ic Here's Why Men Should Take Probiotics By www.medicinenet.com Published On :: Wed, 27 Jul 2022 00:00:00 PDT Title: Here's Why Men Should Take ProbioticsCategory: Health and LivingCreated: 7/27/2022 12:00:00 AMLast Editorial Review: 7/27/2022 12:00:00 AM Full Article
ic 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
ic Pets Have Helped People With HIV Through Two Pandemics By www.medicinenet.com Published On :: Thu, 23 Jun 2022 00:00:00 PDT Title: Pets Have Helped People With HIV Through Two PandemicsCategory: Health NewsCreated: 6/23/2022 12:00:00 AMLast Editorial Review: 6/23/2022 12:00:00 AM Full Article
ic HIV Testing Plummeted During Pandemic By www.medicinenet.com Published On :: Mon, 27 Jun 2022 00:00:00 PDT Title: HIV Testing Plummeted During PandemicCategory: Health NewsCreated: 6/27/2022 12:00:00 AMLast Editorial Review: 6/27/2022 12:00:00 AM Full Article
ic MS (Multiple Sclerosis) vs. ALS (Amyotrophic Lateral Sclerosis) By www.medicinenet.com Published On :: Thu, 4 Aug 2022 00:00:00 PDT Title: MS (Multiple Sclerosis) vs. ALS (Amyotrophic Lateral Sclerosis)Category: Diseases and ConditionsCreated: 6/16/2017 12:00:00 AMLast Editorial Review: 8/4/2022 12:00:00 AM Full Article
ic Motion Sickness By www.medicinenet.com Published On :: Mon, 8 Aug 2022 00:00:00 PDT Title: Motion SicknessCategory: Diseases and ConditionsCreated: 5/30/1999 12:00:00 AMLast Editorial Review: 8/8/2022 12:00:00 AM Full Article
ic Vaccines Have Slashed Rates of HPV Infection in Young American Women By www.medicinenet.com Published On :: Tue, 23 Aug 2022 00:00:00 PDT Title: Vaccines Have Slashed Rates of HPV Infection in Young American WomenCategory: Health NewsCreated: 8/22/2022 12:00:00 AMLast Editorial Review: 8/23/2022 12:00:00 AM Full Article
ic '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
ic Picture of Nickel Contact Dermatitis By www.medicinenet.com Published On :: Thu, 23 Jun 2022 00:00:00 PDT Title: Picture of Nickel Contact DermatitisCategory: ImagesCreated: 2/22/2010 3:07:00 PMLast Editorial Review: 6/23/2022 12:00:00 AM Full Article
ic Picture of Phototoxic Dermatitides By www.medicinenet.com Published On :: Tue, 28 Jun 2022 00:00:00 PDT Title: Picture of Phototoxic DermatitidesCategory: ImagesCreated: 2/23/2010 2:33:00 PMLast Editorial Review: 6/28/2022 12:00:00 AM Full Article
ic Picture of Nickel Contact Dermatitis from Necklace By www.medicinenet.com Published On :: Tue, 28 Jun 2022 00:00:00 PDT Title: Picture of Nickel Contact Dermatitis from NecklaceCategory: ImagesCreated: 2/22/2010 3:21:00 PMLast Editorial Review: 6/28/2022 12:00:00 AM Full Article
ic Salicylate Sensitivity Causes, Symptoms, and Foods to Avoid By www.medicinenet.com Published On :: Fri, 8 Jul 2022 00:00:00 PDT Title: Salicylate Sensitivity Causes, Symptoms, and Foods to AvoidCategory: Health and LivingCreated: 7/8/2022 12:00:00 AMLast Editorial Review: 7/8/2022 12:00:00 AM Full Article
ic 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
ic Prehistoric People Drank Animal Milk, Despite Lactose Intolerance By www.medicinenet.com Published On :: Thu, 28 Jul 2022 00:00:00 PDT Title: Prehistoric People Drank Animal Milk, Despite Lactose IntoleranceCategory: Health NewsCreated: 7/27/2022 12:00:00 AMLast Editorial Review: 7/28/2022 12:00:00 AM Full Article
ic 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
ic Australia's Current Flu Season Is Tough: Will America's Be the Same? By www.medicinenet.com Published On :: Fri, 5 Aug 2022 00:00:00 PDT Title: Australia's Current Flu Season Is Tough: Will America's Be the Same?Category: Health NewsCreated: 8/4/2022 12:00:00 AMLast Editorial Review: 8/5/2022 12:00:00 AM Full Article
ic 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
ic Study Casts Doubt on 'Chemical Imbalance' Theory of Depression By www.medicinenet.com Published On :: Tue, 9 Aug 2022 00:00:00 PDT Title: Study Casts Doubt on 'Chemical Imbalance' Theory of DepressionCategory: Health NewsCreated: 8/9/2022 12:00:00 AMLast Editorial Review: 8/9/2022 12:00:00 AM Full Article
ic Treating central sleep apnoea in heart failure: is positive airway pressure and adaptive servo-ventilation in particular the gold standard? By err.ersjournals.com Published On :: 2024-10-30T01:30:15-07:00 Extract We read with great interest the review article by Randerath et al. [1] recently published in the European Respiratory Review. We would like to congratulate the authors on this clearly structured review, which emphasises the urgent need for an increasingly differentiated view of central sleep apnoea (CSA) in the context of precision medicine. Full Article
