bluuebunny/crossref_metadata_2025_split huggingface dataset:
Honeybee genetics shape the strain-level structure of gut microbiota in social transmission
Authors: Wu Jiaqiang , Lang Haoyu , Mu Xiaohuan , Zhang Zijing , Su Qinzhi , Hu Xiaosong , Zheng Hao 
Published: December 2020

AbstractHoneybee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honeybees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of queen, we hypothesize that the microbiota structure can be shaped by host genetics. We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of individuals from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and “sequence-discrete population”-level. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype ofSnodgrassella alviare preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. A genome-wide association analysis identified that the relative abundance of a cluster ofBifidobacteriumstrains is associated with the host glutamate receptor gene that is specifically expressed in the bee brain. Finally, mono-colonization ofBifidobacteriumwith a specific polysaccharide utilization locus impacts the expression and alternative splicing of thegluR-Bgene, which is associated with an altered circulating metabolomic profile. Our results indicated that host genetics influence the bee gut composition, and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honeybees have been used extensively as a model organism for social behaviors, genetics, and gut microbiome. Further identification of host genetic function as shaping force of microbial structure will advance our understanding of the host-microbe interactions.
League of Brazilian Bioinformatics: a competition framework to promote scientific training
Authors: Carvalho L. M. , Coimbra N. A. R. , Neves M. R. C. , Fonseca N. J. , Costa M. A. , Horacio E. C. A. , Riyuzo R. , Aburjaile F. F. , Nagamatsu S. T. 
Published: December 2020

AbstractBackgroundthe scientific training to become a bioinformatician includes multidisciplinary abilities, which increase the challenges to professional development.Competition frameworkin order to improve and promote the ongoing training of the Brazilian bioinformatics community, we organize a national competition, with the main goal to develop human resources and abilities in Computational Biology at the national level. The competition framework was designed in three phases: 1) a one-day challenge composed of 60 multiple-choice questions covering Biology, Computer Science, and Bioinformatics knowledge; 2) five Computational Biology challenges to be solved in three days; and 3) development of an original project evaluated during the 15th X-meeting.Resultsthe first edition of the League of Brazilian Bioinformatics (LBB) counted 168 competitors and 59 groups, distributed into undergraduate students (14.4%), graduate students (12.6% master and 16.8%, Ph.D.), and other professional fields. The first phase selected 46 teams to proceed in the competition, while the second phase selected the three top-performing teams.Conclusionduring the competition, we were able to stimulate teamwork in the main areas of Bioinformatics, with the engagement of all research-level competitors. Furthermore, we identified opportunities to deliver and offer better training to the community and we intend to apply the acquired experience in the second edition of the LBB, which will occur in 2021.Supplementary informationSupplementary data are available atBioinformatics
Is occupational physical activity associated with all-cause mortality in UK Biobank?
Authors: Pearce Matthew , Strain Tessa , Wijndaele Katrien , Sharp Stephen J. , Mok Alexander , Brage Soren 
Published: December 2020

