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Showing papers by "Makerere University published in 2018"



Journal ArticleDOI
TL;DR: For tuberculosis case detection, sensitivity ofXpert Ultra was superior to that of Xpert in Patients with paucibacillary disease and in patients with HIV, however, this increase in sensitivity came at the expense of a decrease in specificity.
Abstract: Summary Background The Xpert MTB/RIF assay is an automated molecular test that has improved the detection of tuberculosis and rifampicin resistance, but its sensitivity is inadequate in patients with paucibacillary disease or HIV. Xpert MTB/RIF Ultra (Xpert Ultra) was developed to overcome this limitation. We compared the diagnostic performance of Xpert Ultra with that of Xpert for detection of tuberculosis and rifampicin resistance. Methods In this prospective, multicentre, diagnostic accuracy study, we recruited adults with pulmonary tuberculosis symptoms presenting at primary health-care centres and hospitals in eight countries (South Africa, Uganda, Kenya, India, China, Georgia, Belarus, and Brazil). Participants were allocated to the case detection group if no drugs had been taken for tuberculosis in the past 6 months or to the multidrug-resistance risk group if drugs for tuberculosis had been taken in the past 6 months, but drug resistance was suspected. Demographic information, medical history, chest imaging results, and HIV test results were recorded at enrolment, and each participant gave at least three sputum specimen on 2 separate days. Xpert and Xpert Ultra diagnostic performance in the same sputum specimen was compared with culture tests and drug susceptibility testing as reference standards. The primary objectives were to estimate and compare the sensitivity of Xpert Ultra test with that of Xpert for detection of smear-negative tuberculosis and rifampicin resistance and to estimate and compare Xpert Ultra and Xpert specificities for detection of rifampicin resistance. Study participants in the case detection group were included in all analyses, whereas participants in the multidrug-resistance risk group were only included in analyses of rifampicin-resistance detection. Findings Between Feb 18, and Dec 24, 2016, we enrolled 2368 participants for sputum sampling. 248 participants were excluded from the analysis, and 1753 participants were distributed to the case detection group (n=1439) and the multidrug-resistance risk group (n=314). Sensitivities of Xpert Ultra and Xpert were 63% and 46%, respectively, for the 137 participants with smear-negative and culture-positive sputum (difference of 17%, 95% CI 10 to 24); 90% and 77%, respectively, for the 115 HIV-positive participants with culture-positive sputum (13%, 6·4 to 21); and 88% and 83%, respectively, across all 462 participants with culture-positive sputum (5·4%, 3·3 to 8·0). Specificities of Xpert Ultra and Xpert for case detection were 96% and 98% (−2·7%, −3·9 to −1·7) overall, and 93% and 98% for patients with a history of tuberculosis. Xpert Ultra and Xpert performed similarly in detecting rifampicin resistance. Interpretation For tuberculosis case detection, sensitivity of Xpert Ultra was superior to that of Xpert in patients with paucibacillary disease and in patients with HIV. However, this increase in sensitivity came at the expense of a decrease in specificity. Funding Government of Netherlands, Government of Australia, Bill & Melinda Gates Foundation, Government of the UK, and the National Institute of Allergy and Infectious Diseases.

391 citations


Journal ArticleDOI
TL;DR: Despite a low-risk profile and few postoperative complications, patients in Africa were twice as likely to die after surgery when compared with the global average for postoperative deaths, and Initiatives to increase access to surgical treatments in Africa should be coupled with improved surveillance for deteriorating physiology in patients who develop postoperative complication.

353 citations


Journal ArticleDOI
01 Jul 2018
TL;DR: The authors argue that much of the associated challenges and opportunities are found in the global south and call for a renewed research focus on urbanization in the south, and suggest targeted efforts to correct structural biases in the knowledge production system.
Abstract: Urbanization is a global phenomenon with strong sustainability implications across multiple scales. We argue that much of the associated challenges, and opportunities, are found in the global south. We show that urban issues in the global south are distinctly and statistically different from those in the global north, but our current urban knowledge is predominantly shaped by research on and from the global north. Cities in the global south have strong imperatives, and unique but often overlooked capacity, to innovate and experiment for sustainability. We call for a renewed research focus on urbanization in the south, and suggest targeted efforts to correct structural biases in the knowledge production system. Most of the sustainability challenges and opportunities associated with urbanization are found in the global south. This Perspective shows the extent to which urban issues differ between the developed and developing worlds and identifies steps to re-focus the urban research system globally in view of allowing a more prominent role of urban scholarship from the global south.

258 citations


Journal ArticleDOI
TL;DR: A genome-wide association study of multi- and extensively drug-resistant tuberculosis uses 6,465 Mycobacterium tuberculosis clinical isolates to identify novel mutations associated with resistance and suggest the involvement of efflux pumps in the emergence of resistance.
Abstract: To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.

