ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation

MOTIVATION

The acquisition of somatic mutations in hematopoietic stem and progenitor stem cells with resultant clonal expansion, termed clonal hematopoiesis (CH), is associated with increased risk of hematologic malignancies and other adverse outcomes. CH is generally present at low allelic fractions, but clonal expansion and acquisition of additional mutations leads to hematologic cancers in a small proportion of individuals. With high depth and high sensitivity sequencing, CH can be detected in most adults and its clonal trajectory mapped over time. However, accurate CH variant calling is challenging due to the difficulty in distinguishing low frequency CH mutations from sequencing artifacts. The lack of well-validated bioinformatic pipelines for CH calling may contribute to lack of reproducibility in studies of CH.

RESULTS

Here, we developed ArCH, an Artifact filtering Clonal Hematopoiesis variant calling pipeline for detecting single nucleotide variants and short insertions/deletions by combining the output of four variant calling tools and filtering based on variant characteristics and sequencing error rate estimation. ArCH is an end-to-end cloud-based pipeline optimized to accept a variety of inputs with customizable parameters adaptable to multiple sequencing technologies, research questions, and datasets. Using deep targeted sequencing data generated from six acute myeloid leukemia patient tumor: normal dilutions, 31 blood samples with orthogonal validation, and 26 blood samples with technical replicates, we show that ArCH improves the sensitivity and positive predictive value of CH variant detection at low allele frequencies compared to standard application of commonly used variant calling approaches.

AVAILABILITY AND IMPLEMENTATION

The code for this workflow is available at: https://github.com/kbolton-lab/ArCH.

The effect of psychiatric decision unit services on inpatient admissions and mental health presentations in emergency departments: an interrupted time series analysis from two cities and one rural area in England

AIMS

High-quality evidence is lacking for the impact on healthcare utilisation of short-stay alternatives to psychiatric inpatient services for people experiencing acute and/or complex mental health crises (known in England as psychiatric decision units [PDUs]). We assessed the extent to which changes in psychiatric hospital and emergency department (ED) activity were explained by implementation of PDUs in England using a quasi-experimental approach.

METHODS

We conducted an interrupted time series (ITS) analysis of weekly aggregated data pre- and post-PDU implementation in one rural and two urban sites using segmented regression, adjusting for temporal and seasonal trends. Primary outcomes were changes in the number of voluntary inpatient admissions to (acute) adult psychiatric wards and number of ED adult mental health-related attendances in the 24 months post-PDU implementation compared to that in the 24 months pre-PDU implementation.

RESULTS

The two PDUs (one urban and one rural) with longer (average) stays and high staff-to-patient ratios observed post-PDU decreases in the pattern of weekly voluntary psychiatric admissions relative to pre-PDU trend (Rural: -0.45%/week, 95% confidence interval [CI] = -0.78%, -0.12%; Urban: -0.49%/week, 95% CI = -0.73%, -0.25%); PDU implementation in each was associated with an estimated 35-38% reduction in total voluntary admissions in the post-PDU period. The (urban) PDU with the highest throughput, lowest staff-to-patient ratio and shortest average stay observed a 20% (-20.4%, CI = -29.7%, -10.0%) level reduction in mental health-related ED attendances post-PDU, although there was little impact on long-term trend. Pooled analyses across sites indicated a significant reduction in the number of voluntary admissions following PDU implementation (-16.6%, 95% CI = -23.9%, -8.5%) but no significant (long-term) trend change (-0.20%/week, 95% CI = -0.74%, 0.34%) and no short- (-2.8%, 95% CI = -19.3%, 17.0%) or long-term (0.08%/week, 95% CI = -0.13, 0.28%) effects on mental health-related ED attendances. Findings were largely unchanged in secondary (ITS) analyses that considered the introduction of other service initiatives in the study period.

