Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions.

BACKGROUND: Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F1 hybrids can be produced through artificial spawning. F1 hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences. RESULTS: We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as double crossovers, are extremely low among backcross progenies (progenies of channel catfish female × F1 hybrid male), suggesting that the pericentric inversions interrupt postzygotic recombination or survival of recombinants. Identification of channel catfish- and blue catfish-specific genes, along with expansions of immunoglobulin genes and centromeric Xba elements, provides insights into genomic hallmarks of these species. CONCLUSIONS: We generated high-quality reference genome sequences for both blue catfish and channel catfish and identified major chromosomal inversions on chromosomes 6, 11, and 24. These perimetric inversions were validated by additional sequencing analysis, genetic linkage mapping, and PCR analysis across the inversion junctions. The reference genome sequences, as well as the contrasted chromosomal architecture should provide guidance for the interspecific breeding programs.

Ustekinumab Does Not Increase Risk of Adverse Events: A Meta-Analysis of Randomized Controlled Trials.

GOALS AND BACKGROUND: Ustekinumab (UST) is a monoclonal antibody inhibitor of IL-12/IL-23 approved for the treatment of Crohn's disease (CD) and ulcerative colitis (UC). We conducted a meta-analysis to compare rates of adverse events (AEs) in randomized controlled trials (RCTs) of UST for all indications. STUDY: A systematic search was performed of MEDLINE, Embase, and PubMed databases through November 2019. Study inclusion included RCTs comparing UST to placebo or other biologics in patients aged 18 years or older with a diagnosis of an autoimmune condition. RESULTS: Thirty RCTs with 16,068 patients were included in our analysis. Nine thousand six hundred and twenty-six subjects were included in the UST vs placebo analysis. There was no significant difference in serious or mild/moderate AEs between UST and placebo with an OR of 0.83 (95% CI 0.66, 1.05) and 1.08 (95% CI 0.99, 1.18), respectively, over a median follow-up time of 16 weeks. In a sub-analysis of CD and UC trials, no difference in serious or mild/moderate AEs in UST versus placebo was seen. CONCLUSIONS: UST was not associated with an increase in short-term risk of AEs.

SARS-CoV-2 and Stroke in a New York Healthcare System.

BACKGROUND AND PURPOSE: With the spread of coronavirus disease 2019 (COVID-19) during the current worldwide pandemic, there is mounting evidence that patients affected by the illness may develop clinically significant coagulopathy with thromboembolic complications including ischemic stroke. However, there is limited data on the clinical characteristics, stroke mechanism, and outcomes of patients who have a stroke and COVID-19. METHODS: We conducted a retrospective cohort study of consecutive patients with ischemic stroke who were hospitalized between March 15, 2020, and April 19, 2020, within a major health system in New York, the current global epicenter of the pandemic. We compared the clinical characteristics of stroke patients with a concurrent diagnosis of COVID-19 to stroke patients without COVID-19 (contemporary controls). In addition, we compared patients to a historical cohort of patients with ischemic stroke discharged from our hospital system between March 15, 2019, and April 15, 2019 (historical controls). RESULTS: During the study period in 2020, out of 3556 hospitalized patients with diagnosis of COVID-19 infection, 32 patients (0.9%) had imaging proven ischemic stroke. Cryptogenic stroke was more common in patients with COVID-19 (65.6%) as compared to contemporary controls (30.4%, P=0.003) and historical controls (25.0%, P<0.001). When compared with contemporary controls, COVID-19 positive patients had higher admission National Institutes of Health Stroke Scale score and higher peak D-dimer levels. When compared with historical controls, COVID-19 positive patients were more likely to be younger men with elevated troponin, higher admission National Institutes of Health Stroke Scale score, and higher erythrocyte sedimentation rate. Patients with COVID-19 and stroke had significantly higher mortality than historical and contemporary controls. CONCLUSIONS: We observed a low rate of imaging-confirmed ischemic stroke in hospitalized patients with COVID-19. Most strokes were cryptogenic, possibly related to an acquired hypercoagulability, and mortality was increased. Studies are needed to determine the utility of therapeutic anticoagulation for stroke and other thrombotic event prevention in patients with COVID-19.

