bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic and proteomic analysis of marine nematodeLitoditis marinaacclimated to different salinities
Authors: Xie Yusu , Zhang Liusuo 
Published: November 2021

AbstractSalinity is a critical abiotic factor for all living organisms. The ability to adapt to different salinity environments determines an organism’s survival and ecological niches.Litoditis marinais a euryhaline marine nematode widely distributed in coastal ecosystems all over the world, although numerous genes involved in its salinity response have been reported, the adaptive mechanisms underlying its euryhalinity remain unexplored. Here, we utilized worms which have been acclimated to either low salinity or high salinity conditions and evaluated their basal gene expression at both transcriptomic and proteomic levels. We found that several conserved regulators, including osmolytes biosynthesis genes, transthyretin-like family genes, V-type H+-transporting ATPase and potassium channel genes, were involved in both short-term salinity stress response and long-term acclimation processes. In addition, we identified genes related to cell volume regulation, such as actin regulatory genes, Rho family small GTPases and diverse ion transporters, might contribute to hyposaline acclimation, while the glycerol biosynthesis genesgpdh-1andgpdh-2accompanied hypersaline acclimation inL. marina. Furthermore,gpdh-2might play an essential role in transgenerational inheritance of osmotic stress protection inL. marinaas in its relative nematodeCaenorhabditis elegans. Hereby, this study paves the way for further in-depth exploration on adaptive mechanisms underlying euryhalinity, and may also contribute to the studies of healthy ecosystems in the context of global climate change.
Meta-Research: A Poor Research Landscape Hinders the Progression of Knowledge and Treatment of Reproductive Diseases
Authors: Mercuri Natalie D , Cox Brian J 
Published: November 2021

ABSTRACTReproductive diseases have gone under the radar for many years, resulting in insufficient diagnostics and treatments. Infertility rates are rising, preeclampsia claims over 70 000 maternal and 500 000 neonatal lives globally per year, and endometriosis affects 10% of all reproductive-aged women but is often undiagnosed for many years. Changes in policy have been enacted to mitigate the gender inequality in research investigators and subjects of medical research. However, the disparities in reproductive research advancement still exist. Here, we analyzed the reproductive science research landscape in attempt to quantify the gravity of the current situation. We find that non-reproductive organs are annually researched 5-20 times more than reproductive organs leading to an exponentially increasing relative knowledge gap in reproductive sciences. Additionally, reproductive organs (breast and prostate) are mainly researched when there is a disease-focus, leading to a lack of basic understanding of the reproductive organs. This gap in knowledge affects reproductive syndromes, as well as other bodily systems and research areas, such as cancer biology and regenerative medicine. Action must be taken by current researchers, funding organizations, and educators to combat this longstanding disregard of reproductive science.
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Authors: Wu Fei , Liu Yao-Zhong , Ling Binhua 
Published: November 2021

AbstractRNA-seq data contains not only host transcriptomes but also non-host information that comprises transcripts from active microbiota in the host cells. Therefore, joint and integrative analyses of both host and meta-transcriptome can reveal gene expression of microbial community in a given sample as well as the correlative and interactive dynamics of host response to the microbiome. However, there are no convenient tools that can systemically analyze host-microbiota interactions by simultaneously quantifying host and meta-transcriptome in the same sample at the tissue and the single-cell level, which poses a challenge for interested researchers with a limited expertise in bioinformatics. Here, we developed a software pipeline that can comprehensively and synergistically analyze and correlate the host and meta-transcriptome in a single sample using bulk and single-cell RNA-seq data. This pipeline, named MTD, can extensively identify and quantify microbiome, including viruses, bacteria, protozoa, fungi, plasmids, and vectors in the host cells and correlate the microbiome with the host transcriptome. MTD is easy to install and run, involving only a few lines of simple commands. It empowers researchers with unique genomics insights into host immune responses to microorganisms.
Trait Association and Prediction Through Integrative K-mer Analysis
Authors: He Cheng , Washburn Jacob D. , Hao Yangfan , Zhang Zhiwu , Yang Jinliang , Liu Sanzhen 
Published: November 2021

ABSTRACTGenome-wide association study (GWAS) with single nucleotide polymorphisms (SNPs) has been widely used to explore genetic controls of phenotypic traits. Here we employed an GWAS approach using k-mers, short substrings from sequencing reads. Using maize cob and kernel color traits, we demonstrated that k-mer GWAS can effectively identify associated k-mers. Co-expression analysis of kernel color k-mers and pathway genes directly found k-mers from causal genes. Analyzing complex traits of kernel oil and leaf angle resulted in k-mers from both known and candidate genes. Evolution analysis revealed most k-mers positively correlated with kernel oil were strongly selected against in maize populations, while most k-mers for upright leaf angle were positively selected. In addition, phenotypic prediction of kernel oil, leaf angle, and flowering time using k-mer data showed at least a similarly high prediction accuracy to the standard SNP-based method. Collectively, our results demonstrated the bridging role of k-mers for data integration and functional gene discovery.
The relationship between land cover and microbial community composition in European lakes
Authors: Sperlea Theodor , Philip Schenk Jan , Dreßler Hagen , Beisser Daniela , Hattab Georges , Boenigk Jens , Heider Dominik 
Published: November 2021

