bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opposing mechanisms of competition determine species invasions and functional diversity
Authors: Wong Mark K. L. , Lee Roger H. , Leong Chi-Man , Lewis Owen T. , Guénard Benoit 
Published: January 2021

AbstractUnderstanding how species’ phenotypic differences affect competition is key to explaining community assembly and predicting biodiversity responses. Many studies overlook the variable effects that species’ trait differences can have on the direction of competitive exclusion, which reverses depending on the specific mechanism at play. We performed a comprehensive trait-based study of an ant invasion integrating morphological, dietary, physiological and behavioral analyses. We found that trait differences between invasive and resident species were not only associated with niche differences which promoted the coexistence of dissimilar species, but also competitive ability differences which acted in the opposite fashion. Furthermore, competition along separate trait axes led to complex and contrasting patterns in the invaded assemblages, where species were at once similar (clustered) in some traits but also dissimilar (overdispersed) in others. Our results reveal that different aspects of phenotype may distinctly modulate the effect of competition in structuring ecological communities and functional diversity.
Intrinsic reinstatement of induced oscillatory context
Authors: Chantrel Yoann , Trabattoni Valeria , Orton Lydia , Javadi Amir-Homayoun 
Published: January 2021

AbstractDeclarative memory retrieval is thought to rely on the reinstatement, at retrieval, of contextual cues present during encoding, as evidenced in the context and state-dependent literature. Specifically, previous work has shown that reinstating the oscillatory activity present during encoding, at retrieval, is particularly supportive of memory recall. Our study builds on previous findings suggesting that the oscillatory activity present at encoding may be automatically reinstated during retrieval. To explore the roles of consolidation, prefrontal involvement, and frequency specific activity in this process of oscillatory reinstatement, 115 healthy young adults were randomly assigned to one of five conditions. In each condition, transcranial alternating current stimulation (tACS) was administered at either one of two frequencies (60Hz or 6Hz), over the left dorsolateral prefrontal cortex (left-DLPFC, Experimental) or the right primary motor cortex (right-PMC, Control), during learning of written words. This was followed by a retention interval of either 90 minutes or 1 week and a testing phase, during which EEG activity was recorded. Our results showed significant (and frequency specific) oscillatory reinstatement, after stimulation of the left-DLPFC, in the 1-week retention condition. Oscillatory reinstatement effects were non-significant after stimulation of the right-PMC, or in the 90 minutes retention interval condition. Our results highlight that the oscillatory activity induced during encoding is consolidated as context alongside the information and is reinstated intrinsically during retrieval. The implications of our findings for models of human memory, future avenues of research and clinical applications are discussed.
Efficient Precision Dosing Under Estimated Uncertainties via Koopman Expectations of Bayesian Posteriors with Pumas
Authors: Rackauckas Chris , Dixit Vaibhav , Gerlach Adam R. , Ivaturi Vijay 
Published: January 2021

AbstractPersonalized precision dosing is about mathematically determining effective dosing strategies that optimize the probability of containing a patient’s outcome within a therapeutic window. However, the common Monte Carlo approach for generating patient statistics is computationally expensive because thousands of simulations need to be computed. In this manuscript we describe a new method which utilizes the Koopman operator to perform a direct computation of expected patient outcomes with respect to quantified uncertainties of Bayesian posteriors in a nonlinear mixed effect model framework. We detail how quantities such as the probability of being within the therapeutic window can be calculated with a choice of loss function on the Koopman expectation. We demonstrate a high performance parallelized implementation of this methodology in Pumas®and showcase the ability to accelerate the computation of these expectations by 50x-200x over Monte Carlo. We showcase how dosing can be optimized with respect to probabilistic statements respecting variable uncertainties using the Koopman operator. We end by demonstrating an end-to-end workflow, from estimating variable uncertainties via Bayesian estimation to optimizing a dose with respect to parametric uncertainty.
Network-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants
Authors: Saitou Marie. , Masuda Naoki , Gokcumen Omer. 
Published: January 2021

AbstractStructural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a network-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 577 structural variants that show high population distribution. We further showed that 39 and 20 of these putatively adaptive structural variants overlap with coding sequences or are significantly associated with GWAS traits, respectively. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to (i) population differentiation of rapidly evolving multi-allelic variants, (ii) incomplete sweeps, and (iii) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
The urea cycle is transcriptionally controlled by hypoxia-inducible factors
Authors: Singh Charandeep , Benos Andrew , Grenell Allison , Tran Vincent , Hanna Demiana , Anand-Apte Bela , Brunengraber Henri , Sears Jonathan E. 
Published: January 2021

AbstractHere, we demonstrate transcriptional regulation of urea cycle genes CPS1 and ARG1 by hypoxia-inducible factors (HIFs) and demonstrate a hepatic HIF dependent increase in urea cycle activity.
Ecology of active viruses and their bacterial hosts in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics
Authors: Trubl Gareth , Kimbrel Jeffrey A. , Liquet-Gonzalez Jose , Nuccio Erin E. , Weber Peter K. , Pett-Ridge Jennifer , Jansson Janet K. , Waldrop Mark P. , Blazewicz Steven J. 
Published: January 2021

AbstractWinter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake. However, most ecosystem carbon measurements neglect winter months since carbon losses (primarily driven by microbial decomposers) are assumed to be negligible at low temperatures. We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under winter conditions, with an emphasis on viruses and virus-host dynamics. Peat soils from the Bonanza Creek LTER site in Alaska were incubated under subzero anoxic conditions with H218O for 184 and 370 days. We identified 46 bacterial populations (MAGs; spanning 9 bacterial phyla) and 243 viral populations (vOTUs) that actively took up18O and produced significant CO2throughout the incubation. Active hosts, predicted for 33% of the active vOTUs, were some of the most abundant MAGs and capable of fermentation and organic matter degradation. Approximately three-quarters of the active vOTUs carried auxiliary metabolic genes that spanned five functional categories, including carbon utilization, highlighting the potential impact of viruses in this peat soil’s microbial biogeochemistry. These results illustrate significant bacterial and viral activity and interactions occur in frozen soils, revealing viruses are a major community-structuring agent throughout winter months.
Detour learning ability and the effect of novel sensory cues on learning in Australian bull ants,Myrmecia midas
Authors: Islam Muzahid , Deeti Sudhakar , Mahmudah Zakia , Kamhi J. Frances , Cheng Ken 
Published: January 2021

ABSTRACTMany animals navigate in a structurally complex environment which requires them to detour around physical barriers that they encounter. While many studies in animal cognition suggest that they are able to adeptly avoid obstacles, it is unclear whether a new route is learned to navigate around these barriers and, if so, what sensory information may be used to do so. We investigated detour learning ability in the Australian bull ant,Myrmecia midas, which primarily uses visual landmarks to navigate. We first placed a barrier on the ants’ natural path of their foraging tree. Initially, 46% of foragers were unsuccessful in detouring the obstacle. In subsequent trips, the ants became more successful and established a new route. We observed up to eight successful foraging trips detouring around the barrier. When we subsequently changed the position of the barrier, made a new gap in the middle of the obstacle, or removed the barrier altogether, ants mostly maintained their learned motor routine, detouring with a similar path as before, suggesting that foragers were not relying on barrier cues and therefore learned a new route around the obstacle. In additional trials, when foragers encountered new olfactory or tactile cues, or the visual environment was blocked, their navigation was profoundly disrupted. These results suggest that changing sensory information, even in modalities that foragers do not usually need for navigation, drastically affects the foragers’ ability to successful navigate.Subject CategoryNeuroscience and Cognition
Lack of trust and social media echo chambers predict COVID-19 vaccine hesitancy
Authors: Jennings Will , Stoker Gerry , Willis Hannah , Valgardsson Viktor , Gaskell Jen , Devine Daniel , McKay Lawrence , Mills Melinda C. 
Published: January 2021

