Enterococci enhance Clostridioides difficile pathogenesis.

Enteric pathogens are exposed to a dynamic polymicrobial environment in the gastrointestinal tract1. This microbial community has been shown to be important during infection, but there are few examples illustrating how microbial interactions can influence the virulence of invading pathogens2. Here we show that expansion of a group of antibiotic-resistant, opportunistic pathogens in the gut-the enterococci-enhances the fitness and pathogenesis of Clostridioides difficile. Through a parallel process of nutrient restriction and cross-feeding, enterococci shape the metabolic environment in the gut and reprogramme C. difficile metabolism. Enterococci provide fermentable amino acids, including leucine and ornithine, which increase C. difficile fitness in the antibiotic-perturbed gut. Parallel depletion of arginine by enterococci through arginine catabolism provides a metabolic cue for C. difficile that facilitates increased virulence. We find evidence of microbial interaction between these two pathogenic organisms in multiple mouse models of infection and patients infected with C. difficile. These findings provide mechanistic insights into the role of pathogenic microbiota in the susceptibility to and the severity of C. difficile infection.

Leveraging pleiotropy to discover and interpret GWAS results for sleep-associated traits.

Genetic association studies of many heritable traits resulting from physiological testing often have modest sample sizes due to the cost and burden of the required phenotyping. This reduces statistical power and limits discovery of multiple genetic associations. We present a strategy to leverage pleiotropy between traits to both discover new loci and to provide mechanistic hypotheses of the underlying pathophysiology. Specifically, we combine a colocalization test with a locus-level test of pleiotropy. In simulations, we show that this approach is highly selective for identifying true pleiotropy driven by the same causative variant, thereby improves the chance to replicate the associations in underpowered validation cohorts and leads to higher interpretability. Here, as an exemplar, we use Obstructive Sleep Apnea (OSA), a common disorder diagnosed using overnight multi-channel physiological testing. We leverage pleiotropy with relevant cellular and cardio-metabolic phenotypes and gene expression traits to map new risk loci in an underpowered OSA GWAS. We identify several pleiotropic loci harboring suggestive associations to OSA and genome-wide significant associations to other traits, and show that their OSA association replicates in independent cohorts of diverse ancestries. By investigating pleiotropic loci, our strategy allows proposing new hypotheses about OSA pathobiology across many physiological layers. For example, we identify and replicate the pleiotropy across the plateletcrit, OSA and an eQTL of DNA primase subunit 1 (PRIM1) in immune cells. We find suggestive links between OSA, a measure of lung function (FEV1/FVC), and an eQTL of matrix metallopeptidase 15 (MMP15) in lung tissue. We also link a previously known genome-wide significant peak for OSA in the hexokinase 1 (HK1) locus to hematocrit and other red blood cell related traits. Thus, the analysis of pleiotropic associations has the potential to assemble diverse phenotypes into a chain of mechanistic hypotheses that provide insight into the pathogenesis of complex human diseases.

Genomic Epidemiology of Human Respiratory Syncytial Virus, Minnesota, USA, July 2023-February 2024.

We recently expanded the viral genomic surveillance program in Minnesota, USA, to include human respiratory syncytial virus. We performed whole-genome sequencing of 575 specimens collected at Minnesota healthcare facilities during July 2023-February 2024. Subgroups A and B differed in their genomic landscapes, and we identified 23 clusters of genetically identical genomes.

Chemokine CXCL9, a marker of inflammaging, is associated with changes of muscle strength and mortality in older men.