ABSTRACTObjectivesTo investigate associations between occupational physical activity (OPA) and all-cause mortality.MethodsFrom baseline (2006-2010), 452,884 UK Biobank participants (aged 40-69 years) were followed for a median 11.1 (IQR: 10.4-11.8) years. OPA was categorised by cross-tabulating degree of manual work and walking/standing work amongst those in paid employment (n=264,424), whereas categories of occupational status were used for those not in paid employment (n=188,460). Cox proportional hazards models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for all-cause mortality by occupational category, and for working hours/week and non-occupational physical activity stratified by occupational category.ResultsDuring 4,965,616 person-years of follow-up, 23,310 deaths occurred. Compared to those in sedentary jobs, retirement was associated with lower mortality in women (HR=0.74, CI:0.68-0.81) and men (HR=0.85, CI:0.79-0.92), whereas unemployment was associated with higher mortality in men (HR=1.26, CI:1.10-1.45). There was no evidence of mortality differences by OPA category within the working population. Working <35 hours/week versus 35-40 hours/week was associated with lower mortality in both women (HR=0.86, CI:0.79-0.93) and men (HR=0.81, CI:0.75-0.88), with no interaction by OPA. Non-occupational physical activity was associated with lower mortality in both women (HR=0.90 per 5 kJ/day/kg, CI:0.84-0.96) and men (HR=0.88 per 5 kJ/day/kg, CI:0.84-0.92), with no interaction by OPA.ConclusionWork classified as having higher levels of OPA may not be as active as reported, or the types of physical activity performed in those jobs are not health-enhancing. Irrespective of OPA category or employment status, non-occupational physical activity appears to provide health benefits.SUMMARY BOXWhat are the new findings?Retirement was associated with lower all-cause mortality, compared to having a sedentary job in both men and women but unemployment was only associated with higher mortality in men.There were no differences in mortality between categories with different levels of self-reported OPAPhysical activity outside of work was associated with lower hazard of all-cause mortality and there was no interaction with occupational physical activity, indicating similar benefits across different jobs types.How might it impact on clinical practice in the future?Health professionals should be aware that occupations assumed to involve more physical activity may not be as active as reported, or the types of physical activity performed in those jobs may not be health-enhancing.Physical activity during leisure-time should continue to be recommended to adults of all paid and unpaid occupational categories.
Current evidence for COVID-19 therapies: a systematic literature review
Authors: Welte Tobias , Ambrose Lucy J. , Sibbring Gillian C. , Sheikh Shehla , Müllerová Hana , Sabir Ian 
Published: December 2020

AbstractEffective therapeutic interventions for the treatment and prevention of COVID-19 are urgently needed. A systematic review was conducted to identify clinical trials of pharmacological interventions for COVID-19 published between 1 December 2019 and 14 October 2020. Data regarding efficacy of interventions, in terms of mortality, hospitalisation and need for ventilation, were extracted from identified studies and synthesised qualitatively.In total, 42 clinical trials were included. Interventions assessed included antiviral, mucolytic, anti-malarial, anti-inflammatory and immunomodulatory therapies. Some reductions in mortality, hospitalisation and need for ventilation were seen with interferons and remdesivir, particularly when administered early, and with the mucolytic drug, bromhexine. Most studies of lopinavir/ritonavir and hydroxychloroquine did not show significant efficacy over standard care/placebo. Dexamethasone significantly reduced mortality, hospitalisation and need for ventilationversusstandard care, particularly in patients with severe disease. Evidence for other classes of interventions was limited. Many trials had a moderate-to-high risk of bias, particularly in terms of blinding; most were short-term; and some included low patient numbers.This review highlights the need for well-designed clinical trials of therapeutic interventions for COVID-19 to increase the quality of available evidence. It also emphasises the importance of tailoring interventions to disease stage and severity for maximum efficacy.
Bias Reduction through Analysis of Competing Events (BRACE): A Novel Method to Mitigate Bias from Residual Confounding in Observational Data
Authors: Mell Loren K. , Nelson Tyler , Thompson Caroline A. , Williamson Casey W. , Vitzthum Lucas K. , Zou Jingjing 
Published: December 2020

