Background For years, US medical schools have relied on community-based, private clinicians to educate medical students. There has been a steady decline in the number of physicians willing to take on medical students in their clinical practices. Recent issues related to the pandemic raise questions about how many patients students should see to have a meaningful clinical experience. Methods As part of a 16-week longitudinal clinical experience, medical students spend 2 days each week in a family medicine or internal medicine clinic. As repetition enhances learning, maximizing the number of patients students see is important. Using a mixed integer linear program, we sought to determine the optimal schedule that maximizes the number of patients whom students see during a rotation. Patient visits were collected from January to April 2018 for clinics used by the medical school. By maximizing the minimum number of patients per learner over all non-empty day-clinic combinations, we deliver equitable rotation plans based on our assumptions. Results For this pilot study, multiple experiments were performed with different numbers of students assigned to clinics. Each experiment also generated a weekly rotation plan for a given student. Based on this optimization model, the minimum number of patients per student over 16 weeks was 87 (3 patients per day) and actually increased the number of students who could be assigned to one of the clinics from 1 student per rotation to 8 students. Conclusions The mixed integer linear program assigned more students to clinics that have more total visits in order to achieve the optimal and fairest learning quality. In addition, by conducting various experiments on different numbers of students, we observed that we were able to allocate more students without affecting the number of patients students see.
Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
“Race” and “ethnicity” are socially constructed terms, not based on biology - in contrast to biologic ancestry and genetic admixture - and are flexible, contested, and unstable concepts, often driven by power. Although individuals may self-identify with a given race and ethnic group, as multidimensional beings exposed to differential life influencing factors that contribute to disease risk, additional social determinants of health (SDOH) should be explored to understand the relationship of race or ethnicity to health. Potential health effects of structural racism, defined as “the structures, policies, practices, and norms resulting in differential access to goods, services, and opportunities of society by “race,” have been largely ignored in medical research. The Women’s Health Initiative (WHI) was expected to enroll a racially and ethnically diverse cohort of older women at 40 U.S. clinical centers between 1993 and 1998; yet, key information on the racial and ethnic make-up of the WHI cohort of 161,808 women was limited until a 2020–2021 Task Force was charged by the WHI Steering Committee to better characterize the WHI cohort and develop recommendations for WHI investigators who want to include “race” and/or “ethnicity” in papers and presentations. As the lessons learned are of relevance to most cohorts, the essence of the WHI Race and Ethnicity Language and Data Interpretation Guide is presented in this paper. Recommendations from the WHI Race and Ethnicity Language and Data Interpretation Guide include: Studies should be designed to include all populations and researchers should actively, purposefully and with cultural-relevance, commit to recruiting a diverse sample; Researchers should collect robust data on race, ethnicity and SDOH variables that may intersect with participant identities, such as immigration status, country of origin, acculturation, current residence and neighborhood, religion; Authors should use appropriate terminology, based on a participant’s self-identified “race” and “ethnicity”, and provide clear rationale, including a conceptual framework, for including race and ethnicity in the analytic plan; Researchers should employ appropriate analytical methods, including mixed-methods, to study the relationship of these sociocultural variables to health; Authors should address how representative study participants are of the population to which results might apply, such as by age, race and ethnicity.
Cellular reprogramming has rapidly become a promising methodology to generate new cardiomyocytes from non-cardiomyocyte cell types. Using the transient expression of OSKM factors, Chen et al. demonstrate a unique reprogramming strategy involving the modulation of the resident adult cardiomyocyte identity to an immature proliferative state (Science 373:1537–40, 2021). This OSKM-mediated reversion results in the adoption by adult murine cardiomyocytes of a transcriptional profile similar to cardiomyocytes found in developing hearts, as well as increased proliferative capacity of these reprogrammed cardiomyocytes compared to mature cardiomyocytes. Furthermore, this novel approach enhances the regeneration of adult murine hearts post-myocardial injury. Although concerns and questions remain, the encouraging results of this study advance the field of cardiac regeneration by providing a new technique to generate cardiomyocytes as well as insights into cardiomyocyte dedifferentiation and its relation to proliferation.