Our study examined associations of the CXC motif chemokine ligand 9 (CXCL9), a pro-inflammatory protein implicated in age-related inflammation, with musculoskeletal function in elderly men. We found in certain outcomes both cross-sectional and longitudinal significant associations of CXCL9 with poorer musculoskeletal function and increased mortality in older men. This requires further investigation. PURPOSE: We aim to determine the relationship of (CXCL9), a pro-inflammatory protein implicated in age-related inflammation, with both cross-sectional and longitudinal musculoskeletal outcomes and mortality in older men. METHODS: A random sample from the Osteoporotic Fractures in Men (MrOS) Study cohort (N = 300) was chosen for study subjects that had attended the third and fourth clinic visits, and data was available for major musculoskeletal outcomes (6 m walking speed, chair stands), hip bone mineral density (BMD), major osteoporotic fracture, mortality, and serum inflammatory markers. Serum levels of CXCL9 were measured by ELISA, and the associations with musculoskeletal outcomes were assessed by linear regression and fractures and mortality with Cox proportional hazards models. RESULTS: The mean CXCL9 level of study participants (79.1 ± 5.3 years) was 196.9 ± 135.2 pg/ml. There were significant differences for 6 m walking speed, chair stands, physical activity scores, and history of falls in the past year across the quartiles of CXCL9. However, higher CXCL9 was only significantly associated with changes in chair stands (ß = - 1.098, p < 0.001) even after adjustment for multiple covariates. No significant associations were observed between CXCL9 and major osteoporotic fracture or hip BMD changes. The risk of mortality increased with increasing CXCL9 (hazard ratio quartile (Q)4 vs Q1 1.98, 95% confidence interval 1.25-3.14; p for trend < 0.001). CONCLUSIONS: Greater serum levels of CXCL9 were significantly associated with a decline in chair stands and increased mortality. Additional studies with a larger sample size are needed to confirm our findings.

How the EU Soil Observatory contributes to a stronger soil erosion community.

New policy developments have emerged in relation to soil conservation after 2020. The Common Agricultural Policy (CAP) 2023-2027, the proposal for a Soil Monitoring Law and the mission 'A Soil Deal for Europe' have shaped a new policy framework at EU level, which requires updated assessments on soil erosion and land degradation. The EU Soil Observatory (EUSO) successfully organised a scientific workshop on 'Soil erosion for the EU' in June 2022. The event has seen the participation of more than 330 people from 63 countries, addressing important topics such as (i) management practices, (ii) large scale modelling, (iii) the importance of sediments in nutrient cycle, (vi) the role of landslides and (v) laying the foundations for early career scientists. As a follow up, among the 120 abstracts submitted in the workshop, we received fifteen manuscripts, out of which nine were selected for publication in the present special issue. In this editorial, we summarize the major challenges that the soil erosion research community faces in relation to supporting the increasing role of soils in the EU Green Deal.

Validity of the Hawkin Dynamics Wireless Dual Force Platform System Against a Piezoelectric Laboratory Grade System for Vertical Countermovement Jump Variables.

ABSTRACT: Dos'Santos, T, Evans, DT, and Read, DB. Validity of the Hawkin dynamics wireless dual force platform system against a piezoelectric laboratory grade system for vertical countermovement jump variables. J Strength Cond Res 38(6): 1144-1148, 2024-The aim of this study was to determine the criterion validity of the Hawkin Dynamics (HD) wireless dual force platform system for assessing vertical countermovement jump (CMJ) variables, compared with those derived from a Kistler piezoelectric laboratory grade force platform system. During a single testing session, HD force platforms were placed directly on top of 2 adjacent Kistler force platforms to simultaneously collect vertical ground reaction forces produced by 2 male recreational soccer players (age: 29.0 ± 2.8 years, height: 1.79 ± 0.01 m, mass: 85.6 ± 4.7 kg) that performed 25 vertical CMJs each. Sixteen vertical CMJ variables pertaining to jump height (JH), flight time (FT), time-to-take off (TTT), countermovement depth, body weight (BW), propulsive and braking mean, and peak powers, forces, and impulses were compared between systems. Fixed bias was observed for 6 of 16 variables (peak and mean braking power, mean propulsion force, TTT, FT, and BW), while proportional bias was present for 10 of 16 variables (peak and mean propulsive and braking force, TTT, FT, peak and mean braking power, mean propulsive power, and BW). For all variables regardless of fixed or proportional bias, percentage differences were ≤3.4% between force platform systems, with near perfect to perfect correlations (r or ρ = 0.977-1.000) observed for 15 of 16 variables. The HD dual wireless force platform system can be considered a valid alternative to a piezoelectric laboratory grade force platform system for the collection of vertical CMJ variables, particularly outcome (i.e., JH, reactive strength index modified) and strategy variables (countermovement depth).

