Developing site-specific guidelines for orchard soils based on bioaccessibility – Can it be done?

Horticultural land within the periurban fringe of NZ towns and cities increasingly is being developed for residential subdivision. Recent surveys have shown that concentrations of As, Cd, Cu, Pb, and ΣDDT (sum of DDT and its degradation products DDE and DDD) in such soils can exceed criteria protective of human health.¹ Soil ingestion is a key exposure pathway for non-volatile contaminants in soil. Currently in NZ, site-specific risk assessments and the derivation of soil guidelines protective of human health assume that all of the contaminant present in the soil is available for uptake and absorption by the human gastrointestinal tract. This assumption can overestimate health risks and has implications for the remediation of contaminated sites.² In comparison, the bioavailability of contaminants is considered when estimating exposure via dermal absorption and by ingestion of home-grown produce.³ Dermal absorption factors and plant uptake factors are included in the calculations for estimating exposures via these routes

XPHACTOR Clinical Score dataset

The World Health Organization (WHO) recommendation for regular tuberculosis (TB) screening of HIV-positive individuals with Xpert MTB/RIF as the first diagnostic test has major resource implications. The aim of our study was to develop a score, comprising elements readily available in primary care, to predict probability of TB in adults attending for routine HIV care screened for TB and found WHO tool positive. We used data collected for “Xpert for people attending HIV/AIDS care: test or review?” (XPHACTOR), a prospective cohort study evaluating a risk-based algorithm to prioritise Xpert MTB/RIF testing amongst adults attending for routine HIV care in South Africa, to develop and validate our clinical score. This dataset contains data for 1,048 HIV-positive adults attending for routine HIV care and reporting ≥1 symptom on the WHO screening tool. The dataset is split 50:50 to derive, and internally validate the prediction model. It includes basic demographics, TB diagnoses, and candidate predictors considered for the score. Data was collected for the purpose of HIV and TB research and can only be reused for related research, in accordance with the participant consent agreement

Data for: "The utility of repeat Xpert MTB/RIF testing to diagnose tuberculosis in HIV-positive adults with initial negative result"

The World Health Organization recommends regular tuberculosis screening of HIV-positive individuals with Xpert MTB/RIF as the first diagnostic test. Further evaluation of those who are HIV-positive and Xpert-negative comprises clinical reassessment, chest radiograph (if available), sputum for mycobacterial culture, and treatment with antibiotic if clinically indicated. The aim of our study was to describe the diagnostic yield from an immediate repeat sputum tested with Xpert, compared to sequential further investigation guided by South African recommendations , amongst HIV-positive adults in South Africa being investigated for TB whose initial sputum Xpert result is negative. It was a sub-study of “Xpert for people attending HIV/AIDS care: test or review?” (XPHACTOR), a prospective cohort study evaluating a risk-based algorithm to prioritise Xpert testing amongst adults attending for routine HIV care in South Africa. This dataset contains data for 227 adults attending for routine HIV care who have an initial negative sputum Xpert result. It includes basic demographics, TB diagnoses, mycobacteriology and chest radiograph results. Data was collected for the purpose of HIV and TB research and can only be reused for related research, in accordance with the participant consent agreement

Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs

Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Despite the wide application, microarray time course experiments have several limitations in identifying cell cycle genes. We thus propose a computational model to predict human cell cycle genes based on transcription factor (TF) binding and regulatory motif information in their promoters. We utilize ENCODE ChIP-seq data and motif information as predictors to discriminate cell cycle against non-cell cycle genes. Our results show that both the trans- TF features and the cis- motif features are predictive of cell cycle genes, and a combination of the two types of features can further improve prediction accuracy. We apply our model to a complete list of GENCODE promoters to predict novel cell cycle driving promoters for both protein-coding genes and non-coding RNAs such as lincRNAs. We find that a similar percentage of lincRNAs are cell cycle regulated as protein-coding genes, suggesting the importance of non-coding RNAs in cell cycle division. The model we propose here provides not only a practical tool for identifying novel cell cycle genes with high accuracy, but also new insights on cell cycle regulation by TFs and cis-regulatory elements

A geological perspective on potential future sea-level rise

During ice-age cycles, continental ice volume kept pace with slow, multi-millennial scale, changes in climate forcing. Today, rapid greenhouse gas (GHG) increases have outpaced ice-volume responses, likely committing us to > 9 m of long-term sea-level ri

Linkage to care among adults being investigated for tuberculosis in South Africa: pilot study of a case manager intervention.