Background Tuberous sclerosis complex (TSC)–associated neuropsychiatric disorders (TAND) is an umbrella term for the behavioural, psychiatric, intellectual, academic, neuropsychological and psychosocial manifestations of TSC. Although TAND affects 90% of individuals with TSC during their lifetime, these manifestations are relatively under-assessed, under-treated and under-researched. We performed a comprehensive scoping review of all TAND research to date (a) to describe the existing TAND research landscape and (b) to identify knowledge gaps to guide future TAND research. Methods The study was conducted in accordance with stages outlined within the Arksey and O’Malley scoping review framework. Ten research questions relating to study characteristics, research design and research content of TAND levels and clusters were examined. Results Of the 2841 returned searches, 230 articles published between 1987 and 2020 were included (animal studies = 30, case studies = 47, cohort studies = 153), with more than half published since the term TAND was coined in 2012 (118/230; 51%). Cohort studies largely involved children and/or adolescents (63%) as opposed to older adults (16%). Studies were represented across 341 individual research sites from 45 countries, the majority from the USA (89/341; 26%) and the UK (50/341; 15%). Only 48 research sites (14%) were within low–middle income countries (LMICs). Animal studies and case studies were of relatively high/high quality, but cohort studies showed significant variability. Of the 153 cohort studies, only 16 (10%) included interventions. None of these were non-pharmacological, and only 13 employed remote methodologies (e.g. telephone interviews, online surveys). Of all TAND clusters, the autism spectrum disorder–like cluster was the most widely researched (138/230; 60%) and the scholastic cluster the least (53/200; 27%). Conclusions Despite the recent increase in TAND research, studies that represent participants across the lifespan, LMIC research sites and non-pharmacological interventions were identified as future priorities. The quality of cohort studies requires improvement, to which the use of standardised direct behavioural assessments may contribute. In human studies, the academic level in particular warrants further investigation. Remote technologies could help to address many of the TAND knowledge gaps identified.
Background Although survival rates for infants born extremely preterm (gestation < 28 weeks) have improved significantly in recent decades, neurodevelopmental impairment remains a major concern. Children born extremely preterm remain at high risk for cognitive impairment from early childhood to adulthood. However, there is limited evidence on genetic factors associated with cognitive impairment in this population. Methods First, we used a latent profile analysis (LPA) approach to characterize neurocognitive function at age 10 for children born extremely preterm. Children were classified into two groups: (1) no or low cognitive impairment, and (2) moderate-to-severe cognitive impairment. Second, we performed TOPMed-based genotype imputation on samples with genotype array data (n = 528). Third, we then conducted a genome-wide association study (GWAS) for LPA-inferred cognitive impairment. Finally, computational analysis was conducted to explore potential mechanisms underlying the variant x LPA association. Results We identified two loci reaching genome-wide significance (p value < 5e-8): TEA domain transcription factor 4 (TEAD4 at rs11829294, p value = 2.40e-8) and syntaxin 18 (STX18 at rs79453226, p value = 1.91e-8). Integrative analysis with brain expression quantitative trait loci (eQTL), chromatin conformation, and epigenomic annotations suggests tetraspanin 9 (TSPAN9) and protein arginine methyltransferase 8 (PRMT8) as potential functional genes underlying the GWAS signal at the TEAD4 locus. Conclusions We conducted a novel computational analysis by utilizing an LPA-inferred phenotype with genetics data for the first time. This study suggests that rs11829294 and its LD buddies have potential regulatory roles on genes that could impact neurocognitive impairment for extreme preterm born children.
A new generation of community- and population-based research is combining measures of social context, experience, and behavior with direct measures of physiology, gene sequence and function, and health. Studies drawing on models and methods from the social and biological sciences have the potential to illuminate the multilevel mechanisms through which experience becomes biology, and to move past decontextualized and reductionistic approaches to human development, behavior, and health. In this perspective we highlight challenges and opportunities at the biosocial interface, and briefly discuss COVID-19 as a case study demonstrating the importance of linking across levels of analysis.
