bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Seroprevalence in Baixada Santista Metropolitan Area – Brazil
Authors: Batista Karina Barros Calife , Caseiro Marcos Montani , Barros Cláudia Renata , Martins Lourdes Conceição , Chioro Arthur , de Araújo Evaldo Stanislau Affonso , Calvo Marcos , Pereira Luiz Alberto Amador 
Published: September 2020

AbstractBackgroundCOVID-19 reached Brazil in February 2020 after spreading throughout Asia and Europe. The disease first struck in Brazil’s major cities, affecting high-income groups, subsequently spreading to the socially-vulnerable outlying areas. The objective of this preliminary study was to the estimate the seroprevalence of COVID-19 in the Baixada Santista Metropolitan Area - RMBS, to inform policies for prevention and preparation of primary care, hospital services, hospital beds, intensive and critical care in a bid to reduce lethality.MethodsThis study is the first of a four-phase cross-sectional survey to include all cities within the Baixada Santista metropolitan area. The probabilistic population-based sample was based on a 7% prevalence with a 2% delta, a 5% level of significance and 90% power, and considered the estimated population, stratified by age, gender and city. The sample was randomized in each city and street selection was based on data drawn from the 2010 Brazilian census. The serology test was chosen from the available test kits approved by the National Health Agency (ANS) of the National Health Surveillance Agency (ANVISA), for the detection of SARS-CoV-2 antibodies. Information on socioeconomic characteristics, health service use, symptoms and adherence to social distancing measures was collected. All variables were expressed as absolute and relative frequencies and confidence intervals.ResultsThe final sample comprised 2,342 respondents with a mean age of 37.78 (±19.98) years and equal gender distribution. Respondents predominantly lived in an abode with 4 or more rooms, 71.9% had an income of ≤3 minimum wages and no formal employment. Over half of the sample reported being reliant on the National Health Service (SUS) for health care, while 26.5% held private health insurance. Social distancing was practiced by 61.4% of respondents who answered this question. Seroprevalence measured was 1.4% for a 95% CI (0.93-1.93) based on mathematical estimates, with a ratio of 15 actual infections for every case notified, and lethality of 0.48%.ConclusionResults revealed a flattening of the epidemiological curve in the region and high underreporting of cases.
An analysis of genetic diversity actions, indicators and targets in 114 National Reports to the Convention on Biological Diversity
Authors: Hoban Sean , Campbell Catriona , da Silva Jessica , Ekblom Robert , Funk W Chris , Garner Brittany , Godoy Jose A , Kershaw Francine , MacDonald Anna , Mergeay Joachim , Minter Melissa , O'Brien David , Paz-Vinas Ivan , Pearson Sarah Kim , Perez-Espona Silvia , Potter Kevin , Russo Isa-Rita , Segelbacher Gernot , Vernesi Cristiano , Hunter Margaret E 
Published: September 2020

AbstractGenetic diversity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of biodiversity-genes, species and ecosystems-globally. However, assessment and monitoring of genetic diversity are often overlooked, and there are large knowledge and policy gaps regarding genetic diversity conservation. In this study, we present the first quantitative analysis of genetic diversity assessments conducted by Parties to the CBD. We conducted a detailed, systematic analysis of 114 CBD 5th (submitted 2014) and 6th (submitted 2018) National Reports to quantitatively assess actions, progress on targets, values and indicators related to genetic diversity. First, we found that the importance of genetic diversity is recognised by most Parties to the CBD, and that recognition increased over time. However, genetic targets mainly addressed genetic diversity within cultivated plants, farm animals, and crop wild relatives, with little focus on other wild species. Also, actions for conserving genetic diversity primarily concernedex-situfacilities and policy, rather than monitoring and intervention for maintaining genetic diversityin situ. The most commonly used indicators of genetic diversity status were the number of genetic resources in conservation facilities, number of threatened breeds, and Red List Index, which are not well correlated to genetic erosion in most species -- highlighting that genetic change is poorly monitored by current indicators. Lastly, analyses of genetic data observations, indigenous use and knowledge of genetic diversity, and strategies being developed and implemented to conserve genetic diversity are highly under-reported. We make several recommendations for the post-2020 CBD Biodiversity Framework to improve awareness, assessment, and monitoring, and facilitate consistent and complete reporting of progress of genetic diversity in future National Reports.Article Impact StatementAn analysis of genetic diversity in CBD National Reports neglects non-domesticated species and demonstrates need for sufficient indicators.
Serotonergic Effects on Interoception
Authors: Livermore James J A , Holmes Clare L , Moga Gyorgy , Adamatzky Kristian , Critchley Hugo D , Garfinkel Sarah N , Campbell-Meiklejohn Daniel 
Published: September 2020

