A model for uranium mobility in groundwater in the Grand Pré region, Nova Scotia, Canada

Elevated levels of uranium that surpass maximum allowable concentrations have been recognized in some well water samples throughout Nova Scotia. In this study we examine the influence of redox conditions and regional geology on the mobility of uranium in groundwater in the Grand Pré region, located in the eastern end of the Annapolis-Cornwallis Valley in southwestern Nova Scotia. The study site is underlain by carbon-rich shale and arkosic sandstone of the Late Mississippian Horton Bluff Formation and the arenaceous sandstone of the Triassic Wolfville Formation. Water samples from drilled wells were analyzed on site for various water quality parameters (pH, conductivity, temperature, dissolved oxygen) and in the laboratory to determine alkalinity and cation (72) and major anion (9) concentrations. Several samples exceeded Health Canada (2011) limits for uranium (20 μg/L) with values up to 50.8 μg/L and aesthetic objectives (AO) for iron (up to 605 μg/L), manganese (up to 2.28 mg/L) and other cations. Data show that different redox conditions occur in the study area. The geospatial arrangement of the chemical data suggests that the lithology of the underlying aquifer strongly influences the availability of uranium in groundwater. Reduced groundwater in Horton Bluff sandstone typically contains elevated concentrations of Fe 2+ and Mn 2+ , whereas groundwater containing high concentrations of U is found primary in oxidizing environments in quartz arenite sandstone units in the Wolfville Formation. Consumption of groundwater in the Grand Pré region may pose a health risk; however, the level of risk remains unknown. This study emphasizes that in the area of Grand Pré, water that is considered aesthetically undesirable (containing high Fe and Mn) may pose less of a health risk (low U) than waters that are aesthetically pleasing.Des niveaux élevés d’uranium qui dépassent les concentrations maximales admises ont été détectés dans certains échantillons d’eau de puits en Nouvelle Écosse. Dans cette étude, nous examinons les effets de la réduction-oxydation et de la géologie régionale sur la mobilité de l’uranium dans l’eau souterraine de la région de Grand Pré, dans l’extrémité est de la vallée d’Annapolis-Cornwallis, dans le sud ouest de la Nouvelle Écosse. Le site étudié repose sur du schiste charbonneux et du grès arkosique de la Formation de Horton Bluff, du Mississippien tardif, et sur du grès arénacé de la Formation de Wolfville, du Trias. Les échantillons d’eau de puits creusés ont été analysés sur place pour ce qui est de divers paramètres de qualité de l’eau (pH, conductivité, température, oxygène dissous) et des analyses ont eu lieu en laboratoire pour établir l’alcalinité et les concentrations de cations (72) et de principaux anions (9). Plusieurs échantillons dépassaient les limites permises par Santé Canada (2011), en ce qui concerne la teneur en uranium (20 μg/L), certaines teneurs ayant atteint 50,8 μg/L. Il en allait de même en ce qui concerne les critères esthétiques pour le fer (des teneurs ayant atteint 605 μg/L), le manganèse (des teneurs ayant atteint 2,28 mg/L) et d’autres cations. Les données indiquent que divers phénomènes de réduction-oxydation surviennent dans le secteur étudié. Le contexte géospatial des données chimiques porte à croire que la lithologie de la couche aquifère sous jacente exerce une forte influence sur la disponibilité de l’uranium dans l’eau souterraine. L’eau souterraine qui a subi une réduction dans le grès de Horton Bluff contient généralement des concentrations élevées de Fe 2+ et de Mn 2+ , tandis que l’eau souterraine à forte concentration d’uranium est surtout observée dans les milieux oxydants de grès de quartz-arénite de la Formation de Wolfville. La consommation de l’eau souterraine dans la région de Grand Pré peut poser un risque pour la santé, mais le degré de risque demeure inconnu. Cette étude met en lumière le risque moindre pour la santé (faible teneur en U) de l’eau dans la région de Grand Pré, qui a une apparence pouvant laisse à désirer (elle a une forte teneur en Fe et en Mn), comparativement à d’autres sources d’eau d’apparence plus agréable. [Traduit par la redaction

