bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of antibiotic cross-resistance by bacterial sample source: a retrospective cohort study
Authors: Cherny Stacey S. , Chowers Michal , Obolski Uri 
Published: April 2022

AbstractBackground and objectivesAntimicrobial resistance is a major healthcare burden, aggravated when it extends to multiple drugs. While cross-resistance is well-studied experimentally, it is not the case in clinical settings, and especially not while considering confounding variables. In addition, bacteria from different sample sources may have undergone different evolutionary trajectories, therefore examining cross-resistance across sources is desirable.MethodologyWe employed additive Bayesian network (ABN) modelling to examine antibiotic cross-resistance in five major bacterial species, obtained from different sources (urine, wound, blood, and sputum) in a clinical setting, collected in a large hospital in Israel over a 4-year period. ABN modelling allowed for examination of the relationship between resistance to different drugs while controlling for major confounding variables.ResultsPatterns of cross-resistance differed across sample sources. All identified links between resistance to different antibiotics were positive, and most were present in several culture sources. However, in 15 of 18 instances, the magnitudes of the links were significantly different between sources compared. For example, E coli exhibited adjusted odds ratios of gentamicin-ofloxacin cross-resistance ranging from 3.0 (95%CI [2.3,4.0]) in urine samples to 11.0 (95%CI [5.2,26.1]) in blood samples.Conclusions and implicationsOur results highlight the importance of considering sample sources when assessing likelihood of antibiotic cross-resistance and determining antibiotic treatment regimens and policies.Abstract ImportanceWe examine the patterns of antibiotic resistance of a given bacterial species, obtained from different clinical infection locations, while accounting for potentially relevant clinical variables. We find that such patterns of cross-resistance between pairs of antibiotics vary between culture sources (e.g., urine vs blood samples), indicating different selective pressures. These findings have implications on prescription policies aiming to minimize collateral resistance.
The impact of COVID-19 pandemic on influenza surveillance: a systematic review and meta-analysis
Authors: Sabeena Sasidharanpillai , Ravishankar Nagaraja , Robin Sudandiradas 
Published: April 2022

AbstractBackgroundInfluenza activity was reported to be below the seasonal levels during the COVID-19 pandemic globally. However, during the SARS-CoV-2 outbreak, the routine real-time surveillance of influenza like illness (ILI) and acute respiratory infection (ARI) was adversely affected due to the changes in priorities, economic constraints, repurposing of hospitals for COVID care and closure of outpatient services.MethodsA systematic review and meta-analysis were carried out to assess the pooled proportion of symptomatic cases tested for influenza virus before the current pandemic in 2019 and during the pandemic in 2020/21. An electronic search of PubMed/MEDLINE, Scopus and Google Scholar was carried out for the articles reporting the impact of the COVID-19 pandemic on Influenza surveillance among humans using search terms. The study was designed based on PRISMA guidelines and the meta-analysis was performed to synthesise the pooled proportion of patients sampled for influenza with 95% confidence interval (CI).ResultsThe nine qualified studies from the WHO-European region, Canada, Japan, Germany, Italy, Spain, South Africa and the United States were pooled by random-effects meta-analysis. The overall pooled proportion of symptomatic cases sampled for influenza surveillance before and during the pandemic was 2.38% (95% CI 2.08%-2.67%) and 4.18% (95% CI 3.8%-4.52%) respectively. However, the pooled proportion of samples tested for influenza before the pandemic was 0.69% (95% CI 0.45-0.92%) and during the pandemic was 0.48% (95% CI 0.28-0.68%) when studies from Canada were excluded.ConclusionThe meta-analysis concludes that globally there was a decline in influenza surveillance during the COVID-19 pandemic except in Canada.Key MessagesThe nine observational studies from Europe, Canada, Japan, South Africa and the United States were qualified for the meta-analysisA steep decline in the seasonal influenza activity in both northern and southern hemispheres was observedAlmost double the number of symptomatic cases were sampled as part of influenza surveillance during the current pandemic in CanadaExcept in Canada, a decline in influenza surveillance globally during the COVID-19 pandemic was observed
If you build it, will they use it? Use of a Digital Assistant for Self-Reporting of COVID-19 Rapid Antigen Test Results during Large Nationwide Community Testing Initiative
Authors: Herbert Carly , Shi Qiming , Kheterpal Vik , Nowak Chris , Suvarna Thejas , Durnam Basyl , Schrader Summer , Behar Stephanie , Naeem Syed , Tarrant Seanan , Kalibala Ben , Singh Aditi , Gerber Ben , Barton Bruce , Lin Honghuang , Cohen-Wolkowiez Michael , Corbie-Smith Giselle , Kibbe Warren , Marquez Juan , Baek Jonggyu , Hafer Nathaniel , Gibson Laura , O’Connor Laurel , Broach John , Heetderks William , McManus David , Soni Apurv 
Published: April 2022

