Individuals with JAK1 variants are affected by syndromic features encompassing autoimmunity, atopy, colitis, and dermatitis.

Inborn errors of immunity lead to autoimmunity, inflammation, allergy, infection, and/or malignancy. Disease-causing JAK1 gain-of-function (GoF) mutations are considered exceedingly rare and have been identified in only four families. Here, we use forward and reverse genetics to identify 59 individuals harboring one of four heterozygous JAK1 variants. In vitro and ex vivo analysis of these variants revealed hyperactive baseline and cytokine-induced STAT phosphorylation and interferon-stimulated gene (ISG) levels compared with wild-type JAK1. A systematic review of electronic health records from the BioME Biobank revealed increased likelihood of clinical presentation with autoimmunity, atopy, colitis, and/or dermatitis in JAK1 variant-positive individuals. Finally, treatment of one affected patient with severe atopic dermatitis using the JAK1/JAK2-selective inhibitor, baricitinib, resulted in clinically significant improvement. These findings suggest that individually rare JAK1 GoF variants may underlie an emerging syndrome with more common presentations of autoimmune and inflammatory disease (JAACD syndrome). More broadly, individuals who present with such conditions may benefit from genetic testing for the presence of JAK1 GoF variants.

ACE2 acts as a novel regulator of TMPRSS2-catalyzed proteolytic activation of influenza A virus in airway cells.

The transmembrane serine protease 2 (TMPRSS2) activates the outer structural proteins of a number of respiratory viruses including influenza A virus (IAV), parainfluenza viruses, and various coronaviruses for membrane fusion. Previous studies showed that TMPRSS2 interacts with the carboxypeptidase angiotensin-converting enzyme 2 (ACE2), a cell surface protein that serves as an entry receptor for some coronaviruses. Here, by using protease activity assays, we determine that ACE2 increases the enzymatic activity of TMPRSS2 in a non-catalytic manner. Furthermore, we demonstrate that ACE2 knockdown inhibits TMPRSS2-mediated cleavage of IAV hemagglutinin (HA) in Calu-3 human airway cells and suppresses virus titers 100- to 1.000-fold. Transient expression of ACE2 in ACE2-deficient cells increased TMPRSS2-mediated HA cleavage and IAV replication. ACE2 knockdown also reduced titers of MERS-CoV and prevented S cleavage by TMPRSS2 in Calu-3 cells. By contrast, proteolytic activation and multicycle replication of IAV with multibasic HA cleavage site typically cleaved by furin were not affected by ACE2 knockdown. Co-immunoprecipitation analysis revealed that ACE2-TMPRSS2 interaction requires the enzymatic activity of TMPRSS2 and the carboxypeptidase domain of ACE2. Together, our data identify ACE2 as a new co-factor or stabilizer of TMPRSS2 activity and as a novel host cell factor involved in proteolytic activation and spread of IAV in human airway cells. Furthermore, our data indicate that ACE2 is involved in the TMPRSS2-catalyzed activation of additional respiratory viruses including MERS-CoV.IMPORTANCEProteolytic cleavage of viral envelope proteins by host cell proteases is essential for the infectivity of many viruses and relevant proteases provide promising drug targets. The transmembrane serine protease 2 (TMPRSS2) has been identified as a major activating protease of several respiratory viruses, including influenza A virus. TMPRSS2 was previously shown to interact with angiotensin-converting enzyme 2 (ACE2). Here, we report the mechanistic details of this interaction. We demonstrate that ACE2 increases or stabilizes the enzymatic activity of TMPRSS2. Furthermore, we describe ACE2 involvement in TMPRSS2-catalyzed cleavage of the influenza A virus hemagglutinin and MERS-CoV spike protein in human airway cells. These findings expand our knowledge of the activation of respiratory viruses by TMPRSS2 and the host cell factors involved. In addition, our results could help to elucidate a physiological role for TMPRSS2.

Association of hepatokines with markers of endothelial dysfunction and vascular reactivity in obese adolescents.