ABSTRACTPurposeTo introduce a method to mitigate bias from residual confounding in non-randomized data and examine its performance under varying conditions using simulated data.MethodsWe developed a method called Bias Reduction through Analysis of Competing Events (BRACE) based on a proportional relative hazards model. We followed recommended guidelines (ADEMP) established for the conduct of simulation studies. The primary estimand of interest was the treatment effect on the composite hazard for a primary or competing event. We compared the BRACE method to a standard Cox proportional hazards regression model in the presence of an unmeasured confounder, using a parametric (Weibull) simulation model. We examined estimator distributions, bias, mean squared error (MSE), and coverage probability for both methods using ridge, box-and-whisker, forest, and zip plots, respectively. Comparisons with a hypothetical validation estimate treating the confounder as measurable were also performed.ResultsWe presented 16 simulation scenarios under varying parameters. In simulations where residual confounding was present, the BRACE method uniformly reduced both bias and MSE compared to standard Cox models. In the scenario of moderate bias with an effective but non-toxic treatment, MSE was 3.51×10−2 with the standard model vs. 0.259×10−2 with the BRACE method. In the absence of bias, the BRACE method introduced bias toward the null (2.90 x10−2) compared to the standard method (0.331×10−2), albeit with lower MSE (0.341 x10−2 vs. 0.484 x10−2, respectively). Relative to the standard approach, the BRACE method markedly improved coverage probability, but with a tendency toward overcorrection in the case of the effective but non-toxic treatment. Conclusions were similar under different parameter assumptions.ConclusionThe BRACE method can reduce bias and MSE in the setting of residual confounding.
Glycyrrhizin effectively neutralizes SARS-CoV-2 in vitro by inhibiting the viral main protease
Authors: van de Sand L. , Bormann M. , Alt M. , Schipper L. , Heilingloh C.S. , Todt D. , Dittmer U. , Elsner C. , Witzke O. , Krawczyk A. 
Published: December 2020

AbstractThe newly emerged coronavirus, which was designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 disease. High effective and well-tolerated medication for hospitalized and non-hospitalized patients is urgently needed. Traditional herbal medicine substances were discussed as promising candidates for the complementary treatment of viral diseases and recently suggested for the treatment of COVID-19. In the present study, we investigated aqueous licorice root extract for its neutralizing activity against SARS-CoV-2in vitro, identified the active compound glycyrrhizin and uncovered the respective mechanism of viral neutralization. We demonstrated that glycyrrhizin, the primary active ingredient of the licorice root, potently neutralizes SARS-CoV-2 by inhibiting the viral main protease. Our experiments highlight glycyrrhizin as a potential antiviral compound that should be further investigated for the treatment of COVID-19.
Production, Reproduction and Adaptation characteristics of Boran cattle breed under changing climate: A systematic review and meta-analysis
Authors: Bayssa Merga , Yigrem Sintayehu , Betsa Simret , Tolera Adugna 
Published: December 2020

AbstractIntroductionClimate change has devastating effects on livestock production and productivity, which could threaten livestock-based food security in pastoral and agro-pastoral production systems of the tropics and sub-tropics. Hence, to sustain livestock production in an environment challenged by climate change, the animals must have the ability to survive and produce under extreme conditions. Boran cattle breed is one of the hardiest Zebu cattle reared by Borana Oromo pastoralists for milk and meat production. This paper aims to compile the main production, reproduction and adaptation traits of Boran cattle based on systematic review amd meta-analysis of peer reviewed and published articles on the subject.MethodologyCombination of systematic review and meta-analysis based on PRISMA guideline was employed. Accordingly, out of 646 recorded articles identified through database searching, 64 were found to be eligible for production, reproduction and adaptation characteristics of the Boran cattle, twenty-eight articles were included in qualitative systematic review while 36 articles were used for quantitative meta-analysis.ResultBoran cattle have diversity of adaptation (morphological, physiological, biochemical, metabolic, cellular and molecular) responses to the effects of climate change induced challenges - notably high temperature and solar radiation, rangeland degradation, seasonal feed and water shortages and high incidences of tropical diseases. Meta-analysis using a random-effects model showed estimates of heritability and genetic correlations for reproduction and production traits. In addition, heritability and genetic-correlation estimates found in the present study suggest that there is high genetic variability for most traits in Boran cattle, and that genetic improvement is possible for all studied traits in this breed.ConclusionThe review revealed that Boran cattle exhibit better reproduction, production and adaption potentials as compared to other indigenous zebu cattle breeds in Ethiopia under low-land, poor pasture and water conditions. On other hand, the breed is currently challenged by adverse effects of climate change and other management factors such as high rate of genetic dilution, reduced rangeland productivity, lack of organized breed improvement programs and discriminate selection of gene pool. Thus, we recommend strategic breed improvement and genetic conservation program of Boran cattle breed in collaboration with Borana pastoralists through proper quantification of important traits and estimation of the pure Boran cattle population while controlled cross breeding strategy could be used in urban and peri-urban areas for maximum utilization of adapataion and production pottential of this breed.
Meta-analysis of epigenome-wide associations between DNA methylation at birth and childhood cognitive skills
Authors: Caramaschi Doretta , Neumann Alexander , Cardenas Andres , Tindula Gwen , Alemany Silvia , Zillich Lea , Pesce Giancarlo , Lahti Jari M.T. , Havdahl Alexandra , Mulder Rosa , Felix Janine F. , Tiemeier Henning , Sirignano Lea , Frank Josef , Witt Stephanie H. , Rietschel Marcella , Deuschle Michael , Huen Karen , Eskenazi Brenda , Send Tabea Sarah , Ferrer Muriel , Gilles Maria , de Agostini Maria , Baïz Nour , Rifas-Shiman Sheryl L. , Kvist Tuomas , Czamara Darina , Tuominen Samuli T. , Relton Caroline L. , Rai Dheeraj , London Stephanie J. , Räikkönen Katri , Holland Nina , Annesi-Maesano Isabella , Streit Fabian , Hivert Marie-France , Oken Emily , Sunyer Jordi , Cecil Charlotte , Sharp Gemma 
Published: December 2020