AbstractImportanceWide-spread distribution of rapid-antigen tests is integral to the United States’ strategy to address COVID-19; however, it is estimated that few rapid-antigen test results are reported to local departments of health.ObjectiveTo characterize how often individuals in six communities throughout the United States used a digital assistant to log rapid-antigen test results and report them to their local Department of Health.DesignThis prospective cohort study is based on anonymously collected data from the beneficiaries of The Say Yes! Covid Test program, which distributed 3,000,000 rapid antigen tests at no cost to residents of six communities between April and October 2021. We provide a descriptive evaluation of beneficiaries’ use of digital assistant for logging and reporting their rapid antigen test results.Main Outcome and MeasuresNumber and proportion of tests logged and reported to the Department of Health through the digital assistantResultsA total of 178,785 test kits were ordered by the digital assistant, and 14,398 households used the digital assistant to log 41,465 test results. Overall, a small proportion of beneficiaries used the digital assistant (8%), but over 75% of those who used it reported their rapid antigen test results to their state public health department. The reporting behavior varied between communities and was significantly different for communities that were incentivized for reporting test results (p < 0.001). In all communities, positive tests were less reported than negative tests (60.4% vs 75.5%; p<0.001).Conclusions and RelevanceThese results indicate that app-based reporting with incentives may be an effective way to increase reporting of rapid tests for COVID-19; however, increasing the adoption of the digital assistant is a critical first step.
The HIV and STI syndemic following mass scale-up of combination HIV interventions in Uganda: a population-based cross-sectional study
Authors: Grabowski M. Kate , Mpagazi Josephine , Kiboneka Stephen , Ssekubugu Robert , Kereba John Baptiste , Nakayijja Annet , Tukundane Julius , Jackson Jade , Peer Austin D. , Kennedy Caitlin , Kigozi Godfrey , Galiwango Ronald M. , Manabe Yuka , Chang Larry W. , Kalibala Sarah , Gray Ronald H , Wawer Maria J , Reynolds Steven J , Tobian Aaron AR , Serwadda David , Gaydos Charlotte A. , Kagaayi Joseph , Quinn Thomas C 
Published: April 2022

