Covariance analysis of 235U(nth,f) independent and cumulative fission yields: Propositions for JEFF4

The study of fission yields has a major impact on the characterization and understanding of the fission process and its applications. Fission yield evaluations represent the synthesis of experimental and theoretical knowledge in order to perform the best estimation of independent fission yields. Today, the lack of correlations between the different fission observables induces several inconsistencies in the evaluations. Different works proposed to estimate the correlations of the independent fission yields satisfying the consistency to the chain yield evaluations. Nevertheless, none of them introduces a prior correlations of the independent and chain evaluations in the evaluation process. Covariance matrix of fission yields depends on the evaluation method used according to the kinds of existing measurements. The consistency is deeply entangled to the statistical agreement between each dataset considering the covariance of measurements. Moreover, covariance of model parameters does not represent the only contribution to the evaluation covariance matrix. Thus, a new evaluation process is crucial to provide a complete and coherent evaluation file. The LEPh Laboratory of CEA Cadarache is developing this program for the future version of the JEFF-library.

Adjuvant Intravesical Chemohyperthermia Versus Passive Chemotherapy in Patients with Intermediate-risk Non-muscle-invasive Bladder Cancer (HIVEC-II): A Phase 2, Open-label, Randomised Controlled Trial

BACKGROUND

Adjuvant intravesical chemotherapy following tumour resection is recommended for intermediate-risk non-muscle-invasive bladder cancer (NMIBC).

OBJECTIVE

To assess the efficacy and safety of adjuvant intravesical chemohyperthermia (CHT) for intermediate-risk NMIBC.

DESIGN, SETTING, AND PARTICIPANTS

HIVEC-II is an open-label, phase 2 randomised controlled trial of CHT versus chemotherapy alone in patients with intermediate-risk NMIBC recruited at 15 centres between May 2014 and December 2017 (ISRCTN 23639415). Randomisation was stratified by treating hospital.

INTERVENTIONS

Patients were randomly assigned (1:1) to adjuvant CHT with mitomycin C at 43°C or to room-temperature mitomycin C (control). Both treatment arms received six weekly instillations of 40 mg of mitomycin C lasting for 60 min.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The primary endpoint was 24-mo disease-free survival as determined via cystoscopy and urinary cytology. Analysis was by intention to treat.

RESULTS

A total of 259 patients (131 CHT vs 128 control) were randomised. At 24 mo, 42 patients (32%) in the CHT group and 49 (38%) in the control group had experienced recurrence. Disease-free survival at 24 mo was 61% (95% confidence interval [CI] 51-69%) in the CHT arm and 60% (95% CI 50-68%) in the control arm (hazard ratio [HR] 0.92, 95% CI 0.62-1.37; log-rank p = 0.8). Progression-free survival was higher in the control arm (HR 3.44, 95% CI 1.09-10.82; log-rank p = 0.02) on intention-to-treat analysis but was not significantly higher on per-protocol analysis (HR 2.87, 95% CI 0.83-9.98; log-rank p = 0.06). Overall survival was similar (HR 2.55, 95% CI 0.77-8.40; log-rank p = 0.09). Patients undergoing CHT were less likely to complete their treatment (n =75, 59% vs n = 111, 89%). Adverse events were reported by 164 patients (87 CHT vs 77 control). Major (grade III) adverse events were rare (13 CHT vs 7 control).

CONCLUSIONS

CHT cannot be recommended over chemotherapy alone for intermediate-risk NMIBC. Adverse events following CHT were of low grade and short-lived, although patients were less likely to complete their treatment.

PATIENT SUMMARY

The HIVEC-II trial investigated the role of heated chemotherapy instillations in the bladder for treatment of intermediate-risk non-muscle-invasive bladder cancer. We found no cancer control benefit from heated chemotherapy instillations over room-temperature chemotherapy. Adverse events following heated chemotherapy were low grade and short-lived, although these patients were less likely to complete their treatment.

Defining core patient descriptors for perforated peptic ulcer research: international Delphi

BACKGROUND

Perforated peptic ulcer (PPU) remains a common condition globally with significant morbidity and mortality. Previous work has demonstrated variation in reporting of patient characteristics in PPU studies, making comparison of studies and outcomes difficult. The aim of this study was to standardize the reporting of patient characteristics, by creating a core descriptor set (CDS) of important descriptors that should be consistently reported in PPU research.

METHODS

Candidate descriptors were identified through systematic review and stakeholder proposals. An international Delphi exercise involving three survey rounds was undertaken to obtain consensus on key patient characteristics for future research. Participants rated items on a scale of 1-9 with respect to their importance. Items meeting a predetermined threshold (rated 7-9 by over 70 per cent of stakeholders) were included in the final set and ratified at a consensus meeting. Feedback was provided between rounds to allow refinement of ratings.

RESULTS

Some 116 clinicians were recruited from 29 countries. A total of 63 descriptors were longlisted from the literature, and 27 were proposed by stakeholders. After three survey rounds and a consensus meeting, 27 descriptors were included in the CDS. These covered demographic variables and co-morbidities, risk factors for PPU, presentation and pathway factors, need for organ support, biochemical parameters, prognostic tools, perforation details, and surgical history.

CONCLUSION

This study defines the core descriptive items for PPU research, which will allow more robust synthesis of studies.

Integration of Urinary EN2 Protein & Cell-Free RNA Data in the Development of a Multivariable Risk Model for the Detection of Prostate Cancer Prior to Biopsy

Simple Summary

Prostate cancer is a disease responsible for a large proportion of all male cancer deaths but there is a high chance that a patient will die with the disease rather than from. Therefore, there is a desperate need for improvements in diagnosing and predicting outcomes for prostate cancer patients to minimise overdiagnosis and overtreatment whilst appropriately treating men with aggressive disease, especially if this can be done without taking an invasive biopsy. In this work we develop a test that predicts whether a patient has prostate cancer and how aggressive the disease is from a urine sample. This model combines the measurement of a protein-marker called EN2 and the levels of 10 genes measured in urine and proves that integration of information from multiple, non-invasive biomarker sources has the potential to greatly improve how patients with a clinical suspicion of prostate cancer are risk-assessed prior to an invasive biopsy.

Abstract

The objective is to develop a multivariable risk model for the non-invasive detection of prostate cancer prior to biopsy by integrating information from clinically available parameters, Engrailed-2 (EN2) whole-urine protein levels and data from urinary cell-free RNA. Post-digital-rectal examination urine samples collected as part of the Movember Global Action Plan 1 study which has been analysed for both cell-free-RNA and EN2 protein levels were chosen to be integrated with clinical parameters (n = 207). A previously described robust feature selection framework incorporating bootstrap resampling and permutation was applied to the data to generate an optimal feature set for use in Random Forest models for prediction. The fully integrated model was named ExoGrail, and the out-of-bag predictions were used to evaluate the diagnostic potential of the risk model. ExoGrail risk (range 0–1) was able to determine the outcome of an initial trans-rectal ultrasound guided (TRUS) biopsy more accurately than clinical standards of care, predicting the presence of any cancer with an area under the receiver operator curve (AUC) = 0.89 (95% confidence interval(CI): 0.85–0.94), and discriminating more aggressive Gleason ≥ 3 + 4 disease returning an AUC = 0.84 (95% CI: 0.78–0.89). The likelihood of more aggressive disease being detected significantly increased as ExoGrail risk score increased (Odds Ratio (OR) = 2.21 per 0.1 ExoGrail increase, 95% CI: 1.91–2.59). Decision curve analysis of the net benefit of ExoGrail showed the potential to reduce the numbers of unnecessary biopsies by 35% when compared to current standards of care. Integration of information from multiple, non-invasive biomarker sources has the potential to greatly improve how patients with a clinical suspicion of prostate cancer are risk-assessed prior to an invasive biopsy.

Non-contact measurement of the thickness of a surface film using a superimposed ultrasonic standing wave

Most methods used to measure the thickness of thin liquid or solid surface films and coatings need access to the coated surface. In this work reflected ultrasonic pulses were used to measure a coating thickness from a solid back face. Piezoelectric transducers on the solid back face emitted ultrasound waves and received the waves that bounced off the front face. The magnitude of the reflected wave was dependent on the film thickness at the front face. Most pulse-echo ultrasonic approaches use the time-of-flight through the surface layer to determine its thickness. However, as the film becomes thinner, the reflected echoes overlap and there is often an acoustic mismatch between the solid and the surface film that reduces the signal strength. In this work, we propose the use of an ultrasonic continuously repeated chirp longitudinal wave to amplify the effect of the surface film. Multiple reflections interfere within the solid to form a superimposed standing wave whose amplitude spectrum is highly dependent on the surface film thickness thus overcoming the acoustic mismatch problem. Two bare 10 MHz piezoelectric elements were bonded to a 10 mm thick aluminium solid in a pitch-catch arrangement such that one continuously sends repeating chirp ultrasound waves and the other acts as the receiver. The transmitter was set to send a repeating chirp wave of 4 ms duration corresponding to the bandwidth of the transducer in order to maximise signal amplitude. The incident and reflected waves constructively and destructively interfere to form a superimposed standing wave within the solid. The solid/surface film to solid/air boundary condition frequency spectra ratio showed the film resonant frequency modes as minima. Using this technique epoxy coatings ranging from 70 μm to 350 μm were measured and showed a good correlation with independent measurements using a surface profilometer.

Chromatin conformation changes in peripheral blood can detect prostate cancer and stratify disease risk groups

BACKGROUND

Current diagnostic blood tests for prostate cancer (PCa) are unreliable for the early stage disease, resulting in numerous unnecessary prostate biopsies in men with benign disease and false reassurance of negative biopsies in men with PCa. Predicting the risk of PCa is pivotal for making an informed decision on treatment options as the 5-year survival rate in the low-risk group is more than 95% and most men would benefit from surveillance rather than active treatment. Three-dimensional genome architecture and chromosome structures undergo early changes during tumourigenesis both in tumour and in circulating cells and can serve as a disease biomarker.

METHODS

In this prospective study we screened whole blood of newly diagnosed, treatment naïve PCa patients (n = 140) and cancer-free controls (n = 96) for the presence of 14,241 chromosomal loops in the loci of 425 genes.

RESULTS

We have detected specific chromosome conformation changes in the loci of ETS1, MAP3K14, SLC22A3 and CASP2 genes in peripheral blood from PCa patients yielding PCa detection with 80% sensitivity and 80% specificity. Further analysis between PCa risk groups yielded prognostic validation sets consisting of HSD3B2, VEGFC, APAF1, BMP6, ERG, MSR1, MUC1, ACAT1 and DAPK1 genes that achieved 80% sensitivity and 93% specificity stratifying high-risk category 3 vs low risk category 1 and 84% sensitivity and 89% specificity stratifying high risk category 3 vs intermediate risk category 2 disease.