OBJECTIVES: We piloted an intervention to determine if support from a case manager would assist adults being investigated for tuberculosis (TB) to link into TB and HIV care. DESIGN: Pilot interventional cohort study. PARTICIPANTS AND SETTING: Patients identified by primary healthcare clinic staff in South Africa as needing TB investigations were enrolled. INTERVENTION: Participants were supported for 3 months by case managers who facilitated the care pathway by promoting HIV testing, getting laboratory results, calling patients to return for results and facilitating treatment initiation. OUTCOMES MEASURED: Linkage to TB care was defined as starting TB treatment within 28 days in those with a positive test result; linkage to HIV care, for HIV-positive people, was defined as having blood taken for CD4 count and, for those eligible, starting antiretroviral therapy within 3 months. Intervention implementation was measured by number of attempts to contact participants. RESULTS: Among 562 participants (307 (54.6%) female, median age: 36 years (IQR 29-44)), most 477 (84.8%) had previously tested for HIV; of these, 328/475 (69.1%) self-reported being HIV-positive. Overall, 189/562 (33.6%) participants needed linkage to care (132 HIV care linkage only; 35 TB treatment linkage only; 22 both). Of 555 attempts to contact these 189 participants, 407 were to facilitate HIV care linkage, 78 for TB treatment linkage and 70 for both. At the end of 3-month follow-up, 40 participants had not linked to care (29 of the 132 (22.0%) participants needing linkage to HIV care only, 4 of the 35 (11.4%) needing to start on TB treatment only and 7 of the 22 (31.8%) needing both). CONCLUSION: Many people testing for TB need linkage to care. Despite case manager support, non-linkage into HIV care remained higher than desirable, suggesting a need to modify this intervention before implementation. Innovative strategies to enable linkage to care are needed

Predictors of silicosis and variation in prevalence across mines among employed gold miners in South Africa

Background The stated intention to eliminate silicosis from the South African goldmining industry as well as current programmes to find and compensate ex-miners with silicosis require an understanding of variation in silicosis prevalence across the industry. We aimed to identify the predictors of radiological silicosis in a large sample of working miners across gold mines in South Africa. Methods Routine surveillance chest radiographs were collected from 15 goldmine “clusters” in a baseline survey undertaken in preparation for a separate tuberculosis isoniazid prophylaxis trial. All images were read for silicosis by a health professional experienced in using the International Labour Organisation (ILO) classification. Profusion thresholds of > 1/0 and > 1/1 were used. Demographic and occupational information was obtained by questionnaire. Predictors of silicosis were examined in a multivariable logistic regression model, including age, gender, racial ascription, country of origin, years since starting mine employment, mine shaft, skill category, underground work status and tuberculosis. Results The crude silicosis prevalence at ILO > 1/1 was 3.8% [95% confidence interval (CI) 3.5–4.1%]. The range across mine shafts was 0.8–6.9%. After adjustment for covariates, the interquartile range across shafts was reduced from 2.4 to 1.2%. Black miners [adjusted odds ratio (aOR) 2.8; 95% CI 1.1–7.2] and miners in full-time underground work (aOR 2.1; 95% CI 1.3–3.4) had substantially elevated odds of silicosis, while workers from Mozambique had lower odds (aOR 0.54; 95% CI 0.38–0.77). Silicosis odds rose sharply with both age and years since starting in the industry (p for linear trend  15 years since first exposure and 2.2% < 10 years. Conclusions In surveillance of silicosis in working gold miners time since first exposure remains a powerful predictor. Age appears to be an independent predictor, while the detection of radiological silicosis in short-service miners requires attention. Public risk reporting by mines should include factors bearing on silicosis prevalence, specifically dust concentrations, with independent verification. Studies of silicosis and tuberculosis in ex-miners are needed, supported by an accessible electronic database of the relevant medical and dust exposure records of all gold miners

Missed Opportunities for TB Investigation in Primary Care Clinics in South Africa: Experience from the XTEND Trial.