Temporal control by cofactors prevents kinetic trapping in retroviral Gag lattice assembly.

For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature Gag lattice has been structurally characterized and reconstituted in vitro, revealing the sensitivity of lattice assembly to multiple cofactors. Due to this sensitivity, the energetic criterion for forming stable lattices is unknown, as are their corresponding rates. Here, we use a reaction-diffusion model designed from the cryo-ET structure of the immature Gag lattice to map a phase diagram of assembly outcomes controlled by experimentally constrained rates and free energies, over experimentally relevant timescales. We find that productive assembly of complete lattices in bulk solution is extraordinarily difficult due to the large size of this ∼3700 monomer complex. Multiple Gag lattices nucleate before growth can complete, resulting in loss of free monomers and frequent kinetic trapping. We therefore derive a time-dependent protocol to titrate or "activate" the Gag monomers slowly within the solution volume, mimicking the biological roles of cofactors. This general strategy works remarkably well, yielding productive growth of self-assembled lattices for multiple interaction strengths and binding rates. By comparing to the in vitro assembly kinetics, we can estimate bounds on rates of Gag binding to Gag and the cellular cofactor IP6. Our results show that Gag binding to IP6 can provide the additional time delay necessary to support smooth growth of the immature lattice with relatively fast assembly kinetics, mostly avoiding kinetic traps. Our work provides a foundation for predicting and disrupting formation of the immature Gag lattice via targeting specific protein-protein binding interactions.

Genetic and Gene Expression Resources for Osteoporosis and Bone Biology Research.

PURPOSE OF REVIEW: The integration of data from multiple genomic assays from humans and non-human model organisms is an effective approach to identify genes involved in skeletal fragility and fracture risk due to osteoporosis and other conditions. This review summarizes genome-wide genetic variation and gene expression data resources relevant to the discovery of genes contributing to skeletal fragility and fracture risk. RECENT FINDINGS: Genome-wide association studies (GWAS) of osteoporosis-related traits are summarized, in addition to gene expression in bone tissues in humans and non-human organisms, with a focus on rodent models related to skeletal fragility and fracture risk. Gene discovery approaches using these genomic data resources are described. We also describe the Musculoskeletal Knowledge Portal (MSKKP) that integrates much of the available genomic data relevant to fracture risk. The available genomic resources provide a wealth of knowledge and can be analyzed to identify genes related to fracture risk. Genomic resources that would fill particular scientific gaps are discussed.

Targeted Genome Sequencing Identifies Multiple Rare Variants in Caveolin-1 Associated with Obstructive Sleep Apnea.

Rationale: Obstructive sleep apnea (OSA) is a common disorder associated with increased risk for cardiovascular disease, diabetes, and premature mortality. There is strong clinical and epidemiologic evidence supporting the importance of genetic factors influencing OSA but limited data implicating specific genes. Objectives: To search for rare variants contributing to OSA severity. Methods: Leveraging high-depth genomic sequencing data from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and imputed genotype data from multiple population-based studies, we performed linkage analysis in the CFS (Cleveland Family Study), followed by multistage gene-based association analyses in independent cohorts for apnea-hypopnea index (AHI) in a total of 7,708 individuals of European ancestry. Measurements and Main Results: Linkage analysis in the CFS identified a suggestive linkage peak on chromosome 7q31 (LOD = 2.31). Gene-based analysis identified 21 noncoding rare variants in CAV1 (Caveolin-1) associated with lower AHI after accounting for multiple comparisons (P = 7.4 × 10-8). These noncoding variants together significantly contributed to the linkage evidence (P < 10-3). Follow-up analysis revealed significant associations between these variants and increased CAV1 expression, and increased CAV1 expression in peripheral monocytes was associated with lower AHI (P = 0.024) and higher minimum overnight oxygen saturation (P = 0.007). Conclusions: Rare variants in CAV1, a membrane-scaffolding protein essential in multiple cellular and metabolic functions, are associated with higher CAV1 gene expression and lower OSA severity, suggesting a novel target for modulating OSA severity.

