High resolution gamma-ray spectrometer with MHz capabilities for runaway electron studies at ASDEX Upgrade

A new gamma-ray spectrometer with MHz capabilities has been developed to measure the bremsstrahlung emission spectrum in the gamma-ray energy band generated by MeV range runaway electrons in disruption experiments at ASDEX Upgrade. Properties of the runaway electrons are inferred from the measured bremsstrahlung spectrum by a deconvolution technique, particularly with regard to their maximum energy. Changes induced to the runaway electron velocity space are unambiguously observed both in massive gas injection and resonant magnetic perturbation experiments with the detector.

The upgraded JET gamma-ray cameras based on high resolution/high count rate compact spectrometers

The JET gamma-ray cameras have been recently upgraded within the gamma-ray camera upgrade project in support of development of JET high performance deuterium plasma scenarios and in preparation of deuterium-tritium experiments. New, dedicated detectors based on a LaBr₃ crystal and silicon photo-multipliers have been developed and replaced pre-existing CsI detectors in all 19 channels. The new instrument gives opportunity of making two-dimensional gamma-ray measurements with a counting rate capability exceeding 1 MCounts/s (MCps) and energy resolution better than 5% at 1.1 MeV. The upgrade is of relevance for fast ion and runaway electron physics studies in high performance deuterium discharges and also in plasmas with tritium at neutron yields in the range up to about 5 × 10¹⁷ n/s.

Molecular epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) isolated from milk of cows with subclinical mastitis

Bovine mastitis has been a concern for dairy herd for decades. The adaptation capacity of one of the main species responsible for this disease, Staphylococcus aureus (S. aureus), plays a pivotal role in this issue. The aim of this study was to establish a molecular and phenotypic profile of 285 S. aureus strains isolated from milk of subclinical mastitis cows from 18 different farms in São Paulo State using spa typing, multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE), agr cluster (I, II, III and IV) typing, PCR for genes including enterotoxins (sea, seb, sec, sed, see, seg, seh, sei), toxic shock syndrome toxin (tsst-1), and Panton-Valentine leucocidin (pvl), as well as in vitro resistance assays for 12 antibiotics. The results showed a wide variety of strains with a high toxigenic potential; concomitantly, sec, seg and seh were prevalent. In addition, we observed a predominance of the spa types t605 (ST 126, CC126) and t127 (ST1, CC1) and the unusual presence of t321 causing bovine mastitis, which has been previously reported only in swine. The most frequent ST were ST126 (70.5%) and ST1 (10.5%). Regarding PFGE, we observed four major groups and six profile patterns. The highest resistance was observed for streptomycin (9.5%), followed by tetracycline (3.5%), clindamycin (9.3%), and erythromycin (2.8%). The tsst-1 gene was detected in 36.8% of isolates and pvl was not observed. One hundred and thirty-six (47.7%) isolates possessed agr type II, followed by types III (20%) and I (8.1%), with type IV not being detected. We observed that the same spa type could result in different PFGE profiles, so the exclusive use of spa type sequences can lead to incorrect interpretations regarding the spread of clones in an epidemiological context.

Dietary intake and eating behavior in depot medroxyprogesterone acetate users: a systematic review

Because of weight gain, women often discontinue hormonal contraception, especially depot medroxyprogesterone acetate (DMPA). Our objective was to conduct a systematic review of studies describing dietary intake or eating behavior in DMPA users to understand whether the use of DMPA is associated with changes in dietary habits and behaviors leading to weight gain. We searched the PubMed, POPLINE, CENTRAL Cochrane, Web of Science, and EMBASE databases for reports published in English between 1980 and 2017 examining dietary intake or eating behavior in healthy women in reproductive age and adolescents using DMPA (150 mg/mL). Of the 749 publications screened, we excluded 742 due to duplicates (96), not addressing the key research question (638), not reporting dietary intake data (4), and not evaluating the relationship of body weight and dietary or eating behaviors (4). We identified seven relevant studies, including one randomized placebo-controlled trial, one non-randomized paired clinical trial, and five cohort studies. The randomized trial found no association and the other reports were inconsistent. Findings varied from no change in dietary intake or eating behavior with DMPA use to increased appetite in the first six months of DMPA use. Few studies report dietary intake and eating behavior in DMPA users and the available data are insufficient to conclude whether DMPA use is associated with changes in dietary habits or behavior leading to weight gain.

