289 results on '"Homology (anthropology)"'
Search Results
2. <scp>PANTHER</scp> : Making genome‐scale phylogenetics accessible to all
- Author
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Laurent-Philippe Albou, Anushya Muruganujan, Dustin Ebert, Paul Thomas, Tremayne Mushayahama, and Huaiyu Mi
- Subjects
Phylogenetic tree ,Computer science ,Proteins ,Tree of life ,Molecular Sequence Annotation ,Review ,Computational biology ,Biochemistry ,Genome ,Pipeline (software) ,Evolution, Molecular ,Set (abstract data type) ,ComputingMethodologies_PATTERNRECOGNITION ,Sequence Analysis, Protein ,Molecular evolution ,Phylogenetics ,Homology (anthropology) ,Databases, Protein ,Molecular Biology ,Phylogeny ,Software - Abstract
Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their evolutionary relationships to other proteins. However, phylogenetics analyses can be challenging: they are computationally expensive and must be performed carefully in order to avoid systematic errors and artifacts. PANTHER (http://pantherdb.org) is a publicly available, user-focused knowledgebase that stores the results of an extensive phylogenetic reconstruction pipeline that includes computational and manual processes and quality control steps. First, fully reconciled phylogenetic trees (including ancestral protein sequences) are reconstructed for a set of "reference" protein sequences obtained from fully sequenced genomes of organisms across the tree of life. Second, the resulting phylogenetic trees are manually reviewed and annotated with function evolution events: inferred gains and losses of protein function along branches of the phylogenetic tree. Here, we describe in detail the current contents of PANTHER, how those contents are generated, and how they can be used in a variety of applications. The PANTHER knowledgebase can be downloaded or accessed via an extensive API. In addition, PANTHER provides software tools to facilitate the application of the knowledgebase to common protein sequence analysis tasks: exploring an annotated genome by gene function; performing "enrichment analysis" of lists of genes; annotating a single sequence or large batch of sequences by homology; and assessing the likelihood that a genetic variant at a particular site in a protein will have deleterious effects. This article is protected by copyright. All rights reserved.
- Published
- 2021
3. On Chow-weight homology of geometric motives
- Author
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Vladimir Sosnilo and Mikhail V. Bondarko
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Applied Mathematics ,General Mathematics ,Computational biology ,Homology (anthropology) ,Mathematics - Published
- 2021
4. Homology concordance and an infinite rank free subgroup
- Author
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Hugo Zhou
- Subjects
Combinatorics ,Mathematics - Geometric Topology ,Mathematics::K-Theory and Homology ,Concordance ,FOS: Mathematics ,Rank (graph theory) ,Geometric Topology (math.GT) ,Geometry and Topology ,Homology (anthropology) ,Mathematics::Symplectic Geometry ,Mathematics::Algebraic Topology ,Mathematics::Geometric Topology ,Mathematics - Abstract
Two knots are homology concordant if they are smoothly concordant in a homology cobordism. The group $\hat{\mathcal{C}}_{\mathbb{Z}}$ (resp. $\mathcal{C}_{\mathbb{Z}}$) was previously defined as the set of knots in homology spheres that bounds homology balls (resp. in $S^3$), modulo homology concordance. We prove $\hat{\mathcal{C}}_{\mathbb{Z}} / \mathcal{C}_{\mathbb{Z}}$ contains a $\mathbb{Z}^{\infty}$ subgroup. We construct our family of examples by applying the filtered mapping cone formula to $L$--space knots, and prove linear independence with the help of the connected knot complex., Comment: 27 pages, 11 figures. Minor revisions. This is the version to appear in the Journal of Topology
- Published
- 2021
5. Surface Map Homology Inference
- Author
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Janis Born, Marcel Campen, Leif Kobbelt, and Patrick Schmidt
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Surface map ,Inference ,Homology (anthropology) ,Computational biology ,ddc:004 ,Computer Graphics and Computer-Aided Design ,Computing Methodologies ,Mathematics - Abstract
Symposium on Geometry Processing 2021, SGP, online, 12 Jul 2021 - 14 Jul 2021; Computer graphics forum 40(5), 193-203 (2021). doi:10.1111/cgf.14367 special issue: "Symposium on Geometry Processing 2021 : Hosted online July 12 – 14, 2021 / K. Crane and J. Digne (Guest Editors)", Published by Wiley-Blackwell, Oxford
- Published
- 2021
6. Unusual pectoral apparatus in a predatory dinosaur resolves avian wishbone homology
- Author
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Vincent Beyrand, Andrea Cau, Khishigjav Tsogtbaatar, Pascal Godefroit, and Rinchen Barsbold
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0106 biological sciences ,PHASE CONTRAST ,Pectoral girdle ,Sternum ,Science ,BIOLOGY ,010603 evolutionary biology ,01 natural sciences ,Tetrapod ,Article ,Interclavicle ,03 medical and health sciences ,Quadrupedalism ,Homology (anthropology) ,PALEONTOLOGY ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,Articular facet ,biology ,PHASE CONTRAST MICROTOMOGRAPHY ,Palaeontology ,Anatomy ,biology.organism_classification ,Shoulder region ,Medicine ,FOSSIL BONE - Abstract
The furcula is a distinctive element of the pectoral skeleton in birds, which strengthens the shoulder region to withstand the rigor of flight. Although its origin among theropod dinosaurs is now well-supported, the homology of the furcula relative to the elements of the tetrapod pectoral girdle (i.e., interclavicle vs clavicles) remains controversial. Here, we report the identification of the furcula in the birdlike theropod Halszkaraptor escuilliei. The bone is unique among furculae in non-avian dinosaurs in bearing a visceral articular facet in the hypocleideal end firmly joined to and overlapped by the sternal plates, a topographical pattern that supports the primary homology of the furcula with the interclavicle. The transformation of the interclavicle into the furcula in early theropods is correlated to the loss of the clavicles, and reinforced the interconnection between the contralateral scapulocoracoids, while relaxing the bridge between the scapulocoracoids with the sternum. The function of the forelimbs in theropod ancestors shifted from being a component of the locomotory quadrupedal module to an independent module specialized to grasping. The later evolution of novel locomotory modules among maniraptoran theropods, involving the forelimbs, drove the re-acquisition of a tighter connection between the scapulocoracoids and the interclavicle with the sternal complex.
- Published
- 2021
7. Male terminalia of Cercopidae (Hemiptera, Cicadomorpha): towards a consensus terminology
- Author
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Maxime Le Cesne, Elorde Jr. Simpron Crispolon, and Adeline Soulier-Perkins
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Male ,0106 biological sciences ,Systematics ,Entomology ,Consensus ,Science ,010607 zoology ,Genitalia, Male ,010603 evolutionary biology ,01 natural sciences ,Article ,Terminology ,Hemiptera ,Terminology as Topic ,Taxonomy (general) ,Animals ,Homology (anthropology) ,Taxonomy ,Multidisciplinary ,biology ,Phylogenetic tree ,Terminalia ,biology.organism_classification ,Genealogy ,Geography ,Cercopidae ,Medicine - Abstract
The study of male genital appendages is often necessary to identify a species and to characterise the higher systematics ranks for the Cercopidae, a large family of Hemiptera. Therefore, many authors have used them in their work but without any clear consensus on the terms used for each part constituting the male terminalia. A standardised terminology is important for the quality of a taxonomic description but even more essential when we want to compare species and establish a primary homology between states of character and their use in the frame of phylogenetic analysis. The use of a consensus terminology should ensure that we are all observing, speaking and describing the same genital appendage and comparing homologous characters. In order to propose a consensus terminology, we have reviewed all the major works on the anatomy of terminalia for the family since the first description using those characters in 1922. We proposed the use of consensual terms, listed with their definitions. In addition we studied a diversified panel of male specimens, chosen in order to represent as many Cercopidae tribes as possible. We categorised five different groups of Cercopidae according to their male terminalia structures. This opens the reflection on the evolutionary patterns for these structures.