CONCLUSIONS

The introduction of PDUs was associated with an immediate reduction of voluntary psychiatric inpatient admissions. The extent to which PDUs change long-term trends of voluntary psychiatric admissions or impact on psychiatric presentations at ED may be linked to their configuration. PDUs with a large capacity, short length of stay and low staff-to-patient ratio can positively impact ED mental health presentations, while PDUs with longer length of stay and higher staff-to-patient ratios have potential to reduce voluntary psychiatric admissions over an extended period. Taken as a whole, our analyses suggest that when establishing a PDU, consideration of the primary crisis-care need that underlies the creation of the unit is key.

Accuracy of Cytologic vs Histologic Specimens for Assessment of Programmed Cell Death Ligand-1 Expression in Non-Small Cell Lung Cancer: A Systematic Review and Meta-Analysis

BACKGROUND

Programmed cell death ligand-1 (PD-L1) expression on tumor cells, evaluated by immunohistochemistry, guides the use of immunotherapy in advanced non-small cell lung cancer (NSCLC).

RESEARCH QUESTION

What is the sensitivity and specificity of PD-L1 testing performed in cytologic vs paired histologic specimens in patients with NSCLC?

STUDY DESIGN AND METHODS

The MEDLINE, Embase, Web of Science, and Cochrane Library databases were searched through June 1, 2021. The primary outcome was pooled sensitivity and specificity of PD-L1 testing performed on cytologic specimens compared with the reference standard of histologic specimens, analyzed at the PD-L1 expression cutoffs (tumor proportion score) ≥ 1% and ≥ 50%. Pooled sensitivity and specificity, and associated 95% CIs, were estimated using bivariate generalized linear mixed models.

RESULTS

Twenty-six articles were included, encompassing a total of 1,064 pairs of histology specimens and cytology cell blocks, and 267 pairs of histology specimens and direct smears. Among these, 946 paired specimens were acquired without interval treatment between the collection of histology and cytology samples. The pooled sensitivity and specificity of cytology specimens compared with paired histology specimens at the PD-L1 expression cutoff ≥ 1% were 0.84 (95% CI, 0.77-0.89) and 0.88 (95% CI, 0.82-0.93), respectively, whereas the pooled sensitivity and specificity at cutoff ≥ 50% were 0.78 (95% CI, 0.69-0.86) and 0.94 (95% CI, 0.91-0.96), respectively. When only paired specimens acquired without interval treatment were considered, the pooled sensitivity and specificity of cytology specimens at PD-L1 expression cutoff ≥ 1% were 0.84 (95% CI, 0.76-0.90) and 0.89 (95% CI, 0.82-0.94), respectively, whereas the pooled sensitivity and specificity at cutoff ≥ 50% were 0.80 (95% CI, 0.71-0.89) and 0.94 (95% CI, 0.91-0.96), respectively.

INTERPRETATION

Cytologic specimens provide an accurate assessment of PD-L1 expression in most patients with NSCLC, at both ≥ 1% and ≥ 50% cutoffs, when compared with histologic specimens.

TRIAL REGISTRATION

PROSPERO; No.: CRD42020153279; URL: https://www.crd.york.ac.uk/prospero/.

"It's about time they taught us": a qualitative study evaluating the barriers to finding and screening child contacts under five at risk for TB in Gauteng Province, South Africa from the provider and caregiver perspectives

BACKGROUND

Inadequate numbers of children under five years of age who are exposed to tuberculosis (TB) in the home (child contact) are initiated on TB preventive treatment (TPT) in South Africa. We assessed barriers of initiating isoniazid preventive therapy (IPT) in this age group.

METHODS

We conducted a qualitative study at two primary health clinics in the Ekurhuleni district in Gauteng Province. Between April and July 2019, we enrolled facility managers, TB staff and parents or legal guardians of child contacts (caregivers) attending for care, at the two facilities. Semi-structured questionnaires, facility observations and in-depth interviews using a semi-structured interview guide were used to collect data. Findings from the semi-structured questionnaires with facility staff and facility observations were summarized. Thematic analysis with a deductive approach was used to analyse the data from the in-depth interviews with caregivers.

