Identification and analysis of smallholder producers’ constraints: Applications to Tanzania and Uganda

‘The Version of Record of this manuscript has been published and is freely available in Development in Practice 2015 http://www.tandfonline.com/ http://dx.doi.org/10.1080/09614524.2015.1007924’This article puts forward a method for the analysis of constraints faced by developing countries’ smallholder producers. It is consistent with theories of constraints, efficient in terms of cost and researchers’ time, and accessible to a non-technical audience. A hybrid of workshop discussion and individual data collection, it also draws on data and analyses available in most developing countries. The article presents an application to smallholder livestock systems in Tanzania and Uganda, reporting results and analysis relating constraints to households’ characteristics and conditions, and their stated goals. While limitations are identified, it is proposed for application in other development fields

Evaluation of a lateral flow device for in-field detection of Banana Xanthomonas Wilt and its application in tracking the systemicity of Xanthomonas campestris pv. musacearum

Early detection of Banana Xanthomonas Wilt (BXW) in the field and immediate destruction of infected plants or plant tissue are key control methods to prevent the introduction and spread of BXW. This requires rapid, cost effective and an on-site diagnostic tool to detect the bacterium, Xanthomonas campestris pv musacearum (Xcm). Polymerase chain reaction (PCR) detection technique for BXW is efficient but requires expensive equipment and knowledgeable expertise; this limits PCR application to the laboratory. This study therefore was carried out to evaluate the enzyme - linked immunosorbent assay (ELISA) tool configured as a lateral flow device (LFD) for detection of Xcm. Studies on the systemicity of Xcm in banana were carried out using the BXW - LFD in a field trial of 300 banana plants of Pisang Awak inoculated with the Xcm at Kiifu Forest, Mukono District, Uganda. Pseudo-stem samples from symptomatic and asymptomatic suckers were collected and tested with the LFD and the results compared with conventional PCR using the GspDm BXW primers. The LFD was able to detect Xcm3

Relation between falciparum malaria and bacteraemia in Kenyan children: a population-based, case-control study and a longitudinal study.

BACKGROUND: Many investigators have suggested that malaria infection predisposes individuals to bacteraemia. We tested this hypothesis with mendelian randomisation studies of children with the malaria-protective phenotype of sickle-cell trait (HbAS). METHODS: This study was done in a defined area around Kilifi District Hospital, Kilifi, Kenya. We did a matched case-control study to identify risk factors for invasive bacterial disease, in which cases were children aged 3 months to 13 years who were admitted to hospital with bacteraemia between Sept 16, 1999, and July 31, 2002. We aimed to match two controls, by age, sex, location, and time of recruitment, for every case. We then did a longitudinal case-control study to assess the relation between HbAS and invasive bacterial disease as malaria incidence decreased. Cases were children aged 0-13 years who were admitted to hospital with bacteraemia between Jan 1, 1999, and Dec 31, 2007. Controls were born in the study area between Jan 1, 2006, and June 23, 2009. Finally, we modelled the annual incidence of bacteraemia against the community prevalence of malaria during 9 years with Poisson regression. RESULTS: In the matched case-control study, we recruited 292 cases-we recruited two controls for 236, and one for the remaining 56. Sickle-cell disease, HIV, leucocyte haemozoin pigment, and undernutrition were positively associated with bacteraemia and HbAS was strongly negatively associated with bacteraemia (odds ratio 0·36; 95% CI 0·20-0·65). In the longitudinal case-control study, we assessed data from 1454 cases and 10,749 controls. During the study period, the incidence of admission to hospital with malaria per 1000 child-years decreased from 28·5 to 3·45, with a reduction in protection afforded by HbAS against bacteraemia occurring in parallel (p=0·0008). The incidence of hospital admissions for bacteraemia per 1000 child-years also decreased from 2·59 to 1·45. The bacteraemia incidence rate ratio associated with malaria parasitaemia was 6·69 (95% CI 1·31-34·3) and, at a community parasite prevalence of 29% in 1999, 62% (8·2-91) of bacteraemia cases were attributable to malaria. INTERPRETATION: Malaria infection strongly predisposes individuals to bacteraemia and can account for more than half of all cases of bacteraemia in malaria-endemic areas. Interventions to control malaria will have a major additional benefit by reducing the burden of invasive bacterial disease. FUNDING: Wellcome Trust

