The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × âˆ¼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.

Adding Patient-Reported Outcomes to the American College of Surgeons National Surgical Quality Improvement Program: Results of the First 33,842 Patients from 65 Hospitals.

OBJECTIVES: To investigate the initial set of patient-reported outcomes (PROs) in the ACS NSQIP and their associations with 30-day surgical outcomes. BACKGROUND: PROs provide important information that can be used to improve routine care and facilitate quality improvement. The ACS conducted a demonstration project to capture PROs into the NSQIP to complement clinical data. METHODS: From 2/2020-3/2023, 65 hospitals collected PROMIS measures assessing global health, pain interference, fatigue, and physical function from patients accrued into the NSQIP. Using multivariable mixed regression, we compared the scores of patients with and without 30-day complications and further analyzed scores exceeding one standard deviation (1-SD) worse than national benchmarks. RESULTS: Overall, 33842 patients completed the PROMIS measures a median 58 days (IQR 47-72) postoperatively. Among patients without complications (n=31210), 33.9% had PRO scores 1-SD worse than national benchmarks. Patients with complications were 1.7-times more likely to report worse PROs (95% CI 1.6-1.8). Patients with complications had lower scores for global physical health (adjusted mean difference [AMD] 2.6, 95% CI 2.2-3.0), lower for global mental health (AMD 1.8, 95% CI 1.4-2.2), higher for pain interference (AMD 2.4, 95% CI 2.0-2.8), higher fatigue (AMD 2.7, 95% CI 2.3-3.1), and lower physical function (AMD 3.2, 95% CI 2.8-3.5). CONCLUSIONS: Postoperative complications negatively affect multiple key dimensions of patients' health-related quality of life. PROs were well below national benchmarks for many patients, even among those without complications. Identifying solutions to improve PROs after surgery thus remains a tremendous quality opportunity.

Five-year survival prognosis of young, middle-aged, and elderly adult female invasive breast cancer patients by clinical and lifestyle characteristics.

PURPOSE: Early-onset breast cancer incidence has been increasing globally and in Taiwan. However, previous studies have not comprehensively examined how clinical and lifestyle characteristics influence the 5-year survival of breast cancer diagnosed at different stages of adulthood. METHODS: We analyzed the Taiwan National Cancer Registry and Cause of Death datasets to understand how clinical factors (including tumor and treatment characteristics) and lifestyle factors (including body mass index, cigarette smoking, and alcohol consumption) were associated with the 5-year survival of 8471 young, 57,695 middle-aged, and 14,074 elderly female adult invasive breast cancer patients respectively diagnosed at age 20-39, 40-64, and ≥ 65 years between 2002 and 2015, with mortality follow-up to 2020. Poisson regression was used for obtaining the crude and adjusted 5-year survival risk ratios. RESULTS: Clinical and lifestyle characteristics were distributed differently but had mostly similar direction of association with 5-year survival for the three age groups. Receiving any treatment was associated with better survival, especially for elderly patients. Being underweight at initial cancer treatment was associated with worse survival than having normal weight, especially for elderly patients. Current smokers had worse survival than never smokers for middle-aged and elderly patients. The 5-year breast cancer-specific survival was not significantly higher for those of age 45-49 years than 40-44 years, despite the recommended starting screening age is 45 years in Taiwan. CONCLUSION: Our findings contribute to the understanding of early-onset and later-onset female breast cancer characteristics and prognosis, which may inform surveillance and treatment strategies to achieve better breast cancer prognosis.

Patterns of Social Needs Predict Quality-of-Life and Healthcare Utilization Outcomes in Patients from a Large Hospital System.