RESULTS

Two facility managers took part in the study and were assisted to complete the semi-structured questionnaires by TB staff. Fifteen caregivers aged between 18 and 43 years were interviewed of which 13 (87%) were female. Facility managers and TB staff (facility staff) felt that even though caregivers knew of family members who were on TB treatment, they delayed bringing their children for TB screening and TPT. Facility staff perceived caregivers as not understanding the purpose and benefits of TB prevention strategies such as TPT. Caregivers expressed the desire for their children to be screened for TB. However, caregivers lacked knowledge on TB transmission and the value of TB prevention in children at high risk of infection.

CONCLUSION

While facility staff perceived caregivers to lack responsibility, caregivers expressed limited knowledge on the value of screening their children for TB as reasons for not accessing TB preventive services. Health education on TB transmission, screening, and TB prevention strategies at a community level, clinics, creches, schools and via media are important to achieve the global end TB goal of early detection and prevention of TB.

Highly purified cannabidiol in the treatment of drug-resistant epilepsies: A real-life impact on seizure frequency, quality of life, behavior, and sleep patterns from a single Italian center

Seizure frequency in treatment-resistant epilepsies seems to be decreased by cannabidiol (CBD), but contrasting data are available on its effect on sleep, behavior, and quality of life (QoL), and no data is reported on its effect on parental stress in patients with epilepsy (PWE). Thus, we conducted a retrospective study on a cohort of children and adults with drug-resistant epilepsy (DRE) who had been treated with highly purified, pharmaceutical-grade CBD to evaluate its effects on seizure frequency, QoL, behavior, parental stress, and sleep. Eighteen patients (12 adults and 6 children) were included in the cohort and followed for a median of 9 months. At the last follow-up (Tn), nine patients (50%) were considered CBD responders with at least a 50% decrease in seizure frequency. No serious adverse effects were found. No statistically significant differences were found concerning sleep, including daytime sleepiness, and no statistically significant effect was found on parental stress at Tn. An improvement was found for social interaction in quality of life (p < 0.05) for all patients. Our results demonstrate that CBD is a safe and effective antiseizure medication (ASM). CBD doesn't seem to affect sleep measures in adults and children or worsen daytime sleepiness. However, CBD improves specific QoL measures, which could indicate a possible use of CBD for other childhood disabilities. No impact of CBD was seen on parental stress, which could possibly be due to the limited follow-up or could mean that parental stress is not dependent on seizure frequency.

Impact of variation in practice in the prenatal reporting of variants of uncertain significance by commercial laboratories: NEED FOR GREATER ADHERENCE TO PUBLISHED GUIDELINES

OBJECTIVE

To evaluate the impact of implementing commercial whole exome sequencing (WES) and targeted gene panel testing in pregnancies with fetal anomalies.

METHODS

A retrospective chart review of 124 patients with sequencing performed by commercial laboratories.

RESULTS

The diagnostic yield of WES and panel testing was 21.5% and 26% respectively, based on likely pathogenic (LP) or pathogenic (P) variants. Forty-two per cent of exomes and 32% of panels analyzed had one or more variant of uncertain significance (VUS) reported. A multidisciplinary in depth review of the fetal phenotype, disease phenotype, variant data, and, in some patients, additional prenatal or postnatal investigations increased the diagnostic yield by 5% for exome analysis and 6% for panel analysis.

CONCLUSIONS

The diagnostic yield of WES and panel testing combined was 23% based on LP and P variants. Although the reporting of VUS contributed to a 5% increase in diagnostic yield for WES and 6% for panels, the large number of VUS reported by commercial laboratories has significant resource implications. Our results support the need for greater adherence to the recommendations on the prenatal reporting of VUS and the importance of a multidisciplinary approach that brings together clinical and laboratory expertise in prenatal genetics and genomics. This article is protected by copyright. All rights reserved.

Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

BACKGROUND

No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge.

METHODS

The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing.

FINDINGS

2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters.

INTERPRETATION

The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials.

FUNDING

UK Research and Innovation and National Institute for Health Research.

