bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intelligibility improves perception of timing changes in speech
Authors: Zoefel Benedikt , Gilbert Rebecca A. , Davis Matthew H. 
Published: May 2022

AbstractAuditory rhythms are ubiquitous in music, speech, and other everyday sounds. Yet, it is unclear how perceived rhythms arise from the repeating structure of sounds. For speech, it is unclear whether rhythm is solely derived from acoustic properties (e.g., rapid amplitude changes), or if it is also influenced by the linguistic units (syllables, words, etc.) that listeners extract from intelligible speech. Here, we present three experiments in which participants were asked to detect an irregularity in rhythmically spoken speech sequences. In each experiment, we reduce the number of possible stimulus properties that differ between intelligible and unintelligible speech sounds and show that these acoustically-matched intelligibility conditions nonetheless lead to differences in rhythm perception. In Experiment 1, we replicate a previous study showing that rhythm perception is improved for intelligible (16-channel vocoded) as compared to unintelligible (1-channel vocoded) speech – despite near-identical broadband amplitude modulations. In Experiment 2, we use spectrally-rotated 16-channel speech to show the effect of intelligibility cannot be explained by differences in spectral complexity. In Experiment 3, we compare rhythm perception for sine-wave speech signals when they are heard as non-speech (for naïve listeners), and subsequent to training, when identical sounds are perceived as speech. In all cases, detection of rhythmic regularity is enhanced when participants perceive the stimulus as speech compared to when they do not. Together, these findings demonstrate that intelligibility enhances the perception of timing changes in speech, which is hence linked to processes that extract abstract linguistic units from sound.
Prelimbic cortex neural encoding dynamically tracks expected outcome value
Authors: Niedringhaus Mark , West Elizabeth A. 
Published: May 2022

AbstractAnimals must modify their behavior based on updated expected outcomes in a changing environment. Prelimbic cortex (PrL) neural encoding during learning predicts and is necessary for appropriately altering behavior based on new expected outcome value following devaluation. We aimed to determine how PrL neural activity encodes reward predictive cues after the expected outcome value of those cues is decreased following conditioned taste aversion. In one post- devaluation session, rats were tested under extinction to determine their ability alter their behavior to the expected outcome values (i.e., extinction test). In a second post-devaluation session, rats were tested with the newly devalued outcome delivered so that the rats experienced the updated outcome value within the session (i.e., re-exposure test). We found that PrL neural encoding to the cue associated with the devalued reward predicted the ability of rats to suppress behavior in the extinction test session, but not in the re-exposure test session. While all rats were able to successfully devalue the outcome during conditioned taste aversion, a subset of rats continued to consume the devalued outcome in the re-exposure test session. We found differential patterns of PrL neural encoding in the population of rats that did not avoid the devalued outcome during the re-exposure test compared to the rats that successfully avoided the devalued outcome. Our findings suggest that PrL neural encoding dynamically tracks expected outcome values, and differential neural encoding in the PrL to reward predictive cues following expected outcome value changes may contribute to distinct behavioral phenotypes.
Can machine learning with data from wearable devices distinguish disease severity levels and generalise across patients? A pilot study in Mania and Depression
Authors: Li Bryan M. , Corponi Filippo , Anmella Gerard , Mas Ariadna , Sanabra Miriam , Pacchiarotti Isabella , Valentí Marc , Giménez-Palomo Anna , Garriga Marina , Agasi Isabel , Bastidas Anna , Fernández-Plaza Tabatha , Arbelo Néstor , Cavero Myriam , García-Rizo Clemente , Bioque Miquel , Verdolini Norma , Madero Santiago , Murru Andrea , Grande Iria , Amoretti Silvia , Ruiz Victoria , Fico Giovanna , De Prisco Michele , Oliva Vincenzo , Vieta Eduard , Hidalgo-Mazzei Diego 
Published: May 2022

AbstractMood disorders are severe and chronic mental conditions exacting high costs from society. The lack of reliable biomarkers to aid clinicians in tailoring pharmacotherapy based on distinguishable patient-specific traits means that the current prescribing paradigm is largely one of trial and error. Previous studies showed that different biological signatures, such as patterns of heart rate variability or electro-dermal reactivity, are associated with clinically meaningful outcomes. Against this backdrop, the advances in machine learning and the spread of wearable devices capable of providing continuous and ecological monitoring of patients may unlock great opportunities in mental healthcare. We herewith present a pilot study on mania and depression where we moved beyond the simple disease state binary classification but pursued the more informative and clinically meaningful task of differentiating between levels of disease severity. While most previous similar endeavours used recording segments extracted from the same subjects for both training and testing, we explicitly carried out model development and evaluation on segments from different groups of patients, in order to have a fair assessment of the model out-of-sample generalisation. This illustrated how individuals heterogeneity and non-disease-related dimensions of variations (e.g. sex, age, physical fitness) may dominate the signal so that in low sample size regimes a model might learn and overfit subject-specific patterns rather than capturing disease-relevant traits generalisable across disorders. Lastly, we developed a viable baseline for pre-processing raw data from wristband recordings and compared three classical and two deep-learning models to identify levels of disease severity.
Emergence of a Pseudomonas aeruginosa Hypermutator Strain During the Course of Ventilator-Associated Pneumonia
Authors: Nozick Sophie , Ozer Egon A. , Medernach Rachel , Kumar Rebecca , Mills Jori O. , Wunderink Richard G. , Qi Chao , Hauser Alan R. 
Published: May 2022