On-Site Capabilities of a Mobile Laboratory for Aquatic Germplasm Cryopreservation.

Cryopreservation of genetic material can become an important tool for user groups in imperiled fishes, wild fisheries, aquaculture, and biomedical research. Persistent challenges within aquatic species cryopreservation are standardization and reliable collection of diverse, high quality samples. The overall goal of this study was to work with different user groups and cryopreserve sperm on-site at their facilities to evaluate the uses and challenges of a mobile laboratory with high-throughput and quality control capabilities comparable to those of a specialized centralized facility. The objectives were to demonstrate collection and cryopreservation of sperm of: 1) large-bodied freshwater Blue Catfish (Ictalurus furcatus) for aquaculture; 2) small-bodied freshwater Xiphophorus for biomedical and imperiled repository development, and 3) saltwater Red Snapper (Lutjanus campechanus) for wild fisheries research. Over the course of this project, the mobile laboratory traveled more than 4,000 km collecting germplasm from more than 650 male fishes. A total of 136 Blue Catfish were processed in 2015 and 2016 resulting in a total of 6,146 0.5-mL French straws. A total of 521 males from 11 different species in the genus Xiphophorus were processed over 4 d in 2015 resulting in a total of 488 0.25-mL French straws. And, a total of 17 Red Snapper males were processed during 2015 resulting in a total of 316 0.5-mL French straws. This is the first development of a mobile laboratory with high-throughput capability for aquatic species. User groups would no longer be limited to germplasm resources that can only be shipped as samples or transported as live animals to a central cryopreservation facility. Mobile laboratories create opportunities to collect higher quality germplasm, provide access to new species, and enable direct cooperation, including training, with a wide variety of user groups and applications.

Development of genomic predictions for harvest and carcass weight in channel catfish.

BACKGROUND: Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate the use of genomic selection to improve breeding value accuracy and to identify major single nucleotide polymorphisms (SNPs) associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n = 27,160) and residual carcass weight (n = 6020), and 36,365 pedigree records were available. After quality control, genotypes for 54,837 SNPs were available for 2911 fish. Estimated breeding values (EBV) were obtained with traditional pedigree-based best linear unbiased prediction (BLUP) and genomic (G)EBV were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. RESULTS: Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and the results indicated that genomic information reduced breeding value inflation. Genome-wide association studies based on windows of 20 adjacent SNPs indicated that both harvest weight and residual carcass weight have a polygenic architecture with no major SNPs (the largest SNPs explained 0.96 and 1.19% of the additive genetic variation for harvest weight and residual carcass weight respectively). CONCLUSIONS: Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families.

Testing and Treating Small Intestinal Bacterial Overgrowth Reduces Symptoms in Patients with Inflammatory Bowel Disease.

BACKGROUND: Common mechanisms against small intestinal bacterial overgrowth (SIBO), including an intact ileocecal valve, gastric acid secretion, intestinal motility, and an intact immune system, are compromised in inflammatory bowel disease (IBD), and therefore, a relatively high incidence of SIBO has been reported in this population. AIMS: We aimed to determine whether an improvement in IBD clinical activity scores is seen after testing and treating SIBO. METHODS: A retrospective cohort study of 147 patients with inflammatory bowel disease who were referred for SIBO breath testing from 1/2012 to 5/2016 was performed. Characteristics of SIBO positive and treated patients were compared to SIBO negative patients, including the changes in Partial Mayo Score or Harvey Bradshaw Index (HBI), using Student's t test for continuous variables and Chi-squared or Fisher's exact test for categorical variables. RESULTS: 61.9% were SIBO positive and treated, and 38.1% were SIBO negative. In Crohn's disease, the median HBI decreased from 5 to 3 and 5 to 4, in the SIBO positive and negative groups, respectively (p = 0.005). In ulcerative colitis, the Partial Mayo Score decreased from 2 to 1.5 and 2 to 1, respectively (p = 0.607). CONCLUSIONS: This study examines the clinical effect of testing and treating for SIBO in an IBD population. We see a significant reduction in HBI after testing for and treating SIBO. Future prospective studies are necessary to further investigate the role of SIBO in the evaluation and management of IBD.

