Changes in pneumococcal deaths in the United States following the COVID-19 pandemic.

Background: Changes in rates of death due to pneumococcus during the COVID-19 pandemic period from 2020 to 2022 are not well understood.

Methods: We obtained vital statistics data for the United States (National Center for Health Statistics), including age, sex, race/ethnicity, cause of death (ICD-10), 2014-2022. Generalized linear models were fit to the period from January 2014-February 2020 and extrapolated to March 2020-December 2022 to generate an expected number of pneumococcal deaths and a 95% prediction interval.

Unraveling the role of viral interference in disrupting biennial RSV epidemics in northern Stockholm.

Respiratory syncytial virus (RSV) primarily impacts infants and older adults, with seasonal winter outbreaks in temperate countries. Delayed RSV activity was reported worldwide during the 2009 influenza pandemic, and a disrupted biennial pattern of RSV activity was observed in northern Stockholm following the pandemic. Biennial patterns shifted to early/large outbreaks in even-numbered years and late/small outbreaks in odd-numbered years.

: Novel Genes in the locus.

Divergent transcription from bidirectional promoters is frequently observed in eukaryotic genomes, but the biological relevance of divergent RNA transcripts (DT) is unknown. We identified and characterized , a novel DT gene, and , a novel readthrough gene, in the locus containing , a gene with key roles in neuronal development, differentiation, and synaptic plasticity. is independent from the known antisense (), and its expression is developmentally regulated and positively correlated with in human postmortem dorsolateral prefrontal cortex (DLPFC).

Cross-species analysis of adult hippocampal neurogenesis reveals human-specific gene expression but convergent biological processes.

Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine-learning-augmented analysis of published single-nucleus RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development.

Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US.

In 2022, consecutive sweeps of highly transmissible SARS-CoV-2 Omicron-derived lineages (B.1.1.

Temporal changes in pneumococcal carriage among childcare-attending children during the COVID-19 pandemic in the Greater New Haven Area, USA.

Introduction: Non-pharmaceutical interventions (NPIs), which aimed to reduce transmission of SARS-CoV-2, also reduced the circulation of other respiratory pathogens. However, it remains unclear to what extent NPIs disrupted pneumococcal colonization in childcare settings. We investigated pneumococcal colonization dynamics in childcare centers in the Greater New Haven Area (USA) with varying levels of COVID-19-related NPI recommendations.

Utilizing virus genomic surveillance to predict vaccine effectiveness.

As new vaccines are being developed for fast-evolving viruses, determining when and how to update them, and what data should inform these decisions, remains a significant challenge. We developed a model to inform these vaccine updates in near real-time and applied it to SARS-CoV-2 by quantifying the relationship between vaccine effectiveness (VE) and genetic distance from mRNA vaccine formulation sequences using 10,156 genomes from Connecticut (April 2021-July 2024) and data from over one million controls, employing a two-stage statistical approach. We showed a strong inverse correlation between spike gene amino acid distance and VE; every 10 amino acid substitutions away from the vaccine sequences resulted in a 15.

Temporal changes in pneumococcal carriage among childcare-attending children during the COVID-19 pandemic in the Greater New Haven Area, USA.

Introduction: Non-pharmaceutical interventions (NPIs), which aimed to reduce transmission of SARS-CoV-2, also reduced the circulation of other respiratory pathogens. However, it remains unclear to what extent NPIs disrupted pneumococcal colonization in childcare settings. We investigated pneumococcal colonization dynamics in childcare centers in the Greater New Haven Area (USA) with varying levels of COVID-19-related NPI recommendations.

Exploring RSV transmission patterns in different age groups in the United States.

Respiratory syncytial virus (RSV) infections are a significant public health concern for pediatric populations and older adults, with seasonal winter outbreaks in the United States (US). Little is known about the timing of RSV epidemics across age groups and the relative contribution of within-group and between-group transmission of RSV in each age group. In this study, we analyzed RSV timing and transmission across age groups in 12 states from 2018 to 2024.

The Role of Viral Interference in Shaping RSV Epidemics Following the 2009 H1N1 Influenza Pandemic.

Background: Disruptions in respiratory syncytial virus (RSV) activity were observed in different countries following the 2009 influenza pandemic. Given the limited use of non-pharmaceutical interventions, these disruptions provide an opportunity to probe viral interference due to the out-of-season epidemics. The objectives of the study are twofold: to characterize atypical RSV activity in the United States (US) and to explore the mechanisms underlying changes in RSV epidemics following the pandemic.

Altered Brain-Behavior Association During Resting State is a Potential Psychosis Risk Marker.

Alterations in cognitive and neuroimaging measures in psychosis may reflect altered brain-behavior interactions patterns accompanying the symptomatic manifestation of the disease. Using graph connectivity-based approaches, we tested the brain-behavior association between cognitive functioning and functional connectivity at different stages of psychosis. We collected resting-state fMRI of 204 neurotypical controls (NC) in two independent cohorts, 43 patients with chronic psychosis (PSY), and 22 subjects with subthreshold psychotic symptoms (STPS).

Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: A genomic and spatial analysis.

Delays in identifying and treating individuals with infectious tuberculosis (TB) contribute to poor health outcomes and allow ongoing community transmission of M. tuberculosis (Mtb). Current recommendations for screening for tuberculosis specify community characteristics (e.

Global estimates of rotavirus vaccine efficacy and effectiveness: a rapid review and meta-regression analysis.