247 citations


Journal ArticleDOI
TL;DR: World Health Organization (WHO) recommends the use of Xpert Ultra as the initial diagnostic test for suspected tuberculous meningitis, following an evaluation of the diagnostic performance of the new Xpert MTB/RIF Ultra (Xpert Ultra).
Abstract: Summary Background WHO recommends Xpert MTB/RIF as initial diagnostic testing for tuberculous meningitis. However, diagnosis remains difficult, with Xpert sensitivity of about 50–70% and culture sensitivity of about 60%. We evaluated the diagnostic performance of the new Xpert MTB/RIF Ultra (Xpert Ultra) for tuberculous meningitis. Methods We prospectively obtained diagnostic cerebrospinal fluid (CSF) specimens during screening for a trial on the treatment of HIV-associated cryptococcal meningitis in Mbarara, Uganda. HIV-infected adults with suspected meningitis (eg, headache, nuchal rigidity, altered mental status) were screened consecutively at Mbarara Regional Referral Hospital. We centrifuged CSF, resuspended the pellet in 2 mL of CSF, and tested 0·5 mL with mycobacteria growth indicator tube culture, 1 mL with Xpert, and cryopreserved 0·5 mL, later tested with Xpert Ultra. We assessed diagnostic performance against uniform clinical case definition or a composite reference standard of any positive CSF tuberculous test. Findings From Feb 27, 2015, to Nov 7, 2016, we prospectively evaluated 129 HIV-infected adults with suspected meningitis for tuberculosis. 23 participants were classified as probable or definite tuberculous meningitis by uniform case definition, excluding Xpert Ultra results. Xpert Ultra sensitivity was 70% (95% CI 47–87; 16 of 23 cases) for probable or definite tuberculous meningitis compared with 43% (23–66; 10/23) for Xpert and 43% (23–66; 10/23) for culture. With composite standard, we detected tuberculous meningitis in 22 (17%) of 129 participants. Xpert Ultra had 95% sensitivity (95% CI 77–99; 21 of 22 cases) for tuberculous meningitis, which was higher than either Xpert (45% [24–68]; 10/22; p=0·0010) or culture (45% [24–68]; 10/22; p=0·0034). Of 21 participants positive by Xpert Ultra, 13 were positive by culture, Xpert, or both, and eight were only positive by Xpert Ultra. Of those eight, three were categorised as probable tuberculous meningitis, three as possible tuberculous meningitis, and two as not tuberculous meningitis. Testing 6 mL or more of CSF was associated with more frequent detection of tuberculosis than with less than 6 mL (26% vs 7%; p=0·014). Interpretation Xpert Ultra detected significantly more tuberculous meningitis than did either Xpert or culture. WHO now recommends the use of Xpert Ultra as the initial diagnostic test for suspected tuberculous meningitis. Funding National Institute of Neurologic Diseases and Stroke, Fogarty International Center, National Institute of Allergy and Infectious Disease, UK Medical Research Council/DfID/Wellcome Trust Global Health Trials, Doris Duke Charitable Foundation.

222 citations


Journal ArticleDOI
TL;DR: The results showed that PO43- adsorption increased with reaction time and temperature while it decreased with an increase in solution pH, and the good desorption capacity has practical benefits for potential regeneration and re-use of the saturated particles in wastewater treatment systems.

204 citations


Journal ArticleDOI
TL;DR: Adsorption by activated carbon has great potential to improve natural organic matter (NOM) removal from water, but the high production and regeneration costs limit its wide scale application.
Abstract: Adsorption by activated carbon has great potential to improve natural organic matter (NOM) removal from water. However, the high production and regeneration costs limit its wide scale application. ...

198 citations


Journal ArticleDOI
TL;DR: In this paper, the authors demonstrate broad differences between Northern and Southern cities, and deconstructed urban theory derived from experiences of the networked urban regions of the GloVe region of the US.
Abstract: Studies of infrastructure have demonstrated broad differences between Northern and Southern cities, and deconstructed urban theory derived from experiences of the networked urban regions of the Glo...

196 citations


Journal ArticleDOI
TL;DR: Simmons and colleagues discuss potential mechanisms underlying this resistance, such as those mediated by macrophages, T cells and B cells, and how an understanding of these mechanisms might aid in the development of therapies for tuberculosis.
Abstract: Mycobacterium tuberculosis is a leading cause of mortality worldwide and establishes a long-lived latent infection in a substantial proportion of the human population. Multiple lines of evidence suggest that some individuals are resistant to latent M. tuberculosis infection despite long-term and intense exposure, and we term these individuals ‘resisters’. In this Review, we discuss the epidemiological and genetic data that support the existence of resisters and propose criteria to optimally define and characterize the resister phenotype. We review recent insights into the immune mechanisms of M. tuberculosis clearance, including responses mediated by macrophages, T cells and B cells. Understanding the cellular mechanisms that underlie resistance to M. tuberculosis infection may reveal immune correlates of protection that could be utilized for improved diagnostics, vaccine development and novel host-directed therapeutic strategies. Resisters are individuals who show resistance to infection despite long-term, high exposure to Mycobacterium tuberculosis. In this Review, Simmons and colleagues discuss potential mechanisms underlying this resistance, such as those mediated by macrophages, T cells and B cells, and how an understanding of these mechanisms might aid in the development of therapies for tuberculosis.