324 Outcomes of Prostate Artery Embolisation In Catheterised Patients: A Case Series

Aim

Prostate artery embolisation (PAE) is an approved treatment for men with lower urinary tract symptoms secondary to benign prostatic hyperplasia (BPH-LUTS). Evidence of efficacy for PAE in patients who are unable to void urine spontaneously is scant, however. Traditional treatments for BPH-LUTS have evidence in retention patients and this series aims to report outcomes for PAE in catheterised patients.

Method

The records of consecutive men with BPH-LUTS which required either an indwelling bladder catheter or clean intermittent self-catheterisation (CISC) who subsequently underwent PAE were retrospectively reviewed. Basic demographics were collected along with information on the prostate volume and PAE procedure specifics. The primary outcome was whether patients were catheter/CISC free at 3 months. Other outcomes include complications, use of medications and the need for other surgical treatments post-PAE.

Results

63 men underwent PAE for urinary retention and BPH-LUTS between 2013 and 2020. Of these, 7 underwent a unilateral embolisation for aberrant anatomy. The mean prostate volume was 128ml. 61% of men were free from a catheter/CISC post-treatment. 4 patients suffered post-PAE UTI, whilst 3 patients subsequently underwent Transurethral Resection of the Prostate following PAE for failure to become catheter free. 13 men were entirely free from BPH-LUTS medications.

Conclusions

PAE for catheterised men results in a similar catheter-free rate post procedure to several more invasive BPH treatments. It has a low side-effect profile and gives men with poor health an option to try to become catheter free. PAE should be discussed with men with catheters as a treatment option.

Clinical characteristics of two-hundred thirty-two dogs (2006-2018) treated for suspected anaphylaxis in Perth, Western Australia

OBJECTIVE

To describe the clinical features of dogs treated for suspected anaphylaxis in Perth, Western Australia.

DESIGN

Single-centre observational case series with retrospective and prospective phases.

METHODS

This was a two-phase study of dogs with clinical suspicion of anaphylaxis presenting to the emergency service of a university teaching hospital. Dogs required evidence of, and appropriate treatment of, a type 1 hypersensitivity reaction as well as two or more organs affected (or cardiovascular signs alone) to be included. Phase 1 includes retrospective case series of 186 dogs (March 2006-December 2018). Phase 2 includes prospective descriptive case series of 46 dogs (October 2017-July 2018) focused on clinical signs.

RESULTS

In phase 1, 88 (47%) dogs had evidence of insect exposure prior to the acute event. One hundred forty (75%) dogs had dermatological signs, 141 (76%) had gastrointestinal signs and 129 (69%) had cardiovascular signs. Ninety-two (49%) dogs had vasoconstrictive shock (5 with bradycardia), 24 (13%) had vasodilatory shock, 8 (4%) had mixed vasodilatory and vasoconstrictive shock and 5 (3%) had unclassifiable shock. On focused abdominal ultrasound, 42 of 71 (59%) dogs had gallbladder wall oedema and 3 of 71 (4%) dogs had peritoneal free fluid. In phase 2, the distributions of insect exposure, organ dysfunction and sonographic abnormalities were similar to phase 1.

CONCLUSION

Dogs presenting with suspected anaphylaxis showed a broad range of presentations. Dermatological signs were absent in a proportion of dogs, vasoconstrictive shock was more frequent than vasodilatory and unique features of shock were identified. This study highlights the challenges of diagnosis based on presenting features alone.

Reporting of drug trial funding sources and author financial conflicts of interest in Cochrane and non-Cochrane meta-analyses: a cross-sectional study

OBJECTIVE

To (1) investigate the extent to which recently published meta-analyses report trial funding, author-industry financial ties and author-industry employment from included randomised controlled trials (RCTs), comparing Cochrane and non-Cochrane meta-analyses; (2) examine characteristics of meta-analyses independently associated with reporting funding sources of included RCTs; and (3) compare reporting among recently published Cochrane meta-analyses to Cochrane reviews published in 2010.

DESIGN

Review of consecutive sample of recently published meta-analyses.

DATA SOURCES

MEDLINE database via PubMed searched on 19 October 2018.