AbstractInteroception is the signalling, perception, and interpretation of internal physiological states. Much of the psychopharmacology of interoception is still undiscovered. However, psychiatric disorders associated with changes of interoception, including depressive, anxiety, and eating disorders are often treated with selective serotonin reuptake inhibitors (SSRIs). The causal effect of acute changes of serotonin transmission on interoceptive cognition was tested by a within-participant, crossover, placebo-controlled study. Forty-seven healthy human volunteers (31 female, 16 male) were tested both on and off a 20mg oral dose of the commonly prescribed SSRI citalopram. For each randomly ordered session, participants made judgments on the synchrony of their heartbeat to auditory tones and expressed confidence in each of these judgments. Citalopram enhanced insight into the likelihood that one’s interoceptive judgment had been correct, driven primarily by enhanced confidence for correct responses. This effect was independent of measured cardiac and subjective effects of the drug. This novel result is evidence that acute serotonin changes can alter metacognitive insight into the reliability of inferences based on interoceptive information, which is a foundation for considering effects of serotonin on cognition and emotion in terms of effective top-down regulation of interoceptive influence on mental states.
Sex change in aquarium systems establishes the New Zealand spotty wrasse (Notolabrus celidotus) as a temperate model species for the investigation of sequential hermaphroditism
Authors: Goikoetxea A , Muncaster S , Todd EV , Lokman PM , Robertson HA , De Farias e Moraes CE , Damsteegt EL , Gemmell NJ 
Published: September 2020

AbstractThe stunning sexual transformation commonly triggered by age, size or social context in some fishes is one of the best examples of phenotypic plasticity thus far described. To date our understanding of this process is dominated by studies on a handful of subtropical and tropical teleosts, often in wild settings because sex change has been challenging to achieve in captivity. Here we have established the protogynous New Zealand spotty wrasse, Notolabrus celidotus, as a temperate model for the experimental investigation of sex change. Captive fish were induced to change sex using either aromatase inhibition or manipulation of social groups. Complete transition from female to male occurred over 60 days and time-series sampling was used to quantify changes in hormone production, gene expression and gonadal cellular anatomy using radioimmunoassay, nanoString nCounter mRNA and histological analyses, respectively. Early-stage decreases in plasma 17β-estradiol (E2) concentrations or gonadal aromatase (cyp19a1a) expression were not detected in spotty wrasse, despite these being commonly associated with the onset of sex change in subtropical and tropical protogynous (female-to-male) hermaphrodites. In contrast, expression of the masculinising factor amh (anti-Müllerian hormone) increased during early sex change, implying a potential role as a proximate trigger for masculinisation. Expression of male-related genes responsible for androgen production cyp11c1 and hsd11b2 increased from mid sex change. Gonadal expression of the glucocorticoid and mineralocorticoid receptors nr3c1 and nr3c2, putative mediators of the stress hormone cortisol, increased in late stages of sex change. Collectively, these data provide a foundation for the spotty wrasse as a temperate teleost model to study sex change and cell fate in vertebrates.Summary statementThe spotty wrasse, Notolabrus celidotus, is a new temperate model for the study of vertebrate sex change, this work characterises endocrine and genetic markers based on laboratory induced sex change.
Amplitude of circadian rhythms becomes weaker in the north, but there is no cline in the period of rhythm in a beetle
Authors: Abe Masato S. , Matsumura Kentarou , Yoshii Taishi , Miyatake Takahisa 
Published: September 2020

