Background: There are an estimated 1.5 million children living with human immunodeficiency virus (CLHIV), most residing in sub-Saharan Africa. A common hospital presentation of CLHIV is new-onset seizure, for which imaging is helpful but not routinely performed due to scarce resources. We present imaging findings and their association with clinical risk factors and outcomes in a cohort of Zambian CLHIV presenting with new-onset seizure. Methods: In this prospective cohort study, participants were recruited at the University Teaching Hospital in Lusaka, Zambia. Various clinical and demographic characteristics were obtained. Computed tomography (CT), magnetic resonance imaging (MRI), or both were obtained during admission or shortly after discharge. If both studies were available, MRI data was used. Two neuroradiologists interpreted images using REDCap-based NeuroInterp, a tool that quantifies brain imaging findings. Age-dependent neuropsychologic assessments were administered. Results: Nineteen of 39 (49%) children had a brain MRI, 16 of 39 (41%) had CT, and four of 39 (10%) had both. Mean age was 6.8 years (S.D. 1 / 4 4.8). Children with advanced HIV disease had higher odds of atrophy (odds ration [OR] 7.2, 95% confidence interval [CI] 1.1 to 48.3). Focal abnormalities were less likely in children receiving antiretroviral therapy (ART) (OR 0.22, 95% CI 0.05 to 1.0). Children with neurocognitive impairment were more likely to have atrophy (OR 8.4, 95% CI 1.3 to 55.4) and less likely to have focal abnormalities (OR 0.2, 95% CI 0.03 to 0.9). Conclusions: Focal brain abnormalities on MRI were less likely in CLHIV on ART. Brain atrophy was the most common imaging abnormality, which was linked to severe neurocognitive impairment. (c) 2024 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).

Mountaintop removal coal mining (MTR) has been a major source of landscape change in the Central Appalachians of the United States (US). Changes in stream hydrology, channel geomorphology and water quality caused by MTR coal mining can lead to severe impairment of stream ecological integrity. The objective of the Clean Water Act (CWA) is to restore and maintain the ecological integrity of the Nation's waters. Sensitive, readily measured indicators of ecosystem structure and function are needed for the assessment of stream ecological integrity. Most CWA assessments rely on structural indicators; inclusion of functional indicators could make these assessments more holistic and effective. The goals of this study were: (1) test the efficacy of selected carbon (C) and nitrogen (N) cycling and microbial structural and functional indicators for assessing MTR coal mining impacts on streams; (2) determine whether indicators respond to impacts in a predictable manner; and (3) determine if functional indicators are less likely to change than are structural indicators in response to stressors associated with MTR coal mining. The structural indicators are water quality and sediment organic matter concentrations, and the functional indicators relate to microbial activity and biofilm production. Seasonal measurements were conducted over the course of a year in streams draining small MTR-impacted and forested watersheds in the Twentymile Creek watershed of West Virginia (WV). Five of the eight structural parameters measured had significant responses, with all means greater in the MTR-impacted streams than in the forested streams. These responses resulted from changes in source or augmentation of the original source of the C and N structural parameters because of MTR coal mining. Nitrate concentration and the stable carbon isotopic ratio of dissolved inorganic carbon were the most effective indicators evaluated in this study. Only three of the fourteen functional indicators measured had significant responses to MTR coal mining, with all means greater in the forested streams than in the MTR-impacted streams. These results suggest that stressors associated with MTR coal mining caused reduction in some aspects of microbial cycling, but resource subsidies may have counterbalanced some of the inhibition leading to no observable change in most of the functional indicators. The detritus base, which is thought to confer functional stability, was likely sustained in the MTR-impacted streams by channel storage and/or leaf litter inputs from their largely intact riparian zones. Overall, our results largely support the hypothesis that certain functional processes are more resistant to stress induced change than structural properties but also suggest the difficulty of identifying suitable functional indicators for ecological integrity assessment.