ELIGIBILITY CRITERIA FOR SELECTING ARTICLES

We selected the 250 most recent meta-analyses listed in PubMed that included a documented search of at least one database, statistically combined results from ≥2 RCTs and evaluated the effects of a drug or class of drugs.

RESULTS

90 of 107 (84%) Cochrane meta-analyses reported funding sources for some or all included trials compared with 21 of 143 (15%) non-Cochrane meta-analyses, a difference of 69% (95% CI 59% to 77%). Percent reporting was also higher for Cochrane meta-analyses compared with non-Cochrane meta-analyses for trial author-industry financial ties (44% versus 1%; 95% CI for difference 33% to 52%) and employment (17% versus 1%; 95% CI for difference 9% to 24%). In multivariable analysis, compared with Cochrane meta-analyses, the odds ratio (OR) for reporting trial funding was ≤0.11 for all other journal category and impact factor combinations. Compared with Cochrane reviews from 2010, reporting of funding sources of included RCTs among recently published Cochrane meta-analyses improved by 54% (95% CI 42% to 63%), and reporting of trial author-industry financial ties and employment improved by 37% (95% CI 26% to 47%) and 10% (95% CI 2% to 19%).

CONCLUSIONS

Reporting of trial funding sources, trial author-industry financial ties and trial author-industry employment in Cochrane meta-analyses has improved since 2010 and is higher than in non-Cochrane meta-analyses.

What is the impact of psychiatric decision units on mental health crisis care pathways? Protocol for an interrupted time series analysis with a synthetic control study

BACKGROUND

The UK mental health system is stretched to breaking point. Individuals presenting with mental health problems wait longer at the ED than those presenting with physical concerns and finding a bed when needed is difficult - 91% of psychiatric wards are operating at above the recommended occupancy rate. To address the pressure, a new type of facility - psychiatric decision units (also known as mental health decision units) - have been introduced in some areas. These are short-stay facilities, available upon referral, targeted to help individuals who may be able to avoid an inpatient admission or lengthy ED visit. To advance knowledge about the effectiveness of this service for this purpose, we will examine the effect of the service on the mental health crisis care pathway over a 4-year time period; the 2 years proceeding and following the introduction of the service. We use aggregate service level data of key indicators of the performance of this pathway.

METHODS

Data from four mental health Trusts in England will be analysed using an interrupted time series (ITS) design with the primary outcomes of the rate of (i) ED psychiatric presentations and (ii) voluntary admissions to mental health wards. This will be supplemented with a synthetic control study with the same primary outcomes, in which a comparable control group is generated for each outcome using a donor pool of suitable National Health Service Trusts in England. The methods are well suited to an evaluation of an intervention at a service delivery level targeting population-level health outcome and the randomisation or 'trialability' of the intervention is limited. The synthetic control study controls for national trends over time, increasing our confidence in the results. The study has been designed and will be carried out with the involvement of service users and carers.

DISCUSSION

This will be the first formal evaluation of psychiatric decision units in England. The analysis will provide estimates of the effect of the decision units on a number of important service use indicators, providing much-needed information for those designing service pathways.

TRIAL REGISTRATION

primary registry: isrctn.com Identifying number: ISRCTN77588384 Link: Date of registration in primary registry: 27/02/2020.

PRIMARY SPONSOR

St George's, University of London, Cramner Road, Tooting, SW17 ORE. Primary contact: Joe Montebello.

Population Data Centre Profile: The Manitoba Centre for Health Policy

Objective

To profile the Manitoba Centre for Health Policy (MCHP), a population health data centre located at the University of Manitoba in Winnipeg, Canada.

Approach

We describe how MCHP was established and funded, and how it continues to operate based on a foundation of trust and respect between researchers at the University of Manitoba and stakeholders in the Manitoba Government’s Department of Health. MCHP’s research priorities are jointly determined by its scientists’ own research interests and by questions put forward from Manitoba government ministries. Data governance, data privacy, data linkage processes and data access are discussed in detail. We also provide three illustrative examples of the MCHP Data Repository in action, demonstrating how studies using a variety of Repository datasets have had an impact on health and social policies and programs in Manitoba.

