Automated Family Histories Significantly Improve Risk Prediction in an EHR.

We recently demonstrated that electronically constructed family pedigrees (e-pedigrees) have great value in epidemiologic research using electronic health record (EHR) data. Prior to this work, it has been well accepted that family health history is a major predictor for a wide spectrum of diseases, reflecting shared effects of genetics, environment, and lifestyle. With the widespread digitalization of patient data via EHRs, there is an unprecedented opportunity to use machine learning algorithms to better predict disease risk. Although predictive models have previously been constructed for a few important diseases, we currently know very little about how accurately the risk for most diseases can be predicted. It is further unknown if the incorporation of e-pedigrees in machine learning can improve the value of these models. In this study, we devised a family pedigree-driven high-throughput machine learning pipeline to simultaneously predict risks for thousands of diagnosis codes using thousands of input features. Models were built to predict future disease risk for three time windows using both Logistic Regression and XGBoost. For example, we achieved average areas under the receiver operating characteristic curves (AUCs) of 0.82, 0.77 and 0.71 for 1, 6, and 24 months, respectively using XGBoost and without e-pedigrees. When adding e-pedigree features to the XGBoost pipeline, AUCs increased to 0.83, 0.79 and 0.74 for the same three time periods, respectively. E-pedigrees similarly improved the predictions when using Logistic Regression. These results emphasize the potential value of incorporating family health history via e-pedigrees into machine learning with no further human time.

Achieving Equity in EMS Care and Patient Outcomes Through Quality Management Systems: A Position Statement.

Improving health and safety in our communities requires deliberate focus and commitment to equity. Inequities are differences in access, treatment, and outcomes between individuals and across populations that are systemic, avoidable, and unjust. Within health care in general, and Emergency Medical Services (EMS) in particular, there are demonstrated inequities in the quality of care provided to patients based on a number of characteristics linked to discrimination, exclusion, or bias. Given the critical role that EMS plays within the health care system, it is imperative that EMS systems reduce inequities by delivering evidence-based, high-quality care for the communities and patients we serve. To achieve equity in EMS care delivery and patient outcomes, the National Association of EMS Physicians recommends that EMS systems and agencies: make health equity a strategic priority and commit to improving equity at all levels.assess and monitor clinical and safety quality measures through the lens of inequities as an integrated part of the quality management process.ensure that data elements are structured to enable equity analysis at every level and routinely evaluate data for limitations hindering equity analysis and improvement.involve patients and community stakeholders in determining data ownership and stewardship to ensure its ongoing evolution and fitness for use for measuring care inequities.address biases as they translate into the quality of care and standards of respect for patients.pursue equity through a framework rooted in the principles of improvement science.

Closing the Water Balance with a Precision Small-Scale Field Lysimeter.

We developed a set of two precision, small-scale, water balance lysimeters to provide accurate measurements of bare soil evaporation. Each lysimeter comprises a soil tank, a balance assembly with load cell, a wicking drainage system, and a stilling well to measure drained water. Fiberglass wicks installed at the bottom of the soil tanks provide -60 cm of tension to the base of the soil column, and soil water drainage is quantified to close the water balance within the lysimeter. The calibrated lysimeters return mass changes with uncertainties ranging from 3 to 8 g, corresponding to uncertainties of 0.02-0.05 mm of water. Installed at a semi-arid site in northern Nevada, the two lysimeters are filled with uniform construction sand and silt loam. Over a six-month pilot observation period, bare soil evaporation rates of 0.19 and 0.40 mm/day were measured for the construction sand and silt loam, respectively, which is consistent with meteorological data and models of potential evapotranspiration at the site. The design of the lysimeter can be adapted to specific research goals or site restrictions, and these instruments can contribute significantly to our ability to close the soil water balance.

Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types.

Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi ("inactive" X) and Y chromosomes broadly modulate autosomal and Xa ("active" X) gene expression in two cell types. We tested these findings in vivo in two additional cell types. Using linear modeling in CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes, we identified 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo . Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro across all four cell types examined. In contrast, autosomal responses to Xi and/or Y dosage were largely cell-type-specific, with up to 2.6-fold more variation than sex-chromosomal responses. Targets of the X- and Y-encoded transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro . We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable across the four cell types examined, yet they modulate autosomal and Xa genes - and cell function - in a cell-type-specific fashion. These emerging principles offer a foundation for exploring the wide-ranging regulatory roles of the sex chromosomes across the human body.

