Effects of food bar chewing duration on the physiologic, metabolic, and perceptual responses to moderate-intensity running.

PURPOSE: Chewing duration can affect food particle size, gastric processing, and postprandial glycemia, but these effects have not been investigated with exercise. This study examined how the chewing duration of a food bar impacts glycemic and metabolic responses, gastrointestinal (GI) symptoms, psychological affect, and performance during endurance running. METHODS: This randomized, unblinded, crossover study had 15 males (35.2 ± 7.4 years, VO2peak: 56.1 ± 5.2 ml/kg/min) attend three laboratory visits. Visit 1 required a VO2peak test, 10 min familiarization run at 60% VO2peak, and familiarization time-to-exhaustion (TTE) test (10 min at 90% VO2peak, followed by TTE at 100% VO2peak). Visits 2 and 3 consisted of a 60 min run at 60% VO2peak, followed by TTE testing. Participants were fed 45 g of a bar (180 kcal, 4 g fat, 33 g carbohydrate, 3 g protein, 1 g fiber) in 9 g servings 30 min before running, and 27 g of bar in 9 g servings at three timepoints during the 60 min run. Participants consumed the servings in 20 (20CHEW) or 40 (40CHEW) masticatory cycles, at 1 chew/second. Outcomes included blood glucose, substrate use, GI symptoms, perceived exertion (RPE), overall feeling, and TTE. RESULTS: Post-prandial blood glucose, GI symptoms, and RPE increased over time, but there were no significant between-condition or condition-by-time effects. TTE showed no significant between-condition effect (20CHEW: 288 ± 133 s; 40CHEW: 335 ± 299 s; p = 0.240). Overall feeling demonstrated a time-by-condition effect (p = 0.006), suggesting possible better maintenance over time with 40CHEW. CONCLUSION: Cumulatively, the results suggest that extended chewing minimally impacts physiology, perceptions, and performance during 60 min moderate-intensity running.

A hybrid demultiplexing strategy that improves performance and robustness of cell hashing.

Cell hashing, a nucleotide barcode-based method that allows users to pool multiple samples and demultiplex in downstream analysis, has gained widespread popularity in single-cell sequencing due to its compatibility, simplicity, and cost-effectiveness. Despite these advantages, the performance of this method remains unsatisfactory under certain circumstances, especially in experiments that have imbalanced sample sizes or use many hashtag antibodies. Here, we introduce a hybrid demultiplexing strategy that increases accuracy and cell recovery in multi-sample single-cell experiments. This approach correlates the results of cell hashing and genetic variant clustering, enabling precise and efficient cell identity determination without additional experimental costs or efforts. In addition, we developed HTOreader, a demultiplexing tool for cell hashing that improves the accuracy of cut-off calling by avoiding the dominance of negative signals in experiments with many hashtags or imbalanced sample sizes. When compared to existing methods using real-world datasets, this hybrid approach and HTOreader consistently generate reliable results with increased accuracy and cell recovery.

Reframing reentry: Understanding how reentry programming affects the well-being and quality of life of returning citizens.

This study examined the experiences returning citizens (RCs) have in participating in different reentry programs and how these experiences may lead to improved well-being and quality of life (QOL). We conducted 14 semi-structured interviews with RCs participating in employment-oriented reentry programs. The interviews focused on participants' reentry programming experience and areas affecting their well-being (e.g., housing, education, financial stability). QOL was enhanced for RCs when they were able to access stable housing, develop supportive relationships, have a job that permitted them the resources needed to live independently, and increase their perceptions of self-efficacy and social capital. While reentry programs maintain a focus on employment for RCs, housing, healthy relationships, and opportunities for increasing self-efficacy and social capital are tied to well-being and QOL among RCs. Reentry programs have the potential to influence a variety of factors at multiple levels that shape well-being and QOL, and in turn employment and recidivism, among RCs.

Revolutionizing Postoperative Ileus Monitoring: Exploring GRU-D's Real-Time Capabilities and Cross-Hospital Transferability.