ABSTRACTBackgroundCombination HIV interventions (CHIs) have led to significant declines in HIV incidence in sub-Saharan Africa; however, population-level data on non-HIV sexually transmitted infection (STI) burden in the context of CHIs are rare. We aimed to assess STI burden in Uganda following mass scale-up of CHIs, including universal HIV treatment.MethodsThe Sexually Transmitted Infection Prevalence Study (STIPS) was a cross-sectional study nested within the Rakai Community Cohort Study (RCCS), a population-based cohort among inland agrarian and Lake Victoria fishing populations in southern Uganda. STIPS enrolled consenting participants, 18-49 years, between May and October 2019 and measured prevalence ofChlamydia trachomatis(chlamydia),Neisseria gonorrhoeae(gonorrhea),Trichomonas vaginalis(trichomonas), syphilis, and herpes simplex virus type 2 (HSV-2).FindingsSTIPS enrolled 1,825 participants, including 965 women (53%), of whom 9% (n=107) were pregnant. Overall, there was 9.8% prevalence of chlamydia (95%CI:8.5-11%), 6.7% gonorrhea (95%CI:5.7-8.0%), and 11% trichomonas (95%CI:9.5-12%). In the fishing population, syphilis reactivity was 24% (95%CI:22-27%), with 9.4% (95%CI:7.7-11%) having high titer (RPR ≥ 1:8) infection, including 17% (95%CI:12-24%) of HIV-positive men. Prevalence of ≥ 1 curable STI (chlamydia, gonorrhea, trichomonas, or high titer syphilis) was 44% higher among HIV-positive persons (adjusted prevalence risk ratio [adjPRR]=1.44,95%CI:1.22-1.71), with no differences by HIV treatment status. HIV-positive pregnant women were more likely than HIV-negative pregnant women to have a curable STI (adjPRR=1.87, 95%CI: 1.08-3.23).InterpretationSTI burden remains extremely high in Uganda, particularly among HIV-positive persons. There is an urgent need to integrate STI diagnostic testing and treatment with HIV services in African settings.FundingNational Institutes of Health
Latent Factors of Language Disturbance and Relationships to Quantitative Speech Features
Authors: Tang Sunny X. , Hänsel Katrin , Cong Yan , Nikzad Amir H. , Mehta Aarush , Cho Sunghye , Berretta Sarah , Behbehani Leily , Pradhan Sameer , John Majnu , Liberman Mark Y. 
Published: April 2022

AbstractBackground and HypothesisQuantitative acoustic and textual measures derived from speech (“speech features”) may provide valuable biomarkers for psychiatric disorders, particularly schizophrenia spectrum disorders (SSD). We sought to identify cross-diagnostic latent factors for speech disturbance with relevance for SSD and computational modeling.Study DesignClinical ratings for speech disturbance were generated across 14 items for a cross-diagnostic sample (N=343), including SSD (n=97). Speech features were quantified using an automated pipeline for brief recorded samples of free-speech. Factor models for the clinical ratings were generated using exploratory factor analysis, then tested with confirmatory factor analysis in the cross-diagnostic and SSD groups. Relationships among factor scores, speech features and other clinical characteristics were examined using network analysis.Study ResultsWe found a 3-factor model with good fit in the cross-diagnostic group and acceptable fit for the SSD subsample. The model identifies an impaired expressivity factor and two interrelated disorganized factors for inefficient and incoherent speech. Incoherent speech was specific to psychosis groups, while inefficient speech and impaired expressivity showed intermediate effects in people with nonpsychotic disorders. Network analysis showed that the factors had distinct relationships with speech features, and that the patterns were different in the cross-diagnostic versus SSD groups.ConclusionsWe report a cross-diagnostic 3-factor model for speech disturbance which is supported by good statistical measures, intuitive, applicable to SSD, and relatable to linguistic theories. It provides a valuable framework for understanding speech disturbance and appropriate targets for modeling with quantitative speech features.
Hippocampal CA1 represents action and reward events instantly compared to the superficial and deep layers of the lateral entorhinal cortex
Authors: Soma Shogo , Ohara Shinya , Nonomura Satoshi , Yoshida Junichi , Suematsu Naofumi , Pastalkova Eva , Sakai Yutaka , Tsutsui Ken-Ichiro , Isomura Yoshikazu 
Published: April 2022