180 citations


Journal ArticleDOI
31 Aug 2018-Sensors
TL;DR: A spectrogram-based feature extraction approach combined with an ensemble of data augmentations in feature space is proposed to take care of the data scarcity problem and produces state-of-the-art accuracy results in HAR.
Abstract: Wearable inertial measurement unit (IMU) sensors are powerful enablers for acquisition of motion data Specifically, in human activity recognition (HAR), IMU sensor data collected from human motion are categorically combined to formulate datasets that can be used for learning human activities However, successful learning of human activities from motion data involves the design and use of proper feature representations of IMU sensor data and suitable classifiers Furthermore, the scarcity of labelled data is an impeding factor in the process of understanding the performance capabilities of data-driven learning models To tackle these challenges, two primary contributions are in this article: first; by using raw IMU sensor data, a spectrogram-based feature extraction approach is proposed Second, an ensemble of data augmentations in feature space is proposed to take care of the data scarcity problem Performance tests were conducted on a deep long term short term memory (LSTM) neural network architecture to explore the influence of feature representations and the augmentations on activity recognition accuracy The proposed feature extraction approach combined with the data augmentation ensemble produces state-of-the-art accuracy results in HAR A performance evaluation of each augmentation approach is performed to show the influence on classification accuracy Finally, in addition to using our own dataset, the proposed data augmentation technique is evaluated against the University of California, Irvine (UCI) public online HAR dataset and yields state-of-the-art accuracy results at various learning rates

Journal ArticleDOI
Gaya K. Amarasinghe1, Nidia G. Aréchiga Ceballos, Ashley C. Banyard, Christopher F. Basler2, Sina Bavari3, Andrew J. Bennett4, Kim R. Blasdell5, Thomas Briese6, Alexander Bukreyev7, Yíngyún Caì8, Charles H. Calisher9, Cristine Campos Lawson8, Kartik Chandran10, Colin A. Chapman11, Colin A. Chapman12, Colin A. Chapman13, Charles Y. Chiu14, Kang Seuk Choi, Peter L. Collins8, Ralf G. Dietzgen15, Valerian V. Dolja16, Olga Dolnik17, Leslie L. Domier18, Ralf Dürrwald19, John M. Dye3, Andrew J. Easton20, Hideki Ebihara21, Juan Emilio Echevarría22, Anthony R. Fooks, Pierre Formenty23, Ron A. M. Fouchier24, Conrad M. Freuling25, Elodie Ghedin26, Tony L. Goldberg4, Roger Hewson27, Masayuki Horie13, Timothy H. Hyndman28, Dàohóng Jiāng29, Robert Kityo30, Gary P. Kobinger31, Hideki Kondō32, Eugene V. Koonin8, Mart Krupovic33, Gael Kurath34, Robert A. Lamb35, Benhur Lee36, Eric M. Leroy, Piet Maes37, Andrea Maisner17, Denise A. Marston, Sunil K. Mor38, Thomas Müller25, Elke Mühlberger39, Víctor Manuel Neira Ramírez40, Sergey V. Netesov41, Terry Fei Fan Ng14, Norbert Nowotny42, Norbert Nowotny43, Gustavo Palacios3, Jean L. Patterson44, Janusz T. Paweska, Susan Payne45, Karla Prieto3, Bertus K. Rima46, Paul A. Rota47, Dennis Rubbenstroth48, Martin Schwemmle48, Stuart G. Siddell49, Sophie J. Smither50, Qisheng Song51, Timothy Song26, Mark D. Stenglein9, David M. Stone, Ayato Takada52, Robert B. Tesh7, Luciano M. Thomazelli53, Keizō Tomonaga13, Noël Tordo33, Jonathan S. Towner47, Nikos Vasilakis7, Sonia Vázquez-Morón22, Claudio Verdugo54, Viktor E. Volchkov55, Victoria Wahl, Peter J. Walker15, David Wang1, Lin-Fa Wang56, James F. X. Wellehan57, Michael R. Wiley7, Michael R. Wiley58, Anna E. Whitfield59, Yuri I. Wolf8, Gōngyín Yè60, Yǒng Zhèn Zhāng61, Jens H. Kuhn8 
Washington University in St. Louis1, Georgia State University2, United States Army Medical Research Institute of Infectious Diseases3, University of Wisconsin-Madison4, Commonwealth Scientific and Industrial Research Organisation5, Columbia University6, University of Texas Medical Branch7, National Institutes of Health8, Colorado State University9, Yeshiva University10, Wildlife Conservation Society11, McGill University12, Kyoto University13, University of California, San Francisco14, University of Queensland15, Oregon State University16, University of Marburg17, University of Illinois at Chicago18, Robert Koch Institute19, University of Warwick20, Mayo Clinic21, Carlos III Health Institute22, World Health Organization23, Erasmus University Rotterdam24, Friedrich Loeffler Institute25, New York University26, Public Health England27, Murdoch University28, Huazhong Agricultural University29, Makerere University30, Laval University31, Okayama University32, Pasteur Institute33, United States Geological Survey34, Northwestern University35, Icahn School of Medicine at Mount Sinai36, Katholieke Universiteit Leuven37, University of Minnesota38, Boston University39, University of Chile40, Novosibirsk State University41, University of Veterinary Medicine Vienna42, University of Medicine and Health Sciences43, Texas Biomedical Research Institute44, Texas A&M University45, Queen's University Belfast46, Centers for Disease Control and Prevention47, University of Freiburg48, University of Bristol49, Defence Science and Technology Laboratory50, University of Missouri51, Hokkaido University52, University of São Paulo53, Austral University of Chile54, École normale supérieure de Lyon55, National University of Singapore56, University of Florida57, University of Nebraska Medical Center58, North Carolina State University59, Zhejiang University60, Chinese Center for Disease Control and Prevention61
TL;DR: The updated taxonomy of the order Mononegavirales is presented as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and additional taxonomic proposals that may affect the order in the near future are summarized.
Abstract: In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Journal ArticleDOI
TL;DR: This review provides a synopsis of current nematode challenges facing SSA and presents the opportunities to overcome current shortcomings, including a means to increase nematology capacity.
Abstract: Sub-Saharan Africa (SSA) is a region beset with challenges, not least its ability to feed itself. Low agricultural productivity, exploding populations, and escalating urbanization have led to declining per capita food availability. In order to reverse this trend, crop production systems must intensify, which brings with it an elevated threat from pests and diseases, including plant-parasitic nematodes. A holistic systems approach to pest management recognizes disciplinary integration. However, a critical under-representation of nematology expertise is a pivotal shortcoming, especially given the magnitude of the threat nematodes pose under more intensified systems. With more volatile climates, efficient use of water by healthy root systems is especially crucial. Within SSA, smallholder farming systems dominate the agricultural landscape, where a limited understanding of nematode problems prevails. This review provides a synopsis of current nematode challenges facing SSA and presents the opportunities to overcome current shortcomings, including a means to increase nematology capacity.