Background: Postoperative ileus (POI) after colorectal surgery leads to increased morbidity, costs, and hospital stays. Identifying POI risk for early intervention is important for improving surgical outcomes especially given the increasing trend towards early discharge after surgery. While existing studies have assessed POI risk with regression models, the role of deep learning's remains unexplored. Methods: We assessed the performance and transferability (brutal force/instance/parameter transfer) of Gated Recurrent Unit with Decay (GRU-D), a longitudinal deep learning architecture, for real-time risk assessment of POI among 7,349 colorectal surgeries performed across three hospital sites operated by Mayo Clinic with two electronic health records (EHR) systems. The results were compared with atemporal models on a panel of benchmark metrics. Results: GRU-D exhibits robust transferability across different EHR systems and hospital sites, showing enhanced performance by integrating new measurements, even amid the extreme sparsity of real-world longitudinal data. On average, for labs, vitals, and assisted living status, 72.2%, 26.9%, and 49.3% respectively lack measurements within 24 hours after surgery. Over the follow-up period with 4-hour intervals, 98.7%, 84%, and 95.8% of data points are missing, respectively. A maximum of 5% decrease in AUROC was observed in brutal-force transfer between different EHR systems with non-overlapping surgery date frames. Multi-source instance transfer witnessed the best performance, with a maximum of 2.6% improvement in AUROC over local learning. The significant benefit, however, lies in the reduction of variance (a maximum of 86% decrease). The GRU-D model's performance mainly depends on the prediction task's difficulty, especially the case prevalence rate. Whereas the impact of training data and transfer strategy is less crucial, underscoring the challenge of effectively leveraging transfer learning for rare outcomes. While atemporal Logit models show notably superior performance at certain pre-surgical points, their performance fluctuate significantly and generally underperform GRU-D in post-surgical hours. Conclusion: GRU-D demonstrated robust transferability across EHR systems and hospital sites with highly sparse real-world EHR data. Further research on built-in explainability for meaningful intervention would be highly valuable for its integration into clinical practice.

Nucleosome-binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites.

The p53 family of transcription factors plays key roles in driving development and combating cancer by regulating gene expression. TP53, TP63, and TP73-the three members of the p53 family-regulate gene expression by binding to their DNA binding sites, many of which are situated within nucleosomes. To thoroughly examine the nucleosome-binding abilities of the p53 family, we used Pioneer-seq, a technique that assesses a transcription factor's binding affinity to its DNA binding sites at all possible positions within the nucleosome core particle. Using Pioneer-seq, we analyzed the binding affinity of TP53, TP63, and TP73 to 10 p53-family binding sites across the nucleosome core particle. We found that the affinity of TP53, TP63, and TP73 for nucleosomes was largely determined by the positioning of p53-family binding sites within nucleosomes; p53-family members bind strongly to the more accessible edges of nucleosomes but weakly to the less accessible centers of nucleosomes. We also found that the DNA-helical orientation of p53-family binding sites within nucleosomal DNA impacted the nucleosome-binding affinity of p53-family members. The composition of their binding sites also impacted each p53-family member's nucleosome-binding affinities only when the binding site was located in an accessible location. Taken together, our results show that the accessibility, composition, and helical orientation of p53-family binding sites collectively determine the nucleosome-binding affinities of TP53, TP63, and TP73. These findings help explain the rules underlying p53-family-nucleosome binding and thus provide requisite insight into how we may better control gene-expression changes involved in development and tumor suppression.

Differences in urine creatinine and osmolality between black and white Americans after accounting for age, moisture intake, urine volume, and socioeconomic status.