Analysing co-evolution among artificial 3D creatures

This paper is concerned with the analysis of coevolutionary dynamics among 3D artificial creatures, similar to those introduced by Sims (1). Coevolution is subject to complex dynamics which are notoriously difficult to analyse. We introduce an improved analysis method based on Master Tournament matrices [2], which we argue is both less costly to compute and more informative than the original method. Based on visible features of the resulting graphs, we can identify particular trends and incidents in the dynamics of coevolution and look for their causes. Finally, considering that coevolutionary progress is not necessarily identical to global overall progress, we extend this analysis by cross-validating individuals from different evolutionary runs, which we argue is more appropriate than single-record analysis method for evaluating the global performance of individuals

Transcriptional profiles predict treatment outcome in patients with tuberculosis and diabetes at diagnosis and at two weeks after initiation of anti-tuberculosis treatment

Data sharing statement: RNA sequence data have been submitted to NCBI Gene Expression Omnibus (GEO) under accession number GSE193979. dcRT-MLPA data can be found in Supplementary Table S6.Copyright © 2022 The Authors. Background: Globally, the tuberculosis (TB) treatment success rate is approximately 85%, with treatment failure, relapse and death occurring in a significant proportion of pulmonary TB patients. Treatment success is lower among people with diabetes mellitus (DM). Predicting treatment outcome early after diagnosis, especially in TB-DM patients, would allow early treatment adaptation for individuals and may improve global TB control. Methods: Samples were collected in a longitudinal cohort study of adult TB patients from South Africa (n = 94) and Indonesia (n = 81), who had concomitant DM (n = 59), intermediate hyperglycaemia (n = 79) or normal glycaemia/no DM (n = 37). Treatment outcome was monitored, and patients were categorized as having a good (cured) or poor (failed, recurrence, died) outcome during treatment and 12 months follow-up. Whole blood transcriptional profiles before, during and at the end of TB treatment were characterized using unbiased RNA-Seq and targeted gene dcRT-MLPA. Findings: We report differences in whole blood transcriptome profiles, which were observed before initiation of treatment and throughout treatment, between patients with a good versus poor TB treatment outcome. An eight-gene and a 22-gene blood transcriptional signature distinguished patients with a good TB treatment outcome from patients with a poor TB treatment outcome at diagnosis (AUC = 0·815) or two weeks (AUC = 0·834) after initiation of TB treatment, respectively. High accuracy was obtained by cross-validating this signature in an external cohort (AUC = 0·749). Interpretation: These findings suggest that transcriptional profiles can be used as a prognostic biomarker for treatment failure and success, even in patients with concomitant DM.TANDEM Consortium, received funding from the European Community's Seventh Framework Programme (FP7/2007-2013 Grant Agreement No. 305279) and the Netherlands Organization for Scientific Research (NWO-TOP Grant Agreement No. 91214038). The research leading to the results presented in the Indian validation cohort was supported by Research Council of Norway Global Health and Vaccination Research (GLOBVAC) projects: RCN 179342, 192534, and 248042, the University of Bergen (Norway)

Transcriptional profiles predict treatment outcome in patients with tuberculosis and diabetes at diagnosis and at two weeks after initiation of anti-tuberculosis treatment.

BACKGROUND: Globally, the tuberculosis (TB) treatment success rate is approximately 85%, with treatment failure, relapse and death occurring in a significant proportion of pulmonary TB patients. Treatment success is lower among people with diabetes mellitus (DM). Predicting treatment outcome early after diagnosis, especially in TB-DM patients, would allow early treatment adaptation for individuals and may improve global TB control. METHODS: Samples were collected in a longitudinal cohort study of adult TB patients from South Africa (n  =  94) and Indonesia (n  =  81), who had concomitant DM (n  =  59), intermediate hyperglycaemia (n  =  79) or normal glycaemia/no DM (n  =  37). Treatment outcome was monitored, and patients were categorized as having a good (cured) or poor (failed, recurrence, died) outcome during treatment and 12 months follow-up. Whole blood transcriptional profiles before, during and at the end of TB treatment were characterized using unbiased RNA-Seq and targeted gene dcRT-MLPA. FINDINGS: We report differences in whole blood transcriptome profiles, which were observed before initiation of treatment and throughout treatment, between patients with a good versus poor TB treatment outcome. An eight-gene and a 22-gene blood transcriptional signature distinguished patients with a good TB treatment outcome from patients with a poor TB treatment outcome at diagnosis (AUC = 0·815) or two weeks (AUC = 0·834) after initiation of TB treatment, respectively. High accuracy was obtained by cross-validating this signature in an external cohort (AUC = 0·749). INTERPRETATION: These findings suggest that transcriptional profiles can be used as a prognostic biomarker for treatment failure and success, even in patients with concomitant DM. FUNDING: The research leading to these results, as part of the TANDEM Consortium, received funding from the European Community's Seventh Framework Programme (FP7/2007-2013 Grant Agreement No. 305279) and the Netherlands Organization for Scientific Research (NWO-TOP Grant Agreement No. 91214038). The research leading to the results presented in the Indian validation cohort was supported by Research Council of Norway Global Health and Vaccination Research (GLOBVAC) projects: RCN 179342, 192534, and 248042, the University of Bergen (Norway)