CONCLUSIONS

Our results demonstrate specific chromosome conformations in the blood of PCa patients that allow PCa diagnosis and risk stratification with high sensitivity and specificity.

DEVELOPMENT OF MPACT FOR FULL-CORE SIMULATIONS OF MAGNOX GAS-COOLED NUCLEAR REACTORS

The MPACT code, jointly developed by Oak Ridge National Laboratory and University of Michigan, is designed to perform high-fidelity light water reactor (LWR) analysis using wholecore pin-resolved neutron transport calculations on modern parallel-computing hardware. MPACT uses the subgroup method for resonance self-shielding, while the primary neutron transport solver uses a 2D/1D method that is based on the method of characteristics (MoC) for the x-y planes coupled with a 1D diffusion or transport solver in the axial dimension. Additional geometry capabilities are currently being developed in MPACT to support hexagonal-pitched lattices, as well as interstitial geometry (i.e., control rods at the corner of four adjacent pin cells). In this research, the MPACT method is tested on gas-cooled reactors by applying MPACT to full-core MAGNOX reactor test problems. MAGNOX test problems were chosen due to the availability of high-quality reactor design and validation data (available through an ongoing collaboration with the National Nuclear Laboratory in the United Kingdom) and the existence of a relatively complex axial power shape that is expected to challenge the MPACT method. MPACT’s convergence for partial- and full-core problems will be tested and verified. MPACT will be compared with high-fidelity continuous-energy Monte Carlo simulations to verify core reactivity, power distributions, and performance of the available cross section data libraries and energy group structures.

Self-reported motivations for engaging or declining to engage in cyber-dependent offending and the role of autistic traits

Cyber-dependent offending, i.e. criminal behaviour reliant on computing and the online domain, has been reportedly associated with particular characteristics and motivations such as being young, male, autistic and motivated by challenge. These associations are anecdotal however and empirical evidence is limited. The present study investigated reasons for engaging or declining to commit cyber-dependent offending in cyber-skilled non-offenders (n = 175) and offenders (n = 7) via an online survey measuring cyber-dependent criminality. The potential role of autism and autistic traits was also considered. Qualitative interviews about motivations for offending were carried out with the offenders. The cyber-dependent offenders reported seven main reasons for engaging in cyber-dependent offending: (1) lack of understanding; (2) entertainment; (3) peer influence; (4) experience and career; (5) anonymity and risk perception; (6) life events; and (7) morals. Twenty-nine (approximately 17 %) of the non-offenders had been asked to engage in cyber-dependent offending but had declined. Their reasons and motivations for declining to commit cyber-dependent offences were compared with the cyber-dependent offenders reasons and motivations for engaging in cybercrime. Seven main reasons for declining to offend were identified: (1) moral principles; (2) perception of risk; (3) fear of consequences; (4) not wanting to; (5) wanting to adhere to the law; (6) behaviour being too complicated; and (7) price being too low. Implications for practise are discussed.

Methodology for the at-home collection of urine samples for prostate cancer detection

Urine from patients with prostate cancer (PCa) contains gene transcripts that have been used for PCa diagnosis and prognosis. Historically, patient urine samples have been collected after a digital rectal examination of the prostate, which was thought necessary to boost the levels of prostatic secretions in the urine. We herein describe methodology that allows urine to be collected by patients at home and then posted to a laboratory for analysis. RNA yields and quality were comparable to those for post digital rectal examination urine, and there was improved sensitivity for the detection of TMPRSS2:ERG transcripts by RT-PCR. The At-Home collection protocol has opened up the potential to perform large-scale PCa studies without the inconvenience, cost, discomfort and expense of patients having to visit the clinic.

Exercise-induced attenuation of treatment side-effects in patients with newly diagnosed prostate cancer beginning androgen-deprivation therapy: a randomised controlled trial

OBJECTIVES

(i) To assess whether exercise training attenuates the adverse effects of treatment in patients with newly diagnosed prostate cancer beginning androgen-deprivation therapy (ADT), and (ii) to examine whether exercise-induced improvements are sustained after the withdrawal of supervised exercise.

PATIENTS AND METHODS

In all, 50 patients with prostate cancer scheduled for ADT were randomised to an exercise group (n = 24) or a control group (n = 26). The exercise group completed 3 months of supervised aerobic and resistance exercise training (twice a week for 60 min), followed by 3 months of self-directed exercise. Outcomes were assessed at baseline, 3- and 6-months. The primary outcome was difference in fat mass at 3-months. Secondary outcomes included: fat-free mass, cardiopulmonary exercise testing variables, QRISK^® 2 (ClinRisk Ltd, Leeds, UK) score, anthropometry, blood-borne biomarkers, fatigue, and quality of life (QoL).

RESULTS

At 3-months, exercise training prevented adverse changes in peak O₂ uptake (1.9 mL/kg/min, P = 0.038), ventilatory threshold (1.7 mL/kg/min, P = 0.013), O₂ uptake efficiency slope (0.21, P = 0.005), and fatigue (between-group difference in Functional Assessment of Chronic Illness Therapy-Fatigue score of 4.5 points, P = 0.024) compared with controls. After the supervised exercise was withdrawn, the differences in cardiopulmonary fitness and fatigue were not sustained, but the exercise group showed significantly better QoL (Functional Assessment of Cancer Therapy-Prostate difference of 8.5 points, P = 0.034) and a reduced QRISK2 score (-2.9%, P = 0.041) compared to controls.

CONCLUSION

A short-term programme of supervised exercise in patients with prostate cancer beginning ADT results in sustained improvements in QoL and cardiovascular events risk profile.