OBJECTIVE:This study aimed to evaluate the 9-month cost and health-related quality of life (HRQOL) outcomes of resistance versus viral load testing strategies to manage virological failure in low-middle income countries.METHODS:We analyzed secondary outcomes from the REVAMP clinical trial: a pragmatic, open label, parallel-arm randomized trial investigating resistance versus viral load testing for individuals failing first-line treatment in South Africa and Uganda. We collected resource data, valued according to local cost data and used the 3-level version of EQ-5D to measure HRQOL at baseline and 9 months. We applied seemingly unrelated regression equations to account for the correlation between cost and HRQOL. We conducted intention-to-treat analyses with multiple imputation using chained equations for missing data and performed sensitivity analyses using complete cases.RESULTS:For South Africa, resistance testing and opportunistic infections were associated with statistically significantly higher total costs, and virological suppression was associated with lower total cost. Higher baseline utility, higher cluster of differentiation 4 (CD4) count, and virological suppression were associated with better HRQOL. For Uganda, resistance testing and switching to second-line treatment were associated with higher total cost, and higher CD4 was associated with lower total cost. Higher baseline utility, higher CD4 count, and virological suppression were associated with better HRQOL. Sensitivity analyses of the complete-case analysis confirmed the overall results.CONCLUSION:Resistance testing showed no cost or HRQOL advantage in South Africa or Uganda over the 9-month REVAMP clinical trial.

Streamflow-duration assessment methods (SDAMs) are rapid, indicator-based tools for classifying streamflow duration (e.g., intermittent vs perennial flow) at the reach scale. Indicators are easily assessed stream properties used as surrogates of flow duration, which is too resource intensive to measure directly for many reaches. Invertebrates are commonly used as SDAM indicators because many are not highly mobile, and different species have life stages that require flow for different durations and times of the year. The objectives of this study were to 1) identify invertebrate taxa that can be used as SDAM indicators to distinguish between stream reaches having intermittent and perennial flow, 2) to compare indicator strength across different taxonomic and numeric resolutions, and 3) to assess the relative importance of season and habitat type on the ability of invertebrates to predict streamflow-duration class. We used 2 methods, random forest models and indicator species analysis, to analyze aquatic and terrestrial invertebrate data (presence/absence, density, and biomass) at the family and genus levels from 370 samples collected from both erosional and depositional habitats during both wet and dry seasons. In total, 36 intermittent and 53 perennial reaches were sampled along 31 forested headwater streams in 4 level II ecoregions across the United States. Random forest models for family- and genus-level datasets had stream classification accuracy ranging from 88.9 to 93.2%, with slightly higher accuracy for density than for presence/absence and biomass datasets. Season (wet/dry) tended to be a stronger predictor of streamflow-duration class than habitat (erosional/depositional). Many taxa at the family (58.8%) and genus level (61.6%) were collected from both intermittent and perennial reaches, and most taxa that were exclusive to 1 streamflow-duration class were rarely collected. However, 23 family-level or higher taxa (20 aquatic and 3 terrestrial) and 44 aquatic genera were identified as potential indicators of streamflow-duration class for forested headwater streams. The utility of the potential indicators varied across level II ecoregions in part because of representation of intermittent and perennial reaches in the dataset but also because of variable ecological responses to drying among species. Aquatic invertebrates have been an important field indicator of perennial reaches in existing SDAMs, but our findings highlight how including aquatic and terrestrial invertebrates as indicators of intermittent reaches can further maximize the data collected for streamflow-duration classifications.