Impaired resolution of blood transcriptomes through tuberculosis treatment with diabetes comorbidity

Clare Eckold and Cassandra L.R. van Doorn contributed equally to this manuscript. Eleonora Vianello and Jacqueline M. Cliff contributed equally to this manuscript.Data availability statement: The data that support the RNA-Seq findings of this study are openly available in NCBI-GEO at https://www.ncbi.nlm.nih.gov/geo/, accession number GSE193978. The data that support the dcRT-MLPA findings of this study are available in the supplementary material of this article.Copyright © 2023 The Authors. Background: People with diabetes are more likely to develop tuberculosis (TB) and to have poor TB-treatment outcomes than those without. We previously showed that blood transcriptomes in people with TB-diabetes (TB-DM) co-morbidity have excessive inflammatory and reduced interferon responses at diagnosis. It is unknown whether this persists through treatment and contributes to the adverse outcomes. Methods: Pulmonary TB patients recruited in South Africa, Indonesia and Romania were classified as having TB-DM, TB with prediabetes, TB-related hyperglycaemia or TB-only, based on glycated haemoglobin concentration at TB diagnosis and after 6 months of TB treatment. Gene expression in blood at diagnosis and intervals throughout treatment was measured by unbiased RNA-Seq and targeted Multiplex Ligation-dependent Probe Amplification. Transcriptomic data were analysed by longitudinal mixed-model regression to identify whether genes were differentially expressed between clinical groups through time. Predictive models of TB-treatment response across groups were developed and cross-tested. Results: Gene expression differed between TB and TB-DM patients at diagnosis and was modulated by TB treatment in all clinical groups but to different extents, such that differences remained in TB-DM relative to TB-only throughout. Expression of some genes increased through TB treatment, whereas others decreased: some were persistently more highly expressed in TB-DM and others in TB-only patients. Genes involved in innate immune responses, anti-microbial immunity and inflammation were significantly upregulated in people with TB-DM throughout treatment. The overall pattern of change was similar across clinical groups irrespective of diabetes status, permitting models predictive of TB treatment to be developed. Conclusions: Exacerbated transcriptome changes in TB-DM take longer to resolve during TB treatment, meaning they remain different from those in uncomplicated TB after treatment completion. This may indicate a prolonged inflammatory response in TB-DM, requiring prolonged treatment or host-directed therapy for complete cure. Development of transcriptome-based biomarker signatures of TB-treatment response should include people with diabetes for use across populations.European Community's Seventh Framework Programme. Grant Number: 305279; Netherlands Organization for Scientific Research. Grant Number: 9121403

Impaired resolution of blood transcriptomes through tuberculosis treatment with diabetes comorbidity