Detection of Suicidality in Adolescents with Autism Spectrum Disorders: Developing a Natural Language Processing Approach for Use in Electronic Health Records

Over 15% of young people with autism spectrum disorders (ASD) will contemplate or attempt suicide during adolescence. Yet, there is limited evidence concerning risk factors for suicidality in childhood ASD. Electronic health records (EHRs) can be used to create retrospective clinical cohort data for large samples of children with ASD. However systems to accurately extract suicidality-related concepts need to be developed so that putative models of suicide risk in ASD can be explored. We present a systematic approach to 1) adapt Natural Language Processing (NLP) solutions to screen with high sensitivity for reference to suicidal constructs in a large clinical ASD EHR corpus (230,465 documents), and 2) evaluate within a screened subset of 500 patients, the performance of an NLP classification tool for positive and negated suicidal mentions within clinical text. When evaluated, the NLP classification tool showed high system performance for positive suicidality with precision, recall, and F1 scores all > 0.85 at a document and patient level. The application therefore provides accurate output for epidemiological research into the factors contributing to the onset and recurrence of suicidality, and potential utility within clinical settings as an automated surveillance or risk prediction tool for specialist ASD services.

Spatial analysis of polybrominated diphenylethers (PBDEs) and polybrominated biphenyls (PBBs) in fish collected from UK and proximate marine waters

Some commonly consumed marine fish species are considered to display a higher risk of bio-accumulating organic environmental contaminants such as PBDEs. As part of a study to investigate the spatial distribution of these contaminants, data on polybrominated diphenlyethers (PBDEs) and polybrominated biphenyls (PBBs) were collected and analysed by introducing a web-based resource which enables efficient spatial, species and concentration level representations. Furthermore, hierarchical cluster analyses permits correlations within the data to be predicted. The data provide current information on levels of PBDE and PBB occurrence, allowing identification of locations that show higher contaminant levels. 135 fish samples of various species were analysed from UK marine waters, but encompassing the waters around Norway in the North and to the Algarve in the South. PBDEs were observed in all samples with the majority of measured congeners being detected. The concentrations ranged from 0.087 μg/kg to 8.907 μg/kg whole weight (ww) for the sum of all measured PBDE congeners. PBBs occurred less frequently showing a corresponding range of <0.02 μg/kg to 0.97 μg/kg ww for the sum of seven PBB congeners. Concentrations vary depending on species and locations where landed, e.g. PBBs occurred more frequently and at higher levels in grey mullet from French waters. The high frequency of PBDE occurrence makes it prudent to continue the monitoring of these commonly consumed marine fish species. The web-based resource provides a flexible and efficient tool for assessors and policy-makers to monitor and evaluate levels within caught fish species improving evidenced-based decision processes.

Predictors of human PBDE body burdens for a UK cohort

Human exposure to polybrominated diphenyl ethers (PBDEs) was investigated in a cohort of 20 UK adults along with their anthropometric covariates and relevant properties such as room surveys, lifestyle, diet and activity details. Selected PBDE congeners were measured in matched samples of indoor dust (n = 41), vehicles (n = 8), duplicate diet (n = 24), serum (n = 24) and breast milk (n = 6). Combined exposure estimates via dust and diet revealed total PBDE intakes of 104 to 1,440 pg kg^-1 bw d^-1 for ΣBDEs_3-7 and 1,170 to 17,000 pg kg^-1 bw d^-1 for BDE-209. These adult intakes are well within health reference doses suggested by the European Food Safety Authority (EFSA) and the US EPA. Diet was the primary source of intake of BDE_3-7 congeners for the majority of the cohort, with dust the primary source of BDE-209. Primary sources of PBDE exposure vary between countries and regions with differing fire prevention regulations. Estimated infant exposures (ages 1.5-4.5 years) showed that BDE-99 intake for one of the households did not meet EFSA's recommended margin of exposure, a further two households had borderline PBDE exposures for high level dust and diet intake. Males and those having a lower body fat mass had higher serum BDE-153. Higher meat consumption was significantly correlated with higher BDEs_3-7 in serum. A reduction in dietary BDEs_3-7 would therefore result in the greatest reduction in BDE-99 exposure. Rooms containing PUF sofas or armchairs over 20 years old had more BDEs_3-7 in their dust, and rooms with carpets or rugs of that age had higher dust BDE-209. Dusting rooms more frequently resulted in significantly lower concentrations of all major congeners in their dust. Correlation between BDE-209 body burden and dust or diet exposure was limited by its low bioaccessibility. Although vehicle dust contained the highest concentrations of BDEs_3-7 and BDE-209, serum BDEs_3-7 correlated most strongly with bedroom dust.

