The RNase PARN Controls the Levels of Specific miRNAs that Contribute to p53 Regulation.

PARN loss-of-function mutations cause a severe form of the hereditary disease dyskeratosis congenita (DC). PARN deficiency affects the stability of non-coding RNAs such as human telomerase RNA (hTR), but these effects do not explain the severe disease in patients. We demonstrate that PARN deficiency affects the levels of numerous miRNAs in human cells. PARN regulates miRNA levels by stabilizing either mature or precursor miRNAs by removing oligo(A) tails added by the poly(A) polymerase PAPD5, which if remaining recruit the exonuclease DIS3L or DIS3L2 to degrade the miRNA. PARN knockdown destabilizes multiple miRNAs that repress p53 translation, which leads to an increase in p53 accumulation in a Dicer-dependent manner, thus explaining why PARN-defective patients show p53 accumulation. This work also reveals that DIS3L and DIS3L2 are critical 3' to 5' exonucleases that regulate miRNA stability, with the addition and removal of 3' end extensions controlling miRNA levels in the cell.

Sorafenib plus intensive chemotherapy in newly diagnosed FLT3-ITD AML: a randomized, placebo-controlled study by the ALLG.

Sorafenib maintenance improves outcomes after hematopoietic cell transplant (HCT) for patients with FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) acute myeloid leukemia (AML). Although promising outcomes have been reported for sorafenib plus intensive chemotherapy, randomized data are limited. This placebo-controlled, phase 2 study (ACTRN12611001112954) randomized 102 patients (aged 18-65 years) 2:1 to sorafenib vs placebo (days 4-10) combined with intensive induction: idarubicin 12 mg/m2 on days 1 to 3 plus either cytarabine 1.5 g/m2 twice daily on days 1, 3, 5, and 7 (18-55 years) or 100 mg/m2 on days 1 to 7 (56-65 years), followed by consolidation and maintenance therapy for 12 months (post-HCT excluded) in newly diagnosed patients with FLT3-ITD AML. Four patients were excluded in a modified intention-to-treat final analysis (3 not commencing therapy and 1 was FLT3-ITD negative). Rates of complete remission (CR)/CR with incomplete hematologic recovery were high in both arms (sorafenib, 78%/9%; placebo, 70%/24%). With 49.1-months median follow-up, the primary end point of event-free survival (EFS) was not improved by sorafenib (2-year EFS 47.9% vs 45.4%; hazard ratio [HR], 0.87; 95% confidence interval [CI], 0.51-1.51; P = .61). Two-year overall survival (OS) was 67% in the sorafenib arm and 58% in the placebo arm (HR, 0.76; 95% CI, 0.42-1.39). For patients who received HCT in first remission, the 2-year OS rates were 84% and 67% in the sorafenib and placebo arms, respectively (HR, 0.45; 95% CI, 0.18-1.12; P = .08). In exploratory analyses, FLT3-ITD measurable residual disease (MRD) negative status (<0.001%) after induction was associated with improved 2-year OS (83% vs 60%; HR, 0.4; 95% CI, 0.17-0.93; P = .028). In conclusion, routine use of pretransplant sorafenib plus chemotherapy in unselected patients with FLT3-ITD AML is not supported by this study.

LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control.