OBJECTIVES: Obesity-induced insulin resistance (IR) is known to influence hepatic cytokines (hepatokines), including fibroblast growth factor (FGF-21), fetuin-A, and chemerin. This study aimed to investigate the association between hepatokines and markers of endothelial dysfunction and vascular reactivity in obese adolescents. METHODS: A total of 45 obese adolescents were categorized into three groups based on glucose tolerance: normal glucose tolerance (NGT), prediabetes (PD), and type 2 diabetes (T2D). We examined the relationships between FGF-21, fetuin-A, and chemerin with endothelial markers (plasminogen activator inhibitor-1 [PAI-1], intercellular adhesion molecule-1 [ICAM-1], and vascular cell adhesion marker-1 [VCAM-1]) and vascular surrogates (brachial artery reactivity testing [BART] and peak reactive hyperemia [PRH]). RESULTS: Obese adolescents (age 16.2±1.2 years; 62 % female, 65 % Hispanic) with NGT (n=20), PD (n=14), and T2D (n=11) had significant differences between groups in BMI; waist-hip ratio (p=0.05), systolic BP (p=0.008), LDL-C (p=0.02), PAI-1 (p<0.001). FGF-21 pg/mL (mean±SD: NGT vs. PD vs. T2D 54±42; 266±286; 160±126 p=0.006) and fetuin-A ng/mL (266±80; 253±66; 313±50 p=0.018), were significantly different while chemerin ng/mL (26±5; 31±10; 28±2) did not significantly differ between the groups. Positive correlations were found between chemerin and both PAI-1 (r=0.6; p=0.05) and ICAM-1 (r=0.6; p=0.05), FGF-21 and PAI-1 (r=0.6; p<0.001), and fetuin-A with TNFα (r=-0.4; p=0.05). Negative correlations were found between chemerin and PRH (r= -0.5; p=0.017) and fetuin-A and PRH (r=-0.4; p=0.05). CONCLUSIONS: In our cohort, IR predicted higher FGF-21 levels suggesting a linear relationship may exist between the two parameters. Hepatokines can augment alterations in the microvascular milieu in obese adolescents as demonstrated by their associations with the markers PAI-1, ICAM-1, and PRH.

Development of a human genetics-guided priority score for 19,365 genes and 399 drug indications.

Studies have shown that drug targets with human genetic support are more likely to succeed in clinical trials. Hence, a tool integrating genetic evidence to prioritize drug target genes is beneficial for drug discovery. We built a genetic priority score (GPS) by integrating eight genetic features with drug indications from the Open Targets and SIDER databases. The top 0.83%, 0.28% and 0.19% of the GPS conferred a 5.3-, 9.9- and 11.0-fold increased effect of having an indication, respectively. In addition, we observed that targets in the top 0.28% of the score were 1.7-, 3.7- and 8.8-fold more likely to advance from phase I to phases II, III and IV, respectively. Complementary to the GPS, we incorporated the direction of genetic effect and drug mechanism into a directional version of the score called the GPS with direction of effect. We applied our method to 19,365 protein-coding genes and 399 drug indications and made all results available through a web portal.

Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set.

Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. Experimental approaches for identifying GOF and LOF are generally slow and costly, whilst available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, a machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants, trained on a broad range of gene-, protein-, and variant-level features describing diverse biological characteristics. LoGoFunc outperforms other tools trained solely to predict pathogenicity for identifying pathogenic GOF and LOF variants and is available at https://itanlab.shinyapps.io/goflof/ .

The Influence of Social Determinants on Receiving Outpatient Treatment with Monoclonal Antibodies, Disease Risk, and Effectiveness for COVID-19.