Digital approaches are increasingly common in clinical trial recruitment, retention, analysis, and dissemination. Community engagement processes have contributed to the successful implementation of clinical trials and are crucial in enhancing equity in trials. However, few studies focus on how digital approaches can be implemented to enhance community engagement in clinical trials. This narrative review examines three key areas for digital approaches to deepen community engagement in clinical trials—the use of digital technology for trial processes to decentralize trials, digital crowdsourcing to develop trial components, and digital qualitative research methods. We highlight how digital approaches enhanced community engagement through a greater diversity of participants, and deepened community engagement through the decentralization of research processes. We discuss new possibilities that digital technologies offer for community engagement, and highlight potential strengths, weaknesses, and practical considerations. We argue that strengthening community engagement using a digital approach can enhance equity and improve health outcomes.
Four drivers of global change are acting in concert to speed up the ecology of our coastal and open ocean ecosystems. Ocean warming, nutrient pollution, disturbance, and species additions increase biological and ecological rates, favoring weedy communities and causing pervasive human impacts. Ocean warming via greenhouse gas emissions is accelerating metabolic processes, with effects scaling up to populations and ecosystems. Likewise, supercharging primary production via increased resources (e.g., nutrients and light) is leading to faster, weedier communities in estuarine and coastal ecosystems. Disturbances like ocean heat waves are becoming more frequent, resetting succession, and creating permanently young assemblages, while species additions are transporting the quick-growing and the fecund. The speeding up of marine ecosystems will necessitate changes in the ways we do science, attempt conservation, and use ecosystem services.
Objective Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal disease affecting preterm infants. NEC develops suddenly and is characterized by gut barrier destruction, an inflammatory response, intestinal necrosis and multi-system organ failure. There is currently no method for early NEC detection, and the pathogenesis of NEC remains unclear. Design To further understand the molecular mechanisms that support NEC, we used solution phase hybridization and next-generation DNA sequencing of bisulfite converted DNA to perform targeted genome-wide analysis of DNA methylation at high read depth. Results We found that ileal samples from surgical NEC infants ( n = 5) exist in a broadly hypermethylated state relative to their non-NEC counterparts ( n = 9). These trends were not uniform, with hypermethylation being most consistently observed outside CpG islands and promoters. We further identified several biologically interesting gene promoters that displayed differential methylation in NEC and a number of biological pathways that appear dysregulated in NEC. We also found that DNA methylation patterns identified in ileal NEC tissue were correlated with those found and published previously in stool samples from NEC-affected infants. Conclusion We confirmed that surgical NEC is associated with broad DNA hypermethylation in the ileum, and this may be detectable in stool samples of affected individuals. Thus, an epigenomic liquid biopsy of stool may have significant potential as a biomarker with respect to the diagnostic/predictive detection of NEC. Our findings, along with recent similar observations in colon, suggest that epigenomic dysregulation is a significant feature of surgical NEC. These findings motivate future studies which will involve the longitudinal screening of samples obtained prior to the onset of NEC. Our long-term goal is the development of novel screening, diagnostic and phenotyping methods for NEC.
Background Symptoms in patients with advanced cancer are often inadequately captured during encounters with the healthcare team. Emerging evidence demonstrates that weekly electronic home-based patient-reported symptom monitoring with automated alerts to clinicians reduces healthcare utilization, improves health-related quality of life, and lengthens survival. However, oncology practices have lagged in adopting remote symptom monitoring into routine practice, where specific patient populations may have unique barriers. One approach to overcoming barriers is utilizing resources from value-based payment models, such as patient navigators who are ideally positioned to assume a leadership role in remote symptom monitoring implementation. This implementation approach has not been tested in standard of care, and thus optimal implementation strategies are needed for large-scale roll-out. Methods This hybrid type 2 study design evaluates the implementation and effectiveness of remote symptom monitoring for all patients and for diverse populations in two Southern academic medical centers from 2021 to 2026. This study will utilize a pragmatic approach, evaluating real-world data collected during routine care for quantitative implementation and patient outcomes. The Consolidated Framework for Implementation Research (CFIR) will be used to conduct a qualitative evaluation at key time points to assess barriers and facilitators, implementation strategies, fidelity to implementation strategies, and perceived utility of these strategies. We will use a mixed-methods approach for data interpretation to finalize a formal implementation blueprint. Discussion This pragmatic evaluation of real-world implementation of remote symptom monitoring will generate a blueprint for future efforts to scale interventions across health systems with diverse patient populations within value-based healthcare models. Trial registration NCT04809740 ; date of registration 3/22/2021.