Wastewaters and leachates from various inland resource extraction activities contain high ionic concentrations and differ in ionic composition, which complicates the understanding and effective management of their relative risks to stream ecosystems. To this end, we conducted a stream mesocosm dose–response experiment using two dosing recipes prepared from industrial salts. One recipe was designed to generally reflect the major ion composition of deep well brines (DWB) produced from gas wells (primarily Na+, Ca2+, and Cl−) and the other, the major ion composition of mountaintop mining (MTM) leachates from coal extraction operations (using salts dissociating to Ca2+, Mg2+, Na+, SO42− and HCO3−)—both sources being extensive in the Central Appalachians of the USA. The recipes were dosed at environmentally relevant nominal concentrations of total dissolved solids (TDS) spanning 100 to 2000 mg/L for 43 d under continuous flow-through conditions. The colonizing native algal periphyton and benthic invertebrates comprising the mesocosm ecology were assessed with response sensitivity distributions (RSDs) and hazard concentrations (HCs) at the taxa, community (as assemblages), and system (as primary and secondary production) levels. Single-species toxicity tests were run with the same recipes. Dosing the MTM recipe resulted in a significant loss of secondary production and invertebrate taxa assemblages that diverged from the control at all concentrations tested. Comparatively, intermediate doses of the DWB recipe had little consequence or increased secondary production (for emergence only) and had assemblages less different from the control. Only the highest dose of the DWB recipe had a negative impact on certain ecologies. The MTM recipe appeared more toxic, but overall, for both types of resource extraction wastewaters, the mesocosm responses suggested significant changes in stream ecology would not be expected for specific conductivity below 300 µS/cm, a published aquatic life benchmark suggested for the region.

Background Antiretroviral treatment improves health related quality of life (HRQoL) of people with human immunodeficiency virus (PWH). However, one third initiating first-line treatment experience virological failure and the determinants of HRQoL in this key population are unknown. Our study aims to identify determinants of among PWH failing antiretroviral treatment in sub-Saharan Africa. Methods We analysed data from a cohort of PWH having virological failure (> 1,000 copies/mL) on first-line ART in South Africa and Uganda. We measured HRQoL using the EuroQOL EQ-5D-3L and used a two-part regression model to obtain by-country analyses for South Africa and Uganda. The first part identifies risk factors that were associated with the likelihood of participants reporting perfect health (utility = 1) versus non-perfect health (utility < 1). The second part identifies risk factors that were associated with the EQ-5 L-3L utility scores for participants reporting non-perfect health. We performed sensitivity analyses to compare the results between the two-part model using tobit models and ordinary least squares regression. Results In both countries, males were more likely to report perfect health and participants with at least one comorbidity were less likely to report perfect health. In South Africa, participants with side effects and in Uganda those with opportunistic infections were also less likely to report perfect health. In Uganda, participants with 100% ART adherence were more likely to report perfect health. In South Africa, high HIV viral load, experiencing ART side effects, and the presence of opportunistic infections were each associated with lower HRQoL, whereas participants with 100% ART adherence reported higher HRQoL. In Uganda participants with lower CD4 count had lower HRQoL. Conclusion Markers of advanced disease (opportunistic infection, high viral load, low CD4), side effects, comorbidities and lack of ART adherence negatively impacted HRQoL for PWH experiencing virological failure. Trial registration ClinicalTrials.gov: NCT02787499.

Interest in developing periphytic diatom and bacterial indicators of nutrient effects continues to grow in support of the assessment and management of stream ecosystems and their watersheds. However, temporal variability could confound relationships between indicators and nutrients, subsequently affecting assessment outcomes. To document how temporal variability affects measures of diatom and bacterial assemblages obtained from DNA metabarcoding, we conducted weekly periphyton and nutrient sampling from July to October 2016 in 25 streams in a 1293 km2 mixed land use watershed. Measures of both diatom and bacterial assemblages were strongly associated with the percent agriculture in upstream watersheds and total phosphorus (TP) and total nitrogen (TN) concentrations. Temporal variability in TP and TN concentrations increased with greater amounts of agriculture in watersheds, but overall diatom and bacterial assemblage variability within sites-measured as mean distance among samples to corresponding site centroids in ordination space-remained consistent. This consistency was due in part to offsets between decreasing variability in relative abundances of taxa typical of low nutrient conditions and increasing variability in those typical of high nutrient conditions as mean concentrations of TP and TN increased within sites. Weekly low and high nutrient diatom and bacterial metrics were more strongly correlated with site mean nutrient concentrations over the sampling period than with same day measurements and more strongly correlated with TP than with TN. Correlations with TP concentrations were consistently strong throughout the study except briefly following two major precipitation events. Following these events, biotic relationships with TP reestablished within one to three weeks. Collectively, these results can strengthen interpretations of survey results and inform monitoring strategies and decision making. These findings have direct applications for improving the use of diatoms and bacteria, and the use of DNA metabarcoding, in monitoring programs and stream site assessments.

Indicators based on nutrient-biota relationships in streams can inform water quality restoration and protection programs. Bacterial assemblages could be particularly useful indicators of nutrient effects because they are species-rich, important contributors to ecosystem processes in streams, and responsive to rapidly changing conditions. Here, we sampled 25 streams weekly (12–14 times each) and used 16S rRNA gene metabarcoding of periphyton-associated bacteria to quantify the effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis identified assemblage-level changes and amplicon sequence variants (ASVs) that increased or decreased with increasing TP and TN concentrations (i.e., low P, high P, low N, and high N ASVs). Boosted regression trees confirmed that relative abundances of gene sequence reads for these four indicator groups were associated with nutrient concentrations. Gradient forest analysis complemented these results by using multiple predictors and random forest models for each ASV to identify portions of TP and TN gradients at which the greatest changes in assemblage structure occurred. Synthesized statistical results showed bacterial assemblage structure began changing at 24 µg TP/L with the greatest changes occurring from 110 to 195 µg/L. Changes in the bacterial assemblages associated with TN gradually occurred from 275 to 855 µg/L. Taxonomic and phylogenetic analyses showed that low nutrient ASVs were commonly Firmicutes, Verrucomicrobiota, Flavobacteriales, and Caulobacterales, Pseudomonadales, and Rhodobacterales of Proteobacteria, whereas other groups, such as Chitinophagales of Bacteroidota, and Burkholderiales, Rhizobiales, Sphingomonadales, and Steroidobacterales of Proteobacteria comprised the high nutrient ASVs. Overall, the responses of bacterial ASV indicators in this study highlight the utility of metabarcoding periphyton-associated bacteria for quantifying biotic responses to nutrient inputs in streams.

Beaver are recolonizing previously occupied regions, expanding into new territories, and increasingly being introduced and protected for stream conservation and restoration across numerous biomes. However, beaver dam effects on the physical, chemical, and biological characteristics of streams may vary within and among biomes. A comprehensive review of these impacts is lacking. The goals of this review were to: 1) summarize the distribution of studies by biome on beaver dam effects related to channel morphology, hydrology, water quality, and aquatic biota, as well as on beaver habitat selection, 2) summarize the extent to which beaver dam impacts have been consistent within and among biomes, and 3) share testable hypotheses regarding beaver impacts within understudied biomes. We quantify the directionality of beaver dam impacts from 267 peer-reviewed studies. Results show that the majority of studies have been completed within temperate forest environments and that many biomes are understudied. Across biomes, beaver preferred sites for dam development characterized by relatively low gradients and unconfined reaches with small drainage areas. Overall, parameters related to stream morphology and hydrology showed relatively consistent responses to beaver dams within and among biomes, yet water quality and biotic responses were variable among biomes. Responses also varied by parameter within water quality and biotic impact categories. The findings of this study can be useful for stream conservation and restoration efforts that introduce or protect beaver. Additional studies are needed within arid and cold biomes historically occupied by beaver and in novel biomes where beaver populations are currently expanding.

