bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electronic health record biobank cohort recapitulates an association between theMUC5Bpromoter polymorphism and ARDS in critically ill adults
Authors: Kerchberger V. Eric , McNeil J. Brennan , Zheng Neil , Chang Diana , Rosenberger Carrie , Rogers Angela J. , Bastarache Julie A. , Feng QiPing , Wei Wei-Qi , Ware Lorraine B. 
Published: August 2024

ABSTRACTBackgroundLarge population-based DNA biobanks linked to electronic health records (EHRs) may provide novel opportunities to identify genetic drivers of ARDS.Research QuestionCan we develop an EHR-based algorithm to identify ARDS in a biobank database, and can this validate a previously reported ARDS genetic risk factor?Study Design and MethodsWe analyzed two parallel genotyped cohorts: a prospective biomarker cohort of critically ill adults (VALID), and a retrospective cohort of hospitalized participants enrolled in a de-identified EHR biobank (BioVU). ARDS was identified by clinician-investigator review in VALID and an EHR algorithm in BioVU (EHR-ARDS). We tested the association between theMUC5Bpromoter polymorphism rs35705950 with development of ARDS, and assessed if age modified this genetic association in each cohort.ResultsIn VALID, 2,795 patients were included, age was 55 [43, 66] (median [IQR]) years, and 718 (25.7%) developed ARDS. In BioVU, 9,025 hospitalized participants were included, age was 60 [48, 70] years, and 1,056 (11.7%) developed EHR-ARDS. We observed a significant age-related interaction effect on ARDS in VALID: among older patients, rs35705950 was associated with increased ARDS risk (OR: 1.44; 95%CI 1.08-1.92; p=0.012) whereas among younger patients this effect was absent (OR: 0.84; 95%CI: 0.62-1.14; p=0.26). In BioVU, rs35705950 was associated with increased risk for EHR-ARDS among all participants (OR: 1.20; 95%CI: 1.00-1.43, p=0.043) and this did not vary by age. The polymorphism was also associated worse oxygenation in mechanically ventilated BioVU participants, but had no association with oxygenation in VALID.InterpretationTheMUC5Bpromoter polymorphism was associated with ARDS in two cohorts of at-risk adults. Although age-related effect modification was observed only in VALID, BioVU identified a consistent association betweenMUC5Band ARDS risk regardless of age, and a novel association with oxygenation impairment. Our study highlights the potential for EHR biobanks to enable precision-medicine ARDS studies.
Novel RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria
Authors: Ignatov Dmitriy , Shanmuganathan Vivekanandan , Ahmed-Begrich Rina , Alagesan Kathirvel , Frese Christian Karl , Wang Chu , Krause Kathrin , Charpentier Emmanuelle 
Published: August 2024

AbstractThe ribosome employs a set of highly conserved translation factors to efficiently synthesise proteins. Some translation factors interact with the ribosome in a transient manner and are thus challenging to identify. However, proteins involved in translation can be specifically identified by their interaction with ribosomal RNAs. Using a combination of proteomics approaches, we identified novel RNA binding proteins in the pathogenic bacteriumStreptococcus pyogenes. One of these, a universally conserved protein YebC, was shown to transiently interact with 23S rRNA near the peptidyl-transferase centre. Deletion ofyebCmoderately affected the physiology and virulence ofS. pyogenes. We performed ribosome profiling and detected increased pausing at proline-rich amino acid stretches in the absence of functional YebC. Further results obtained within vivoreporters andin vitrotranslation system suggest that YebC is a novel translation factor required for efficient translation of proteins with proline-rich motifs.
Exploring the role of the rich club in network control of neurocognitive states
Authors: Podschun Alina N. , Betzel Richard F. , Braun Urs , Markett Sebastian 
Published: August 2024