Functional outcomes of Fournier's gangrene: a multi-institutional experience.

INTRODUCTION: Fournier's gangrene (FG), is a progressive, necrotizing soft tissue infection of the external genitalia, perineum, and/or anorectal region. How treatment and recovery from FG impacts quality of life related to sexual and general health is poorly characterized. Our purpose is to evaluate the long term impact of FG on overall and sexual quality of life using standardized questionnaires through a multi-institutional observational study. MATERIALS AND METHODS: Multi-institutional retrospective data were collected by standardized questionnaires on patient-reported outcome measures including the Changes in Sexual Functioning Questionnaire (CSFQ) and the Veterans RAND 36 (VR-36) survey of general health-related quality of life. Data were collected via telephone call, email, and certified mail, with a 10% response rate. There was no incentive for patient participation. RESULTS: Thirty-five patients responded to the survey, with 9 female and 26 male patients. All patients in the study underwent surgical debridement between 2007-2018 at three tertiary care centers. Further reconstructions were performed for 57% of respondents. Values for respondents with overall lower sexual function were reduced in all component categories (pleasure, desire/ frequency, desire/interest, arousal/excitement, orgasm/ completion), and trended toward male sex, older age, longer time from initial debridement to reconstruction, and poorer self-reported general health-related quality of life metrics. CONCLUSION: FG is associated with high morbidity and significant decreases in quality of life across general and sexual functional domains.

Gaussian process linking functions for mind, brain, and behavior.

The link between mind, brain, and behavior has mystified philosophers and scientists for millennia. Recent progress has been made by forming statistical associations between manifest variables of the brain (e.g., electroencephalogram [EEG], functional MRI [fMRI]) and manifest variables of behavior (e.g., response times, accuracy) through hierarchical latent variable models. Within this framework, one can make inferences about the mind in a statistically principled way, such that complex patterns of brain-behavior associations drive the inference procedure. However, previous approaches were limited in the flexibility of the linking function, which has proved prohibitive for understanding the complex dynamics exhibited by the brain. In this article, we propose a data-driven, nonparametric approach that allows complex linking functions to emerge from fitting a hierarchical latent representation of the mind to multivariate, multimodal data. Furthermore, to enforce biological plausibility, we impose both spatial and temporal structure so that the types of realizable system dynamics are constrained. To illustrate the benefits of our approach, we investigate the model's performance in a simulation study and apply it to experimental data. In the simulation study, we verify that the model can be accurately fitted to simulated data, and latent dynamics can be well recovered. In an experimental application, we simultaneously fit the model to fMRI and behavioral data from a continuous motion tracking task. We show that the model accurately recovers both neural and behavioral data and reveals interesting latent cognitive dynamics, the topology of which can be contrasted with several aspects of the experiment.

Evolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients.

