bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global environmental drivers of local abundance-mass scaling in soil animal communities
Authors: Antunes Ana Carolina , Gauzens Benoit , Brose Ulrich , Potapov Anton M. , Jochum Malte , Santini Luca , Eisenhauer Nico , Ferlian Olga , Cesarz Simone , Scheu Stefan , Hirt Myriam R. 
Published: July 2022

AbstractThe relationship between species’ body masses and densities is strongly conserved around a three-quarter power law when pooling data across communities. However, studies of local within-community relationships have revealed major deviations from this general pattern, which has profound implications for their stability and functioning. Despite multiple contributions of soil communities to people, there is limited knowledge on the drivers of body mass-abundance relationship in these communities. We compiled a dataset comprising 155 soil-animal communities across four countries (Canada, Germany, Indonesia, USA), all sampled using the same methodology. We tested if variation in local climatic and edaphic conditions drives differences in local body mass-abundance scaling relationships. We found substantial variation in the slopes of this power-law relationship across local communities. Structural equation modeling showed that soil temperature and water content have a positive and negative net effect, respectively, on soil communities. These effects are mediated by changes in local edaphic conditions (soil pH and carbon content) and the body-mass range of the communities. These results highlight ways in which alterations of soil climatic and edaphic conditions interactively impact the distribution of abundance, and thus energy, between populations of small and large animals. These quantitative mechanistic relationships facilitate our understanding of how global changes in environmental conditions, such as temperature and precipitation, will affect community-abundance distributions and thus the stability and functioning of soil-animal communities.
CoxMKF: A Knockoff Filter for High-Dimensional Mediation Analysis with a Survival Outcome in Epigenetic Studies
Authors: Tian Peixin , Yao Minhao , Huang Tao , Liu Zhonghua 
Published: July 2022

AbstractMotivationIt is of scientific interest to identify DNA methylation CpG sites that might mediate the effect of an environmental exposure on a survival outcome in high-dimensional mediation analysis. However, there is a lack of powerful statistical methods that can provide a guarantee of false discovery rate (FDR) control in finite-sample settings.ResultsIn this article, we propose a novel method called CoxMKF, which applies aggregation of multiple knockoffs to a Cox proportional hazards model for a survival outcome with high-dimensional mediators. The proposed CoxMKF can achieve FDR control even in finite-sample settings, which is particularly advantageous when the sample size is not large. Moreover, our proposed CoxMKF can overcome the randomness of the unstable model-X knockoffs. Our simulation results show that CoxMKF controls FDR well in finite samples. We further apply CoxMKF to a lung cancer data set from The Cancer Genome Atlas (TCGA) project with 754 subjects and 365 306 DNA methylation CpG sites, and identify four DNA methylation CpG sites that might mediate the effect of smoking on the overall survival among lung cancer patients.AvailabilityThe R packageCoxMKFis publicly available athttps://github.com/MinhaoYaooo/CoxMKF.Contactzl2509@cumc.columbia.edu.
Negative and positive interspecific interactions involving jellyfish polyps in marine sessile communities
Authors: Boughton Jade , Hirst Andrew G. , Lucas Cathy H. , Spencer Matthew 
Published: July 2022

AbstractSessile marine invertebrates on hard substrates are one of the two canonical examples of communities structured by competition, but some aspects of their dynamics remain poorly understood. Jellyfish polyps are an important but under-studied component of these communities.We determined how jellyfish polyps interact with their potential competitors in sessile marine hard-substrate communities, using a combination of experiments and modelling.We carried out an experimental study of the interaction between polyps of the moon jellyfish Aurelia aurita and potential competitors on settlement panels, in which we determined the effects of reduction in relative abundance of either A. aurita or potential competitors at two depths. We predicted that removal of potential competitors would result in a relative increase in A. aurita that would not depend on depth, and that removal of A. aurita would result in a relative increase in potential competitors that would be stronger at shallower depths, where oxygen is less likely to be limiting.Removal of potential competitors resulted in a relative increase in A. aurita at both depths, as predicted. Unexpectedly, removal of A. aurita resulted in a relative decrease in potential competitors at both depths. We investigated a range of models of competition for space, of which the most successful involved enhanced overgrowth of A. aurita by potential competitors, but none of these models was completely able to reproduce the observed pattern.Our results suggest that interspecific interactions in this canonical example of a competitive system are more complex than is generally believed.
Decisive Roles of Sequence Distributions in the Generalizability ofde novoDeep Learning Models for RNA Secondary Structure Prediction
Authors: Qiu Xiangyun 
Published: July 2022