AbstractWe present a systematic analysis of the rich club as a possible control center of brain dynamics. Contrary to research stressing control properties of the rich club, our results indicate that the rich club and high-degree regions were not involved in optimally controlling the human connectome for a set of data-driven and task-evoked patterns of activity. Indeed, low-degree peripheral regions were more suited towards this. Findings were stable across group-level and individual-level rich club definitions, various cognitively meaningful brain state transitions, and different parameter settings. A region’s contribution to optimal control processes was associated with its affiliation with certain intrinsic connectivity networks and its position on the secondary, but not primary, cortical gradient. These results do not negate an integratory role of the rich club, but merely question its proposed role as a driver of control. Indeed, if it would inhabit such a role, we would have expected opposite results. Our findings fit with a position describing the rich club as a passive “data-highway” which, by means of its high connectivity, can be easily controlled by peripheral regions and thus facilitate relevant communication channels between them. We call for methodological expansions of the control theoretical toolbox allowing for elaborations on the temporal dynamics of control processes.
Tameness selection pressure affects gut virome diversity in mice
Authors: Biswa Bhim B. , Fujiwara Kazumichi , Toyoda Atsushi , Koide Tsuyoshi 
Published: August 2024

AbstractThe gut microbiome, a complex ecosystem comprising bacteria, viruses, archaea, fungi, and other microorganisms, plays a pivotal role in host health, immunity, and behaviour. Among its components, bacteriophages and viruses that infect bacteria significantly influence microbial community dynamics by affecting bacterial diversity, function, and evolution. Despite extensive research on bacterial components, the viral metagenome (virome) remains relatively unexplored. This study investigated the effect of selective breeding for tameness on the gut virome of wild heterogeneous stock (WHS) mice. WHS mice were selectively bred for active tameness, resulting in four groups: S1 and S2 (selected for tameness), and C1 and C2 (non-selected). In previous study, we observed an increased abundance ofLimosilactobacillus reuteriin tame groups compared to non-selected groups, as well as a tameness-promoting effect ofL. reuteriwith long-term administration. Given the regulatory role of phages in bacterial populations, this study focused on analysing the gut virome using shotgun metagenome sequencing data. From the 84 samples, we generated 6078 non-redundant viral operational taxonomic units (vOTUs) and identified the hosts of 3,065 of these vOTUs. Significant differences in gut virome beta diversity were observed between the selectively bred and control groups, suggesting that tameness selection exerts distinct pressure on the virome. Additionally, phage-host interaction analysis revealed strong correlations between specific phages and their bacterial hosts, indicating a co-occurrence that influences host behaviour. Overall, this study provides novel insights into the role of the gut virome in shaping host behaviour and highlights the broader implications of microbial contributions to domestication and selective breeding outcomes.
An exploration of unusual antimicrobial resistance phenotypes inSalmonellaTyphi from Blantyre, Malawi reveals the ongoing role of IncHI1 plasmids
Authors: Zuza Allan , Wailan Alexander M , Anscombe Catherine , Feasey Nicholas A , Heinz Eva 
Published: August 2024

AbstractTyphoid fever is a significant public health problem endemic in Southeast Asia and Sub- Saharan Africa. Antimicrobial treatment of typhoid is however threatened by the increasing prevalence of antimicrobial resistant (AMR)S.Typhi, especially in the globally successful lineage (4.3.1) which has rapidly spread in East and Southern Africa. AMR elements can be found either on plasmids or in one of the three chromosomal integration sites, and there is variability of this across the lineage. Several previous studies with Malawian isolates indicated a clonal, locally spreading lineage with chromosomally integrated resistance genes. In a recent study however we noted three isolates with unusual predicted resistance profiles, and we here present the resolved genomes of these isolates using long- and short-read sequencing. Our work shows that these isolates are potentially imported cases, most closely related to the recently described sub-lineage 4.3.1.EA1, and encode IncHI1 plasmids with reduced resistance profiles compared to the major reference sequence of these plasmids spreading in East Africa. Similar reduced resistance plasmids were reported in a recent large-scale study in five isolates from Tanzania, highlighting the urgency for better coverage of the African continent in genome studies to better understand the dynamics of these potentially co-circulating plasmids.
Estimates of the Prevalence of Autism Spectrum Disorder in the Middle East and North Africa Region: A Systematic Review and Meta-Analysis
Authors: Akomolafe Aishat F. , Abdallah Bushra M. , Mahmood Fathima R. , Elshoeibi Amgad M. , Al-Khulaifi Aisha Abdulla , Mahmoud Elhassan , Dweidri Yara , Darwish Nour , Yousif Duaa , Khalid Hafsa , Al-Theyab Majed , Azeem Muhammad Waqar , Shahwar Durre , Kamal Madeeha , Alabdulla Majid , Khaled Salma M. , Chivese Tawanda 
Published: August 2024

AbstractBackground and ObjectiveEstimates of the prevalence of the autism spectrum disorder (ASD) in the Middle East and North Africa (MENA) region are not readily available, amid a lack of recent evidence. In this study, we estimated the prevalence of ASD in the MENA region by synthesising evidence from published studies in the region.MethodsIn this systematic review and meta-analysis, we searched PubMed, EMBASE, Scopus, and CINAHL databases for studies which assessed ASD prevalence in the MENA region. Risk of bias was assessed using the Newcastle Ottawa scale. A bias-adjusted inverse variance heterogeneity meta-analysis model was used to pool prevalence estimates from included studies. Cochran’s Q statistic and the I2statistic were used to assess heterogeneity, and publication bias assessed using funnel and Doi plots.ResultsA total of 3075 studies were identified, 16 studies of which met the inclusion criteria and involved 3,727,731 individuals. The studies were published during the period 2007-2022, and included individuals from Iran, Oman, Libya, Egypt, Kingdom of Saudi Arabia (KSA), Lebanon, United Arab Emirates (UAE), Bahrain and Qatar. Estimates of ASD prevalence ranged from 0.01% in Oman during the period June 2009-December 2009, to a high of 2.51% in the Kingdom of Saudi Arabia during the period December 2017-March 2018. The pooled prevalence of ASD was 0.13% (95% CI: 0.01% – 0.33%), with significant heterogeneity (I2= 99.8%). For Iran, the only country with multiple analysable studies, an overall prevalence of 0.06% (95% CI: 0.00 – 0.19, I2=97.5%, n= 6 studies) was found. A review of data from countries with repeated studies suggested that the prevalence of ASD is increasing.ConclusionEstimates of the prevalence of ASD vary widely across the MENA region, from 0.01% in Oman to 2.51% in Saudi, with an overall prevalence of 0.13%. Existing data suggests a trend towards increasing prevalence in the region. More and better-quality research is needed to provide up to date ASD prevalence estimates.RegistrationThe protocol for this systematic review and meta-analysis was registered on the International Prospective Register of Systematic Reviews (PROSPERO) with registration ID CRD42024499837.
Neuropathologic and proteomic analysis of human hippocampal CA1 pyramidal neuron sublayers in human Alzheimer’s disease
Authors: Reyes Isabel , Kanshin Evgeny , Tian Chengju , Faustin Arline , Ueberheide Beatrix M. , Masurkar Arjun V. 
Published: August 2024

AbstractHippocampal area CA1 is vulnerable to Alzheimer’s disease (AD) pathology, but if and how CA1 pyramidal neuron (PN) subpopulations are impacted is unclear. Specifically, CA1 PNs can be divided into a superficial (sPN) and deep (dPN) layer that have distinct molecular and functional properties. Understanding AD pathophysiology at the level of these CA1 PN subpopulations may inform on mechanisms of vulnerability and cognitive dysfunction. We first quantified amyloid plaque and tau pathology in Braak stage V-VI human AD cases, revealing that the sPN layer shows much higher levels of AD pathology compared to the dPN layer. We then performed quantitative localized proteomics of sPN and dPN layers in Braak stage VI human AD cases, which revealed that the two layers show disease- and function-related molecular differences that support relative hyperexcitability of sPNs and markers of delayed neurodegeneration in dPNs. In sum, these findings support that sPNs are differentially vulnerable in human AD.
Marine spatial planning to enhance coral adaptive potential
Authors: Forrest Daniel L. , McManus Lisa C. , Tekwa Eden W. , Schindler Daniel E. , Colton Madhavi A. , Webster Michael M. , Fox Helen E. , Essington Timothy E. , Palumbi Stephen R. , Mumby Peter J. , DeFilippo Lukas , Schill Steven R. , Pollock F. Joseph , Pinsky Malin L. 
Published: August 2024

