Predicting freshwater habitat integrity using land-use surrogates

Freshwater biodiversity is globally threatened due to human disturbances, but freshwater ecosystems have been accorded lessprotection than their terrestrial and marine counterparts. Few criteria exist for assessing the habitat integrity of rivers and data used for such assessments are generally of limited geographical coverage. Here, we use a fine-scale dataset describing river integrity in north-western South Africa to explore the extent to which measures of freshwater habitat integrity can be predicted from remotely sensed data, which are readily available in many parts of the world. A spatial statistical model was built using broad land-cover variables to predict the habitat integrity (subdivided into riparian and instream integrity) of rivers.We also explored the importance of the spatial scale. Results showed that riparian and, to a lesser degree, instream habitat integrity of river systems could be predicted with reasonable accuracy. The total area under natural vegetation was the most significant predictor of riparian integrity, which is best predicted by land-use activities at catchment level, rather than more locally. Our GIS-based model thus provides a fine-scale approach to assessing river habitat integrity as a supplement to landscape-level conservation plans for river systems, and represents a significant contribution towards the monitoring componentof the River Health Programme (RHP), which reports on the state of rivers in South Africa

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

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

Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project

Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04-0.06) for all ages, 0.05 (0.04-0.05) for <5 years of age, 0.08 (0.06-0.09) for 5-17 years, 0.06 (0.05-0.08) for 18-49 years, 0.06 (0.05-0.07) for 50-64 years, and 0.05 (0.04-0.06) for ≥65 years. PCV10/13 use in infant immunization programs was followed by a 95% reduction in ST1 IPD in all ages after approximately 6 years. Limited data availability from the highest ST1 disease burden countries using a 3+0 schedule constrains generalizability and data from these settings are needed

Global Landscape Review of Serotype-Specific Invasive Pneumococcal Disease Surveillance among Countries Using PCV10/13: The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) Project.

Serotype-specific surveillance for invasive pneumococcal disease (IPD) is essential for assessing the impact of 10- and 13-valent pneumococcal conjugate vaccines (PCV10/13). The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project aimed to evaluate the global evidence to estimate the impact of PCV10/13 by age, product, schedule, and syndrome. Here we systematically characterize and summarize the global landscape of routine serotype-specific IPD surveillance in PCV10/13-using countries and describe the subset that are included in PSERENADE. Of 138 countries using PCV10/13 as of 2018, we identified 109 with IPD surveillance systems, 76 of which met PSERENADE data collection eligibility criteria. PSERENADE received data from most (n = 63, 82.9%), yielding 240,639 post-PCV10/13 introduction IPD cases. Pediatric and adult surveillance was represented from all geographic regions but was limited from lower income and high-burden countries. In PSERENADE, 18 sites evaluated PCV10, 42 PCV13, and 17 both; 17 sites used a 3 + 0 schedule, 38 used 2 + 1, 13 used 3 + 1, and 9 used mixed schedules. With such a sizeable and generally representative dataset, PSERENADE will be able to conduct robust analyses to estimate PCV impact and inform policy at national and global levels regarding adult immunization, schedule, and product choice, including for higher valency PCVs on the horizon

Land-Cover Separability Analysis of MODIS Time-Series Data Using a Combined Simple Harmonic Oscillator and a Mean Reverting Stochastic Process

It is proposed that the time series extracted from moderate resolution imaging spectroradiometer satellite data be modeled as a simple harmonic oscillator with additive colored noise. The colored noise is modeled with an Ornstein–Uhlenbeck process. The Fourier transform and maximum-likelihood parameter estimation are used to estimate the harmonic and noise parameters of the colored simple harmonic oscillator. Two case studies in South Africa show that reliable class differentiation can be obtained between natural vegetation and settlement land cover types, when using the parameters of the colored simple harmonic oscillator as input features to a classifier. The two case studies were conducted in the Gauteng and Limpopo provinces of South Africa. In the case of the Gauteng case study, we obtained an average for single-band classification, while standard harmonic features only achieved an average . In conclusion, the results obtained from the colored simple harmonic oscillator approach outperformed standard harmonic features and the minimum distance classifier.http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?reload=true&punumber=4609443ai201

Using Page's Cumulative Sum Test on MODIS Time Series to Detect Land-Cover Changes

Human settlement expansion is one of the most pervasive forms of land cover change in South Africa. The use of Page’s Cumulative Sum Test is proposed as a method to detect new settlement developments in areas that were previously covered by natural vegetation using 500 m MODIS time series satellite data. The method is a sequential per pixel change alarm algorithm that can take into account positive detection delay, probability of detection and false alarm probability to construct a threshold. Simulated change data was generated to determine a threshold during a preliminary off-line optimization phase. After optimization the method was evaluated on examples of known land cover change in the Gauteng and Limpopo provinces of South Africa. The experimental results indicated that CUSUM performs better than band differencing in the before mentioned study areas.http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=8859hb2013ai201

Pretoriana, no. 030, Aug. 1959

Heloise Greenlees : in memoriam / W. Punt -- Bulldozing history -- Die Suid-Afrikaanse museumwese / H. Muller -- Pretoria's oldest building to be demolished and dumped on a waste lot -- Verslag van 'n onderhoud / G.W. Eybers -- Byskrif by 'n foto van Dr. G.W. Eybers -- Die oudste huis in die omgewing van Pretoria / F.C. Calitz -- Hartebeespoort nr. 308 -- Enkele grepe uit die geskiedenis van Silverton / B. Auret, A. Bester -- A building almost as old as Johannesburg -- 'n Petisie in sake "De Botanischen Tuin" (Burgerspark) -- KNoffel en kanfer / J.P. Kleynhan