AbstractMany species show rhythmicity in activity, from the timing of flowering in plants to that of foraging behaviour in animals. The free-running periods and amplitude (sometimes called strength or power) of circadian rhythms are often used as indicators of biological clocks. Many reports have shown that these traits highly geographically variable, and interestingly, they often show latitudinal or altitudinal clines. In many cases, the higher the latitude is, the longer the free-running circadian period (i.e., period of rhythm) in insects and plants. However, reports of positive correlations between latitude or longitude and circadian rhythm traits, including free-running periods, the power of the rhythm and locomotor activity, are limited to certain taxonomic groups. Therefore, we collected a cosmopolitan stored-product pest species, the red flour beetleTribolium castaneum, in various parts of Japan and examined its rhythm traits, including the power of the rhythm and period of the rhythm, which were calculated from locomotor activity. The analysis revealed that power was significantly lower for beetles collected in northern areas compared with southern areas in Japan. However, it is worth noting that the period of circadian rhythm did not show any clines; specifically, it did not vary among the sampling sites, despite the very large sample size (n = 1585). We discuss why these cline trends were observed inT. castaneum.
Idiosyncratic Tower of Babel: Individual differences in word meaning representation increase along abstractness
Authors: Wang Xiaosha , Bi Yanchao 
Published: September 2020

AbstractHumans primarily rely on language to communicate, based on a shared understanding of the basic building blocks of communication: words. However, words also have idiosyncratic aspects of meaning. Do we mean the same things when we use the same words? Classical philosophers disagreed on this point, speculating that words have more similar meanings across individuals if they are either more experiential (John Locke) or more abstract (Bertrand Russell). Here, we empirically characterize the individual variation pattern of 90 words using both behavioral and neuroimaging measures. We show that the magnitude of individual meaning disagreement is a function of how much language or sensory experience a word associates with, and this variation increases with abstractness of a word. Uncovering the cognitive and neural origins of word meaning disagreements across individuals has implications for potential mechanisms to modulate such disagreements.
Temporal and genomic analysis of additive genetic variance in breeding programmes
Authors: Lara Letícia A. de C. , Pocrnic Ivan , Gaynor R. Chris , Gorjanc Gregor 
Published: September 2020

AbstractThis study demonstrates a framework for temporal and genomic analysis of additive genetic variance in a breeding programme. Traditionally we used specific experimental designs to estimate genetic variance for a specific group of individuals and a general pedigree-based model to estimate genetic variance for pedigree founders. However, with the pedigree-based model we can also analyse temporal changes in genetic variance by summarising sampled realisations of genetic values from a fitted model. Here we extend this analysis to a marker-based model and build a framework for temporal and genomic analyses of genetic variance. The framework involves three steps: (i) fitting a marker-based model to data, (ii) sampling realisations of marker effects from the fitted model and for each sample calculating realisations of genetic values, and (iii) calculating variance of the sampled genetic values by time and genome partitions. Genome partitions enable estimation of contributions from chromosomes and chromosome pairs and genic and linkage-disequilibrium variances. We demonstrate the framework by analysing data from a simulated breeding programme involving a complex trait with additive gene action. We use the full Bayesian and empirical Bayesian approaches to account for the uncertainty due to model fitting. We also evaluate the use of principal component approximation. Results show good concordance between the simulated and estimated variances for temporal and genomic analyses and give insight into genetic processes. For example, we observe reduction of genic variance due to selection and drift and buildup of negative linkage-disequilibrium (the Bulmer effect) due to directional selection. In this study the popular empirical Bayesian approach estimated the variances well but it underestimated uncertainty of the estimates. The principal components approximation biases estimates, in particular for the genic variance. This study gives breeders a framework to analyse genetic variance and its components in different stages of a programme and over time.
Anatomy, transcription dynamics and evolution of wheat ribosomal RNA loci deciphered by a multi-omics approach
Authors: Tulpová Zuzana , Kovařík Aleš , Toegelová Helena , Navrátilová Pavla , Kapustová Veronika , Hřibová Eva , Vrána Jan , Macas Jiří , Doležel Jaroslav , Šimková Hana 
Published: September 2020