Urine osmolality is used throughout research to determine hydration levels. Prior studies have found black individuals to have elevated urine creatinine and osmolality, but it remains unclear which factors explain these findings. This cross-sectional, observational study sought to understand the relationship of self-reported race to urine creatinine and urine osmolality after accounting for age, socioeconomic status, and fluid intake. Data from 1,386 participants of the 2009-2012 National Health and Nutrition Examination Survey were utilized. Age, poverty-to-income ratio (PIR), urine flow rate (UFR), fluid intake, estimated lean body mass (LBM), urine creatinine, and urine osmolality were measured. In a sex-specific manner, black and white participants were matched on age, dietary moisture, UFR, and PIR. Urine creatinine was greater in black men (171 mg/dL) than white men (150 mg/dL) and greater in black women (147 mg/dL) than white women (108 mg/dL) (p < .001). Similarly, urine osmolality was greater in black women than white women (723 vs. 656 mOsm/kg, p = .001), but no difference was observed between white and black men (737 vs. 731 mOsm/kg, p = .417). Estimated LBM was greater in black men (61.8 kg) and women (45.5 kg) than in white men (58.9 kg) and women (42.2 kg) (p≤.001). The strongest correlate of urine osmolality in all race-sex groups was urine creatinine (Spearman ρ = .68-.75). These results affirm that individuals identifying as black produce higher urine creatinine concentrations and, in women, higher urine osmolality after matching for age, fluid intake, and socioeconomic status. The findings suggest caution when comparing urine hydration markers between racial groups.

Preliminary findings from the Dynamics of the Immune Responses to Repeat Influenza Vaccination Exposures (DRIVE I) Study: a Randomized Controlled Trial.

Background: Studies have reported that repeated annual vaccination may influence the effectiveness of the influenza vaccination in the current season. The mechanisms underlying these differences are unclear but might include "focusing" of the adaptive immune response to older strains. Methods: We established a 5-year randomized placebo-controlled trial of repeated influenza vaccination (Flublok, Sanofi Pasteur) in adults 18-45 years of age. Participants were randomized equally between five groups, with planned annual receipt of vaccination (V) or saline placebo (P) as follows: P-P-P-P-V, P-P-P-V-V, P-P-V-V-V, P-V-V-V-V, or V-V-V-VV. Serum samples were collected each year just before vaccination and after 30 and 182 days. A subset of sera were tested by hemagglutination inhibition assays, focus reduction neutralization tests and enzyme-linked immunosorbent assays against vaccine strains. Results: From 23 October 2020 through 11 March 2021 we enrolled and randomized 447 adults. We selected sera from 95 participants at five timepoints from the first two study years for testing. Among vaccinated individuals, antibody titers increased between days 0 and 30 against each of the vaccine strains, with substantial increases for first-time vaccinees and smaller increases for repeat vaccinees, who had higher pre-vaccination titers in year 2. There were statistically significant reductions in the proportion of participants achieving a four-fold greater rise in antibody titer for the repeat vaccinees for A(H1N1), B/Victoria and B/Yamagata, but not for influenza A(H3N2). There were no statistically significant differences between groups in geometric mean titers at day 30 or the proportions of participants with antibody titers ≥40 at day 30 for any of the vaccine strains. Conclusions: In the first two years, repeat vaccinees and first-time vaccinees had similar post-vaccination geometric mean titers to all four vaccine strains, indicative of similar levels of clinical protection. The vaccine strains of A(H1N1) and A(H3N2) were updated in year 2, providing an opportunity to explore antigenic distances between those strains in humans in subsequent years.

Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.

Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NPRBD) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NPRBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NPRBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.

Technology Access and Perceptions of Telehealth Services Among Young Adults Involved in the Court System.

PURPOSE: This study examined access to technology and telehealth among young adults (ages 18-24) who were court-involved and were recruited from an alternative sentencing program in New York City. METHODS: Using sequential mixed methods design, we examined demographic factors linked with access to technology and perceived usefulness of the Internet among n = 321 young adults who were court-involved (75% male, 65% African American, 35% Latinx). We then conducted in-depth interviews with 27 young adults to elicit first-person account of their access to, interest in, and experience with technology and telehealth. RESULTS: Although most participants had access to a phone with a data plan, a substantial proportion reported inconsistent access to the technology critical to telehealth. Certain young adults were more likely to lack consistent access to the technology needed for telehealth, including Black young adults, males, those with less than a high school diploma, those with a history of homelessness, and those who had difficulties paying for basic necessities. Qualitative interviews revealed that most had a strong self-efficacy using technology, while distrust of technology, inexperience with and skepticism of telehealth, low perceived need for care, and medical mistrust were common significant barriers in this underserved population. DISCUSSION: Findings underscored the critical need to address medical mistrust and increase access to and utilization of care among young adults who are court-involved. Results can inform the development and implementation of interventions designed to improve accessibility and acceptability of telehealth.

