Establishment of “The South African Bioinformatics Student Council” and activity highlights:

The South African Society for Bioinformatics1 (SASBi) was officially formed in September 2012 during a joint Congress with the South African Genetics Society (SAGS). Prior to this there was no official body to represent bioinformatic researchers and students in the country. The establishment of SASBi also led to the establishment of the Student Society as a platform for students to meet and discuss their research activities, but also to socialise and broaden their network of knowledge and friendships. A small group of students joined as volunteers to pioneer and set up a SASBi Student Council (SASBiSC). As a first step, one representative, selected from the attendees present at the first Joint Congress of SASBi and SAGS, was elected to the main SASBi Council

GenGraph: a python module for the simple generation and manipulation of genome graphs

Abstract Background As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is closely related to the isolate, or one that is annotated in detail. One promising solution to this problem is through the graph based representation of collections of genomes as a single genome graph. Though there are currently a handful of tools that can create genome graphs and have demonstrated the advantages of this new paradigm, there still exists a need for flexible tools that can be used by researchers to overcome challenges in genomics studies. Results We present GenGraph, a Python toolkit and accompanying modules that use existing multiple sequence alignment tools to create genome graphs. Python is one of the most popular coding languages for the biological sciences, and by providing these tools, GenGraph makes it easier to experiment and develop new tools that utilise genome graphs. The conceptual model used is highly intuitive, and as much as possible the graph structure represents the biological relationship between the genomes. This design means that users will quickly be able to start creating genome graphs and using them in their own projects. We outline the methods used in the generation of the graphs, and give some examples of how the created graphs may be used. GenGraph utilises existing file formats and methods in the generation of these graphs, allowing graphs to be visualised and imported with widely used applications, including Cytoscape, R, and Java Script. Conclusions GenGraph provides a set of tools for generating graph based representations of sets of sequences with a simple conceptual model, written in the widely used coding language Python, and publicly available on Github

A survey of psychological support provision for people with inflammatory arthritis in secondary care in England

© 2014 The Authors. Objectives: The consequences of inflammatory arthritis can include depression, anxiety and low mood, reducing patients' quality of life and increasing pressure on the healthcare system. Treatment guidelines recommend psychological support, but data are lacking on the provision available. Methods: A postal survey concerning psychological support provision was sent to rheumatology units in 143 acute trusts across England. Nurses from 73 rheumatology units (51%) responded. Results: Overall, 73% rated their unit's psychological support provision as 'inadequate' and only 4% rated it as 'good'. Few units believed that psychological support did not fall within their remit (12%), yet only 8% had a psychologist in the team. Most units (68%) did not routinely screen patients to identify psychological difficulties. Referral to other service providers was reported in 42% of units, with 3% very satisfied with this provision. Within units, services containing elements of psychological support ranged from occupational therapy (81%) to psychology/counselling (14%). Psychological approaches used by team members ranged from shared decision making (77%) to cognitive-behavioural approaches (26%). The current barriers to providing psychological support were lack of clinical time and available training (86% and 74%, respectively), and delivery costs (74%). Future facilitators included management support (74%) and availability of skills training (74%). Conclusions: Rheumatology units viewed psychological support provision as part of their remit but rated their overall provision as inadequate, despite some team members using psychological skills. To improve provision, clinicians' training needs must be addressed and organizational support generated, and further research needs to define adequate psychological support provision from the patient perspective

Patients’ Perspectives on the Psychological Impact of Inflammatory Arthritis and Meeting the Associated Support Needs: Open-Ended Responses in a Multi-Centre Survey