Prospective Identification of Malaria Parasite Genes under Balancing Selection

BACKGROUND: Endemic human pathogens are subject to strong immune selection, and interrogation of pathogen genome variation for signatures of balancing selection can identify important target antigens. Several major antigen genes in the malaria parasite Plasmodium falciparum have shown such signatures in polymorphism-versus-divergence indices (comparing with the chimpanzee parasite P. reichenowi), and in allele frequency based indices. METHODOLOGY/PRINCIPAL FINDINGS: To compare methods for prospective identification of genes under balancing selection, 26 additional genes known or predicted to encode surface-exposed proteins of the invasive blood stage merozoite were first sequenced from a panel of 14 independent P. falciparum cultured lines and P. reichenowi. Six genes at the positive extremes of one or both of the Hudson-Kreitman-Aguade (HKA) and McDonald-Kreitman (MK) indices were identified. Allele frequency based analysis was then performed on a Gambian P. falciparum population sample for these six genes and three others as controls. Tajima's D (TjD) index was most highly positive for the msp3/6-like PF10_0348 (TjD = 1.96) as well as the positive control ama1 antigen gene (TjD = 1.22). Across the genes there was a strong correlation between population TjD values and the relative HKA indices (whether derived from the population or the panel of cultured laboratory isolates), but no correlation with the MK indices. CONCLUSIONS/SIGNIFICANCE: Although few individual parasite genes show significant evidence of balancing selection, analysis of population genomic and comparative sequence data with the HKA and TjD indices should discriminate those that do, and thereby identify likely targets of immunity

The incidence and clinical burden of respiratory syncytial virus disease identified through hospital outpatient presentations in Kenyan children

There is little information that describe the burden of respiratory syncytial virus (RSV) associated disease in the tropical African outpatient setting. Methods We studied a systematic sample of children aged <5 years presenting to a rural district hospital in Kenya with acute respiratory infection (ARI) between May 2002 and April 2004. We collected clinical data and screened nasal wash samples for RSV antigen by immunofluorescence. We used a linked demographic surveillance system to estimate disease incidence. Results Among 2143 children tested, 166 (8%) were RSV positive (6% among children with upper respiratory tract infection and 12% among children with lower respiratory tract infection (LRTI). RSV was more likely in LRTI than URTI (p<0.001). 51% of RSV cases were aged 1 year or over. RSV cases represented 3.4% of hospital outpatient presentations. Relative to RSV negative cases, RSV positive cases were more likely to have crackles (RR = 1.63; 95% CI 1.34–1.97), nasal flaring (RR = 2.66; 95% CI 1.40–5.04), in-drawing (RR = 2.24; 95% CI 1.47–3.40), fast breathing for age (RR = 1.34; 95% CI 1.03–1.75) and fever (RR = 1.54; 95% CI 1.33–1.80). The estimated incidence of RSV-ARI and RSV-LRTI, per 100,000 child years, among those aged <5 years was 767 and 283, respectively. Conclusion The burden of childhood RSV-associated URTI and LRTI presenting to outpatients in this setting is considerable. The clinical features of cases associated with an RSV infection were more severe than cases without an RSV diagnosis

Persistence of Gamma-H2AX Foci in Irradiated Bronchial Cells Correlates with Susceptibility to Radiation Associated Lung Cancer in Mice

The risk of developing radiation-induced lung cancer differs between different strains of mice, but the underlying cause of the strain differences is unknown. Strains of mice also differ in their ability to efficiently repair DNA double strand breaks resulting from radiation exposure. We phenotyped mouse strains from the CcS/Dem recombinant congenic strain set for their efficacy in repairing DNA double strand breaks during protracted radiation exposures. We monitored persistent gamma-H2AX radiation induced foci (RIF) 24 hours after exposure to chronic gamma-rays as a surrogate marker for repair deficiency in bronchial epithelial cells for 17 of the CcS/Dem strains and the BALB/cHeN founder strain. We observed a very strong correlation R2 = 79.18%, P < 0.001) between the level of persistent RIF and radiogenic lung cancer percent incidence measured in the same strains. Interestingly, spontaneous levels of foci in non-irradiated strains also showed good correlation with lung cancer incidence (R2=32.74%, P =0.013). These results suggest that genetic differences in DNA repair capacity largely account for differing susceptibilities to radiation-induced lung cancer among CcS/Dem mouse strains and that high levels of spontaneous DNA damage is also a relatively good marker of cancer predisposition. In a smaller pilot study, we found that the repair capacity measured in peripheral blood leucocytes also correlated well with radiogenic lung cancer susceptibility, raising the possibility that such phenotyping assay could be used to detect radiogenic lung cancer susceptibility in humans

Mapping spatial distribution and geographic shifts of east African highland banana (Musa spp.) in Uganda