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

Budesonide foam induces remission in patients with mild to moderate ulcerative proctitis and ulcerative proctosigmoiditis.

BACKGROUND & AIMS: Budesonide is a high-potency, second-generation corticosteroid designed to minimize systemic adverse consequences of conventional corticosteroids. We performed 2 randomized, phase 3 trials to evaluate the ability of budesonide rectal foam, formulated to optimize retention and provide uniform delivery of budesonide to the rectum and distal colon, to induce remission in patients with ulcerative proctitis or ulcerative proctosigmoiditis. METHODS: Two identically designed, randomized, double-blind, placebo-controlled trials evaluated the efficacy of budesonide foam for induction of remission in 546 patients with mild to moderate ulcerative proctitis or ulcerative proctosigmoiditis who received budesonide foam 2 mg/25 mL twice daily for 2 weeks, then once daily for 4 weeks, or placebo. RESULTS: Remission at week 6 occurred significantly more frequently among patients receiving budesonide foam than placebo (Study 1: 38.3% vs 25.8%; P = .0324; Study 2: 44.0% vs 22.4%; P < .0001). A significantly greater percentage of patients receiving budesonide foam vs placebo achieved rectal bleeding resolution (Study 1: 46.6% vs 28.0%; P = .0022; Study 2: 50.0% vs 28.6%; P = .0002) and endoscopic improvement (Study 1: 55.6% vs 43.2%; P = .0486; Study 2: 56.0% vs 36.7%; P = .0013) at week 6. Most adverse events occurred at similar frequencies between groups, although events related to changes in cortisol values were reported more frequently with budesonide foam. There were no cases of clinically symptomatic adrenal insufficiency. CONCLUSIONS: Budesonide rectal foam was well tolerated and more efficacious than placebo in inducing remission in patients with mild to moderate ulcerative proctitis and ulcerative proctosigmoiditis. ClinicalTrials.gov ID: NCT01008410 and NCT01008423.

Risk of New or Recurrent Cancer in Patients With Inflammatory Bowel Disease and Previous Cancer Exposed to Immunosuppressive and Anti-Tumor Necrosis Factor Agents.

BACKGROUND & AIMS: Our understanding of malignancy associated with immunosuppression in patients with inflammatory bowel disease (IBD) comes from studies of individuals with no history of cancer. We investigated whether patients with IBD and a history of cancer who were subsequently immunosuppressed have an increased risk of developing incident cancer. METHODS: We performed a retrospective analysis of data from 333 patients with IBD treated at 8 academic medical centers who developed cancer and subsequently received treatment with anti-tumor necrosis factor (TNF), anti-TNF with an antimetabolite (thiopurines, methotrexate), antimetabolites, or no subsequent exposure to immunosuppressive agents (controls). We collected data on their primary outcomes of incident cancers (new or recurrent). Hazard ratios (HRs) were calculated by using Cox proportional hazards and Kaplan-Meier survival curves; study groups were compared by using the log-rank test. RESULTS: During the follow-up period, 90 patients (27%) developed an incident cancer. Patient characteristics between groups differed, but matching was not possible because of the relatively small sample sizes. There was no difference in time to incident cancer (P = .14) or type of incident cancer (P = .61) among the 4 groups. After adjusting for recurrence risk for type of prior cancer, there was no difference in risk of incident cancer (HR for anti-TNF, 0.32; 95% confidence interval [CI], 0.09-1.09; HR for anti-TNF with an antimetabolite, 0.64; 95% CI, 0.26-1.59; HR for an antimetabolite, 1.08; 95% CI, 0.54-2.15) or time to subsequent cancer between study arms (P = .22). CONCLUSION: On the basis of a retrospective study, in patients with IBD and a history of cancer, exposure to an anti-TNF agent or an antimetabolite after cancer was not associated with an increased risk of incident cancer, compared with patients who did not receive immunosuppression. Larger, matched, prospective studies are needed to confirm these findings.