Journal ArticleDOI
TL;DR: This investigation demonstrated PFASs entry into the terrestrial food chain and drinking water resources in Kampala, Uganda and demonstrates PFAS-specific partitioning behaviour in different matrices.


Journal ArticleDOI
TL;DR: Household air pollution exposure was associated with a higher prevalence of COPD, particularly among women, and it is likely a leading population‐attributable risk factor for COPD in resource‐poor settings.
Abstract: Rationale: Forty percent of households worldwide burn biomass fuels for energy, which may be the most important contributor to household air pollution.Objectives: To examine the association between...

Journal ArticleDOI
TL;DR: Replacement of SFM with BSFPM did not affect daily feed intake, daily body weight gain, feed conversion ratio, aroma or taste of cooked breast meat, and their potential for income generation and job creation particularly in developing countries is discussed.
Abstract: The ever-increasing animal feed costs are driving many vulnerable communities involved in animal husbandry out of business. The high cost is mainly driven by the protein source, which represents the most expensive component in animal feed. In conventional feed, protein is obtained mainly from soybean and fish meal (SFM). The present study explored potential of partially replacing this SFM with black soldier fly prepupae meal (BSFPM) in Cobb 500 broiler chicken diets. A SFM-based diet was compared to three experimental diets formulated by partially substituting SFM with BSFPM at 13.8, 27.4, and 42.0% of the crude protein (CP) in the starter feed and 11.0, 37.2, and 55.5% of the CP in the finisher feed of diets D1, D2, and D3, respectively. Dietary effects on average daily feed intake, average daily body weight gain, feed conversion ratio, carcass characteristics, breast meat sensory attributes, and the economic implication of their use in broiler production were evaluated. Replacement of SFM with BSFPM did not affect daily feed intake, daily body weight gain, feed conversion ratio, aroma or taste of cooked breast meat. A 16.0% higher Cost Benefit Ratio and 25.0% better Return on Investment was recorded when the birds were reared on the highest concentration of black soldier fly (D3) compared to the conventional diet which was 19.0% more expensive. The implication of these findings for the promotion of insect mass production enterprises for animal feed protein, and their potential for income generation and job creation particularly in developing countries is discussed.

Journal ArticleDOI
TL;DR: It is argued that PBF as it is currently implemented in many contexts does not satisfy the promises, and entry points for alternative approaches are proposed.
Abstract: This paper questions the view that performance-based financing (PBF) in the health sector is an effective, efficient and equitable approach to improving the performance of health systems in low-income and middle-income countries (LMICs). PBF was conceived as an open approach adapted to specific country needs, having the potential to foster system-wide reforms. However, as with many strategies and tools, there is a gap between what was planned and what is actually implemented. This paper argues that PBF as it is currently implemented in many contexts does not satisfy the promises. First, since the start of PBF implementation in LMICs, concerns have been raised on the basis of empirical evidence from different settings and disciplines that indicated the risks, cost and perverse effects. However, PBF implementation was rushed despite insufficient evidence of its effectiveness. Second, there is a lack of domestic ownership of PBF. Considering the amounts of time and money it now absorbs, and the lack of evidence of effectiveness and efficiency, PBF can be characterised as a donor fad. Third, by presenting itself as a comprehensive approach that makes it possible to address all aspects of the health system in any context, PBF monopolises attention and focuses policy dialogue on the short-term results of PBF programmes while diverting attention and resources from broader processes of change and necessary reforms. Too little care is given to system-wide and long-term effects, so that PBF can actually damage health services and systems. This paper ends by proposing entry points for alternative approaches.