Open Access Journal; Published online: 17 Feb 2022East African highland banana (Musa acuminata genome group AAA-EA; hereafter referred to as banana) is critical for Uganda’s food supply, hence our aim to map current distribution and to understand changes in banana production areas over the past five decades. We collected banana presence/absence data through an online survey based on high-resolution satellite images and coupled this data with independent covariates as inputs for ensemble machine learning prediction of current banana distribution. We assessed geographic shifts of production areas using spatially explicit differences between the 1958 and 2016 banana distribution maps. The biophysical factors associated with banana spatial distribution and geographic shift were determined using a logistic regression model and classification and regression tree, respectively. Ensemble models were superior (AUC = 0.895; 0.907) compared to their constituent algorithms trained with 12 and 17 covariates, respectively: random forests (AUC = 0.883; 0.901), gradient boosting machines (AUC = 0.878; 0.903), and neural networks (AUC = 0.870; 0.890). The logistic regression model (AUC = 0.879) performance was similar to that for the ensemble model and its constituent algorithms. In 2016, banana cultivation was concentrated in the western (44%) and central (36%) regions, while only a small proportion was in the eastern (18%) and northern (2%) regions. About 60% of increased cultivation since 1958 was in the western region; 50% of decreased cultivation in the eastern region; and 44% of continued cultivation in the central region. Soil organic carbon, soil pH, annual precipitation, slope gradient, bulk density and blue reflectance were associated with increased banana cultivation while precipitation seasonality and mean annual temperature were associated with decreased banana cultivation over the past 50 years. The maps of spatial distribution and geographic shift of banana can support targeting of context-specific intensification options and policy advocacy to avert agriculture driven environmental degradation

Cyst nematode bio-communication with plants: implications for novel management approaches

Bio‐communication occurs when living organisms interact with each other, facilitated by the exchange of signals including visual, auditory, tactile and chemical. The most common form of bio‐communication between organisms is mediated by chemical signals, commonly referred to as ‘semiochemicals’, and it involves an emitter releasing the chemical signal that is detected by a receiver leading to a phenotypic response in the latter organism. The quality and quantity of the chemical signal released may be influenced by abiotic and biotic factors. Bio‐communication has been reported to occur in both above‐ and below‐ground interactions and it can be exploited for the management of pests, such as cyst nematodes, which are pervasive soil‐borne pests that cause significant crop production losses worldwide. Cyst nematode hatching and successful infection of hosts are biological processes that are largely influenced by semiochemicals including hatching stimulators, hatching inhibitors, attractants and repellents. These semiochemicals can be used to disrupt interactions between host plants and cyst nematodes. Advances in RNAi techniques such as host‐induced gene silencing to interfere with cyst nematode hatching and host location can also be exploited for development of synthetic resistant host cultivars. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry

Targeted Next Generation Sequencing for malaria research in Africa:Current status and outlook

Targeted Next Generation Sequencing (TNGS) is an efficient and economical Next Generation Sequencing (NGS) platform and the preferred choice when specific genomic regions are of interest. So far, only institutions located in middle and high-income countries have developed and implemented the technology, however, the efficiency and cost savings, as opposed to more traditional sequencing methodologies (e.g. Sanger sequencing) make the approach potentially well suited for resource-constrained regions as well. In April 2018, scientists from the Plasmodium Diversity Network Africa (PDNA) and collaborators met during the 7th Pan African Multilateral Initiative of Malaria (MIM) conference held in Dakar, Senegal to explore the feasibility of applying TNGS to genetic studies and malaria surveillance in Africa. The group of scientists reviewed the current experience with TNGS platforms in sub-Saharan Africa (SSA) and identified potential roles the technology might play to accelerate malaria research, scientific discoveries and improved public health in SSA. Research funding, infrastructure and human resources were highlighted as challenges that will have to be mitigated to enable African scientists to drive the implementation of TNGS in SSA. Current roles of important stakeholders and strategies to strengthen existing networks to effectively harness this powerful technology for malaria research of public health importance were discussed

A hyperchaotic system without equilibrium

Abstract: This article introduces a new chaotic system of 4-D autonomous ordinary differential equations, which has no equilibrium. This system shows a hyper-chaotic attractor. There is no sink in this system as there is no equilibrium. The proposed system is investigated through numerical simulations and analyses including time phase portraits, Lyapunov exponents, and Poincaré maps. There is little difference between this chaotic system and other chaotic systems with one or several equilibria shown by phase portraits, Lyapunov exponents and time series methods, but the Poincaré maps show this system is a chaotic system with more complicated dynamics. Moreover, the circuit realization is also presented