AbstractOcean warming interacts with local stressors to negatively affect coral reefs. The adaptive capacity of reefs to survive these stressors is driven by ecological and evolutionary processes occurring at multiple spatial scales. Marine protected area (MPA) networks are one solution that can address both local and regional threats, yet the impacts of MPA network design on adaptive processes remains unclear. In this paper, we used an eco-evolutionary model to simulate hypothetical MPA configurations in the Caribbean, Southwest Pacific and Coral Triangle under projected warming. We found that protecting thermal refugia (i.e., cooler reefs) largely benefited corals inside the refugia while other reefs declined. In contrast, protecting a diverse habitat portfolio led to increased coral cover both inside and outside of the MPA network. We then quantified the thermal habitat and connectivity representations of reefs both inside and outside existing MPA networks across each region. Most strikingly, reefs in current MPA networks in the Southwest Pacific and Coral Triangle are approximately 2 °C cooler than reefs outside the MPA networks, while the Caribbean’s MPA network is approximately 1 °C warmer than reefs outside the network, based on mean temperatures from 2008-2018. These results suggest that the Caribbean MPA network is poised to protect sources of warm-adapted larvae but not destinations, and the opposite is true of the Southwest Pacific and Coral Triangle. Our results suggest that 1) by protecting sites with particular temperature and connectivity characteristics, marine spatial planning may alter eco-evolutionary processes to enhance or inhibit the adaptive capacity of a reef network and 2) the distribution, extent, and effectiveness of local interventions have the potential to affect regional distributions of coral cover beyond what would be expected from local benefits alone, due to the potentially wide-reaching effects of larval dispersal and gene flow.
Distribution and Temporal Changes of Autoantibody-Mediated Pathogenic Mechanisms Among Acetylcholine Receptor-Positive Myasthenia Gravis Patients
Authors: Khani-Habibabadi Fatemeh , Roy Bhaskar , Pham Minh C , Obaid Abeer H , Filipek Beata , Nowak Richard J , O’Connor Kevin C 
Published: August 2024

AbstractObjectiveGiven that acetylcholine receptor-positive (AChR+) myasthenia gravis (MG) is mediated by AChR- specific autoantibodies, the emergence of new therapeutics underscores the importance of investigating AChR-specific autoantibody repertoire. This study aimed to assess the distribution of AChR-specific autoantibody isotypes, IgG subclasses, and the pathogenic mechanisms they mediate in AChR+ MG patients. Furthermore, we investigated longitudinal changes in autoantibody repertoire and the associated pathogenic mechanisms.MethodsSerum samples (N=210) from 50 AChR+ generalized MG patients collected longitudinally over two years as part of the B-Cell Targeted Treatment in MG (BeatMG) study were evaluated using a set of cell-based assays.ResultsIn cross-sectional samples, IgA and IgM AChR-specific autoantibodies were observed in the co-occurrence of IgG in 10% and 12% of patients, respectively. Among them, 4% had all three isotypes. AChR-IgG1 was found in 67.4%, followed by IgG3 (21.7%) and IgG2 (17.4%). Complement was active in 84.8%, followed by AChR internalization (63%) and blocking (30.4%). Complement and AChR internalization were simultaneously active in 45.6%, complement and blocking were active in 10.8%, and all three pathomechanisms were active in 17.4%. Blocking alone was active in only 2.1%; AChR internalization alone was not found. Temporal fluctuations of autoantibody isotypes/ IgG subclasses and the associated pathogenic mechanisms were observed.InterpretationThese results demonstrate that a subset of patients have autoantibodies that can mediate pathogenic mechanisms and include isotypes/IgG subclasses that current therapeutics may not effectively target. Accordingly, defining individual patient AChR-specific autoantibody profiles may afford more accurate application of therapeutics designed to target specific autoantibody-mediated mechanisms.
A Rapid Assessment of Mortality Surveillance in Uganda
Authors: Zalwango Marie Gorreti , Kyozira Caroline , Nambuya Mariam , Bulamu Martin , Muruta Allan 
Published: August 2024