Limits of Ultra: Towards an Interdisciplinary Understanding of Ultra-Endurance Running Performance.

Ultra-endurance running (UER) poses extreme mental and physical challenges that present many barriers to completion, let alone performance. Despite these challenges, participation in UER events continues to increase. With the relative paucity of research into UER training and racing compared with traditional endurance running distance (e.g., marathon), it follows that there are sizable improvements still to be made in UER if the limitations of the sport are sufficiently understood. The purpose of this review is to summarise our current understanding of the major limitations in UER. We begin with an evolutionary perspective that provides the critical background for understanding how our capacities, abilities and limitations have come to be. Although we show that humans display evolutionary adaptations that may bestow an advantage for covering large distances on a daily basis, these often far exceed the levels of our ancestors, which exposes relative limitations. From that framework, we explore the physiological and psychological systems required for running UER events. In each system, the factors that limit performance are highlighted and some guidance for practitioners and future research are shared. Examined systems include thermoregulation, oxygen delivery and utilisation, running economy and biomechanics, fatigue, the digestive system, nutritional and psychological strategies. We show that minimising the cost of running, damage to lower limb tissue and muscle fatigability may become crucial in UER events. Maintaining a sustainable core body temperature is critical to performance, and an even pacing strategy, strategic heat acclimation and individually calculated hydration all contribute to sustained performance. Gastrointestinal issues affect almost every UER participant and can be due to a variety of factors. We present nutritional strategies for different event lengths and types, such as personalised and evidence-based approaches for varying types of carbohydrate, protein and fat intake in fluid or solid form, and how to avoid flavour fatigue. Psychology plays a vital role in UER performance, and we highlight the need to be able to cope with complex situations, and that specific long and short-term goal setting improves performance. Fatigue in UER is multi-factorial, both physical and mental, and the perceived effort or level of fatigue have a major impact on the ability to continue at a given pace. Understanding the complex interplay of these limitations will help prepare UER competitors for the different scenarios they are likely to face. Therefore, this review takes an interdisciplinary approach to synthesising and illuminating limitations in UER performance to assist practitioners and scientists in making informed decisions in practice and applicable research.

Biochemical and biophysical characterization of natural polyreactivity in antibodies.

To become specialized binders, antibodies undergo a process called affinity maturation to maximize their binding affinity. Despite this process, some antibodies retain low-affinity binding to diverse epitopes in a phenomenon called polyreactivity. Here we seek to understand the molecular basis of this polyreactivity in antibodies. Our results highlight that polyreactive antigen-binding fragments (Fabs) bind their targets with low affinities, comparable to T cell receptor recognition of autologous classical major histocompatibility complex. Extensive mutagenic studies find no singular amino acid residue or biochemical property responsible for polyreactive interaction, suggesting that polyreactive antibodies use multiple strategies for engagement. Finally, our crystal structures and all-atom molecular dynamics simulations of polyreactive Fabs show increased rigidity compared to their monoreactive relatives, forming a neutral and accessible platform for diverse antigens to bind. Together, these data support a cooperative strategy of rigid neutrality in establishing the polyreactive status of an antibody molecule.

Effects of drinking water treatment residual amendments to biosolids on plant uptake of per- and polyfluoroalkyl substances.