Journal ArticleDOI
TL;DR: In this paper, the authors investigated the contribution of training and employee engagement on employee performance using evidence from Uganda's health sector using cross-sectional data from the National Health Service (NHS).
Abstract: The purpose of this study was to investigate the contribution of training and employee engagement on employee performance using evidence from Uganda’s health sector. This study is cross sectional a...

Journal ArticleDOI
25 Jul 2018-eLife
TL;DR: This work used detailed clinical and entomological data from parallel cohort studies conducted across the malaria transmission spectrum in Uganda to quantify the development of immunity against symptomatic P. falciparum as a function of age and transmission intensity.
Abstract: Fundamental gaps remain in our understanding of how immunity to malaria develops. We used detailed clinical and entomological data from parallel cohort studies conducted across the malaria transmission spectrum in Uganda to quantify the development of immunity against symptomatic P. falciparum as a function of age and transmission intensity. We focus on: anti-parasite immunity (i.e. ability to control parasite densities) and anti-disease immunity (i.e. ability to tolerate higher parasite densities without fever). Our findings suggest a strong effect of age on both types of immunity, not explained by cumulative-exposure. They also show an independent effect of exposure, where children living in moderate/high transmission settings develop immunity faster as transmission increases. Surprisingly, children in the lowest transmission setting appear to develop immunity more efficiently than those living in moderate transmission settings. Anti-parasite and anti-disease immunity develop in parallel, reducing the probability of experiencing symptomatic malaria upon each subsequent P. falciparum infection.

Journal ArticleDOI
Mehdi Rahmati1, Mehdi Rahmati2, Lutz Weihermüller1, Jan Vanderborght1, Yakov Pachepsky3, Lili Mao, Seyed Hamidreza Sadeghi4, Niloofar Moosavi1, Hossein Kheirfam5, Carsten Montzka1, Kris Van Looy1, Brigitta Tóth6, Brigitta Tóth7, Zeinab Hazbavi4, Wafa Al Yamani8, Ammar Albalasmeh9, Ma'in Z. Alghzawi9, Rafael Angulo-Jaramillo10, Antonio Celso Dantas Antonino11, George Arampatzis, Robson André Armindo, Hossein Asadi12, Yazidhi Bamutaze13, Jordi Batlle-Aguilar14, Jordi Batlle-Aguilar15, Béatrice Bechet16, Fabian Becker17, Günter Blöschl18, Klaus Bohne19, Isabelle Braud, Clara Castellano20, Artemi Cerdà21, Maha Chalhoub15, Rogerio Cichota22, Milena Cislerova23, Brent Clothier22, Yves Coquet24, Yves Coquet15, Wim Cornelis25, Corrado Corradini26, Artur Paiva Coutinho11, Muriel Bastista de Oliveira, José Ronaldo de Macedo27, Matheus Fonseca Durães, Hojat Emami28, Iraj Eskandari, A Farajnia, Alessia Flammini26, Nándor Fodor7, Mamoun A. Gharaibeh9, Mohamad Hossein Ghavimipanah4, Teamrat A. Ghezzehei29, Simone Giertz30, Evangelos G. Hatzigiannakis, Rainer Horn31, Juan J. Jiménez20, Diederik Jacques, Saskia Keesstra32, Saskia Keesstra33, Hamid Kelishadi34, Mahboobeh Kiani-Harchegani4, Mehdi Kouselou2, Madan K. Jha35, Laurent Lassabatere10, Xiaoyan Li36, Mark A. Liebig3, Lubomir Lichner37, M.V. López20, Deepesh Machiwal38, Dirk Mallants39, Micael Stolben Mallmann40, Jean Dalmo de Oliveira Marques, Miles R. Marshall, Jan Mertens, Félicien Meunier41, Mohammad Hossein Mohammadi12, Binayak P. Mohanty42, Mansonia Pulido-Moncada43, Suzana Maria Gico Lima Montenegro11, Renato Morbidelli26, David Moret-Fernández20, Ali Akbar Moosavi44, Mohammad Reza Mosaddeghi34, Seyed Bahman Mousavi2, Hasan Mozaffari44, K. Nabiollahi45, Mohammad Reza Neyshabouri46, Marta Vasconcelos Ottoni, Theophilo Benedicto Ottoni Filho47, Mohammad Reza Pahlavan-Rad, Andreas Panagopoulos, Stephan Peth48, Pierre-Emmanuel Peyneau16, Tommaso Picciafuoco18, Tommaso Picciafuoco26, Jean Poesen49, Manuel Pulido50, Dalvan José Reinert40, Sabine Reinsch, Meisam Rezaei25, Francis Parry Roberts, David A. Robinson, Jesús Rodrigo-Comino51, Jesús Rodrigo-Comino52, Otto Corrêa Rotunno Filho47, Tadaomi Saito53, Hideki Suganuma54, Carla Saltalippi26, Renáta Sándor7, Brigitta Schütt17, Manuel Seeger51, Nasrollah Sepehrnia34, Ehsan Sharifi Moghaddam4, Manoj K. Shukla55, Shiraki Shutaro, Ricardo Sorando, Ajayi Asishana Stanley56, Peter Strauss, Zhongbo Su57, Ruhollah Taghizadeh-Mehrjardi, Encarnación V. Taguas58, Wenceslau Geraldes Teixeira27, Ali Reza Vaezi59, Mehdi Vafakhah4, Tomas Vogel23, Iris Vogeler22, Jana Votrubova23, Steffen Werner60, Thierry Winarski10, Deniz Yilmaz61, Michael H. Young62, Steffen Zacharias, Yijian Zeng57, Ying Zhao63, Hong Zhao57, Harry Vereecken1 
Forschungszentrum Jülich1, University of Maragheh2, Agricultural Research Service3, Tarbiat Modares University4, Urmia University5, University of Pannonia6, Hungarian Academy of Sciences7, Environment Agency Abu Dhabi8, Jordan University of Science and Technology9, Claude Bernard University Lyon 110, Federal University of Pernambuco11, University of Tehran12, Makerere University13, University of Paris-Sud14, Institut national de la recherche agronomique15, IFSTTAR16, Free University of Berlin17, Vienna University of Technology18, University of Rostock19, Spanish National Research Council20, University of Valencia21, Plant & Food Research22, Czech Technical University in Prague23, University of Orléans24, Ghent University25, University of Perugia26, Empresa Brasileira de Pesquisa Agropecuária27, Ferdowsi University of Mashhad28, University of California, Merced29, University of Bonn30, University of Kiel31, University of Newcastle32, Wageningen University and Research Centre33, Isfahan University of Technology34, Indian Institute of Technology Kharagpur35, Beijing Normal University36, Slovak Academy of Sciences37, Central Arid Zone Research Institute38, Commonwealth Scientific and Industrial Research Organisation39, Universidade Federal de Santa Maria40, Université catholique de Louvain41, Texas A&M University42, Aarhus University43, Shiraz University44, University of Kurdistan45, University of Tabriz46, Federal University of Rio de Janeiro47, University of Kassel48, Catholic University of Leuven49, University of Extremadura50, University of Trier51, University of Málaga52, Tottori University53, Seikei University54, New Mexico State University55, Ahmadu Bello University56, University of Twente57, University of Córdoba (Spain)58, University of Zanjan59, Ruhr University Bochum60, Tunceli University61, University of Texas at Austin62, Ludong University63
TL;DR: Rahmati et al. as mentioned in this paper presented and analyzed a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG)database, which covers research from 1976 to late 2017.
Abstract: . In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements ( ∼ 76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76 % of the experimental sites with agricultural land use as the dominant type ( ∼ 40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in *.xlsx and *.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it.

