bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensory- and memory-related drivers for altered ventriloquism effects and aftereffects in older adults
Authors: Park Hame , Nannt Julia , Kayser Christoph 
Published: February 2020

ABSTRACTThe manner in which humans exploit multisensory information for subsequent decisions changes with age. Multiple causes for such age-effects are being discussed, including a reduced precision in peripheral sensory representations, changes in cognitive inference about causal relations between sensory cues, and a decline in memory contributing to altered sequential patterns of multisensory behaviour. To dissociate these putative contributions, we investigated how healthy young and older adults integrate audio-visual spatial information within trials (the ventriloquism effect) and between trials (the ventriloquism aftereffect). With both a model-free and (Bayesian) model-based analyses we found that both biases differed between groups. Our results attribute the age-change in the ventriloquism bias to a decline in spatial hearing rather than a change in cognitive processes. This decline in peripheral function, combined with a more prominent influence from preceding responses rather than preceding stimuli in the elderly, can also explain the observed age-effect in the ventriloquism aftereffect. Our results suggest a transition from a sensory- to a behavior-driven influence of past multisensory experience on perceptual decisions with age, due to reduced sensory precision and change in memory capacity.
Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast
Authors: Malecki Michal , Kamrad Stephan , Ralser Markus , Bähler Jürg 
Published: February 2020

AbstractWhen glucose is available, many organisms repress mitochondrial respiration in favour of aerobic glycolysis, or fermentation in yeast, that suffices for ATP production. Fission yeast cells, however, rely partially on respiration for rapid proliferation under fermentative conditions. Here we determined the limiting factors that require respiratory function during fermentation. When the electron transport chain was inhibited, supplementation with arginine was necessary and sufficient to restore rapid cell proliferation. Accordingly, a systematic screen for mutants growing poorly without arginine identified not only mutants defective in arginine synthesis but also mutants defective in mitochondrial oxidative metabolism. Genetic or pharmacological inhibition of respiration triggered a drop in intracellular levels of arginine and amino acids derived from the Krebs-cycle metabolite alpha-ketoglutarate: glutamine, lysine and glutamic acid. Conversion of arginine into these amino acids was required for rapid proliferation when the respiratory chain was blocked. The respiratory block triggered an immediate gene-expression response diagnostic of TOR inhibition, which was muted by arginine supplementation or without the AMPK-activating kinase Ssp1. The TOR-controlled proteins featured biased composition of amino acids reflecting their shortage after respiratory inhibition. We conclude that respiration supports rapid proliferation in fermenting cells of fission yeast by boosting the supply of Krebs-cycle derived amino acids.
Cryptic diversity in the model fern genusCeratopteris(Pteridaceae)
Authors: Kinosian Sylvia P. , Pearse William D. , Wolf Paul G. 
Published: February 2020

AbstractCryptic species are present throughout the tree of life. They are especially prevalent in ferns, because of processes such hybridization, polyploidy, and reticulate evolution. In addition, the morphological simple body plan of ferns limits phenotypic variation and makes it difficult to detect crypic species in ferns without molecular work. The model fern genusCeratopterishas long been suspected to harbor cryptic diversity, specifically in the highly polymorphicC. thalictroides. Yet no studies have included samples from throughout the pan-tropical range ofCeratopterisor utilized genomic sequencing, making it difficult to assess the full extent of cryptic variation within this genus. Here, we present the first multilocus phylogeny of the genus using reduced representation genomic sequencing (RADseq) and examine population structure, phylogenetic relationships, and ploidy level variation. We recover similar species relationships found in previous studies, find support for a named cryptic species as genetically distinct, and identify a novel putative species from withinC. thalictroides sensu latuin Central and South America.
The estrogenic pathway modulates non-breeding female aggression in a teleost fish
Authors: Zubizarreta Lucía , Silva Ana C. , Quintana Laura 
Published: February 2020