Characteristics and changes in characteristics of women and babies admitted to residential parenting services in New South Wales, Australia in the first year following birth: a population-based data linkage study 2000-2012

OBJECTIVE

To examine the characteristics of women and babies admitted to the residential parenting services (RPS) of Tresillian and Karitane in the first year following birth.

DESIGN

A linked population data cohort study was undertaken for the years 2000-2012.

SETTING

New South Wales (NSW), Australia.

PARTICIPANTS

All women giving birth and babies born in NSW were compared with those admitted to RPS.

RESULTS

During the time period there were a total of 1 097 762 births (2000-2012) in NSW and 32 991 admissions to RPS. Women in cohort 1: (those admitted to RPS) were older at the time of birth, more likely to be admitted as a private patient at the time of birth, be born in Australia and be having their first baby compared with women in cohort 2 (those not admitted to an RPS). Women admitted to RPS experienced more birth intervention (induction, instrumental birth, caesarean section), had more multiple births and were more likely to have a male infant. Their babies were also more likely to be resuscitated and have experienced birth trauma to the scalp. Between 2000 and 2012 the average age of women in the RPS increased by nearly 2 years; their infants were older on admission and women were less likely to smoke. Over the time period there was a drop in the numbers of women admitted to RPS having a normal vaginal birth and an increase in women having an instrumental birth.

CONCLUSION

Women who access RPS in the first year after birth are more socially advantaged and have higher birth intervention than those who do not, due in part to higher numbers birthing in the private sector where intervention rates are high. The rise in women admitted to RPS (2000-2012) who have had instrumental births is intriguing as overall rates did not increase.

Patient perspectives of vigorous intensity aerobic interval exercise prehabilitation prior to radical cystectomy: a qualitative focus group study

PURPOSE

Preoperative cardiopulmonary fitness is increasingly being recognized as an important factor influencing postoperative recovery outcomes in cancer patients. The aim of this study was to explore patient perspectives of preoperative high intensity aerobic interval exercise before radical cystectomy.

MATERIALS AND METHODS

Focus groups involving a purposive convenience sample of patients with bladder cancer (N = 14; mean age ± SD: 72.3 ± 6.0 years) were undertaken in a hospital education department. Data were analyzed using Framework analysis.

RESULTS

Participants identified physical (e.g., fitness) psychological (e.g., preparing for their operation) and social (e.g., peer support) benefits of the program. Key motivational factors for engaging in exercise prehabiliation were identified as social support, previous exercise experience and objective measures of progression. The need for clear information from healthcare providers to ensure that patients are adequately prepared for sessions was highlighted.

CONCLUSIONS

This qualitative study provides new insights into the perspectives and experiences of patients with bladder cancer regarding participation in preoperative vigorous intensity aerobic exercise. The study yielded novel perceptions on the physical, psychological and social health benefits accruing from the exercise program and patient views on program design features, which are important for informing future interventions and implementation strategies.IMPLICATIONS FOR REHABILITATIONA preoperative high intensity aerobic interval exercise program before radical cystectomy provides physical, psychological and social benefits to individuals living with bladder cancer.Supervised exercise, objective improvement, and peer and family support all contribute to motivation to engage with preoperative high intensity aerobic interval exercise.Individuals may require support post-radical cystectomy in order to continue with exercise due to the uncertainty around this.

epiCaPture: A Urine DNA Methylation Test for Early Detection of Aggressive Prostate Cancer

Purpose

Liquid biopsies that noninvasively detect molecular correlates of aggressive prostate cancer (PCa) could be used to triage patients, reducing the burdens of unnecessary invasive prostate biopsy and enabling early detection of high-risk disease. DNA hypermethylation is among the earliest and most frequent aberrations in PCa. We investigated the accuracy of a six-gene DNA methylation panel (Epigenetic Cancer of the Prostate Test in Urine [epiCaPture]) at detecting PCa, high-grade (Gleason score greater than or equal to 8) and high-risk (D’Amico and Cancer of the Prostate Risk Assessment] PCa from urine.

Patients and Methods

Prognostic utility of epiCaPture genes was first validated in two independent prostate tissue cohorts. epiCaPture was assessed in a multicenter prospective study of 463 men undergoing prostate biopsy. epiCaPture was performed by quantitative methylation-specific polymerase chain reaction in DNA isolated from prebiopsy urine sediments and evaluated by receiver operating characteristic and decision curves (clinical benefit). The epiCaPture score was developed and validated on a two thirds training set to one third test set.

Results

Higher methylation of epiCaPture genes was significantly associated with increasing aggressiveness in PCa tissues. In urine, area under the receiver operating characteristic curve was 0.64, 0.86, and 0.83 for detecting PCa, high-grade PCa, and high-risk PCa, respectively. Decision curves revealed a net benefit across relevant threshold probabilities. Independent analysis of two epiCaPture genes in the same clinical cohort provided analytical validation. Parallel epiCaPture analysis in urine and matched biopsy cores showed added value of a liquid biopsy.

Conclusion

epiCaPture is a urine DNA methylation test for high-risk PCa. Its tumor specificity out-performs that of prostate-specific antigen (greater than 3 ng/mL). Used as an adjunct to prostate-specific antigen, epiCaPture could aid patient stratification to determine need for biopsy.