ic Impaired lung function and associated risk factors in children born prematurely: a systematic review and meta-analysis By err.ersjournals.com Published On :: 2024-10-09T00:15:15-07:00 Background Immature lung development and respiratory morbidity place preterm-born children at high risk of long-term pulmonary sequelae. This systematic review and meta-analysis aims to quantify lung function in preterm-born children and identify risk factors for a compromised lung function. Methods We searched MEDLINE, Embase, Cochrane Library, Web of Science and Scopus for relevant studies published on preterm cohorts born since 1990. Studies comparing forced expiratory volume in 1 s (FEV1) in preterm-born children aged ≥5 years to term-born controls or normative data were included. Study quality was assessed using the Newcastle–Ottawa Scale for cohort studies. Standardised mean differences in FEV1 and secondary spirometry outcomes per study were pooled using meta-analysis. The impact of different demographic and neonatal variables on studies’ FEV1 effect sizes was investigated by meta-regression analyses. Certainty of evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluations framework. Results We identified 42 studies with unique cohorts including 4743 preterm children and 9843 controls. Median gestational age in the studies was 28.0 weeks and age at assessment ranged from 6.7 to 16.7 years. Preterm children had lower FEV1 than controls (–0.58 sd, 95% CI –0.69– –0.47 sd, p<0.001) resulting in a relative risk of 2.9 (95% CI 2.4–3.4) for abnormal outcome, with high certainty of evidence. FEV1 was significantly associated with gestational age, birthweight, bronchopulmonary dysplasia and invasive mechanical ventilation in univariate meta-regression analyses (R2=36–96%). Conclusion This systematic review shows robust evidence of impaired lung function in preterm-born children with a high certainty of evidence. Full Article
ic Epidemiology of severe asthma in children: a systematic review and meta-analysis By err.ersjournals.com Published On :: 2024-10-09T00:15:15-07:00 Background Severe asthma significantly impacts a minority of children with asthma, leading to frequent symptoms, hospitalisations and potential long-term health consequences. However, accurate global data on severe asthma epidemiology is lacking. This study aims to address this gap, providing data on severe asthma epidemiology, regional differences and associated comorbidities. Methods We conducted a rigorous systematic review and meta-analysis following a registered protocol (PROSPERO CRD42023472845). We searched PubMed, Scopus and Web of Science for cohort or cross-sectional studies published since 2003, evaluating severe asthma incidence and prevalence in children. Study quality and risk of bias were assessed using STROBE guidelines. Results Nine studies investigating European children with asthma (aged 5–18 years) were included in the meta-analysis. No significant publication bias was found. The overall severe asthma prevalence in children with asthma was 3% (95% CI 1–6; I2=99.9%; p<0.001), with no significant difference between males and females. Prevalence estimates varied significantly depending on the diagnostic criteria used (Global Initiative for Asthma: 6%; European Respiratory Society/American Thoracic Society: 1%; other: 3%). Because none of the examined studies were prospectively designed, incidence rates could not be determined. Conclusions This systematic review and meta-analysis provide the first robust assessment of severe asthma prevalence among European children. Our findings underscore the need for comprehensive research to address knowledge gaps in severe asthma, including determining incidence rates, standardising definitions, investigating regional differences and evaluating comorbidities and treatment strategies. Full Article
ic 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
ic The ageing of people living with cystic fibrosis: what to expect now? By err.ersjournals.com Published On :: 2024-10-30T01:30:15-07:00 The prognosis of people with cystic fibrosis (pwCF) has improved dramatically with the introduction of cystic fibrosis transmembrane conductance regulator (CFTR) modulators (CFTRm). The ageing of the cystic fibrosis (CF) population is changing the disease landscape with the emergence of different needs and increasing comorbidities related to both age and long-term exposure to multiple treatments including CFTRm. Although the number of pwCF eligible for this treatment is expected to increase, major disparities in care and outcomes still exist in this population. Moreover, the long-term impact of the use of CFTRm is still partly unknown due to the current short