AbstractAggressive behaviors are widespread among animals and are critical in the competition for resources. The physiological mechanisms underlying aggression have mostly been examined in breeding males, in which gonadal androgens, acting in part through their aromatization to estrogens, have a key role. There are two alternative models that contribute to further understanding hormonal mechanisms underlying aggression: aggression displayed in the non-breeding season, when gonadal steroids are low, and female aggression. In this study we approach, for the first time, the modulatory role of estrogens and androgens upon non-breeding aggression in a wild female teleost fish. We characterized female aggression in the weakly electric fishGymnotus omarorumand carried out acute treatments 1 h prior to agonistic encounters with either an aromatase inhibitor or an antagonist of androgen receptors. Aromatase inhibition caused a strong distortion of aggressive behavior whereas anti-androgen treatment had no effect on behavior. Territorial non-breeding aggression in femaleG. omarorumis robust and depended on rapid estrogen actions to maintain high levels of aggression, and ultimately reach conflict resolution from which dominant/subordinate status emerged. Our results taken together with our own reports in males and the contributions from non-breeding aggression in bird and mammal models, suggest a conserved strategy involving fast-acting estrogens in the control of this behavior across species. In addition, further analysis of female non-breeding aggression may shed light on potential sexual differences in the fine tuning of social behaviors.HighlightsFemaleGymnotus omarorumdisplayed robust territorial aggression in lab settings.Acute treatment with aromatase inhibitor lowered aggression levels.Aromatase inhibition increased first attack latency and decreased conflict resolution.Acute treatment with anti-androgens showed no effects.This is the first report of estrogens underlying teleost non-breeding female aggression.
How young is your Muscle? A Machine Learning framework for motor functional assessment with ageing by NMF based analysis of HD-sEMG signal
Authors: Banerjee Swati , Boudaoud Sofiane , Kinugawa-Burron Kiyoka 
Published: February 2020

AbstractObjectiveWith ageing, there are various changes in the autonomic nervous system and a simultaneous decline in the motor functional abilities of the human body. This study falls within the framework improvement of the clinical tools dedicated to the robust evaluation of motor function efficiency with ageing.MethodAnalysis of HD-sEMG signals recorded from 32 channels during Sit To Stand (STS) test are used for the functional assessment of body muscles. For this purpose, five primary characteristic features,iEMG, ARV, RMS, Skewness, Kurtosis, are employed for the study. A channel clustering approach is proposed based on the parameters using Non Negative Matrix Factorization (NMF).ResultsThe NMF based clustering of the HD-sEMG channels seems to be sensitive toward modifications of the muscle activation strategy with ageing during STS test.ConclusionThis manuscript provides a framework for the assessment of Motor Functional Age(MFA) of subjects having a range of chronological from 25 yrs to 75 yrs. The groups were made a decade apart and it was found that the MFA varies with the level of activeness of the muscle under study and a premature ageing is observed according to the change in activation pattern of the HD-sEMG grid.
Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties
Authors: Danczak Robert E. , Goldman Amy E. , Chu Rosalie K. , Toyoda Jason G. , Garayburu-Caruso Vanessa A. , Tolić Nikola , Graham Emily B. , Morad Joseph W. , Renteria Lupita , Wells Jacqueline R. , Herzog Skuyler P. , Ward Adam S. , Stegen James C. 
Published: February 2020

AbstractStream and river systems transport and process substantial amounts of dissolved organic matter (DOM) from terrestrial and aquatic sources to the ocean, with global biogeochemical implications. However, the underlying mechanisms affecting the spatiotemporal organization of DOM composition are under-investigated. To understand the principles governing DOM composition, we leverage the recently proposed synthesis of metacommunity ecology and metabolomics, termed ‘meta-metabolome ecology.’ Applying this novel approach to a freshwater ecosystem, we demonstrated that despite similar molecular properties across metabolomes, metabolite identity significantly diverged due to environmental filtering. We refer to this phenomenon as ‘thermodynamic redundancy,’ which is analogous to the ecological concept of functional redundancy. We suggest that under thermodynamic redundancy, divergent metabolomes can support equivalent biogeochemical function just as divergent ecological communities can support equivalent ecosystem function. As these analyses are performed in additional ecosystems, potentially generalizable principles, like thermodynamic redundancy, can be revealed and provide insight into DOM dynamics.
No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells
Authors: McGinnis Christopher S. , Siegel David A. , Xie Guorui , Stone Mars , Gartner Zev J. , Roan Nadia R. , Lee Sulggi A. 
Published: February 2020

