A simple field based method for rapid wood density estimation for selected tree species in Western Kenya

Wood density is an important variable for accurate quantification of woody biomass and carbon stocks. Conventional destructive methods for wood density estimation are resource intensive, prohibiting their use, limiting the application of approaches that would minimize uncertainties in tree biomass estimates. We tested an alternative method involving tree coring with a carpenter's auger to estimate wood density of seven tropical tree species in Western Kenya. We used conventional water immersion method to validate results from the auger core method. The mean densities (and 95% confidence intervals) ranged from 0.36 g cm−3 (0.25–0.47) to 0.67 g cm−3 (0.61–0.73) for the auger core method, and 0.46 g cm−3 (0.42–0.50) to 0.67 g cm−3 (0.61–0.73) for the water immersion method. The auger core and water immersion methods were not significantly different for four out of seven tree species namely; Acacia mearnsii, Mangifera indica, Eucalyptus grandis and Grevillea robusta. However, wood densities estimated from the auger core method were lower (t (61) = 7.992, P = <0.001). The ease of the auger core method application, as a non-destructive method in acquiring wood density data, is a worthy alternative in biomass and carbon stocks quantification. This method could protect trees outside forests found in most parts of Africa

K-Deep Simplex: Deep Manifold Learning via Local Dictionaries

We propose K-Deep Simplex (KDS), a unified optimization framework for nonlinear dimensionality reduction that combines the strengths of manifold learning and sparse dictionary learning. Our approach learns local dictionaries that represent a data point with reconstruction coefficients supported on the probability simplex. The dictionaries are learned using algorithm unrolling, an increasingly popular technique for structured deep learning. KDS enjoys tremendous computational advantages over related approaches and is both interpretable and flexible. In particular, KDS is quasilinear in the number of data points with scaling that depends on intrinsic geometric properties of the data. We apply KDS to the unsupervised clustering problem and prove theoretical performance guarantees. Experiments show that the algorithm is highly efficient and performs competitively on synthetic and real data sets.Comment: 14 pages, 6 figure

Exploratory analysis of time from HIV diagnosis to ART start, factors and effect on survival: A longitudinal follow up study at seven teaching hospitals in Ethiopia

Background: the HIV care in Ethiopia has reached 79% coverage. The timeliness of the care provided at the different levels in the course of the disease starting from knowing HIV positive status to ART initiation is not well known. This study intends to explore the timing of the care seeking, the care provision and associated factors.Methods: This is a longitudinal follow-up study at seven university hospitals. Patients enrolled in HIV care from September 2005 to December 2013 and aged ≥14 years were studied. Different times in the cascade of HIV care were examined including the duration from date HIV diagnosed to enrollment in HIV care, duration from enrollment to eligibility for ART and time from eligibility to initiation of ART. Ordinal logistic regression was used to investigate their determinants while the effect of these periods on survival of patients was determined using cox-proportional hazards regression.Results: 4159 clients were studied. Time to enrollment after HIV test decreased from 39 days in 2005 to 1 day after 2008. It took longer if baseline CD4 was higher, and eligibility for ART was assessed late. Young adults, lower baseline CD4, HIV diagnosis&lt;2008, late enrollment, and early eligibility assessment were associated with early ART initiation. Male gender, advanced disease stage and lower baseline CD4 were consistent risk factors for mortality.Conclusion and recommendation: Time to enrollment and duration of ART eligibility assessment as well as ART initiation time after eligibility is improving. Further study is required to identify why mortality is slightly increasing after 2010.Key words: HIV, HIV testing, enrollment, eligibility, antiretroviral therapy, mortality, Ethiopia

