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The homology group of a tiling introduced by M. Reid is studied for certain topological tilings. As in the planar case, for finite square grids on topological surfaces, the method of homology groups, namely the non-triviality of some specific element in the group allows a "coloring proof" of impossibility of a tiling. Several results about the non-existence of polyomino tilings on certain square-tiled surfaces are proved in the paper.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

International audience

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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?

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.

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.

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’.

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.