Implementation of the new multichannel X-mode edge density profile reflectometer for the ICRF antenna on ASDEX Upgrade

A new multichannel frequency modulated continuous-wave reflectometry diagnostic has been successfully installed and commissioned on ASDEX Upgrade to measure the plasma edge electron density profile evolution in front of the Ion Cyclotron Range of Frequencies (ICRF) antenna. The design of the new three-strap ICRF antenna integrates ten pairs (sending and receiving) of microwave reflectometry antennas. The multichannel reflectometer can use three of these to measure the edge electron density profiles up to 2 × 10¹⁹ m^-3, at different poloidal locations, allowing the direct study of the local plasma layers in front of the ICRF antenna. ICRF power coupling, operational effects, and poloidal variations of the plasma density profile can be consistently studied for the first time. In this work the diagnostic hardware architecture is described and the obtained density profile measurements were used to track outer radial plasma position and plasma shape.

Performance of the prototype LaBr3 spectrometer developed for the JET gamma-ray camera upgrade

In this work, we describe the solution developed by the gamma ray camera upgrade enhancement project to improve the spectroscopic properties of the existing JET γ-ray camera. Aim of the project is to enable gamma-ray spectroscopy in JET deuterium-tritium plasmas. A dedicated pilot spectrometer based on a LaBr₃ crystal coupled to a silicon photo-multiplier has been developed. A proper pole zero cancellation network able to shorten the output signal to a length of 120 ns has been implemented allowing for spectroscopy at MHz count rates. The system has been characterized in the laboratory and shows an energy resolution of 5.5% at E_γ = 0.662 MeV, which extrapolates favorably in the energy range of interest for gamma-ray emission from fast ions in fusion plasmas.

Cohort profile of the South London and Maudsley NHS Foundation Trust Biomedical Research Centre (SLaM BRC) Case Register: current status and recent enhancement of an Electronic Mental Health Record-derived data resource

PURPOSE

The South London and Maudsley National Health Service (NHS) Foundation Trust Biomedical Research Centre (SLaM BRC) Case Register and its Clinical Record Interactive Search (CRIS) application were developed in 2008, generating a research repository of real-time, anonymised, structured and open-text data derived from the electronic health record system used by SLaM, a large mental healthcare provider in southeast London. In this paper, we update this register's descriptive data, and describe the substantial expansion and extension of the data resource since its original development.

PARTICIPANTS

Descriptive data were generated from the SLaM BRC Case Register on 31 December 2014. Currently, there are over 250,000 patient records accessed through CRIS.

FINDINGS TO DATE

Since 2008, the most significant developments in the SLaM BRC Case Register have been the introduction of natural language processing to extract structured data from open-text fields, linkages to external sources of data, and the addition of a parallel relational database (Structured Query Language) output. Natural language processing applications to date have brought in new and hitherto inaccessible data on cognitive function, education, social care receipt, smoking, diagnostic statements and pharmacotherapy. In addition, through external data linkages, large volumes of supplementary information have been accessed on mortality, hospital attendances and cancer registrations.

FUTURE PLANS

Coupled with robust data security and governance structures, electronic health records provide potentially transformative information on mental disorders and outcomes in routine clinical care. The SLaM BRC Case Register continues to grow as a database, with approximately 20,000 new cases added each year, in addition to extension of follow-up for existing cases. Data linkages and natural language processing present important opportunities to enhance this type of research resource further, achieving both volume and depth of data. However, research projects still need to be carefully tailored, so that they take into account the nature and quality of the source information.

Influence of oestrogen deficiency on the development of apical periodontitis

AIM

To evaluate the effects of a long period of oestrogen deficiency on the development of apical periodontitis in rats.

METHODOLOGY

Wistar rats (n = 24), 3 months old, evaluated by vaginal cytology, were included in the study. Twelve animals were ovariectomized (OVX group) and the other 12 were sham operated (control group). One hundred and twenty days after castration, the pulps of the left mandibular first molars were exposed to induce the development of apical periodontitis. Body mass was verified on a weekly basis. Following 21 and 40 days of lesion induction, the animals were sacrificed. Blood was collected for biochemical analysis, and mandibles were removed for radiographic analysis. Comparative analysis of the data was performed by the nonparametric Kruskal-Wallis and Dunn's multiple-comparisons tests. The t-test was applied to compare the oestrogen levels between control and OVX groups.