ABSTRACTTaking sequences as the only inputs, the class ofde novodeep learning (DL) models for RNA secondary structure prediction has achieved far superior performances than traditional algorithms. However, key questions remain over the statistical underpinning of such models that make no use of physical laws or co-evolutionary information. We present a quantitative study of the capacity and generalizability of a series ofde novoDL models, with a minimal two-module architecture and no post-processing, under varied distributions of the seen and unseen sequences. Our DL models outperform existing methods on commonly used benchmark datasets and demonstrate excellent learning capacities under all sequence distributions. These DL models generalize well over non-identical unseen sequences, but the generalizability degrades rapidly as the sequence distributions of the seen and unseen datasets become dissimilar. Examinations of RNA family-specific behaviors manifest not only disparate familydependent performances but substantial generalization gaps within the same family. We further determine how model generalization decreases with the decrease of sequence similarity via pairwise sequence alignment, providing quantitative insights into the limitations of statistical learning. Model generalizability thus poses a major hurdle for practical uses ofde novoDL models and several tenable avenues for future advances are discussed.
Shared and ethnic background site-specific dietary patterns in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
Authors: De Vito Roberta , Stephenson Briana , Sotres-Alvarez Daniela , Siega-Riz Anna-Maria , Mattei Josiemer , Parpinel Maria , Peters Brandilyn A. , Bainter Sierra A. , Daviglus Martha L. , Van Horn Linda , Edefonti Valeria 
Published: July 2022

AbstractDietary patterns (DPs) synthesize multiple related dietary components in one or more combined variables. A drawback of DPs is their limited reproducibility across subpopulations, especially adoptinga posterioriDPs, derived using standard multivariate methods [e.g., factor analysis (FA)]. Standard approaches assessing reproducibility of FA-based DPs mostly rely on correlation coefficients/agreement measures between pairs of factors and do not consider any statistical model. Multi-study factor analysis builds upon standard FA model to identify DPs shared across all subpopulations and those specific to some subpopulations. Pattern reproducibility is investigated from a different perspective: a shared DP identified within multi-study factor analysis is “reproducible” since it is common to all subpopulations. Bayesian multi-study factor analysis (BMSFA) has been developed to improve DP retention and identification, two critical issues as the number of subpopulations analyzed increases.Using baseline (2008-2011) 24-hour dietary recalls from the Hispanic Community Health Study/Study of Latinos (n=16,415), we applied the BMSFA on 42 common nutrients to identify shared and subpopulation-specific DPs where subpopulations were defined as the cross-classification of ethnic background and study site (EBS).Overall, 4 shared DPs were identified:Plant-based foods, Processed foods, Dairy products, andSeafood. At the subpopulation level, we identified 12 EBS-specific DPs, one for each EBS category, primarily representing variants of foods from animal sources. Different nuances were expressed by subsets of fairly similar EBS-specific DPs, including anAnimal vs. vegetable source, anAnimal source only, and aPoultry vs. dairy productsoverarching DPs. Shared DPs from BMSFA were similar to their counterparts from standard FA and frequentist multi-study factor analysis; EBS-specific DPs from BMSFA were better characterized than those from frequentist multi-study factor analysis.In conclusion, the BMSFA successfully captured sources of both dietary homogeneity and heterogeneity in a large well-characterized study of US Hispanics/Latino adults by ethnic background and site.
Rucaparib blocks SARS-CoV-2 virus binding to cells and interleukin-6 release in a model of COVID-19
Authors: Papp Henrietta , Bóvári-Biri Judit , Bánfai Krisztina , Juhász Péter , Mahdi Mohamed , Russo Lilian Cristina , Bajusz Dávid , Sipos Adrienn , Petri László , Kemény Ágnes , Madai Mónika , Kuczmog Anett , Batta Gyula , Mózner Orsolya , Vaskó Dorottya , Hirsch Edit , Bohus Péter , Méhes Gábor , Tőzsér József , Curtin Nicola J. , Helyes Zsuzsanna , Tóth Attila , Hoch Nicolas C. , Jakab Ferenc , M. Keserű György , Pongrácz Judit E. , Bai Péter 
Published: July 2022

AbstractCoronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 virus, is a major global health challenge, as there is no efficient treatment for the moderate to severe disease. ADP-ribosylation events are involved in regulating the life cycle of coronaviruses and the inflammatory reactions of the host, hence we assessed the repurposing of registered PARP inhibitors for the treatment of COVID-19. We detected high levels of oxidative stress and strong PARylation in all cell types in the lungs of COVID-19 patients. Interestingly, rucaparib, unlike other PARP inhibitors, reduced SARS-CoV-2 infection rate through binding to the conserved 493-498 amino acid region located in the spike-ACE2 interface in the spike protein and prevented viruses from binding to ACE2. In addition, the spike protein-induced overexpression of IL-6, a key cytokine in COVID-19, was inhibited by rucaparib at pharmacologically relevant concentrations. These findings build a case for repurposing rucaparib for treating COVID-19 disease.
Risk Factors of Developing Contralateral Breast Cancer After Treatment of a First Primary Breast Cancer
Authors: Avatefi Maryam , Hadavand-Siri Fatemeh , Hashemi-Nazari Seyed-Saeed , Akbari Mohammad Esmaeil 
Published: July 2022

AbstractIntroductionBreast cancer (BC) is the most common cancer among women worldwide. This study aimed to determine the disease-free interval (DFI) and the effect of risk factors and characteristics of first primary breast cancer survivors on the progression of contralateral breast cancer (CBC).MethodIn this retrospective cohort study, we identified 5003 women (containing 145 CBC and 4858 BC survivors) diagnosed with BC between 2000 and 2020 in the cancer research center. CBC was diagnosed at least 6 months after detection of primary BC. Kaplan–Meier method was used to indicate DFI and survival curves. To determine the risk factors of CBC, the Cox proportional hazard regression model was employed.ResultsThe median time interval among primary BC and CBC was 7.10 years (average: 7.57, range: 0.49-19.95). The 5-year DFI was 97%. The median age of CBC and primary BC patients was 47 (range 17-78) and 48 (range 17-90), respectively. ER+, PR+, and HER2+ were reported in 72.13%, 66.67%, and 30% of CBC patients. Also, 69.57% of patients had IDC pathology type and 81.90% and 83.64% of the patients were treated with adjuvant chemotherapy and external radiotherapy. More than half of the participants had no family history of BC (69.57%). The hazard ratio indicates that women 60-70 years old, a higher number of involved lymph nodes, and recurrence had significant relationships with CBC.ConclusionThis is the first study to investigate the risk factors of CBC and disease-free interval among BC survivors. Women with higher lymph node metastasis have a lower chance to develop CBC and patients with recurrence are at higher risk for CBC.
Evaluating the impact of e-registration and mHealth on institutional delivery in hazard-prone areas of Bangladesh: A protocol for a non-randomized controlled cluster trial
Authors: Chowdhury Anika Tasneem , Jabeen Sabrina , Sultana Zeeba Zahra , Rahman Ahmed Ehsanur , Arifeen Shams El , Hossain Ahmed 
Published: July 2022