AbstractAs COVID-19 vaccines are rolled out across the world, there are growing concerns about the role that trust, belief in conspiracy theories and spread of misinformation through social media impact vaccine hesitancy. We use a nationally representative survey of 1,476 adults in the UK between December 12 to 18, 2020 and five focus groups conducted in the same period. Trust is a core predictor, with distrust in vaccines in general and mistrust in government raising vaccine hesitancy. Trust in health institutions and experts and perceived personal threat are vital, with focus groups revealing that COVID-19 vaccine hesitancy is driven by a misunderstanding of herd immunity as providing protection, fear of rapid vaccine development and side effects, belief the virus is man- made and related to population control. Particularly those who obtain information from relatively unregulated social media sources such as YouTube that have recommendations tailored by watch history are less likely to be willing to become vaccinated. Those who hold general conspiratorial beliefs are less willing to be vaccinated. Since an increasing number of individuals use social media for gathering health information, interventions require action from governments, health officials and social media companies. More attention needs to help people understand their own risks, unpack complex concepts and fill knowledge voids.
Efficacy of Colchicine in Non-Hospitalized Patients with COVID-19
Authors: Tardif Jean-Claude , Bouabdallaoui Nadia , L’Allier Philippe L. , Gaudet Daniel , Shah Binita , Pillinger Michael H. , Lopez-Sendon Jose , da Luz Protasio , Verret Lucie , Audet Sylvia , Dupuis Jocelyn , Denault André , Pelletier Martin , Tessier Philippe A. , Samson Sarah , Fortin Denis , Tardif Jean-Daniel , Busseuil David , Goulet Elisabeth , Lacoste Chantal , Dubois Anick , Joshi Avni Y. , Waters David D. , Hsue Priscilla , Lepor Norman E. , Lesage Frédéric , Sainturet Nicolas , Roy-Clavel Eve , Bassevitch Zohar , Orfanos Andreas , Grégoire Jean C. , Busque Lambert , Lavallée Christian , Hétu Pierre-Olivier , Paquette Jean-Sébastien , Levesque Sylvie , Cossette Mariève , Nozza Anna , Chabot-Blanchet Malorie , Dubé Marie-Pierre , Guertin Marie-Claude , Boivin Guy ,   for the COLCORONA Investigators
Published: January 2021

ABSTRACTBackgroundEvidence suggests the role of an inflammatory storm in COVID-19 complications. Colchicine is an orally administered, anti-inflammatory medication beneficial in gout, pericarditis and coronary disease.MethodsWe performed a randomized, double-blind trial involving non-hospitalized patients with COVID-19 diagnosed by polymerase chain reaction (PCR) testing or clinical criteria. The patients were randomly assigned to receive colchicine (0.5 mg twice daily for 3 days and once daily thereafter) or placebo for 30 days. The primary efficacy endpoint was the composite of death or hospitalization for COVID-19.ResultsA total of 4488 patients were enrolled. The primary endpoint occurred in 4.7% of the patients in the colchicine group and 5.8% of those in the placebo group (odds ratio, 0.79; 95.1% confidence interval (CI), 0.61 to 1.03; P=0.08). Among the 4159 patients with PCR-confirmed COVID-19, the primary endpoint occurred in 4.6% and 6.0% of patients in the colchicine and placebo groups, respectively (odds ratio, 0.75; 95% CI, 0.57 to 0.99; P=0.04). In these patients with PCR-confirmed COVID-19, the odds ratios were 0.75 (95% CI, 0.57 to 0.99) for hospitalization due to COVID-19, 0.50 (95% CI, 0.23 to 1.07) for mechanical ventilation, and 0.56 (95% CI, 0.19 to 1.66) for death. Serious adverse events were reported in 4.9% and 6.3% in the colchicine and placebo groups (P=0.05); pneumonia occurred in 2.9% and 4.1% of patients (P=0.02). Diarrhea was reported in 13.7% and 7.3% in the colchicine and placebo groups (P<0.0001).ConclusionAmong non-hospitalized patients with COVID-19, colchicine reduces the composite rate of death or hospitalization. (COLCORONAClinicalTrials.govnumber:NCT04322682)
The Association Between Hypoglycemic Agents and Clinical Outcomes of COVID-19 in Patients with Diabetes: A Systematic Review and Meta-Analysis
Authors: Han Tiantian , Ma Shaodi , Sun Chenyu , Zhang Huimei , Qu Guangbo , Chen Yue , Cheng Ce , Chen Eric L. , Ahmed Mubashir Ayaz , Kim Keun Young , Manem Reveena , Chen Mengshi , Guo Zhichun , Yang Hongru , Yan Yue , Zhou Qin 
Published: January 2021