AbstractBackground and AimsThree out of four RNA components of ribosomes are encoded by 45S rDNA loci, whose transcripts are processed into 18S, 5.8S and 26S ribosomal RNAs. The loci are organized as long head-to-tail tandem arrays of nearly identical units spanning over several megabases of sequence. Due to this peculiar structure, the number of rRNA genes, their sequence composition and expression status remain unclear, especially in complex polyploid genomes harbouring multiple loci. Here we conducted a complex study to decipher structure and activity of both major and minor rRNA loci in hexaploid bread wheat (Triticum aestivum).MethodsWe employed an original, multi-omics approach, combining chromosome flow sorting and optical mapping with transcriptome and methylome sequencing.Key ResultsThe former two techniques enabled unbiased quantification of rDNA units in particular loci of the wheat genome. Total number of rRNA genes organized in tandem arrays was 4388, with 64.1, 31.4, 3.9 and 0.7% located in short arms of chromosomes 6B, 1B, 5D and 1A, respectively. At the expression level, only 1B and 6B loci contributed to transcription at roughly 2:1 ratio. The 1B:6B ratio varied among five analysed tissues (embryo, coleoptile, root tip, primary leaf, mature leaf), being the highest (2.64:1) in mature leaf and lowest (1.72:1) in coleoptile. Cytosine methylation was considerably higher in CHG contexts in the silenced 5D locus compared to the active 1B and 6B loci.ConclusionsA fine genomic organization and tissue-specific expression of rRNA loci were deciphered, for the first time, in a complex polyploid species. We documented various mechanisms of rRNA dosage control, including gene elimination and stable inactivation related to nucleolar subdominance of A and D-genome loci, and a subtle, developmentally regulated silencing of one of the major loci. The results are discussed in the context of wheat evolution and transcription regulation.
Grazing impacts on ground beetle (Coleoptera: Carabidae) abundance and diversity on a semi-natural grassland
Authors: Pozsgai Gabor , Quinzo-Ortega Luis , Littlewood Nick A. 
Published: September 2020

AbstractSemi-natural grasslands are commonly managed as a grazing resource for domestic livestock but, due to their unique biodiversity, they are also of conservation interest. Numerous drivers have impacted on the status of these grasslands in recent decades, most importantly changing grazing management strategies. These changes have the potential to affect the biodiversity associated with these habitats, including on some rich invertebrate assemblages. Responses, however, are often dissimilar between different invertebrate taxa.We investigated the responses of ground beetles to different grazing regimes within a long-term grazing experiment on upland semi-natural grassland in Scotland. Although there was substantial overlap between ground beetle assemblages in different grazing treatments, species richness, mean abundance and Shannon diversity of ground beetles were significantly lower in ungrazed plots than in plots subject to high- or low-intensity sheep grazing. Ground beetle abundance (but not species richness or diversity) were lower in ungrazed plots compared to those with low-intensity mixed grazing by sheep and cattle. However, no differences were identified in abundance, species richness or diversity between the three grazed treatments.Our results suggest that ground beetles may show different responses to grazing compared to responses of some other invertebrate groups and demonstrates the difficulty of carrying out management for a multi-taxon benefit.
Haplotype-resolved genome assembly enables gene discovery in the red palm weevilRhynchophorus ferrugineus
Authors: Dias Guilherme B. , Altammami Musaad A. , El-Shafie Hamadttu A.F. , Alhoshani Fahad M. , Al-Fageeh Mohamed B. , Bergman Casey M. , Manee Manee M. 
Published: September 2020