Test-retest reliability of a mobile application of the patient reported outcomes burdens and experiences (PROBE) study.

INTRODUCTION: The Patient Reported Outcomes, Burdens, and Experiences (PROBE) questionnaire is a patient-reported outcome tool that assesses quality of life and disease burden in people with haemophilia (PWH). AIM: To assesses the test-retest reliability of PROBE when completed using the mobile phone application. METHODS: We recruited PWH, including carriers, and individuals with no bleeding disorders who attended haemophilia-related workshops or via social media. Participants completed PROBE three times (twice on the app: T1 and T2, and once on the web, T3). Test-retest reliability was analysed for T1 versus T2 (app to app, time period one) and T2 versus T3 (app to web, time period two). RESULTS: We enrolled 48 participants (median age = 56 [range 27-78] years). Eighteen participants (37.5%) were PWH and seven (14.6%) were carriers. On general health domain questions, we found almost perfect agreement, except for a question on the frequency of use of pain medication in the last 12 months [Kappa coefficient (κ) .72 and .37 for time period one and two, respectively] and any use of pain medications (κ .75) for time period two. For haemophilia-related questions, we found substantial to perfect agreement, except for the questions on the number of joint bleeds in the previous 6 months for time period one (κ .49) and the number of bleeds in the previous two weeks for time period two (κ .34). CONCLUSIONS: The results demonstrate the reliability of the PROBE app. The app can be used interchangeably with the paper and web platforms for PROBE administration.

Preoperative immune checkpoint inhibition and cryoablation in early-stage breast cancer.

Local cryoablation can engender systemic immune activation/anticancer responses in tumors otherwise resistant to immune checkpoint blockade (ICB). We evaluated the safety/tolerability of preoperative cryoablation plus ipilimumab and nivolumab in 5 early-stage/resectable breast cancers. The primary endpoint was met when all 5 patients underwent standard-of-care primary breast surgery undelayedly. Three patients developed transient hyperthyroidism; one developed grade 4 liver toxicity (resolved with supportive management). We compared this strategy with cryoablation and/or ipilimumab. Dual ICB plus cryoablation induced higher expression of T cell activation markers and serum Th1 cytokines and reduced immunosuppressive serum CD4+PD-1hi T cells, improving effector-to-suppressor T cell ratio. After dual ICB and before cryoablation, T cell receptor sequencing of 4 patients showed increased T cell clonality. In this small subset of patients, we provide preliminary evidence that preoperative cryoablation plus ipilimumab and nivolumab is feasible, inducing systemic adaptive immune activation potentially more robust than cryoablation with/without ipilimumab.

David C. Page.

We talk to David C. Page, corresponding author of "The human Y and inactive X chromosomes similarly modulate autosomal gene expression" in this issue of Cell Genomics, about his paper, the most exciting findings in the paper, and his advice for other scientists.

*SMARTSIM* A multicenter prospective randomized trial of 3D virtual reality versus traditional patient simulation.

Objective: Simulations are an integral part of paramedic education. Technological advancements have introduced three-dimensional virtual reality patient simulations (3DVRS), offering a low-cost, accessible alternative. This study compares the impact of 3DVRS and traditional simulation on paramedic students. Methods: Students selected from a convenience sample of 11 cohorts in 10 accredited programs distributed across the United States were allocated to 2 groups using a stratified random sampling. One group received simulations via 3DVRS, the second used traditional in-person simulation. Students were exposed to 6 scenarios over 2 h from the National Association of Emergency Medical Technicians (NAEMT) Advanced Medical Life Support (AMLS) program. Altered mental status scenarios were selected a priori by the research team containing approximately 30 potential differential diagnoses. A 50-item posttest was administered using validated cognitive items provided by Fisdap. Results: A multicenter prospective randomized trial of 174 paramedic students was undertaken from April until August of 2022. The traditional simulation group was comprised of 88 students and the 3DVRS group had 86 students. A Mann-Whitney U test (U = 4064.5, n 1 = 88, n 2 = 86, p = 0.396) detected no statistical difference between two distributions or median exam score (70%), the range of values and interquartile range (IQR) for both groups: TS IQR = 64-75 (range, 32-82); 3DVRS IQR = 64-76 (range, 34-86). Conclusion: No difference in exam scores using 3DVRS versus traditional simulation was detected. Paramedic programs may have an effective new option when incorporating simulation with 3DVRS, potentially reducing financial and real-estate resources required with in-person simulations. Larger studies are needed to truly evaluate the impact and usability of virtual reality on paramedic education.

Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer.

Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

The human Y and inactive X chromosomes similarly modulate autosomal gene expression.

Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.

Thrombin generation, bleeding and hemostasis in humans: Protocol for a scoping review of the literature.

INTRODUCTION: Hemostasis and bleeding are difficult to measure. Thrombin generation assays (TGAs) can measure both procoagulant and anticoagulant contributions to coagulation. TGAs might prove useful for the study of bleeding disorders. There has been much progress in TGA methodology over the past two decades, but its clinical significance is uncertain. We will undertake a scoping review of the literature to synthesize available information on the application of TGAs towards the study of bleeding and hemostasis, TGA methodologies being used and to summarize available literature on associations between TGA parameters, bleeding and hemostatic outcomes. METHODS AND ANALYSIS: MEDLINE, EMBASE and the Cochrane Central Register of Controlled Trials (CENTRAL) will be searched in collaboration with an information specialist. Title/abstract and full-text screening will be carried out independently and in duplicate; eligible study types will include randomized controlled trials, non-randomized studies, systematic reviews, and case series reporting TGA results and bleeding/hemostatic outcomes among humans. Mapping the information identified will be carried out with results presented using qualitative data analytical techniques. ETHICS AND DISSEMINATION: This scoping review will use published, publicly available information. Research ethics approval will not be required. We will disseminate our findings using conference presentations, peer-reviewed publications, social media, and engagement with knowledge users. This review will outline knowledge gaps concerning TGAs, better delineate its applicability as a clinically relevant assay for bleeding. and seek to identify ongoing barriers to its widespread adoption in clinical research, and eventually, in the clinical setting. TRAIL REGULATIONS: Registration ID with Open Science Framework: osf.io/zp4ge.

Post-transcriptional repression of mRNA enhances competence to transit from mitosis to meiosis in mouse spermatogenic cells.

The special cell cycle known as meiosis transforms diploid germ cells into haploid gametes. In mammalian testes, diploid spermatogenic cells become competent to transition from mitosis to meiosis in response to retinoic acid. In mice, previous studies revealed that MEIOC, alongside binding partners YTHDC2 and RBM46, represses mitotic genes and promotes robust meiotic gene expression in spermatogenic cells that have already initiated meiosis. Here, we molecularly dissect MEIOC-dependent regulation in mouse spermatogenic cells and find that MEIOC actually shapes the transcriptome much earlier, even before meiotic initiation. MEIOC, acting with YTHDC2 and RBM46, destabilizes mRNA targets, including transcriptional repressors E2f6 and Mga, in mitotic spermatogonia. MEIOC thereby derepresses E2F6- and MGA-repressed genes, including Meiosin and other meiosis-associated genes. This confers on spermatogenic cells the molecular competence to, in response to retinoic acid, fully activate the STRA8-MEIOSIN transcriptional regulator, which is required for the meiotic G1/S cell cycle transition and meiotic gene expression. We conclude that in mice, mRNA decay mediated by MEIOC-YTHDC2-RBM46 enhances the competence of mitotic spermatogonia to transit from mitosis to meiosis.

Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection.