AbstractThe entorhinal cortex (EC) is the main interface between the hippocampus and the neocortex. The EC plays a critical role in learning and memory. We investigated the neuronal representation of behavioral events during operant learning in the hippocampal-entorhinal circuit of head-fixed rats. Both CA1 and lateral entorhinal cortex (LEC) neurons develop task-related activities after learning. Among diverse task-related activities, we compared the transient peak activities that represent action and reward and found a distinct difference in the timing of behavioral event representation between CA1 and LEC. CA1 represents action and reward events in close to real-time, whereas both the superficial and deep layers of the LEC showed delayed representation of those events. Our results suggest that subpopulations exist within which CA1 and LEC neurons process the information in a different order from the anatomically defined hippocampal-entorhinal circuit.
Antibody evolution to SARS-CoV-2 after single-dose Ad26.COV2.S vaccine
Authors: Cho Alice , Muecksch Frauke , Wang Zijun , Tanfous Tarek Ben , DaSilva Justin , Raspe Raphael , Johnson Brianna , Bednarski Eva , Ramos Victor , Schaefer-Babajew Dennis , Shimeliovich Irina , Dizon Juan , Yao Kai-Hui , Schmidt Fabian , Millard Katrina G. , Turroja Martina , Jankovic Mila , Oliveira Thiago Y. , Gazumyan Anna , Gaebler Christian , Caskey Marina , Hatziioannou Theodora , Bieniasz Paul D. , Nussenzweig Michel C. 
Published: April 2022

AbstractThe single dose Ad.26.COV.2 (Janssen) vaccine elicits lower levels of neutralizing antibodies and shows more limited efficacy in protection against infection than either of the available mRNA vaccines. In addition, the Ad.26.COV.2 has been less effective in protection against severe disease during the Omicron surge. Here, we examined the memory B cell response to single dose Ad.26.COV.2 vaccination. Compared to mRNA vaccines, Ad.26.COV.2 recipients had significantly lower numbers of RBD-specific memory B cells 1.5 or 6 months after vaccination. Memory antibodies elicited by both vaccine types show comparable neutralizing potency against SARS-CoV-2 and Delta. However, the number of memory cells producing Omicron neutralizing antibodies was somewhat lower after Ad.26.COV.2 than mRNA vaccination. The data help explain why boosting Ad.26.COV.2 vaccine recipients with mRNA vaccines is effective, and why the Janssen vaccine appears to have been less protective against severe disease during the Omicron surge than the mRNA vaccine.One-Sentence SummaryAd.26.COV.2 vaccine results in lower quantity but comparable quality of protective memory B cells compared to mRNA vaccines.
Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike
Authors: Yu Xiaodi , Juraszek Jarek , Rutten Lucy , Bakkers Mark J. G. , Blokland Sven , van den Broek Niels J.F. , Verwilligen Annemiek Y.W. , Abeywickrema Pravien , Vingerhoets Johan , Neefs Jean-Marc , Mohamed Bakhash Shah A. , Roychoudhury Pavitra , Greninger Alex , Sharma Sujata , Langedijk Johannes P. M. 
Published: April 2022

AbstractThe SARS-CoV-2 spike protein is the target of neutralizing antibodies and the immunogen used in all currently approved vaccines. The global spread of the virus has resulted in emergence of lineages which are of concern for the effectiveness of immunotherapies and vaccines based on the early Wuhan isolate. Here we describe two SARS-CoV-2 isolates with large deletions in the N-terminal domain (NTD) of the spike. Cryo-EM structural analysis showed that the deletions result in complete reshaping of the antigenic surface of the NTD supersite. The remodeling of the NTD affects binding of all tested NTD-specific antibodies in and outside of the NTD supersite for both spike variants. A unique escape mechanism with high antigenic impact observed in the ΔN135 variant was based on the loss of the Cys15-Cys136 disulfide due to the P9L-mediated shift of the signal peptide cleavage site and deletion of residues 136-144. Although the observed large loop and disulfide deletions are rare, similar modifications became independently established in several other lineages, highlighting the possibility of a general escape mechanism via the NTD supersite. The observed plasticity of the NTD foreshadows its broad potential for immune escape with the continued spread of SARS-CoV-2.
History of previous midlife estradiol treatment permanently alters interactions of brain insulin-like growth factor-1 signaling and hippocampal estrogen synthesis to enhance cognitive aging in a rat model of menopause
Authors: Baumgartner Nina E. , McQuillen Shannon M. , Perry Samantha F. , Miller Sangtawan , Gibbs Robert , Daniel Jill M 
Published: April 2022