Patients with hematological malignancies or undergoing hematopoietic stem cell transplantation are vulnerable to colonization and infection with multidrug-resistant organisms, including vancomycin-resistant Enterococcus faecium (VREfm). Over a 10-y period, we collected and sequenced the genomes of 110 VREfm isolates from gastrointestinal and blood cultures of 24 pediatric patients undergoing chemotherapy or hematopoietic stem cell transplantation for hematological malignancy at St. Jude Children's Research Hospital. We used patient-specific reference genomes to identify variants that arose over time in subsequent gastrointestinal and blood isolates from each patient and analyzed these variants for insight into how VREfm adapted during colonization and bloodstream infection within each patient. Variants were enriched in genes involved in carbohydrate metabolism, and phenotypic analysis identified associated differences in carbohydrate utilization among isolates. In particular, a Y585C mutation in the sorbitol operon transcriptional regulator gutR was associated with increased bacterial growth in the presence of sorbitol. We also found differences in biofilm-formation capability between isolates and observed that increased biofilm formation correlated with mutations in the putative E. faecium capsular polysaccharide (cps) biosynthetic locus, with different mutations arising independently in distinct genetic backgrounds. Isolates with cps mutations showed improved survival following exposure to lysozyme, suggesting a possible reason for the selection of capsule-lacking bacteria. Finally, we observed mutations conferring increased tolerance of linezolid and daptomycin in patients who were treated with these antibiotics. Overall, this study documents known and previously undescribed ways that VREfm evolve during intestinal colonization and subsequent bloodstream infection in immunocompromised pediatric patients.

Relationships Between Lower Extremity Power and Fastball Spin Rate and Ball Velocity in Professional Baseball Pitchers.

ABSTRACT: Wong, R, Laudner, K, Amonette, W, Vazquez, J, Evans, D, and Meister, K. Relationships between lower extremity power and fastball spin rate and ball velocity in professional baseball pitchers. J Strength Cond Res 37(4): 823-828, 2023-Lower extremity power has been hypothesized to increase ball spin and velocity during pitching in baseball. Therefore, the purpose of this study was to determine the relationship between lower extremity power and fastball spin rate in professional baseball pitchers. A secondary purpose was to determine the relationship between lower extremity power and ball velocity. Fifty-three asymptomatic professional pitchers participated (24.5 ± 3.6 years; 189.9 ± 6.1 cm; 92.6 ± 10.3 kg). Each athlete performed 3 separate bilateral jump tests on force plates: countermovement jump (CMJ), squat jump (SJ), and drop jump (DJ). The average fastball spin rate and ball velocity for each pitcher was calculated using a 3-dimensional Doppler radar and video system over the course of a competitive season. Standard multiple regression analyses ( p ≤ 0.05) revealed significant relationship between ball spin and summation of variables for the CMJ (peak force, peak power, rate of power development, and jump height) ( R2 = 0.20, F = 3.1, p = 0.03). However, no individual variable was significantly associated ( p > 0.09). There was also a significant amount of variance in ball spin explained by summation of variables for the SJ (peak force, peak power, rate of power development, and jump height) ( R2 = 0.19, F = 2.8, p = 0.04); rate of power development was the only variable that significantly predicted ball spin within this model ( B = 0.27; 95% confidence interval [CI]: 0.003-0.75, p = 0.05). Ball spin was not associated with summation of DJ variables (peak power, rate of power development, jump height, reactive strength index, and total peak power in watts) ( R2 = 0.18, F = 2.0, p = 0.09). For ball velocity, there were no significant relationships for the summation of either the CMJ variables ( R2 = 0.10, p = 0.28) or the SJ variables ( R2 = 0.07, p = 0.44). However, there was a significant amount of variance in ball velocity explained by summation of variables for the DJ ( R2 = 0.30, F = 3.93, p = 0.005). The reactive strength index was the sole unique contribution to this model ( B = 1.18; 95% CI: -10.34 to 2.36, p = 0.002). These findings highlight the relevance of increased lower extremity power on increasing fastball spin rate and ball velocity.

Distributed Neural Systems Support Flexible Attention Updating during Category Learning.

