bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota (Fungi) and a potential to switch between hosts
Authors: Strassert Jürgen F. H. , Wurzbacher Christian , Hervé Vincent , Antany Taraha , Brune Andreas , Radek Renate 
Published: October 2020

AbstractNephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate and uninucleate cells, and sporogonial plasmodia that form uninucleate spores. Nephridiophagids are poor in morphological characteristics, and although they have been tentatively identified as early-branching fungi based on the SSU rRNA gene sequences of three species, their exact position within the fungal tree of live remained unclear. In this study, we described two new species of nephridiophagids (Nephridiophaga posticiandNephridiophaga javanicae) from cockroaches. Using long-read sequencing of the entire rDNA operon of numerous further species obtained from cockroaches and earwigs to improve the resolution of the phylogenetic analysis, we found a robust affiliation of nephridiophagids with the Chytridiomycota — a group of zoosporic fungi that comprises parasites of diverse host taxa, such as microphytes, plants, and amphibians. The presence of the same nephridiophagid species in two only distantly related cockroaches indicates their host specificity is not a strict as generally assumed.
Heterozygous deletion of SYNGAP enzymatic domains in rats causes selective learning, social and seizure phenotypes
Authors: Katsanevaki D. , Till SM. , Buller-Peralta I. , Watson TC. , Nawaz MS. , Arkell D. , Tiwari S. , Kapgal V. , Biswal S. , Smith JAB. , Anstey NJ. , Mizen L. , Perentos N. , Jones MW. , Cousin MA. , Chattarji S. , Gonzalez-Sulser A. , Hardt O. , Wood ER. , Kind PC. 
Published: October 2020

AbstractPathogenic variants inSYNGAP1are one of the most common genetic causes of nonsyndromic intellectual disability (ID) and are considered a risk for autism spectrum disorder (ASD).SYNGAP1encodes asynapticGTPaseactivatingprotein that modulates the intrinsic GTPase activity of several small G-proteins and is implicated in regulating the composition of the postsynaptic density. By targeting the deletion of exons encoding the calcium/lipid binding (C2) andGTPaseactivatingprotein (GAP) domains, we generated a novel rat model to study SYNGAP related pathophysiology. We find that rats heterozygous for the C2/GAP domain deletion (Syngap+/Δ-GAP) exhibit reduced exploration and fear extinction, altered social behaviour, and spontaneous seizures, while homozygous mutants die within days after birth. This new rat model reveals that the enzymatic domains of SYNGAP are essential for normal brain function and provide an important new model system in the study of both ID/ASD and epilepsy.
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
Authors: Whiting James R. , Paris Josephine R. , van der Zee Mijke J. , Parsons Paul J. , Weigel Detlef , Fraser Bonnie A. 
Published: October 2020

ABSTRACTStudies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signalling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
“Sifarchaeota” a novel Asgard phylum capable of polysaccharide degradation and anaerobic methylotrophy
Authors: Farag Ibrahim F. , Zhao Rui , Biddle Jennifer F. 
Published: October 2020

AbstractThe Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode for diverse metabolic capacities and play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name “Sifarchaeota” for this phylum. The two “Sifarchaeota” MAGs encode for an anaerobic methylotrophy pathway enabling the utilization of C1-C3 compounds (methanol and methylamines) to synthesize acetyl CoA. Also, the MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded for diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di- and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of Asgard lineages revealed the close relation between “Sifarchaeota” and Odinarchaeota MAGs, which suggested a similar metabolic potentials and ecological roles. Furthermore, we identified multiple potential horizontal gene transfer (HGT) events from different bacterial donors within “Sifarchaetoa” MAGs, which hypothetically expanded “Sifarchaeota” capacities for substrate utilization, energy production and niche adaptation.ImportanceDeep marine sediments are the home of multiple poorly described archaeal lineages, many of which have ecological and evolutionary importance. We recovered metagenome-assembled genomes (MAGs) belonging to a novel Asgard phylum from the deep sediment of the Costa Rica margin. We proposed the name “Sifarchaeota” to describe the members of this phylum. Representative genomes of the “Sifarchaeota” showed remarkable saccharolytic capacities extending the known metabolic features encoded by the Asgard lineages. We attribute its ability to survive under the deep sediment conditions to its putative capacities to utilize different (C1-C3) compounds commonly encountered in deep sediment environments via anaerobic methylotrophy pathway. Also, we showed the importance of horizontal gene transfer in enhancing the “Sifarchaeota” collective adaptation strategies.
EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture
Authors: Costa-Neto Germano , Galli Giovanni , Carvalho Humberto Fanelli , Crossa José , Fritsche-Neto Roberto 
Published: October 2020