A urine-based DNA methylation assay, ProCUrE, to identify clinically significant prostate cancer

Background

Prevention of unnecessary biopsies and overtreatment of indolent disease remains a challenge in the management of prostate cancer. Novel non-invasive tests that can identify clinically significant (intermediate-risk and high-risk) diseases are needed to improve risk stratification and monitoring of prostate cancer patients. Here, we investigated a panel of six DNA methylation biomarkers in urine samples collected post-digital rectal exam from patients undergoing prostate biopsy, for their utility to guide decision making for diagnostic biopsy and early detection of aggressive prostate cancer.

Results

We recruited 408 patients in risk categories ranging from benign to low-, intermediate-, and high-risk prostate cancer from three international cohorts. Patients were separated into 2/3 training and 1/3 validation cohorts. Methylation biomarkers were analyzed in post-digital rectal exam urinary sediment DNA by quantitative MethyLight assay and investigated for their association with any or aggressive prostate cancers.

We developed a Prostate Cancer Urinary Epigenetic (ProCUrE) assay based on an optimal two-gene (HOXD3 and GSTP1) LASSO model, derived from methylation values in the training cohort, and assessed ProCUrE’s diagnostic and prognostic ability for prostate cancer in both the training and validation cohorts.

ProCUrE demonstrated improved prostate cancer diagnosis and identification of patients with clinically significant disease in both the training and validation cohorts. Using three different risk stratification criteria (Gleason score, D’Amico criteria, and CAPRA score), we found that the positive predictive value for ProCUrE was higher (59.4–78%) than prostate specific antigen (PSA) (38.2–72.1%) for all risk category comparisons. ProCUrE also demonstrated additive value to PSA in identifying GS ≥ 7 PCa compared to PSA alone (DeLong’s test p = 0.039), as well as additive value to the PCPT risk calculator for identifying any PCa and GS ≥ 7 PCa (DeLong’s test p = 0.011 and 0.022, respectively).

Conclusions

ProCUrE is a promising non-invasive urinary methylation assay for the early detection and prognostication of prostate cancer. ProCUrE has the potential to supplement PSA testing to identify patients with clinically significant prostate cancer.

Electronic supplementary material

The online version of this article (10.1186/s13148-018-0575-z) contains supplementary material, which is available to authorized users.

Characteristics of prisoners with intellectual disabilities

BACKGROUND

Previous studies have found high rates of intellectual disabilities (ID) in prison. However, little is understood about prisoners with ID. This study aimed to identify prisoners with ID and compare their characteristics with prisoners without neurodevelopmental disorders with regard to demographic profile, mental health, suicide risk and offences.

METHOD

This was a descriptive, cross-sectional study carried out using face-to-face interviews with 240 participants in a London Category C prison. Standardised tools were used to assess prisoners for ID and mental disorder.

RESULTS

The study identified 18 prisoners as having ID. Participants with ID were less likely to be from a black or minority ethnic background, be over 35 years of age or have any qualifications. They were more likely to have been single, homeless or unemployed before coming into prison. Prisoners with ID were significantly more likely to have mental health problems and 25% had thought about suicide in the last month and 63% had attempted suicide in the past. Prisoners with ID were also more likely to be housed in the vulnerable prisoners' wing and significantly more likely to have committed robbery than other prisoners.

CONCLUSIONS

The findings confirm the presence of significant numbers of people with ID with high levels of mental illness in a male prison. Services across the CJS are required for this group, specifically, there is a need for raised awareness among those working in prison about ID and improved skills to recognise offenders with ID and address major gaps in current healthcare provision in prison.

Design and operating characteristic of a vacuum furnace for time-of-flight inelastic neutron scattering measurements

We present the design and operating characteristics of a vacuum furnace used for inelastic neutron scattering experiments on a time-of-flight chopper spectrometer. The device is an actively water cooled radiant heating furnace capable of performing experiments up to 1873 K. Inelastic neutron scattering studies performed with this furnace include studies of phonon dynamics and metallic liquids. We describe the design, control, characterization, and limitations of the equipment. Further, we provide comparisons of the neutron performance of our device with commercially available options. Finally we consider upgrade paths to improve performance and reliability.

Combination of RAD001 (everolimus) and docetaxel reduces prostate and breast cancer cell VEGF production and tumour vascularisation independently of sphingosine-kinase-1

Resistance to docetaxel is a key problem in current prostate and breast cancer management. We have recently discovered a new molecular mechanism of prostate cancer docetaxel chemoresistance mediated by the mammalian target of rapamycin (mTOR)/sphingosine-kinase-1 (SK1) pathway. Here we investigated the influence of this pathway on vascular endothelial growth factor (VEGF) production and tumour vascularisation in hormone resistant prostate and breast cancer models. Immunofluorescent staining of tumour sections from human oestrogen receptor (ER)-negative breast cancer patients showed a strong correlation between phosphorylated P70S6 kinase (mTOR downstream target), VEGF and SK1 protein expression. In hormone-insensitive prostate (PC3) and breast (MDA-MB-231 and BT-549) cancer cell lines the mTOR inhibitor RAD001 (everolimus) has significantly inhibited SK1 and VEGF expression, while low dose (5 nM) docetaxel had no significant effect. In these cell lines, SK1 overexpression slightly increased the basal levels of VEGF, but did not block the inhibitory effect of RAD001 on VEGF. In a human prostate xenograft model established in nude mice, RAD001 alone or in combination with docetaxel has suppressed tumour growth, VEGF expression and decreased tumour vasculature. Overall, our data demonstrate a new mechanism of an independent regulation of SK1 and VEGF by mTOR in hormone-insensitive prostate and breast cancers.