BACKGROUND: Unmet social needs (SNs) often coexist in distinct patterns within specific population subgroups, yet these patterns are understudied. OBJECTIVE: To identify patterns of social needs (PSNs) and characterize their associations with health-related quality-of-life (HRQoL) and healthcare utilization (HCU). DESIGN: Observational study using data on SNs screening, HRQoL (i.e., low mental and physical health), and 90-day HCU (i.e., emergency visits and hospital admission). Among patients with any SNs, latent class analysis was conducted to identify unique PSNs. For all patients and by race and age subgroups, compared with no SNs, we calculated the risks of poor HRQoL and time to first HCU following SNs screening for each PSN. PATIENTS: Adult patients undergoing SNs screening at the Mass General Brigham healthcare system in Massachusetts, United States, between March 2018 and January 2023. MAIN MEASURES: SNs included: education, employment, family care, food, housing, medication, transportation, and ability to pay for household utilities. HRQoL was assessed using the Patient-Reported Outcomes Measurement Information System Global-10. KEY RESULTS: Six unique PSNs were identified: "high number of social needs," "food and utility access," "employment needs," "interested in education," "housing instability," and "transportation barriers." In 14,230 patients with HRQoL data, PSNs increased the risks of poor mental health, with risk ratios ranging from 1.07(95%CI:1.01-1.13) to 1.80(95%CI:1.74-1.86). Analysis of poor physical health yielded similar findings, except that the "interested in education" showed a mild protective effect (0.97[95%CI:0.94-1.00]). In 105,110 patients, PSNs increased the risk of 90-day HCU, with hazard ratios ranging from 1.09(95%CI:0.99-1.21) to 1.70(95%CI:1.52-1.90). Findings were generally consistent in subgroup analyses by race and age. CONCLUSIONS: Certain SNs coexist in distinct patterns and result in poorer HRQoL and more HCU. Understanding PSNs allows policymakers, public health practitioners, and social workers to identify at-risk patients and implement integrated, system-wide, and community-based interventions.

Patient-reported outcome measures for primary hyperparathyroidism: a systematic review of measurement properties.

BACKGROUND: The quality of patient-reported outcome measures (PROMs) used to assess the outcomes of primary hyperparathyroidism (PHPT), a common endocrine disorder that can negatively affect patients' health-related quality of life due to chronic symptoms, has not been rigorously examined. This systematic review aimed to summarize and evaluate evidence on the measurement properties of PROMs used in adult patients with PHPT, and to provide recommendations for appropriate measure selection. METHODS: After PROSPERO registration (CRD42023438287), Medline, EMBASE, CINAHL Complete, Web of Science, PsycINFO, and Cochrane Trials were searched for full-text articles in English investigating PROM development, pilot studies, or evaluation of at least one PROM measurement property in adult patients with any clinical form of PHPT. Two reviewers independently identified studies for inclusion and conducted the review following the Consensus-Based Standards for the Selection of Health Measurement Instruments (COSMIN) Methodology to assess risk of bias, evaluate the quality of measurement properties, and grade the certainty of evidence. RESULTS: From 4989 records, nine PROM development or validation studies were identified for three PROMs: the SF-36, PAS, and PHPQoL. Though the PAS demonstrated sufficient test-retest reliability and convergent validity, and the PHPQoL sufficient test-retest reliability, convergent validity, and responsiveness, the certainty of evidence was low-to-very low due to risk of bias. All three PROMs lacked sufficient evidence for content validity in patients with PHPT. CONCLUSIONS: Based upon the available evidence, the SF-36, PAS, and PHPQoL cannot currently be recommended for use in research or clinical care, raising important questions about the conclusions of studies using these PROMs. Further validation studies or the development of more relevant PROMs with strong measurement properties for this patient population are needed.

Skin cancer survivorship and sun protection behaviors in the United States.