AbstractAcross species, including humans, elevated levels of brain estrogen receptor (ER) α are associated with enhanced cognitive aging even in the absence of circulating estrogens. In rodents, short-term estrogen treatment—such as that commonly used in the menopausal transition—results in long-term increases in levels of ERα in the hippocampus, leading to enhanced memory long after termination of estrogen treatment. However, mechanisms by which increased levels of brain ERα enhances cognitive aging remain unclear. Here we show that in the hippocampus, insulin-like growth factor-1 (IGF-1)—which can activate ER via ligand-independent mechanisms—requires concomitant synthesis of brain-derived neuroestrogens to phosphorylate ERα via MAPK signaling, ultimately resulting in enhanced memory. In a rat model of menopause involving long-term ovarian hormone deprivation, hippocampal neuroestrogen activity decreases, altering IGF-1 activity and resulting in impaired memory. However, this process is reversed by short-term estradiol treatment. Forty-days of estradiol exposure following ovariectomy results in maintenance of neuroestrogen levels that persist beyond the period of hormone treatment, allowing for continued interactions between IGF-1 and neuroestrogen signaling, elevated levels of hippocampal ERα, and ultimately enhanced memory. Collectively, results demonstrate that short-term estradiol use following loss of ovarian function has long-lasting effects on hippocampal function and memory by dynamically regulating cellular mechanisms that promote activity of ERα in the absence of circulating estrogens. Translational impacts of these findings suggest lasting cognitive benefits of short-term estrogen use near menopause and highlight the importance of hippocampal ERα—independent from the role of circulating estrogens—in regulating memory in aging females.Significance statementDeclines in ovarian hormones following menopause coincide with increased risk of cognitive decline. Due to potential health risks, current recommendations are that menopausal estrogen therapy be limited to a few years. Long-term consequences for the brain and memory of this short-term midlife estrogen therapy are unclear. Here, in a rodent model of menopause, we determined mechanisms by which short-term midlife estrogen exposure can enhance hippocampal function and memory with cognitive benefits and molecular changes enduring long after termination of estrogen exposure. Our model indicates long-lasting benefits of maintaining hippocampal estrogen receptor function in the absence of ongoing estrogen exposure and suggests potential strategies for combating age-related cognitive decline.
An Open and Continuously Updated Fern Tree of Life
Authors: Nitta Joel H. , Schuettpelz Eric , Ramírez-Barahona Santiago , Iwasaki Wataru 
Published: April 2022

1AbstractFerns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated.Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification.The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies.FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.
Direct and indirect impacts of positive selection on genomic variation in Drosophila serrata
Authors: Wang Yiguan , Reddiex Adam J. , Allen Scott L. , Chenoweth Stephen F. 
Published: April 2022

AbstractUnderstanding the extent to which microevolutionary adaptation relies on novel beneficial mutations, as opposed to previously neutral standing genetic variation, is an important goal of evolutionary genetics. Progress towards this goal has been enhanced during the genomic era through the study of selective sweeps. Selective sweeps fall into two categories: hard sweeps via new mutations and soft sweeps via pre-existing mutations. However, data are currently lacking on the relative frequency of these two types of selective sweep. In this study, we examined 110 whole genome sequences from Drosophila serrata sampled from eastern Australia and searched for hard and soft sweeps using a deep learning algorithm (diploS/HIC). Analyses revealed that approximately 15% of the D. serrata genome was directly impacted by soft sweeps, and that 46% of the genome was indirectly influenced via linkage to these soft sweeps. In contrast, hard sweep signatures were very rare, only accounting for 0.1% of the scanned genome. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under frequent selection due to evolutionary arms races (e.g. immunity and sperm competition) were detected. Within soft sweep regions and those flanking them, there was an over-representation of SNPs with predicted deleterious effects, suggesting positive selection drags deleterious variants to higher frequency due to their linkage with beneficial loci. This study provides insight into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.