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- 2021
8. The social positions of taste between and within music genres: From omnivore to snob
- Author
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Jean-François Nault, Shyon Baumann, Craig M. Rawlings, and Clayton Childress
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Cultural Studies ,050402 sociology ,Taste (sociology) ,media_common.quotation_subject ,05 social sciences ,0506 political science ,Education ,Epistemology ,0504 sociology ,Arts and Humanities (miscellaneous) ,050602 political science & public administration ,Homology (anthropology) ,Sociology ,Omnivore ,Snob ,Construct (philosophy) ,media_common - Abstract
Are higher status cultural tastes in the modern United States better described as being inclusive and broad or exclusive and narrow? We construct an original dataset in response to conflicting answers to this question. We fill a major gap in the literature on cultural tastes by simultaneously considering taste for both musical genres and artists within genres. By examining the compositional balance of respondents’ taste portfolios, we reconcile seemingly incommensurate theoretical frameworks of class homology and omnivorousness. The results indicate that an omnivorous disposition to music is a relatively middle-status position in the social structure. In contrast, positions characterized by higher levels of cultural capital map onto exclusive and narrower tastes for consecrated culture.
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- 2021
9. A Biomimetic Covering Learning Method Based on Principle of Homology Continuity
- Author
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Weiwei Cai, Liang Liu, Weijuan Tian, Xin Ning, and Yuebao Wang
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Theoretical computer science ,Basis (linear algebra) ,Computer science ,business.industry ,Deep learning ,Learning methods ,Effective method ,Biological neuron model ,Artificial intelligence ,Homology (anthropology) ,Pattern recognition problem ,business - Abstract
The Principle of Homology Continuity (PHC) based covering learning method is an effective method to solve the pattern recognition problem. However, PHC and the existence of optimal coverage are not mathematical proven. To address this issue, we firstly give the mathematical description and theoretical proof of PHC. On this basis, the theoretical definition of optimal coverage is introduced. Optimal coverage can determine the internal connections among samples as prior knowledge and use covering neurons to learn prior knowledge. Finally, we propose a kind of covering neuron model, and the effectiveness of which is demonstrated through extensive experiments conducted on the CIFAR-10, LFW, and YTF datasets.
- Published
- 2021
10. The myth of the hippo-like anthracothere: The eternal problem of homology and convergence
- Author
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Martin Pickford
- Subjects
Ghost lineage ,Body proportions ,Paleontology ,Convergence (relationship) ,Homology (anthropology) ,Mythology ,Biology ,hippopotamidae, anthracotheriidae, palaeochoeridae, evolution, homology, convergence, early/late divergence, history, phylogeny ,QE701-760 ,Genealogy - Abstract
The notion that anthracotheres had hippo-like body proportions, locomotion and lifestyles has been in the literature for so long, and has been repeated so many times, that it has taken on the aura of unquestionable truth. However, right from the beginning of studies into hippo-anthracothere relationships over a century and a half ago, observations were made that revealed the existence of fundamental differences in dental, cranial and postcranial anatomy in the two groups. The aim of this paper is to review the possible role of anthracotheres in the evolution of hippopotamids. It is concluded that they played no part in it, whereas palaeochoerids could well represent the ghost lineage that has evaded scientists for more than a century.
- Published
- 2021
11. Research Progress of Osteoporosis Based on the Theory of 'Homology of Liver and Kidney'
- Author
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Hua Zhang, Sen Li, Zhenxing Qu, and Zhibin Li
- Subjects
Postmenopausal women ,business.industry ,Liver and kidney ,Osteoporosis ,medicine ,Traditional Chinese medicine ,Homology (anthropology) ,medicine.disease ,business ,Bioinformatics ,Clinical treatment ,Metabolic bone disease ,Western medicine - Abstract
Osteoporosis is a systemic chronic metabolic bone disease, mainly in the elderly and postmenopausal women. At present, most of the clinical treatment is western medicine, but the curative effect is not very significant. In the treatment of osteoporosis, traditional Chinese medicine (TCM) is mainly based on the overall concept of TCM. This article briefly analyzes osteoporosis from the theory of “liver and kidney homology,” discusses the research on osteoporosis in TCM, and hopes to provide reference for the clinical treatment and research of osteoporosis.
- Published
- 2021
12. Enrichment of Remote Homology Detection using Cascading Maximum Entropy Markov Model
- Author
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Muthu C, N. Sajithra, D. Ramyachitra, and P. Manikandan
- Subjects
Combinatorics ,Aging ,Maximum-entropy Markov model ,General Health Professions ,Dentistry (miscellaneous) ,Homology (anthropology) ,Health Professions (miscellaneous) ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,General Dentistry ,General Biochemistry, Genetics and Molecular Biology ,Mathematics - Published
- 2021
13. Heegaard Floer homology and splicing homology spheres
- Author
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a r Karakurt, Eamonn Tweedy, Tye Lidman, and Cagri Karakurt
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Floer homology ,General Mathematics ,RNA splicing ,Computational biology ,Homology (anthropology) ,Mathematics - Published
- 2021
14. Magnitude homology, diagonality, and median spaces
- Author
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Tom Kaiser and Rémi Bottinelli
- Subjects
Combinatorics ,Metric space ,Mathematics (miscellaneous) ,Magnitude (mathematics) ,Homology (anthropology) ,Mathematics - Published
- 2021
15. Advances in Imaging of Tumor Homology
- Subjects
business.industry ,Strategy and Management ,Mechanical Engineering ,Metals and Alloys ,Medicine ,Homology (anthropology) ,Computational biology ,business ,Industrial and Manufacturing Engineering - Published
- 2021
16. Characters from the deciduous dentition and its interest for phylogenetic reconstruction in Hippopotamoidea (Cetartiodactyla: Mammalia)
- Author
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Maeva J. Orliac, Fabrice Lihoreau, Jean-Renaud Boisserie, Helder Gomes Rodrigues, Centre de Recherche en Paléontologie - Paris (CR2P), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Centre Français des Etudes Ethiopiennes (CFEE), CFEE, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre Français des Études Ethiopiennes (CFEE), and Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0106 biological sciences ,010506 paleontology ,Phylogenetic tree ,Anthracotheres ,homology ,molarization ,Biology ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Deciduous dentition ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,maximum-likelihood analysis ,Hippopotamidae ,Deciduous ,Taxon ,parsimony analyses ,Phylogenetics ,Evolutionary biology ,dental ontogeny ,Animal Science and Zoology ,Mammal ,Homology (anthropology) ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Abstract
Teeth are frequently used in phylogeny in order to better characterize the evolution of extinct mammal species. While most studies have focused on the adult dentition, the consideration of characters from the deciduous dentition could also contribute to reinforce phylogenetic assumptions or disentangle phylogenetic issues. We chose to investigate the characters of the deciduous dentition in cetartiodactyl taxa in relation to the disputed relationships within hippopotamoids, especially the position of Hippopotamidae. We describe the deciduous dentition of 51 species, among a dataset of 70 cetartiodactyls. We noticed that second and third deciduous premolars have a much lower degree of molarization, and are more suitable for coding than fourth deciduous premolars. Thirty-nine resulting characters were thus added to a previously published matrix, and parsimony and maximum-likelihood analyses were performed. Both analyses provided a better resolved topology for most taxa than without these characters, and with better support for most nodes in the parsimony analysis. Moreover, this analysis provides additional characters supporting the hypothesis of an emergence of hippopotamids within bothriodontine anthracotheres from the Palaeogene of Africa. The promising use of characters from the deciduous dentition in phylogeny should allow discussion of the underlying ontogenetic mechanisms at the origin of dental homology.