ABSTRACTSingle-cell RNA sequencing (scRNA-seq) provides high-dimensional measurement of transcript counts in individual cells. However, high assay costs limit the study of large numbers of samples. Sample multiplexing technologies such as antibody hashing and MULTI-seq use sample-specific sequence tags to enable individual samples (e.g., different patients) to be sequenced in a pooled format before downstream computational demultiplexing. Critically, no study to date has evaluated whether the mixing of samples from different donors in this manner results in significant changes in gene expression resulting from alloreactivity (i.e., response to non-self immune antigens). The ability to demonstrate minimal to no alloreactivity is crucial to avoid confounded data analyses, particularly for cross-sectional studies evaluating changes in immunologic gene signatures,. Here, we compared the expression profiles of peripheral blood mononuclear cells (PBMCs) from a single donor with and without pooling with PBMCs isolated from other donors with different blood types. We find that there was no evidence of alloreactivity in the multiplexed samples following three distinct multiplexing workflows (antibody hashing, MULTI-seq, andin silicogenotyping using souporcell). Moreover, we identified biases amongst antibody hashing sample classification results in this particular experimental system, as well as gene expression signatures linked to PBMC preparation method (e.g., Ficoll-Paque density gradient centrifugation with or without apheresis using Trima filtration).
Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants
Authors: Hicks Allison L. , Kissler Stephen M. , Mortimer Tatum D. , Ma Kevin C. , Taiaroa George , Ashcroft Melinda , Williamson Deborah A. , Lipsitch Marc , Grad Yonatan H. 
Published: February 2020

AbstractGenotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate and ineffective antibiotic use. However, because such assays infer resistance phenotypes based on the presence or absence of known genetic markers, their utility will wane in response to the emergence of novel resistance. Maintenance of these diagnostics will therefore require surveillance designed to ensure early detection of novel resistance variants, but efficient strategies to do so remain to be defined. Here, we evaluate the efficiency of targeted sampling approaches informed by patient and pathogen characteristics in detecting genetic variants associated with antibiotic resistance or diagnostic escape inNeisseria gonorrhoeae, focusing on this pathogen because of its high burden of disease, the imminent threat of treatment resistance, and the use and ongoing development of genotype-based diagnostics. We show that incorporating patient characteristics, such as demographics, geographic regions, or anatomical sites of isolate collection, into sampling approaches is not a reliable strategy for increasing variant detection efficiency. In contrast, sampling approaches informed by pathogen characteristics, such as genomic diversity and genomic background, are significantly more efficient than random sampling in identifying genetic variants associated with antibiotic resistance and diagnostic escape.
Metagenomic insights into the metabolism and ecologic functions of the widespread DPANN archaea from deep-sea hydrothermal vents
Authors: Cai Ruining , Zhang Jing , Liu Rui , Sun Chaomin 
Published: February 2020