ABSTRACTHypermutator lineages of Pseudomonas aeruginosa arise frequently during the years of lung infection seen in patients with cystic fibrosis and bronchiectasis but are rare in the absence of structural lung disease. Since the onset of the COVID-19 pandemic, large numbers of patients have remained mechanically ventilated for extended periods of time. These patients are prone to acquire bacterial pathogens that persist for many weeks and have the opportunity to evolve within the pulmonary environment. However, little is known about what types of adaptations occur in these bacteria and whether these adaptations mimic those described in chronic infections. We describe a COVID-19 patient with a secondary Pseudomonas aeruginosa lung infection in which the causative bacterium persisted for >90 days. During the course of this infection, a hypermutator lineage of P. aeruginosa emerged and co-existed with a non-hypermutator lineage. Compared to the parental lineage, the hypermutator lineage evolved to be more extensively resistant to antibiotics, to change its type III secretion profile, and to grow more slowly. Genomic analyses of the hypermutator lineage identified numerous mutations, including in the mismatch repair gene mutL and other genes frequently mutated in individuals with cystic fibrosis. Together, these findings demonstrate that hypermutator phenotypes can emerge when clearance of P. aeruginosa fails to occur in typically acute infections such as ventilator-associated pneumonia and suggest that hypermutator lineages can affect patient treatments and outcomes.
Extensive acquisition of carbapenem-resistant Acinetobacter baumannii in Intensive Care Unit patients is driven by widespread environmental contamination
Authors: Doughty Emma L. , Liu Haiyang , Moran Robert A. , Hua Xiaoting , Ba Xiaoliang , Guo Feng , Chen Xiangping , Zhang Linghong , Holmes Mark , van Schaik Willem , McNally Alan , Yu Yunsong 
Published: May 2022

AbstractCarbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations. A three-month prospective observational study was conducted in a 28-bed intensive care unit (ICU) in Hangzhou, China. A total of 3985, 964 and 119 samples were collected from the hospital environment, patients and staff, respectively. CRAB were isolated from 10.75% of collected samples (n = 551) and whole-genome sequenced. The ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.27 % of all isolates) that could be divided into 20 distinct clusters. CRAB was persistently present in the ICU, driven by regular introductions of distinct clusters. The hospital environment was heavily contaminated, with CRAB isolated from bed units on 183/335 (54.63 %) sampling occasions but from patients on only 72/299 (24.08 %) occasions. CRAB was spread to adjacent bed units and rooms and following re-location of patients within the ICU. We also observed that, over the course of this study, three different plasmids had transferred between CRAB strains in the ICU. The epidemiology of CRAB in this setting contrasted with previously described clonal outbreaks in high-income countries, highlighting the importance of environmental CRAB reservoirs in ICU epidemiology. There is an urgent need for targeted infection prevention and control interventions in endemic settings that can address the global threat posed by this against this multidrug-resistant opportunistic pathogen.
A Functional Genomics Pipeline to Identify High-Value Asthma and Allergy CpGs in the Human Methylome
Authors: Morin Andréanne , Thompson Emma E. , Helling Britney A. , Shorey-Kendrick Lyndsey E. , Faber Pieter , Gebretsadik Tebeb , Bacharier Leonard B. , Kattan Meyer , O’Connor George T. , Rivera-Spoljaric Katherine , Wood Robert A. , Barnes Kathleen C. , Mathias Rasika A. , Altman Matthew C. , Hansen Kasper , McEvoy Cindy T. , Spindel Eliot R. , Hartert Tina , Jackson Daniel J. , Gern James E. , McKennan Chris G. , Ober Carole 
Published: May 2022