Malignant testicular germ cells tumors (TGCTs) are the most common solid cancers in young men. Current TGCT diagnostics include conventional serum protein markers, but these lack the sensitivity and specificity to serve as accurate markers across all TGCT subtypes. MicroRNAs (miRNAs) are small non-coding regulatory RNAs and informative biomarkers for several diseases. In humans, miRNAs of the miR-371-373 cluster are detectable in the serum of patients with malignant TGCTs and outperform existing serum protein markers for both initial diagnosis and subsequent disease monitoring. We previously developed a genetically engineered mouse model featuring malignant mixed TGCTs consisting of pluripotent embryonal carcinoma (EC) and differentiated teratoma that, like the corresponding human malignancies, originate in utero and are highly chemosensitive. Here, we report that miRNAs in the mouse miR-290-295 cluster, homologs of the human miR-371-373 cluster, were detectable in serum from mice with malignant TGCTs but not from tumor-free control mice or mice with benign teratomas. miR-291-293 were expressed and secreted specifically by pluripotent EC cells, and expression was lost following differentiation induced by the drug thioridazine. Notably, miR-291-293 levels were significantly higher in the serum of pregnant dams carrying tumor-bearing fetuses compared to that of control dams. These findings reveal that expression of the miR-290-295 and miR-371-373 clusters in mice and humans, respectively, is a conserved feature of malignant TGCTs, further validating the mouse model as representative of the human disease. These data also highlight the potential of serum miR-371-373 assays to improve patient outcomes through early TGCT detection, possibly even prenatally.

A national assessment of standards of care for inherited bleeding disorders in Canada.

AIM: The Canadian Integrated and Comprehensive Care Standards for Inherited Bleeding Disorders were adopted in June 2020. In early 2023, a self-assessment of each of the 26 Canadian inherited bleeding disorder treatment centre's (IBDTCs) capacity to meet the Standards was conducted. The goal was to validate the standards by assessing appropriateness and adherence. As a result, centres can compare their own practices and capacity against those of all centres, identify barriers to adherence, identify opportunities for remedial actions and use the results locally as evidence for needed resources. METHODS: Healthcare providers (HCPs) in the 26 IBDTCs were provided with a checklist to assess adherence to each of the 66 standards of care. Centre participation was voluntary but strongly encouraged by the healthcare provider and patient associations. RESULTS: All 26 centres completed the self-assessments. Collectively, centres reported meeting 88.8% of the standards. Adherence to each standard ranged from 40% to 100%. Forty-one (41) of the standards were adhered to by 90% or more of the centres, 12 by 80%-89% of the centres and 13 by fewer than 80% of the centres. A report consolidating all the assessments was sent to the 26 centres. CONCLUSION: None of the comments received in the self-assessment reports indicated that a given standard was irrelevant, unrealistic or unnecessary. These data are strong indicators that the standards, as written, are appropriate. The self-assessments, however, reveal alarming deficiencies in staffing levels, notably in physiotherapy, psychosocial support and data entry and data management. These constitute a barrier to comprehensive care for many centres. The findings echo similar conclusions from a previous assessment conducted in 2015.

Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer.

Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for describing or analyzing spatial immune cell data, and most reported spatial analyses are rudimentary. In this review, we provide an overview of two approaches for reporting and analyzing spatial data (raster versus vector-based). We then provide a compendium of spatial immune cell metrics that have been reported in the literature, summarizing prognostic associations in the context of a variety of cancers. We conclude by discussing two well-described clinical biomarkers, the breast cancer stromal tumor infiltrating lymphocytes score and the colon cancer Immunoscore, and describe investigative opportunities to improve clinical utility of these spatial biomarkers. © 2023 The Pathological Society of Great Britain and Ireland.

Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer

The clinical significance of the tumor-immune interaction in breast cancer is now established, and tumor-infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2-negative) breast cancer and HER2-positive breast cancer. How computational assessments of TILs might complement manual TIL assessment in trial and daily practices is currently debated. Recent efforts to use machine learning (ML) to automatically evaluate TILs have shown promising results. We review state-of-the-art approaches and identify pitfalls and challenges of automated TIL evaluation by studying the root cause of ML discordances in comparison to manual TIL quantification. We categorize our findings into four main topics: (1) technical slide issues, (2) ML and image analysis aspects, (3) data challenges, and (4) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns or design choices in the computational implementation. To aid the adoption of ML for TIL assessment, we provide an in-depth discussion of ML and image analysis, including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial and routine clinical management of patients with triple-negative breast cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Human microglia maturation is underpinned by specific gene regulatory networks.