ABSTRACTDue to the particularity of metabolism and the importance of ecological roles, the archaea living in deep-sea hydrothermal system always attract great attention. Included, the DPANN superphylum archaea, which are massive radiation of organisms, distribute widely in hydrothermal environment, but their metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes comprised in 43 reconstructed genomes from deep-sea hydrothermal sediments, presenting high abundance in the archaea kingdom. Phylogenetic analysis shows 6 phyla comprising Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota and a new candidate phylum designated DPANN-HV-2 are included in the 20 DPANN archaeal members, indicating their wide diversity in this extreme environment. Metabolic analysis presents their metabolic deficiencies because of their reduced genome size, such as gluconeogenesis,de novonucleotide and amino acid synthesis. However, they possess alternative and economical strategies to fill this gap. Furthermore, they were detected to have multiple capacities of assimilating carbon dioxide, nitrogen and sulfur compounds, suggesting their potentially important ecologic roles in the hydrothermal system.IMPORTANCEDPANN archaea show high distribution in the hydrothermal system. However, they possess small genome size and some incomplete biological process. Exploring their metabolism is helpful to know how such small lives adapt to this special environment and what ecological roles they play. It was ever rarely noticed and reported. Therefore, in this study, we provide some genomic information about that and find their various abilities and potential ecological roles. Understanding their lifestyles is helpful for further cultivating, exploring deep-sea dark matters and revealing microbial biogeochemical cycles in this extreme environment.
Quantifying bias of COVID-19 prevalence and severity estimates in Wuhan, China that depend on reported cases in international travelers
Authors: Niehus Rene , De Salazar Pablo M. , Taylor Aimee R. , Lipsitch Marc 
Published: February 2020

AbstractRisk of COVID-19 infection in Wuhan has been estimated using imported case counts of international travelers, often under the assumption that all cases in travelers are ascertained. Recent work indicates variation among countries in detection capacity for imported cases. Singapore has historically had very strong epidemiological surveillance and contact-tracing capacity and has shown in the COVID-19 epidemic evidence of a high sensitivity of case detection. We therefore used a Bayesian modeling approach to estimate the relative imported case detection capacity for other countries compared to that of Singapore.We estimate that the global ability to detect imported cases is 38% (95% HPDI 22% - 64%) of Singapore’s capacity. Equivalently, an estimate of 2.8 (95% HPDI 1.5 - 4.4) times the current number of imported cases, could have been detected, if all countries had had the same detection capacity as Singapore. Using the second component of the Global Health Security index to stratify likely case-detection capacities, we found that the ability to detect imported cases relative to Singapore among high surveillance locations is 40% (95% HPDI 22% - 67%), among intermediate surveillance locations it is 37% (95% HPDI 18% - 68%), and among low surveillance locations it is 11% (95% HPDI 0% - 42%). Using a simple mathematical model, we further find that treating all travelers as if they were residents (rather than accounting for the brief stay of some of these travelers in Wuhan) can modestly contribute to underestimation of prevalence as well. We conclude that estimates of case counts in Wuhan based on assumptions of perfect detection in travelers may be underestimated by several fold, and severity correspondingly overestimated by several fold. Undetected cases are likely in countries around the world, with greater risk in countries of low detection capacity and high connectivity to the epicenter of the outbreak.
Concurrent of stunting and overweight/obesity among children: evidence from Ethiopia
Authors: Farah Alinoor Mohamed , Nour Tahir Yousuf , Endris Bilal Shikur , Gebreyesus Seifu Hagos 
Published: February 2020