- Published
- 2020
17. An Ecofeminist Homology as Reflected in Salwa Bakr's Thirty-One Beautiful Green Trees and Han Kang's The Vegetarian : A Comparative Study
- Author
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Eman Mohamed Mohamed and AL Bayomy
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Oppression ,Ecofeminism ,media_common.quotation_subject ,Spirituality ,Identity (social science) ,Sociology ,Homology (anthropology) ,Religious studies ,media_common - Abstract
This paper intends to illustrate the close similarities between Salwa Bakr's short story Thirty-One Beautiful Green Trees (1986) and Han Kang's novel The Vegetarian (2007) through the lens of the ecofeminism theory as a comparative study that has not been attempted so far. Ecofeminism is a theory that mainly linked the oppression of women and nature. Both of them are exploited under the patriarchal culture of the Egyptian and the South Korean societies as it will be depicted in the present paper. Bakr's Thirty-One Beautiful Green Trees tackles social ecofeminism that portrays the colonization of women's identity and body as well as nature. While Kang's The Vegetarian handles vegetarian ecofeminism that rejects the idea of dealing harshly with women and animals as objects that have no rights. Both of these works explore the spiritual side that the protagonists adhere to and their psychological suffering.
- Published
- 2020
18. Comparability in evolutionary biology: The case of Darwin’s barnacles
- Author
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Lindell Bromham
- Subjects
0106 biological sciences ,0301 basic medicine ,Linguistics and Language ,Comparability ,Analogy ,Biology ,010603 evolutionary biology ,01 natural sciences ,Language and Linguistics ,Linguistic typology ,03 medical and health sciences ,030104 developmental biology ,Evolutionary biology ,Darwin (ADL) ,Cognate ,Homology (anthropology) - Abstract
Language change and biological evolution are sufficiently similar that biologists and linguists often face similar challenges in reconstructing paths of historical change connecting different species or languages. Tracing evolutionary change over time requires us to consider how shared features have been modified in different lineages since they shared a common ancestor, and this means we have to be able to establish meaningful comparability between traits. In some cases, we may wish to understand how the same ancestral trait has been modified in each lineage in response to different pressures. But in other cases, we may wish to ask whether particular traits often arise in response to certain circumstances. Biologists must therefore consider different reasons for similarities between species, and choose to compare those traits that are relevant to the story they want to tell. To reconstruct histories of change, we need to compare homologous traits (those similar due to shared ancestry). But comparing analogous traits (independently derived but similar traits) highlights how separate evolutionary lineages can find similar solutions to common problems. I will illustrate the importance of comparability in constructing evolutionary explanations using one of the more obscure yet fascinating examples of Charles Darwin’s scientific researches, his multi-volume taxonomic treatise on barnacles. Darwin faced the challenge of how to explain the evolutionary trajectory of unique and highly modified traits that appear to have no equivalents in related taxa. He did this by tracing the development of unique traits within growing individuals, looking for variation in these strange adaptations between individuals, and comparing them across species that varied in their degree of modification from their ancestor. Using meticulous observations to establish comparability, even in such an incomparable animal as the barnacle, he could reconstruct plausible evolutionary explanations for even the most bizarrely modified traits, such as the presence of parasitic males and the invention of the cement that sticks barnacles to rocks, boats and whales. Nowadays, scientists increasingly rely on DNA evidence to trace evolutionary paths, which brings both advantages and challenges in establishing comparability. Even if you, like most people, are not particularly interested in barnacles, Darwin’s underappreciated taxonomic work is a surprisingly good place to go to if you want to think about the issue of comparability and why it matters to understanding evolution.
- Published
- 2020
19. A Dança das formas em Perisséia , de Tom Zé e Macunaíma, de Mário de Andrade
- Author
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Alex Alves Fogal
- Subjects
General Computer Science ,media_common.quotation_subject ,HERO ,Character (symbol) ,Homology (anthropology) ,Art ,Humanities ,media_common - Abstract
O presente trabalho visa comparar a forma composicional da canção, “Perisséia” de Tom Zé à de Macunaíma: o herói sem nenhum caráter, de Mário de Andrade. Conforme espera-se demonstrar, a canção do músico baiano estabelece uma homologia criativa com os princípios formais do livro do escritor modernista.
- Published
- 2020
20. Marks i terror. Kilka uwag o ideach, które miały konsekwencje
- Author
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Marcin Hylewski
- Subjects
Politics ,media_common.quotation_subject ,Philosophy ,Institutionalism ,Historicism ,Marxist philosophy ,Ideology ,Homology (anthropology) ,Collective memory ,Communism ,media_common ,Epistemology - Abstract
The aim of this article is to develop and supplement arguments in support of Leszek Kolakowski’s thesis concerning the ideological and practical continuity of Marx’s philosophy and the 20th-century political attempts to implement it (‘institutionalism of Marxism’). The forms of the indicated homology have been divided into three categories: unjustified prophecies (historicism), propagation of violence and scientific misconduct. The article also explores numerous 19th-century exante sources that show the dangerous consequences of the Marxist philosophy of history long before they were confirmed by the revolutionary experiences of the 20th century. The final part describes the consequences of the conceptual ferment related to the attempts to separate Marx’s theory (in particular by giving up its systemic lectures) and modern totalitarian experiments with communism which are still present in political discourse and preserved in the dominant forms of collective memory.
- Published
- 2019
21. New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources
- Author
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Kalpana Karra, Shuai Weng, Stuart R. Miyasato, Matt Simison, J. Michael Cherry, Marek S. Skrzypek, Suzi Aleksander, Robert S. Nash, Edith D. Wong, Stacia R. Engel, Eric Douglass, and Micheal Alexander
- Subjects
biology ,ved/biology ,Saccharomyces cerevisiae ,ved/biology.organism_classification_rank.species ,Computational biology ,biology.organism_classification ,Genome ,Saccharomyces ,Annotation ,Alliance ,Databases, Genetic ,Genetics ,Humans ,Homology (anthropology) ,Genome, Fungal ,Allele ,Model organism ,Alleles ,Reference genome - Abstract
Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.