BACKGROUND: Limited research has studied the influence of social determinants of health (SDoH) on the receipt, disease risk, and subsequent effectiveness of neutralizing monoclonal antibodies (nMAbs) for outpatient treatment of COVID-19. OBJECTIVE: To examine the influence of SDoH variables on receiving nMAb treatments and the risk of a poor COVID-19 outcome, as well as nMAb treatment effectiveness across SDoH subgroups. DESIGN: Retrospective observational study utilizing electronic health record data from four health systems. SDoH variables analyzed included race, ethnicity, insurance, marital status, Area Deprivation Index, and population density. PARTICIPANTS: COVID-19 patients who met at least one emergency use authorization criterion for nMAb treatment. MAIN MEASURE: We used binary logistic regression to examine the influence of SDoH variables on receiving nMAb treatments and risk of a poor outcome from COVID-19 and marginal structural models to study treatment effectiveness. RESULTS: The study population included 25,241 (15.1%) nMAb-treated and 141,942 (84.9%) non-treated patients. Black or African American patients were less likely to receive treatment than white non-Hispanic patients (adjusted odds ratio (OR) = 0.86; 95% CI = 0.82-0.91). Patients who were on Medicaid, divorced or widowed, living in rural areas, or living in areas with the highest Area Deprivation Index (most vulnerable) had lower odds of receiving nMAb treatment, but a higher risk of a poor outcome. For example, compared to patients on private insurance, Medicaid patients had 0.89 (95% CI = 0.84-0.93) times the odds of receiving nMAb treatment, but 1.18 (95% CI = 1.13-1.24) times the odds of a poor COVID-19 outcome. Age, comorbidities, and COVID-19 vaccination status had a stronger influence on risk of a poor outcome than SDoH variables. nMAb treatment benefited all SDoH subgroups with lower rates of 14-day hospitalization and 30-day mortality. CONCLUSION: Disparities existed in receiving nMAbs within SDoH subgroups despite the benefit of treatment across subgroups.

Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures.

Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs, which enable kinases to adopt various conformational states. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the kinase conformation(s) they bind. However, the limited availability of experimentally determined structural data for kinases in inactive states restricts drug discovery efforts for this major protein family. Modern AI-based structural modeling methods hold potential for exploring the previously experimentally uncharted druggable conformational space for kinases. Here, we first evaluated the currently explored conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) (1) and ESMFold (2), two prominent AI-based structure prediction methods. We then investigated AF2's ability to predict kinase structures in different conformations at various multiple sequence alignment (MSA) depths, based on this parameter's ability to explore conformational diversity. Our results showed a bias within the PDB and predicted structural models generated by AF2 and ESMFold toward structures of kinases in the active state over alternative conformations, particularly those conformations controlled by the DFG motif. Finally, we demonstrate that predicting kinase structures using AF2 at lower MSA depths allows the exploration of the space of these alternative conformations, including identifying previously unobserved conformations for 398 kinases. The results of our analysis of structural modeling by AF2 create a new avenue for the pursuit of new therapeutic agents against a notoriously difficult-to-target family of proteins. Significance Statement: Greater abundance of kinase structural data in inactive conformations, currently lacking in structural databases, would improve our understanding of how protein kinases function and expand drug discovery and development for this family of therapeutic targets. Modern approaches utilizing artificial intelligence and machine learning have potential for efficiently capturing novel protein conformations. We provide evidence for a bias within AlphaFold2 and ESMFold to predict structures of kinases in their active states, similar to their overrepresentation in the PDB. We show that lowering the AlphaFold2 algorithm's multiple sequence alignment depth can help explore kinase conformational space more broadly. It can also enable the prediction of hundreds of kinase structures in novel conformations, many of whose models are likely viable for drug discovery.

Location Factors Impact the Career Choice of German Dental Practitioners - An Empirical Analytical Approach to Multi-Criteria Decision-Making.

Objectives: In light of the increasing number of employed dentists and the decreasing rate of self-employed dentists, the factors that impact the decision to set up a dental office in Germany were investigated. Central to this approach is the provision of comprehensive dental care. Methods: Using a pairwise comparison technique, the analytic hierarchy process (AHP), location factors identified as relevant in a systematic literature review and then prioritized by the professionals were weighted and ranked. Results: According to this, five factors generally dominate the decision to open a dental office. These are, in descending order: environment for the family, quality of life in the private environment, real income, perception of location, and good infrastructure. The strongest impact on the rank order of the influencing factors is the socio-demographic characteristic of gender. For female dentists, the family environment is in the first place (p = .3196/C.R. = 0.1502). For male colleagues, this influence ranks third (p = .1550/C.R. = 0.1468) and real income receives the first place (p = .244/C.R. = 0.1468). For female dentists, the influence of income ranks fifth (p = .076/C.R. = 0.1502). Female and male dentists who grew up in rural areas were less likely to prefer employment (13.6%) than subjects of urban origin (40.2%). Conclusion: The method of AHP is a way to map a priority list of all relevant factors. It can successfully show variations related to specific personal attributes. Obviously, there are factors that are of greater importance for the decision-making process to set up a dental office.