follow-up and experience with their use, thus generating some uncertainties. The future spread and initiation of these drugs at an earlier stage of the disease is expected to reduce the systemic burden of systemic inflammation and its consequences on health. However, the prolonged life expectancy is accompanied by an increasing burden of age-related comorbidities, especially in the context of chronic disease. The clinical manifestations of the comorbidities directly or indirectly associated with CFTR dysfunction are changing, along with the disease dynamics and outcomes. Current protocols used to monitor slow disease progression will need continuous updates, including the composition of the multidisciplinary team for CF care, with a greater focus on the needs of the adult population. Full Article
ic 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
ic The effect of graded exercise therapy on fatigue in people with serious respiratory illness: a systematic review By err.ersjournals.com Published On :: 2024-10-09T00:15:15-07:00 Background In adults with serious respiratory illness, fatigue is prevalent and under-recognised, with few treatment options. The aim of this review was to assess the impact of graded exercise therapy (GET) on fatigue in adults with serious respiratory illness. Methods Electronic databases were searched to identify randomised controlled trials (RCTs) testing GET (involving incremental increases in exercise from an established baseline) in adults with serious respiratory illness. The primary outcome was fatigue and secondary outcomes were health-related quality of life (HRQoL) and adverse events. Two authors independently screened for inclusion, evaluated risk of bias and extracted data. Results 76 RCTs were included with 3309 participants, most with a diagnosis of COPD or asthma. Reductions in fatigue measured by the Chronic Respiratory Disease Questionnaire fatigue domain score were demonstrated following GET consisting of aerobic with/without resistance training (mean difference (MD) 0.53 points, 95% CI 0.41–0.65, 11 RCTs, 624 participants) and GET using resistance training alone (MD 0.58 points, 95% CI 0.21–0.96, two RCTs, 82 participants) compared with usual care. Although the mean effect exceeded the minimal important difference, the lower end of the confidence intervals did not always exceed this threshold so the clinical significance could not be confirmed. GET consistently improved HRQoL in people with a range of chronic respiratory diseases on multiple HRQoL measures. No serious adverse events related to GET were reported. Conclusion GET may improve fatigue alongside consistent improvements in HRQoL in people with serious respiratory illness. These findings support the use of GET in the care of people with serious respiratory illness. Full Article
ic Breathing techniques to reduce symptoms in people with serious respiratory illness: a systematic review By err.ersjournals.com Published On :: 2024-10-30T01:30:15-07:00 Background In adults with serious respiratory illness, breathlessness is prevalent and associated with reduced health-related quality of life. The aim of this review was to assess the impact of breathing techniques on breathlessness in adults with serious respiratory illness. Methods Electronic databases were searched to identify randomised controlled trials testing breathing techniques (techniques that aim to alter the respiratory pattern, excluding respiratory muscle training) in people with serious respiratory illness. The primary outcome was breathlessness and secondary outcomes were health-related quality of life and adverse events. Two authors independently screened for inclusion, evaluated risk of bias and extracted data. Results 73 randomised controlled trials were included with 5479 participants, most with COPD or asthma. Breathing exercises (pursed lip and/or diaphragmatic breathing) reduced breathlessness measured by the modified Medical Research Council scale compared to usual care (mean difference (MD) –0.40 points, 95% CI –0.70– –0.11, eight studies, n=323), although the effect did not exceed the minimal important difference. Yoga breathing also improved modified Medical Research Council score compared to usual care (MD –1.05 points, 95% CI –2.45–0.35, three studies, n=175). Breathing techniques consistently improved health-related quality of life in people with COPD and asthma on multiple health-related quality of life measures in comparison to usual care, with effects that generally exceeded the minimal important difference. No adverse events related to breathing techniques were reported. Conclusion Breathing techniques may improve breathlessness, and consistently improve health-related quality of life, in people with serious respiratory illness. These findings support the use of breathing exercises in the care of people with serious respiratory illness. Full Article