ABSTRACTThe red palm weevilRhynchophorus ferrugineus(Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function inR. ferrugineushas the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly forR. ferrugineusfrom a single heterozygous individual with modest sequencing coverage (~62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in ourR. ferrugineusgenome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci inR. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6,000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% ofR. ferrugineuschemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.
RetroCHMP3 Blocks Budding of Enveloped Viruses Without Blocking Cytokinesis
Authors: Rheinemann Lara , Downhour Diane Miller , Bredbenner Kate , Mercenne Gaelle , Davenport Kristen A. , Schmitt Phuong Tieu , Necessary Christina R. , McCullough John , Schmitt Anthony P. , Simon Sanford M. , Sundquist Wesley I. , Elde Nels C. 
Published: September 2020

SummaryMany enveloped viruses require the endosomal sorting complexes required for transport (ESCRT) pathway to exit infected cells. This highly conserved pathway mediates essential cellular membrane fission events, which restricts the acquisition of adaptive mutations to counteract viral co-option. Here, we describe duplicated and truncated copies of the ESCRT-III factor CHMP3 that block ESCRT-dependent virus budding and that arose independently in New World monkeys and mice. When expressed in human cells, these retroCHMP3 proteins potently inhibit release of retroviruses, paramyxoviruses, and filoviruses. Remarkably, retroCHMP3 proteins have evolved to reduce interactions with other ESCRT-III factors and to have little effect on cellular ESCRT processes, revealing routes for decoupling cellular ESCRT functions from viral exploitation. The repurposing of duplicated ESCRT-III proteins thus provides a mechanism to generate broad-spectrum viral budding inhibitors without blocking highly conserved essential cellular ESCRT functions.
Theta oscillations shift towards optimal frequency for cognitive control
Authors: Senoussi Mehdi , Verbeke Pieter , Desender Kobe , De Loof Esther , Talsma Durk , Verguts Tom 
Published: September 2020

AbstractCognitive control is supported by theta band (4-7Hz) neural oscillations coordinating neural populations for task implementation. Task performance has been shown to depend on theta amplitude but a second critical aspect of theta oscillations, its peak frequency, has mostly been overlooked. Using modelling, behavioral and electrophysiological recordings, we show that theta oscillations adapt to task demands by shifting towards the optimal frequency.
Rab2 is a potent new target for enhancing autophagy in the treatment of Parkinson’s disease
Authors: Szinyákovics Janka , Kiss Eszter , Keresztes Fanni , Vellai Tibor , Kovács Tibor 
Published: September 2020

AbstractMacroautophagy is a lysosomal-dependent degradational pathway of eukaryotic cells, during which toxic, unnecessary, and damaged intracellular components are broken down. Autophagic activity declines with age, and this change could contribute to the accumulation of intracellular damage at advanced ages, causing cells to lose their functionality and vitality. This could be particularly problematic in post-mitotic cells include neurons, the mass destruction of which leads to different neurodegenerative diseases.We aim to discover new regulation points where autophagy could be specifically activated, and test these potential drug targets in Drosophila neurodegenerative disease models. One possible way to activate autophagy is through the enhancement of autophagosome-lysosome fusion to become autolysosome. This fusion is regulated by HOPS (homotypic fusion and protein sorting) and SNARE (Snap receptor) complexes. The HOPS complex forms a bridge between lysosome and autophagosome with the assistance of small GTPase Rab (Ras-associated binding) proteins. Thus, Rab proteins are essential for autolysosome maturation, and among Rab proteins, Rab2 is required for the degradation of autophagic cargo.Our results revealed that GTP-locked (constitutively active) Rab2 (Rab2 CA) expression reduces the levels of the autophagic substrate p62/Ref2P in dopaminergic neurons, and improved the climbing ability of animals during aging. The expression of Rab2 CA also increased lifespan in a Parkinson’s disease model (human mutant alpha-synuclein [A53T] overexpressed animals). In these animals, Rab2 CA expression significantly increased autophagic degradation as compared to control. These results may reveal a new, more specific drug target for autophagic activation treating today’s incurable neurodegenerative diseases.