AbstractBackgroundDuring the current Coronavirus Disease 2019 (COVID-19) pandemic, diabetic patients face disproportionately more. Anti-inflammatory effects of hypoglycemic agents have been reported, and their beneficial or harmful effects in patients with diabetes and COVID-19 remain controversial.PurposeThis study was performed to clarify this association.Data SourcesRelevant literature was searched on China National Knowledge Infrastructure (CNKI), Wanfang Data Knowledge Service Platform, Chinese periodical service platform VIP Database, Sinomed (China Biology Medicine, CBM), MedRxiv, PubMed, ScienceDirect, Web of Science, Ovid Databases (LWW), Springer Link, Wiley Online Library, Oxford Academic, Nature Press Group, Cochrane Library and BMJ Evidence-Based Medicine up to November 14, 2020.Study SelectionOnly observational studies of hypoglycemic agents vs. drugs or therapy without hypoglycemic agents in adult diabetic patients with COVID-19 were included.Data ExtractionData of death and poor composite outcomes were extracted.Data SynthesisThe pooled effects were calculated using the fixed-effects or random-effects models based on heterogeneity assessment.LimitationMost studies were retrospective cohort studies with relative weak capability to verify causality.ConclusionHome use of metformin might be beneficial in decreasing mortality in diabetic patients infected with SARS-CoV-2. There is insufficient evidence to conclude that metformin and other hypoglycemic agents are associated with poor composite outcomes. More prospective studies, especially RCTs are needed.Registration-PROSPEROCRD42020221951.
Bolstering fitness via opportunistic CO2fixation: mixotroph dominance in modern groundwater
Authors: Taubert Martin , Overholt Will A. , Heinze Beatrix M. , Matanfack Georgette Azemtsop , Houhou Rola , Jehmlich Nico , von Bergen Martin , Rösch Petra , Popp Jürgen , Küsel Kirsten 
Published: January 2021

AbstractThe current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically-fixed carbon, the flux of CO2-derived carbon through various subpopulations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here, we implement novel stable isotope cluster analysis to render a time-resolved and quantitative evaluation of13CO-derived carbon flow through a groundwater microbiome stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not obligate chemolithoautotrophs, were the most abundant active organisms in groundwater microcosms. Species ofHydrogenophaga,Polaromonas,Dechloromonas, and other metabolically versatile mixotrophs drove the recycling of organic carbon and, when chance afforded, supplemented their carbon requirements via chemolithoautotrophy and uptake of available organic compounds. Mixotrophic activity facilitated the replacement of 43 and 80% of total microbial carbon stores with13C in just 21 and 70 days, respectively. This opportunistic “utilize whatever pathways net the greatest advantage in fitness” strategy may explain the great abundances of mixotrophs in other oligotrophic habitats, like the upper ocean and boreal lakes.
Determining significant correlation between pairs of extant characters in a small parsimony framework
Authors: Khandai Kaustubh , Navarro-Martinez Cristian , Smith Brendan , Buonopane Rebecca , Byun S. Ashley , Patterson Murray 
Published: January 2021