ic 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
ic Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level [RESOURCES] By genome.cshlp.org Published On :: 2024-10-29T06:46:08-07:00 Retrotransposable elements (RTEs) are common mobile genetic elements comprising ~42% of the human genome. RTEs play critical roles in gene regulation and function, but how they are specifically involved in complex diseases is largely unknown. Here, we investigate the cellular heterogeneity of RTEs using 12 single-cell transcriptome profiles covering three neurodegenerative diseases, Alzheimer's disease (AD), Parkinson's disease, and multiple sclerosis. We identify cell type marker RTEs in neurons, astrocytes, oligodendrocytes, and oligodendrocyte precursor cells that are related to these diseases. The differential expression analysis reveals the landscape of dysregulated RTE expression, especially L1s, in excitatory neurons of multiple neurodegenerative diseases. Machine learning algorithms for predicting cell disease stage using a combination of RTE and gene expression features suggests dynamic regulation of RTEs in AD. Furthermore, we construct a single-cell atlas of retrotransposable elements in neurodegenerative disease (scARE) using these data sets and features. scARE has six feature analysis modules to explore RTE dynamics in a user-defined condition. To our knowledge, scARE represents the first systematic investigation of RTE dynamics at the single-cell level within the context of neurodegenerative diseases. Full Article
ic Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis [METHODS] By genome.cshlp.org Published On :: 2024-10-29T06:46:08-07:00 Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. There is a need for tools that can process this growing volume of bacterial genome data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split k-mer analysis (SKA2), a method that supports both reference-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or genome assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can also accurately map variants to a reference and be used with recombination detection methods to rapidly reconstruct vertical evolutionary history. SKA2 is many times faster than comparable methods and can be used to add new genomes to an existing call set, allowing sequential use without the need to reanalyze entire collections. With an inherent absence of reference bias, high accuracy, and a robust implementation, SKA2 has the potential to become the tool of choice for genotyping bacteria. SKA2 is implemented in Rust and is freely available as open-source software. Full Article
ic 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
ic 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
ic Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories [METHODS] By genome.cshlp.org Published On :: 2024-10-29T06:46:08-07:00 Most studies of genome organization have focused on intrachromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Interchromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework that uses Hi-C data to identify sets of loci that jointly interact in trans. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum var genes, the mouse olfactory receptor "Greek islands," and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes coregulated by the same trans-acting element (i.e., a transcription or splicing factor) colocalize in three dimensions to form "RNA factories" that maximize the efficiency and accuracy of RNA biogenesis. We find that many loci with multiple binding sites of the same DNA-binding proteins interact with one another in trans, especially those bound by factors with intrinsically disordered domains. Similarly, clustered binding of a subset of RNA-binding proteins correlates with trans interaction of the encoding loci. We observe that these trans-interacting loci are close to nuclear speckles. These findings support the existence of trans-interacting chromatin domains (TIDs) driven by RNA biogenesis. Trans-C provides an efficient computational framework for studying these and other types of trans interactions, empowering studies of a poorly understood aspect of genome architecture. Full Article
ic Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:08-07:00 Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility. Full Article