Compositional analysis is based on the premise that a relatively small proportion of taxa are differentially abundant, while the ratios of the relative abundances of the remaining taxa remain unchanged. Most existing methods use log-transformed data, but log-transformation of data with pervasive zero counts is problematic, and these methods cannot always control the false discovery rate (FDR). Further, high-throughput microbiome data such as 16S amplicon or metagenomic sequencing are subject to experimental biases that are introduced in every step of the experimental workflow. McLaren et al. [eLife 8, e46923 (2019)] have recently proposed a model for how these biases affect relative abundance data. Motivated by this model, we show that the odds ratios in a logistic regression comparing counts in two taxa are invariant to experimental biases. With this motivation, we propose logistic compositional analysis (LOCOM), a robust logistic regression approach to compositional analysis, that does not require pseudocounts. Inference is based on permutation to account for overdispersion and small sample sizes. Traits can be either binary or continuous, and adjustment for confounders is supported. Our simulations indicate that LOCOM always preserved FDR and had much improved sensitivity over existing methods. In contrast, analysis of composition of microbiomes (ANCOM) and ANCOM with bias correction (ANCOM-BC)/ANOVA-Like Differential Expression tool (ALDEx2) had inflated FDR when the effect sizes were small and large, respectively. Only LOCOM was robust to experimental biases in every situation. The flexibility of our method for a variety of microbiome studies is illustrated by the analysis of data from two microbiome studies. Our R package LOCOM is publicly available.

Compositional analysis of microbiome data using the linear decomposition model (LDM).

SUMMARY: There are compelling reasons to test compositional hypotheses about microbiome data. We present here linear decomposition model-centered log ratio (LDM-clr), an extension of our LDM approach to allow fitting linear models to centered-log-ratio-transformed taxa count data. As LDM-clr is implemented within the existing LDM program, this extension enjoys all the features supported by LDM, including a compositional analysis of differential abundance at both the taxon and community levels, while allowing for a wide range of covariates and study designs for either association or mediation analysis. AVAILABILITY AND IMPLEMENTATION: LDM-clr has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.

Expert Consensus on Pediatric Urodynamics Reporting Using Modified Delphi Technique.

PURPOSE: Urodynamic testing (UDS) is an important tool in the management of pediatric lower urinary tract conditions. There have been notable efforts to standardize pediatric UDS nomenclature and technique, but no formal guidelines exist on essential elements to include in a clinical report. We sought to identify ideal structure and elements of a pediatric UDS assessment based on expert consensus. MATERIALS AND METHODS: Pediatric urologists regularly performing UDS were queried using a Delphi process. Participants were invited representing varied geographic, experience, and societal involvement. Participants underwent 3 rounds of questionnaires between November 2022 and August 2023 focusing on report organization, elements, definitions, and automated electronic health record clinical decision support. Professional billing requirements were also considered. Consensus was defined as 80% agreeing either in favor of or against a topic. Elements without consensus were discussed in subsequent rounds. RESULTS: A diverse sample of 30 providers, representing 27 institutions across 21 US states; Washington, District of Columbia; and Canada completed the study. Participants reported interpreting an average number of 5 UDS reports per week (range 1-22). The finalized consensus report identifies 93 elements that should be included in a pediatric UDS report based on applicable study conditions and findings. CONCLUSIONS: This consensus report details the key elements and structure agreed upon by an expert panel of pediatric urologists. Further standardization of documentation should aid collaboration and research for patients undergoing UDS. Based on this information, development of a standardized UDS report template using electronic health record implementation principles is underway, which will be openly available for pediatric urologists.

Clinical grade multiparametric cell sorting and gene-marking of regulatory T cells.

BACKGROUND AIMS: Regulatory T cells (Tregs) are the main mediators of peripheral tolerance. Treg-directed therapy has shown promising results in preclinical studies of diverse immunopathologies. At present, the clinical applicability of adoptive Treg transfer is limited by difficulties in generating Tregs at sufficient cell dose and purity. METHODS: We developed a Good Manufacturing Practice (GMP) compliant method based on closed-system multiparametric Fluorescence-Activated Cell Sorting (FACS) to purify Tregs, which are then expanded in vitro and gene-marked with a clinical grade retroviral vector to enable in vivo fate tracking. Following small-scale optimization, we conducted four clinical-scale processing runs. RESULTS: We showed that Tregs could be enriched to 87- 92% purity following FACS-sorting, and expanded and transduced to yield clinically relevant cell dose of 136-732×106 gene-marked cells, sufficient for a cell dose of at least 2 × 106 cells/kg. The expanded Tregs were highly demethylated in the FOXP3 Treg-specific demethylated region (TSDR), consistent with bona fide natural Tregs. They were suppressive in vitro, but a small percentage could secrete proinflammatory cytokines, including interferon-γ and interleukin-17A. CONCLUSIONS: This study demonstrated the feasibility of isolating, expanding and gene-marking Tregs in clinical scale, thus paving the way for future phase I trials that will advance knowledge about the in vivo fate of transferred Tregs and its relationship with concomitant Treg-directed pharmacotherapy and clinical response.