ABSTRACTEnvirotyping is an essential technique used to unfold the non-genetic drivers associated with the phenotypic adaptation of living organisms. Here we introduce theEnvRtypeR package, a novel toolkit developed to interplay large-scale envirotyping data (enviromics) into quantitative genomics. To start a user-friendly envirotyping pipeline, this package offers: (1) remote sensing tools for collecting (get_weather and extract_GIS functions) and processing ecophysiological variables (processWTH function) from raw environmental data at single locations or worldwide; (2) environmental characterization by typing environments and profiling descriptors of environmental quality (env_typing function), in addition to gathering environmental covariables as quantitative descriptors for predictive purposes (W_matrix function); and (3) identification of environmental similarity that can be used as an enviromic-based kernel (env_typing function) in whole-genome prediction (GP), aimed at increasing ecophysiological knowledge in genomic best-unbiased predictions (GBLUP) and emulating reaction norm effects (get_kernel and kernel_model functions). We highlight literature mining concepts in fine-tuning envirotyping parameters for each plant species and target growing environments. We show that envirotyping for predictive breeding collects raw data and processes it in an eco-physiologically-smart way. Examples of its use for creating global-scale envirotyping networks and integrating reaction-norm modeling in GP are also outlined. We conclude thatEnvRtypeprovides a cost-effective envirotyping pipeline capable of providing high quality enviromic data for a diverse set of genomic-based studies, especially for increasing accuracy in GP across untested growing environments.
Bayesian Encoding and Decoding as Distinct Perspectives on Neural Coding
Authors: Lange Richard D. , Shivkumar Sabyasachi , Chattoraj Ankani , Haefner Ralf M. 
Published: October 2020

AbstractOne of the most influential, and controversial, ideas in neuroscience has been to understand the brain in terms of Bayesian computations. Unstated differences in how Bayesian ideas are operationalized across different models make it difficult to ascertain both which empirical data support which models, and how Bayesian computations might be implemented by neural circuits. In this paper, we make one such difference explicit by identifying two distinct philosophies that underlie existing neural models of Bayesian inference: one in which the brain recovers experimenter-defined structures in the world from sensory neural activity (Decoding), and another in which the brain represents latent quantities in an internal model that explains its inputs (Encoding). These philosophies require profoundly different assumptions about the nature of inference in the brain, and lead to different interpretations of empirical data. Here, we characterize and contrast both philosophies in terms of motivations, empirical support, and relationship to neural data. We also show that this implicit difference in philosophy underlies some of the debate on whether neural activity is better described as a sampling-based, or a parametric, distributional code. Using a simple model of primary visual cortex as an example, we show mathematically that it is possible that the very same neural activity can be described as probabilistic inference by neural sampling in theEncodingframework while also forming a linear probabilistic population code (PPC) in theDecodingframework. This demonstrates that certain families of Encoding and Decoding models are compatible with each other rather than competing explanations of data. In sum, Bayesian Encoding and Bayesian Decoding are distinct, non-exclusive philosophies, and appreciating their similarities and differences will help organize future work and allow for stronger empirical tests about the nature of inference in the brain.
Sculpting New Visual Categories into the Human Brain
Authors: Iordan Coraline Rinn , Ritvo Victoria J. H. , Norman Kenneth A. , Turk-Browne Nicholas B. , Cohen Jonathan D. 
Published: October 2020

