120 research outputs found
Perils of Genome Assembly: Data types and sequencing platform defines optimal genome assembly in prokaryotes and eukaryotes
No full textCorrection to: Monitoring changes in malaria epidemiology and effectiveness of interventions in Ethiopia and Uganda: Beyond Garki Project baseline survey
No full textThis is the final version. Available on open access from BMC via the DOI in this recordThe article to which this is the correction is available in ORE at http://hdl.handle.net/10871/19983Correction to: Malar J (2015) 14:337 https://doi.org/10.1186/s12936-015-0852-7
Please be advised that one of the author names is incorrectly spelled in the published article: ‘Irene Kyomuhagi’ should be ‘Irene Kyomuhangi’.
The corrected name can be found in the author list of this article
Regulation of mating genes during arbuscular mycorrhizal isolate co-existence—where is the evidence?
No full textA recent study published by Mateus et al. [1] claimed that 18 “mating-related” genes are differentially expressed in the model arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis when genetically distinct fungal strains co-colonize a host plant. To clarify the level of evidence for this interesting conclusion, we first aimed to validate the functional annotation of these 18 R. irregularis genes using orthology predictions. These analyses revealed that, although sequence relationship exists, only 2 of the claimed 18 R. irregularis mating genes are potential orthologues to validated fungal mating genes. We also investigated the RNA-seq data from Mateus et al. [1] using classical RNA-seq methods and statistics. This analysis found that the over-expression during strain co-existence was not significant at the typical cut-off of the R. irregularis strains DAOM197198 and B1 in plants. Overall, we do not find convincing evidence that the genes involved have functions in mating, or that they are reproducibly up or down regulated during co-existence in plants
Comparative genomics of Westiellopsis prolifica a freshwater cyanobacteria uncovers the prolific and distinctive metabolic potentials
No full textAcceptability - a neglected dimension of access to health care: findings from a study on childhood convulsions in rural Tanzania.
No full textABSTRACT: BACKGROUND: Acceptability is a poorly conceptualized dimension of access to health care. Using a study on childhood convulsion in rural Tanzania, we examined social acceptability from a user perspective. The study design is based on the premise that a match between health providers' and clients' understanding of disease is an important dimension of social acceptability, especially in trans-cultural communication, for example if childhood convulsions are not linked with malaria and local treatment practices are mostly preferred. The study was linked to health interventions with the objective of bridging the gap between local and biomedical understanding of convulsions. METHODS: The study combined classical ethnography with the cultural epidemiology approach using EMIC (Explanatory Model Interview Catalogue) tool. EMIC interviews were conducted in a 2007/08 convulsion study (n = 88) and results were compared with those of an earlier 2004/06 convulsion study (n = 135). Earlier studies on convulsion in the area were also examined to explore longer-term changes in treatment practices. RESULTS: The match between local and biomedical understanding of convulsions was already high in the 2004/06 study. Specific improvements were noted in form of (1) 46% point increase among those who reported use of mosquito nets to prevent convulsion (2) 13% point decrease among caregivers who associated convulsion with 'evil eye and sorcery', 3) 14% point increase in prompt use of health facility and 4)16% point decrease among those who did not use health facility at all. Such changes can be partly attributed to interventions which explicitly aimed at increasing the match between local and biomedical understanding of malaria. Caregivers, mostly mothers, did not seek advice on where to take an ill child. This indicates that treatment at health facility has become socially acceptable for severe febrile with convulsion. CONCLUSION: As an important dimension of access to health care 'social acceptability' seems relevant in studying illnesses that are perceived not to belong to the biomedical field, specifically in trans-cultural societies. Understanding the match between local and biomedical understanding of disease is fundamental to ensure acceptability of health care services, successful control and management of health problems. Our study noted some positive changes in community knowledge and management of convulsion episodes, changes which might be accredited to extensive health education campaigns in the study area. On the other hand it is difficult to make inference out of the findings as a result of small sample size involved. In return, it is clear that well ingrained traditional beliefs can be modified with communication campaigns, provided that this change resonates with the beneficiaries
Health Worker Factors Associated with Prescribing of Artemisinin Combination Therapy for Uncomplicated Malaria in Rural Tanzania.
No full textImproving malaria case management is partially dependent on health worker compliance with clinical guidelines. This study assessed health worker factors associated with correct anti-malarial prescribing practices at two sites in rural Tanzania. Repeated cross-sectional health facility surveys were conducted during high and low malaria transmission seasons in 2010 and collected information on patient consultations and health worker characteristics. Using logistic regression, the study assessed health worker factors associated with correct prescription for uncomplicated malaria defined as prescription of artemisinin-based combination therapy (ACT) for patients with fever and Plasmodium falciparum asexual infection based on blood slide or malaria rapid diagnostic test (RDT) according to national treatment guidelines. The analysis included 685 patients with uncomplicated malaria who were seen in a health facility with ACT in stock, and 71 health workers practicing in 30 health facilities. Overall, 58% of malaria patients were correctly treated with ACT. Health workers with three or more years' work experience were significantly more likely than others to prescribe correctly (adjusted odds ratio (aOR) 2.9; 95% confidence interval (CI) 1.2-7.1; p = 0.019). Clinical officers (aOR 2.2; 95% CI 1.1-4.5; p = 0.037), and nurse aide or lower cadre (aOR 3.1; 95% CI 1.3-7.1; p = 0.009) were more likely to correctly prescribe ACT than medical officers. Training on ACT use, supervision visits, and availability of job aids were not significantly associated with correct prescription. Years of working experience and health worker cadre were associated with correct ACT prescription for uncomplicated malaria. Targeted interventions to improve health worker performance are needed to improve overall malaria case management
Bayesian variable selection in modelling geographical heterogeneity in malaria transmission from sparse data : an application to Nouna Health and Demographic Surveillance System (HDSS) data, Burkina Faso
No full textQuantification of malaria heterogeneity is very challenging, partly because of the underlying characteristics of mosquitoes and also because malaria is an environmentally driven disease. Furthermore, in order to assess the spatial and seasonal variability in malaria transmission, vector data need to be collected repeatedly over time (at fixed geographical locations). