for COVID Vaccine Safe for Pregnant Women: Study By www.medicinenet.com Published On :: Mon, 15 Aug 2022 00:00:00 PDT Title: COVID Vaccine Safe for Pregnant Women: StudyCategory: Health NewsCreated: 8/15/2022 12:00:00 AMLast Editorial Review: 8/15/2022 12:00:00 AM Full Article
for Premature Birth Tied to Higher Risk for ADHD By www.medicinenet.com Published On :: Tue, 16 Aug 2022 00:00:00 PDT Title: Premature Birth Tied to Higher Risk for ADHDCategory: Health NewsCreated: 8/16/2022 12:00:00 AMLast Editorial Review: 8/16/2022 12:00:00 AM Full Article
for Pregnancy Can Be Anxious Time for Women With Epilepsy By www.medicinenet.com Published On :: Thu, 18 Aug 2022 00:00:00 PDT Title: Pregnancy Can Be Anxious Time for Women With EpilepsyCategory: Health NewsCreated: 8/18/2022 12:00:00 AMLast Editorial Review: 8/18/2022 12:00:00 AM Full Article
for Family History of Mental Illness Ups Odds for Postpartum Depression By www.medicinenet.com Published On :: Tue, 23 Aug 2022 00:00:00 PDT Title: Family History of Mental Illness Ups Odds for Postpartum DepressionCategory: Health NewsCreated: 8/22/2022 12:00:00 AMLast Editorial Review: 8/23/2022 12:00:00 AM Full Article
for Gout Flare-Ups Could Raise Heart Risk for Weeks After By www.medicinenet.com Published On :: Thu, 4 Aug 2022 00:00:00 PDT Title: Gout Flare-Ups Could Raise Heart Risk for Weeks AfterCategory: Health NewsCreated: 8/3/2022 12:00:00 AMLast Editorial Review: 8/4/2022 12:00:00 AM Full Article
for What Does a Neurologist Do for a Vestibular Migraine? By www.medicinenet.com Published On :: Wed, 22 Jun 2022 00:00:00 PDT Title: What Does a Neurologist Do for a Vestibular Migraine?Category: Diseases and ConditionsCreated: 6/22/2022 12:00:00 AMLast Editorial Review: 6/22/2022 12:00:00 AM Full Article
for Pandemic Brought More Woes for Kids Prone to Headaches By www.medicinenet.com Published On :: Wed, 10 Aug 2022 00:00:00 PDT Title: Pandemic Brought More Woes for Kids Prone to HeadachesCategory: Health NewsCreated: 8/9/2022 12:00:00 AMLast Editorial Review: 8/10/2022 12:00:00 AM Full Article
for Having Ideal Heart Health May Lessen the Risk for Brain Vessel Disease By www.medicinenet.com Published On :: Thu, 18 Aug 2022 00:00:00 PDT Title: Having Ideal Heart Health May Lessen the Risk for Brain Vessel DiseaseCategory: Health NewsCreated: 8/17/2022 12:00:00 AMLast Editorial Review: 8/18/2022 12:00:00 AM Full Article
for Breakfast Might Be Good for a Child's Emotional Health, Too By www.medicinenet.com Published On :: Wed, 24 Aug 2022 00:00:00 PDT Title: Breakfast Might Be Good for a Child's Emotional Health, TooCategory: Health NewsCreated: 8/24/2022 12:00:00 AMLast Editorial Review: 8/24/2022 12:00:00 AM Full Article
for Here Are the Top 15 Anti-Inflammatory Foods for Your Diet To Reduce Inflammation By www.medicinenet.com Published On :: Fri, 26 Aug 2022 00:00:00 PDT Title: Here Are the Top 15 Anti-Inflammatory Foods for Your Diet To Reduce InflammationCategory: Health and LivingCreated: 8/26/2022 12:00:00 AMLast Editorial Review: 8/26/2022 12:00:00 AM Full Article
for 7 Healthy Sushi Options, Plus Ingredients to Look Out For By www.medicinenet.com Published On :: Fri, 26 Aug 2022 00:00:00 PDT Title: 7 Healthy Sushi Options, Plus Ingredients to Look Out ForCategory: Health and LivingCreated: 8/26/2022 12:00:00 AMLast Editorial Review: 8/26/2022 12:00:00 AM Full Article
for What Is Oolong Tea Good For? By www.medicinenet.com Published On :: Fri, 26 Aug 2022 00:00:00 PDT Title: What Is Oolong Tea Good For?Category: Health and LivingCreated: 8/26/2022 12:00:00 AMLast Editorial Review: 8/26/2022 12:00:00 AM Full Article
for Why Is Coconut Oil Good for Your Teeth? By www.medicinenet.com Published On :: Fri, 26 Aug 2022 00:00:00 PDT Title: Why Is Coconut Oil Good for Your Teeth?Category: Health and LivingCreated: 8/26/2022 12:00:00 AMLast Editorial Review: 8/26/2022 12:00:00 AM Full Article
for Are Green Mussels Good for You? By www.medicinenet.com Published On :: Fri, 26 Aug 2022 00:00:00 PDT Title: Are Green Mussels Good for You?Category: Health and LivingCreated: 8/26/2022 12:00:00 AMLast Editorial Review: 8/26/2022 12:00:00 AM Full Article
for U.S. Government Extends Baby Formula Waivers, Rebates for WIC Families By www.medicinenet.com Published On :: Sat, 27 Aug 2022 00:00:00 PDT Title: U.S. Government Extends Baby Formula Waivers, Rebates for WIC FamiliesCategory: Health NewsCreated: 8/25/2022 12:00:00 AMLast Editorial Review: 8/26/2022 12:00:00 AM Full Article
for Are Plant Sterols Good for Lowering Cholesterol? By www.medicinenet.com Published On :: Thu, 12 May 2022 00:00:00 PDT Title: Are Plant Sterols Good for Lowering Cholesterol?Category: Diseases and ConditionsCreated: 5/12/2022 12:00:00 AMLast Editorial Review: 5/12/2022 12:00:00 AM Full Article
for What Fish Is Best for Lowering Cholesterol? By www.medicinenet.com Published On :: Thu, 19 May 2022 00:00:00 PDT Title: What Fish Is Best for Lowering Cholesterol?Category: Health and LivingCreated: 5/19/2022 12:00:00 AMLast Editorial Review: 5/19/2022 12:00:00 AM Full Article
for California Will Produce Its Own Insulin to Bring Down Prices By www.medicinenet.com Published On :: Fri, 8 Jul 2022 00:00:00 PDT Title: California Will Produce Its Own Insulin to Bring Down PricesCategory: Health NewsCreated: 7/8/2022 12:00:00 AMLast Editorial Review: 7/8/2022 12:00:00 AM Full Article
for Even Chores, Socializing Might Lower Your Odds for Dementia By www.medicinenet.com Published On :: Fri, 29 Jul 2022 00:00:00 PDT Title: Even Chores, Socializing Might Lower Your Odds for DementiaCategory: Health NewsCreated: 7/28/2022 12:00:00 AMLast Editorial Review: 7/29/2022 12:00:00 AM Full Article
for Everyday Activities That Can Cut Your Odds for Dementia By www.medicinenet.com Published On :: Mon, 15 Aug 2022 00:00:00 PDT Title: Everyday Activities That Can Cut Your Odds for DementiaCategory: Health NewsCreated: 8/12/2022 12:00:00 AMLast Editorial Review: 8/15/2022 12:00:00 AM Full Article
for AHA News: People With Dementia May Be Less Likely to Receive an Advanced Treatment For Stroke By www.medicinenet.com Published On :: Wed, 24 Aug 2022 00:00:00 PDT Title: AHA News: People With Dementia May Be Less Likely to Receive an Advanced Treatment For StrokeCategory: Health NewsCreated: 8/24/2022 12:00:00 AMLast Editorial Review: 8/24/2022 12:00:00 AM Full Article
for 3 Big Pharmacy Chains Must Pay $650 Million to Ohio Counties for Role in Opioid Crisis By www.medicinenet.com Published On :: Thu, 18 Aug 2022 00:00:00 PDT Title: 3 Big Pharmacy Chains Must Pay $650 Million to Ohio Counties for Role in Opioid CrisisCategory: Health NewsCreated: 8/18/2022 12:00:00 AMLast Editorial Review: 8/18/2022 12:00:00 AM Full Article
for Many Who Need Opioid OD Antidote the Most Can't Afford It By www.medicinenet.com Published On :: Mon, 22 Aug 2022 00:00:00 PDT Title: Many Who Need Opioid OD Antidote the Most Can't Afford ItCategory: Health NewsCreated: 8/22/2022 12:00:00 AMLast Editorial Review: 8/22/2022 12:00:00 AM Full Article
for Qigong Meditation for Beginners: Techniques, Benefits, and More By www.medicinenet.com Published On :: Wed, 24 Aug 2022 00:00:00 PDT Title: Qigong Meditation for Beginners: Techniques, Benefits, and MoreCategory: Health and LivingCreated: 8/24/2022 12:00:00 AMLast Editorial Review: 8/24/2022 12:00:00 AM Full Article
for Playing Football, Hockey in High School Ups Odds for Stimulant Abuse By www.medicinenet.com Published On :: Mon, 15 Aug 2022 00:00:00 PDT Title: Playing Football, Hockey in High School Ups Odds for Stimulant AbuseCategory: Health NewsCreated: 8/15/2022 12:00:00 AMLast Editorial Review: 8/15/2022 12:00:00 AM Full Article
for As Pandemic Eases, It's Boom Times for Cosmetic Surgeons By www.medicinenet.com Published On :: Wed, 24 Aug 2022 00:00:00 PDT Title: As Pandemic Eases, It's Boom Times for Cosmetic SurgeonsCategory: Health NewsCreated: 8/24/2022 12:00:00 AMLast Editorial Review: 8/24/2022 12:00:00 AM Full Article
for What Is a Good Height for a Man? By www.medicinenet.com Published On :: Thu, 7 Jul 2022 00:00:00 PDT Title: What Is a Good Height for a Man?Category: Health and LivingCreated: 7/7/2022 12:00:00 AMLast Editorial Review: 7/7/2022 12:00:00 AM Full Article
for Why Do Men Often Die Before Women? By www.medicinenet.com Published On :: Fri, 15 Jul 2022 00:00:00 PDT Title: Why Do Men Often Die Before Women?Category: Health NewsCreated: 7/14/2022 12:00:00 AMLast Editorial Review: 7/15/2022 12:00:00 AM Full Article
for Foreign Objects or Insects in the Ear By www.medicinenet.com Published On :: Wed, 3 Aug 2022 00:00:00 PDT Title: Foreign Objects or Insects in the EarCategory: Diseases and ConditionsCreated: 11/29/1998 12:00:00 AMLast Editorial Review: 8/3/2022 12:00:00 AM Full Article
for What Therapeutic Options Are Available for Treating an Antiretroviral Naive Patient? By www.medicinenet.com Published On :: Thu, 16 Jun 2022 00:00:00 PDT Title: What Therapeutic Options Are Available for Treating an Antiretroviral Naive Patient?Category: Diseases and ConditionsCreated: 6/16/2022 12:00:00 AMLast Editorial Review: 6/16/2022 12:00:00 AM Full Article
for New Approach Cuts Odds for Anal Cancer in People With HIV By www.medicinenet.com Published On :: Thu, 16 Jun 2022 00:00:00 PDT Title: New Approach Cuts Odds for Anal Cancer in People With HIVCategory: Health NewsCreated: 6/16/2022 12:00:00 AMLast Editorial Review: 6/16/2022 12:00:00 AM Full Article
for Do You Use Mouthwash Before or After Brushing? By www.medicinenet.com Published On :: Fri, 5 Aug 2022 00:00:00 PDT Title: Do You Use Mouthwash Before or After Brushing?Category: Health and LivingCreated: 8/5/2022 12:00:00 AMLast Editorial Review: 8/5/2022 12:00:00 AM Full Article
for Vegetarian Women at Higher Odds for Hip Fracture By www.medicinenet.com Published On :: Fri, 12 Aug 2022 00:00:00 PDT Title: Vegetarian Women at Higher Odds for Hip FractureCategory: Health NewsCreated: 8/11/2022 12:00:00 AMLast Editorial Review: 8/12/2022 12:00:00 AM Full Article
for Senior Sex: Tips for Senior Citizens By www.medicinenet.com Published On :: Mon, 11 Jul 2022 00:00:00 PDT Title: Senior Sex: Tips for Senior CitizensCategory: Health and LivingCreated: 7/11/2022 12:00:00 AMLast Editorial Review: 7/11/2022 12:00:00 AM Full Article
for U.S. Hospitals Are Getting Safer for Patients, Study Finds By www.medicinenet.com Published On :: Wed, 20 Jul 2022 00:00:00 PDT Title: U.S. Hospitals Are Getting Safer for Patients, Study FindsCategory: Health NewsCreated: 7/20/2022 12:00:00 AMLast Editorial Review: 7/20/2022 12:00:00 AM Full Article
for 'Virtual' Museum Visits Are Good Medicine for Seniors By www.medicinenet.com Published On :: Tue, 16 Aug 2022 00:00:00 PDT Title: 'Virtual' Museum Visits Are Good Medicine for SeniorsCategory: Health NewsCreated: 8/16/2022 12:00:00 AMLast Editorial Review: 8/16/2022 12:00:00 AM Full Article
for Health Care Plans Keep Allergy Rescue Injectors Pricey for Some By www.medicinenet.com Published On :: Fri, 15 Jul 2022 00:00:00 PDT Title: Health Care Plans Keep Allergy Rescue Injectors Pricey for SomeCategory: Health NewsCreated: 7/15/2022 12:00:00 AMLast Editorial Review: 7/15/2022 12:00:00 AM Full Article
for Looking for Reliable Hay Fever Advice? It's Probably Not on YouTube By www.medicinenet.com Published On :: Tue, 16 Aug 2022 00:00:00 PDT Title: Looking for Reliable Hay Fever Advice? It's Probably Not on YouTubeCategory: Health NewsCreated: 8/16/2022 12:00:00 AMLast Editorial Review: 8/16/2022 12:00:00 AM Full Article
for Smoking Rates Drop for Americans Battling Depression, Substance Abuse By www.medicinenet.com Published On :: Wed, 27 Apr 2022 00:00:00 PDT Title: Smoking Rates Drop for Americans Battling Depression, Substance AbuseCategory: Health NewsCreated: 4/27/2022 12:00:00 AMLast Editorial Review: 4/27/2022 12:00:00 AM Full Article
for Noninvasive diagnostic modalities and prediction models for detecting pulmonary hypertension associated with interstitial lung disease: a narrative review By err.ersjournals.com Published On :: 2024-10-09T00:15:15-07:00 Pulmonary hypertension (PH) is highly prevalent in patients with interstitial lung disease (ILD) and is associated with increased morbidity and mortality. Widely available noninvasive screening tools are warranted to identify patients at risk for PH, especially severe PH, that could be managed at expert centres. This review summarises current evidence on noninvasive diagnostic modalities and prediction models for the timely detection of PH in patients with ILD. It critically evaluates these approaches and discusses future perspectives in the field. A comprehensive literature search was carried out in PubMed and Scopus, identifying 39 articles that fulfilled inclusion criteria. There is currently no single noninvasive test capable of accurately detecting and diagnosing PH in ILD patients. Estimated right ventricular pressure (RVSP) on Doppler echocardiography remains the single most predictive factor of PH, with other indirect echocardiographic markers increasing its diagnostic accuracy. However, RVSP can be difficult to estimate in patients due to suboptimal views from extensive lung disease. The majority of existing composite scores, including variables obtained from chest computed tomography, pulmonary function tests and cardiopulmonary exercise tests, were derived from retrospective studies, whilst lacking validation in external cohorts. Only two available scores, one based on a stepwise echocardiographic approach and the other on functional parameters, predicted the presence of PH with sufficient accuracy and used a validation cohort. Although several methodological limitations prohibit their generalisability, their use may help physicians to detect PH earlier. Further research on the potential of artificial intelligence may guide a more tailored approach, for timely PH diagnosis. Full Article
for Patient-managed interventions for adults with bronchiectasis: evidence, challenges and prospects By err.ersjournals.com Published On :: 2024-10-30T01:30:15-07:00 Bronchiectasis is a chronic lung condition which is characterised by recurrent chest infections, chronic sputum production and cough, and limited exercise tolerance. While bronchiectasis may be caused by various aetiologies, these features are shared by most patients with bronchiectasis regardless of the cause. This review consolidates the existing evidence on patient-managed interventions for adults with bronchiectasis, while also outlining areas for future research. Airway clearance techniques and hyperosmolar agents are key components of the bronchiectasis management and consistently recommended for clinical implementation. Questions around their prescription, such as optimal sequence of delivery, are still to be answered. Pulmonary rehabilitation and exercise are also recommended for patients with bronchiectasis. Relatively strong evidence underpins this recommendation during a clinically stable stage of the disease, although the role of pulmonary rehabilitation following an exacerbation is still unclear. Additionally, self-management programmes feature prominently in bronchiectasis treatment, yet the lack of consensus regarding their definition and outcomes presents hurdles to establishing a cohesive evidence base. Moreover, cough, a cardinal symptom of bronchiectasis, warrants closer examination. Although managing cough in bronchiectasis may initially appear risky, further research is necessary to ascertain whether strategies employed in other respiratory conditions can be safely and effectively adapted to bronchiectasis, particularly through identifying patient responder populations and criteria where cough may not enhance airway clearance efficacy and its control is needed. Overall, there is a growing recognition of the importance of patient-managed interventions in the bronchiectasis management. Efforts to improve research methodologies and increase research funding are needed to further advance our understanding of these interventions, and their role in optimising patient care and outcomes. Full Article
for Multicomponent services for symptoms in serious respiratory illness: a systematic review and meta-analysis By err.ersjournals.com Published On :: 2024-10-30T01:30:15-07:00 Background People living with serious respiratory illness experience a high burden of symptoms. This review aimed to determine whether multicomponent services reduce symptoms in people with serious illness related to respiratory disease. Methods Electronic databases were searched to identify randomised controlled trials (RCTs) evaluating multicomponent services that enrolled patients due to symptoms, rather than underlying disease, and provided at least one nonpharmacological intervention. The primary outcome was chronic breathlessness and secondary outcomes were health-related quality of life (HRQoL), cough, fatigue and adverse events. At least two authors independently screened studies, assessed risk of bias and extracted data. Results Five RCTs, involving 439 patients, were included. In comparison to usual