AbstractBackgroundDespite substantial progress, Bangladesh still has a high rate of maternal deaths owing to difficulties during pregnancy, delivery, and the postpartum period. Increasing facility delivery is mandatory to reach the goal of bringing down the MMR to <70 deaths/100,000 live births by 2030. In the era of digitalization, the introduction of e-registration and mHealth may aid the government in reaching this target. The southern part of Bangladesh is a hazard-prone area, where service uptake from institutions is low. This study aimed to determine the effect of an e-registration tracking system and mHealth counseling on institutional deliveries to pregnant mothers in hazard-prone areas of southern Bangladesh.MethodsWe will conduct an open-label, two-arm, non-randomized controlled cluster trial for six months and use three hazard-prone areas for intervention and another three hazard-prone areas for control. We will collect data at baseline and end-line of the study period using a structured questionnaire. We will enroll at least 268 pregnant mothers from the intervention and 268 pregnant mothers from the control areas after screening based on the inclusion and exclusion criteria. Pregnancy information will be obtained from the Family Welfare Assistant register. We will follow the participants until their delivery and exclude those respondents from the study who will have post-dated delivery, migrate out, lost to follow-up, or die during the study period. Random-intercept mixed-effect logistic regression will be performed to explain the relationship of e-registration and mHealth package with institutional delivery.DiscussionInstitutional delivery is still uncommon in Southern Bangladesh despite several interventions. Innovative approaches like e-registration and mHealth counseling may be helpful to bring women to health facilities.Trial registrationThis experiment is registered in the open science framework (registration number: DOI 10.17605/OSF.IO/YZE5C) and https://www.clinicaltrials.gov/ (registration number: NCT05398978).
Mitigation of gastrointestinal graft versus host disease with tocilizumab prophylaxis is accompanied by preservation of microbial diversity and attenuation of enterococcal domination
Authors: Chhabra Saurabh , Szabo Aniko , Clurman Annelie , McShane Katelynn , Waters Nicholas , Eastwood Daniel , Samanas Lisa , Fei Teng , Armijo Gabriel , Abedin Sameen , Longo Walter , Hari Parameswaran , Hamadani Mehdi , Shah Nirav N. , Runaas Lyndsey , Jerkins James H. , van den Brink Marcel , Peled Jonathan U. , Drobyski William R. 
Published: July 2022

ABSTRACTA common feature in the gastrointestinal (GI) tract during allogeneic hematopoietic stem cell transplantation is the loss of microbial diversity and emergence of opportunistic pathogens that can adversely impact survival. Consequently, preventing transplant-associated dysbiosis is an emerging strategy for optimizing treatment outcomes. In this study, we examined the effect of an extended tocilizumab administration schedule in addition to tacrolimus/methotrexate (Tac/MTX) as graft versus host disease (GVHD) prophylaxis on microbial composition in the GI tract along with overall transplant outcomes. Twenty-nine patients received busulfan-based myeloablative conditioning and were transplanted with HLA-matched related or unrelated peripheral blood stem cell grafts. The primary end point of the trial was GVHD-free relapse-free survival (GRFS) at 12 months. The cumulative incidences of grades 2-4 and 3-4 acute GVHD were 10.5% and 7% at day 180, respectively. There was one case of GVHD of the lower GI tract within the first 12 months. Non-relapse mortality and relapse-free survival were 3.4% and 86.2% at one year, respectively. GRFS was 38% at one year which was significantly higher than the pre-specified historical control rate of 20% (p=0.02) and therefore met the primary end point of the trial. Fecal samples from this patient population were sequenced and computationally analyzed centrally along with a demographically matched control cohort that received only Tac/MTX for GVHD prophylaxis. This comparative analysis revealed significantly less loss of α-diversity and reduced emergence of pathogenic organisms such as enterococcus in tocilizumab-treated recipients, demonstrating that loss of microbial diversity and enterococcal domination is attenuated in these patients. (Clinicaltrial.gov Identifier: NCT03699631).
Real World Evidence of Effectiveness of COVID-19 Vaccines and Anti SARS-CoV-2 Monoclonal Antibodies Against Post-Acute Sequelae of SARS-CoV-2 Infection
Authors: Tannous Jonika , Pan Alan P. , Potter Thomas , Bako Abdulaziz , Dlouhy Katharine , Drews Ashley , Sostman H. Dirk , Vahidy Farhaan S. 
Published: July 2022