Barriers and Facilitators to Pediatric Resident Education in the Emergency Department: A Qualitative Study.

Objective Local resident evaluations of the pediatric emergency department (ED) declined over the last five years. Sparse literature exists on resident perspectives of educational experiences. This study explored the barriers and facilitators to resident education in the Pediatric ED. Methods This qualitative study utilized focus groups at a large pediatric training hospital. Trained facilitators performed semi-structured interviews prompting discussion of resident experiences in the pediatric ED. One pilot and six focus groups (38 pediatric residents) achieved data saturation. Sessions were audio recorded, de-identified and transcribed by a professional service. Three authors (CJ, JM, SS) analyzed the transcripts independently using line-by-line coding. Following code agreement, authors identified central themes drawing on grounded theory. Results Six categories emerged: (1) ED environment, (2) consistent goals, expectations, and resources, (3) ED workflow, (4) preceptor accessibility, (5) resident growth and development, (6) ED preconceived notions. Residents value a respectful work environment despite the chaotic nature of the ED. They need clear goals and expectations with a strong orientation. Autonomy, open communication and shared decision-making allow residents to feel like team members. Residents gravitate toward welcoming, available preceptors that enthusiastically teach. More ED environment exposure increases comfort and efficiency and helps develop medical decision-making skills. Residents admit ED preconceptions and personality traits affect performance. Conclusion Residents self-identified barriers and facilitators to ED education. Educators must provide a safe and open learning environment, clear rotation expectations and goals, consistent positivity supporting shared decision making, and allow residents autonomy to build their practice styles.

Neutralizing Monoclonal Antibody Use and COVID-19 Infection Outcomes.

Importance: Evidence on the effectiveness and safety of COVID-19 therapies across a diverse population with varied risk factors is needed to inform clinical practice. Objective: To assess the safety of neutralizing monoclonal antibodies (nMAbs) for the treatment of COVID-19 and their association with adverse outcomes. Design, Setting, and Participants: This retrospective cohort study included 167 183 patients from a consortium of 4 health care systems based in California, Minnesota, Texas, and Utah. The study included nonhospitalized patients 12 years and older with a positive COVID-19 laboratory test collected between November 9, 2020, and January 31, 2022, who met at least 1 emergency use authorization criterion for risk of a poor outcome. Exposure: Four nMAb products (bamlanivimab, bamlanivimab-etesevimab, casirivimab-imdevimab, and sotrovimab) administered in the outpatient setting. Main Outcomes and Measures: Clinical and SARS-CoV-2 genomic sequence data and propensity-adjusted marginal structural models were used to assess the association between treatment with nMAbs and 4 outcomes: all-cause emergency department (ED) visits, hospitalization, death, and a composite of hospitalization or death within 14 days and 30 days of the index date (defined as the date of the first positive COVID-19 test or the date of referral). Patient index dates were categorized into 4 variant epochs: pre-Delta (November 9, 2020, to June 30, 2021), Delta (July 1 to November 30, 2021), Delta and Omicron BA.1 (December 1 to 31, 2021), and Omicron BA.1 (January 1 to 31, 2022). Results: Among 167 183 patients, the mean (SD) age was 47.0 (18.5) years; 95 669 patients (57.2%) were female at birth, 139 379 (83.4%) were White, and 138 900 (83.1%) were non-Hispanic. A total of 25 241 patients received treatment with nMAbs. Treatment with nMAbs was associated with lower odds of ED visits within 14 days (odds ratio [OR], 0.76; 95% CI, 0.68-0.85), hospitalization within 14 days (OR, 0.52; 95% CI, 0.45-0.59), and death within 30 days (OR, 0.14; 95% CI, 0.10-0.20). The association between nMAbs and reduced risk of hospitalization was stronger in unvaccinated patients (14-day hospitalization: OR, 0.51; 95% CI, 0.44-0.59), and the associations with hospitalization and death were stronger in immunocompromised patients (hospitalization within 14 days: OR, 0.31 [95% CI, 0.24-0.41]; death within 30 days: OR, 0.13 [95% CI, 0.06-0.27]). The strength of associations of nMAbs increased incrementally among patients with a greater probability of poor outcomes; for example, the ORs for hospitalization within 14 days were 0.58 (95% CI, 0.48-0.72) among those in the third (moderate) risk stratum and 0.41 (95% CI, 0.32-0.53) among those in the fifth (highest) risk stratum. The association of nMAb treatment with reduced risk of hospitalizations within 14 days was strongest during the Delta variant epoch (OR, 0.37; 95% CI, 0.31-0.43) but not during the Omicron BA.1 epoch (OR, 1.29; 95% CI, 0.68-2.47). These findings were corroborated in the subset of patients with viral genomic data. Treatment with nMAbs was associated with a significant mortality benefit in all variant epochs (pre-Delta: OR, 0.16 [95% CI, 0.08-0.33]; Delta: OR, 0.14 [95% CI, 0.09-0.22]; Delta and Omicron BA.1: OR, 0.10 [95% CI, 0.03-0.35]; and Omicron BA.1: OR, 0.13 [95% CI, 0.02-0.93]). Potential adverse drug events were identified in 38 treated patients (0.2%). Conclusions and Relevance: In this study, nMAb treatment for COVID-19 was safe and associated with reductions in ED visits, hospitalization, and death, although it was not associated with reduced risk of hospitalization during the Omicron BA.1 epoch. These findings suggest that targeted risk stratification strategies may help optimize future nMAb treatment decisions.