MERIT: Controlling Monte-Carlo error rate in large-scale Monte-Carlo hypothesis testing.

The use of Monte-Carlo (MC) p $$ p $$ -values when testing the significance of a large number of hypotheses is now commonplace. In large-scale hypothesis testing, we will typically encounter at least some p $$ p $$ -values near the threshold of significance, which require a larger number of MC replicates than p $$ p $$ -values that are far from the threshold. As a result, some incorrect conclusions can be reached due to MC error alone; for hypotheses near the threshold, even a very large number (eg, 1 0 6 $$ 1{0}^6 $$ ) of MC replicates may not be enough to guarantee conclusions reached using MC p $$ p $$ -values. Gandy and Hahn (GH)6-8 have developed the only method that directly addresses this problem. They defined a Monte-Carlo error rate (MCER) to be the probability that any decisions on accepting or rejecting a hypothesis based on MC p $$ p $$ -values are different from decisions based on ideal p $$ p $$ -values; their method then makes decisions by controlling the MCER. Unfortunately, the GH method is frequently very conservative, often making no rejections at all and leaving a large number of hypotheses "undecided". In this article, we propose MERIT, a method for large-scale MC hypothesis testing that also controls the MCER but is more statistically efficient than the GH method. Through extensive simulation studies, we demonstrate that MERIT controls the MCER while making more decisions that agree with the ideal p $$ p $$ -values than GH does. We also illustrate our method by an analysis of gene expression data from a prostate cancer study.

Applying the antecedent, behaviour, and consequence taxonomy to unintentional firearm injury as determined by a collaborative firearm injury database.

BACKGROUND: Unintentional firearm injury (UFI) remains a significant problem in the USA with respect to preventable injury and death. The antecedent, behaviour and consequence (ABC) taxonomy has been used by law enforcement agencies to evaluate unintentional firearm discharge. Using an adapted ABC taxonomy, we sought to categorise civilian UFI in our community to identify modifiable behaviours. METHODS: Using a collaborative firearm injury database (containing both a university-based level 1 trauma registry and a metropolitan law enforcement database), all UFIs from August 2008 through December 2021 were identified. Perceived threat (antecedent), behaviour and injured party (consequence) were identified for each incident. RESULTS: During the study period, 937 incidents of UFI were identified with 64.2% of incidents occurring during routine firearm tasks. 30.4% of UFI occurred during neglectful firearm behaviour such as inappropriate storage. Most injuries occurred under situations of low perceived threat. UFI involving children was most often due to inappropriate storage of weapons, while cleaning a firearm was the most common behaviour in adults. Overall, 16.5% of UFI involved injury to persons other than the one handling the weapon and approximately 1.3% of UFI resulted in mortality. CONCLUSIONS: The majority of UFI occurred during routine and expected firearm tasks such as firearm cleaning. Prevention programmes should not overlook these modifiable behaviours in an effort to reduce UFIs, complications and deaths.

Nursing and allied health workforce in Australian public rheumatology departments is inadequate: a cross-sectional observational study.