Journal ArticleDOI
TL;DR: In this paper, the authors developed briquettes from coffee and rice husks agricultural wastes as sustainable fuel sources for domestic cooking applications, using both clay and cassava starch as binders.

Journal ArticleDOI
TL;DR: This study shows that pre-HIV infection frequencies of α4β7+ peripheral blood CD4+ T cells, independent of other T cell phenotypes and genital inflammation, were associated with increased rates of HIV acquisition in South African women and supported further evaluation of targeting α4 β7 integrin as a clinical intervention during HIV infection.
Abstract: The gastrointestinal (GI) mucosa is central to HIV pathogenesis, and the integrin α4β7 promotes the homing of immune cells to this site, including those that serve as viral targets. Data from simian immunodeficiency virus (SIV) animal models suggest that α4β7 blockade provides prophylactic and therapeutic benefits. We show that pre-HIV infection frequencies of α4β7+ peripheral blood CD4+ T cells, independent of other T cell phenotypes and genital inflammation, were associated with increased rates of HIV acquisition in South African women. A similar acquisition effect was observed in a Kenyan cohort and in nonhuman primates (NHPs) after intravaginal SIV challenge. This association was stronger when infection was caused by HIV strains containing V2 envelope motifs with a preference for α4β7 binding. In addition, pre-HIV α4β7+ CD4+ T cells predicted a higher set-point viral load and a greater than twofold increased rate of CD4+ T cell decline. These results were confirmed in SIV-infected NHPs. Increased frequencies of pre-HIV α4β7+ CD4+ T cells were also associated with higher postinfection expression of lipopolysaccharide binding protein, a microbial translocation marker, suggestive of more extensive gut damage. CD4+ T cells expressing α4β7 were rapidly depleted very early in HIV infection, particularly from the GI mucosa, and were not restored by early antiretroviral therapy. This study provides a link between α4β7 expression and HIV clinical outcomes in humans, in line with observations made in NHPs. Given the availability of a clinically approved anti-α4β7 monoclonal antibody for treatment of inflammatory bowel disease, these data support further evaluation of targeting α4β7 integrin as a clinical intervention during HIV infection.