AbstractBackgroundMortality surveillance aids in identifying and addressing their causes allowing health systems to adapt and respond effectively. This rapid assessment aimed to create awareness on the state of mortality surveillance in Uganda, highlight existing gaps and provide recommendations required for an improved mortality system hence the eventual improvement of public health in the country.MethodsAn assessment of mortality surveillance in Uganda was conducted from November 2023 to June 2024 through data reviews and plenary discussions engaging various stakeholders in Uganda. Eight (8) workshops/meetings were conducted over a period of eight months to generate information on mortality data sources, processes of data generation and challenges affecting the system. Reports generated from the meetings and workshops were summarized and presented as descriptive narratives. Data from DHIS2 was analyzed using excel and presented using charts and tables.ResultsThe rapid assessment of mortality surveillance in Uganda highlighted opportunities for improved mortality surveillance through the existence of various sources of data. It was highlighted that 66.9% of the death occur in communities, however, there is a major data completeness gaps where suboptimal data from the community is feed into the national health statistics database (DHIS2) to enable stakeholder analysis and utilization. Furthermore, a number of data quality issues were identified in the health facility generated data where 33% of the deaths occur. These include: data completeness where the national referral specialized health institutes do not feed their data into the national data base, late reporting and the lack of coordination and standardisation of reporting among the various partners.ConclusionThe existence of structures to conduct mortality surveillance in Uganda presents an opportunity for improved mortality surveillance despite the highlighted gaps and challenges. Adoption of strategies aimed to enable the successful implementation of an efficient mortality surveillance program like: strengthening governance and operations of death reporting activities, establishing a clear definition of institutional roles and responsibilities, raising awareness and advocacy at all levels, building technical capacities, improving allocation of resources, and leveraging on shared interests by both implementing and development partners could improve mortality surveillance and the health of the population through utilisation of the generated data.
Antidepressant efficacy of administering repetitive transcranial magnetic stimulation (rTMS) concurrently with psychological tasks or interventions: a scoping review and meta-analysis
Authors: Giron Cristian G. , Tang Alvin H.P. , Jin Minxia , Kranz Georg S. 
Published: August 2024

ABSTRACTCurrent approaches to optimize the efficacy of repetitive transcranial magnetic stimulation (rTMS) for depressive symptoms focus on personalizing targets and parameters. But what should occur during these three-to-forty-minute sessions remains under-investigated. Specific concerns include evidence suggesting brain state modulates the brain’s response to stimulation, and the potential to boost antidepressant efficacy by administering rTMS concurrently with psychological methods. Thus, conducted a scoping review and meta-analysis, per PRISMA-ScR guidelines, to pool studies that administered rTMS during psychological tasks or interventions. PubMed and Web of Science databases were searched from inception to 10 July 2024. Inclusion criteria: neuropsychiatric patients underwent rTMS; studies assessed depressive symptom severity; psychological tasks or interventions were administered during rTMS, or intentionally did not include a wash-out period. Of 8442 hits, 20 studies combined rTMS with aerobic exercise, bright light therapy, cognitive training or reactivation, psychotherapy, sleep deprivation, or a psychophysical task. Meta-analyses with random effects models pooled the efficacy of these combinations, based on change scores on depressive severity scales. The effect size was large and therapeutic for uncontrolled pretest-posttest comparisons (17 studies, 20 datasets, g=-1.91, SE=0.45, 95%CI= −2.80 to −1.03, p<0.01); medium when studies compared active combinations with sham rTMS plus active psychological methods (8 studies, g=-0.55, SE=0.14, 95%CI= −0.82 to −0.28, p<0.01); and non-significant when active combinations were compared with active rTMS plus sham psychological methods (4 studies, p= 0.96). These findings suggest that the antidepressant efficacy of combining rTMS with psychological methods is promising, but not an improvement over rTMS alone.
SARS-CoV-2 Surveillance in US Wastewater: Leading Indicators and Data Variability Analysis in the 2023-2024 Season
Authors: Schenk Hannes , Rauch Wolfgang , Zulli Alessandro , Boehm Alexandria B. 
Published: August 2024

AbstractWastewater-Based Epidemiology (WBE) has become a powerful tool for assessing disease occurrence in communities. This study investigates the coronavirus disease 2019 (COVID-19) epidemic in the United States during the 2023-2024 season using wastewater data from 189 wastewater treatment plants in 40 states and the District of Columbia. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pepper-mild mottle virus normalized SARS-CoV-2 concentration data were compared with COVID-19 hospitalization admission data at both national and state levels. We further investigate temporal features in wastewater viral abundance, with peak timing and cross-correlation lag analyses indicating that wastewater SARS-CoV-2 concentrations precede hospitalization admissions by 2 to 12 days. Lastly, we demonstrate that wastewater treatment plant size, assessed by number of population served, has a significant effect on the variability of measured SARS-CoV-2 concentrations. This study highlights the effectiveness of WBE as a non-invasive, timely and resource-efficient disease monitoring strategy, especially in the context of declining COVID-19 clinical reporting.