Rheumatological conditions are complex and impact many facets of daily life. Management of people with rheumatological conditions can be optimised through multidisciplinary care. However, the current access to nursing and allied health professionals in Australia is unknown. A cross-sectional study of nursing and allied health professionals in Australian public rheumatology departments for adult and paediatric services was conducted. The heads of Australian public rheumatology departments were invited to report the health professionals working within their departments, referral pathways, and barriers to greater multidisciplinary care. A total of 27/39 (69.2%) of the hospitals responded. The most common health professionals within departments were nurses (n = 23; 85.2%) and physiotherapists (n = 10; 37.0%), followed by pharmacists (n = 5; 18.5%), psychologists (n = 4; 14.8%), and occupational therapists (n = 4; 14.8%). No podiatrists were employed within departments. Referral pathways were most common for physiotherapy (n = 20; 74.1%), followed by occupational therapy (n = 15; 55.5%), podiatry (n = 13; 48.1%), and psychology (n = 6; 22%). The mean full-time equivalent of nursing and allied health professionals per 100,000 population in Australia was 0.29. Funding was identified as the most common barrier. In Australia, publicly funded multidisciplinary care from nurses and allied health professionals in rheumatology departments is approximately 1.5 days per week on average. This level of multidisciplinary care is unlikely to meet the needs of rheumatology patients. Research is needed to determine the minimum staffing requirements of nursing and allied health professionals to provide optimal care.

Building and maintaining interprofessional collaborative practice in eyecare: Learnings from the Queensland Paediatric Optometry Alignment Program.

PURPOSE: The Queensland Children's Hospital Paediatric Optometry Alignment Program commenced with a pilot phase to assess its feasibility, effectiveness and acceptability. This study identified the barriers that hinder effective interprofessional collaboration and the facilitators that contribute to its success, and assessed changes in optometrists' satisfaction since the pilot phase of the collaborative care programme. METHODS: Qualitative deductive and inductive content analysis was applied to open-ended free-text survey responses collected in 2018 from the optometrists involved in the Program's pilot phase. The responses were coded using the Theoretical Domains Framework (TDF) to categorise barriers and facilitators into key themes. Key behavioural determinants were mapped to the COM-B (Capability, Opportunity, Motivation-Behaviour) elements of the Behaviour Change Wheel model to identify intervention strategies. Intervention recommendations were derived from behaviour change mapping and compared with programme quality improvement initiatives. A cross-sectional explanatory survey informed by the TDF was conducted within the current 2023 cohort, and a longitudinal comparative analysis was carried out using data from the 2018 survey. RESULTS: Among the 97 surveys distributed in 2018, 44 respondents participated; from this group, 38 individuals contributed a total of 200 free-text responses. Facilitators (240 comments) outnumbered barriers (65 comments). Key facilitators were accessible and timely care, professional development, confidence and positive outcome beliefs. Barriers included communication, information handover, credibility, relationships and skill gaps. Optometrists actively engaged in the programme in 2023 reported heightened satisfaction with their involvement, increased confidence and greater engagement in paediatric eyecare delivery. However, challenges in clinical information transfer persist. CONCLUSION: The interprofessional collaborative model of paediatric eyecare has contributed efficiencies within the health system by building paediatric care capacity in the community, fostering professional credibility and promoting interdisciplinary trust. Insights gained should prove valuable for other paediatric eyecare services exploring hospital-to-community care models.

Carbohydrates and protein digestive traits in beef cattle grazing fertilised or mixed tropical pasture.

This study was performed to investigate the nitrogen (N) and carbohydrate digestive traits of grazing heifers. The experiment was carried out at the Federal University of Lavras. The treatments were a Marandu palisadegrass (Urochloa brizantha [Syn, Brachiaria brizantha] Stapf. A. Rich. cv. Marandu) monoculture fertilised with 150 kg N/[ha ∙ year] (FP) or Marandu palisadegrass mixed pasture with forage peanut (MP). The pastures were grazed by six rumen-cannulated zebu heifers. A double cross-over design was used in four periods. Nutritive value, intake and apparent digestibility of forage, ruminal traits and kinetics and N balance were evaluated. Apparent total-tract digestibility of dry matter (DM) and neutral detergent fibre (NDF) were greater for FP than for MP. There was no effect in apparent total-tract digestibility of N. The estimated intestinal digestibility of nutrients was greater on MP than FP. Even though N intake and faecal N output were greater on MP than FP, there was no effect in urine N output. The N balance tended to be greater on MP than FP. The forage peanut, which contains condensed tannins, decreased ruminal fibre degradation, apparent digestibility and ruminal protein degradation, increased N flow from the rumen. Inclusion of forage peanut in the mixed pasture decreased the ruminal fibre degradability but increased N retention by the animals.