- Published
- 2021
22. Is ACCTRAN better than DELTRAN?
- Author
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Jeremy A. Miller and Ingi Agnarsson
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Root (linguistics) ,Character (mathematics) ,Transformation (function) ,Character evolution ,Phylogenetic tree ,Feature (machine learning) ,Homology (anthropology) ,Biology ,Mathematical economics ,Ecology, Evolution, Behavior and Systematics ,Simple (philosophy) - Abstract
When parsimony ancestral character reconstruction is ambiguous, it is often resolved in favour of the more complex character state. Hence, secondary loss (secondary ‘‘absence’’) of a complex feature is favoured over parallel gains of that feature as this preserves the stronger hypothesis of homology. We believe that such asymmetry in character state complexity is important information for understanding character evolution in general. However, we here point out an inappropriate link that is commonly made between this approach and the accelerated transformation (ACCTRAN) algorithm. In ACCTRAN, changes are assigned along branches of a phylogenetic tree as close to the root as possible. This has been taken to imply that ACCTRAN will minimize hypotheses of parallel origins of complex traits and thus that ACCTRAN is philosophically better justified than the alternatives, such as delayed transformation (DELTRAN), where changes are assigned along branches as close to the tips as possible. We provide simple examples to show that such views are mistaken and that neither ACCTRAN nor DELTRAN consistently minimize parallel gain of complex traits. We therefore do not see theoretical grounds for favouring the popular ACCTRAN algorithm. � The Willi Hennig Society 2008.
- Published
- 2021
23. On the Nature of Organs and Organ Systems – A Chapter in the History and Philosophy of Biology
- Author
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Alessandro Minelli
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Structure (mathematical logic) ,body part ,Ecology ,Evolution ,Comparative method ,Philosophy ,media_common.quotation_subject ,Morphology (biology) ,hermaphroditism ,Owen ,Epistemology ,Dohrn ,Philosophy of biology ,Character (mathematics) ,organ ,organ system ,QH359-425 ,Homology (anthropology) ,Function (engineering) ,Archetype ,QH540-549.5 ,Ecology, Evolution, Behavior and Systematics ,media_common - Abstract
Contrasting definitions of organs based either on function or on strictly morphological criteria are the legacy of a tradition starting with Aristotle. This floating characterization of organs in terms of both form and function extends also to organ systems. The first section of this review outlines the notions of organ and body part as defined, explicitly or implicitly, in representative works of nineteenth century’s comparative morphology. The lack of a clear distinction between the two notions led to problems in Owen’s approach to the comparative method (definition of homolog vs. nature of the vertebrate archetype) and to a paradoxical formulation, by Anton Dohrn, of the principle of functional change. Starting from the second half of the twentieth century, with the extensive use of morphological data in phylogenetic analyses, both terms – organ and body part – have been often set aside, to leave room for a comparison between variously characterized attributes (character states) of the taxa to be compared. Throughout the last two centuries, there have been also efforts to characterize organs or body parts in terms of the underlying developmental dynamics, both in the context of classical descriptive embryology and according to models suggested by developmental genetics. Functionally defined organ are occasionally co-extensive with morphologically defined body parts, nevertheless a clear distinction between the former and the latter is a necessary prerequisite to a study of their evolution: this issue is discussed here on the example of the evolution of hermaphroditism and gonad structure and function.
- Published
- 2021
24. I Dream of Siri: Magic and Female Voice Assistants
- Author
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Jason Toncic
- Subjects
Magic (illusion) ,Ghost in the machine ,Aesthetics ,media_common.quotation_subject ,Isolation (psychology) ,Female voice ,General Medicine ,Sociology ,Homology (anthropology) ,Dream ,Structural anthropology ,Feminism ,media_common - Abstract
Recent advances in science and engineering have facilitated the development of artificial intelligence voice assistants. While this is true from a technical aspect, smart speakers and voice assistants did not develop in isolation from the rest of human society. The devices may be new, but the practices and patterns in their development and use are not. Using Lévi-Strauss’s structural anthropology, I map homologous practices of smart speaker interaction onto historical conceptions of supernatural magic use. This structural comparison suggests that practices and patterns that were essential to magic use have re-emerged in smart speaker utilization in similar forms. Some of these practices are noteworthy for their homology alone. However, other homologous behaviors revive patterns of inequity that, in Western magical traditions, had privileged the traditionally educated man. The goal of this paper is to elucidate the ghost in the machine: the prejudiced social practices of supernatural magic that were asserted to be eradicated yet which are now, nevertheless, newly instantiated within our most cutting-edge devices.
- Published
- 2021
25. Functional Precision Profiling: The Way Forward for Personalized Medicine
- Author
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Siobhan Glavey, Triona Ni Chonghaile, and Lyndsey Flanagan
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business.industry ,Profiling (information science) ,Medicine ,Homology (anthropology) ,Computational biology ,Personalized medicine ,business - Published
- 2021
26. The first homology of a real cubic is generated by lines
- Author
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Sergey Finashin, Viatcheslav Kharlamov, Institut de Recherche Mathématique Avancée (IRMA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Middle East Technical University (METU), and Middle East Technical University [Ankara] (METU)
- Subjects
[MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT] ,010102 general mathematics ,0103 physical sciences ,010307 mathematical physics ,Homology (anthropology) ,Computational biology ,[MATH.MATH-AG]Mathematics [math]/Algebraic Geometry [math.AG] ,0101 mathematics ,01 natural sciences ,ComputingMilieux_MISCELLANEOUS ,Mathematics - Abstract
International audience
- Published
- 2021
27. Bioinformatics and 3D homology modelling of AsAlaDH from Amycolatopsis sulphurea
- Author
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Fatih Aktaş
- Subjects
Biochemistry ,Alanine dehydrogenase ,Homology (anthropology) ,Biology ,Amycolatopsis sulphurea - Published
- 2021
28. Consciousness in Jawless Fishes
- Author
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Daichi G. Suzuki
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ammocoetes ,Cognitive Neuroscience ,media_common.quotation_subject ,hagfish ,Neuroscience (miscellaneous) ,lamprey ,Neurosciences. Biological psychiatry. Neuropsychiatry ,primary consciousness ,Cellular and Molecular Neuroscience ,Primary consciousness ,Developmental Neuroscience ,biology.animal ,Homology (anthropology) ,minimal consciousness ,Metamorphosis ,media_common ,biology ,Lamprey ,biology.organism_classification ,Evolutionary biology ,Forebrain ,Perspective ,%22">Fish ,cyclostome ,Consciousness ,RC321-571 ,Hagfish ,Neuroscience - Abstract
Jawless fishes were the first vertebrates to evolve. It is thus important to investigate them to determine whether consciousness was acquired in the common ancestor of all vertebrates. Most jawless fish lineages are extinct, and cyclostomes (lampreys and hagfish) are the sole survivors. Here, I review the empirical knowledge on the neurobiology of cyclostomes with special reference to recently proposed “markers” of primary, minimal consciousness. The adult lamprey appears to meet the neuroanatomical criteria but there is a practical limitation to behavioral examination of its learning ability. In addition, the consciousness-related neuroarchitecture of larvae and its reconstruction during metamorphosis remain largely uninvestigated. Even less is known of hagfish neurobiology. The hagfish forebrain forms the central prosencephalic complex, and the homology of its components to the brain regions of other vertebrates needs to be confirmed using modern techniques. Nevertheless, as behavioral responses to olfactory stimuli in aquariums have been reported, it is easier to investigate the learning ability of the hagfish than that of the lamprey. Based on these facts, I finally discuss the potential future directions of empirical studies for examining the existence of consciousness in jawless fishes.