BACKGROUND: Skin cancer survivors are more vulnerable to subsequent skin cancers and other malignancies, but previous studies have not examined in detail their sun protection behavior prevalence by sociodemographic factors. We aimed to understand the sociodemographic disparities in the prevalence of three important types of sun protection behaviors: using sunscreen, seeking shade, and wearing protective clothing, among skin cancer survivors and those without skin cancer history. METHODS: We used the 2015 U.S. National Health Interview Survey to analyze 29,523 participants, of which 772 were skin cancer survivors and 28,751 were those without skin cancer history. We assessed overall and specific sun protection behavior prevalence based on using sunscreen, seeking shade, and wearing protective clothing. Weighted Poisson regression was used to estimate prevalence ratios. RESULTS: Melanoma and nonmelanoma skin cancer survivors had similar overall sun protection behavior (p > .05). Among all skin cancer survivors, 36.0% infrequently used sunscreen, 50.2% infrequently wore protective clothing, 47.8% infrequently sought shade, and 30.0% lacked frequent overall sun protection, which significantly differed from those without skin cancer history (p < .0001). The prevalence of frequent overall sun protection behavior was lower for those who were younger at survey, males, less educated, single or never married, or lived in poverty, regardless of their skin cancer history (p < .01). CONCLUSIONS: By identifying subpopulations with higher prevalence of infrequent sun protection among those with or without skin cancer history, our findings may encourage efforts to reduce sociodemographic disparities in sun protection behaviors and promote primary and tertiary skin cancer prevention.

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.

In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. To this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. The resulting model contains information about biological properties in its representations. The representations are learned from sequence data alone. The learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction.

Prevalence of Current Cigarette Smoking by Sociodemographic Characteristics in U.S. Cancer Survivors.

BACKGROUND: Cancer survivors are especially vulnerable to the carcinogenic effects of tobacco smoking, but there lacks a study comprehensively examining the sociodemographic disparities in current smoking prevalence in this population. In this study, we quantified the current cigarette smoking prevalence in cancer survivors and those without cancer history by sociodemographic factors, to identify subpopulations with high current smoking burden. METHODS: We conducted a cross-sectional study of 3,679 cancer survivors and 27,350 participants without cancer history who were 18 years of age or above in the 2019 National Health Interview Survey. Data for the study variables were obtained from computer-assisted personal or telephone interviews. Weighted Poisson regression was used to estimate prevalence ratios and 95% confidence intervals. RESULTS: Although the current smoking prevalence for cancer survivors was slightly lower than for those without cancer history, the prevalence exceeded 30% in cancer survivors in poverty or without health insurance. Individuals with significantly higher current smoking prevalence had lower education levels, were unmarried, did not have health insurance, or lived in poverty. The associations of age, sex, race, health insurance status, and poverty status with current smoking significantly differed between cancer survivors and those without cancer history. Sociodemographic disparities in current smoking prevalence were found in survivors of either smoking-related or nonsmoking-related cancers. CONCLUSION: High current smoking prevalence still exists in subpopulations of cancer survivors and those without cancer history. Our findings may strengthen efforts to reduce sociodemographic disparities in current smoking prevalence and to lower the overall smoking prevalence.

COVID-19 Diagnosis and SARS-CoV-2 Strain Identification by a Rapid, Multiplexed, Point-of-Care Antibody Microarray.

Antigen tests to detect SARS-CoV-2 have emerged as a promising rapid diagnostic method for COVID-19, but they are unable to differentiate between variants of concern (VOCs). Here, we report a rapid point-of-care test (POC-T), termed CoVariant-SPOT, that uses a set of antibodies that are either tolerant or intolerant to spike protein mutations to identify the likely SARS-CoV-2 strain concurrent with COVID-19 diagnosis using antibodies targeting the nucleocapsid protein. All reagents are incorporated into a portable, multiplexed, and sensitive diagnostic platform built upon a nonfouling polymer brush. To validate CoVariant-SPOT, we tested recombinant SARS-CoV-2 proteins, inactivated viruses, and nasopharyngeal swab samples from COVID-19 positive and negative individuals and showed that CoVariant-SPOT can readily distinguish between two VOCs: Delta and Omicron. We believe that CoVariant-SPOT can serve as a valuable adjunct to next-generation sequencing to rapidly identify variants using a scalable and deployable POC-T, thereby enhancing community surveillance efforts worldwide and informing treatment selection.

Associations between sociodemographic factors and breast, cervical, and colorectal cancer screening in the United States.