AbstractLearning requires changing the brain. This typically occurs through experience, study, or instruction. We report a proof-of-concept for a new way for humans to acquire visual knowledge by directly sculpting activity patterns in the human brain that mirror those expected to arise through learning. We used a non-invasive technique (closed-loop real-time functional magnetic resonance imaging neurofeedback) to create new categories of visual objects in the brain, without the participants’ explicit awareness. After neural sculpting, participants exhibited behavioral and neural biases for the sculpted, but not for the control categories. The ability to sculpt new perceptual distinctions in the human brain offers a new paradigm for human fMRI research that allows for non-invasive, causal testing of the link between neural representations and behavior. As such, beyond its current application to perception, our work potentially has broad relevance to other domains of cognition such as decision-making, memory, and motor control.Significance StatementObjects that belong to the same category tend to elicit similar patterns of brain activity. Here we reverse this mapping and ask whether neural similarity is sufficient to induce increased perceptual discrimination and categorical perception. We do this by using real-time fMRI to modify neural representations of objects in high-level visual cortex. Participants viewed an object and received closed-loop neurofeedback that pushed them to represent the object more similarly to a brain activity pattern we chose for that category. After successfully self-modulating their brain activity, participants began to perceive objects assigned to the same brain pattern as more categorically distinct from those assigned to a different brain pattern. These findings open a new avenue for understanding and accelerating human learning.
Multivariate distributions of behavioural, morphological, and ontogenetic traits in hybrids bring new insights into the divergence of sympatric Arctic charr morphs
Authors: Horta-Lacueva Quentin J.B. , Snorrason Sigurður S. , Morrissey Michael B. , Leblanc Camille A. , Kapralova Kalina H. 
Published: October 2020

AbstractStudying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of phenotypic traits suspected to be involved in the divergence of two recently evolved morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. We observed differences among morphs in overall phenotypic variance and in trait correlations. Phenotypic contrainsts also tended to be reduced in the hybrids, which corroborates the narrative of hybridization facilitating adaptive divergence by relaxing trait covariance. However, the hybrids were associated with reduced phenotypic variance at different scales (i.e. at the scale of the entirePmatrix and in different parts of the multivariate space), and we identified stronger correlations between several ontogenetic and morphological traits in the hybrids than in both morphs. These findings suggest a limited potential for hybridization to generate phenotypic novelty, and emphasise the need for multivariate approaches conciliating ontogenetic, morphological and behavioural processes to study the processes of adaptive divergence and speciation.
Acis-regulatory element promoting increased transcription at low temperature in cultured ectothermicDrosophilacells
Authors: Bai Yu , Caussinus Emmanuel , Leo Stefano , Bosshardt Fritz , Myachina Faina , Rot Gregor , Robinson Mark D. , Lehner Christian F. 
Published: October 2020

AbstractCells of many ectothermic species, includingDrosophila melanogaster, maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation are still poorly understood. At the transcriptional level, the heat shock response has been extensively analyzed. The opposite has received less attention. Here, using culturedDrosophilacells, we have identified genes with increased transcript levels at the lower end of the readily tolerated temperature range, as well as chromatin regions with increased DNA accessibility. Candidatecis-regulatory elements (CREs) for transcriptional upregulation at low temperature were selected and evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from thepastrelgene, which expresses more transcript and protein at reduced temperatures. The CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D.
Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation
Authors: Xu Pengfei , Yu Haoze Vincent , Tseng Kuo-Chang , Flath Mackenzie , Fabian Peter , Segil Neil , Crump J. Gage 
Published: October 2020

AbstractThe specification of cartilage requires Sox9, a transcription factor with broad roles for organogenesis outside the skeletal system. How Sox9 gains selective access to cartilage-specific cis-regulatory regions during skeletal development had remained unclear. By analyzing chromatin accessibility during the differentiation of neural crest cells into chondrocytes of the zebrafish head, we find that cartilage-associated chromatin accessibility is dynamically established. Cartilage-associated regions that become accessible after neural crest migration are co-enriched for Sox9 and Fox transcription factor binding motifs. In zebrafish lacking Foxc1 paralogs, we find a global decrease in chromatin accessibility in chondrocytes, consistent with a later loss of dorsal facial cartilages. Zebrafish transgenesis assays confirm that many of these Foxc1-dependent elements function as enhancers with region- and stage-specific activity in facial cartilages. We propose that Foxc1-dependent chromatin accessibility helps directs the versatile Sox9 protein to a chondrogenic program in the face.HighlightsDynamic chromatin accessibility across facial cartilage developmentCo-enrichment of Fox- and Sox-binding motifs in accessible regionsFoxc1 establishes accessibility in a subset of facial cartilage enhancersModular activity of Foxc1-dependent cartilage enhancers in zebrafish
How do followers infer the motives behind an influencer's advertising disclosures?
Authors: Han Haejoo , Yi Jisu , Jun Sunghee , Ahn Sungsook 
Published: October 2020