Factors associated with mortality of TB/HIV co-infected patients in Ethiopia

Background: Despite the large number of TB patients on ART in Ethiopia, their mortality remains high. This study reports the effect of TB on HIV related mortality and determinants of TB/HIV co-infection related mortality.Methods: A longitudinal study design was employed as part of the Advanced Clinical Monitoring of ART (ACM) in Ethiopia. All patients started on ART at or after January 1, 2005 were included. Survival analysis was done to compare survival patterns of HIV patients with TB against HIV patients without TB. In addition, determinants of survival among TB/HIV co-infected patients were analyzed. Adjusted effects of the different factors on time to death were generated using Cox-proportional hazards regression.Results: A total of 3,889 patients were enrolled in the ACM study, of which 355 TB cases were identified, making the crude prevalence 9% (95% CI 8.3 – 10.2). Overall, incidence of TB was 2.2 (95% CI 1.9-2.4) per 100 person-years. TB was highest in the first 2 months and declined with time on ART to reach 1 per 100 person years after 24 months on ART. TB was significantly associated with mortality among HIV patients on HAART (AHR 2.0, 95% CI 1.47-2.75). Male gender was associated with mortality among TB/HIV co-infected patients.Conclusion: Tuberculosis plays a key role in HIV associated mortality. Targeted interventions which can keep patients free of TB in the early stages of their treatment are required to reduce TB related mortality.Key Words: Tuberculosis, Antiretroviral therapy, Mortalit

Magnitude of Antiretroviral Drug toxicity in adult HIV patients in Ethiopia: A cohort study at seven teaching hospitals

Background: The introduction of antiretroviral therapy (ART) has resulted in significant mortality reduction and improvement in the quality of life. However, this has come at a cost of increased drug toxicity. The objective of this study was to assess the patterns and predictors of ART toxicity in adult HIV patients in Ethiopia.Methods: This is a prospective cohort study conducted at seven teaching hospitals between September 2009 and December 2013 involving 3921 HIV patients on ART. Adverse drug reactions (ADR) due to ART were identified based on clinical assessment and/or laboratory parameters. Multivariable random effects Poisson regression analysis was used to identify factors independently associated with toxicity.Result: ADR due to ART drugs was reported in 867 (22.1 %) of the participants; 374 (9.5%) had severe forms. About 87% of reported toxicities were limited to three organ systems – the skin, nervous system and blood. The overall incidence of ADR was 9 per 100 person years. About a third of toxicities occurred during the first six months after ART initiation with the incidence rate of 22.4 per 100 person years. Concomitant anti-tuberculosis treatment was the strongest independent predictor of toxicity.Conclusion: ADR was found to be highly prevalent in HIV patients on ART at tertiary hospitals in Ethiopia. Most of these conditions occurred early after ART initiation and in those with concomitant anti-tuberculosis treatment. Thus, routine monitoring of patients on ART should be strengthened with particular emphasis in the first 6 months. Strategies should also be devised to replace older and more toxic agents with newer and safer drugs available.Key words: HIV, ART, adverse drug reaction, incidence rate, ACM, Ethiopi

Importance of Ethnicity, CYP2B6 and ABCB1 Genotype for Efavirenz Pharmacokinetics and Treatment Outcomes: A Parallel-group Prospective Cohort Study in two sub-Saharan Africa Populations.

We evaluated the importance of ethnicity and pharmacogenetic variations in determining efavirenz pharmacokinetics, auto-induction and immunological outcomes in two African populations. ART naïve HIV patients from Ethiopia (n = 285) and Tanzania (n = 209) were prospectively enrolled in parallel to start efavirenz based HAART. CD4+ cell counts were determined at baseline, 12, 24 and 48 weeks. Plasma and intracellular efavirenz and 8-hydroxyefvairenz concentrations were determined at week 4 and 16. Genotyping for common functional CYP2B6, CYP3A5, ABCB1, UGT2B7 and SLCO1B1 variant alleles were done. Patient country, CYP2B6*6 and ABCB1 c.4036A>G (rs3842A>G) genotype were significant predictors of plasma and intracellular efavirenz concentration. CYP2B6*6 and ABCB1 c.4036A>G (rs3842) genotype were significantly associated with higher plasma efavirenz concentration and their allele frequencies were significantly higher in Tanzanians than Ethiopians. Tanzanians displayed significantly higher efavirenz plasma concentration at week 4 (p<0.0002) and week 16 (p = 0.006) compared to Ethiopians. Efavirenz plasma concentrations remained significantly higher in Tanzanians even after controlling for the effect of CYP2B6*6 and ABCB1 c.4036A>G genotype. Within country analyses indicated a significant decrease in the mean plasma efavirenz concentration by week 16 compared to week 4 in Tanzanians (p = 0.006), whereas no significant differences in plasma concentration over time was observed in Ethiopians (p = 0.84). Intracellular efavirenz concentration and patient country were significant predictors of CD4 gain during HAART. We report substantial differences in efavirenz pharmacokinetics, extent of auto-induction and immunologic recovery between Ethiopian and Tanzanian HIV patients, partly but not solely, due to pharmacogenetic variations. The observed inter-ethnic variations in efavirenz plasma exposure may possibly result in varying clinical treatment outcome or adverse event profiles between populations