HIV and Hepatitis C Virus Screening Practices in a Geographically Diverse Sample of American Community Health Centers

Because of the advent of highly effective treatments, routine screening for HIV and hepatitis C virus (HCV) has been recommended for many Americans. This study explored the perceived barriers surrounding routine HIV and HCV screening in a diverse sample of community health centers (CHCs). The Community Health Applied Research Network (CHARN) is a collaboration of CHCs, with a shared clinical database. In July, 2013, 195 CHARN providers working in 12 CHCs completed a survey of their attitudes and beliefs about HIV and HCV testing. Summary statistics were generated to describe the prevalence of HIV and HCV and associated demographics by CHCs. HIV and HCV prevalence ranged from 0.1% to 5.7% for HIV and from 0.1% to 3.7% for HCV in the different CHCs. About 15% of the providers cared for at least 50 individuals with HIV and the same was true for HCV. Two-thirds saw less than 10 patients with HIV and less than half saw less than 10 patients with HCV. Less than two-thirds followed USPHS guidelines to screen all patients for HIV between the ages of 13 and 64, and only 44.4% followed the guidance to screen all baby boomers for HCV. Providers with less HIV experience tended to be more concerned about routine screening practices. More experienced providers were more likely to perceive lack of time being an impediment to routine screening. Many US CHC providers do not routinely screen their patients for HIV and HCV. Although additional education about the rationale for routine screening may be indicated, incentives to compensate providers for the additional time they anticipate spending in counseling may also facilitate increased screening rates.

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

Genetic variants identified by genome-wide association studies explain only a modest proportion of heritability, suggesting that meaningful associations lie 'hidden' below current thresholds. Here, we integrate information from association studies with epigenomic maps to demonstrate that enhancers significantly overlap known loci associated with the cardiac QT interval and QRS duration. We apply functional criteria to identify loci associated with QT interval that do not meet genome-wide significance and are missed by existing studies. We demonstrate that these 'sub-threshold' signals represent novel loci, and that epigenomic maps are effective at discriminating true biological signals from noise. We experimentally validate the molecular, gene-regulatory, cellular and organismal phenotypes of these sub-threshold loci, demonstrating that most sub-threshold loci have regulatory consequences and that genetic perturbation of nearby genes causes cardiac phenotypes in mouse. Our work provides a general approach for improving the detection of novel loci associated with complex human traits.

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

Genetic variants identified by genome-wide association studies explain only a modest proportion of heritability, suggesting that meaningful associations lie 'hidden' below current thresholds. Here, we integrate information from association studies with epigenomic maps to demonstrate that enhancers significantly overlap known loci associated with the cardiac QT interval and QRS duration. We apply functional criteria to identify loci associated with QT interval that do not meet genome-wide significance and are missed by existing studies. We demonstrate that these 'sub-threshold' signals represent novel loci, and that epigenomic maps are effective at discriminating true biological signals from noise. We experimentally validate the molecular, gene-regulatory, cellular and organismal phenotypes of these sub-threshold loci, demonstrating that most sub-threshold loci have regulatory consequences and that genetic perturbation of nearby genes causes cardiac phenotypes in mouse. Our work provides a general approach for improving the detection of novel loci associated with complex human traits.

DOI:http://dx.doi.org/10.7554/eLife.10557.001

Most complex traits are governed by a large number of genetic contributors, each playing only a modest effect. This makes it difficult to identify the genetic variants that increase disease risk, hindering the discovery of new drug targets and the development of new therapeutics.

To overcome this limitation in discovery power, the field of human genetics has traditionally sought increasingly large groups, or cohorts, of afflicted and non-afflicted individuals. Studies of large cohorts are a powerful approach for discovering new disease genes, but such groups are often impractical and sometimes impossible to obtain. However, it has become possible to complement the genetic evidence found in disease association studies with biological evidence of the effects of disease-associated genetic variants.

Wang et al. focus specifically on genetic sites, or loci, that do not affect protein sequence but instead affect the non-coding control regions. These are known as enhancer elements, as they can enhance the expression of nearby genes. These loci constitute the majority of disease regions, and thus are extremely important, but their discovery has been hindered by our relatively poor understanding of the human genome.

Chemical modifications known as epigenomic marks are indicative of enhancer regions. By studying the factors that affect heart rhythm, Wang et al. show that specific combinations of epigenomic marks are enriched in known trait-associated regions. This knowledge was then used to prioritize the further investigation of genetic regions that genome-wide association studies had only weakly linked to heart rhythm alterations. Wang et al. directly confirmed that genetic differences in “sub-threshold” regions indeed alter the activity of these regulatory regions in human heart cells. Furthermore, mutating or perturbing the predicted target genes of the sub-threshold enhancers caused heart defects in mouse and zebrafish.

Wang et al. have demonstrated that epigenome maps can help to distinguish which sub-threshold regions from genome-wide association studies are more likely to contribute to a disease. This allows for the discovery of new disease genes with much smaller cohorts than would be needed otherwise, thus speeding up the development of new therapeutics by many years.

DOI:http://dx.doi.org/10.7554/eLife.10557.002

Characteristics of prisoners with neurodevelopmental disorders and difficulties

BACKGROUND

Previous studies have found high rates of attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD) and intellectual disability (ID) within the criminal justice system (CJS). However, little is understood about prisoners with neurodevelopmental disorders and difficulties (NDD) or their needs. This study aimed to identify prisoners with NDD and compare their characteristics with prisoners without NDD on a range of socio-demographic and social functioning measures.