Background People with diabetes are more likely to develop tuberculosis (TB) and to have poor TB-treatment outcomes than those without. We previously showed that blood transcriptomes in people with TB-diabetes (TB-DM) co-morbidity have excessive inflammatory and reduced interferon responses at diagnosis. It is unknown whether this persists through treatment and contributes to the adverse outcomes. Methods Pulmonary TB patients recruited in South Africa, Indonesia and Romania were classified as having TB-DM, TB with prediabetes, TB-related hyperglycaemia or TB-only, based on glycated haemoglobin concentration at TB diagnosis and after 6 months of TB treatment. Gene expression in blood at diagnosis and intervals throughout treatment was measured by unbiased RNA-Seq and targeted Multiplex Ligation-dependent Probe Amplification. Transcriptomic data were analysed by longitudinal mixed-model regression to identify whether genes were differentially expressed between clinical groups through time. Predictive models of TB-treatment response across groups were developed and cross-tested. Results Gene expression differed between TB and TB-DM patients at diagnosis and was modulated by TB treatment in all clinical groups but to different extents, such that differences remained in TB-DM relative to TB-only throughout. Expression of some genes increased through TB treatment, whereas others decreased: some were persistently more highly expressed in TB-DM and others in TB-only patients. Genes involved in innate immune responses, anti-microbial immunity and inflammation were significantly upregulated in people with TB-DM throughout treatment. The overall pattern of change was similar across clinical groups irrespective of diabetes status, permitting models predictive of TB treatment to be developed. Conclusions Exacerbated transcriptome changes in TB-DM take longer to resolve during TB treatment, meaning they remain different from those in uncomplicated TB after treatment completion. This may indicate a prolonged inflammatory response in TB-DM, requiring prolonged treatment or host-directed therapy for complete cure. Development of transcriptome-based biomarker signatures of TB-treatment response should include people with diabetes for use across populations

Concurrent evaluation of cytokines improves the accuracy of antibodies against Mycobacterium tuberculosis antigens in the diagnosis of active tuberculosis

Data availability statement: All the important data relevant to this study was reported in the manuscript. Any additional data will be made available upon request from the corresponding author.Copyright © 2022 The Authors. Background: Antibodies against mycobacterial proteins are highly specific, but lack sensitivity, whereas cytokines have been shown to be sensitive but not very specific in the diagnosis of tuberculosis (TB). We assessed combinations between antibodies and cytokines for diagnosing TB. Methods: Immuoglubulin (Ig) A and IgM antibody titres against selected mycobacterial antigens including Apa, NarL, Rv3019c, PstS1, LAM, “Kit 1” (MTP64 and Tpx)”, and “Kit 2” (MPT64, Tpx and 19 kDa) were evaluated by ELISA in plasma samples obtained from individuals under clinical suspicion for TB. Combinations between the antibody titres and previously published cytokine responses in the same participants were assessed for diagnosing active TB. Results: Antibody responses were more promising when used in combination (AUC of 0.80), when all seven antibodies were combined. When anti-“Kit 1”-IgA levels were combined with five host cytokine biomarkers, the AUC increased to 97% (92–100%) with a sensitivity of 95% (95% CI, 73–100%), and specificity of 88.5% (95% CI, 68.7–97%) achieved after leave-one-out cross validation. Conclusion: When used in combination, IgA titres measured with ELISA against multiple Mycobacterium tuberculosis antigens may be useful in the diagnosis of TB. However, diagnostic accuracy may be improved if the antibodies are used in combination with cytokines.This work was part of the EDCTP1 programme supported by the European Union (grant number IP_2009_32040, AE-TBC; awarded to GW). The project was also supported by the South African Government through the National Research Foundation (NRF, awarded to NC) and the South African Medical Research Council (SAMRC, postgraduate scholarship to RJ)

Impact of Intermediate Hyperglycemia and Diabetes on Immune Dysfunction in Tuberculosis