OBJECTIVES:There is conflicting evidence on the impact of pre-existing HIV drug resistance mutations (DRMs) in patients infected with non-B subtype virus.METHODS:We performed a case-cohort substudy of the AIDS Drug Resistance Surveillance Study, which enrolled South African patients initiating first-line efavirenz/emtricitabine/tenofovir. Pre-ART DRMs were detected by Illumina sequencing of HIV pol and DRMs present at <20% of the viral population were labelled as minority variants (MVs). Weighted Cox proportional hazards models estimated the association between pre-ART DRMs and risk of virological failure (VF), defined as confirmed HIV-1 RNA ≥1000 copies/mL after ≥5 months of ART.RESULTS:The evaluable population included 178 participants from a randomly selected subcohort (16 with VF, 162 without VF) and 83 additional participants with VF. In the subcohort, 16% of participants harboured ≥1 majority DRM. The presence of any majority DRM was associated with a 3-fold greater risk of VF (P = 0.002), which increased to 9.2-fold (P < 0.001) in those with <2 active drugs. Thirteen percent of participants harboured MV DRMs in the absence of majority DRMs. Presence of MVs alone had no significant impact on the risk of VF. Inclusion of pre-ART MVs with majority DRMs improved the sensitivity but reduced the specificity of predicting VF.CONCLUSIONS:In a South African cohort, the presence of majority DRMs increased the risk of VF, especially for participants receiving <2 active drugs. The detection of drug-resistant MVs alone did not predict an increased risk of VF, but their inclusion with majority DRMs affected the sensitivity/specificity of predicting VF.

AbstractNutrient pollution from human activities remains a common problem facing stream ecosystems. Identifying ecological responses to phosphorus and nitrogen can inform decisions affecting the protection and management of streams and their watersheds. Diatoms are particularly useful because they are a highly diverse group of unicellular algae found in nearly all aquatic environments and are sensitive responders to increased nutrient concentrations. Here, we used DNA metabarcoding of stream diatoms as an approach to quantifying effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis (TITAN) identified operational taxonomic units (OTUs) that increased or decreased along TP and TN gradients along with nutrient concentrations at which assemblages had substantial changes in the occurrences and relative abundances of OTUs. Boosted regression trees showed that relative abundances of gene sequence reads for OTUs identified by TITAN as low P, high P, low N, or high N diatoms had strong relationships with nutrient concentrations, which provided support for potentially using these groups of diatoms as metrics in monitoring programs. Gradient forest analysis provided complementary information by characterizing multi‐taxa assemblage change using multiple predictors and results from random forest models for each OTU. Collectively, these analyses showed that notable changes in diatom assemblage structure and OTUs began around 20 µg TP/L, low P diatoms decreased substantially and community change points occurred from 75 to 150 µg/L, and high P diatoms became increasingly dominant from 150 to 300 µg/L. Diatoms also responded to TN with large decreases in low N diatoms occurring from 280 to 525 µg TN/L and a transition to dominance by high N diatoms from 525–850 µg/L. These diatom responses to TP and TN could be used to inform protection efforts (i.e., anti‐degradation) and management goals (i.e., nutrient reduction) in streams and watersheds. Our results add to the growing support for using diatom metabarcoding in monitoring programs.

Linked foraging and bioenergetics models allow for increased understanding of fish growth potential and behavior by incorporating prey availability coupled to environmental conditions including temperature and prey visibility. To inform our understanding of growth and vertical migration patterns of Chinook salmon (Oncorhynchus tshawytscha) inhabiting lentic ecosystems, we linked foraging and bioenergetics models to create GrowChinook ( http://growchinook.fw.oregonstate.edu/ ). This multimodel design and optimization routine has broad applications in examining growth potential and predicting habitat use in stratified environments. We demonstrate the use of GrowChinook for the spring–summer rearing period in three Willamette River basin reservoirs, Oregon, USA. These reservoirs support juvenile spring Chinook salmon that exhibit a novel reservoir-reared life history that includes larger juvenile fish compared with nearby stream-reared subyearlings. Model outputs of predicted growth and depth use patterns based on observed prey distributions and environmental conditions were corroborated by observed empirical size and growth data from other years. Our simulations support diel vertical migration as a tactic that increases growth potential and contribute to understanding juvenile Chinook salmon growth in stratified systems.