PurposeIn the context of influencer marketing, this study examines the effects of explicit advertising disclosure on consumers' inference regarding influencers' sincere recommendation intent, and its consequences for consumers' purchase intentions.Design/methodology/approachIn Study 1, participants were randomly assigned to the conditions of explicit advertising disclosure (e.g. #AD, #Sponsored) and subtle advertising disclosure (e.g. #ThankYou), and indicated their inference regarding influencers' recommendation motives and their own purchase intentions. One-way ANOVA analysis reveals the effect of advertising disclosure on consumers' purchase intentions and the PROCESS model indicates the mediating role of consumers' inferences regarding influencers' sincere recommendation intent. In Study 2, we implemented a 2 (explicit vs. subtle advertising disclosure) × 2 (moderate vs. large size of followers) between-subjects design, using a two-way ANOVA analysis. We analyzed the moderated mediation effect via the PROCESS model.FindingsConsumers are less inclined to purchase products when influencers express explicit advertising disclosures, compared to when the advertising disclosures are subtle (Study 1). These negative effects of advertising disclosure can be caused by consumers' inferences regarding influencers' sincere recommendation intent in terms of posting content (Studies 1 and 2). Additionally, the negative effect is particularly prominent when an influencer has a large (vs. moderate) number of followers (Study 2).Originality/valueBy examining (1) the effects of explicit advertising disclosure on consumers' inference regarding influencers' persuasion motives and (2) the role of the influencer's number of followers, this research provides both theoretical and practical insights for understanding how best to implement influencer marketing.
Benchmarking health-care supply chain by implementing Industry 4.0: a fuzzy-AHP-DEMATEL approach
Authors: Hossain Md Kamal , Thakur Vikas 
Published: October 2020

PurposeWith the rising needs of health-care (HC) services during the health outbreaks, it is essential to upgrade the existing HC delivery infrastructure. The study aims to prioritize and highlight the interrelationships among the key factors of the smart health-care supply chain (HCSC) by implementing the concept of Industry 4.0.Design/methodology/approachThe key factors of implementing Industry 4.0 in HCSC have been identified through extensive literature review and stakeholders' opinions. To achieve the abovementioned objectives, the present study proposed hybrid multi-criteria decision-making (MCDM) tools, namely, the fuzzy-analytic hierarchy process (AHP) and fuzzy- decision-making trial and evaluation laboratory (DEMATEL). The Fuzzy-AHP prioritized the factors of implementing Industry 4.0 in HCSC, while the cause–effect relationships among the factors have been explored using fuzzy-DEMATEL.FindingsThe results of the study indicated that HC logistics management (HCLM) is the most prioritized factor of implementing Industry 4.0 in HCSC, followed by the integrated HCSC, then sustainable HCSC practices, HCSC innovation and technological aspects, HCSC institutional perspectives, HCSC competitiveness, social aspects and economic factors of HCSC. The cause–effect analysis has highlighted integrated HCSC, HCLM, HCSC competitiveness and social aspects as the cause group factors and they are the critical success parameters for implementing Industry 4.0 in the HCSC.Practical implicationsThe results of the study can be useful for policymakers, humanitarian organizations, health administrators and other decision makers considering the smartening of HCSC to enhance the operational performance of health facilities.Originality/valueThis is one of the few studies to have been conducted so far in which the subfactors of HCSC implementing Industry 4.0 have been identified and analyzed using the fuzzy-AHP and fuzzy-DEMATEL hybrid approach.
Gray clustering model based on the degree of dynamic weighted incidence for panel data and its application
Authors: Wu Honghua , Qu Zhongfeng 
Published: October 2020

PurposeThe paper aims to propose a clustering model for panel data. More specifically, the paper aims to construct a gray incidence model for panel data to solve the classification with multi-factors and multi-attributes.Design/methodology/approachThe paper opted for a clustering theory study using gray incidence theory based on dynamic weighted function. The paper presents an example to verify the rationality of the new model, which suggests that the new model can reflect the incidence degree of panel data.FindingsThe paper provides a new gray incidence model based on a dynamic weighted function that can amplify the characteristics of the sample to some extent. The properties of the new incidence model, such as normalization, symmetry and nearness, are all satisfied. The paper also shows that the new incidence model performs very well on cluster discrimination.Originality/valueThe new model in this paper has supplemented and improved the gray incidence analysis theory for panel data.