ic Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 Somatic mutations arise and accumulate during tissue culture and vegetative propagation, potentially affecting various traits in horticultural crops, but their characteristics are still unclear. Here, somatic mutations in regenerated woodland strawberry derived from tissue culture of shoot tips under different conditions and 12 cultivated strawberry individuals are analyzed by whole genome sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 x 10–8–3.0 x 10–6 mutations per site. CG methylation shows a stable reduction (0.71%–8.03%) in regenerated plants, and hypoCG-DMRs are more heritable after sexual reproduction. A high-quality haplotype-resolved genome is assembled for the strawberry cultivar "Beni hoppe." The 12 "Beni hoppe" individuals randomly selected from different locations show 4731–6005 mutations relative to the reference genome, and the mutation frequency varies among the subgenomes. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale and nucleotide resolution in plants. Full Article
ic Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 The poly(A) signal, together with auxiliary elements, directs cleavage of a pre-mRNA and thus determines the 3' end of the mature transcript. In many species, including humans, the poly(A) signal is an AAUAAA hexamer, but we recently found that the deeply branching eukaryote Giardia lamblia uses a distinct hexamer (AGURAA) and lacks any known auxiliary elements. Our discovery prompted us to explore the evolutionary dynamics of poly(A) signals and auxiliary elements in the eukaryotic kingdom. We use direct RNA sequencing to determine poly(A) signals for four protists within the Metamonada clade (which also contains G. lamblia) and two outgroup protists. These experiments reveal that the AAUAAA hexamer serves as the poly(A) signal in at least four different eukaryotic clades, indicating that it is likely the ancestral signal, whereas the unusual Giardia version is derived. We find that the use and relative strengths of auxiliary elements are also plastic; in fact, within Metamonada, species like G. lamblia make use of a previously unrecognized auxiliary element where nucleotides flanking the poly(A) signal itself specify genuine cleavage sites. Thus, despite the fundamental nature of pre-mRNA cleavage for the expression of all protein-coding genes, the motifs controlling this process are dynamic on evolutionary timescales, providing motivation for future biochemical and structural studies as well as new therapeutic angles to target eukaryotic pathogens. Full Article
ic Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 The transcription factor (TF) cone-rod homeobox (CRX) is essential for the differentiation and maintenance of photoreceptor cell identity. Several human CRX variants cause degenerative retinopathies, but most are variants of uncertain significance. We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitutions in CRX using a cell-based transcriptional reporter assay, curating a high-confidence list of nearly 2000 variants with altered transcriptional activity. In the structured homeodomain, activity scores closely aligned to a predicted structure and demonstrated position-specific constraints on amino acid substitution. In contrast, the intrinsically disordered transcriptional effector domain displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. These compositional constraints were consistent with the acidic exposure model of transcriptional activation. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, identifying pathogenic variants with high specificity and moderate sensitivity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate utility for integration into the clinical variant classification pipeline. Full Article
ic 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
ic Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 As a major type of structural variants, tandem duplication plays a critical role in tumorigenesis by increasing oncogene dosage. Recent work has revealed that noncoding enhancers are also affected by duplications leading to the activation of oncogenes that are inside or outside of the duplicated regions. However, the prevalence of enhancer duplication and the identity of their target genes remains largely unknown in the cancer genome. Here, by analyzing whole-genome sequencing data in a non-gene-centric manner, we identify 881 duplication hotspots in 13 major cancer types, most of which do not contain protein-coding genes. We show that the hotspots are enriched with distal enhancer elements and are highly lineage-specific. We develop a HiChIP-based methodology that navigates enhancer–promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63, and VEGFA, as well as potentially novel oncogenes such as GRHL2, IRF2BP2, and CREB3L1. In particular, we identify a duplication hotspot on Chromosome 10p15 harboring a cluster of enhancers, which skips over two genes, through a long-range chromatin interaction, to activate an oncogenic isoform of the NET1 gene to promote migration of gastric cancer cells. Focusing on tandem duplications, our study substantially extends the catalog of noncoding driver alterations in multiple cancer types, revealing attractive targets for functional characterization and therapeutic intervention. Full Article
ic 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
ic AGAP duplicons associate with structural diversity at Chromosome 10q11.22 [RESEARCH] By genome.cshlp.org Published On :: 2024-10-29T06:46:07-07:00 The 10q11.22 chromosomal region is a duplication-rich interval of the human genome and one of the last to be fully assembled. It carries copy number–variable genes associated with intellectual disability, bipolar disorder, and obesity. In this study, we characterized the structural diversity at this locus by analyzing 64 haploid assemblies produced by the Human Pangenome Reference Consortium. We identified 11 alternative haplotypes that differ in the copy number and/or orientation of large genomic segments, ranging from hundreds of kilobase pairs (kbp) to over one megabase pair (Mbp). We uncovered a 2.4 Mbp size difference between the shortest and longest haplotypes. Breakpoint analysis revealed that genomic instability results from nonallelic homologous recombination between segmental duplication (SD) pairs with varying similarity (94.4%–99.6%). Nonetheless, these pairs generally recombine at positions where their identity is higher (>99.6%). Recurrent inversions occur with different breakpoints within the same inverted SD pair. Inversion polymorphisms shuffle the entire SD arrangement, creating new predispositions to copy-number variations. The SD architecture is associated with a catarrhine-specific subgroup of the AGAP gene family, which likely triggered the accumulation of SDs at this locus over the past 25 million years of human evolution. Our results reveal extensive structural diversity and genomic instability at the 10q11.22 locus, and expand the general understanding of the mutational mechanisms behind SD-mediated rearrangements. Full Article
ic Re: Friendship as Medicine By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Full Article
ic Wonca Europe 2023 Definition of General Practice/Family Medicine: New Needs New Content By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Full Article
ic 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
ic Impact of COVID-19 on Chronic Ambulatory-Care-Sensitive Condition Emergency Department Use Among Older Adults By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Background: The COVID-19 pandemic social distancing requirements encouraged patients to avoid public spaces including in-office health care visits. Ambulatory-care-sensitive conditions (ACSCs) represent conditions that can be managed with quality primary care and when access is limited, these conditions can lead to avoidable emergency department (ED) visits. Methods: Using national data on ED visits from 2019 to 2021 in the National Hospital Ambulatory Care Survey, we examined the impact of COVID-19 pandemic on ACSC ED visits among older adults (aged ≥65). Results: The proportion of ED visits among older adults that were for ACSCs increased between 2019 (17.4%) and 2021 (18.5%). The trend in both rural (26.4%–28.6%) and urban areas (15.4%–16.8%) shows a significant jump from 2019 to 2021 (P < .001). Conclusions: This rise in ACSC ED use is consistent with a delay in normal primary care during the pandemic. Full Article
ic Impact of Point of Care Hemoglobin A1c Testing on Time to Therapeutic Intervention By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Without compromising accuracy, point of care testing (POCT) provides immediate results at the time of in person patient consultation. The purpose of this study was to evaluate time until therapeutic intervention with POCT HbA1c versus venipuncture, where venipuncture was considered standard of care. The primary outcome was time (hours) to implementation of a therapeutic intervention based on POCT HbA1c result, as compared with most recent venipuncture HbA1c before the study and its associated therapeutic intervention. A total of 94 POCT HbA1c tests were included in the primary analysis. For the POCT HbA1c, the mean time to therapeutic intervention was 1.6 ± 3.14 hours. For the previous venipuncture HbA1c, the mean time to therapeutic intervention was 1376.66 ± 3356.6 hours (P < .001). Overall, this trial showed that POCT HbA1c results in a significantly faster time to therapeutic intervention than venipuncture in a primary care clinic that serves a rural population. Full Article