AbstractBackgroundDNA methylation of cytosines at CpG dinucleotides is a widespread epigenetic mark; but genome-wide variation has been relatively unexplored due to the limited representation of variable CpGs on commercial high-throughput arrays.ObjectiveTo explore this hidden portion of the epigenome, we combined whole-genome bisulfite sequencing (WGBS) with in silico evidence of gene regulatory regions to design a custom array of high-value CpGs. We focused these studies in airway epithelial cells from children with and without allergic asthma because these cells mediate the effects of inhaled microbes, pollution, and allergens on asthma and allergic disease risk.MethodsWe identified differentially methylated regions (DMRs) from WGBS in nasal epithelial cell (NEC) DNA from 39 children with and without allergic asthma of both European and African ancestries. We selected CpGs from DMRs, previous allergy or asthma Epigenome-Wide Association Studies (EWAS), or Genome-Wide Association Study (GWAS) loci, and overlapped them with functional annotations for inclusion on a custom Asthma&Allergy array. Using both the Custom and EPIC arrays, we performed EWAS of allergic sensitization (AS) in NEC DNA from children in the URECA birth cohort and using the Custom array in the INSPIRE birth cohort. We assigned each CpG on the arrays to its nearest gene and its promotor capture Hi-C interacting gene and performed expression quantitative trait methylation (eQTM) studies for both sets of genes.ResultsCustom array CpGs were enriched for intermediate methylation (IM) levels compared to EPIC CpGs. IM CpGs were further enriched among those associated with AS and for eQTMs on both arrays.ConclusionsOur study revealed signature features of high-value CpGs and evidence for epigenetic regulation of genes at AS EWAS loci that are robust to race/ethnicity, ascertainment, age, and geography.Clinical ImplicationsThese studies identified allergic sensitization-associated differentially methylated CpGs and their target genes in airway epithelium, providing potential epigenetic mechanisms in the development of allergic diseases and suggesting novel drug targets.Capsule SummaryThis study of previously unexplored regions of the airway epithelial methylome revealed novel epigenetic mechanisms regulating genes previously implicated in the pathogenesis of asthma and allergic diseases.
Estimating Vaccine-Preventable COVID-19 Deaths Under Counterfactual Vaccination Scenarios in the United States
Authors: Zhong Ming , Kshirsagar Meghana , Johnston Richard , Dodhia Rahul , Glazer Tammy , Kim Allen , Michael Divya , Nair-Desai Sameer , Tsai Thomas C. , Friedhoff Stefanie , Lavista Ferres Juan M. 
Published: May 2022

AbstractImportanceWith an abundant supply of COVID-19 vaccines becoming available in spring and summer 2021, the major barrier to high vaccination rates in the United States has been a lack of vaccine demand. This has contributed to a higher rate of deaths from SARS-CoV-2 infections amongst unvaccinated individuals as compared to vaccinated individuals. It is important to understand how low vaccination rates directly impact deaths resulting from SARS-CoV-2 infections in unvaccinated populations across the United States.ObjectiveTo estimate a lower bound on the number of vaccine-preventable deaths from SARS-CoV-2 infections under various scenarios of vaccine completion, for every state of the United States.Design, Setting, and ParticipantsThis counterfactual simulation study varies the rates of complete vaccination coverage under the scenarios of 100%, 90% and 85% coverage of the adult (18+) population of the United States. For each scenario, we use U.S. state-level demographic information in conjunction with county-level vaccination statistics to compute a lower bound on the number of vaccine-preventable deaths for each state.ExposuresCOVID-19 vaccines, SARS-CoV-2 infectionMain Outcomes and MeasuresDeath from SARS-CoV-2 infectionResultsBetween January 1st, 2021 and April 30th, 2022, there were 641,305 deaths due to COVID-19 in the United States. Assuming each state continued peak vaccination capacity after initially achieving its peak vaccination rate, a vaccination rate of 100% would have led to 322,324 deaths nationally, that of 90% would have led to 415,878 deaths, and that of 85% would have led to 463,305 deaths. As a comparison, using the state with the highest peak vaccination rate (per million population each week) for all the states, a vaccination rate of 100% would have led to 302,344 deaths nationally, that of 90% would have led to 398,289 deaths, and that of 85% would have led to 446,449 deaths.Conclusions and RelevanceOnce COVID-19 vaccine supplies peaked across the United States, if there had been 100% COVID-19 vaccination coverage of the over 18+ population, a conservative estimate of 318,981 deaths could have been potentially avoided through vaccination. For a 90% vaccination coverage, we estimate at least 225,427 deaths averted through vaccination, and at least 178,000 lives saved through vaccination for an 85% vaccination coverage.
Sex differences in the change in cardiorespiratory fitness and additional physical and mental health outcomes after exercise training in adults with atrial fibrillation: a systematic review protocol
Authors: Vidal-Almela Sol , Marçal Isabela R. , Terada Tasuku , O’Neill Carley D. , Reed Jennifer L. 
Published: May 2022