- Published
- 2021
29. Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs
- Author
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Benjamin D. Knick, Ashley Elias, Madeline L. Fudala, Amanda N. Cass, and Marcus C. Davis
- Subjects
QH301-705.5 ,Morphology (biology) ,Tetrapod ,03 medical and health sciences ,Hox genes ,Limb development ,Homology (anthropology) ,Biology (General) ,Hox gene ,Deep homology ,030304 developmental biology ,Nature and Landscape Conservation ,Appendage ,0303 health sciences ,Ecology ,biology ,deep homology ,Ecological Modeling ,030302 biochemistry & molecular biology ,evo-devo ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Evolutionary biology ,limb development ,Evolutionary developmental biology ,paired fins ,fin-to-limb transition - Abstract
The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.
- Published
- 2021
30. The developmental biology of Charnia and the eumetazoan affinity of the Ediacaran rangeomorphs
- Author
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Dmitriy V. Grazhdankin, Frances S. Dunn, Alexander G. Liu, Simon Harris, Emily Green, Joseph Flannery-Sutherland, Philip C. J. Donoghue, Philip Vixseboxse, Philip R. Wilby, Dunn, Frances S [0000-0001-7080-5283], Liu, Alexander G [0000-0002-3985-982X], Grazhdankin, Dmitriy V [0000-0003-0797-1347], Flannery-Sutherland, Joseph [0000-0001-8232-6773], Green, Emily [0000-0002-7070-0534], Harris, Simon [0000-0002-7408-7255], Donoghue, Philip CJ [0000-0003-3116-7463], and Apollo - University of Cambridge Repository
- Subjects
0106 biological sciences ,0303 health sciences ,Multidisciplinary ,MSci Palaeontology and Evolution ,biology ,Phylogenetic tree ,3104 Evolutionary Biology ,37 Earth Sciences ,3705 Geology ,Rangeomorph ,biology.organism_classification ,Fossil evidence ,010603 evolutionary biology ,01 natural sciences ,Charnia ,03 medical and health sciences ,Taxon ,Evolutionary biology ,Homology (anthropology) ,Developmental biology ,31 Biological Sciences ,030304 developmental biology - Abstract
Molecular timescales estimate that early animal lineages diverged tens of millions of years before their earliest unequivocal fossil evidence. The Ediacaran macrobiota (~574–538 million years ago) are largely eschewed from this debate, primarily due to their extreme phylogenetic uncertainty, but they remain germane. We characterize the development of Charnia masoni and establish the phylogenetic affinity of rangeomorphs, among the oldest and most enigmatic components of the Ediacaran macrobiota. We provide the first direct evidence for the internal interconnected nature of rangeomorphs, and show Charnia was constructed of repeated branches that derived successively from pre-existing branches. We find homology and rationalise morphogenesis between disparate rangeomorph taxa, before producing a new phylogenetic analysis, resolving Charnia as a stem-eumetazoan and expanding the anatomical disparity of that group to include a long-extinct bodyplan. These data bring competing records of early animal evolution into closer agreement, reformulating our understanding of the evolutionary emergence of animal bodyplans.
- Published
- 2021
31. Deep learning classification of bacteria clones explained by persistence homology
- Author
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Dorota Ochońska, Bartosz Zieliński, Monika Brzychczy-Włoch, Dawid Rymarczyk, and Adriana Borowa
- Subjects
Persistence (psychology) ,Artificial neural network ,Similarity (network science) ,Cloning (programming) ,business.industry ,Computer science ,Deep learning ,Bacterial taxonomy ,Homology (anthropology) ,Artificial intelligence ,Computational biology ,business - Abstract
In this work, we automatically distinguish between different clones of the same bacteria species (Klebsiella pneumoniae) based only on microscopic images. It is a challenging task, previously seemed unreachable due to the high clones' similarity. For this purpose, we apply a multi-step algorithm with attention-based deep multiple instance learning, which returns parts of the image crucial to the prediction. Except for obtaining high accuracy, we introduce extensive explainability based on persistence homology, increasing the understandability and trust in the model. Our work opens a plethora of research pathways towards cheaper and faster epidemiological management.
- Published
- 2021
32. The Integrative Approach to Inferring Homology: Morphology and Development Combined
- Author
-
Arsham Nejad Kourki, Nejad Kourki, Arsham [0000-0002-4508-4653], and Apollo - University of Cambridge Repository
- Subjects
Morphology (biology) ,Computational biology ,Biology ,Article ,animal_sciences_zoology ,Homology ,Developmental mechanism ,Phylogenetics ,Philosophy ,History and Philosophy of Science ,Eumetazoan body plan ,Evidential integration ,Homology (anthropology) ,General Agricultural and Biological Sciences - Abstract
Reconstructing ancestral species is a challenging endeavour: fossils are often scarce or enigmatic, and inferring ancestral characters based on novel molecular approaches (e.g. comparative genomics or developmental genetics) has long been controversial. A key philosophical challenge pertinent at present is the lack of a theoretical framework capable of evaluating inferences of homology made through integration of multiple kinds of evidence (e.g. molecular, developmental, or morphological). Here, I present just such a framework. I start with a brief history and critical assessment of attempts at inferring morphological homology through developmental genetics. I then bring attention to a recent model of homology, namely Character Identity Mechanisms (DiFrisco et al. 2020), intended partly to elucidate the relationships between morphological characters, developmental genetics, and homology. I utilise and build on this model to construct the evaluative framework mentioned above, which judges the epistemic value of evidence of each kind in each particular case based on three proposed criteria: effectiveness, admissibility, and informativity, as well as providing a generalised guideline on how it can be scientifically operationalised. I then point out the evolution of the eumetazoan body plan as a case in point where the application of this framework can yield satisfactory results, both empirically and conceptually. I will conclude with a discussion on some potential implications for more general philosophy of biology and philosophy of science, especially surrounding evidential integration, models and explanation, and reductionism.
- Published
- 2021
33. PHROG: families of prokaryotic virus proteins clustered using remote homology
- Author
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Rubén Enrique Pérez Bucio, Julien Lossouarn, Eric Olo Ndela, Clovis Galiez, François Enault, Robin Mom, Marie-Agnès Petit, Paul Terzian, Ariane Toussaint, Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Université libre de Bruxelles (ULB), H2020 European Research Council685778INRAE, Statistique pour le Vivant et l’Homme (SVH), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut de Biologie et de Médecine Moléculaires [Gosselies] (ULB/IBMM), Faculté des Sciences [Bruxelles] (ULB), and Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB)
- Subjects
AcademicSubjects/SCI01140 ,AcademicSubjects/SCI01060 ,Protein family ,Viral protein ,Ecology (disciplines) ,AcademicSubjects/SCI00030 ,Standard Article ,Computational biology ,Biology ,AcademicSubjects/SCI01180 ,medicine.disease_cause ,03 medical and health sciences ,Annotation ,medicine ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Homology (anthropology) ,Cluster analysis ,030304 developmental biology ,Sequence (medicine) ,0303 health sciences ,prokaryotic virus proteins ,[INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB] ,MOBILE GENETIC ELEMENTS ,030302 biochemistry & molecular biology ,homology ,Classification ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,AcademicSubjects/SCI00980 ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,PHROG ,Reference genome - Abstract
Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both in terms of the number of different protein families encountered and in the sequence heterogeneity of each protein family. The recent increase in sequenced viral genomes constitutes a great opportunity to gain new insights into this diversity and consequently urges the development of annotation resources to help functional and comparative analysis. Here, we introduce PHROG (Prokaryotic Virus Remote Homologous Groups), a library of viral protein families generated using a new clustering approach based on remote homology detection by HMM profile-profile comparisons. Considering 17 473 reference (pro)viruses of prokaryotes, 868 340 of the total 938 864 proteins were grouped into 38 880 clusters that proved to be a 2-fold deeper clustering than using a classical strategy based on BLAST-like similarity searches, and yet to remain homogeneous. Manual inspection of similarities to various reference sequence databases led to the annotation of 5108 clusters (containing 50.6 % of the total protein dataset) with 705 different annotation terms, included in 9 functional categories, specifically designed for viruses. Hopefully, PHROG will be a useful tool to better annotate future prokaryotic viral sequences thus helping the scientific community to better understand the evolution and ecology of these entities.