I-CARE, a European Prospective Cohort Study Assessing Safety and Effectiveness of Biologics in Inflammatory Bowel Disease.

BACKGROUND AND AIMS: There is a need to evaluate the benefit-risk ratio of current therapies in inflammatory bowel disease (IBD) patients to provide the best quality of care. The primary objective of I-CARE (IBD Cancer and serious infections in Europe) was to assess prospectively safety concerns in IBD, with specific focus on the risk of cancer/lymphoma and serious infections in patients treated with anti-tumor necrosis factor and other biologic monotherapy as well as in combination with immunomodulators. METHODS: I-CARE was designed as a European prospective longitudinal observational multicenter cohort study to include patients with a diagnosis of Crohn's disease, ulcerative colitis, or IBD unclassified established at least 3 months prior to enrollment. RESULTS: A total of 10,206 patients were enrolled between March 2016 and April 2019, including 6169 (60.4%) patients with Crohn's disease, 3853 (37.8%) with ulcerative colitis, and 184 (1.8%) with a diagnosis of IBD unclassified. Thirty-two percent of patients were receiving azathioprine/thiopurines, 4.6% 6-mercaptopurine, and 3.2% methotrexate at study entry. At inclusion, 47.3% of patients were treated with an anti-tumor necrosis factor agent, 8.8% with vedolizumab, and 3.4% with ustekinumab. Roughly one-quarter of patients (26.8%) underwent prior IBD-related surgery. Sixty-six percent of patients had been previously treated with systemic steroids. Three percent of patients had a medical history of cancer prior to inclusion and 1.1% had a history of colonic, esophageal, or uterine cervix high-grade dysplasia. CONCLUSIONS: I-CARE is an ongoing investigator-initiated observational European prospective cohort study that will provide unique information on the long-term benefits and risks of biological therapies in IBD patients. (EudraCT, Number: 2014-004728-23; ClinicalTrials.gov, Number: NCT02377258).

Dichotomous effects of in vivo and in vitro ionizing radiation exposure on lymphatic function.

On the one hand, lymphatic dysfunction induces interstitial edema and inflammation. On the other hand, the formation of edema and inflammation induce lymphatic dysfunction. However, informed by the earlier reports of undetected apoptosis of irradiated lymphatic endothelial cells (LECs) in vivo, lymphatic vessels are commonly considered inconsequential to ionizing radiation (IR)-induced inflammatory injury to normal tissues. Primarily because of the lack of understanding of the acute effects of IR exposure on lymphatic function, acute edema and inflammation, common sequelae of IR exposure, have been ascribed solely to blood vessel damage. Therefore, in the present study, the lymphatic acute responses to IR exposure were quantified to evaluate the hypothesis that IR exposure impairs lymphatic pumping. Rat mesenteric lymphatic vessels were irradiated in vivo or in vitro, and changes in pumping were quantified in isolated vessels in vitro. Compared with sham-treated vessels, pumping was lowered in lymphatic vessels irradiated in vivo but increased in vessels irradiated in vitro. Furthermore, unlike in blood vessels, the acute effects of IR exposure in lymphatic vessels were not mediated by nitric oxide-dependent pathways in either in vivo or in vitro irradiated vessels. After cyclooxygenase blockade, pumping was partially restored in lymphatic vessels irradiated in vitro but not in vessels irradiated in vivo. Taken together, these findings demonstrated that lymphatic vessels are radiosensitive and LEC apoptosis alone may not account for all the effects of IR exposure on the lymphatic system.NEW & NOTEWORTHY Earlier studies leading to the common belief that lymphatic vessels are radioresistant either did not characterize lymphatic pumping, deemed necessary for the resolution of edema and inflammation, or did it in vivo. By characterizing pumping in vitro, the present study, for the first time, demonstrated that lymphatic pumping was impaired in vessels irradiated in vivo and enhanced in vessels irradiated in vitro. Furthermore, the pathways implicated in ionizing radiation-induced blood vessel damage did not mediate lymphatic responses.

A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome.

MOTIVATION: PERMANOVA is currently the most commonly used method for testing community-level hypotheses about microbiome associations with covariates of interest. PERMANOVA can test for associations that result from changes in which taxa are present or absent by using the Jaccard or unweighted UniFrac distance. However, such presence-absence analyses face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias but at the potential costs of information loss and the introduction of a stochastic component into the analysis. RESULTS: Here, we develop a non-stochastic approach to PERMANOVA presence-absence analyses that aggregates information over all potential rarefaction replicates without actual resampling, when the Jaccard or unweighted UniFrac distance is used. We compare this new approach to three possible ways of aggregating PERMANOVA over multiple rarefactions obtained from resampling: averaging the distance matrix, averaging the (element-wise) squared distance matrix and averaging the F-statistic. Our simulations indicate that our non-stochastic approach is robust to confounding by library size and outperforms each of the stochastic resampling approaches. We also show that, when overdispersion is low, averaging the (element-wise) squared distance outperforms averaging the unsquared distance, currently implemented in the R package vegan. We illustrate our methods using an analysis of data on inflammatory bowel disease in which samples from case participants have systematically smaller library sizes than samples from control participants. AVAILABILITY AND IMPLEMENTATION: We have implemented all the approaches described above, including the function for calculating the analytical average of the squared or unsquared distance matrix, in our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM.

SUMMARY: We previously developed the LDM for testing hypotheses about the microbiome that performs the test at both the community level and the individual taxon level. The LDM can be applied to relative abundance data and presence-absence data separately, which work well when associated taxa are abundant and rare, respectively. Here, we propose LDM-omni3 that combines LDM analyses at the relative abundance and presence-absence data scales, thereby offering optimal power across scenarios with different association mechanisms. The new LDM-omni3 test is available for the wide range of data types and analyses that are supported by the LDM. AVAILABILITY AND IMPLEMENTATION: The LDM-omni3 test has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A phase 3 double-blind study of the addition of tocilizumab vs placebo to cyclosporin/methotrexate GVHD prophylaxis.

We determined the efficacy of tocilizumab (TCZ) in preventing grade 2-4 acute graft-versus-host disease (aGVHD) in patients with acute leukemia or myelodysplasia undergoing matched sibling donor (MSD) or volunteer unrelated donor (VUD) allogeneic stem cell transplantation after myeloablative or reduced-intensity conditioning across 5 Australian centers. A total of 145 patients (50 MSD, 95 VUD) were randomly assigned to placebo or TCZ on day -1. All patients received T-cell-replete peripheral blood stem cell grafts and graft-versus-host disease (GVHD) prophylaxis with cyclosporin/methotrexate. A planned substudy analyzed the VUD cohort. With a median follow-up of 746 days, the incidence of grade 2-4 aGVHD at day 100 for the entire cohort was 36% for placebo vs 27% for TCZ (hazard ratio [HR], 0.69; 95% confidence interval [CI], 0.38-1.26; P = .23) and 45% vs 32% (HR, 0.61; 95% CI, 0.31-1.22; P = .16) for the VUD subgroup. The incidence of grade 2-4 aGVHD at day 180 for the entire cohort was 40% for placebo vs 29% for TCZ (HR, 0.68; 95% CI, 0.38-1.22; P = .19) and 48% vs 32% (HR, 0.59; 95% CI, 0.30-1.16; P = .13) for the VUD subgroup. Reductions in aGVHD were predominantly in grade 2 disease. For the entire cohort, transplant-related mortality occurred in 8% vs 11% of placebo-treated vs TCZ-treated patients, respectively (P = .56), and overall survival was 79% vs 71% (P = .27). Median day to neutrophil and platelet engraftment was delayed by 2 to 3 days in TCZ-treated patients, whereas liver toxicity and infectious complications were similar between groups. In this phase 3 randomized double-blind trial, TCZ showed nonsignificant trends toward reduced incidence of grade 2-4 aGVHD in recipients from HLA-matched VUDs but no improvements in long term-survival.

Utilization pattern of prophylactic measures for prevention of post-ERCP pancreatitis: a National Survey Study.

BACKGROUND AND AIMS: Post-ERCP pancreatitis (PEP) is the most frequent adverse event of ERCP. Various prophylactic measures are endorsed by the American Society for Gastrointestinal Endoscopy and the European Society of Gastrointestinal Endoscopy to both lower the incidence of PEP and to decrease its severity. The extent to which these interventions are practiced throughout the United States is unclear. The aim of this study was to describe the utilization pattern of various PEP measures and determine factors that affect utilization of these measures. METHODS: A 27-question electronic survey was distributed using a cloud-based program (Qualtrics). The questions assessed ERCP training, practice setting, experience, practice patterns, and perceptions for PEP prophylaxis interventions. Endoscopists with practices based in the United States listed in the American Society for Gastrointestinal Endoscopy member directory received a survey invitation via e-mail. The invitation outlined the study and contained a link with instructions to complete the voluntary survey if they had an active ERCP practice. Data were de-identified for the purposes of analysis. RESULTS: Of survey respondents (N = 319), 46% reported therapeutic endoscopy fellowship training and 37% practiced in teaching programs. Annualized ERCP volume of >100 cases per year were reported by 47%, with pancreatic ERCP comprising ≤5% of procedure volume reported by the majority of respondents (61%). The majority of respondents used prophylactic pancreatic stent (PPS), and 54% reported frequent use during high-risk ERCP. The most common indications for PPS were difficult cannulation, to assist biliary access, and multiple pancreatic duct injections. Most respondents reported frequent use of indomethacin (89%). Of physicians who did not use PPS, use of indomethacin was the most common reason (80%). Variables associated with frequent use of PPS were ERCP fellowship training (P ≤ .001), practice at a teaching program (P ≤ .001), <10 years in practice (P = .005), higher procedure volume (P ≤ .001), and higher proportion of pancreatic cases (P ≤ .001). CONCLUSIONS: Physicians with higher annual ERCP volume, who teach at hospital-based ERCP practices, and who regularly perform pancreatic ERCP are more likely to use PPS. Therapeutic ERCP fellowship training and recent entry into practice were also associated with PPS utilization. Indomethacin use seems to be more frequent than PPS. Our findings suggest that indomethacin is supplanting PPS as the preferred method of PEP prophylaxis.

The effects of crank power and cadence on muscle fascicle shortening velocity, muscle activation and joint-specific power during cycling.