ic A Comprehensive Guide to Long-Acting Injectable Antipsychotics for Primary Care Clinicians By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 We propose a paper that provides education on commonly used long-acting injectable antipsychotics (LAIs) to improve primary care based mental health interventions in patients with severe mental illnesses (SMIs) such as schizophrenia, schizoaffective disorder, and bipolar disorders. With the expanding interface of primary care and psychiatry across all healthcare settings, it has become increasingly important for primary care clinicians to have a broader understanding of common psychiatric treatments, including LAIs. Long-acting injectable antipsychotics have been shown to be helpful in significantly improving treatment adherence, preventing disease progression, improving treatment response, decreasing readmission rates, and reducing social impairment. We discuss evidence-based indications and guidelines for use of long-acting injectable antipsychotics. We provide an overview of the treatment of SMI with LAIs, mainly focusing on the most commonly used long-acting injectable antipsychotics, advantages and disadvantages of each, along with outlining important clinical pearls for ease of practical application. Equipped with increased familiarity and understanding of these essential therapies, primary care clinicians can better facilitate early engagement with psychiatric care, promote more widespread use, and thus significantly improve the wellbeing and quality of life of patients with severe mental illness. Full Article
ic Potential Drawbacks of Noninvasive Diagnostic Methods for Nonalcoholic Fatty Liver Disease By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 The rising obesity epidemic is a phenomenon that has gained increasing attention from health providers and health policy makers. This led to recognition of nonalcoholic fatty liver disease (MASLD). The standard for its assessment has been histologic, which is neither practical nor acceptable by patients. Subsequently, a number of noninvasive assessment methods have been developed. However, despite ease of implementation, their confounding variables do hinder their accuracy. Nonetheless, the development of the liver stiffness measurement (LSM) and incorporation of other biological parameters has minimized but not eliminated the need for liver biopsy. Imaging methods are useful in evaluation, estimation, and following the progression of steatosis and fibrosis with particular attention to controlled attenuation parameter (CAP) and MRI–Proton Density Fat Fraction (MRI-PDFF). The choices for the family physician are broad and rely on tests’ availability, cost, and patient acceptance. Great efforts have been undertaken to produce more robust and novel noninvasive markers that indicate fibrinogenesis directly in an implementable and cost-effective way. Full Article
ic Assessing Patient Readiness for Hospital Discharge, Discharge Communication, and Transitional Care Management By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Background: Discharge communication between hospitalists and primary care clinicians is essential to improve care coordination, minimize adverse events, and decrease unplanned health services use. Health-related social needs are key drivers of health, and hospitalists and primary care clinicians value communicating social needs at discharge. Objective: To 1) characterize the current state of discharge communications between an academic medical center hospital and primary care clinicians at associated clinics; 2) seek feedback about the potential usefulness of discharge readiness information to primary care clinicians. Design: Exploratory, convergent mixed methods. Participants: Primary care clinicians from Family Medicine and General Internal Medicine of an academic medical center in the US Intermountain West. Approach: Literature-informed REDCap survey. Semistructured interview guide developed with key informants, grounded in current literature. Survey data were descriptively summarized; interview data were deductively and inductively coded, organized by topics. Results: Two key topics emerged: 1) discharge communication, with interrelated topics of transitional care management and follow-up appointment challenges, and recommendations for improving discharge