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TL;DR: Five community‐based trials have been implemented in sub‐Saharan Africa to measure the effects of various UTT strategies at population level and the contexts, research methodologies, intervention packages, themes explored, evolution of study designs and interventions related to each of these five UTT trials are described.
Abstract: DESIGN: Universal voluntary HIV counselling and testing followed by prompt initiation of antiretroviral therapy (ART) for all those diagnosed HIV-infected (universal test and treat, UTT) is now a global health standard. However, its population-level impact, feasibility and cost remain unknown. Five community-based trials have been implemented in sub-Saharan Africa to measure the effects of various UTT strategies at population level: BCPP/YaTsie in Botswana, MaxART in Swaziland, HPTN 071 (PopART) in South Africa and Zambia, SEARCH in Uganda and Kenya and ANRS 12249 TasP in South Africa. This report describes and contrasts the contexts, research methodologies, intervention packages, themes explored, evolution of study designs and interventions related to each of these five UTT trials. METHODS: We conducted a comparative assessment of the five trials using data extracted from study protocols and collected during baseline studies, with additional input from study investigators. We organized differences and commonalities across the trials in five categories: trial contexts, research designs, intervention packages, trial themes and adaptations. RESULTS: All performed in the context of generalized HIV epidemics, the trials highly differ in their social, demographic, economic, political and health systems settings. They share the common aim of assessing the impact of UTT on the HIV epidemic but differ in methodological aspects such as study design and eligibility criteria for trial populations. In addition to universal ART initiation, the trials deliver a wide range of biomedical, behavioural and structural interventions as part of their UTT strategies. The five studies explore common issues, including the uptake rates of the trial services and individual health outcomes. All trials have adapted since their initiation to the evolving political, economic and public health contexts, including adopting the successive national recommendations for ART initiation. CONCLUSIONS: We found substantial commonalities but also differences between the five UTT trials in their design, conduct and multidisciplinary outputs. As empirical literature on how UTT may improve efficiency and quality of HIV care at population level is still scarce, this article provides a foundation for more collaborative research on UTT and supports evidence-based decision making for HIV care in country and internationally.

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TL;DR: This is the first study to establish the occurrence of several bacteria species infecting fish; and to determine antibiotic susceptibility of fish bacteria in Uganda, suggesting minimal levels of acquired antibiotic resistance in fish bacteria from the study area.
Abstract: The intention of this study was to identify the bacterial pathogens infecting Oreochromis niloticus (Nile tilapia) and Clarias gariepinus (African catfish), and to establish the antibiotic susceptibility of fish bacteria in Uganda. A total of 288 fish samples from 40 fish farms (ponds, cages, and tanks) and 8 wild water sites were aseptically collected and bacteria isolated from the head kidney, liver, brain and spleen. The isolates were identified by their morphological characteristics, conventional biochemical tests and Analytical Profile Index test kits. Antibiotic susceptibility of selected bacteria was determined by the Kirby-Bauer disc diffusion method. The following well-known fish pathogens were identified at a farm prevalence of; Aeromonas hydrophila (43.8%), Aeromonas sobria (20.8%), Edwardsiella tarda (8.3%), Flavobacterium spp. (4.2%) and Streptococcus spp. (6.3%). Other bacteria with varying significance as fish pathogens were also identified including Plesiomonas shigelloides (25.0%), Chryseobacterium indoligenes (12.5%), Pseudomonas fluorescens (10.4%), Pseudomonas aeruginosa (4.2%), Pseudomonas stutzeri (2.1%), Vibrio cholerae (10.4%), Proteus spp. (6.3%), Citrobacter spp. (4.2%), Klebsiella spp. (4.2%) Serratia marcescens (4.2%), Burkholderia cepacia (2.1%), Comamonas testosteroni (8.3%) and Ralstonia picketti (2.1%). Aeromonas spp., Edwardsiella tarda and Streptococcus spp. were commonly isolated from diseased fish. Aeromonas spp. (n = 82) and Plesiomonas shigelloides (n = 73) were evaluated for antibiotic susceptibility. All isolates tested were susceptible to at-least ten (10) of the fourteen antibiotics evaluated. High levels of resistance were however expressed by all isolates to penicillin, oxacillin and ampicillin. This observed resistance is most probably intrinsic to those bacteria, suggesting minimal levels of acquired antibiotic resistance in fish bacteria from the study area. To our knowledge, this is the first study to establish the occurrence of several bacteria species infecting fish; and to determine antibiotic susceptibility of fish bacteria in Uganda. The current study provides baseline information for future reference and fish disease management in the country.

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TL;DR: In this paper, the authors presented a projected climate over the Greater Horn of Africa under 1.5 degrees C and 2 degrees C global warming, respectively, under the assumption of a 2.5 degree C and 3 degree C scenario.
Abstract: Projected climate over the Greater Horn of Africa under 1.5 degrees C and 2 degrees C global warming