PURPOSE: Cancer is the second leading cause of death globally and in the U.S., but screening can reduce cancer-related deaths. We analyzed data from a nationwide survey to compare how sociodemographic factors were associated with never or not timely screening for multiple types of cancer, and the use of different colorectal cancer screening procedures. METHODS: We analyzed data from the 2019 U.S. National Health Interview Survey. To understand breast, cervical, and colorectal cancer screening participation among those recommended to screen, we respectively analyzed 8,110 women 45 to 74 years of age, 9,583 women 21 to 65 years of age, and 13,497 individuals 50 to 75 years of age at survey. Weighted Poisson regression was used to estimate the unadjusted and confounding-adjusted prevalence ratio and 95% confidence intervals. RESULTS: In our analysis populations, 6.9% never had a mammogram, 14.6% never screened for cervical cancer, and 26.8% never screened for colorectal cancer; the prevalence respectively increased to 24.7%, 23.8%, and 32.3% for not timely screening according to national guidelines. The prevalence of never screening was 81.9% for non-invasive colorectal cancer tests, compared with 32.5% for colonoscopy or sigmoidoscopy. Individuals with lower education level, with no health insurance, or in poverty had higher prevalence of never screening for all three cancers. There was low sociodemographic disparity for the use of non-invasive colorectal cancer screening tests. CONCLUSION: Socioeconomically disadvantaged individuals have higher prevalence of never or not timely screening. The utilization of non-invasive colorectal cancer screening procedures remains low across sociodemographic groups.

Comparative cardiovascular safety of LABA/LAMA FDC versus LABA/ICS FDC in patients with chronic obstructive pulmonary disease: a population-based cohort study with a target trial emulation framework.

BACKGROUND: Use of combinations of long-acting ß2 agonists/long-acting muscarinic antagonists (LABA/LAMA) in patients with chronic obstructive pulmonary disease (COPD) is increasing. Nevertheless, existing evidence on cardiovascular risk associated with LABA/LAMA versus another dual combination, LABA/inhaled corticosteroids (ICS), was limited and discrepant. AIM: The present cohort study aimed to examine comparative cardiovascular safety of LABA/LAMA and LABA/ICS with a target trial emulation framework, focusing on dual fixed-dose combination (FDC) therapies. METHODS: We identified patients with COPD who initiated LABA/LAMA FDC or LABA/ICS FDC from a nationwide Taiwanese database during 2017-2020. The outcome of interest was a hospitalized composite cardiovascular events of acute myocardial infarction, unstable angina, heart failure, cardiac dysrhythmia, and ischemic stroke. Cox regression models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for composite and individual cardiovascular events after matching up to five LABA/LAMA FDC initiators to one LABA/ICS FDC initiator using propensity scores (PS). RESULTS: Among 75,926 PS-matched patients, use of LABA/LAMA FDC did not show a higher cardiovascular risk compared to use of LABA/ICS FDC, with a HR of 0.89 (95% CI, 0.78-1.01) for the composite events, 0.80 (95% CI, 0.61-1.05) for acute myocardial infarction, 1.48 (95% CI, 0.68-3.25) for unstable angina, 1.00 (95% CI, 0.80-1.24) for congestive heart failure, 0.62 (95% CI, 0.37-1.05) for cardiac dysrhythmia, and 0.82 (95% CI, 0.66-1.02) for ischemic stroke. The results did not vary substantially in several pre-specified sensitivity and subgroup analyses. CONCLUSION: Our findings provide important reassurance about comparative cardiovascular safety of LABA/LAMA FDC treatment among patients with COPD.

Anisotropic material depletion in epitaxial polymer crystallization.

The physical properties of a semicrystalline polymer thin film are intimately related to the morphology of its crystalline domains. While the mechanisms underlying crystallization of flat-on oriented polymer crystals are well known, similar mechanisms remain elusive for edge-on oriented thin films due to the propensity of substantially thin films to adopt flat-on orientations. Here, we employ an epitaxial polymer-substrate relationship to enforce edge-on crystallization in thin films. Using matrix-assisted pulsed laser evaporation (MAPLE), we deposit films in which crystal nucleation is spatially separated from subsequent epitaxial crystallization. These experiments, together with phase-field simulations, demonstrate a highly anisotropic and localized material depletion during edge-on crystallization. These results provide deeper insight into the physics of polymer crystallization under confinement and introduce a processing motif in the crystallization of ultrathin structured films.