Drinking water treatment residuals (DWTRs), solid by-products of drinking water treatment, are dominated by calcium (Ca), iron (Fe), or aluminum (Al), depending on the coagulant used. DWTRs are often landfilled, but current research is exploring options for beneficial reuse. Previous studies have shown that Al- and Fe-rich materials have potential to reduce the mobility of per- and polyfluoroalkyl substances (PFAS). Here, we investigated how amending biosolids with 5% wt/wt DWTRs affected plant bioavailable PFAS in two different simulated scenarios: (1) agricultural scenario with Solanum lycopersicum (tomato) grown in soil amended with an agronomically relevant rate of DWTR-amended biosolids (0.9% w/w, resulting in 0.045% w/w DWTR in the biosolids-amended soil) and (2) mine reclamation scenario examining PFAS uptake by Lolium perenne (perennial ryegrass) grown in soil that received DWTR-amended biosolids amendment at a rate consistent with the mine remediation (13% w/w, resulting in 0.65% w/w DWTR in the biosolids-amended soil). Amending biosolids with Ca-DWTR significantly reduced perfluorobutanoic acid (PFBA) uptake in ryegrass and perfluorohexanoic acid uptake in tomatoes, possibly due to DWTR-induced pH elevation, while Fe-DWTR amendment reduced PFBA bioaccumulation in ryegrass. The Al-DWTR did not induce a significant reduction in accumulated PFAS compared to controls. Although the reasons for this finding are unclear, the relatively low PFAS concentrations in the biosolids and relatively high Al content in the biosolids and soil may be partially responsible.

Trunk-to-leg-volume ratio is not associated with bone density or fracture risk in middle-aged adults: results from the National Health and Nutrition Examination Survey.

Unlike a high body mass index or waist circumference, a high trunk-to-leg-volume ratio does not associate with a lower risk of osteopenia/osteoporosis at the femoral neck. While elevated TLVR showed a suggestive association with a history of wrist fracture in women, additional research is needed to confirm this suggestion. PURPOSE: Body mass index (BMI) and waist circumference (WC) are commonly used to predict bone health, which is typically assessed via bone mineral density (BMD). Trunk-to-leg-volume ratio (TLVR), a relatively novel measure, predicts cardiometabolic outcomes, but its relationships with BMD and fracture remain unstudied. This study evaluated these anthropometric measures' associations with BMD and fracture in Americans aged 40-60 years. METHODS: Analyses of middle-aged adults from the 2013-2014 to 2017-2018 National Health and Nutrition Examination Survey were conducted. Whole-body, dual-energy X-ray absorptiometry was used to quantify TLVR as well as BMD at the lumbar spine, while a femur-specific scan was used to quantify femoral neck BMD. Fracture history was self-reported. Linear and logistic regression models were constructed with age, diabetes, smoking, race/ethnicity, education, and physical activity as confounding variables. RESULTS: TLVR was generally not associated with BMD, while WC and BMI showed positive associations with femoral neck BMD. Odds of osteopenia/osteoporosis at the femoral neck were ~ 65-80% lower among participants in the highest tertile of BMI and WC versus the lowest (p < 0.001). There were no statistically significant associations between anthropometric predictors and fracture. Women in tertiles 2 or 3 of TLVR (p = 0.097 and 0.079, respectively) did have 2.66 times the odds of wrist fracture than women in tertile 1, but this was not significant. CONCLUSION: As shown in previous research, BMI and WC show positive associations with femoral BMD. In contrast, the more novel anthropometric marker TLVR shows no association with femoral BMD, and no clear association with fracture.

Health Challenges in South Dakota: Creation of Healthcare Provider Referral List for Special Olympic Athletes.