AbstractMicrobes such as bacteria, archaea, and protists are essential for element cycling and ecosystem functioning, but many questions central to the understanding of the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the land cover surrounding the lakes. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. We identify microbial bioindicators for these land cover categories. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop two novel similarity metrics that facilitate insights into the ecology of the lake microbiome. We show that the bioindicator network, i.e., the graph linking OTUs indicative of the same environmental parameters, corresponds to microbial co-occurrence patterns. Taken together, we demonstrate the strength of machine learning approaches to identify correlations between microbial diversity and environmental factors, potentially opening new approaches to integrate environmental molecular diversity into monitoring and water quality assessments.
Quantifying asymmetry in non-symmetrical morphologies, with an example from Cetacea
Authors: Coombs Ellen. J. , Felice Ryan. N. 
Published: November 2021

Abstract1. Three-dimensional measurements of morphology are key to gaining an understanding of a species’ biology and to answering subsequent questions regarding the processes of ecology (or palaeoecology), function, and evolution. However, the collection of morphometric data is often focused on methods designed to produce data on bilaterally symmetric morphologies which may mischaracterise asymmetric structures.2. Using 3D landmark and curve data on 3D surface meshes of specimens, we present a method for first quantifying the level of asymmetry in a specimen and second, accurately capturing the morphology of asymmetric specimens for further geometric analyses.3. We provide an example of the process from initial landmark placement, including details on how to place landmarks to quantify the level of asymmetry, and then on how to use this information to accurately capture the morphology of asymmetric morphologies or structures. We use toothed whales (odontocetes) as a case study and include examples of the consequences of mirroring landmarks and curves, a method commonly used in bilaterally symmetrical specimens, on asymmetric specimens.4. We conclude by presenting a step-by-step method to collecting 3D landmark data on asymmetric specimens. Additionally, we provide code for placing landmarks and curves on asymmetric specimens in a manner designed to both save time and ultimately accurately quantify morphology. This method can be used as a first crucial step in morphometric analyses of any biological specimens by assessing levels of asymmetry and then if required, accurately quantifying this asymmetry. The latter not only saves the researcher time, but also accurately represents the morphology of asymmetric structures.
Assessing the Use of Prescription Drugs in Obese Respondents in the National Health and Nutrition Examination Survey
Authors: Barrett Laura A. , Xing Aiwen , Sheffler Julia , Steidley Elizabeth , Adam Terrence J. , Zhang Rui , He Zhe 
Published: November 2021

AbstractIntroductionObesity is a common disease and a known risk factor for many other conditions such as hypertension, type 2 diabetes, and cancer. Treatment options for obesity include lifestyle changes, pharmacotherapy, and surgical interventions such as bariatric surgery. In this study, we examine the use of prescription drugs and dietary supplements by the individuals with obesity.MethodsWe conducted a cross-sectional analysis of the National Health and Nutrition Examination Survey (NHANES) data 2003-2014. We used multivariate logistic regression to analyze the correlations of demographics and obesity status with the use of prescription drugs and dietary supplement use. We also built machine learning models to classify prescription drug and dietary supplement use using demographic data and obesity status.ResultsIndividuals with obesity are more likely to take cardiovascular agents (OR=1.265, 95% CI 1.222-1.311) and metabolic agents (OR=1.398, 95% CI 1.343-1.456) than individuals without obesity. The best performing model for classifying prescription drug use had the accuracy of 74.5% and the AUROC of 0.817.ConclusionsThis study can inform clinical practice and patient education of the use of prescription drugs and dietary supplements and their correlation with obesity.
The clinical efficacy of faecal microbiota transplantation: An umbrella review of randomized controlled trials
Authors: Liu Nanyang , Zhang Tingting , Sun Jiahui , Fu Jianhua , Li Hao 
Published: November 2021