AbstractWhen studying the evolutionary relationships among a set of species, the principle of parsimony states that a relationship involving the fewest number of evolutionary events is likely the correct one. Due to its simplicity, this principle was formalized in the context of computational evolutionary biology decades ago by,e.g., Fitch and Sankoff. Because the parsimony framework does not require a model of evolution, unlike maximum likelihood or Bayesian approaches, it is often a good starting point when no reasonable estimate of such a model is available.In this work, we devise a method for determining if pairs of discrete characters are significantly correlated across all most parsimonious reconstructions, given a set of species on these characters, and an evolutionary tree. The first step of this method is to use Sankoff’s algorithm to computeallmost parsimonious assignments of ancestral states (of each character) to the internal nodes of the phylogeny. Correlation between a pair of evolutionary events (e.g., absent to present) for a pair of characters is then determined by the (co-) occurrence patterns between the sets of their respective ancestral assignments. The probability of obtaining a correlation this extreme (or more) under a null hypothesis where the events happen randomly on the evolutionary tree is then used to assess the significance of this correlation. We implement this method:parcours(PARsimonious CO-occURrenceS) and use it to identify significantly correlated evolution among vocalizations and morphological characters in the Felidae family.Theparcourstool is freely available athttps://github.com/murraypatterson/parcours
Proteomic characterization of GSK3β knockout shows altered cell adhesion and metabolic pathway utilisation in colorectal cancer cells.
Authors: Bowler-Barnett E.H. , Martinez-Garcia F. D. , Sherwood M. , Weston S. , Wang Y. , Divecha N. , Skipp P. , Ewing R.M. 
Published: January 2021

ABSTRACTGlycogen-specific kinase (GSK3β) is an integral regulator of the Wnt signalling pathway as well as many other diverse signalling pathways and processes. Dys-regulation of GSK3β is implicated in many different pathologies, including neurodegenerative disorders as well as many different tumour types. In the context of tumour development, GSK3β has been shown to play both oncogenic and tumour suppressor roles, depending upon tissue, signalling environment or disease progression. Although multiple substrates of the GSK3β kinase have been identified, the wider protein networks within which GSK3β participates are not well known, and the consequences of these interactions not well understood. In this study, LC-MS/MS expression analysis was performed using knockout GSK3β colorectal cancer cells and isogenic controls in colorectal cancer cell lines carrying dominant stabilizing mutations of β-Catenin. Consistent with the role GSK3β, we found that β-Catenin levels and canonical Wnt activity are unaffected by knockout of GSK3β and therefore use this knockout cell model to identify other processes in which GSK3β is implicated. Quantitative proteomic analysis revealed perturbation of proteins involved in cell-cell adhesion, and we characterize the phenotype and altered proteomic profiles associated with this. We also characterize the perturbation of metabolic pathways resulting from GSK3β knockout and identify defects in glycogen metabolism. In summary, using a precision colorectal cancer cell-line knockout model with constitutively activated β-Catenin we are able to identify several of the diverse pathways and processes associated with GSK3β function.
Modulation of the spontaneous brain activity and functional connectivity in the triple resting-state networks following the visual oddball paradigm
Authors: Sbaihat Hasan , Rajkumar Ravichandran , Ramkiran Shukti , Assi Abed Al-Nasser , Shah N. Jon , Veselinović Tanja , Neuner Irene 
Published: January 2021

AbstractThe default mode network (DMN), the salience network (SN), and the central executive network (CEN) could be considered as the core resting-state brain networks (RSN) due to their involvement in a wide range of cognitive tasks. Despite the large body of knowledge relating to their regional spontaneous activity (RSA) and functional connectivity (FC) of these networks, less is known about the influence of task-associated activity on these parameters and on the interaction between these three networks. We have investigated the effects of the visual-oddball paradigm on three fMRI measures (amplitude of low-frequency fluctuations for RSA, regional homogeneity for local FC, and degree centrality for global FC) in these three core RSN networks. A rest-task-rest paradigm was used and the RSNs were identified using independent component analysis (ICA) on the resting-state data. We found that the task-related brain activity induced different patterns of significant changes within the three RS networks. Most changes were strongly associated with the task performance. Furthermore, the task-activity significantly increased the inter-network correlations between the SN and CEN as well as between the DMN and CEN, but not between the DMN and SN. A significant dynamical change in RSA, alongside local and global FC within the three core resting-state networks following a simple cognitive activity may be an expression of the distinct involvement of these networks in the performance of the task and their various outcomes.