- Published
- 2021
34. Small sparking flies: systematics of Pholeomyia Bilimek, 1867 (Diptera: Milichiidae: Milichiinae)
- Author
-
Heloísa Fernandes Flores
- Subjects
Systematics ,biology ,Evolutionary biology ,Pholeomyia ,Homology (anthropology) ,Milichiidae ,biology.organism_classification ,Cladistics - Published
- 2021
35. Homology of process: developmental dynamics in comparative biology
- Author
-
Johannes Jaeger and James DiFrisco
- Subjects
0303 health sciences ,Dynamical systems theory ,Computer science ,Process (engineering) ,Biomedical Engineering ,Biophysics ,Gene regulatory network ,Bioengineering ,Comparative biology ,Articles ,Biochemistry ,Biomaterials ,Structuralism (biology) ,03 medical and health sciences ,0302 clinical medicine ,Evolutionary biology ,Segmentation ,Homology (anthropology) ,Developmental biology ,030217 neurology & neurosurgery ,030304 developmental biology ,Biotechnology - Abstract
Comparative biology builds up systematic knowledge of the diversity of life, across evolutionary lineages and levels of organization, starting with evidence from a sparse sample of model organisms. In developmental biology, a key obstacle to the growth of comparative approaches is that the concept of homology is not very well defined for levels of organization that are intermediate between individual genes and morphological characters. In this paper, we investigate what it means for ontogenetic processes to be homologous, focusing specifically on the examples of insect segmentation and vertebrate somitogenesis. These processes can be homologous without homology of the underlying genes or gene networks, since the latter can diverge over evolutionary time, while the dynamics of the process remain the same. Ontogenetic processes like these therefore constitute a dissociable level and distinctive unit of comparison requiring their own specific criteria of homology. In addition, such processes are typically complex and nonlinear, such that their rigorous description and comparison requires not only observation and experimentation, but also dynamical modelling. We propose six criteria of process homology, combining recognized indicators (sameness of parts, morphological outcome and topological position) with novel ones derived from dynamical systems modelling (sameness of dynamical properties, dynamical complexity and evidence for transitional forms). We show how these criteria apply to animal segmentation and other ontogenetic processes. We conclude by situating our proposed dynamical framework for homology of process in relation to similar research programmes, such as process structuralism and developmental approaches to morphological homology. ispartof: Interface Focus vol:11 issue:3 pages:1-18 ispartof: location:England status: published
- Published
- 2021
36. A fast, general synteny detection engine
- Author
-
Kristen J. Wade, Ahrens Jb, and David D. Pollock
- Subjects
Identification (information) ,Common descent ,Computer science ,Directionality ,Computational biology ,Homology (anthropology) ,False positive rate ,Divergence (statistics) ,Genome ,Synteny - Abstract
The increasingly widespread availability of genomic data has created a growing need for fast, sensitive and scalable comparative analysis methods. A key aspect of comparative genomic analysis is the study of synteny, co-localized gene clusters shared among genomes due to descent from common ancestors. Synteny can provide unique insight into the origin, function, and evolution of genome architectures, but methods to identify syntenic patterns in genomic datasets are often inflexible and slow, and use diverse definitions of what counts as likely synteny. Moreover, the reliable identification of putatively syntenic regions (i.e., whether they are truly indicative of homology) with different lengths and signal to noise ratios can be difficult to quantify. Here, we present Mology, a fast, flexible, alignment-free, nonparametric method to detect regions of syntenic elements among genomes or other datasets. The core algorithm operates on consecutive, rank-ordered elements, which could be genes, operons, motifs, sequence fragments, or any other orderable element. It is agnostic to the physical distance between distinct elements and also to directionality and order within syntenic regions, although such considerations can be addressed post hoc. We describe the underlying statistical theory behind our analysis method, and employ a Monte Carlo approach to estimate the false positive rate and positive predictive values for putative syntenic regions. We also evaluate how varying amounts of noise affect recovery of true syntenic regions among Saccharomycetaceae yeast genomes with up to ~100 million years of divergence. We discuss different strategies for recursive application of our method on syntenic regions with sparser signal than considered here, as well as the general applicability of the core algorithm.
- Published
- 2021
37. The ultimate database to (re)set the evolutionary history of primate genital bones
- Author
-
Massimiliano Scalici, Federica Spani, Gabriele Gentile, Matteo Bettuzzi, Maria Pia Morigi, Monica Carosi, Spani, Federica, Morigi, Maria Pia, Bettuzzi, Matteo, Scalici, Massimiliano, Gentile, Gabriele, Carosi, Monica, Spani F., Morigi M.P., Bettuzzi M., Scalici M., Gentile G., and Carosi M.
- Subjects
MAMMALIAN BACULUM ,Primates ,0106 biological sciences ,0301 basic medicine ,Settore BIO/05 ,Databases, Factual ,Science ,computer.software_genre ,010603 evolutionary biology ,01 natural sciences ,SEXUAL SELECTION ,Article ,Set (abstract data type) ,Databases ,03 medical and health sciences ,Species level ,Taxonomy (general) ,biology.animal ,Animals ,Sex organ ,Primate ,Genitalia ,Homology (anthropology) ,ALLOMETRY ,Multidisciplinary ,biology ,Database ,OS-PENIS ,Evolutionary theory ,COPULATORY-BEHAVIOR ,Data acquisition ,EXTERNAL GENITALIA ,X-Ray Microtomography ,Biological Evolution ,ANATOMY ,Phylogenetics ,030104 developmental biology ,Geography ,Baculum ,MORPHOLOGY ,Medicine ,Data integration ,Raw data ,computer - Abstract
Scientific literature concerning genital bones in primates consists of both ancient works (dating back to the nineteenth century) and more recent revisions/meta-analyses, which, however, are not always so detailed or exhaustive. Based on a thorough analysis, several conflicting data, inaccurate references, and questionable claims have emerged. We generated a binary matrix of genital bone occurrence data, considering only data at the species level, based on (1) a rigorous literature search protocol, (2) raw data (collected exclusively from primary literature), (3) an updated taxonomy (often tracing back to the species taxonomic history) and (4) new occurrence data from scanned genitals of fresh and museum specimens (using micro-computed tomography-micro-CT). Thanks to this methodological approach, we almost doubled available occurrence data so far, avoiding any arbitrary extension of generic data to conspecific species. This practice, in fact, has been recently responsible for an overestimation of the occurrence data, definitively flattening the interspecific variability. We performed the ancestral state reconstruction analysis of genital bone occurrence and results were mapped onto the most updated phylogeny of primates. As for baculum, we definitively demonstrated its simplesiomorphy for the entire order. As for baubellum, we interpreted all scattered absences as losses, actually proposing (for the first time) a simplesiomorphic state for the clitoral bone as well. The occurrence data obtained, while indirectly confirming the baculum/baubellum homology (i.e., for each baubellum a baculum was invariably present), could also directly demonstrate an intra-specific variability affecting ossa genitalia occurrence. With our results, we established a radically improved and updated database about the occurrence of genital bones in primates, available for further comparative analyses.