care, multicomponent services improved breathlessness mastery (Chronic Respiratory Questionnaire (CRQ) mastery scale, mean difference (MD) 0.43 points, 95% CI 0.20–0.67, three RCTs, 327 participants) and HRQoL (CRQ total score, MD 0.24 points, 95% CI 0.04–0.40, two RCTs, 237 participants). Fatigue did not improve with multicomponent services and no studies evaluated cough. No serious adverse events were reported. The one study evaluating mortality found increased survival in those accessing a multicomponent service. The certainty of evidence was very low, mainly due to detection and reporting bias. Conclusion Multicomponent services improve breathlessness mastery and HRQoL, with minimal risk. These findings support the use of multicomponent symptom-directed services for people living with serious respiratory illness. Full Article
for Opioids for the palliation of symptoms in people with serious respiratory illness: a systematic review and meta-analysis By err.ersjournals.com Published On :: 2024-10-09T00:15:15-07:00 Background People living with serious respiratory illness experience a high burden of distressing symptoms. Although opioids are prescribed for symptom management, they generate adverse events, and their benefits are unclear. Methods We examined the efficacy and safety of opioids for symptom management in people with serious respiratory illness. Embase, MEDLINE and the Cochrane Central Register of Controlled Trials were searched up to 11 July 2022. Reports of randomised controlled trials administering opioids to treat symptoms in people with serious respiratory illness were included. Key exclusion criteria included <80% of participants having a nonmalignant lung disease. Data were extracted regarding study characteristics, outcomes of breathlessness, cough, health-related quality of life (HRQoL) and adverse events. Treatment effects were pooled using a generic inverse variance model with random effects. Risk of bias was assessed using the Cochrane Risk of Bias tool version 1. Results Out of 17 included trials, six were laboratory-based exercise trials (n=70), 10 were home studies measuring breathlessness in daily life (n=788) and one (n=18) was conducted in both settings. Overall certainty of evidence was "very low" to "low". Opioids reduced breathlessness intensity during laboratory exercise testing (standardised mean difference (SMD) –0.37, 95% CI –0.67– –0.07), but not breathlessness measured in daily life (SMD –0.10, 95% CI –0.64–0.44). No effects on HRQoL (SMD –0.42, 95% CI –0.98–0.13) or cough (SMD –1.42, 95% CI –3.99–1.16) were detected. In at-home studies, opioids led to increased frequency of nausea/vomiting (OR 3.32, 95% CI 1.70–6.51), constipation (OR 3.08, 95% CI 1.69–5.61) and drowsiness (OR 1.37, 95% CI 1.01–1.86), with serious adverse events including hospitalisation and death identified. Conclusions Opioids improved exertional breathlessness in laboratory exercise studies, but did not improve breathlessness, cough or HRQoL measured in daily life at home. There were significant adverse events, which may outweigh any benefits. Full Article
for PWAS Hub for exploring gene-based associations of common complex diseases [RESOURCES] By genome.cshlp.org Published On :: 2024-10-29T06:46:08-07:00 PWAS (proteome-wide association study) is an innovative genetic association approach that complements widely used methods like GWAS (genome-wide association study). The PWAS approach involves consecutive phases. Initially, machine learning modeling and probabilistic considerations quantify the impact of genetic variants on protein-coding genes’ biochemical functions. Secondly, for each individual, aggregating the variants per gene determines a gene-damaging score. Finally, standard statistical tests are activated in the case-control setting to yield statistically significant genes per phenotype. The PWAS Hub offers a user-friendly interface for an in-depth exploration of gene–disease associations from the UK Biobank (UKB). Results from PWAS cover 99 common diseases and conditions, each with over 10,000 diagnosed individuals per phenotype. Users can explore genes associated with these diseases, with separate analyses conducted for males and females. For each phenotype, the analyses account for