AbstractBackgroundWe evaluated the effectiveness of COVID-19 vaccines and monoclonal antibodies (mAb) against Post-Acute Sequelae of SARS-CoV-2 infection (PASC), an emerging public health problem.Methods and FindingsIn a retrospective cohort study, we identified patients with clinically significant PASC using a COVID-19 specific, electronic medical record-based surveillance and outcomes registry from an 8-hospital tertiary healthcare system in the greater Houston metropolitan (primary analyses). Analyses were then replicated across a global research network database. We included all adults (>= 18) who survived beyond 28-days of their index infection. PASC was defined as experiencing constitutional (palpitations, malaise / fatigue, headache) or systemic (sleep disorder, shortness of breath, mood / anxiety disorders, cough, and cognitive impairment) symptoms beyond 28-day post-infection period. Instances of PASC were excluded if the symptoms were present pre-COVID or if they resolved within four weeks of initial infection. We fit multivariable logistic regression models and report estimated likelihood of PASC associated with vaccination or mAb treatment as adjusted odds ratios (aOR) with 95% confidence intervals (CI).Primary analyses included 53,239 subjects (54.9% female), of whom 5,929, 11.1% (CI: 10.9 - 11.4), experienced PASC. Both, vaccinated breakthrough cases (vs. unvaccinated) and mAb treated patients (vs. untreated) had lower likelihoods for developing PASC, aOR (CI): 0.58 (0.52, 0.66), and 0.77 (0.69, 0.86), respectively. Vaccination was associated with decreased odds of developing all constitutional and systemic symptoms except for taste and smell changes. For all symptoms, vaccination was associated with lower likelihood of experiencing PASC compared to mAb treatment. Replication analysis found almost identical frequency of PASC (11.2%) and similar protective effects against PASC for the COVID-19 vaccine: aOR (CI) 0.25 (0.21 - 0.30) and mAb treatment: 0.62 (0.59 - 0.66).DiscussionAlthough both COVID-19 vaccines and mAbs decreased the likelihood of PASC, at present, vaccination is the most effective tool to potentially prevent long-term clinical and socio-economic consequences of COVID-19.
GeoWaVe: Geometric median clustering with weighted voting for ensemble clustering of cytometry data
Authors: Burton Ross J. , Cuff Simone M. , Morgan Matt P. , Artemiou Andreas , Eberl Matthias 
Published: July 2022

AbstractMotivationClustering is an unsupervised method for identifying structure in unlabelled data. In the context of cytometry, is typically used to categorise cells into subpopulations of similar phenotype. However, clustering is greatly dependent on hyperparameters and the data to which it is applied as each algorithm makes different assumptions and generates a different ‘view’ of the dataset. As such, the choice of clustering algorithm can significantly influence results, and there is often not one preferred method but different insights to be obtained from different methods. To overcome these limitations, consensus approaches are needed that directly address the effect of competing algorithms, which to our knowledge has not been applied to cytometry.ResultsWe present a novel ensemble clustering methodology based on geometric median clustering with weighted voting (GeoWaVe). Compared to graph ensemble clustering methods that have gained popularity in scRNA-seq analysis, GeoWaVe performed favourably on different sets of high-dimensional mass and flow cytometry data. Our findings provide proof of concept for the power of consensus methods to make the analysis, visualisation and interpretation of cytometry data more robust and reproducible. The wide availability of ensemble clustering methods is likely to have a profound impact on our understanding of cellular responses, clinical conditions, and therapeutic and diagnostic options.Availability and implementationGeoWaVe is available as part of the CytoCluster packagehttps://github.com/burtonrj/CytoCluster.ContactRoss.Burton@wales.nhs.uk
Temnothorax rugatulus ants do not change their nest walls in response to environmental humidity
Authors: Chism Greg T. , Faron Wiley , Dornhaus Anna 
Published: July 2022

AbstractAnimal architectures are interesting biological phenomena that can greatly increase the fitness of the builder and exist in a variety of forms and functions across taxa. Among the most intricate architectures are social insect nests, which may have several functions, one of which is the control of internal microclimate. In social insects, the regulation particularly of humidity in the nest can be crucial for the survival and growth of the brood. Though much is known on how nest excavating social insects respond to environmental humidity, little is known about how ants that build on to pre-existing cavities respond. Here we use the rock ant Temnothorax rugatulus to determine whether and how colonies respond to environmental humidity by building and changing their nest architectures in pre-existing nest spaces. We specifically test the hypothesis that T. rugatulus colonies build different nest walls, e.g. wider or denser ones, in response to lower environmental humidity. We allowed T. rugatulus colonies to build nest walls with two substrates across a 0-100% relative humidity gradient. We further compare the porosity - empty volume in built nest walls - of natural T. rugatulus nest walls with these artificial building substrates and the substrate compositions of built walls from our experiment. We found that humidity did not influence the nest walls T. rugatulus colonies built in our experiment, concluding that regulating humidity is likely not a key function of T. rugatulus nest wall architecture. We also found that the porosities of the artificial substrate that was predominantly used by the ants in our experiment were like the porosity of natural T. rugatulus nest walls, indicating that ants had constant preferences for particular substrates. Physical nest wall features, including porosity, are therefore unlikely to be flexibly regulated in response to external humidity, but may be adaptations in other ways.