Id1 expression in endothelial cells of the colon is required for normal response to injury.

Inhibitor of DNA binding (ID)-1 is important for angiogenesis during embryogenesis and tumor development. Whether ID1 expression in endothelial cells of the colon is required for normal response to injury is unknown. We demonstrate that Id1 is up-regulated in colonic endothelial cells in an experimental model of colitis and in the inflamed mucosa of patients with inflammatory bowel disease. Because prostaglandin E2 and tumor necrosis factor-α are also elevated in colitis, we determined whether these factors could induce ID1 transcription in cultured endothelial cells. Tumor necrosis factor-α stimulated ID1 transcription via early growth response 1 protein (Egr-1). By contrast, the induction of ID1 by prostaglandin E2 was mediated by cAMP response element-binding protein (CREB). To determine whether the increased ID1 levels in the endothelial cells of inflamed mucosa were an adaptive response that modulated the severity of tissue injury, Id1 was conditionally depleted in the endothelium of mice, which sensitized the mice to more severe chemical colitis, including more severe diarrhea, bleeding, and histological injury, and shorter colon compared with control mice. Moreover, depletion of Id1 in the vasculature was associated with increased CD31(+) aggregates and increased vascular permeability in inflamed mucosa compared with those in Id1 wild-type control mice. These results suggest that endothelial ID1 up-regulation in inflamed colonic mucosa is an adaptive response that modulates the severity of tissue injury.

Exercise and Self-Reported Limitations in Patients with Inflammatory Bowel Disease.

BACKGROUND: Limited evidence suggests that exercise may have beneficial, anti-inflammatory effects in patients with inflammatory bowel disease (IBD). AIMS: The purpose of this study was to evaluate the prevalence of exercise in patients with IBD and the limitations they experience secondary to their disease. METHODS: Two hundred and fifty IBD patients were prospectively enrolled in this study at an academic medical center at the time of their outpatient visits between March and October 2013. Subjects were asked to complete a one-time survey that asks questions about medical and surgical history, exercise frequency and intensity, and the limitations and barriers they experience. RESULTS: Two hundred and twenty-seven patients (148 female patients) completed the survey. Crohn's disease was present in 140 patients (61.5 %), while 87 had ulcerative colitis. Forty-one patients (16.4 %) never exercised, 82 patients (32.8 %) exercised 1-2 times per week, 59 (23.6 %) exercised 3-4 times per week, and 45 (18.0 %) exercised more than four times per week. Of the 186 who regularly exercise, 95 (51 %) reported moderate exercise intensity, 61 (33 %) reported light intensity, and 30 (16 %) reported vigorous intensity. Ninety-nine patients (44 %) reported that their IBD limited their exercise for reasons including fatigue (n = 81), joint pain (n = 37), embarrassment (n = 23), weakness (n = 21), and others. CONCLUSIONS: Although they may benefit from exercise, IBD patients experience considerable barriers to regular exercise secondary to the relapsing and remitting nature of IBD. Larger studies are needed to determine the effects of exercise on disease symptomatology and activity.

Segmental liver ischemia/infarction after elective transjugular intrahepatic portosystemic shunt creation: clinical outcomes in 10 patients.