Discussion

MCHP has experienced tremendous growth over the last three decades. We discuss emerging research directions as the capacity for innovation at MCHP continues to expand, including a focus on natural language processing and other applications of artificial intelligence techniques, a leadership role in the new SPOR Canadian Data Platform, and a foray into social policy evaluation and analysis. With these and other exciting opportunities on the horizon, the future at MCHP looks exceptionally bright.

Endometrial development during the transition to menopause: preliminary associations with follicular dynamics

Objective: This study aimed to test the hypothesis that the development of functional luteal phase dominant follicles (LPDFs) is associated with increased endometrial growth as women transition to menopause.Methods: Endometrial thickness (ET), follicle development, and hormone production were characterized in ovulatory women of mid-reproductive age (MRA; 18-35 years, n = 10) and advanced reproductive age (ARA; 45-55 years, n = 16). Transvaginal ultrasonography was conducted every 1-3 days during one interovulatory interval to quantify ET and the diameters of follicles ≥2 mm. Blood was drawn at each visit to measure progesterone, estradiol, inhibin A, follicle stimulating hormone, and luteinizing hormone.Results: In the MRA group, ET was lower (8.87 vs. 10.1 mm) in women with typical versus no LPDFs, in association with greater luteal phase estradiol (91.1 vs. 48.8 ng/l). In the ARA group, luteal phase endometrial growth was greater (12.0 vs. 10.4 mm) in women with typical versus no LPDFs, in association with lower progesterone (10.7 vs. 13.8 μg/l; LPDF effect p < 0.1) and inhibin A (35.6 vs. 51.17 ng/l; p < 0.10).Conclusions: Preliminary findings suggest that ET may be increased in women who develop LPDFs, in association with reduced luteal phase progesterone and inhibin A, during the transition to menopause. Continued research is required to confirm these findings.

The Concept Dictionary and Glossary at MCHP: Tools and Techniques to Support a Population Research Data Repository

The Manitoba Centre for Health Policy’s Concept Dictionary and Glossary, and the Data Repository they document, broaden the analytic possibilities associated with administrative data. The aim of the Repository is to describe and explain patterns of health care and illness, while the Concept Dictionary and Glossary create consistency in documenting research methodologies. The Concept Dictionary alone contains detailed operational definitions and programming code for measures used in MCHP research that are reusable in future projects.

Making these tools available on the internet allows reaching a heterogeneous audience of academic and government health service partners, epidemiologists, planners, programmers, clinicians, and students extending around the globe. They aid in the retention of corporate knowledge, facilitate researcher/analyst communication, and enhance the Centre’s knowledge translation activities. Such documentation has saved countless hours for programmers, analysts and researchers who frequently need to tread paths previously taken by others.

Quantification of the duodenal eosinophil content in adults: a necessary step for an evidence-based diagnosis of duodenal eosinophilia

BACKGROUND

The normal content of eosinophils in the adult duodenum remains undefined. Therefore, there is no foundation for evidence-based criteria to diagnose eosinophilic duodenitis.

AIM

This study aimed at: (1) establishing the range of the eosinophil density in the mucosa of the duodenum of normal adults, and (2) determining the biopsy-based prevalence of isolated eosinophilic duodenitis in a large population of adults.

METHODS

We counted intact eosinophils in three separate high-power fields (hpf area = 0.237 mm² each) with the highest densities of eosinophils from the duodenal biopsy specimens of 370 consecutive adults (60% women) with no history of small intestinal disease and a normal duodenal histology. From a large database we also extracted patients with a diagnosis of elevated duodenal eosinophilia and reviewed their biopsies and clinical history.

RESULTS

The mean eosinophil count for the 370 patients was 8.2 eos/hpf with a standard deviation of ± 6.3. Twenty-seven of the 370 had eosinophil counts outside the 95% range, which was calculated as: mean + 1.96 × SD = 20.4 eos/hpf. In a database of 458 668 adult subjects, 31 patients (6.8/100 000) had elevated duodenal eosinophilia; 21 of these had other gastrointestinal organs involved by eosinophilia, suggesting eosinophilic gastroenteritis. No significant association between duodenal eosinophilia and any specific symptom was observed.