Microglia phenotypes are highly regulated by the brain environment, but the transcriptional networks that specify the maturation of human microglia are poorly understood. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia and acquired corresponding data in induced pluripotent stem cell (iPSC)-derived microglia, in cerebral organoids, and following engraftment into humanized mice. Parallel development of computational approaches that considered transcription factor (TF) co-occurrence and enhancer activity allowed prediction of shared and state-specific gene regulatory networks associated with fetal and postnatal microglia. Additionally, many features of the human fetal-to-postnatal transition were recapitulated in a time-dependent manner following the engraftment of iPSC cells into humanized mice. These data and accompanying computational approaches will facilitate further efforts to elucidate mechanisms by which human microglia acquire stage- and disease-specific phenotypes.

Cell type-specific role of CBX2 and its disordered region in spermatogenesis.

Polycomb group (PcG) proteins maintain the repressed state of lineage-inappropriate genes and are therefore essential for embryonic development and adult tissue homeostasis. One critical function of PcG complexes is modulating chromatin structure. Canonical Polycomb repressive complex 1 (cPRC1), particularly its component CBX2, can compact chromatin and phase-separate in vitro. These activities are hypothesized to be critical for forming a repressed physical environment in cells. While much has been learned by studying these PcG activities in cell culture models, it is largely unexplored how cPRC1 regulates adult stem cells and their subsequent differentiation in living animals. Here, we show in vivo evidence of a critical nonenzymatic repressive function of cPRC1 component CBX2 in the male germline. CBX2 is up-regulated as spermatogonial stem cells differentiate and is required to repress genes that were active in stem cells. CBX2 forms condensates (similar to previously described Polycomb bodies) that colocalize with target genes bound by CBX2 in differentiating spermatogonia. Single-cell analyses of mosaic Cbx2 mutant testes show that CBX2 is specifically required to produce differentiating A1 spermatogonia. Furthermore, the region of CBX2 responsible for compaction and phase separation is needed for the long-term maintenance of male germ cells in the animal. These results emphasize that the regulation of chromatin structure by CBX2 at a specific stage of spermatogenesis is critical, which distinguishes this from a mechanism that is reliant on histone modification.

Prophylactic Administration of Vasopressors Prior to Emergency Intubation in Critically Ill Patients: A Secondary Analysis of Two Multicenter Clinical Trials.

Hypotension affects approximately 40% of critically ill patients undergoing emergency intubation and is associated with an increased risk of death. The objective of this study was to examine the association between prophylactic vasopressor administration and the incidence of peri-intubation hypotension and other clinical outcomes. DESIGN: A secondary analysis of two multicenter randomized clinical trials. The clinical effect of prophylactic vasopressor administration was estimated using a one-to-one propensity-matched cohort of patients with and without prophylactic vasopressors. SETTING: Seven emergency departments and 17 ICUs across the United States. PATIENTS: One thousand seven hundred ninety-eight critically ill patients who underwent emergency intubation at the study sites between February 1, 2019, and May 24, 2021. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The primary outcome was peri-intubation hypotension defined as a systolic blood pressure less than 90 mm Hg occurring between induction and 2 minutes after tracheal intubation. A total of 187 patients (10%) received prophylactic vasopressors prior to intubation. Compared with patients who did not receive prophylactic vasopressors, those who did were older, had higher Acute Physiology and Chronic Health Evaluation II scores, were more likely to have a diagnosis of sepsis, had lower pre-induction systolic blood pressures, and were more likely to be on continuous vasopressor infusions prior to intubation. In our propensity-matched cohort, prophylactic vasopressor administration was not associated with reduced risk of peri-intubation hypotension (41% vs 32%; p = 0.08) or change in systolic blood pressure from baseline (-12 vs -11 mm Hg; p = 0.66). CONCLUSIONS: The administration of prophylactic vasopressors was not associated with a lower incidence of peri-intubation hypotension in our propensity-matched analysis. To address potential residual confounding, randomized clinical trials should examine the effect of prophylactic vasopressor administration on peri-intubation outcomes.

The human Y and inactive X chromosomes similarly modulate autosomal gene expression.

Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.