Feature Guided Training and Rotational Standardisation for the Morphological Classification of Radio Galaxies

State-of-the-art radio observatories produce large amounts of data which can be used to study the properties of radio galaxies. However, with this rapid increase in data volume, it has become unrealistic to manually process all of the incoming data, which in turn led to the development of automated approaches for data processing tasks, such as morphological classification. Deep learning plays a crucial role in this automation process and it has been shown that convolutional neural networks (CNNs) can deliver good performance in the morphological classification of radio galaxies. This paper investigates two adaptations to the application of these CNNs for radio galaxy classification. The first adaptation consists of using principal component analysis (PCA) during preprocessing to align the galaxies' principal components with the axes of the coordinate system, which will normalize the orientation of the galaxies. This adaptation led to a significant improvement in the classification accuracy of the CNNs and decreased the average time required to train the models. The second adaptation consists of guiding the CNN to look for specific features within the samples in an attempt to utilize domain knowledge to improve the training process. It was found that this adaptation generally leads to a stabler training process and in certain instances reduced overfitting within the network, as well as the number of epochs required for training.Comment: 20 pages, 17 figures, this is a pre-copyedited, author-produced PDF of an article accepted for publication in the Monthly Notices of the Royal Astronomical Societ

Late-night simulation: Opinions of fourth- and fifth-year medical students at the University of the Free State, Bloemfontein, South Africa

Background. Sleep deprivation is a problem for medical students and practitioners due to long and late working hours, which may result in a decline in their performance in practising medicine. Objectives. To investigate whether educational practices require altering with regard to the time at which simulation classes are presented, or identify any other possible suggestions for improving the preparation of students for shift work in their profession as medical doctors as a potential solution to reduce sleep-deprivation-related adverse outcomes. Methods. In this quantitative cross-sectional study, an anonymous questionnaire was distributed to 111 fourth-year and 141 fifth-year medical students at the Faculty of Health Sciences, University of the Free State (UFS), Bloemfontein, South Africa, during the second half of 2018. The researchers interpreted the responses and the Department of Biostatistics, UFS, analysed the data. Results. The majority of the fourth-year (88.6%) and fifth-year (90.4%) student groups responded that late-night simulation classes between 01h00 and 04h00 would not be beneficial to their preparation for shift work. The motivation for negative responses was that it might worsen sleep deprivation due to time constraints in an already demanding course. The fourth-year (61.4%) and fifth-year (80.5%) student groups did not regard simulation as realistic and felt that late-night simulation training sessions would not prepare them better for future shift work. However, both groups believed ‘practice makes perfect’ and, as such, their confidence with procedures would improve as they practise more during simulation. Conclusion. The majority of students were negative towards the idea of late-night simulation classes, because of the effect it would have on their already full programme. Students are familiar with the effects of sleep deprivation and felt that late-night simulation classes would add pressure to their busy lives and worsen their sleep deprivation. Further investigation and practical testing would be required to conclude the impact of late-night simulation classes in preparation for shift work of medical doctors and the resultant effect on clinical performance

Survey of Citrus tristeza virus (CTV) diversity in pigmented Citrus x paradisi (Macfad.) (Grapefruit) trees in north-western Argentina

Citrus tristeza virus (CTV) is the most severe viral pathogen of citrus and elicits a wide range of devastating disease symptoms. Grapefruit cultivars (Citrus x paradisi) are the most sensitive among citrus to the effects of CTV infections. Grapefruit is an important crop within the north-western Argentine citrus industry; however, production has been affected by CTV stem-pitting. In general, CTV diversity within South America is poorly studied, with data on grapefruit CTV populations being particularly limited. In this study, 50 samples were collected from Star Ruby, Henninger’s Ruby and Ruben Pink cultivars, within the provinces of Tucumán, Salta and Jujuy in north-western Argentina. The CTV p33 gene was PCR amplified and the resulting amplicons sequenced with Sanger sequencing. A subset of these amplicons was sequenced with Illumina MiSeq sequencing. AT-1-like sequences were dominant within the majority of populations, as determined by Sanger sequencing, followed by sequences clustering within the unresolved Kpg3/SP/T3 and RB clades. Sequencing by Illumina MiSeq confirmed this, as well as detecting minor sequence types within the HA 16–5, VT, B165 and A18 clades.The National Research Foundation (South Africa) and Ministerio de Ciencia, Tecnologia e Innovación Productiva (Argentina) via the South Africa-Argentina Bilateral agreement programme.http://link.springer.com/journal/106582019-06-01hj2017Microbiology and Plant Patholog

Survey of citrus tristeza virus (CTV) strains in Citrus x limon (L) Burm f. (lemon) in Tucumán Province, Argentina