ABSTRACTCognitive skills are a strong predictor of a wide range of later life outcomes. Genetic and epigenetic associations across the genome explain some of the variation in general cognitive abilities in the general population and it is plausible that epigenetic associations might arise from prenatal environmental exposures and/or genetic variation early in life. We investigated the association between cord blood DNA methylation at birth and cognitive skills assessed in children from eight pregnancy cohorts (N=2196-3798) within the Pregnancy And Childhood Epigenetics (PACE) Consortium across overall, verbal and non-verbal cognitive scores. The associations at single CpG sites were weak for all of the cognitive domains investigated. One region nearDUSP22on chromosome 6 was associated with non-verbal cognition in a model adjusted for maternal IQ. We conclude that there is little evidence to support the idea that cord blood DNA methylation at single CpGs can predict cognitive skills and further studies are needed to confirm regional differences.
Urban fox squirrels exhibit tolerance to humans but respond to stimuli from natural predators
Authors: Kittendorf Anna , Dantzer Ben 
Published: December 2020

AbstractAnimals in urban areas that experience frequent exposure to humans often behave differently than those in less urban areas, such as exhibiting less vigilance or anti-predator behavior. These behavioral shifts may be an adaptive response to urbanization, but it may be costly if animals in urban areas also exhibit reduced anti-predator behavior in the presence of natural predators. In trials with only a human observer as the stimulus, urban squirrels exhibited reduced vigilance and anti-predator behavior compared to those in less urban areas. Next, we exposed squirrels in multiple urban and less urban sites to acoustic playbacks of a control stimulus (non-predatory bird calls), a natural predator (hawk), and dogs and recorded their vigilance and three different anti-predator behaviors when a human approached them while either broadcasting one of these three playbacks or no playbacks at all. Squirrels at urban sites also did not differ in their behavioral responses to the playbacks from possible predators (hawks or dogs) when they were compared to those at less urban sites exposed to these playbacks. Urban squirrels also exhibited increased vigilance and anti-predator behavior when exposed to a human paired with hawk playbacks compared to the control playbacks. Together, our results indicate that urban squirrels did perceive and assess risk to the natural predator appropriately despite exhibiting increased tolerance to humans. These results provide little support for the hypothesis that increased tolerance to humans causes animals to lose their fear of natural predators.
The plot thickens: haploid and triploid-like thalli, hybridization, and biased mating type ratios inLetharia
Authors: Ament-Velásquez S. Lorena , Tuovinen Veera , Bergström Linnea , Spribille Toby , Vanderpool Dan , Nascimbene Juri , Yamamoto Yoshikazu , Thor Göran , Johannesson Hanna 
Published: December 2020