Global, regional, and national burden of chronic kidney disease, 1990–2017 : a systematic analysis for the Global Burden of Disease Study 2017

Background Health system planning requires careful assessment of chronic kidney disease (CKD) epidemiology, but data for morbidity and mortality of this disease are scarce or non-existent in many countries. We estimated the global, regional, and national burden of CKD, as well as the burden of cardiovascular disease and gout attributable to impaired kidney function, for the Global Burden of Diseases, Injuries, and Risk Factors Study 2017. We use the term CKD to refer to the morbidity and mortality that can be directly attributed to all stages of CKD, and we use the term impaired kidney function to refer to the additional risk of CKD from cardiovascular disease and gout. Methods The main data sources we used were published literature, vital registration systems, end-stage kidney disease registries, and household surveys. Estimates of CKD burden were produced using a Cause of Death Ensemble model and a Bayesian meta-regression analytical tool, and included incidence, prevalence, years lived with disability, mortality, years of life lost, and disability-adjusted life-years (DALYs). A comparative risk assessment approach was used to estimate the proportion of cardiovascular diseases and gout burden attributable to impaired kidney function. Findings Globally, in 2017, 1·2 million (95% uncertainty interval [UI] 1·2 to 1·3) people died from CKD. The global all-age mortality rate from CKD increased 41·5% (95% UI 35·2 to 46·5) between 1990 and 2017, although there was no significant change in the age-standardised mortality rate (2·8%, −1·5 to 6·3). In 2017, 697·5 million (95% UI 649·2 to 752·0) cases of all-stage CKD were recorded, for a global prevalence of 9·1% (8·5 to 9·8). The global all-age prevalence of CKD increased 29·3% (95% UI 26·4 to 32·6) since 1990, whereas the age-standardised prevalence remained stable (1·2%, −1·1 to 3·5). CKD resulted in 35·8 million (95% UI 33·7 to 38·0) DALYs in 2017, with diabetic nephropathy accounting for almost a third of DALYs. Most of the burden of CKD was concentrated in the three lowest quintiles of Socio-demographic Index (SDI). In several regions, particularly Oceania, sub-Saharan Africa, and Latin America, the burden of CKD was much higher than expected for the level of development, whereas the disease burden in western, eastern, and central sub-Saharan Africa, east Asia, south Asia, central and eastern Europe, Australasia, and western Europe was lower than expected. 1·4 million (95% UI 1·2 to 1·6) cardiovascular disease-related deaths and 25·3 million (22·2 to 28·9) cardiovascular disease DALYs were attributable to impaired kidney function. Interpretation Kidney disease has a major effect on global health, both as a direct cause of global morbidity and mortality and as an important risk factor for cardiovascular disease. CKD is largely preventable and treatable and deserves greater attention in global health policy decision making, particularly in locations with low and middle SDI

Combating the effects of climatic change on forests by mitigation strategies

<p>Abstract</p> <p>Background</p> <p>Forests occur across diverse biomes, each of which shows a specific composition of plant communities associated with the particular climate regimes. Predicted future climate change will have impacts on the vulnerability and productivity of forests; in some regions higher temperatures will extend the growing season and thus improve forest productivity, while changed annual precipitation patterns may show disadvantageous effects in areas, where water availability is restricted. While adaptation of forests to predicted future climate scenarios has been intensively studied, less attention was paid to mitigation strategies such as the introduction of tree species well adapted to changing environmental conditions.</p> <p>Results</p> <p>We simulated the development of managed forest ecosystems in Germany for the time period between 2000 and 2100 under different forest management regimes and climate change scenarios. The management regimes reflect different rotation periods, harvesting intensities and species selection for reforestations. The climate change scenarios were taken from the IPCC's Special Report on Emission Scenarios (SRES). We used the scenarios A1B (rapid and successful economic development) and B1 (high level of environmental and social consciousness combined with a globally coherent approach to a more sustainable development). Our results indicate that the effects of different climate change scenarios on the future productivity and species composition of German forests are minor compared to the effects of forest management.</p> <p>Conclusions</p> <p>The inherent natural adaptive capacity of forest ecosystems to changing environmental conditions is limited by the long life time of trees. Planting of adapted species and forest management will reduce the impact of predicted future climate change on forests.</p

Pharmacogenetic & Pharmacokinetic Biomarker for Efavirenz Based ARV and Rifampicin Based Anti-TB Drug Induced Liver Injury in TB-HIV Infected Patients

BACKGROUND: Implication of pharmacogenetic variations and efavirenz pharmacokinetics in concomitant efavirenz based antiviral therapy and anti-tubercular drug induced liver injury (DILI) has not been yet studied. We performed a prospective case-control association study to identify the incidence, pharmacogenetic, pharmacokinetic and biochemical predictors for anti-tubercular and antiretroviral drugs induced liver injury (DILI) in HIV and tuberculosis (TB) co-infected patients. METHODS AND FINDINGS: Newly diagnosed treatment naïve TB-HIV co-infected patients (n = 353) were enrolled to receive efavirenz based ART and rifampicin based anti-TB therapy, and assessed clinically and biochemically for DILI up to 56 weeks. Quantification of plasma efavirenz and 8-hydroxyefaviernz levels and genotyping for NAT2, CYP2B6, CYP3A5, ABCB1, UGT2B7 and SLCO1B1 genes were done. The incidence of DILI and identification of predictors was evaluated using survival analysis and the Cox Proportional Hazards Model. The incidence of DILI was 30.0%, or 14.5 per 1000 person-week, and that of severe was 18.4%, or 7.49 per 1000 person-week. A statistically significant association of DILI with being of the female sex (p = 0.001), higher plasma efavirenz level (p = 0.009), efavirenz/8-hydroxyefavirenz ratio (p = 0.036), baseline AST (p = 0.022), ALT (p = 0.014), lower hemoglobin (p = 0.008), and serum albumin (p = 0.007), NAT2 slow-acetylator genotype (p = 0.039) and ABCB1 3435TT genotype (p = 0.001). CONCLUSION: We report high incidence of anti-tubercular and antiretroviral DILI in Ethiopian patients. Between patient variability in systemic efavirenz exposure and pharmacogenetic variations in NAT2, CYP2B6 and ABCB1 genes determines susceptibility to DILI in TB-HIV co-infected patients. Close monitoring of plasma efavirenz level and liver enzymes during early therapy and/or genotyping practice in HIV clinics is recommended for early identification of patients at risk of DILI

Preterm care during the COVID-19 pandemic: A comparative risk analysis of neonatal deaths averted by kangaroo mother care versus mortality due to SARS-CoV-2 infection.

BACKGROUND: COVID-19 is disrupting health services for mothers and newborns, particularly in low- and middle-income countries (LMIC). Preterm newborns are particularly vulnerable. We undertook analyses of the benefits of kangaroo mother care (KMC) on survival among neonates weighing ≤2000 g compared with the risk of SARS-CoV-2 acquired from infected mothers/caregivers. METHODS: We modelled two scenarios over 12 months. Scenario 1 compared the survival benefits of KMC with universal coverage (99%) and mortality risk due to COVID-19. Scenario 2 estimated incremental deaths from reduced coverage and complete disruption of KMC. Projections were based on the most recent data for 127 LMICs (~90% of global births), with results aggregated into five regions. FINDINGS: Our worst-case scenario (100% transmission) could result in 1,950 neonatal deaths from COVID-19. Conversely, 125,680 neonatal lives could be saved with universal KMC coverage. Hence, the benefit of KMC is 65-fold higher than the mortality risk of COVID-19. If recent evidence of 10% transmission was applied, the ratio would be 630-fold. We estimated a 50% reduction in KMC coverage could result in 12,570 incremental deaths and full disruption could result in 25,140 incremental deaths, representing a 2·3-4·6% increase in neonatal mortality across the 127 countries. INTERPRETATION: The survival benefit of KMC far outweighs the small risk of death due to COVID-19. Preterm newborns are at risk, especially in LMICs where the consequences of disruptions are substantial. Policymakers and healthcare professionals need to protect services and ensure clearer messaging to keep mothers and newborns together, even if the mother is SARS-CoV-2-positive. FUNDING: Eunice Kennedy Shriver National Institute of Child Health & Human Development; Bill & Melinda Gates Foundation; Elma Philanthropies; Wellcome Trust; and Joint Global Health Trials scheme of Department of Health and Social Care, Department for International Development, Medical Research Council, and Wellcome Trust