Citrus tristeza virus (CTV) causes various syndromes of citrus and consists of diverse strains which may cause symptoms of differing severity. Lemon is the most important citrus crop produced in Tucumán province, Argentina, but the diversity of CTV strains within this region has been poorly studied. In this study we identified strains of CTV in lemons in 29 trees of five commonly planted lemon cultivars from this area using direct Sanger and next generation sequencing (NGS) of amplicons derived from the CTV p33 gene. The Kpg3/SP/T3 genotype was dominant in 28 of the 29 samples analysed, with one sample being dominant for a genotype of RB. This was confirmed with NGS in all but one instance. In addition, all thirteen samples tested by NGS were infected with RB, Kpg3/SP/T3 and HA 16–5 genotypes. One sample also had a minor VT component, while a further two samples also had a minor AT-1 component.The National Research Foundation (South Africa) and Ministerio de Ciencia, Tecnologia e Innovación Productiva (Argentina) via the South Africa-Argentina Bilateral agreement programme.http://link.springer.com/journal/106582018-12-01hj2018Microbiology and Plant Patholog

Can pneumococcal meningitis surveillance be used to assess the impact of pneumococcal conjugate vaccine on total invasive pneumococcal disease? A case-study from South Africa, 2005–2016

INTRODUCTION : South Africa introduced seven-valent pneumococcal conjugate vaccine (PCV7) in 2009 and PCV13 in 2011. We aimed to compare the estimated impact of PCV on pneumococcal meningitis (PM) to impact of PCV on total invasive pneumococcal disease (tIPD) based on risk reduction after PCV introduction. METHODS : We conducted national, laboratory-based surveillance for tIPD during 2005–2016. We estimated and compared rates of PCV13 and non-PCV13 serotype disease among tIPD and PM in individuals aged <5 years and ≥5 years, and compared these rates between the 2005–2008 pre-PCV introduction period and two time points after PCV introduction, 2012 and 2016. RESULTS : We enrolled 45,853 tIPD cases; 17,251 (38%) were PM. By 2016, IPD caused by all serotypes decreased 55% (95%CI −57% to −53%) for tIPD, and 54% for PM (95%CI −58% to −51%), 0.7% difference between estimates (p = 0.7). No significant differences were observed between PCV7-serotype disease reduction in tIPD and PM in both age groups or the additional 6 serotypes included in PCV13 in <5 year olds in 2012 and 2016. In 2012 there was a significant difference between increases in non-PCV13 serotype disease in those ≥5 years for tIPD and PM (32% greater increase in PM, p < 0.001), but this difference was absent by 2016. There was a significant difference between the estimated decrease in additional PCV13 type disease in 2016 between tIPD and PM for those aged ≥5 years (28% greater reduction in PM, p = 0.008). CONCLUSION : PM showed similar reductions to tIPD seven years after PCV introduction in vaccine serotype disease in those <5 years, and increases in non-vaccine serotype disease in all ages.The National Institute for Communicable Diseases a division of the National Health Laboratory Service, South Africa; the United States Agency for International Development’s Antimicrobial Resistance Initiative, United States of America, transferred via a cooperative agreement [U60/CCU022088] from the United States Centers for Disease Control and Prevention, United States if Ameriva; and the United States Centers for Disease Control and Prevention [U62/CCU022901], United States of America.http://www.elsevier.com/locate/vaccine2020-09-10hj2019School of Health Systems and Public Health (SHSPH

Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis

Mycobacterium tuberculosis (M.tb) causes tuberculosis (TB) and remains one of the leading causes of mortality due to an infectious pathogen. Host immune responses have been implicated in driving the progression from infection to severe lung disease. We analyzed longitudinal RNA sequencing (RNAseq) data from the whole blood of 74 TB progressors whose samples were grouped into four six-month intervals preceding diagnosis (the GC6-74 study). We additionally analyzed RNAseq data from an independent cohort of 90 TB patients with positron emission tomography-computed tomography (PET-CT) scan results which were used to categorize them into groups with high and low levels of lung damage (the Catalysis TB Biomarker study). These groups were compared to non-TB controls to obtain a complete whole blood transcriptional profile for individuals spanning from early stages of M.tb infection to TB diagnosis. The results revealed a steady increase in the number of genes that were differentially expressed in progressors at time points closer to diagnosis with 278 genes at 13-18 months, 742 at 7-12 months and 5,131 detected 1-6 months before diagnosis and 9,205 detected in TB patients. A total of 2,144 differentially expressed genes were detected when comparing TB patients with high and low levels of lung damage. There was a large overlap in the genes upregulated in progressors 1-6 months before diagnosis (86%) with those in TB patients. A comprehensive pathway analysis revealed a potent activation of neutrophil and platelet mediated defenses including neutrophil and platelet degranulation, and NET formation at both time points. These pathways were also enriched in TB patients with high levels of lung damage compared to those with low. These findings suggest that neutrophils and platelets play a critical role in TB pathogenesis, and provide details of the timing of specific effector mechanisms that may contribute to TB lung pathology

Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study

BACKGROUND: People with human immunodeficiency virus (HIV; PWH) have increased cardiovascular risk. Higher leukocyte count has been associated with coronary artery disease (CAD) events in the general population. It is unknown whether the leukocyte-CAD association also applies to PWH. METHODS: In a case-control study nested within the Swiss HIV Cohort Study, we obtained uni- and multivariable odds ratios (OR) for CAD events, based on traditional and HIV-related CAD risk factors, leukocyte count, and confounders previously associated with leukocyte count. RESULTS: We included 536 cases with a first CAD event (2000-2021; median age, 56 years; 87% male; 84% with suppressed HIV RNA) and 1464 event-free controls. Cases had higher latest leukocyte count before CAD event than controls (median [interquartile range], 6495 [5300-7995] vs 5900 [4910-7200]; P 11 000/µL) was uncommon (4.3% vs 2.1%; P = .01). In the highest versus lowest leukocyte quintile at latest time point before CAD event, participants had univariable CAD-OR = 2.27 (95% confidence interval, 1.63-3.15) and multivariable adjusted CAD-OR = 1.59 (1.09-2.30). For comparison, univariable CAD-OR for dyslipidemia, diabetes, and recent abacavir exposure were 1.58 (1.29-1.93), 2.19 (1.59-3.03), and 1.73 (1.37-2.17), respectively. Smoking and, to a lesser degree, alcohol and ethnicity attenuated the leukocyte-CAD association. Leukocytes measured up to 8 years before the event were significantly associated with CAD events. CONCLUSIONS: PWH in Switzerland with higher leukocyte counts have an independently increased risk of CAD events, to a degree similar to traditional and HIV-related risk factors

Initial assessment of well-being in South African armed services personnel

As professionals in law enforcement and defence (armed services) function under high pressure, the maintenance of overall health should be emphasized and closely monitored in training facilities. The aim of this research was to assess current health status and risk factors of the members of three armed service training facilities. This represents the first step in an integrated approach toward health maintenance in this important sector. The sample consisted of 323 members from three different armed service training facilities in South Africa. The subjects completed a questionnaire on health history and coping with stress. Heart health, body composition, general fitness and co-ordination were then examined. The mean age of the sample was 38.08 years (SD=8.81). The mean blood pressure readings were pre-hypertensive (Systolic 127.4mmHg, SD=16.67; Diastolic 82.74mmHg, SD=10.94) and the mean BMI was in the overweight category (27.97kg/m2, SD=8.81). The percentage (more than 40 %) of subjects that require physical fitness intervention reflects an urgent need for effective implementation of wellness programmes in this sector.http://www.ajol.info/journal_index.php?jid=153&ab=ajpher

Mycobacterium tuberculosis-stimulated whole blood culture to detect host biosignatures for tuberculosis treatment response

Supplementary data are available online at https://www.sciencedirect.com/science/article/pii/S1472979221000329?via%3Dihub#appsec1 .Host markers to monitor the response to tuberculosis (TB) therapy hold some promise. We evaluated the changes in concentration of Mycobacterium tuberculosis (M.tb)-induced soluble biomarkers during early treatment for predicting short- and long-term treatment outcomes. Whole blood samples from 30 cured and 12 relapsed TB patients from diagnosis, week 1, 2, and 4 of treatment were cultured in the presence of live M.tb for seven days and patients followed up for 24 weeks after the end of treatment. 57 markers were measured in unstimulated and antigen-stimulated culture supernatants using Luminex assays. Top performing multi-variable models at diagnosis using unstimulated values predicted outcome at 24 months after treatment completion with a sensitivity of 75.0% (95% CI, 42.8–94.5%) and specificity of 72.4% (95% CI, 52.8–87.3%) in leave-one-out cross validation. Month two treatment responder classification was correctly predicted with a sensitivity of 79.2% (95% CI, 57.8–92.9%) and specificity of 92.3% (95% CI, 64.0–99.8%). This study provides evidence of the early M.tb-specific treatment response in TB patients but shows that the observed unstimulated marker models are not outperformed by stimulated marker models. Performance of unstimulated predictive host marker signatures is promising and requires validation in larger studies.Bill and Melinda Gates Foundation (TB Drug Accelerator Program, grant number 48941); Action TB by GSK; EDCTP (01.T.d1, Grant number 2004.1.R.d1); the South African Technology for Human Resources and Industry Program (THRIP); and an International Collaborations in Infectious Diseases Research grant from the National Institute of Allergy and Infectious Diseases (grant number 5U01IA115619). This research was also partially funded by the South African government through the South African Medical Research Council, through a grant from the Strategic Health Innovations Partnership (SHIP) unit, by the South African National Research Foundation through a South African Research Chair Initiative: Biomarkers for TB (grant number 86535) and a South African Department of Science and Innovation/National Research Foundation funded Centre of Excellence in Biomedical Tuberculosis Research

TB epidemiology: where are the young women? Know your tuberculosis epidemic, know your response.

CAPRISA, 2018.Abstract available in pdf