AbstractThe study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex and symbiotic lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal inLetharia. Here, we used genomic data from a pure culture and from thalli, together with a PCR survey of the MAT locus, to infer the genome organization and reproduction inLetharia. We found that the read count variation in the fourLethariaspecimens, including the pure culture derived from a single sexual spore ofL. lupina, is consistent with haploidy. By contrast, theL. lupinaread counts from a thallus’ metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America forL. vulpinaandL. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe forL. vulpina, consistent with predominant asexuality. Taken together, we propose thatLethariafungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are rare hybrids betweenL. lupinaand an unknownLetharialineage, reconciling classic systematic and genetic studies with recent genomic observations.
Neural heterogeneity promotes robust learning
Authors: Perez-Nieves Nicolas , Leung Vincent C. H. , Dragotti Pier Luigi , Goodman Dan F. M. 
Published: December 2020

AbstractThe brain has a hugely diverse, heterogeneous structure. Whether or not heterogeneity at the neural level plays a functional role remains unclear, and has been relatively little explored in models which are often highly homogeneous. We compared the performance of spiking neural networks trained to carry out tasks of real-world difficulty, with varying degrees of heterogeneity, and found that it substantially improved task performance. Learning was more stable and robust, particularly for tasks with a rich temporal structure. In addition, the distribution of neuronal parameters in the trained networks closely matches those observed experimentally. We suggest that the heterogeneity observed in the brain may be more than just the byproduct of noisy processes, but rather may serve an active and important role in allowing animals to learn in changing environments.SummaryNeural heterogeneity is metabolically efficient for learning, and optimal parameter distribution matches experimental data.
Alterations in excitatory and inhibitory synaptic development within the mesolimbic dopamine pathway in a mouse model of prenatal drug exposure
Authors: Boggess Taylor , Williamson James C. , Niebergall Ethan B. , Sexton Hannah , Mazur Anna , Egleton Richard D. , Grover Lawrence M. , Risher W. Christopher 
Published: December 2020

AbstractThe rise in rates of opioid abuse in recent years has led to an increase in the incidence of neonatal abstinence syndrome (NAS). Despite having a greater understanding of NAS and its symptoms, there still remains a lack of information surrounding the long-term effects of prenatal exposure to drugs of abuse on neurological development. One potential outcome of prenatal drug exposure that has been increasingly explored is disruption in normal synaptogenesis within the central nervous system. Both opioids and gabapentin, an antiepileptic drug commonly co-abused by opioid abuse disorder patients, have been shown to interfere with the normal functioning of astrocytes, non-neuronal glial cells known to serve many functions, including regulation of synaptic development. The goal of this study was to investigate the effects of prenatal drug exposure on synaptogenesis within brain regions associated with the mesolimbic dopamine pathway, the primary reward pathway within the brain associated with drug abuse and addiction, in a pregnant mouse model. Immunohistochemistry (IHC) and confocal fluorescence microscopy imaging studies on the brains of postnatal day 21 (P21) mouse pups revealed a significant increase in the mean number of excitatory synapses within the anterior cingulate cortex (ACC), nucleus accumbens (NAc), and prefrontal cortex (PFC) in mice that were prenatally exposed to either the opioid drug buprenorphine or gabapentin. These studies also revealed a significant decrease in the mean number of inhibitory synapses within the NAc and PFC of mice treated with buprenorphine. This observed net increase in excitatory signaling capability within the developing mesolimbic dopamine pathway suggests that exposure to drugs of abusein uterocan trigger maladaptive neuronal connectivity that persists beyond the earliest stages of life.