INTRODUCTION: Individuals with intellectual and developmental disabilities (IDD) face significant health challenges affecting their overall morbidity and mortality. Special Olympics is one of the largest non-profit organizations that focuses on the promotion of health and fitness for individuals with IDD (referred to as athletes) year-round. At the state level, Special Olympics South Dakota (SOSD) hosts an annual Summer Games where athletes are provided the opportunity to obtain free health screenings. If an area is identified as needing further attention, a referral is made for the athlete to obtain more in-depth care. The referral process often leads to difficulties for athletes, ranging from finding a healthcare provider (HCP) who is comfortable working with individuals with disabilities, to ensuring the acceptance of a wide range of health insurances (such as Medicaid). Obstacles to finding a HCP for a referral is what necessitates the need for a statewide HCP referral list. The purpose of this project is to increase the ease of accessibility to HCPs for individuals with IDD who are Special Olympics South Dakota athletes. METHODS: Data from Special Olympics and the CDC Disability and Health Data System (DHDS) was gathered to compare health outcomes between those with disabilities nationwide to those with disabilities in South Dakota. The referral list obtained HCPs via an online two-part survey. Survey 1 focused on demographic information on HCP and place of practice and Survey 2 focused on HCP training and professional work with those with IDD. The surveys were sent to individual providers via their respective professional state associations as well as through convenience sampling (relationship with Clinical Directors for SOSD). Survey 1 gathered 233 responses total, with 95 meeting completion criteria. Survey 2 offered to those 95 and gathered 66 responses total. RESULTS: Data on multiple health outcomes from the Special Olympics and CDC DHDS revealed individualized areas of concern with little overlap between the two datasets. Of the 95 HCPs added to the referral list (40% completion rate from Survey 1), the majority were localized to areas of higher population density in South Dakota (Sioux Falls and Rapid City areas). In Survey 2, 90% of HCPs indicated some level of training for working with individuals with IDD and 74% of responding HCPs were interested in obtaining further training. All HCPs that responded to Survey 2 had encounters with individuals with IDD in their current professional role, with 94% having 4 or more encounters. CONCLUSIONS: The Special Olympics South Dakota HCP referral list provides a direct method for SOSD athletes to find referral care. Currently, this is the only database of health care providers that is accessible to individuals with IDD that are members of SOSD. Geographically however, much of South Dakota is not represented on the current HCP referral list. While 90% of HCPs have training, 30% indicate not having received formal training on working with individuals with IDD during their professional training, also showcasing a need for HCPs to strive to limit potential gaps in care.

Germline-encoded specificities and the predictability of the B cell response.

Antibodies result from the competition of B cell lineages evolving under selection for improved antigen recognition, a process known as affinity maturation. High-affinity antibodies to pathogens such as HIV, influenza, and SARS-CoV-2 are frequently reported to arise from B cells whose receptors, the precursors to antibodies, are encoded by particular immunoglobulin alleles. This raises the possibility that the presence of particular germline alleles in the B cell repertoire is a major determinant of the quality of the antibody response. Alternatively, initial differences in germline alleles' propensities to form high-affinity receptors might be overcome by chance events during affinity maturation. We first investigate these scenarios in simulations: when germline-encoded fitness differences are large relative to the rate and effect size variation of somatic mutations, the same germline alleles persistently dominate the response of different individuals. In contrast, if germline-encoded advantages can be easily overcome by subsequent mutations, allele usage becomes increasingly divergent over time, a pattern we then observe in mice experimentally infected with influenza virus. We investigated whether affinity maturation might nonetheless strongly select for particular amino acid motifs across diverse genetic backgrounds, but we found no evidence of convergence to similar CDR3 sequences or amino acid substitutions. These results suggest that although germline-encoded specificities can lead to similar immune responses between individuals, diverse evolutionary routes to high affinity limit the genetic predictability of responses to infection and vaccination.

IgG3 subclass antibodies recognize antigenically drifted influenza viruses and SARS-CoV-2 variants through efficient bivalent binding.

The constant domains of antibodies are important for effector functions, but less is known about how they can affect binding and neutralization of viruses. Here, we evaluated a panel of human influenza virus monoclonal antibodies (mAbs) expressed as IgG1, IgG2, or IgG3. We found that many influenza virus-specific mAbs have altered binding and neutralization capacity depending on the IgG subclass encoded and that these differences result from unique bivalency capacities of the subclasses. Importantly, subclass differences in antibody binding and neutralization were greatest when the affinity for the target antigen was reduced through antigenic mismatch. We found that antibodies expressed as IgG3 bound and neutralized antigenically drifted influenza viruses more effectively. We obtained similar results using a panel of SARS-CoV-2-specific mAbs and the antigenically advanced B.1.351 and BA.1 strains of SARS-CoV-2. We found that a licensed therapeutic mAb retained neutralization breadth against SARS-CoV-2 variants when expressed as IgG3, but not IgG1. These data highlight that IgG subclasses are not only important for fine-tuning effector functionality but also for binding and neutralization of antigenically drifted viruses.

Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis.