Impact of Obesity on Risk of Hypocalcemia After Total Thyroidectomy: Targeted National Surgical Quality Improvement Program Analysis of 16,277 Patients.

INTRODUCTION: Hypocalcemia following total thyroidectomy (TT) is common due to postoperative parathyroid dysfunction and vitamin D deficiency. Given the association between obesity and vitamin D deficiency, we sought to correlate body mass index (BMI) with hypocalcemia after TT. METHODS: Patients undergoing TT between 2016 and 2020 were identified from the American College of Surgeons National Surgical Quality Improvement Program thyroidectomy-targeted database. Univariable and multivariable regressions, stratified by BMI category (normal, overweight, obese), identified factors associated with hypocalcemia prior to discharge, within 30 d, and severe hypocalcemic events (emergent evaluation, intravenous calcium supplementation, or readmission). RESULTS: Sixteen thousand two hundred seventy seven TT were performed with available BMI data. Three thousand five hundred thirty one (21.7%) patients had normal BMI, 4823 (29.6%) were overweight, and 7772 (47.7%) were obese. Patients with BMI ≥ 25 had decreased risk of hypocalcemia before discharge (9.8% versus 13%, odds ratio [OR] 0.73, P < 0.001), 30 d (8.1% versus 10.4%, OR 0.76, P < 0.001), and severe hypocalcemic events (5.5% versus 6.4%, OR 0.84, P = 0.029) compared to normal BMI patients. On multivariable analysis for normal BMI patients, age < 45 y was a risk factor for hypocalcemia before discharge, 30 d, and severe hypocalcemic events (P < 0.05 for all). Additional risk factors in this group for 30-d hypocalcemia included parathyroid autotransplant and central neck dissection (P < 0.05) and recurrent laryngeal nerve injury for severe hypocalcemic events (P = 0.01). CONCLUSIONS: Younger patients with BMI < 25 are at an increased risk for hypocalcemia and severe hypocalcemic events after TT. These patients may benefit from preoperative counseling and increased calcium/vitamin D supplementation to reduce prolonged hospitalization and mitigate morbidity.

Imaging of Small-Bowel Neuroendocrine Neoplasms: AJR Expert Panel Narrative Review.

Neuroendocrine neoplasms (NENs) of the small bowel are typically slow-growing lesions that remain asymptomatic until reaching an advanced stage. Imaging modalities for lesion detection, staging, and follow-up in patients with known or suspected NEN include CT enterography, MR enterography, and PET/CT using a somatostatin receptor analog. FDG PET/CT may have a role in the evaluation of poorly differentiated NENs. Liver MRI, ideally with a hepatocyte-specific contrast agent, should be used in the evaluation of hepatic metastases. Imaging informs decisions regarding both surgical approaches and systematic therapy (specifically, peptide receptor radionuclide therapy). This AJR Expert Panel Narrative Review describes the multimodality imaging features of small-bowel NENs; explores the optimal imaging modalities for their diagnosis, staging, and follow-up; and discusses how imaging may be used to guide therapy.

Interrelationships Between Pregnancy Intention, Antenatal Care, and Sociodemographic Factors: Analysis of a Nationwide Population-Based Cross-Sectional Study in Vietnam.