To accurately categorize items, humans learn to selectively attend to the stimulus dimensions that are most relevant to the task. Models of category learning describe how attention changes across trials as labeled stimuli are progressively observed. The Adaptive Attention Representation Model (AARM), for example, provides an account in which categorization decisions are based on the perceptual similarity of a new stimulus to stored exemplars, and dimension-wise attention is updated on every trial in the direction of a feedback-based error gradient. As such, attention modulation as described by AARM requires interactions among processes of orienting, visual perception, memory retrieval, prediction error, and goal maintenance to facilitate learning. The current study explored the neural bases of attention mechanisms using quantitative predictions from AARM to analyze behavioral and fMRI data collected while participants learned novel categories. Generalized linear model analyses revealed patterns of BOLD activation in the parietal cortex (orienting), visual cortex (perception), medial temporal lobe (memory retrieval), basal ganglia (prediction error), and pFC (goal maintenance) that covaried with the magnitude of model-predicted attentional tuning. Results are consistent with AARM's specification of attention modulation as a dynamic property of distributed cognitive systems.

Patient-level interventions to reduce alcohol-related harms in low- and middle-income countries: A systematic review and meta-summary.

BACKGROUND: Disease and disability from alcohol use disproportionately impact people in low- and middle-income countries (LMICs). While varied interventions have been shown to reduce alcohol use in high-income countries, their efficacy in LMICs has not been assessed. This systematic review describes current published literature on patient-level alcohol interventions in LMICs and specifically describes clinical trials evaluating interventions to reduce alcohol use in LMICs. METHODS AND FINDINGS: In accordance with PRISMA, we performed a systematic review using an electronic search strategy from January 1, 1995 to December 1, 2020. Title, abstract, as well as full-text screening and extraction were performed in duplicate. A meta-summary was performed on randomized controlled trials (RCTs) that evaluated alcohol-related outcomes. We searched the following electronic databases: PubMed, EMBASE, Scopus, Web of Science, Cochrane, WHO Global Health Library, and PsycINFO. Articles that evaluated patient-level interventions targeting alcohol use and alcohol-related harm in LMICs were eligible for inclusion. No studies were excluded based on language. After screening 5,036 articles, 117 articles fit our inclusion criteria, 75 of which were RCTs. Of these RCTs, 93% were performed in 13 middle-income countries, while 7% were from 2 low-income countries. These RCTs evaluated brief interventions (24, defined as any intervention ranging from advice to counseling, lasting less than 1 hour per session up to 4 sessions), psychotherapy or counseling (15, defined as an interaction with a counselor longer than a brief intervention or that included a psychotherapeutic component), health promotion and education (20, defined as an intervention encouraged individuals' agency of taking care of their health), or biologic treatments (19, defined as interventions where the biological function of alcohol use disorder (AUD) as the main nexus of intervention) with 3 mixing categories of intervention types. Due to high heterogeneity of intervention types, outcome measures, and follow-up times, we did not conduct meta-analysis to compare and contrast studies, but created a meta-summary of all 75 RCT studies. The most commonly evaluated intervention with the most consistent positive effect was a brief intervention; similarly, motivational interviewing (MI) techniques were most commonly utilized among the diverse array of interventions evaluated. CONCLUSIONS: Our review demonstrated numerous patient-level interventions that have the potential to be effective in LMICs, but further research to standardize interventions, populations, and outcome measures is necessary to accurately assess their effectiveness. Brief interventions and MI techniques were the most commonly evaluated and had the most consistent positive effect on alcohol-related outcomes. TRIAL REGISTRATION: Protocol Registry: PROSPERO CRD42017055549.

Antibiotic Prophylaxis for Megaprosthetic Reconstructions: Drug and Dosing May Matter More than Duration.