METHOD

This was a descriptive, cross-sectional study carried out using face-to-face interviews with 240 participants in a London Category C prison. Standardised tools were used to assess prisoners for ADHD, ASD and ID.

RESULTS

The study identified 87 prisoners who screened positive for one or more type of NDD. Participants with NDD were significantly younger and more likely to be single [(odds ratio) OR = 2.1], homeless (OR = 3.4) or unemployed (OR = 2.6) before they came into prison. They also had poorer educational achievements that those without NDD. Over 80% of those with NDD had a previous conviction or imprisonment.

CONCLUSIONS

The findings confirm the presence of significant numbers of people with NDD in a male prison. Services across the CJS are required for this group; specifically, there is a need for raised awareness among those working in the CJS to improve the recognition of offenders with NDD. Services in the community need to work with individuals with NDD who are at risk of offending, targeting those who are homeless, unemployed and have poor employment opportunities.

A new apparatus design for high temperature (up to 950°C) quasi-elastic neutron scattering in a controlled gaseous environment

A design for a sample cell system suitable for high temperature Quasi-Elastic Neutron Scattering (QENS) experiments is presented. The apparatus was developed at the Spallation Neutron Source in Oak Ridge National Lab where it is currently in use. The design provides a special sample cell environment under controlled humid or dry gas flow over a wide range of temperature up to 950 °C. Using such a cell, chemical, dynamical, and physical changes can be studied in situ under various operating conditions. While the cell combined with portable automated gas environment system is especially useful for in situ studies of microscopic dynamics under operational conditions that are similar to those of solid oxide fuel cells, it can additionally be used to study a wide variety of materials, such as high temperature proton conductors. The cell can also be used in many different neutron experiments when a suitable sample holder material is selected. The sample cell system has recently been used to reveal fast dynamic processes in quasi-elastic neutron scattering experiments, which standard probes (such as electrochemical impedance spectroscopy) could not detect. In this work, we outline the design of the sample cell system and present results demonstrating its abilities in high temperature QENS experiments.

Direct load monitoring of rolling bearing contacts using ultrasonic time of flight

The load applied by each rolling element on a bearing raceway controls friction, wear and service life. It is possible to infer bearing load from load cells or strain gauges on the shaft or bearing housing. However, this is not always simply and uniquely related to the real load transmitted by rolling elements directly to the raceway. Firstly, the load sharing between rolling elements in the raceway is statically indeterminate, and secondly, in a machine with non-steady loading, the load path is complex and highly transient being subject to the dynamic behaviour of the transmission system. This study describes a method to measure the load transmitted directly by a rolling element to the raceway by using the time of flight (ToF) of a reflected ultrasonic pulse. A piezoelectric sensor was permanently bonded onto the bore surface of the inner raceway of a cylindrical roller bearing. The ToF of an ultrasonic pulse from the sensor to the roller–raceway contact was measured. This ToF depends on the speed of the wave and the thickness of the raceway. The speed of an ultrasonic wave changes with the state of the stress, known as the acoustoelastic effect. The thickness of the material varies when deflection occurs as the contacting surfaces are subjected to load. In addition, the contact stiffness changes the phase of the reflected signal and in simple peak-to-peak measurement, this appears as a change in the ToF. In this work, the Hilbert transform was used to remove this contact dependent phase shift. Experiments have been performed on both a model line contact and a single row cylindrical roller bearing from the planet gear of a wind turbine epicyclic gearbox. The change in ToF under different bearing loads was recorded and used to determine the deflection of the raceway. This was then related to the bearing load using a simple elastic contact model. Measured load from the ultrasonic reflection was compared with the applied bearing load with good agreement. The technique shows promise as an effective method for load monitoring in real-world bearing applications.

Building Data-Driven Pathways From Routinely Collected Hospital Data: A Case Study on Prostate Cancer

BACKGROUND

Routinely collected data in hospitals is complex, typically heterogeneous, and scattered across multiple Hospital Information Systems (HIS). This big data, created as a byproduct of health care activities, has the potential to provide a better understanding of diseases, unearth hidden patterns, and improve services and cost. The extent and uses of such data rely on its quality, which is not consistently checked, nor fully understood. Nevertheless, using routine data for the construction of data-driven clinical pathways, describing processes and trends, is a key topic receiving increasing attention in the literature. Traditional algorithms do not cope well with unstructured processes or data, and do not produce clinically meaningful visualizations. Supporting systems that provide additional information, context, and quality assurance inspection are needed.

OBJECTIVE

The objective of the study is to explore how routine hospital data can be used to develop data-driven pathways that describe the journeys that patients take through care, and their potential uses in biomedical research; it proposes a framework for the construction, quality assessment, and visualization of patient pathways for clinical studies and decision support using a case study on prostate cancer.

METHODS

Data pertaining to prostate cancer patients were extracted from a large UK hospital from eight different HIS, validated, and complemented with information from the local cancer registry. Data-driven pathways were built for each of the 1904 patients and an expert knowledge base, containing rules on the prostate cancer biomarker, was used to assess the completeness and utility of the pathways for a specific clinical study. Software components were built to provide meaningful visualizations for the constructed pathways.

RESULTS

The proposed framework and pathway formalism enable the summarization, visualization, and querying of complex patient-centric clinical information, as well as the computation of quality indicators and dimensions. A novel graphical representation of the pathways allows the synthesis of such information.