CONCLUSIONS

This study suggests that in this diverse US population, a cut-off count of 20 eos/hpf would be useful to separate patients with normal from those with elevated duodenal eosinophilic infiltrations. The clinical implications of duodenal eosinophilia, particularly when it is not an expression of eosinophilic gastroenteritis, remain to be established.

The impact of complications and errors on surgeons

Do surgeons need support – and, if so, what kind?

Developing a mHealth intervention to promote uptake of HIV testing among African communities in the UK: a qualitative study

BACKGROUND

HIV-related mHealth interventions have demonstrable efficacy in supporting treatment adherence, although the evidence base for promoting HIV testing is inconclusive. Progress is constrained by a limited understanding of processes used to develop interventions and weak theoretical underpinnings. This paper describes a research project that informed the development of a theory-based mHealth intervention to promote HIV testing amongst city-dwelling African communities in the conditions.

METHODS

A community-based participatory social marketing design was adopted. Six focus groups (48 participants in total) were undertaken and analysed using a thematic framework approach, guided by constructs from the Health Belief Model. Key themes were incorporated into a set of text messages, which were pre-tested and refined.

RESULTS

The focus groups identified a relatively low perception of HIV risk, especially amongst men, and a range of social and structural barriers to HIV testing. In terms of self-efficacy around HIV testing, respondents highlighted a need for communities and professionals to work together to build a context of trust through co-location in, and co-involvement of, local communities which would in turn enhance confidence in, and support for, HIV testing activities of health professionals. Findings suggested that messages should: avoid an exclusive focus on HIV, be tailored and personalised, come from a trusted source, allay fears and focus on support and health benefits.

CONCLUSIONS

HIV remains a stigmatized and de-prioritized issue within African migrant communities in the UK, posing barriers to HIV testing initiatives. A community-based participatory social marketing design can be successfully used to develop a culturally appropriate text messaging HIV intervention. Key challenges involved turning community research recommendations into brief text messages of only 160 characters. The intervention needs to be evaluated in a randomized control trial. Future research should explore the application of the processes and methodologies described in this paper within other communities.

Audit on the management of epididymo-orchitis by the Department of Urology in Edinburgh

Epididymo-orchitis among men younger than 35 years is mainly caused by chlamydial infection. National guidelines for the management of this condition have been published. The aim of this study was to audit the management of epididymo-orchitis in a major teaching hospital. To this end we performed a retrospective study of patients with epididymo-orchitis admitted to the Department of Urology in the Western General Hospital, Edinburgh between 1998 and 2003. Case-notes of 108 cases of epididymo-orchitis were reviewed. The diagnosis was established by ultrasound in 94% of cases. Patients were not tested routinely for chlamydial infection and the majority of men younger than 35 years were treated inappropriately with ciprofloxacin. The management of patients younger than 35 years was not in accordance with the recommendations of national guidelines. Chlamydia trachomatis is sexually transmissible and is not responsive to ciproflcxacin. As a result of this audit, each patient will be tested for chlamydial infection and men younger than 35 years will be treated with ofloxacin. Sexual partners of patients with chlamydial infection will be treated in the department of genitourinary medicine.

The effects of ergot alkaloids on the breeding stallion reproductive system

REASONS FOR PERFORMING STUDY

Ergot alkaloids cause a range of pathological conditions in mares. There is no evaluation of the effects of ergot alkaloids from endophyte-infected tall fescue on the stallion breeding soundness examination spermiogram.

OBJECTIVES

The objective of this study was to investigate the effect of ergot alkaloids from endophyte-infected tall fescue on the stallion's reproductive functions.

STUDY DESIGN

Crossover toxicology experiment.