In orthopedic oncology, the implant of a megaprosthetic device is standard of care after large-scale tumor resection involving segmental removal of bone. Infection remains the leading cause of implant failure, often resulting in major morbidity. Perioperative antibiotic practices for megaprosthetic reconstructions are not standardized and are based on guidelines for conventional joint arthroplasties. This study aims to evaluate the efficacy of current prophylactic strategies for megaprosthetic reconstructions. We conducted a retrospective review of megaprosthetic reconstructions performed at Duke University from 2001 to 2021. Logistic regression with GEE was used to assess whether a prolonged course of postoperative antibiotics is associated with infection risk. We assessed the microbial profile and corresponding susceptibilities of megaprosthetic infections through record review. Additionally, we designed a pharmacokinetic subgroup analysis using liquid chromatography-tandem mass spectrometry to quantify antibiotic concentrations in surgical tissue. Wilcoxon rank-sum tests were used to correlate tissue concentrations with infection risk. Out of 184 cases, 23 (12.5%) developed infection within 1 year. Extended postoperative antibiotics were not significantly associated with infection risk (P = 0.23). Among 18 culture-positive cases, 4 (22.2%) were caused by cefazolin-susceptible organisms. Median bone and muscle concentrations of cefazolin among cases that developed postoperative infection (0.065 ng/mL and 0.2 ng/mL, respectively) were significantly lower than those of cases that did not (0.42 ng/mL and 1.95 ng/mL, P < 0.01 and P = 0.03). This study is the first to comprehensively assess aspects of perioperative prophylaxis for megaprosthetic reconstructions. Extending postoperative antibiotics did not reduce infection risk. We detected a high frequency of cefazolin nonsusceptible organisms among postoperative infections. Additionally, intraoperative antibiotic tissue concentrations may be predictive of later infection. Future studies ought to examine optimal drug choices and dosing strategies.

Sequencing Analysis at 8p23 Identifies Multiple Rare Variants in DLC1 Associated with Sleep-Related Oxyhemoglobin Saturation Level.

Average arterial oxyhemoglobin saturation during sleep (AvSpO2S) is a clinically relevant measure of physiological stress associated with sleep-disordered breathing, and this measure predicts incident cardiovascular disease and mortality. Using high-depth whole-genome sequencing data from the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) project and focusing on genes with linkage evidence on chromosome 8p23,1,2 we observed that six coding and 51 noncoding variants in a gene that encodes the GTPase-activating protein (DLC1) are significantly associated with AvSpO2S and replicated in independent subjects. The combined DLC1 association evidence of discovery and replication cohorts reaches genome-wide significance in European Americans (p = 7.9 × 10-7). A risk score for these variants, built on an independent dataset, explains 0.97% of the AvSpO2S variation and contributes to the linkage evidence. The 51 noncoding variants are enriched in regulatory features in a human lung fibroblast cell line and contribute to DLC1 expression variation. Mendelian randomization analysis using these variants indicates a significant causal effect of DLC1 expression in fibroblasts on AvSpO2S. Multiple sources of information, including genetic variants, gene expression, and methylation, consistently suggest that DLC1 is a gene associated with AvSpO2S.

Identifying Modifiable and Non-modifiable Risk Factors of Readmission and Short-Term Mortality in Chondrosarcoma: A National Cancer Database Study.