Copyright © 2016 John Wiley & Sons, Ltd. Objectives: Psychological support for inflammatory arthritis is recommended in rheumatology treatment guidelines. Previous research found that high numbers of patients would access such support but that provision is often inconsistent and inadequate. The present study explored patients’ perspectives on the nature of the psychological impact of inflammatory arthritis and how to meet the associated support needs. Methods: A cross-sectional survey was conducted, using questionnaires which included three open-ended questions about helpful and unhelpful psychological support. The questionnaires were administered to 1,080 patients at six regional rheumatology units across England, and 1,200 members of a national patient charity. Results: A total of 1,210 (53%) patients completed the questionnaire, with 779 (64%) responding to the open-ended questions: 80% female; mean age 59 years (12.6); disease duration 10 years (40%). Data were analysed using a hybrid content analysis. Four categories emerged: challenges of an altered life course (negative emotions, isolation and loneliness, a dysfunctional body, loss, strained relationships, and fears for the future); poor communication (feeling unheard, clinicians’ reluctance to address psychological issues, a lack of help to manage pain and fatigue, and struggling to ask for help); understood by others (sharing with people who have arthritis, supportive family and friends, whole team support, and understanding from clinicians); and acquiring strategies (ways of coping). Conclusions: Psychological distress was commonplace, and often attributed to fatigue and pain. In addition to peers and family, patients looked to the rheumatology team for validation and support. Further research will address the skills training needs of rheumatology teams to meet patients’ psychological support requirements

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Search for direct stau production in events with two hadronic tau-leptons in root s=13 TeV pp collisions with the ATLAS detector

A search for the direct production of the supersymmetric partners ofτ-leptons (staus) in final stateswith two hadronically decayingτ-leptons is presented. The analysis uses a dataset of pp collisions corresponding to an integrated luminosity of139fb−1, recorded with the ATLAS detector at the LargeHadron Collider at a center-of-mass energy of 13 TeV. No significant deviation from the expected StandardModel background is observed. Limits are derived in scenarios of direct production of stau pairs with eachstau decaying into the stable lightest neutralino and oneτ-lepton in simplified models where the two staumass eigenstates are degenerate. Stau masses from 120 GeV to 390 GeV are excluded at 95% confidencelevel for a massless lightest neutralino

Search for chargino-neutralino production with mass splittings near the electroweak scale in three-lepton final states in √s=13 TeV pp collisions with the ATLAS detector

A search for supersymmetry through the pair production of electroweakinos with mass splittings near the electroweak scale and decaying via on-shell W and Z bosons is presented for a three-lepton final state. The analyzed proton-proton collision data taken at a center-of-mass energy of √s=13  TeV were collected between 2015 and 2018 by the ATLAS experiment at the Large Hadron Collider, corresponding to an integrated luminosity of 139  fb−1. A search, emulating the recursive jigsaw reconstruction technique with easily reproducible laboratory-frame variables, is performed. The two excesses observed in the 2015–2016 data recursive jigsaw analysis in the low-mass three-lepton phase space are reproduced. Results with the full data set are in agreement with the Standard Model expectations. They are interpreted to set exclusion limits at the 95% confidence level on simplified models of chargino-neutralino pair production for masses up to 345 GeV

Baseline factors associated with early and late death in intracerebral haemorrhage survivors

Background and purpose: The aim of this study was to determine whether early and late death are associated with different baseline factors in intracerebral haemorrhage (ICH) survivors. Methods: This was a secondary analysis of the multicentre prospective observational CROMIS‐2 ICH study. Death was defined as ‘early’ if occurring within 6 months of study entry and ‘late’ if occurring after this time point. Results: In our cohort (n = 1094), there were 306 deaths (per 100 patient‐years: absolute event rate, 11.7; 95% confidence intervals, 10.5–13.1); 156 were ‘early’ and 150 ‘late’. In multivariable analyses, early death was independently associated with age [per year increase; hazard ratio (HR), 1.05, P = 0.003], history of hypertension (HR, 1.89, P = 0.038), pre‐event modified Rankin scale score (per point increase; HR, 1.41, P < 0.0001), admission National Institutes of Health Stroke Scale score (per point increase; HR, 1.11, P < 0.0001) and haemorrhage volume >60 mL (HR, 4.08, P < 0.0001). Late death showed independent associations with age (per year increase; HR, 1.04, P = 0.003), pre‐event modified Rankin scale score (per point increase; HR, 1.42, P = 0.001), prior anticoagulant use (HR, 2.13, P = 0.028) and the presence of intraventricular extension (HR, 1.73, P = 0.033) in multivariable analyses. In further analyses where time was treated as continuous (rather than dichotomized), the HR of previous cerebral ischaemic events increased with time, whereas HRs for Glasgow Coma Scale score, National Institutes of Health Stroke Scale score and ICH volume decreased over time. Conclusions: We provide new evidence that not all baseline factors associated with early mortality after ICH are associated with mortality after 6 months and that the effects of baseline variables change over time. Our findings could help design better prognostic scores for later death after ICH