Purpose Anterior cruciate ligament rupture is associated with characteristic bone contusions in approximately 80% of patients, and these have been correlated with higher pain scores. Bone bruising may indicate joint damage that increases inflammation and the likelihood of posttraumatic osteoarthritis. We sought to characterize the severity of bone bruising following acute anterior cruciate ligament injury and determine if it correlates with synovial fluid and serum levels of the proinflammatory chemokine monocyte chemoattractant protein-1 associated with posttraumatic osteoarthritis. Methods This was a retrospective analysis of data collected prospectively from January 2014 through December 2016. All patients who sustained an acute ligament rupture were evaluated within 15 days of injury, obtained a magnetic resonance imaging study, and underwent bone-patellar-tendon-bone autograft reconstruction were offered enrollment. The overall severity of bone bruising on magnetic resonance imaging was graded (sum of 0–3 grades in 13 sectors of the articular surfaces). Serum and synovial fluid levels of monocyte chemoattractant protein-1 were measured within 14 days of injury, and serum levels were again measured 6 and 12 months following surgery. Separate univariate linear regression models were constructed to determine the association between monocyte chemoattractant protein-1 and bone bruising severity at each time point. Results Forty-eight subjects were included in this study. They had a mean age of 21.4 years and were 48% female. Median overall bone bruising severity was 5 (range 0–14). Severity of bone bruising correlated with higher synovial fluid concentrations of monocyte chemoattractant protein-1 preoperatively (R ² = 0.18, p = 0.009) and with serum concentrations at 12 months post-reconstruction (R ² = 0.12, p = 0.04). Conclusions The severity of bone bruising following anterior cruciate ligament rupture is associated with higher levels of the proinflammatory cytokine monocyte chemoattractant protein-1 in synovial fluid acutely post-injury and in serum 12-months following anterior cruciate ligament reconstruction. This suggests that severe bone bruising on magnetic resonance imaging after ligament rupture may indicate increased risk for persistent joint inflammation and posttraumatic osteoarthritis. Level of evidence III ― retrospective cohort study.
Background This update describes changes to the Brief Educational Tool to Enhance Recovery (BETTER) trial in response to the COVID-19 pandemic. Methods/design The original protocol was published in Trials . Due to the COVID-19 pandemic, the BETTER trial converted to remote recruitment in April 2020. All recruitment, consent, enrollment, and randomization now occur by phone within 24 h of the acute care visit. Other changes to the original protocol include an expansion of inclusion criteria and addition of new recruitment sites. To increase recruitment numbers, eligibility criteria were expanded to include individuals with chronic pain, non-daily opioid use within 2 weeks of enrollment, presenting musculoskeletal pain (MSP) symptoms for more than 1 week, hospitalization in past 30 days, and not the first time seeking medical treatment for presenting MSP pain. In addition, recruitment sites were expanded to other emergency departments and an orthopedic urgent care clinic. Conclusions Recruiting from an orthopedic urgent care clinic and transitioning to remote operations not only allowed for continued participant enrollment during the pandemic but also resulted in some favorable outcomes, including operational efficiencies, increased enrollment, and broader generalizability. Trial registration ClinicalTrials.gov NCT04118595 . Registered on October 8, 2019.
Background Marijuana’s putative anti-inflammatory properties may benefit HIV-associated comorbidities. How recreational marijuana use affects gene expression in peripheral blood cells (PBC) among youth with HIV-1 (YWH) is unknown. Approach YWH with defined substance use (n = 54) receiving similar antiretroviral therapy (ART) were assigned to one of four analysis groups: YWH with detectable plasma HIV-1 (> 50 RNA copies/ml) who did not use substances (H+V+S−), and YWH with undetectable plasma HIV-1 who did not use substances (H+V−S−), or used marijuana alone (H+V−S+[M]), or marijuana in combination with tobacco (H+V−S+[M/T]). Non-substance using youth without HIV infection (H−S−, n = 25) provided a reference group. PBC mRNA was profiled by Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Differentially expressed genes (DEG) within outcome groups were identified by Significance Analysis of Microarrays and used for Hierarchical Clustering, Principal Component Analysis, and Ingenuity Pathways Analysis. Results HIV-1 replication resulted in > 3000 DEG involving 27 perturbed pathways. Viral suppression reduced DEG to 313, normalized all 27 pathways, and down-regulated two additional pathways, while marijuana use among virally suppressed YWH resulted in 434 DEG and no perturbed pathways. Relative to H+V−S−, multiple DEG normalized in H+V−S+[M]. In contrast, H+V−S+[M/T] had 1140 DEG and 10 dysregulated pathways, including multiple proinflammatory genes and six pathways shared by H+V+S−. Conclusions YWH receiving ART display unique transcriptome bioprofiles based on viral replication and substance use. In the context of HIV suppression, marijuana use, alone or combined with tobacco, has opposing effects on inflammatory gene expression.