RESULTS

Radiographs revealed that apical periodontitis lesions were significantly larger in the 40-day OVX group when compared with both 40-day (P < 0.05) and 21-day (P < 0.001) control groups. Serum oestrogen levels were significantly lower in the OVX group (P < 0.01), confirming the efficacy of castration. Oestrogen deficiency resulted in significantly greater body mass gain (P < 0.01) in 40-day OVX group when compared with 40-day control group. Serum concentrations of calcium were similar between groups (P > 0.05). Alkaline phosphatase levels, although higher in the OVX groups (21 and 40 days), were not significantly different.

CONCLUSIONS

Ovariectomized rats had significantly larger apical periodontitis lesions after 40 days of pulp exposure when compared with controls. These findings suggest that bone alterations as a result of long periods of oestrogen deficiency can influence the progression of apical periodontitis.

Electrochemical oxidation of humic acid and sanitary landfill leachate: Influence of anode material, chloride concentration and current density

The influence of applied current density and chloride ion concentration on the ability of Ti/Pt/PbO2 and Ti/Pt/SnO2-Sb2O4 anodes for the electrochemical oxidation of humic acid and sanitary landfill leachate samples was assessed and compared with that of BDD anode. For the experimental conditions used, results show that both organic load and nitrogen removal rates increase with the applied current density and chloride ion concentration, although there is an optimum COD/[Cl-]0 ratio below which there is no further increase in COD removal. Metal oxide anodes present a similar performance to that of BDD, being the results obtained for Ti/Pt/PbO2 slightly better than for Ti/Pt/SnO2-Sb2O4. Contrary to BDD, Ti/Pt/PbO2 promotes lower nitrate formation and is the most suitable material for total nitrogen elimination. The importance of the optimum ratio of Cl-/COD/NH4 +initial concentrations is discussed.

Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid

BACKGROUND

Dietary exposure to cytotoxic and carcinogenic aristolochic acid (AA) causes severe nephropathy typically associated with urologic cancers. Monitoring of AA exposure uses biomarkers such as aristolactam-DNA adducts, detected by mass spectrometry in the kidney cortex, or the somatic A>T transversion pattern characteristic of exposure to AA, as revealed by previous DNA-sequencing studies using fresh-frozen tumors.

METHODS

Here, we report a low-coverage whole-exome sequencing method (LC-WES) optimized for multisample detection of the AA mutational signature, and demonstrate its utility in 17 formalin-fixed paraffin-embedded urothelial tumors obtained from 15 patients with endemic nephropathy, an environmental form of AA nephropathy.

RESULTS

LC-WES identified the AA signature, alongside signatures of age and APOBEC enzyme activity, in 15 samples sequenced at the average per-base coverage of approximately 10×. Analysis at 3 to 9× coverage revealed the signature in 91% of the positive samples. The exome-wide distribution of the predominant A>T transversions exhibited a stochastic pattern, whereas 83 cancer driver genes were enriched for recurrent nonsynonymous A>T mutations. In two patients, pairs of tumors from different parts of the urinary tract, including the bladder, harbored overlapping mutation patterns, suggesting tumor dissemination via cell seeding.

CONCLUSIONS

LC-WES analysis of archived tumor tissues is a reliable method applicable to investigations of both the exposure to AA and its biologic effects in human carcinomas.

IMPACT

By detecting cancers associated with AA exposure in high-risk populations, LC-WES can support future molecular epidemiology studies and provide evidence-base for relevant preventive measures.

Chemical characterization of a red raspberry fruit extract and evaluation of its pharmacological effects in experimental models of acute inflammation and collagen-induced arthritis

Berries are an important dietary source of fibres, vitamins, minerals and some biologically active non-nutrients. A red raspberry fruit extract was characterized in terms of phenolic content and the anti-inflammatory properties and protective effects were evaluated in two experimental models of inflammation. The antioxidant potential of the extract, the cellular antioxidant activity and the effects over neutrophils' oxidative burst were also studied to provide a mechanistic insight for the anti-inflammatory effects observed. The extract was administered in a dose of 15 mg kg(-1), i.p. and significantly inhibited paw oedema formation in the rat. The same dose was administered via i.p. and p.o. routes in the collagen-induced arthritis model in the rat. The extract showed pharmacological activity and was able to significantly reduce the development of clinical signs of arthritis and markedly reduce the degree of bone resorption, soft tissue swelling and osteophyte formation, preventing articular destruction in treated animals.