Primary sclerosing cholangitis (PSC) is an immune-mediated disease of the bile ducts that co-occurs with inflammatory bowel disease (IBD) in almost 90% of cases. Colorectal cancer is a major complication of patients with PSC and IBD, and these patients are at a much greater risk compared to patients with IBD without concomitant PSC. Combining flow cytometry, bulk and single-cell transcriptomics, and T and B cell receptor repertoire analysis of right colon tissue from 65 patients with PSC, 108 patients with IBD and 48 healthy individuals we identified a unique adaptive inflammatory transcriptional signature associated with greater risk and shorter time to dysplasia in patients with PSC. This inflammatory signature is characterized by antigen-driven interleukin-17A (IL-17A)+ forkhead box P3 (FOXP3)+ CD4 T cells that express a pathogenic IL-17 signature, as well as an expansion of IgG-secreting plasma cells. These results suggest that the mechanisms that drive the emergence of dysplasia in PSC and IBD are distinct and provide molecular insights that could guide prevention of colorectal cancer in individuals with PSC.

A hybrid demultiplexing strategy that improves performance and robustness of cell hashing.

Recent advances in single cell RNA sequencing allow users to pool multiple samples and demultiplex in downstream analysis, which greatly increase experimental efficiency and cost-effectiveness. Among all the demultiplexing methods, nucleotide barcode-based cell hashing has gained widespread popularity due to its compatibility and simplicity. Despite these advantages, certain issues of this technic remain to be solved, such as challenges in distinguishing true positive from background, high reagent cost for samples with large cell numbers, and unpredictable false negative and false doublet rates. Here, we propose a hybrid demultiplexing strategy that increases calling accuracy and cell recovery of cell hashing without adding experimental cost. In this approach, we computationally cluster all single cells based on their natural genetic variations and assign donor identity by finding the dominant hashtag in each genotype cluster. This hybrid strategy assigns donor identity to any cell that is identified as singlet by either genotype clustering or cell hashing, which allows us to demultiplex most majority of cells even if only a small fraction of cells are labeled with hashtags. When comparing its performance with cell hashing on multiple real-world datasets, this hybrid approach consistently generates reliable demultiplexing results with increased cell recovery and accuracy.

Proposing the observational-implementation hybrid approach: designing observational research for rapid translation.

We propose the observational-implementation hybrid approach-the incorporation of implementation science methods and measures into observational studies to collect information that would allow researchers to anticipate, estimate, or infer the effects of interventions and implementation strategies. Essentially, we propose that researchers collect implementation data early in the research pipeline, in situations where they might not typically be thinking about implementation science. We describe three broad contextual scenarios through which the observational-implementation hybrid approach would most productively be applied. The first application is for observational cohorts that individually enroll participants-either for existing (to which implementation concepts could be added) or for newly planned studies. The second application is with routinely collected program data, at either the individual or aggregate levels. The third application is to the collection of data from study participants enrolled in an observational cohort study who are also involved in interventions linked to that study (e.g., collecting data about their experiences with those interventions). Examples of relevant implementation data that could be collected as part of observational studies include factors relevant to transportability, participant preferences, and participant/provider perspectives regarding interventions and implementation strategies. The observational-implementation hybrid model provides a practical approach to make the research pipeline more efficient and to decrease the time from observational research to health impact. If this approach is widely adopted, observational and implementation science studies will become more integrated; this will likely lead to new collaborations, will encourage the expansion of epidemiological training, and, we hope, will push both epidemiologists and implementation scientists to increase the public health impact of their work.

Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants.

The rapid evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identified S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) that was derived from an individual previously infected with WT SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrated broad cross-neutralization of all dominant variants, including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1/XBB). Furthermore, S728-1157 protected hamsters against in vivo challenges with WT, Delta, and BA.1 viruses. Structural analysis showed that this antibody targets a class 1/RBS-A epitope in the receptor binding domain via multiple hydrophobic and polar interactions with its heavy chain complementarity determining region 3 (CDR-H3), in addition to common motifs in CDR-H1/CDR-H2 of class 1/RBS-A antibodies. Importantly, this epitope was more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared with diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential and may inform target-driven vaccine designs against future SARS-CoV-2 variants.