Supplementary Data: Supplementary materials are available at Clinical Infectious Diseases online at https://academic.oup.com/cid/article/72/1/69/5857148#274319223 . Consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author.Copyright © The Author(s) 2020. Background: People with diabetes have an increased risk of developing active tuberculosis (TB) and are more likely to have poor TB-treatment outcomes, which may impact on control of TB as the prevalence of diabetes is increasing worldwide. Blood transcriptomes are altered in patients with active TB relative to healthy individuals. The effects of diabetes and intermediate hyperglycemia (IH) on this transcriptomic signature were investigated to enhance understanding of immunological susceptibility in diabetes-TB comorbidity. Methods: Whole blood samples were collected from active TB patients with diabetes (glycated hemoglobin [HbA1c] ≥6.5%) or IH (HbA1c = 5.7% to <6.5%), TB-only patients, and healthy controls in 4 countries: South Africa, Romania, Indonesia, and Peru. Differential blood gene expression was determined by RNA-seq (n = 249). Results: Diabetes increased the magnitude of gene expression change in the host transcriptome in TB, notably showing an increase in genes associated with innate inflammatory and decrease in adaptive immune responses. Strikingly, patients with IH and TB exhibited blood transcriptomes much more similar to patients with diabetes-TB than to patients with only TB. Both diabetes-TB and IH-TB patients had a decreased type I interferon response relative to TB-only patients. Conclusions: Comorbidity in individuals with both TB and diabetes is associated with altered transcriptomes, with an expected enhanced inflammation in the presence of both conditions, but also reduced type I interferon responses in comorbid patients, suggesting an unexpected uncoupling of the TB transcriptome phenotype. These immunological dysfunctions are also present in individuals with IH, showing that altered immunity to TB may also be present in this group. The TB disease outcomes in individuals with IH diagnosed with TB should be investigated further.European Union’s Seventh Framework Programme (FP7 2007-2013 - Health) under grant agreement No 305279

A collaborative approach to adopting/adapting guidelines - the Australian 24-hour Movement Guidelines for the early years (birth to 5 years): an integration of physical activity, sedentary behavior, and sleep

BACKGROUND: In 2017, the Australian Government funded the update of the National Physical Activity Recommendations for Children 0-5&nbsp;years, with the intention that they be an integration of movement behaviours across the 24-h period. The benefit for Australia was that it could leverage research in Canada in the development of their 24-h guidelines for the early years. Concurrently, the Grading of Recommendations Assessment, Development and Evaluation (GRADE) working group published a model to produce guidelines based on adoption, adaption and/or de novo development using the GRADE evidence-to-decision framework. Referred to as the GRADE-ADOLOPMENT approach, it allows guideline developers to follow a structured and transparent process in a more efficient manner, potentially avoiding the need to unnecessarily repeat costly tasks such as conducting systematic reviews. The purpose of this paper is to outline the process and outcomes for adapting the Canadian 24-Hour Movement Guidelines for the Early Years to develop the Australian 24-Hour Movement Guidelines for the Early Years guided by the GRADE-ADOLOPMENT framework. METHODS: The development process was guided by the GRADE-ADOLOPMENT approach. A Leadership Group and Consensus Panel were formed and existing credible guidelines identified. The draft Canadian 24-h integrated movement guidelines for the early years best met the criteria established by the Panel. These were evaluated based on the evidence in the GRADE tables, summaries of findings tables and draft recommendations from the Canadian Draft Guidelines. Updates to each of the Canadian systematic reviews were conducted and the Consensus Panel reviewed the evidence for each behaviour separately and made a decision to adopt or adapt the Canadian recommendations for each behaviour or create de novo recommendations. An online survey was then conducted (n&nbsp;=&nbsp;302) along with five focus groups (n&nbsp;=&nbsp;30) and five key informant interviews (n&nbsp;=&nbsp;5) to obtain feedback from stakeholders on the draft guidelines. RESULTS: Based on the evidence from the Canadian systematic reviews and the updated systematic reviews in Australia, the Consensus Panel agreed to adopt the Canadian recommendations and, apart from some minor changes to the wording of good practice statements, keep the wording of the guidelines, preamble and title of the Canadian Guidelines. The Australian Guidelines provide evidence-informed recommendations for a healthy day (24-h), integrating physical activity, sedentary behaviour (including limits to screen time), and sleep for infants (&lt;1&nbsp;year), toddlers (1-2&nbsp;years) and preschoolers (3-5&nbsp;years). CONCLUSIONS: To our knowledge, this is only the second time the GRADE-ADOLOPMENT approach has been used. Following this approach, the judgments of the Australian Consensus Panel did not differ sufficiently to change the directions and strength of the recommendations and as such, the Canadian recommendations were adopted with very minor alterations. This allowed the Guidelines to be developed much faster and at lower cost. As such, we would recommend the GRADE-ADOLOPMENT approach, especially if a credible set of guidelines, with all supporting materials and developed using a transparent process, is available. Other countries may consider using this approach when developing and/or revising national movement guidelines

Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020–December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population