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TL;DR: Findings were based on nucleic acid detection by PCR, and future studies should seek to isolate the virus from fish in Lake Victoria and show its ability to cause disease and virulence in susceptible fish.
Abstract: Tilapia lake virus disease (TiLVD) has emerged to be an important viral disease of farmed Nile tilapia (Oreochromis niloticus) having the potential to impede expansion of aquaculture production. There is a need for rapid diagnostic tools to identify infected fish to limit the spread in individual farms. We report the first detection of TiLV infection by PCR in farmed and wild Nile tilapia from Lake Victoria. There was no difference in prevalence between farmed and wild fish samples (p = .65), and of the 442 samples examined from 191 fish, 28 were positive for TiLV by PCR. In terms of tissue distribution, the head kidney (7.69%, N = 65) and spleen (10.99%, N = 191), samples had the highest prevalence (p < .0028) followed by heart samples (3.45%, N = 29). Conversely, the prevalence was low in the liver (0.71%, N = 140) and absent in brain samples (0.0%, N = 17), which have previously been shown to be target organs during acute infections. Phylogenetic analysis showed homology between our sequences and those from recent outbreaks in Israel and Thailand. Given that these findings were based on nucleic acid detection by PCR, future studies should seek to isolate the virus from fish in Lake Victoria and show its ability to cause disease and virulence in susceptible fish.

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TL;DR: Janowski and Tomaszewski as mentioned in this paper proposed a method to solve the problem by using the Danube University Krems (DUK) in Australia and Gdansk University of Technology (GDT).

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TL;DR: The majority of women in Tanzania took appropriate healthcare seeking action after recognizing danger signs during pregnancy, but the majority had low knowledge of pregnancy danger signs.
Abstract: Tanzania is among the countries with a high maternal mortality ratio. However, it remains unclear how information and education on danger signs of pregnancy translate into appropriate actions when a woman recognizes danger signs. This study aimed to determine women’s knowledge of obstetric danger signs during pregnancy and their subsequent healthcare seeking actions. The study design was a health facility-based cross-sectional study. Quantitative data were collected through interviewer-administered questionnaires. Descriptive and inferential statistics were used to analyze the data. The study enrolled 384 women from two health centers in Kinondoni Municipality, Dar es Salaam, Tanzania. A woman who had not mentioned any danger sign was categorized as having no knowledge, mentioned one to three danger signs as having low knowledge, and mentioned four or more danger signs as having sufficient knowledge. Among the 384 participants, 67 (17.4%) had experienced danger signs during their pregnancy and reported their healthcare seeking actions after recognizing the danger signs. Among those who recognized danger signs, 61 (91%) visited a healthcare facility. Among the 384 participants, five (1.3%) had no education, 175 (45.6%) had primary education, 172 (44.8%) had secondary education, and 32 (8.3%) had post-secondary education as their highest educational levels. When asked to spontaneously mention the danger signs, more than half of the participants (n = 222, 57.8%) were able to mention only one to three danger signs. Only 104 (31%) had correct knowledge of at least four danger signs and nine (2.7%) were not able to mention any item. The most commonly known pregnancy danger signs were vaginal bleeding (81%); swelling of the fingers, face, and legs (46%); and severe headache (44%). Older women were 1.6 times more likely to have knowledge of danger signs than young women (OR 1.61; 95% CI 1.05-2.46)”. Women took appropriate healthcare seeking action after recognizing danger signs during pregnancy. However, the majority had low knowledge of pregnancy danger signs. Additional studies are warranted to address the knowledge gap and to plan interventions for improving health education under limited resource settings.

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TL;DR: The implications of the diverse examples of gender and health systems research highlighted indicate that policy-makers, health practitioners and others interested in enhancing health system research and delivery have solid grounds to advance their enquiry and that one-size-fits-all heath interventions that ignore gender and intersectionality dimensions require caution.
Abstract: Gender is often neglected in health systems, yet health systems are not gender neutral. Within health systems research, gender analysis seeks to understand how gender power relations create inequities in access to resources, the distribution of labour and roles, social norms and values, and decision-making. This paper synthesises findings from nine studies focusing on four health systems domains, namely human resources, service delivery, governance and financing. It provides examples of how a gendered and/or intersectional gender approach can be applied by researchers in a range of low- and middle-income settings (Cambodia, Zimbabwe, Uganda, India, China, Nigeria and Tanzania) to issues across the health system and demonstrates that these types of analysis can uncover new and novel ways of viewing seemingly intractable problems. The research used a combination of mixed, quantitative, qualitative and participatory methods, demonstrating the applicability of diverse research methods for gender and intersectional analysis. Within each study, the researchers adapted and applied a variety of gender and intersectional tools to assist with data collection and analysis, including different gender frameworks. Some researchers used participatory tools, such as photovoice and life histories, to prompt deeper and more personal reflections on gender norms from respondents, whereas others used conventional qualitative methods (in-depth interviews, focus group discussion). Findings from across the studies were reviewed and key themes were extracted and summarised. Five core themes that cut across the different projects were identified and are reported in this paper as follows: the intersection of gender with other social stratifiers; the importance of male involvement; the influence of gendered social norms on health system structures and processes; reliance on (often female) unpaid carers within the health system; and the role of gender within policy and practice. These themes indicate the relevance of and need for gender analysis within health systems research. The implications of the diverse examples of gender and health systems research highlighted indicate that policy-makers, health practitioners and others interested in enhancing health system research and delivery have solid grounds to advance their enquiry and that one-size-fits-all heath interventions that ignore gender and intersectionality dimensions require caution. It is essential that we build upon these insights in our efforts and commitment to move towards greater equity both locally and globally.