Self-organized intracellular twisters.

Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy, and information flows is disrupted. Global coordination is no less important in single cells, especially in large oocytes and newly formed embryos, which commonly use fast fluid flows for dynamic reorganization of their cytoplasm. Here, we combine theory, computing, and imaging to investigate such flows in the Drosophila oocyte, where streaming has been proposed to spontaneously arise from hydrodynamic interactions among cortically anchored microtubules loaded with cargo-carrying molecular motors. We use a fast, accurate, and scalable numerical approach to investigate fluid-structure interactions of 1000s of flexible fibers and demonstrate the robust emergence and evolution of cell-spanning vortices, or twisters. Dominated by a rigid body rotation and secondary toroidal components, these flows are likely involved in rapid mixing and transport of ooplasmic components.

Self-organized intracellular twisters.

Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy, and information flows is disrupted. Global coordination is no less important in single cells, especially in large oocytes and newly formed embryos, which commonly use fast fluid flows for dynamic reorganization of their cytoplasm. Here, we combine theory, computing, and imaging to investigate such flows in the Drosophila oocyte, where streaming has been proposed to spontaneously arise from hydrodynamic interactions among cortically anchored microtubules loaded with cargo-carrying molecular motors. We use a fast, accurate, and scalable numerical approach to investigate fluid-structure interactions of 1000s of flexible fibers and demonstrate the robust emergence and evolution of cell-spanning vortices, or twisters. Dominated by a rigid body rotation and secondary toroidal components, these flows are likely involved in rapid mixing and transport of ooplasmic components.

Structural Analysis of Genomic and Proteomic Signatures Reveal Dynamic Expression of Intrinsically Disordered Regions in Breast Cancer and Tissue.

Structural features of proteins capture underlying information about protein evolution and function, which enhances the analysis of proteomic and transcriptomic data. Here we develop Structural Analysis of Gene and protein Expression Signatures (SAGES), a method that describes expression data using features calculated from sequence-based prediction methods and 3D structural models. We used SAGES, along with machine learning, to characterize tissues from healthy individuals and those with breast cancer. We analyzed gene expression data from 23 breast cancer patients and genetic mutation data from the COSMIC database as well as 17 breast tumor protein expression profiles. We identified prominent expression of intrinsically disordered regions in breast cancer proteins as well as relationships between drug perturbation signatures and breast cancer disease signatures. Our results suggest that SAGES is generally applicable to describe diverse biological phenomena including disease states and drug effects.

Influence of Selected Environmental Factors on the Business Type of Dentist's Practice in Germany: A Multi-Criteria Decision-Making Process With an Analytical Hierarchy Process.