ABSTRACTINTRODUCTIONFaecal microbiota transplantation (FMT) therapeutic strategy has been associated with positive outcomes in multiple diseases. We conducted an umbrella review of the meta-analysis to summarize the available evidence and assess its credibility.METHODSWe evaluated a meta-analysis of randomized controlled trials that investigated the efficacy and safety of FMT for any condition. We used the random-effects model to obtain estimates and corresponding 95% confidence intervals, heterogeneity estimates, and small-study effects. We used AMSTAR 2 to assess methodological quality and GRADE tools to grade the evidence.RESULTSSeven meta-analyses with a total of 33 outcomes were included in the current umbrella review to evaluate the efficacy and safety of FMT. Overall, there is a moderate certainty of evidence supporting the associations of the use of FMT with better clinical remission in patients with Clostridium difficile infection (RR = 1.74; 95% CI: 1.37-2.22) and inflammatory bowel disease (RR = 1.70; 95% CI: 1.12-2.56). A very low certainty evidence supports the use of FMT to treat antibiotic-resistant bacteria (RR = 5.67; 95% CI: 2.20-14.63) and functional constipation (RR = 1.35; 95% CI: 1.14-1.60) but does not support irritable bowel syndrome (RR = 1.08; 95% CI: 0.65-1.77).DISCUSSIONThe umbrella review of the current meta-analysis demonstrates that FMT intervention is associated with positive outcomes for several diseases. However, the credibility of the evidence is not high. Further high-quality randomized controlled trials should be carried out to improve the strength and credibility of the evidence base.
The critical role of the ventral temporal lobe in word retrieval
Authors: Snyder Kathryn M. , Forseth Kiefer J. , Donos Cristian , Rollo Patrick S. , Fischer-Baum Simon , Breier Joshua , Tandon Nitin 
Published: November 2021

AbstractDeficits in word retrieval are a hallmark of a variety of neurological illnesses spanning from dementia to traumatic injuries. The role of the dominant temporal lobe in fluent naming has been characterized by lesional analyses, functional imaging, and intracranial recordings, but limitations of each of these measures preclude a clear assessment of which specific constituent of the temporal lobe is critical for naming. We studied a large cohort of patients undergoing surgical resections or laser ablations of the dominant temporal lobe for medically intractable epilepsy (n=95). These techniques are exceedingly effective for seizure control but often result in language declines, particularly in confrontation naming, which can be socio-economically disabling. We used a multivariate voxel-based lesion symptom mapping analysis to localize brain regions significantly associated with visual object naming deficits. We observed that posterior inferior temporal regions, centered around the middle fusiform gyrus, were significantly associated with a decline in confrontation naming. Furthermore, we found that the posterior margin of anterior temporal lobectomies was linearly correlated to a decline in visual naming with a clinically significant decline occurring once the resection extended 6 cm from the anterior tip of the temporal lobe. We integrated these findings with electrocorticography during naming in a subset of this population and found that the majority of cortical regions whose resection was associated with a significant decline overlapped with regions that were functionally most active prior to articulation. Importantly, these loci coincide with the sites of susceptibility artifacts during echo-planar imaging, which explains why this region has not previously been implicated. Taken together, these data highlight the crucial contribution of the posterior ventral temporal cortex in lexical access and its important role in the pathophysiology of anomia following temporal lobe resections. Surgical strategies, including the use of laser ablation to target the medial temporal lobe as well as microsurgical approaches, should attempt to preserve this region to mitigate postoperative language deficits.
Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England
Authors: Borek Aleksandra J. , Maitland Katherine , McLeod Monsey , Campbell Anne , Hayhoe Benedict , Butler Christopher C. , Morrell Liz , Roope Laurence , Holmes Alison , Walker A. Sarah , Tonkin-Crine Sarah 
Published: November 2021

AbstractThe COVID-19 pandemic has had a profound impact on the delivery of primary care services. We aimed to identify general practitioners’ (GPs’) perceptions and experiences of how the COVID-19 pandemic influenced antibiotic prescribing and antimicrobial stewardship (AMS) in general practice in England. Twenty-four semi-structured interviews were conducted with 18 GPs at two time-points: autumn 2020 (14 interviews) and spring 2021 (10 interviews). Interviews were audio-recorded, transcribed and analysed thematically, taking a longitudinal approach. Participants reported a lower threshold for antibiotic prescribing (and fewer consultations) for respiratory infections and COVID-19 symptoms early in the pandemic, then returning to more usual (pre-pandemic) prescribing. They perceived less impact on antibiotic prescribing for urinary and skin infections. Participants perceived the changing ways of working and consulting (e.g., proportions of remote and in-person consultations), and the changing patient presentations and GP workload as influencing the fluctuations in antibiotic prescribing. This was compounded by decreased engagement with, and priority of, AMS due to COVID-19-related urgent priorities. Re-engagement with AMS is needed, e.g., through reviving antibiotic prescribing feedback and targets/incentives. While the pandemic disrupted the usual ways of working, it also produced opportunities, e.g., for re-organising ways of managing infections and AMS in the future.
Childhood Immuno-metabolic Markers and Risk of Depression and Psychosis in Adulthood: A Prospective Birth Cohort Study
Authors: Donnelly NA , Perry BI , Jones HJ , Khandaker GM 
Published: November 2021