ABSTRACTBackgroundPatients with atrial fibrillation (AF), the most common sustained cardiac arrhythmia, often have a low cardiorespiratory fitness (CRF) and poor physical and mental health due to disabling AF symptoms. This is more pronounced in females, who also report worse AF symptoms and quality of life (QoL) than males. Improving CRF through exercise training is an important AF management target associated with lower hospitalization and mortality rates. Emerging research suggests smaller CRF improvements in females than males following the same exercise training program. Yet, this has not been systematically reviewed in the AF population. The primary purpose of this systematic review is to compare changes in CRF following exercise training between females and males with AF. Secondary aims will compare changes in AF symptoms, QoL and additional physical and mental health outcomes between sexes.MethodsWe will adhere to the reporting guidelines of the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) statement. Five electronic bibliographic databases are being searched to identify studies with prospective cohort and experimental designs, implementing exercise training of any form (e.g. aerobic, strength) for at least 4 weeks, in adults (≥18 years old) with an AF diagnosis. Eligible studies must report a baseline and follow-up measure of at least one primary or secondary outcome. CRF (primary outcome) can be estimated or directly measured as peak oxygen consumption (VO2peak). When eligible results are not segregated by sex, authors will be contacted to obtain sex-specific data. Study quality and risk of bias will be assessed using the Tool for the assEssment of Study qualiTy and reporting in EXercise (TESTEX) scale and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Meta-analyses will be conducted to synthesize the measures of effect in studies with sufficient homogeneity.DiscussionThis review will address the lack of sex-based analyses in exercise studies in the AF population. By using a sex lens, we will provide evidence on the physical and mental health effects of exercise training in females and males with AF. Our findings will be of value to patients with AF, researchers and healthcare providers involved in AF management.Systematic review registrationPROSPERO #CRD42022302310
Direct and indirect phenotypic effects on sociability indicate potential to evolve
Authors: Fisher David N. 
Published: May 2022

AbstractThe decision to leave or join a group is important as group size influences many aspects of organisms’ lives and their fitness. This tendency to socialise with others, sociability, should be influenced by genes carried by focal individuals (direct genetic effects) and by genes in partner individuals (indirect genetic effects), indicating the trait’s evolution could be slower or faster than expected. However, estimating these genetic parameters is difficult. Here, in a laboratory population of the cockroachBlaptica dubia, I estimate phenotypic parameters for sociability: repeatability (R) and repeatable influence (RI), that indicate whether direct and indirect genetic effects respectively are likely. I also estimate the interaction coefficient (Ψ), which quantifies how strongly a partner’s trait influences the phenotype of the focal individual and is key in models for the evolution of interacting phenotypes. Focal individuals were somewhat repeatable for sociability across a three-week period (R= 0.083), and partners also had marginally consistent effects on focal sociability (RI= 0.055). The interaction coefficient was non-zero, although in opposite sign for the sexes; males preferred to associate with larger individuals (Ψmale= −0.129) while females preferred to associate with smaller individuals (Ψfemale= 0.068). Individual sociability was consistent between dyadic trials and in social networks of groups. These results provide phenotypic evidence that direct and indirect genetic effects have limited influence on sociability, with perhaps most evolutionary potential stemming from heritable effects of the body mass of partners. Sex-specific interaction coefficients may produce sexual conflict and the evolution of sexual dimorphism in social behaviour.
Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota
Authors: Baldo Laura , Tavecchia Giacomo , Rotger Andreu , Igual José Manuel , Riera Joan Lluís 
Published: May 2022

AbstractIntegrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Islands provide ideal natural systems to understand the biogeographic patterns that shape these symbiotic associations, their resilience and plasticity over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Here we used the Balearic wall lizard Podarcis lilfordi to address the diversification of the holobiont in an insular context by dissecting the drivers of the gut microbiota diversity within and across host allopatric populations. By extensive fecal sampling of individually identified lizards from three closed populations/islets in the South of Mallorca (Na Moltona, Na Guardis and En Curt) along two years and two seasons (spring and autumn), we sorted out the effect of islet, year, season, sex and partly life stage on the microbiota composition. We further related microbiota distances to host genetics and trophic ecology. Overall, the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (as inferred by microsatellites) and trophic niche distances (as inferred by stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) persisted along the four sampling dates. Microbial diversity was driven by life stage and season, with no annual or sex effect. Seasonal changes within islets were mainly associated with fluctuations in the relative abundances of few bacterial taxa (mostly families Lachnospiraceae and Ruminococcaceae), consistently in both sampled years and without any major compositional turnover. These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also suggest an undergoing process of parallel diversification of the holobiont. The cyclic seasonal fluctuations in gut microbiota composition hint to an important plasticity of these bacterial communities in response to the host annual physiological/metabolic shifts. The importance of these microbial community dynamics in the host ecology and dietary flexibility remains to be investigated.