sex-based genetic effects, inheritance modes (dominant and recessive), and the pleiotropic nature of associated genes. The PWAS Hub showcases its usefulness for asthma by navigating through proteomic-genetic analyses. Inspecting PWAS asthma-listed genes (a total of 27) provide insights into the underlying cellular and molecular mechanisms. Comparison of PWAS-statistically significant genes for common diseases to the Open Targets benchmark shows partial but significant overlap in gene associations for most phenotypes. Graphical tools facilitate comparing genetic effects between PWAS and coding GWAS results, aiding in understanding the sex-specific genetic impact on common diseases. This adaptable platform is attractive to clinicians, researchers, and individuals interested in delving into gene–disease associations and sex-specific genetic effects. Full Article
for Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change [METHODS] By genome.cshlp.org Published On :: 2024-10-29T06:46:08-07:00 The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pangenomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of clinical, pooled, or wastewater sequence. Quantifying diversity is central to ecology. Hill numbers, or the effective number of species in a sample, provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k-mer an individual and each genome a transect in the pangenome of the species. Structured in this way, Hill numbers summarize the temporal trajectory of pandemic variants, collapsing each day's assemblies into genome equivalents. For pooled or wastewater sequence, we instead compare days using survey sequence divorced from individual infections. Across data from the UK, USA, and South Africa, we trace the ascendance of new variants of concern as they emerge in local populations well before these variants are named and added to phylogenetic databases. Using data from San Diego wastewater, we monitor these same population changes from raw, unassembled sequence. This history of emerging variants senses all available data as it is sequenced, intimating variant sweeps to dominance or declines to extinction at the leading edge of the COVID-19 pandemic. Full Article
for Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data [METHODS] By genome.cshlp.org Published On :: 2024-10-29T06:46:08-07:00 High-throughput sequencing (HTS) technologies have been instrumental in investigating biological questions at the bulk and single-cell levels. Comparative analysis of two HTS data sets often relies on testing the statistical significance for the difference of two negative binomial distributions (DOTNB). Although negative binomial distributions are well studied, the theoretical results for DOTNB remain largely unexplored. Here, we derive basic analytical results for DOTNB and examine its asymptotic properties. As a state-of-the-art application of DOTNB, we introduce DEGage, a computational method for detecting differentially expressed genes (DEGs) in scRNA-seq data. DEGage calculates the mean of the sample-wise differences of gene expression levels as the test statistic and determines significant differential expression by computing the P-value with DOTNB. Extensive validation using simulated and real scRNA-seq data sets demonstrates that DEGage outperforms five popular DEG analysis tools: DEGseq2, DEsingle, edgeR, Monocle3, and scDD. DEGage is robust against high dropout levels and exhibits superior sensitivity when applied to balanced and imbalanced data sets, even with small sample sizes. We utilize DEGage to analyze prostate cancer scRNA-seq data sets and identify marker genes for 17 cell types. Furthermore, we apply DEGage to scRNA-seq data sets of mouse neurons with and without fear memory and reveal eight potential memory-related genes overlooked in previous analyses. The theoretical results and supporting software for DOTNB can be widely applied to comparative analyses of dispersed count data in HTS and broad research questions. Full Article