PURPOSE: To determine the clinical significance and potential mechanisms of segmental liver ischemia and infarction following elective creation of a transjugular intrahepatic portosystemic shunt (TIPS). MATERIALS AND METHODS: A retrospective review of 374 elective TIPS creations between March 2006 and September 2014 was performed, yielding 77 contrast-enhanced scans for review. Patients with imaging evidence of segmental perfusion defects were identified. Model for End-stage Liver Disease scores, liver volume, and percentage of liver ischemia/infarct were calculated. Clinical outcomes after TIPS creation were reviewed. RESULTS: Ten patients showed segmental liver ischemia/infarction on contrast-enhanced imaging after elective TIPS creation. Associated imaging findings included thrombosis of the posterior division (n = 7) and anterior division (n = 3) of the right portal vein (PV). The right hepatic vein was thrombosed in 5 patients, as was the middle hepatic vein in 3 and the left hepatic vein in 1. One patient had acute thrombosis of the shunt and main PV. Three patients developed acute liver failure: 2 died within 30 days and 1 required emergent liver transplantation. One patient died of acute renal failure 20 days after TIPS creation. A large infarct in a transplant recipient resulted in biloma formation. Five patients survived without additional interventions with follow-up times ranging from 3 months to 5 years. CONCLUSIONS: Segmental perfusion defects are not an uncommon imaging finding after elective TIPS creation. Segmental ischemia was associated with thrombosis of major branches of the PVs and often of the hepatic veins. Clinical outcomes varied significantly, from transient problems to acute liver failure with high mortality rates.

Budesonide Foam Has a Favorable Safety Profile for Inducing Remission in Mild-to-Moderate Ulcerative Proctitis or Proctosigmoiditis.

BACKGROUND: Budesonide foam, a rectally administered, second-generation corticosteroid with extensive hepatic first-pass metabolism, is efficacious for the treatment of mild-to-moderate ulcerative proctitis and ulcerative proctosigmoiditis. AIM: The aim of this study was to comprehensively assess the safety and pharmacokinetic profile of budesonide foam. METHODS: Data from five phase III studies were pooled to further evaluate safety, including an open-label study (once-daily treatment for 8 weeks), an active-comparator study (once-daily treatment for 4 weeks), and two placebo-controlled studies and an open-label extension study (twice-daily treatment for 2 weeks, then once daily for 4 weeks). Data from the placebo-controlled studies and two phase I studies (i.e., patients with mild-to-moderate ulcerative colitis and healthy volunteers) were pooled to evaluate the pharmacokinetics of budesonide foam. RESULTS: A similar percentage of patients reported adverse events in the budesonide foam and placebo groups, with the majority of adverse events being mild or moderate in intensity (93.3 vs 96.0%, respectively). Adverse events occurred in 41.4 and 36.3% of patients receiving budesonide foam and placebo, respectively. Mean morning cortisol concentrations remained within the normal range for up to 8 weeks of treatment; there were no clinically relevant effects of budesonide foam on the hypothalamic-pituitary-adrenal axis. Population pharmacokinetic analysis demonstrated low systemic exposure after budesonide foam administration. CONCLUSIONS: This integrated analysis demonstrated that budesonide foam for the induction of remission of distal ulcerative colitis is safe overall, with no clinically relevant effects on the hypothalamic-pituitary-adrenal axis.

S1P1 localizes to the colonic vasculature in ulcerative colitis and maintains blood vessel integrity.

Signaling through sphingosine-1-phosphate receptor1 (S1P1) promotes blood vessel barrier function. Degradation of S1P1 results in increased vascular permeability in the lung and may explain side effects associated with administration of FTY720, a functional antagonist of the S1P1 receptor that is currently used to treat multiple sclerosis. Ulcerative colitis (UC) is characterized by an increased density of abnormal vessels. The expression or role of S1P1 in blood vessels in the colon has not been investigated. In the present study, we show that S1P1 is overexpressed in the colonic mucosa of UC patients. This increase in S1P1 levels reflects increased vascular density in the inflamed mucosa. Genetic deletion of S1pr1 in mice increases colonic vascular permeability under basal conditions and increases bleeding in experimental colitis. In contrast, neither FTY720 nor AUY954, two S1P receptor-targeting agents, increases bleeding in experimental colitis. Taken together, our findings demonstrate that S1P1 is critical to maintaining colonic vascular integrity and may play a role in UC pathogenesis.