OBJECTIVES: This study aimed to improve the understanding of the interrelationships between sociodemographic factors, pregnancy intention, and antenatal care by: (1) identifying sociodemographic predictors of unintended pregnancy; (2) examining associations between unintended pregnancy types and antenatal care (ANC) inadequacy; (3) examining how the association between unintended pregnancy and ANC inadequacy is modified by maternal characteristics; and (4) identifying sociodemographic predictors of ANC inadequacy by pregnancy intention status. METHODS: We analyzed women 15-49 years of age who participated in the nationwide cross-sectional Vietnam Multiple Indicator Cluster Survey. Pregnancy intention and ANC adequacy were assessed for the most recent live birth within two years preceding survey completion. Weighted Poisson regression was used to estimate risk ratios. RESULTS: Of the 1,474 study participants, 17.8% had unintended pregnancy and 29.0% had inadequate ANC. There was no significant confounding-adjusted association between unintended pregnancy and ANC inadequacy, except in those currently not working. Women with intended pregnancy or unintended pregnancy had significantly higher ANC inadequacy risk if they lived in rural areas, were less educated, and had no media exposure, lower wealth status, or more than two children. Younger age, ever given birth, having child loss, and positive attitude towards partner violence were significant predictors of ANC inadequacy only in women with intended pregnancy. CONCLUSIONS FOR PRACTICE: ANC inadequacy was more strongly predicted by sociodemographic characteristics rather than pregnancy intention, and the sociodemographic variables' prediction of ANC inadequacy was stronger in women with intended pregnancy than unintended pregnancy.

Piperacillin-Tazobactam Compared With Cefoxitin as Antimicrobial Prophylaxis for Pancreatoduodenectomy: A Randomized Clinical Trial.

Importance: Despite improvements in perioperative mortality, the incidence of postoperative surgical site infection (SSI) remains high after pancreatoduodenectomy. The effect of broad-spectrum antimicrobial surgical prophylaxis in reducing SSI is poorly understood. Objective: To define the effect of broad-spectrum perioperative antimicrobial prophylaxis on postoperative SSI incidence compared with standard care antibiotics. Design, Setting, and Participants: Pragmatic, open-label, multicenter, randomized phase 3 clinical trial at 26 hospitals across the US and Canada. Participants were enrolled between November 2017 and August 2021, with follow-up through December 2021. Adults undergoing open pancreatoduodenectomy for any indication were eligible. Individuals were excluded if they had allergies to study medications, active infections, chronic steroid use, significant kidney dysfunction, or were pregnant or breastfeeding. Participants were block randomized in a 1:1 ratio and stratified by the presence of a preoperative biliary stent. Participants, investigators, and statisticians analyzing trial data were unblinded to treatment assignment. Intervention: The intervention group received piperacillin-tazobactam (3.375 or 4 g intravenously) as perioperative antimicrobial prophylaxis, while the control group received cefoxitin (2 g intravenously; standard care). Main Outcomes and Measures: The primary outcome was development of postoperative SSI within 30 days. Secondary end points included 30-day mortality, development of clinically relevant postoperative pancreatic fistula, and sepsis. All data were collected as part of the American College of Surgeons National Surgical Quality Improvement Program. Results: The trial was terminated at an interim analysis on the basis of a predefined stopping rule. Of 778 participants (378 in the piperacillin-tazobactam group [median age, 66.8 y; 233 {61.6%} men] and 400 in the cefoxitin group [median age, 68.0 y; 223 {55.8%} men]), the percentage with SSI at 30 days was lower in the perioperative piperacillin-tazobactam vs cefoxitin group (19.8% vs 32.8%; absolute difference, -13.0% [95% CI, -19.1% to -6.9%]; P < .001). Participants treated with piperacillin-tazobactam, vs cefoxitin, had lower rates of postoperative sepsis (4.2% vs 7.5%; difference, -3.3% [95% CI, -6.6% to 0.0%]; P = .02) and clinically relevant postoperative pancreatic fistula (12.7% vs 19.0%; difference, -6.3% [95% CI, -11.4% to -1.2%]; P = .03). Mortality rates at 30 days were 1.3% (5/378) among participants treated with piperacillin-tazobactam and 2.5% (10/400) among those receiving cefoxitin (difference, -1.2% [95% CI, -3.1% to 0.7%]; P = .32). Conclusions and Relevance: In participants undergoing open pancreatoduodenectomy, use of piperacillin-tazobactam as perioperative prophylaxis reduced postoperative SSI, pancreatic fistula, and multiple downstream sequelae of SSI. The findings support the use of piperacillin-tazobactam as standard care for open pancreatoduodenectomy. Trial Registration: ClinicalTrials.gov Identifier: NCT03269994.