Whilst people typically choose to locomote in the most economical fashion, during bicycling they will, unusually, chose cadences that are higher than metabolically optimal. Empirical measurements of the intrinsic contractile properties of the vastus lateralis (VL) muscle during submaximal cycling suggest that the cadences that people self-selected might allow for optimal muscle fascicle shortening velocity for the production of knee extensor muscle power. It remains unclear, however, whether this is consistent across different power outputs where the self-selected cadence (SSC) varies. We examined the effect of cadence and external power requirements on muscle neuromechanics and joint power during cycling. VL fascicle shortening velocity, muscle activation and joint-specific power were measured during cycling between 60 and 120 rpm (including SSC), while participants produced 10%, 30% and 50% of peak maximal power. VL shortening velocity increased as cadence increased but was similar across the different power outputs. Although no differences were found in the distribution of joint power across cadence conditions, the absolute knee joint power increased with increasing crank power output. Muscle fascicle shortening velocity increased in VL at the SSC as pedal power demands increased from submaximal towards maximal cycling. A secondary analysis of muscle activation patterns showed minimized activation of VL and other muscles near the SSC at the 10% and 30% power conditions. Minimization of activation with progressively increasing fascicle shortening velocities at the SSC may be consistent with the theory that the optimum shortening velocity for maximizing power increases with the intensity of exercise and recruitment of fast twitch fibers.

Linking muscle mechanics to the metabolic cost of human hopping.

Many models have been developed to predict metabolic energy expenditure based on biomechanical proxies of muscle function. However, current models may only perform well for select forms of locomotion, not only because the models are rarely rigorously tested across subtle and broad changes in locomotor task but also because previous research has not adequately characterised different forms of locomotion to account for the potential variability in muscle function and thus metabolic energy expenditure. To help to address the latter point, the present study imposed frequency and height constraints to hopping and quantified gross metabolic power as well as the activation requirements of medial gastrocnemius (MG), lateral gastrocnemius (GL), soleus (SOL), tibialis anterior (TA), vastus lateralis (VL), rectus femoris (RF) and biceps femoris (BF), and the work requirements of GL, SOL and VL. Gross metabolic power increased with a decrease in hop frequency and increase in hop height. There was no hop frequency or hop height effect on the mean electromyography (EMG) data of ankle musculature; however, the mean EMG of VL and RF increased with a decrease in hop frequency and that of BF increased with an increase in hop height. With a reduction in hop frequency, GL, SOL and VL fascicle shortening, fascicle shortening velocity and fascicle to MTU shortening ratio increased, whereas with an increase in hop height, only SOL fascicle shortening velocity increased. Therefore, within the constraints that we imposed, decreases in hop frequency and increases in hop height resulted in increases in metabolic power that could be explained by increases in the activation requirements of knee musculature and/or increases in the work requirements of both knee and ankle musculature.

Testing microbiome associations with survival times at both the community and individual taxon levels.

BACKGROUND: Finding microbiome associations with possibly censored survival times is an important problem, especially as specific taxa could serve as biomarkers for disease prognosis or as targets for therapeutic interventions. The two existing methods for survival outcomes, MiRKAT-S and OMiSA, are restricted to testing associations at the community level and do not provide results at the individual taxon level. An ad hoc approach testing each taxon with a survival outcome using the Cox proportional hazard model may not perform well in the microbiome setting with sparse count data and small sample sizes. METHODS: We have previously developed the linear decomposition model (LDM) for testing continuous or discrete outcomes that unifies community-level and taxon-level tests into one framework. Here we extend the LDM to test survival outcomes. We propose to use the Martingale residuals or the deviance residuals obtained from the Cox model as continuous covariates in the LDM. We further construct tests that combine the results of analyzing each set of residuals separately. Finally, we extend PERMANOVA, the most commonly used distance-based method for testing community-level hypotheses, to handle survival outcomes in a similar manner. RESULTS: Using simulated data, we showed that the LDM-based tests preserved the false discovery rate for testing individual taxa and had good sensitivity. The LDM-based community-level tests and PERMANOVA-based tests had comparable or better power than MiRKAT-S and OMiSA. An analysis of data on the association of the gut microbiome and the time to acute graft-versus-host disease revealed several dozen associated taxa that would not have been achievable by any community-level test, as well as improved community-level tests by the LDM and PERMANOVA over those obtained using MiRKAT-S and OMiSA. CONCLUSIONS: Unlike existing methods, our new methods are capable of discovering individual taxa that are associated with survival times, which could be of important use in clinical settings.