BACKGROUND: Limited data are available to inform the risk of readmission and short-term mortality in musculoskeletal oncology. The goal of this study was to identify factors independently associated with 30-day readmission and 90-day mortality following surgical resection of chondrosarcoma. METHODS: We retrospectively reviewed 6653 patients following surgical resection of primary chondrosarcoma in the National Cancer Database (2004-2017). Both demographic and clinicopathologic variables were assessed for correlation with readmission and short-term mortality utilizing univariate and multivariate logistic regression modeling. RESULTS: Of 220 readmissions (3.26%), risk factors independently associated with an increased risk of unplanned 30-day readmission included Charlson-Deyo Comorbidity Index (CDCC) (odds ratio [OR] 1.31; p = 0.027), increasing American Joint Committee on Cancer (AJCC) stage (OR 1.31; p = 0.004), undergoing major amputation (OR 2.38; p = 0.001), and axial skeletal location (OR 1.51; p = 0.028). A total of 137 patients died within 90 days of surgery (2.25%). Risk factors associated with increased mortality included the CDCC (OR 1.60; p = 0.001), increasing age (OR 1.06; p < 0.001), having Medicaid insurance status (OR 3.453; p = 0.005), living in a zip code with a higher educational attainment (OR 1.59; p = 0.003), increasing AJCC stage (OR 2.32; p < 0.001), longer postoperative length of stay (OR 1.015; p = 0.033), and positive surgical margins (OR 2.75; p = 0.001). Although a majority of the cohort did not receive radiation therapy (88.8%), receiving radiotherapy (OR 0.132; p = 0.010) was associated with a decreased risk of short-term mortality. CONCLUSIONS: Several tumor, treatment, and patient factors can help inform the risk of readmission and short-term mortality in patients with surgically treated chondrosarcoma.

From Passive Gatekeeper to Quarterback: Evolving Perceptions of Primary Care Among Medical Students in Longitudinal Outpatient Clerkships.

BACKGROUND: Longitudinal clerkships provide students with meaningful clinical care roles that promote learning and professional development. It remains unclear how longitudinal primary care clerkships inform students' perceptions of primary care. OBJECTIVE: To explore perceptions of primary care among medical students enrolled in longitudinal primary care clerkships. DESIGN: Qualitative, semi-structured interviews with medical students over 4 years. PARTICIPANTS: Thirty-eight medical students participated at baseline; 35 participated in a 2-year follow-up interview; 24 participated at 4 years. Each student was enrolled in one of two longitudinal primary care clerkships: a team-based Education-Centered Medical Home (ECMH) or a one-on-one individual preceptorship (IP). APPROACH: De-identified interview transcripts were analyzed using a process of open and axial coding, followed by elaborative coding for longitudinal analysis. Codes were compiled into a set of themes and compared across time periods and between clerkships. KEY RESULTS: Students reported that primary care serves as a first point of contact, emphasizing longitudinal care with a wide scope of practice and approaching patient care with a biopsychosocial perspective. Student perceptions of primary care greatly expanded over the course of 4 years: for instance, initial perceptions of primary care physicians evolved from "passive gatekeeper" to a more nuanced "quarterback." Students in ECMH, whose clerkship provided more opportunity for patient continuity, further reflected on the relationships they themselves developed with patients. CONCLUSIONS: Regardless of their eventual specialty choice, longitudinal experiences may aid all students in fostering a sense of the broad scope and importance of primary care. However, without numerous opportunities to witness continuity of care, students may perceive primary care as having limited scope and importance. Longitudinal clerkships, emphasizing continuity with patients and preceptors, may foster in students a broad and nuanced perspective of the scope of primary care as a field.

signatureSearch: environment for gene expression signature searching and functional interpretation.

signatureSearch is an R/Bioconductor package that integrates a suite of existing and novel algorithms into an analysis environment for gene expression signature (GES) searching combined with functional enrichment analysis (FEA) and visualization methods to facilitate the interpretation of the search results. In a typical GES search (GESS), a query GES is searched against a database of GESs obtained from large numbers of measurements, such as different genetic backgrounds, disease states and drug perturbations. Database matches sharing correlated signatures with the query indicate related cellular responses frequently governed by connected mechanisms, such as drugs mimicking the expression responses of a disease. To identify which processes are predominantly modulated in the GESS results, we developed specialized FEA methods combined with drug-target network visualization tools. The provided analysis tools are useful for studying the effects of genetic, chemical and environmental perturbations on biological systems, as well as searching single cell GES databases to identify novel network connections or cell types. The signatureSearch software is unique in that it provides access to an integrated environment for GESS/FEA routines that includes several novel search and enrichment methods, efficient data structures, and access to pre-built GES databases, and allowing users to work with custom databases.