AbstractBackgroundMetabolic and inflammatory disorders commonly co-occur with depression and psychosis, with emerging evidence implicating immuno-metabolic dysfunction in their aetiology. Previous studies have reported metabolic dysfunction and inflammation in adults with depression and psychosis. However, longitudinal studies testing the direction of association, and the effects of different dimensions of early-life immuno-metabolic dysfunction on adult psychopathology, are limited.MethodsUsing data from 3875 birth cohort participants we examined longitudinal associations of three metabolic hormones (leptin, adiponectin, insulin) at age 9 with risks for depression- and psychosis-spectrum outcomes at age 24. In addition, using nine immuno-metabolic biomarkers, we constructed an exploratory bifactor model showing a general immuno-metabolic factor and three specific factors (adiposity, inflammation, and insulin resistance), which were also used as exposures.ResultsChildhood leptin was associated with adult depressive episode (adjusted odds ratio (aOR)=1.28; 95% CI, 1.00-1.64) and negative symptoms (aOR=1.12; 95% CI, 1.05-1.20). The general immuno-metabolic factor was associated with depressive symptoms (aOR=1.05; 95% CI, 1.01-1.08) and psychotic experiences (aOR=1.20; 95% CI, 1.01-1.42). The adiposity factor was associated with negative symptoms (aOR=1.07; 95% CI 1.02-1.12). All associations tended to be stronger in women, though 95% credible intervals overlapped with that for men. In women, the inflammatory factor was associated with depressive episode (aOR=1.23; 95% CI, 1.01-1.47) and atypical depressive symptoms (aOR=1.10; 95% CI, 1.02-1.19).ConclusionsWhile general immuno-metabolic dysfunction in childhood may contribute to risks for both psychotic and depressive symptoms in adulthood, childhood adiposity and inflammation are linked to affective (depressive, atypical, and negative) symptoms.
When less is more – A fast TurboID KI approach for high sensitivity endogenous interactome mapping
Authors: Stockhammer Alexander , Spalt Carissa , Benz Laila S. , Harel Shelly , Natalia Vini , Wiench Lukas , Freund Christian , Kuropka Benno , Bottanelli Francesca 
Published: November 2021

AbstractIn recent years, proximity labelling has established itself as an unbiased and powerful approach to map the interactome of specific proteins. While physiological expression of the labelling enzyme is beneficial for the mapping of interactors, generation of the desired cell lines remains time-consuming and challenging. Using our established pipeline for the rapid generation of C- and N-terminal CRISPR-Cas9 knock-ins (KIs) based on antibiotic selection, we were able to compare the performance of commonly used labelling enzymes when endogenously expressed. Endogenous tagging of the μ subunit of the AP-1 complex with TurboID allowed identification of known interactors and cargo proteins that simple overexpression of a labelling enzyme fusion protein could not reveal. We used the KI-strategy to compare the interactome of the different adaptor protein (AP) complexes and clathrin and were able to assemble lists of potential interactors and cargo proteins that are specific for each sorting pathway. Our approach greatly simplifies the execution of proximity labelling experiments for proteins in their native cellular environment and allows going from CRISPR transfection to mass spectrometry analysis and interactome data in just over a month.
Simulation of particles screening in pulsating negative pressure shale shaker by coupling CFD and DEM
Authors: Yin Peng , Hou Yongjun , Wu Xianjin 
Published: November 2021

PurposeThe purpose of this paper is to obtain the combination of working parameters suitable for pulsating negative pressure shale shaker through simulation, which is conducive to efficient recovery of clean drilling fluid and relatively dry cuttings.Design/methodology/approachShale shaker is still one of the main equipment in solid–solid and solid–liquid separation processes in drilling industry. This research is based on a new drilling fluids circulation treatment device, namely pulsating negative pressure shale shaker. In this work, a numerical study of particle flow and separation in the pulsating negative pressure shale shaker is carried out by coupling computational fluid dynamics/discrete element method (CFD-DEM). The effect of vibration parameters and negative pressure parameters are studied in terms of conveyance velocity and percent through screen.FindingsThe results show that, conveyance velocity of particle is mainly affected by vibration parameters, negative pressure in pulsating form can effectively prevent cuttings from sticking to the screen. Vibration parameters and pulsating airflow velocity peak have great influence on percent through screen, while vibration frequency and screen slope have influence on the time when the percent through screen reaches stability.Originality/valueIn this paper, the authors put forward a new kind of drilling waste fluid treatment equipment, and focused on the study of particle movement law. The results have important guiding significance for the selection of structural design parameters and rational use of equipment. In addition, the new device provides a new idea for solid–liquid separation method, which is one of the hot topics in current research.