Rifaximin resistance in Escherichia coli associated with inflammatory bowel disease correlates with prior rifaximin use, mutations in rpoB, and activity of Phe-Arg-ß-naphthylamide-inhibitable efflux pumps.

Escherichia coli is implicated in the pathogenesis of inflammatory bowel disease (IBD). Rifaximin, a nonabsorbable derivative of rifampin effective against E. coli, improves symptoms in mild-to-moderate IBD. However, rifaximin resistance can develop in a single step in vitro. We examined the prevalence and mechanisms of rifaximin resistance in 62 strains of E. coli isolated from the ileal mucosa of 50 patients (19 with ileal Crohn's disease [L1+L3], 6 with colonic Crohn's disease [L2], 13 with ulcerative colitis [UC], 4 with symptomatic non-IBD diagnoses [NI], and 8 healthy [H]). Resistance (MIC > 1,024 mg/liter) was present in 12/48 IBD-associated ileal E. coli strains. Resistance correlated with prior rifaximin treatment (P < 0.00000001) but not with the presence of ileal inflammation (P = 0.73) or E. coli phylogroup. Mutations in a 1,057-bp region of rpoB, which encodes the bacterial target of rifaximin, were identified in 10/12 resistant strains versus 0/50 sensitive strains (P < 0.000000001) and consisted of seven amino acid substitutions. The efflux pump inhibitor Phe-Arg-ß-naphthylamide (PAßN) lowered the MIC of 9/12 resistant strains 8- to 128-fold. Resistance was stable in the absence of rifaximin in 10/12 resistant strains after 30 passages. We conclude that IBD-associated ileal E. coli frequently manifest resistance to rifaximin that correlates with prior rifaximin use, amino acid substitutions in rpoB, and activity of PAßN-inhibitable efflux pumps, but not with the presence of ileal inflammation or E. coli phylogroup. These findings have significant implications for treatment trials targeting IBD-associated E. coli.

Low prevalence of coeliac disease in patients with systemic sclerosis: a cross-sectional study of a registry cohort.

OBJECTIVES: Two prior studies suggested that coeliac disease (CD) has a higher prevalence rate (8%) in SSc than in the general population (1%), but these studies were limited by small numbers and the use of traditional coeliac screening antibody tests, where newer ones with improved accuracy have since emerged. Our aim was to determine the prevalence of CD in a larger SSc population using a more modern serological approach to coeliac testing and to correlate coeliac antibody status with gastrointestinal symptoms. METHODS: Stored sera from 72 SSc patients in the Scleroderma Registry at the Hospital for Special Surgery were tested for anti-tissue transglutaminase (traditional) and anti-deamidated gliadin peptide (novel) antibodies. If any of these antibodies were positive, anti-endomysial antibodies were tested and confirmatory small-bowel endoscopy and biopsy were obtained. Registry clinical data were used to determine whether antibody status correlated with gastrointestinal symptoms. RESULTS: The prevalence of coeliac antibodies in our SSc population was 3/72 (4%). No significant differences with respect to gastrointestinal symptoms were seen in the coeliac antibody-positive compared with -negative SSc patients. No cases of confirmed CD were seen in our cohort. CONCLUSION: Contrary to the only two previously published studies, the low prevalence of CD that we found does not suggest that concurrent CD is a common cause of gastrointestinal complaints in SSc patients.

Novel Note Templates to Enhance Signal and Reduce Noise in Medical Documentation: Prospective Improvement Study.