In the interests of satisfying the dental services demands of German citizens area-wide, constant, and thoughtful planning of supply and demand is essential. With an anonymous online survey of 375 dentists a pairwise comparison of 9 factors extracted as relevant from the existing scientific literature were analyzed with an analytic hierarchy process (AHP) and ranked considering the various business types. In general, 5 local environmental factors have a dominant impact on founders' decision in German dentistry. In order: environment for the family, quality of life in private environment, real income, location of the practice, infrastructure. Real income is in first place (p = 0.287) for dentists who want to start a new single practice. For preferring a new community practice, it is on third place (p = 0.177) and for dentists who favor a takeover a single practice (p = 0.130) or joining a community practice (p = 0.096) or employment (p = 0.111) it is fourth place. For this purpose, the location of the practice is of greater priority than the real income for dentists who prefer not to start a new practice. The AHP method is a way to picture a priority list out of all relevant factors for setting up of a dental practice.

Hybridization Chain Reaction Fluorescence In Situ Hybridization (HCR-FISH) in Ambystoma mexicanum Tissue.

In situ hybridization is a standard procedure for visualizing mRNA transcripts in tissues. The recent adoption of fluorescent probes and new signal amplification methods have facilitated multiplexed RNA imaging in tissue sections and whole tissues. Here we present protocols for multiplexed hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) staining, imaging, cell segmentation, and mRNA quantification in regenerating axolotl tissue sections. We also present a protocol for whole-mount staining and imaging of developing axolotl limbs.

Common and species-specific molecular signatures, networks, and regulators of influenza virus infection in mice, ferrets, and humans.

Molecular responses to influenza A virus (IAV) infections vary between mammalian species. To identify conserved and species-specific molecular responses, we perform a comparative study of transcriptomic data derived from blood cells, primary epithelial cells, and lung tissues collected from IAV-infected humans, ferrets, and mice. The molecular responses in the human host have unique functions such as antigen processing that are not observed in mice or ferrets. Highly conserved gene coexpression modules across the three species are enriched for IAV infection-induced pathways including cell cycle and interferon (IFN) signaling. TDRD7 is predicted as an IFN-inducible host factor that is up-regulated upon IAV infection in the three species. TDRD7 is required for antiviral IFN response, potentially modulating IFN signaling via the JAK/STAT/IRF9 pathway. Identification of the common and species-specific molecular signatures, networks, and regulators of IAV infection provides insights into host-defense mechanisms and will facilitate the development of novel therapeutic interventions against IAV infection.

Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues.

Structural features of proteins provide powerful insights into biological function and similarity. Specifically, previous work has demonstrated that structural features of tissue and drug-treated cell line samples can be used to predict tissue type and characterize drug relationships, respectively. We have developed structural signatures, a web server for annotating and analyzing protein features from gene sets that are often found in transcriptomic and proteomic data. This platform provides access to a structural feature database derived from normal and disease human tissue samples. We show how analysis using this database can shed light on the relationship between states of single-cell RNA-sequencing lung cancer samples. These various structural feature signatures can be visualized on the server itself or downloaded for additional analysis. The structural signatures server tool is freely available at https://structural-server.kinametrix.com/.

Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline.

The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age correction representing ~ 2% annual decline is often applied to account for this change in mutation level. Here we report that recent data indicate that the dynamics of m.3243A > G are more complex and depend on the mutation level in blood in a bi-phasic way. Consequently, the traditional 2% correction, which is adequate 'on average', creates opposite predictive biases at high and low mutation levels. Unbiased age correction is needed to circumvent these drawbacks of the standard model. We propose to eliminate both biases by using an approach where age correction depends on mutation level in a biphasic way to account for the dynamics of m.3243A > G in blood. The utility of this approach was further tested in estimating germline selection of m.3243A > G. The biphasic approach permitted us to uncover patterns consistent with the possibility of positive selection for m.3243A > G. Germline selection of m.3243A > G shows an 'arching' profile by which selection is positive at intermediate mutant fractions and declines at high and low mutant fractions. We conclude that use of this biphasic approach will greatly improve the accuracy of modelling changes in mtDNA mutation frequencies in the germline and in somatic cells during aging.