Background: Rotavirus is the leading cause of diarrhoea worldwide, particularly affecting young children. While national rotavirus immunization programs have reduced rotavirus morbidity and mortality, vaccine performance varies considerably between high-income and low-income settings.

Methods: We updated a previous systematic review of studies reporting rotavirus vaccine efficacy and vaccine effectiveness against severe rotavirus-associated gastroenteritis (RVGE) by performing a rapid review from July 1, 2020 through October 16, 2024.

Relating in vivo RSV infection kinetics to host infectiousness in different age groups.

Respiratory syncytial virus (RSV) infections are a major public health concern for pediatric populations and older adults. Viral kinetics, the dynamic processes of viral infection within an individual over time, vary across different populations. However, RSV transmission in different age groups is incompletely understood from the perspective of individual-level viral kinetics.

Estimated Effectiveness of Nirsevimab Against Respiratory Syncytial Virus.

Importance: Nirsevimab, a long-acting monoclonal antibody, demonstrated efficacy against respiratory syncytial virus (RSV)-associated lower respiratory tract infections (LRTI) in clinical trials. Postlicensure monitoring is essential to confirm these benefits in clinical settings.

Objective: To estimate the effectiveness of nirsevimab against medically attended RSV infections in infants and to assess how effectiveness varies by disease severity, dosage, and time since immunization.

Decline of community-acquired alveolar pneumonia positive for respiratory syncytial virus in hospitalized children following implementation of PCV in Israel.

Background: We assessed the impact of pneumococcal conjugate vaccine (PCV) implementation on respiratory syncytial virus-positive community-acquired alveolar pneumonia (RSV-CAAP) in young children in southern Israel.

Methods: This study was nested within a prospective population-based active surveillance system during 2004-2019. All children <60 months residing in the region and served by the region's only hospital were included.

Estimating the Serotype-Specific Association Between the Concentration of Vaccine-Induced Serum Antibodies and Protection Against Pneumococcal Colonization.

Background: Pneumococcal conjugate vaccines (PCVs) offer indirect protection by reducing pneumococcal colonization in the vaccinated children and thus transmission. As higher-valency PCVs may trigger a weaker immune response, it is important to understand how differences in immunogenicity between PCVs translate to effectiveness against colonization.

Methods: We estimated the serotype-specific relationship between the concentration of vaccine-induced serum immunoglobulin G (IgG) and protection against colonization using a hierarchical Bayesian model with the longitudinal data from a randomized controlled trial.

Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans.

Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development.

Deep learning imputes DNA methylation states in single cells and enhances the detection of epigenetic alterations in schizophrenia.

DNA methylation (DNAm) is a key epigenetic mark with essential roles in gene regulation, mammalian development, and human diseases. Single-cell technologies enable profiling DNAm at cytosines in individual cells, but they often suffer from low coverage for CpG sites. We introduce scMeFormer, a transformer-based deep learning model for imputing DNAm states at each CpG site in single cells.

The Complex Landscape of Updated Pneumococcal Conjugate Vaccines.

Pneumococcus is a major cause of serious infections, especially among vulnerable populations. While pneumococcal conjugate vaccines (PCVs) provide effective protection against disease caused by the included serotypes, a substantial burden of disease remains. Several new PCVs are under development or were recently recommended for use to counteract the remaining disease burden.

Advancing adoptability and sustainability of digital prediction tools for climate-sensitive infectious disease prevention and control.

Few forecasting models have been translated into digital prediction tools for prevention and control of climate-sensitive infectious diseases. We propose a 3-U (useful, usable, and used) research framework for advancing the adoptability and sustainability of these tools. We make recommendations for 1) developing a tool with a high level of accuracy and sufficient lead time to permit effective proactive interventions (useful); 2) conducting a needs assessment to ensure that a tool meets the needs of end-users (usable); and 3) demonstrating the efficacy and cost-effectiveness of a tool to secure its adoption into routine surveillance and response systems (used).

Detection of Pneumococcal Carriage in Asymptomatic Healthcare Workers.

Background: Healthcare workers are at increased risk of exposure to respiratory pathogens including (pneumococcus). While little asymptomatic carriage has been reported in young-to-middle-aged adults, this may be due to nonsensitive diagnostic methods. The aim of the current study was to investigate the rates of pneumococcal carriage in a large cohort of healthcare workers, using saliva as a respiratory specimen.

Classification of schizophrenia, bipolar disorder and major depressive disorder with comorbid traits and deep learning algorithms.

Many psychiatric disorders share genetic liabilities, but whether these shared liabilities can be utilized to classify and differentiate psychiatric disorders remains unclear. In this study, we use polygenic risk scores (PRSs) of 42 traits comorbid with schizophrenia (SCZ), bipolar disorder (BIP), and major depressive disorder (MDD) to evaluate their utilities. We found that combining target specific PRS with PRSs of comorbid traits can improve the classification of the target disorders.

Estimating the burden of RSV- and influenza-associated hospitalizations, ICU admissions, and deaths across age and socioeconomic groups in New York State, 2005-2019.

Background: Multiple prophylactic products are now available to protect against respiratory syncytial virus (RSV) in different age groups. Assessing the pre-intervention burden of RSV infections across various severity levels and risk groups is crucial, as it provides a baseline for evaluating the impact of these products.

Methods: We obtained monthly time series data on hospitalizations, intensive care unit (ICU) admissions, and deaths by age group, ZIP code, and cause for New York state from 2005 to 2019.