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.

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.