Cerebral microbleeds and intracranial haemorrhage risk in patients anticoagulated for atrial fibrillation after acute ischaemic stroke or transient ischaemic attack (CROMIS-2):a multicentre observational cohort study

Background: Cerebral microbleeds are a potential neuroimaging biomarker of cerebral small vessel diseases that are prone to intracranial bleeding. We aimed to determine whether presence of cerebral microbleeds can identify patients at high risk of symptomatic intracranial haemorrhage when anticoagulated for atrial fibrillation after recent ischaemic stroke or transient ischaemic attack. Methods: Our observational, multicentre, prospective inception cohort study recruited adults aged 18 years or older from 79 hospitals in the UK and one in the Netherlands with atrial fibrillation and recent acute ischaemic stroke or transient ischaemic attack, treated with a vitamin K antagonist or direct oral anticoagulant, and followed up for 24 months using general practitioner and patient postal questionnaires, telephone interviews, hospital visits, and National Health Service digital data on hospital admissions or death. We excluded patients if they could not undergo MRI, had a definite contraindication to anticoagulation, or had previously received therapeutic anticoagulation. The primary outcome was symptomatic intracranial haemorrhage occurring at any time before the final follow-up at 24 months. The log-rank test was used to compare rates of intracranial haemorrhage between those with and without cerebral microbleeds. We developed two prediction models using Cox regression: first, including all predictors associated with intracranial haemorrhage at the 20% level in univariable analysis; and second, including cerebral microbleed presence and HAS-BLED score. We then compared these with the HAS-BLED score alone. This study is registered with ClinicalTrials.gov, number NCT02513316. Findings: Between Aug 4, 2011, and July 31, 2015, we recruited 1490 participants of whom follow-up data were available for 1447 (97%), over a mean period of 850 days (SD 373; 3366 patient-years). The symptomatic intracranial haemorrhage rate in patients with cerebral microbleeds was 9·8 per 1000 patient-years (95% CI 4·0–20·3) compared with 2·6 per 1000 patient-years (95% CI 1·1–5·4) in those without cerebral microbleeds (adjusted hazard ratio 3·67, 95% CI 1·27–10·60). Compared with the HAS-BLED score alone (C-index 0·41, 95% CI 0·29–0·53), models including cerebral microbleeds and HAS-BLED (0·66, 0·53–0·80) and cerebral microbleeds, diabetes, anticoagulant type, and HAS-BLED (0·74, 0·60–0·88) predicted symptomatic intracranial haemorrhage significantly better (difference in C-index 0·25, 95% CI 0·07–0·43, p=0·0065; and 0·33, 0·14–0·51, p=0·00059, respectively). Interpretation: In patients with atrial fibrillation anticoagulated after recent ischaemic stroke or transient ischaemic attack, cerebral microbleed presence is independently associated with symptomatic intracranial haemorrhage risk and could be used to inform anticoagulation decisions. Large-scale collaborative observational cohort analyses are needed to refine and validate intracranial haemorrhage risk scores incorporating cerebral microbleeds to identify patients at risk of net harm from oral anticoagulation. Funding: The Stroke Association and the British Heart Foundation

Electron and photon energy calibration with the ATLAS detector using 2015–2016 LHC proton-proton collision data

This paper presents the electron and photon energy calibration obtained with the ATLAS detector using about 36 fb−1 of LHC proton-proton collision data recorded at √s = 13 TeV in 2015 and 2016. The different calibration steps applied to the data and the optimization of the reconstruction of electron and photon energies are discussed. The absolute energy scale is set using a large sample of Z boson decays into electron-positron pairs. The systematic uncertainty in the energy scale calibration varies between 0.03% to 0.2% in most of the detector acceptance for electrons with transverse momentum close to 45 GeV. For electrons with transverse momentum of 10 GeV the typical uncertainty is 0.3% to 0.8% and it varies between 0.25% and 1% for photons with transverse momentum around 60 GeV. Validations of the energy calibration with J/ψ → e + e − decays and radiative Z boson decays are also presented