Patient-Reported Outcomes and Surgical Quality.

Delivering high-quality surgical care requires knowing how best to define and measure quality in surgery. Patient-reported outcomes (PROs) enable surgeons, health care systems, and payers to understand meaningful health outcomes from the patient's perspective and can be measured using patient-reported outcome measures (PROMs). As a result, there is much interest in using PROMs in routine surgical care, to guide quality improvement and to inform reimbursement pay structures. This chapter defines PROs and PROMs, differentiates PROMs from other quality measures such as patient-reported experience measures, describes PROMs in the context of routine clinical care, and provides an overview of interpreting PROM data. This chapter also describes how PROMs may be applied to quality improvement and value-based reimbursement in surgery.

Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization.

MOTIVATION: Traditionally, an individual can only query and retrieve information from a genome browser by using accessories such as a mouse and keyboard. However, technology has changed the way that people interact with their screens. We hypothesized that we could leverage technological advances to use voice recognition as an interactive input to query and visualize genomic information. RESULTS: We developed an Amazon Alexa skill called Gene Tracer that allows users to use their voice to find disease-associated gene information, deleterious mutations and gene networks, while simultaneously enjoy a genome browser-like visualization experience on their screen. As the voice can be well recognized and understood, Gene Tracer provides users with more flexibility to acquire knowledge and is broadly applicable to other scenarios. AVAILABILITYAND IMPLEMENTATION: Alexa skill store (https://www.amazon.com/LT-Gene-tracer/dp/B08HCL1V68/) and a demonstration video (https://youtu.be/XbDbx7JDKmI). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments.

SUMMARY: scATAC-seq is a powerful approach for characterizing cell-type-specific regulatory landscapes. However, it is difficult to benchmark the performance of various scATAC-seq analysis techniques (such as clustering and deconvolution) without having a priori a known set of gold-standard cell types. To simulate scATAC-seq experiments with known cell-type labels, we introduce an efficient and scalable scATAC-seq simulation method (SCAN-ATAC-Sim) that down-samples bulk ATAC-seq data (e.g. from representative cell lines or tissues). Our protocol uses a consistent but tunable signal-to-noise ratio across cell types in a scATAC-seq simulation for integrating bulk experiments with different levels of background noise, and it independently samples twice without replacement to account for the diploid genome. Because it uses an efficient weighted reservoir sampling algorithm and is highly parallelizable with OpenMP, our implementation in C++ allows millions of cells to be simulated in less than an hour on a laptop computer. AVAILABILITY AND IMPLEMENTATION: SCAN-ATAC-Sim is available at scan-atac-sim.gersteinlab.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.

MOTIVATION: Mapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods with limited training data. Moreover, past approaches have implemented enhancer discovery as a binary classification problem without accurate boundary detection, producing low-resolution annotations with superfluous regions and reducing the statistical power for downstream analyses (e.g. causal variant mapping and functional validations). Here, we addressed these challenges via a two-step model called Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays (DECODE). First, we employed direct enhancer-activity readouts from novel functional characterization assays, such as STARR-seq, to train a deep neural network for accurate cell-type-specific enhancer prediction. Second, to improve the annotation resolution, we implemented a weakly supervised object detection framework for enhancer localization with precise boundary detection (to a 10 bp resolution) using Gradient-weighted Class Activation Mapping. RESULTS: Our DECODE binary classifier outperformed a state-of-the-art enhancer prediction method by 24% in transgenic mouse validation. Furthermore, the object detection framework can condense enhancer annotations to only 13% of their original size, and these compact annotations have significantly higher conservation scores and genome-wide association study variant enrichments than the original predictions. Overall, DECODE is an effective tool for enhancer classification and precise localization. AVAILABILITY AND IMPLEMENTATION: DECODE source code and pre-processing scripts are available at decode.gersteinlab.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.