METHODS

Six stallions were fed either toxic endophyte-infected tall fescue seed or a nontoxic endophyte tall fescue seed (Flecha AR-542, MaxQ). The fescue seed content was compounded at 45% of a grain diet and the stallions were fed the grain diet at 1% of their body weight. The stallions were fed the diet for 70 days, then rested for at least 70 days (no fescue seed) and then fed fescue seed for a second 70 days. At regular intervals blood sampling and a breeding soundness examination were performed.

RESULTS

The mean time to maximal systemic toxicity was 8.33 h after starting toxic seed ingestion with a mean toxicity level of 49.98 ng alkaloid/mg creatinine. After cessation of feeding toxic seed, the systemic alkaloid concentration fell to control levels within 48 h. There were no significant changes in sperm motility, sperm concentration, sperm cell morphology, total number of sperm cells, number of breeding doses, testicular volume, baseline and human chorionic gonadotropin stimulated testosterone levels. There were no changes in core body temperature and superficial scrotal temperature. The ejaculate from stallions consuming endophyte-infected tall fescue seed had significantly lower gel-free volume (47.5 ± 4.1 ml) than stallions consuming nontoxic endophyte tall fescue seed (62.8 + 4.3 ml, P<0.01).

CONCLUSION

Ergot alkaloids decreased the gel-free volume of stallions consuming high levels of ergot alkaloids but statistically significant effects on the spermiogram of adult breeding stallions were not found.

Multicentre study of neoadjuvant chemotherapy for stage I and II oesophageal cancer

Background

The benefit of neoadjuvant chemotherapy (NCT) for early-stage oesophageal cancer is unknown. The aim of this study was to assess whether NCT improves the outcome of patients with stage I or II disease.

Methods

Data were collected from 30 European centres from 2000 to 2010. Patients who received NCT for stage I or II oesophageal cancer were compared with patients who underwent primary surgery with regard to postoperative morbidity, mortality, and overall and disease-free survival. Propensity score matching was used to adjust for differences in baseline characteristics.

Results

Of 1173 patients recruited (181 NCT, 992 primary surgery), 651 (55·5 per cent) had clinical stage I disease and 522 (44·5 per cent) had stage II disease. Comparisons of the NCT and primary surgery groups in the matched population (181 patients in each group) revealed in-hospital mortality rates of 4·4 and 5·5 per cent respectively (P = 0·660), R0 resection rates of 91·7 and 86·7 per cent (P = 0·338), 5-year overall survival rates of 47·7 and 38·6 per cent (hazard ratio (HR) 0·68, 95 per cent c.i. 0·49 to 0·93; P = 0·016), and 5-year disease-free survival rates of 44·9 and 36·1 per cent (HR 0·68, 0·50 to 0·93; P = 0·017).

Conclusion

NCT was associated with better overall and disease-free survival in patients with stage I or II oesophageal cancer, without increasing postoperative morbidity.

Point prevalence survey of urinary catheterisation in care homes and where they were inserted, 2012

The extent to which the use of catheter care bundles and other interventions has led to a reduction in urinary catheterisation rates is unknown. We aimed to determine current urinary catheterisation rates in care homes with residents over 65 years old, and determine the extent to which residents are discharged from the hospital setting with urinary catheters. A point prevalence questionnaire survey was used in care homes that looked after residents over 65 years in six UK health boards or primary care trusts, to determine urinary catheterisation rates, and where these catheters were inserted. Questionnaires for 445 of 461 care homes (96.5%) were completed, 425 of 445 care homes cared for residents over 65 years; 888 (6.9%) of 12,827 residents had a urethral (82.5%) or supra-pubic (17.5%) urinary catheter. Over half of all catheters (both urethral and suprapubic, 57.4%, 509 of 888 catheters), and 3.1% of all residents had a catheter inserted while the residents were hospital inpatients, and then discharged back to the care home still catheterised. There was a significant variation in urinary catheterisation rates in the care homes surveyed, and rates remain similar to previous English surveys in 2003 and 2009. More still needs to be done to understand the variation in urinary catheterisation rates in care homes and reduce these rates, including the numbers of residents that are discharged from hospital with a urinary catheter.