for Evidence for compensatory evolution within pleiotropic regulatory elements [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 Pleiotropy, measured as expression breadth across tissues, is one of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly half a million CREs. To assess the functional conservation of CREs, we generated ATAC-seq and RNA-seq data from humans and macaques. We found that more pleiotropic CREs exhibit greater conservation in accessibility, and the mRNA expression levels of the associated genes are more conserved. This trend of higher conservation for higher degrees of pleiotropy persists when analyzing the transcription factor binding repertoire. In contrast, simple DNA sequence conservation of orthologous sites between species tends to be even lower for pleiotropic CREs than for species-specific CREs. Combining various lines of evidence, we propose that the lack of sequence conservation in functionally conserved pleiotropic CREs is owing to within-element compensatory evolution. In summary, our findings suggest that pleiotropy is also a good predictor for the functional conservation of CREs, even though this is not reflected in the sequence conservation of pleiotropic CREs. Full Article
for Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 The human major histocompatibility complex (MHC) is a ~4 Mb genomic segment on Chromosome 6 that plays a pivotal role in the immune response. Despite its importance in various traits and diseases, its complex nature makes it challenging to accurately characterize on a routine basis. We present a novel approach allowing targeted sequencing and de novo haplotypic assembly of the MHC region in heterozygous samples, using long-read sequencing technologies. Our approach is validated using two reference samples, two family trios, and an African-American sample. We achieved excellent coverage (96.6%–99.9% with at least 30x depth) and high accuracy (99.89%–99.99%) for the different haplotypes. This methodology offers a reliable and cost-effective method for sequencing and fully characterizing the MHC without the need for whole-genome sequencing, facilitating broader studies on this important genomic segment and having significant implications in immunology, genetics, and medicine. Full Article
for The chromatin tapestry as a framework for neurodevelopment [MINI-REVIEW] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 The neuronal nucleus houses a meticulously organized genome. Within this structure, genetic material is not simply compacted but arranged into a precise and functional 3D chromatin landscape essential for cellular regulation. This mini-review highlights the importance of this chromatin landscape in healthy neurodevelopment, as well as the diseases that occur with aberrant chromatin architecture. We discuss insights into the fundamental mechanistic relationship between histone modifications, DNA methylation, and genome organization. We then discuss findings that reveal how these epigenetic features change throughout normal neurodevelopment. Finally, we highlight single-gene neurodevelopmental disorders that illustrate the interdependence of epigenetic features, showing how disruptions in DNA methylation or genome architecture can ripple across the entire epigenome. As such, we emphasize the importance of measuring multiple chromatin architectural aspects, as the disruption of one mechanism can likely impact others in the intricate epigenetic network. This mini-review underscores the vast gaps in our understanding of chromatin structure in neurodevelopmental diseases and the substantial research needed to understand the interplay between chromatin features and neurodevelopment. Full Article
for Only One Quarter of Family Physicians Are Very Satisfied with Their Electronic Health Records Platform By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Two decades into the era of Electronic Health Records (EHRs), the promise of streamlining clinical care, reducing burden, and improving patient outcomes has yet to be realized. A cross-sectional family physician census conducted by the American Board of Family Medicine in 2022 and 2023 included self-reported physician EHR satisfaction. Of the nearly 10,000 responding family physicians, only one-in-four (26.2%) report being very satisfied and one-in-three (33.8%) were not satisfied. These low levels of satisfaction point to the need for greater transparency in the marketplace and pressure to increase user-centric EHR design. Full Article