BACKGROUND: The introduction of electronic workflows has allowed for the flow of raw uncontextualized clinical data into medical documentation. As a result, many electronic notes have become replete of "noise" and deplete clinically significant "signals." There is an urgent need to develop and implement innovative approaches in electronic clinical documentation that improve note quality and reduce unnecessary bloating. OBJECTIVE: This study aims to describe the development and impact of a novel set of templates designed to change the flow of information in medical documentation. METHODS: This is a multihospital nonrandomized prospective improvement study conducted on the inpatient general internal medicine service across 3 hospital campuses at the New York University Langone Health System. A group of physician leaders representing each campus met biweekly for 6 months. The output of these meetings included (1) a conceptualization of the note bloat problem as a dysfunction in information flow, (2) a set of guiding principles for organizational documentation improvement, (3) the design and build of novel electronic templates that reduced the flow of extraneous information into provider notes by providing link outs to best practice data visualizations, and (4) a documentation improvement curriculum for inpatient medicine providers. Prior to go-live, pragmatic usability testing was performed with the new progress note template, and the overall user experience was measured using the System Usability Scale (SUS). Primary outcome measures after go-live include template utilization rate and note length in characters. RESULTS: In usability testing among 22 medicine providers, the new progress note template averaged a usability score of 90.6 out of 100 on the SUS. A total of 77% (17/22) of providers strongly agreed that the new template was easy to use, and 64% (14/22) strongly agreed that they would like to use the template frequently. In the 3 months after template implementation, general internal medicine providers wrote 67% (51,431/76,647) of all inpatient notes with the new templates. During this period, the organization saw a 46% (2768/6191), 47% (3505/7819), and 32% (3427/11,226) reduction in note length for general medicine progress notes, consults, and history and physical notes, respectively, when compared to a baseline measurement period prior to interventions. CONCLUSIONS: A bundled intervention that included the deployment of novel templates for inpatient general medicine providers significantly reduced average note length on the clinical service. Templates designed to reduce the flow of extraneous information into provider notes performed well during usability testing, and these templates were rapidly adopted across all hospital campuses. Further research is needed to assess the impact of novel templates on note quality, provider efficiency, and patient outcomes.

The impact of COVID-19 monoclonal antibodies on clinical outcomes: A retrospective cohort study.

PURPOSE: Despite progress in the treatment of coronavirus disease 2019 (COVID-19), including the development of monoclonal antibodies (mAbs), more clinical data to support the use of mAbs in outpatients with COVID-19 is needed. This study is designed to determine the impact of bamlanivimab, bamlanivimab/etesevimab, or casirivimab/imdevimab on clinical outcomes within 30 days of COVID-19 diagnosis. METHODS: A retrospective cohort study was conducted at a single academic medical center with 3 campuses in Manhattan, Brooklyn, and Long Island, NY. Patients 12 years of age or older who tested positive for COVID-19 or were treated with a COVID-19-specific therapy, including COVID-19 mAb therapies, at the study site between November 24, 2020, and May 15, 2021, were included. The primary outcomes included rates of emergency department (ED) visit, inpatient admission, intensive care unit (ICU) admission, or death within 30 days from the date of COVID-19 diagnosis. RESULTS: A total of 1,344 mAb-treated patients were propensity matched to 1,344 patients with COVID-19 patients who were not treated with mAb therapy. Within 30 days of diagnosis, among the patients who received mAb therapy, 101 (7.5%) presented to the ED and 79 (5.9%) were admitted. Among the patients who did not receive mAb therapy, 165 (12.3%) presented to the ED and 156 (11.6%) were admitted (relative risk [RR], 0.61 [95% CI, 0.50-0.75] and 0.51 [95% CI, 0.40-0.64], respectively). Four mAb patients (0.3%) and 2.64 control patients (0.2%) were admitted to the ICU (RR, 01.51; 95% CI, 0.45-5.09). Six mAb-treated patients (0.4%) and 3.37 controls (0.3%) died and/or were admitted to hospice (RR, 1.61; 95% CI, 0.54-4.83). mAb therapy in ambulatory patients with COVID-19 decreases the risk of ED presentation and hospital admission within 30 days of diagnosis.