communication; and 2) usefulness of the discharge readiness information, included interrelated topics related to lack of shared understanding about roles and responsibilities across settings and ethical concerns related to identifying problems that may not have solutions. Conclusions: While reiterating perennial discharge communication and transitional care management challenges, this study reveals new evidence about how these issues are interrelated with assessing and responding to patients’ lack of readiness for discharge and unmet social needs during care transitions. Primary care clinicians had mixed views on the usefulness of discharge readiness information. We offer recommendations for improving discharge communication and transitional care management (TCM) processes, which may be applicable in other care settings. Full Article
ic Sexual Misconduct by Board Certified Family Physicians By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Purpose: Sexual misconduct by physicians is a consequential violation of patient trust. The purpose of this study was to determine the frequency and patterns of sexual misconduct by physicians certified by the American Board of Family Medicine (ABFM). Methods: We described a cohort of current or formerly ABFM certified physicians ("Diplomates") disciplined for sexual misconduct in 2016 to 2022. Results: Ninety-four physicians, representing only 0.1% of ABFM Diplomates, were identified as having received disciplinary action(s) for reported sexual misconduct. These constituted 8.9% of the 1122 cases that resulted in a physician losing board certification or eligibility for any cause in 2016 to 2022. Ninety-three of the 94 physicians identified as male, with an average age of 56 (range 22 to 88 years). Eighty-nine percent of victims were female, and 90% were patients of the physician. Unwanted sexual behavior/assault occurred in more than half of the cases, whereas one third described an ongoing sexual relationship between patient and physician. Nearly 1 in 5 cases also included controlled substance prescribing. Seven cases involved minors. Noncontact ("grooming") behaviors were described in 34 cases, 28 of which included subsequent physical sexual behavior. A clinical setting was the site of misconduct in 84% of cases. Conclusions: Reports of sexual misconduct among board-certified family physicians are infrequent. However, any sexual misconduct by physicians is harmful to patients and the profession. The specialty should work to enhance education and change professional culture to mitigate this important problem. Full Article
ic How Early Career Family Medicine Women Physicians Negotiate Their First Job After Residency By www.jabfm.org Published On :: 2024-10-25T09:26:14-07:00 Background: Nested within a growing body of evidence of a gender pay gap in medicine are more alarming recent findings from family medicine: a gender pay gap of 16% can be detected at a very early career stage. This article explores qualitative evidence of women’s experiences negotiating for their first job out of residency to ascertain women’s engagement with and approach to the negotiation process. Methods: We recruited family physicians who graduated residency in 2019 and responded to the American Board of Family Medicine 2022 graduate survey. We developed a semistructured interview guide following a modified life history approach to uncover women’s experiences through the transitory stages from residency to workforce. A qualitative researcher used Zoom to interview 19 geographically and racially diverse early career women physicians. Interviews were transcribed verbatim and analyzed using NVivo software following an Inductive Content Analysis approach. Results: Three main themes emerged from the data. First, salary was found to be nonnegotiable, exemplified by participants’ inability to change initial salary offers. Second, the role of peer support throughout residency and early career was crucial to uncovering and rectifying salary inequity. Third, a pay expectation gap was identified among women from minority and low-income households. Conclusion: To rectify the gender pay gap in medicine, a systems-level approach is required. This can be achieved through various levels of interventions: societally expanding the use of and removing the stigma around parental leave, recognizing the importance of contributions not currently valued by productivity-based payment models, examining assumptions about leadership; and institutionally moving away from fee-for-service systems, encouraging flexible schedules, increasing salary transparency, and improving advancement transparency. Full Article