Impact of Clinician Linkage on Unequal Access to High-Volume Hospitals for Colorectal Cancer Surgery.

BACKGROUND: Understanding drivers of persistent surgical disparities remains an important area of cancer care delivery and policy. The degree to which clinician linkages contribute to disparities in access to quality colorectal cancer surgery is unknown. Using hospital surgical volume as a proxy for quality, the study team evaluated how clinician linkages impact access to colorectal cancer surgery at high-volume hospitals (HVHs). STUDY DESIGN: Maryland's Health Services Cost Review Commission was used to evaluate 6,909 patients who underwent colon or rectal cancer operations from 2013 to 2018. Two linkages based on patient sharing were examined separately for colon and rectal cancer surgery: (1) from primary care clinicians to specialists (gastroenterologist or medical oncologist) and (2) from specialists to surgeons (general or colorectal). A referral link was defined as 9 or more shared patients between 2 clinicians. Adjusted regression models examined associations between referral links and odds of receiving colon or rectal cancer operations at HVHs. RESULTS: The cohort included 5,645 colon and 1,264 rectal cancer patients across 52 hospitals. Every additional referral link between a primary care clinician and a specialist connected to a HVH was associated with a 12% and 14% increased likelihood of receiving colon (odds ratio [OR] 1.12, CI 1.07 to 1.17) and rectal (OR 1.14, CI 1.08 to 1.20]) cancer operations at a HVH, respectively. Every additional referral link between a specialist and a surgeon at a HVH was associated with at least a 25% increased likelihood of receiving colon (OR 1.28, CI 1.20 to 1.36) and rectal (OR 1.25, CI 1.15 to 1.36) cancer operation at a HVH. CONCLUSIONS: Patients of clinicians with linkages to HVHs are more likely to have their colorectal cancer operations at these hospitals. These findings suggest that policy interventions targeting clinician relationships are an important step in providing equitable surgical care.

Prognosis of Chronically Ventilated Patients in a Long-Term Ventilation Facility: Association with Age, Consciousness and Cognitive State.

Background: The number of adults requiring prolonged mechanical ventilation (PMV) including those with cognitive impairment or disorders of consciousness is escalating. We aimed to compare in a long-term acute care hospital (LTACH) mortality and length of stay (LOS) among three age groups (40-59y, 60-79y, ≥80y) of hospitalized PMV patients, and according to consciousness and cognitive state at admission. Methods: We obtained data from the health records of 308 adults aged ≥40 years requiring PMV hospitalized at a Chronic Ventilator Dependent Unit in a LTACH between 01/01/2015 to 06/30/2019 and followed-up until discharge or death or until 12/31/2019. Results: At admission to LTACH, 42.2% of PMV patients were in a vegetative state/ minimally conscious state (VS/MCS); 32.5% were severely cognitively impaired, 11.0% were mildly to moderately cognitively impaired, 12.3% had no cognitive impairment, and 1.9% had intellectual disability/psychiatric disorder. In-LTACH LOS (months) decreased from 34.6 ± 42.6 at age 40-59y, 19.1 ± 22.3 at 60-79y to 14.4 ± 19.3 at age ≥80y (p = .006). In-LTACH mortality was 30.6% for 40-59y, 41.1% for 60-79y and 54.8% for age ≥80y. In-LTACH LOS (months) was 23.8 ± 30.7 for VS/MCS, 15.1 ± 19.5 for the severely cognitively impaired, 10.0 ± 12.8 for mild to moderate cognitive impairment and 18.9 ± 21.9 for those without cognitive impairment (p = .02). In-LTACH mortality was 50.8% for VS/MCS, 58.0% for the severely cognitively impaired, 26.5% for mild to moderate cognitive impairment and 13.2% for those without cognitive impairment (p < .001). Conclusion: In this population requiring PMV, mortality and in-LTACH LOS worsened with age. In-LTACH LOS was longest for VS/MCS patients, who had a mean survival of about two years, followed by those without cognitive impairment and then those with severe cognitive impairment. Mortality was associated with worse consciousness and cognitive state. These findings highlight the importance of discussing end-of-life decisions with patients and family members regarding resuscitation/intubation and the long-term management of these patients.