- Published
- 2021
38. Three-stage multiscale modelling of the NMDA neuroreceptor
- Author
-
Fabio Sterpone, Simone Melchionna, Sauro Succi, Marco Lauricella, Franck Pérot, Francesco Di Palma, Istituto Italiano di Tecnologia (IIT), Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Istituto per le Applicazioni del Calcolo 'Mauro Picone' (IAC), Consiglio Nazionale delle Ricerche [Roma] (CNR), and Istituto Sistemi Complessi [ROME] (ISC)
- Subjects
Physics ,Three stage ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,010304 chemical physics ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,[PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] ,Biophysics ,Crystal structure ,Computational biology ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,molecular dynamics ,0104 chemical sciences ,Molecular dynamics ,0103 physical sciences ,NMDA receptor ,Homology (anthropology) ,Physical and Theoretical Chemistry ,Molecular Biology - Abstract
International audience; We present a new multistage method to study the N-Methyl-D-Aspartate (NMDA) neuroreceptor starting from the reconstruction of its crystallographic structure. Thanks to the combination of Homology Modelling, Molecular Dynamics and Lattice Boltzmann simulations, we analyse the allosteric transition of NDMA upon ligand binding and compute the receptor response to ionic passage across the membrane.
- Published
- 2021
39. Testing the Omnivore Hypothesis in Russia
- Author
-
Iuliia Papushina
- Subjects
omnivore ,tolerance ,Sociology and Political Science ,Taste (sociology) ,media_common.quotation_subject ,Economics, Econometrics and Finance (miscellaneous) ,urbanization ,Musical ,cultural consumption ,HM401-1281 ,Popular music ,Argument ,Urbanization ,Sociology (General) ,Omnivore ,Homology (anthropology) ,Sociology ,Positive economics ,Preference (economics) ,media_common ,music preferences in russia - Abstract
In the last thirty years, a significant shift from the homology to omnivore argument has occurred in musical preference studies. Studies on the omnivore argument mainly come from North and South America, Western and sometimes Eastern Europe. To the best of our knowledge, there are no empirical tests of musical omnivorousness in Russia. The aim of this paper is to reveal omnivore musical preferences in Russia, and analyzes the links between musical preferences, social-demographic profiles, and tolerance. Our research also emphasizes the territory dimension. The research setting is the Perm Region. A survey of 2,400 Perm Region citizens is analyzed using principal component analysis and linear regression provides evidence for the research. Our findings do not indicate omnivore musical tastes in Russia that contradicts the conclusions of the research in other cultures. Instead of finding the omnivore pattern, we found Bourdieu-like patterns of classical versus pop music taste and nostalgic taste versus contemporary taste. Representatives of each taste pattern have a specific social-demographic profile. The urbanization factor influences musical preferences as well. The paper discusses the limitations of the research and directions for further work. Acknowledgements. The publication was prepared within the framework of the project “Intergenerational cultural dynamics” No 18-011-00548А supported by Russian Fundamental Research Fund.
- Published
- 2021
40. Structural and Functional Analyses of the Gelsolin Homology Domains of Flightless‐I in Actin Dynamics
- Author
-
Andrea Vig, Rauan Sakenov, Réka Pintér, Rahmah Hanifatul, Beáta Bugyi, Mónika Ágnes Tóth, Tamás Huber, Péter Gaszler, and Péter Bukovics
- Subjects
Actin dynamics ,Genetics ,Homology (anthropology) ,Computational biology ,Biology ,Molecular Biology ,Biochemistry ,Gelsolin ,Biotechnology - Published
- 2021
41. Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading
- Author
-
Sutanu Bhattacharya, Rahmatullah Roche, Md Hossain Shuvo, and Debswapna Bhattacharya
- Subjects
0301 basic medicine ,Computer science ,QH301-705.5 ,Mini Review ,homology modeling ,Computational biology ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Biochemistry ,03 medical and health sciences ,inter-residue interaction map ,Molecular Biosciences ,Homology (anthropology) ,Homology modeling ,Biology (General) ,Molecular Biology ,Sequence (medicine) ,030102 biochemistry & molecular biology ,Artificial neural network ,protein homology ,protein threading ,Protein superfamily ,Protein structure prediction ,protein structure prediction ,030104 developmental biology ,Protein homology ,Threading (protein sequence) - Abstract
Sequence-based protein homology detection has emerged as one of the most sensitive and accurate approaches to protein structure prediction. Despite the success, homology detection remains very challenging for weakly homologous proteins with divergent evolutionary profile. Very recently, deep neural network architectures have shown promising progress in mining the coevolutionary signal encoded in multiple sequence alignments, leading to reasonably accurate estimation of inter-residue interaction maps, which serve as a rich source of additional information for improved homology detection. Here, we summarize the latest developments in protein homology detection driven by inter-residue interaction map threading. We highlight the emerging trends in distant-homology protein threading through the alignment of predicted interaction maps at various granularities ranging from binary contact maps to finer-grained distance and orientation maps as well as their combination. We also discuss some of the current limitations and possible future avenues to further enhance the sensitivity of protein homology detection.
- Published
- 2021
42. O pensamento estético de Georg Lukács: continuidade ou ruptura?
- Author
-
Renata Altenfelder Garcia Gallo
- Subjects
Lebensphilosophie ,Aesthetics ,media_common.quotation_subject ,Philosophy ,Hegelianism ,Homology (anthropology) ,Maturity (psychological) ,media_common - Abstract
Ao longo de seu percurso intelectual, o filósofo húngaro Georg Lukács (1885- 1971) demonstrou vasto interesse sobre a esfera artística, o que o levou a escrever duas estéticas. A primeira delas, redigida em dois momentos diversos de sua juventude, resultou em dois textos complementares, intitulados Filosofia da Arte (1912-14) e Estética de Heidelberg (1916-18). Dentre as influências que os textos apresentam, as mais marcantes são aquelas da filosofia neokantiana, da Lebensphilosophie e dos escritos de Hegel. A redação da segunda estética Lukácsiana veio a público em 1963 e foi pensada a partir da teoria marxista. Apesar de, aproximadamente, 45 anos separarem essas publicações, as indagações que Lukács colecionava acerca da esfera estética eram muito semelhantes, dentre as quais, citamos a preocupação do autor em elucidar o estatuto categorial particular do campo da arte no conjunto das criações humanas, a fim de garantir a autonomia da referida esfera. Diante de tais problemas, este estudo visa apresentar e discutir alguns pontos importantes das estéticas Lukácsianas para que seja possível respondermos à seguinte pergunta: É possível afirmar a existência de uma homologia entre as estéticas de juventude e de maturidade de Georg Lukács?