Recent concerns about the viability of zoo populations have motivated studies on the historic and current status of animal populations in North American and European zoos. However, these evaluations may not accurately reflect the populations' long-term viability in the decades to come. Here, we assessed the projected future status of North American zoo populations by conducting standardized population viability analyses (PVAs) for 137 cooperative breeding programs. We summarized PVA results to describe patterns in viability across populations, and examined whether viability can be predicted by biological or management-based factors. Under recent management practices and without imports or exports of animals, 64% of populations will decline in size over the next 25 years, and only 18% would retain ≥90% of the founding gene diversity (GD) in 100 years. However, viability would improve if programs can implement management changes (e.g., increasing reproduction, increasing holding space, and importing genetically unique individuals, as appropriate): only 16% of populations would still decline in 25 years, and 49% would retain ≥90% GD in 100 years. Programs with more participating institutions and a "green" Association of Zoos and Aquariums animal program designation were projected to have higher metrics of demographic viability, and those with longer lifespans and lower recent death rates were projected to have higher metrics of genetic viability. Due to the large variation in species life history, management goals, and constraints across programs, our findings suggest there is unlikely to be a single path to long-term viability that would be appropriate for all zoo populations.

Headwater ephemeral tributaries are interfaces between uplands and downstream waters. Terrestrial coarse particulate organic matter (CPOM) is important in fueling aquatic ecosystems; however, the extent to which ephemeral tributaries are functionally connected to downstream waters through fluvial transport of CPOM has been little studied. Hydrology and deposition of leaf and wood, and surrogate transport (Ginkgo biloba leaves and wood dowels) were measured over month-long intervals through the winter and spring seasons (6 months) in 10 ephemeral tributaries (1.3-5.4 ha) in eastern Kentucky. Leaf deposition and surrogate transport varied over time, reflecting the seasonality of litterfall and runoff. Leaf deposition was higher in December than February and May but did not differ from January, March, and April. Mean percent of surrogate leaf transport from the ephemeral tributaries was highest in April (3.6% per day) and lowest in February (2.5%) and May (2%). Wood deposition and transport had similar patterns. No CPOM measures were related to flow frequency. Ephemeral tributaries were estimated to annually contribute 110.6 kg AFDM.km(-1).yr(-1) of leaves to the downstream mainstem. Ephemeral tributaries are functionally connected to downstream waters through CPOM storage and subsequent release that is timed when CPOM is often limited in downstream waters.

Spatial patterns in major dissolved solute concentrations were examined to better understand impact of surface coal mining in headwaters on downstream water chemistry. Sixty sites were sampled seasonally from 2012 to 2014 in an eastern Kentucky watershed. Watershed areas (WA) ranged from 1.6 to 400.5 km2 and were mostly forested (58%-95%), but some drained as much as 31% surface mining. Measures of total dissolved solutes and most component ions were positively correlated with mining. Analytes showed strong convergent spatial patterns with high variability in headwaters (<15 km2 WA) that stabilized downstream (WA > 75 km2), indicating hydrologic mixing primarily controls downstream values. Mean headwater solute concentrations were a good predictor of downstream values, with % differences ranging from 0.55% (Na+) to 28.78% (Mg2+). In a mined scenario where all headwaters had impacts, downstream solute concentrations roughly doubled. Alternatively, if mining impacts to headwaters were minimized, downstream solute concentrations better approximated the 300 μS/cm conductivity criterion deemed protective of aquatic life. Temporal variability also had convergent spatial patterns and mined streams were less variable due to unnaturally stable hydrology. The highly conserved nature of dissolved solutes from mining activities and lack of viable treatment options suggest forested, unmined watersheds would provide dilution that would be protective of downstream aquatic life.