Background Sleep is important for healthy functioning in children. Numerous genetic and environmental factors, from conception onwards, may influence this phenotype. Epigenetic mechanisms such as DNA methylation have been proposed to underlie variation in sleep or may be an early-life marker of sleep disturbances. We examined if DNA methylation at birth or in school age is associated with parent-reported and actigraphy-estimated sleep outcomes in children. Methods We meta-analysed epigenome-wide association study results. DNA methylation was measured from cord blood at birth in 11 cohorts and from peripheral blood in children (4–13 years) in 8 cohorts. Outcomes included parent-reported sleep duration, sleep initiation and fragmentation problems, and actigraphy-estimated sleep duration, sleep onset latency and wake-after-sleep-onset duration. Results We found no associations between DNA methylation at birth and parent-reported sleep duration (n = 3658), initiation problems (n = 2504), or fragmentation (n = 1681) (p values above cut-off 4.0 × 10–8). Lower methylation at cg24815001 and cg02753354 at birth was associated with longer actigraphy-estimated sleep duration (p = 3.31 × 10–8, n = 577) and sleep onset latency (p = 8.8 × 10–9, n = 580), respectively. DNA methylation in childhood was not cross-sectionally associated with any sleep outcomes (n = 716–2539). Conclusion DNA methylation, at birth or in childhood, was not associated with parent-reported sleep. Associations observed with objectively measured sleep outcomes could be studied further if additional data sets become available.
Here, we report a lack of diversity in epigenome-wide association studies (EWAS) and DNA methylation (DNAm) data, discuss current challenges, and propose solutions for EWAS and DNAm research in diverse populations. The strategies we propose include fostering community involvement, new data generation, and cost-effective approaches such as locus-specific analysis and ancestry variable region analysis.
In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.
Background The etiology of hamstring strain injury (HSI) in American football is multi-factorial and understanding these risk factors is paramount to developing predictive models and guiding prevention and rehabilitation strategies. Many player-games are lost due to the lack of a clear understanding of risk factors and the absence of effective methods to minimize re-injury. This paper describes the protocol that will be followed to develop the HAMstring InjuRy (HAMIR) index risk prediction models for HSI and re-injury based on morphological, architectural, biomechanical and clinical factors in National Collegiate Athletic Association Division I collegiate football players. Methods A 3-year, prospective study will be conducted involving collegiate football student-athletes at four institutions. Enrolled participants will complete preseason assessments of eccentric hamstring strength, on-field sprinting biomechanics and muscle–tendon volumes using magnetic-resonance imaging (MRI). Athletic trainers will monitor injuries and exposure for the duration of the study. Participants who sustain an HSI will undergo a clinical assessment at the time of injury along with MRI examinations. Following completion of structured rehabilitation and return to unrestricted sport participation, clinical assessments, MRI examinations and sprinting biomechanics will be repeated. Injury recurrence will be monitored through a 6-month follow-up period. HAMIR index prediction models for index HSI injury and re-injury will be constructed. Discussion The most appropriate strategies for reducing risk of HSI are likely multi-factorial and depend on risk factors unique to each athlete. This study will be the largest-of-its-kind (1200 player-years) to gather detailed information on index and recurrent HSI, and will be the first study to simultaneously investigate the effect of morphological, biomechanical and clinical variables on risk of HSI in collegiate football athletes. The quantitative HAMIR index will be formulated to identify an athlete’s propensity for HSI, and more importantly, identify targets for injury mitigation, thereby reducing the global burden of HSI in high-level American football players. Trial Registration The trial is prospectively registered on ClinicalTrials.gov (NCT05343052; April 22, 2022).
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