SETTING: 40 primary health clinics (PHCs) in four provinces in South Africa, June 2012 -February 2013. OBJECTIVE: To determine whether health care worker (HCW) practice in investigating people with TB symptoms was altered when the initial test for TB was changed from smear microscopy to Xpert MTB/RIF. DESIGN: Cross-sectional substudy at clinics participating in a pragmatic cluster randomised trial, Xpert for TB: Evaluating a New Diagnostic "XTEND", which evaluated the effect of Xpert MTB/RIF implementation in South Africa. METHODS: Consecutive adults exiting PHCs reporting at least one TB symptom (defined as any of cough, weight loss, night sweats and fever) were enrolled. The main outcome was the proportion who self-reported having sputum requested by HCW during the clinic encounter just completed. RESULTS: 3604 adults exiting PHCs (1676 in Xpert arm, 1928 in microscopy arm) were enrolled (median age 38 years, 71.4% female, 38.8% reported being HIV-positive, 70% reported cough). For 1267 participants (35.2%) the main reason for attending the clinic was TB symptom(s). Overall 2130/3604 (59.1%) said they reported their symptom(s) to HCW. 22.7% (818/3604) reported having been asked to give sputum for TB investigation. Though participants in the Xpert vs. microscopy arm were more likely to have sputum requested by HCW, this was not significantly different: overall (26.0% [436/1676] vs 19.8% [382/1928]; adjusted prevalence ratio [aPR] 1.31, [95% CI 0.78-2.20]) and when restricted to those presenting at clinics due to symptoms (49.1% [260/530] vs 29.9% [220/737]; aPR 1.38 [0.89-2.13]) and those reporting being HIV-positive (29.4% [190/647] vs 20.8% [156/749]; aPR 1.38[0.88-2.16]). Those attending clinic due to TB symptoms, were more likely to have sputum requested if they had increasing number of symptoms; longer duration of cough, unintentional weight loss and night sweats and if they reported symptoms to HCW. CONCLUSIONS: A large proportion of people exiting PHCs reporting TB symptoms did not get tested. Implementation of Xpert MTB/RIF did not substantially change the probability of testing for TB. Better systems are needed to ensure that opportunities to identify active TB among PHC attendees are not missed

Low haemoglobin predicts early mortality among adults starting antiretroviral therapy in an HIV care programme in South Africa: a cohort study

BACKGROUND: Antiretroviral therapy (ART) has dramatically reduced morbidity and mortality among people with HIV infection; however, mortality after the start of ART is high in resource-limited settings. We investigated risk factors for mortality among adults starting ART in a multi-clinic community programme in South Africa. METHODS: Cohort of adults starting ART at 27 clinics between February 2005 and June 2006, followed to 31st March 2007. Kaplan-Meier survival estimates were used to describe overall mortality. Shared frailty Cox regression was used to identify baseline risk factors for early mortality. RESULTS: Among 1350 participants (median age 35.5 years, 60% female, median CD4 count 83/microL [interquartile range (27-147)], median follow-up 13.4 months), there were 185 deaths, overall mortality rate 13/100 pyrs; for 0-3, 3-9 and >9 months from ART start mortality rates were 24, 13 and 6/100 pyrs respectively. 43% of the deaths were in the first 3 months of treatment. Risk factors for mortality in univariable analysis were baseline CD4 count, viral load, haemoglobin and body mass index, in multivariable analysis adjusting for age and gender, only CD4 count and haemoglobin remained independently associated with proportional hazards not being satisfied for haemoglobin. Adjusted hazard ratios (aHR) for participants with haemoglobin 11.9(f)/12.9 (m) g/mL were 4.99, 3.05 and 0.12 respectively comparing to 10-11.9 (f)/12.9 (m)g/mL in the first 3 months of ART. aHRs for CD4 counts were 0.40, 0.38 and 0.34 for 50-99, 100-200 and >200/microL comparing to <50/microL. CONCLUSIONS: The high mortality rate in the first 3 months underlines the need for earlier HIV diagnosis so that ART can be initiated earlier. Low haemoglobin and low CD4 count are both strong predictors of mortality, and could be used to identify individuals at high risk who might benefit from intensive case management

Identification of Cell Cycle–Regulated Genes Periodically Expressed in U2OS Cells and their Regulation by FOXM1 and E2F Transcription Factors

We identify the cell cycle–regulated mRNA transcripts genome-wide in the osteosarcoma-derived U2OS cell line. This results in 2140 transcripts mapping to 1871 unique cell cycle–regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identify genomic loci bound by the G2/M transcription factor FOXM1 by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associate these with cell cycle–regulated genes. FOXM1 is bound to cell cycle–regulated genes with peak expression in both S phase and G2/M phases. We show that ChIP-seq genomic loci are responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly activates promoters of G2/M phase genes and weakly activates those induced in S phase. Analysis of ChIP-seq data from a panel of cell cycle transcription factors (E2F1, E2F4, E2F6, and GABPA) from the Encyclopedia of DNA Elements and ChIP-seq data for the DREAM complex finds that a set of core cell cycle genes regulated in both U2OS and HeLa cells are bound by multiple cell cycle transcription factors. These data identify the cell cycle–regulated genes in a second cancer-derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle