epub Date: 2020-11-21 DOI: 10.1007/s12064-020-00330-6

Rituparno Sen, Jörg Fallmann, Maria Emília M T Walter, Peter F Stadler

{"title":"Are spliced ncRNA host genes distinct classes of lncRNAs?","authors":"Rituparno Sen, Jörg Fallmann, Maria Emília M T Walter, Peter F Stadler","doi":"10.1007/s12064-020-00330-6","DOIUrl":"10.1007/s12064-020-00330-6","url":null,"abstract":"Many small nucleolar RNAs and many of the hairpin precursors of miRNAs are processed from long non-protein-coding host genes. In contrast to their highly conserved and heavily structured payload, the host genes feature poorly conserved sequences. Nevertheless, there is mounting evidence that the host genes have biological functions beyond their primary task of carrying a ncRNA as payload. So far, no connections between the function of the host genes and the function of their payloads have been reported. Here we investigate whether there is evidence for an association of host gene function or mechanisms with the type of payload. To assess this hypothesis we test whether the miRNA host genes (MIRHGs), snoRNA host genes (SNHGs), and other lncRNA host genes can be distinguished based on sequence and/or structure features unrelated to their payload. A positive answer would imply a functional and mechanistic correlation between host genes and their payload, provided the classification does not depend on the presence and type of the payload. A negative answer would indicate that to the extent that secondary functions are acquired, they are not strongly constrained by the prior, primary function of the payload. We find that the three classes can be distinguished reliably when the classifier is allowed to extract features from the payloads. They become virtually indistinguishable, however, as soon as only sequence and structure of parts of the host gene distal from the snoRNAs or miRNA payload is used for classification. This indicates that the functions of MIRHGs and SNHGs are largely independent of the functions of their payloads. Furthermore, there is no evidence that the MIRHGs and SNHGs form coherent classes of long non-coding RNAs distinguished by features other than their payloads.","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"139 4","pages":"349-359"},"PeriodicalIF":1.3,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7719101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38722544","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