CONCLUSIONS

Clinical pathways built from routinely collected hospital data can unearth information about patients and diseases that may otherwise be unavailable or overlooked in hospitals. Data-driven clinical pathways allow for heterogeneous data (ie, semistructured and unstructured data) to be collated over a unified data model and for data quality dimensions to be assessed. This work has enabled further research on prostate cancer and its biomarkers, and on the development and application of methods to mine, compare, analyze, and visualize pathways constructed from routine data. This is an important development for the reuse of big data in hospitals.

Impact of delivery models on understanding genomic risk for type 2 diabetes

BACKGROUND

Genetic information, typically communicated in-person by genetic counselors, can be challenging to comprehend; delivery of this information online--as is becoming more common--has the potential of increasing these challenges.

METHODS

To address the impact of the mode of delivery of genomic risk information, 300 individuals were recruited from the general public and randomized to receive genomic risk information for type 2 diabetes mellitus in-person from a board-certified genetic counselor or online through the testing company's website.

RESULTS

Participants were asked to indicate their genomic risk and overall lifetime risk as reported on their test report as well as to interpret their genomic risk (increased, decreased, or same as population). For each question, 59% of participants correctly indicated their risk. Participants who received their results in-person were more likely than those who reviewed their results on-line to correctly interpret their genomic risk (72 vs. 47%, p = 0.0002) and report their actual genomic risk (69 vs. 49%, p = 0.002).

CONCLUSIONS

The delivery of personal genomic risk through a trained health professional resulted in significantly higher comprehension. Therefore, if the online delivery of genomic test results is to become more widespread, further evaluation of this method of communication may be needed to ensure the effective presentation of results to promote comprehension.

Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility

BACKGROUND

Genetic studies have identified numerous genes reproducibly associated with asthma, yet these studies have focussed almost entirely on single nucleotide polymorphisms (SNPs), and virtually ignored another highly prevalent form of genetic variation: Copy Number Variants (CNVs).

OBJECTIVE

To survey the prevalence of CNVs in genes previously associated with asthma, and to assess whether CNVs represent the functional asthma-susceptibility variants at these loci.

METHODS

We genotyped 383 asthmatic trios participating in the Childhood Asthma Management Program (CAMP) using a competitive genomic hybridization (CGH) array designed to interrogate 20 092 CNVs. To ensure comprehensive assessment of all potential asthma candidate genes, we purposely used liberal asthma gene inclusion criteria, resulting in consideration of 270 candidate genes previously implicated in asthma. We performed statistical testing using FBAT-CNV.

RESULTS

Copy number variation in asthma candidate genes was prevalent, with 21% of tested genes residing near or within one of 69 CNVs. In six instances, the complete candidate gene sequence resides within the CNV boundaries. On average, asthmatic probands carried six asthma-candidate CNVs (range 1-29). However, the vast majority of identified CNVs were of rare frequency (< 5%) and were not statistically associated with asthma. Modest evidence for association with asthma was observed for 2 CNVs near NOS1 and SERPINA3. Linkage disequilibrium analysis suggests that CNV effects are unlikely to explain previously detected SNP associations with asthma.

CONCLUSIONS AND CLINICAL RELEVANCE

Although a substantial proportion of asthma-susceptibility genes harbour polymorphic CNVs, the majority of these variants do not confer increased asthma risk. The lack of linkage disequilibrium (LD) between CNVs and asthma-associated SNPs suggests that these CNVs are unlikely to represent the functional variant responsible for most known asthma associations.

Abstract 285: Overexpression of SK3 in a Murine Model Results in Sudden Cardiac Death

Background: Recently, the gene responsible for encoding SK3, KCNN3, was implicated in a genome-wide association study as a susceptibility locus for atrial fibrillation. SK3 is one of a family of three small conductance, voltage-independent, calcium-activated potassium channels which is abundantly expressed in cardiac tissues. Therefore, we hypothesized that transcriptional misregulation of the KCNN3 gene could result in arrhythmogenesis.

Methods: We characterized a mouse line which had constitutive ubiquitous overexpression of Kcnn3 using ambulatory cardiac rhythm monitoring, optical mapping and in vivo electrophysiology studies. Both homozygote (SK3 T/T ) and heterozygote (SK3 T/+ ) animals were compared to their wild-type (SK3 +/+ ) littermates for assessment of cardiac phenotypes.

Results: SK3 T/T mice displayed increased expression of SK3, as assessed by qRT-PCR, in all four chambers of the heart, although highest increase of expression was observed in the ventricles. Examinations of SK3 T/T mice revealed no gross morphological changes in the myocardium, no observable cardiac fibrosis, and normal echocardiograms when compared to SK3 +/+ mice. However, pups from SK3 T/+ crosses did not produce expected Mendelian ratios (SK3 +/+ = 17%), and 7 out of 19 SK3 +/+ mice died suddenly by 3 months of age, whereas all of the SK3 T/+ or SK3 +/+ survived. To address potential mechanisms, we performed ambulatory monitoring on mice beginning at approximately one month of age. Of the 6 SK3 +/+ mice, 4 died suddenly, whereas neither of the wild-type controls expired. The cardiac rhythm recorded at the time of death in three of the four mice was heart block followed by severe bradycardia. Additionally, during the period of ambulatory monitoring, SK3 T/T mice had a lower mean heart rate compared to the SK3 +/+ control mice, and SK3 T/T mice also displayed frequent episodes of atrioventricular dissociation, both at rest and during periods of activity. SK3 T/T mice also displayed more pronounced variability of the heart rate and the PR interval. Optical mapping revealed slower ventricular conduction velocity.

Conclusion: These data suggest a mechanism whereby overexpression of SK3 leads to sudden death due to bradyarrhythmias and heart block.