AbstractBackgroundNutrition transition in many low- and middle-income countries (LMICs) has led to childhood nutritional outcomes to shift from a predominance of undernutrition to a dual burden of under- and overnutrition. Yet, Infant and young child feeding programs in Ethiopia mainly focus on undernutrition. It is therefore crucial to assess the prevalence and determinants to better inform infant young child feeding programs.MethodsWe analyzed anthropometric, sociodemographic and dietary data of children aged 6-23 months from 2016 Ethiopian Demographic and Health Survey (EDHS). A total of 2,674 children were included in the current study. Concurrent of Stunting and Overweight/Obesity (CSO) prevalence was estimated by distal, intermediate and proximal factors. To identify factors associated with CSO, we conducted hierarchical logistic regression analyses.ResultsThe overall prevalence of CSO was 2.45%. The odds of CSO was significantly higher in children of low household wealth category, compared to their counter parts in the richest category (AOR=2.07, 95%CI=1.06–4.03, P=0.033). In boys, the likelihood of CSO was 1.60 times that of girls (95%CI =1.03–2.49, P=0.038). Above 12months of age was significantly associated with a higher odd of CSO, compared to below 12months of age (AOR=1.76, 95% CI=1.07– 2.88, P=0.026).Small birth size was significantly associated with a higher odd of CSO, compared to large birth size (AOR=2.53, 95%CI=1.45–4.41, P=0.001). Children who did not take vitamin A supplement within the previous six months had a higher odd of CSO, compared to those who took (AOR=1.91, 95%CI =1.19–3.07, P =0.007).ConclusionOur study provided evidence on the co-existence of stunting and overweight/obesity among infants and young children in Ethiopia. CSO was associated with various factors originating from community and child levels. Therefore, identifying children at risk of growth flattering and excess weight gain provides IYCF programs in Ethiopia and beyond with an opportunity of earlier interventions.
Causal dynamical modelling predicts novel regulatory genes of FOXP3 in human regulatory T cells
Authors: Sawlekar Rucha , Magni Stefano , Capelle Christophe , Baron Alexandre , Zeng Ni , Mombaerts Laurent , Yue Zuogong , Yuan Ye , He Feng Q. , Gonçalves Jorge 
Published: February 2020

AbstractRegulatory T cells (Tregs), characterized as a CD4+CD25+FOXP3+ subset of T cells, are vital to the induction of immune tolerance and the maintenance of immune homeostasis. While target genes of Treg master regulator FOXP3 have been identified, the upstream regulatory machinery of FOXP3 still remains largely unknown. Here we dynamically modelcausalrelationships among genes from available time-series genome-scale datasets, to predict direct or indirect regulatory genes of FOXP3 in human primary Tregs. From the whole genome, we selected five top ranked candidates for further experimental validation. Following knockdown, three out of the five candidates indeed showed significant effects on the mRNA expression of FOXP3. Further experiments showed that one out of these three predicted candidates, namely nuclear receptor binding factor 2 (NRBF2), also affected FOXP3 protein expression. These results open new doors to identify potential new mechanisms of immune related diseases.
Alteration of Power Law Scaling of Spontaneous Brain Activity in Schizophrenia
Authors: Lee Yi-Ju , Huang Su-Yun , Lin Ching-Po , Tsai Shih-Jen , Yang Albert C. 
Published: February 2020

AbstractNonlinear dynamical analysis has been used to quantify the complexity of brain signal at temporal scales. Power law scaling is a well-validated method in physics that has been used to describe the complex nature of a system across different time scales. In this research, we investigated the change of power-law characteristics in a large-scale resting-state fMRI data of schizophrenia (N = 200) and healthy participants (N = 200) derived from Taiwan Aging and Mental Illness cohort. Fourier transform was used to determine the power spectral density (PSD) of resting-state fMRI signal. We estimated the power law scaling of PSD of resting-state fMRI signal by determining the slope of the regression line fitting to the log-log plot of PSD. The power law scaling represents the dynamical properties of resting-state fMRI signal ranging from noisy oscillation (e.g., white noise) to complex fluctuations (e.g., slope approaches −1). Linear regression model was used to assess the statistical difference in power law scaling between schizophrenia and healthy participants. The significant differences in power law scaling were found in six brain regions. Schizophrenia patients has significantly more positive power law scaling (i.e., frequency components become more homogenous) at four brain regions: left precuneus, left medial dorsal nucleus, right inferior frontal gyrus, and right middle temporal gyrus, compared with healthy participants. Additionally, schizophrenia exhibited less positive power law scaling (i.e., frequency components are more dominant at lower frequency range) in bilateral putamen. Significant correlations of power law scaling with the severity of psychosis were found in these identified brain areas in schizophrenia. These findings suggest that schizophrenia has abnormal brain signal complexity toward random patterns, which is linked to psychotic symptoms. The power law scaling analysis may serve as a novel functional brain imaging marker for evaluating patients with mental illness.