- Published
- 2019
43. 냉전의 경쟁과 모방―북한 전쟁첩보영화 <이름 없는 영웅들>에 나타난 냉전/분단의 상동성―
- Author
-
Ha-Na Lee
- Subjects
Competition (economics) ,History ,Cold war ,Imitation (music) ,Homology (anthropology) ,Ancient history ,Division (mathematics) - Published
- 2019
44. A Human Behavior Strategy Estimation Method Using Homology Search for Rock-Scissors-Paper Game
- Author
-
Hiroaki Kurokawa, Song-Ju Kim, Takuji Kousaka, and Takahiro Komai
- Subjects
Computer science ,Homology (anthropology) ,Computational biology - Published
- 2019
45. Toward a theory of homology: development and the de-coupling of morphological and molecular evolution
- Author
-
James DiFrisco
- Subjects
Coupling (electronics) ,Physics ,Philosophy ,History ,Development (topology) ,History and Philosophy of Science ,Stereochemistry ,Molecular evolution ,Homology (anthropology) - Published
- 2021
46. Homology sequence analysis using GPU acceleration
- Author
-
Huan Truong
- Subjects
Physics ,Sequence analysis ,Acceleration (differential geometry) ,Homology (anthropology) ,Computational biology - Abstract
A number of problems in bioinformatics, systems biology and computational biology field require abstracting physical entities to mathematical or computational models. In such studies, the computational paradigms often involve algorithms that can be solved by the Central Processing Unit (CPU). Historically, those algorithms benefit from the advancements of computing power in the serial processing capabilities of individual CPU cores. However, the growth has slowed down over recent years, as scaling out CPU has been shown to be both cost-prohibitive and insecure. To overcome this problem, parallel computing approaches that employ the Graphics Processing Unit (GPU) have gained attention as complementing or replacing traditional CPU approaches. The premise of this research is to investigate the applicability of various parallel computing platforms to several problems in the detection and analysis of homology in biological sequence. I hypothesize that by exploiting the sheer amount of computation power and sequencing data, it is possible to deduce information from raw sequences without supplying the underlying prior knowledge to come up with an answer. I have developed such tools to perform analysis at scales that are traditionally unattainable with general-purpose CPU platforms. I have developed a method to accelerate sequence alignment on the GPU, and I used the method to investigate whether the Operational Taxonomic Unit (OTU) classification problem can be improved with such sheer amount of computational power. I have developed a method to accelerate pairwise k-mer comparison on the GPU, and I used the method to further develop PolyHomology, a framework to scaffold shared sequence motifs across large numbers of genomes to illuminate the structure of the regulatory network in yeasts. The results suggest that such approach to heterogeneous computing could help to answer questions in biology and is a viable path to new discoveries in the present and the future.
- Published
- 2021
47. 'I would sooner die than give up': Huxley and Darwin's deep disagreement
- Author
-
Winsor, Mary P.
- Subjects
0106 biological sciences ,History ,History of taxonomy ,Richard Owen ,Analogy ,050905 science studies ,010603 evolutionary biology ,01 natural sciences ,History and Philosophy of Science ,Arts and Humanities (miscellaneous) ,Homology (anthropology) ,Lagostomus ,Biology ,Archetype ,History of science ,Naturalism ,Literature ,Original Paper ,Philosophy of science ,William Whewell ,business.industry ,John Stuart Mill ,05 social sciences ,History of systematics ,History, 19th Century ,Biological Evolution ,Dissent and Disputes ,Homology ,Philosophy of biology ,Charles Darwin ,Darwin (ADL) ,Thomas Henry Huxley ,0509 other social sciences ,Hugh Strickland ,business ,Natural History - Abstract
Thomas Henry Huxley and Charles Darwin discovered in 1857 that they had a fundamental disagreement about biological classification. Darwin believed that the natural system should express genealogy while Huxley insisted that classification must stand on its own basis, independent of evolution. Darwin used human races as a model for his view. This private and long-forgotten dispute exposes important divisions within Victorian biology. Huxley, trained in physiology and anatomy, was a professional biologist while Darwin was a gentleman naturalist. Huxley agreed with John Stuart Mill's rejection of William Whewell's sympathy for Linnaeus. The naturalists William Sharp Macleay, Hugh Strickland, and George Waterhouse worked to distinguish two kinds of relationship, affinity and analogy. Darwin believed that his theory could explain the difference. Richard Owen introduced the distinction between homology and analogy to anatomists, but the word homology did not enter Darwin's vocabulary until 1848, when he used the morphological concept of archetype in his work on Cirripedia. Huxley dropped the word archetype when Richard Owen linked it to Plato's ideal forms, replacing it with common plan. When Darwin wrote in the Origin of Species that the word plan gives no explanation, he may have had Huxley in mind. Darwin's preposterous story in the Origin about a bear giving birth to a kangaroo, which he dropped in the second edition, was in fact aimed at Huxley.
- Published
- 2021
48. MolluscDB: a genome and transcriptome database for molluscs
- Author
-
Mark Blaxter, Sujai Kumar, Dominik R. Laetsch, Karim Gharbi, Carlos Caurcel, and Richard Challis
- Subjects
Web server ,Computer science ,Genomics ,computer.software_genre ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Resource (project management) ,Phylogenetics ,Databases, Genetic ,Ensembl ,Animals ,Homology (anthropology) ,protein families ,genome ,database ,molluscs ,Database ,Phylum ,Gene Expression Profiling ,ComputingMethodologies_PATTERNRECOGNITION ,Mollusca ,shell matrix proteins ,General Agricultural and Biological Sciences ,Transcriptome ,computer ,transcriptome - Abstract
As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
- Published
- 2021
49. Homology thinking reconciles the conceptual conflict between typological and population thinking
- Author
-
Daichi G. Suzuki
- Subjects
0106 biological sciences ,Typology ,0303 health sciences ,education.field_of_study ,Essentialism ,Modern evolutionary synthesis ,Interpretation (philosophy) ,Population ,010603 evolutionary biology ,01 natural sciences ,Epistemology ,03 medical and health sciences ,Philosophy ,Philosophy of biology ,History and Philosophy of Science ,Darwinism ,Sociology ,Homology (anthropology) ,General Agricultural and Biological Sciences ,education ,030304 developmental biology - Abstract
This paper attempts to reconcile the conceptual conflict between typological and population thinking to provide a philosophical foundation for extended evolutionary synthesis (EES). Typological thinking has been considered a pre-Darwinian, essentialist dogma incompatible with population thinking, which is the core notion of Darwinism. More recent philosophical and historical studies suggest that a non-essentialist form of typology (i.e., representational typology) has some advantages in the study of evolutionary biology. However, even if we adopt such an epistemological interpretation of typological thinking, there still remains an epistemological and methodological conflict between these two styles of thinking. How can we relate typological thinking with population thinking in pursuit of more integrated or interconnected research into evolutionary biology? I propose that homology thinking, which is another style of thinking that recognizes homologous characters, provides a common basis for typological representations of character states and for character dynamics in an evolving population. Good examples of this bridging role are found in teratology and breeding, where variation and novelty are recognized in developmental and morphological traits, gene expression patterns, and so on. Essentialism-free, dynamic views of homology have great potential to reconcile typological and population thinking and to set the stage for the EES.
- Published
- 2021
50. Corrigendum to Complete homology and related dimensions of groups [J. Group Theory 12 (2009), 431–448]
- Author
-
Jang Hyun Jo
- Subjects
Algebra and Number Theory ,Homology (anthropology) ,Computational biology ,Group theory ,Mathematics - Published
- 2021
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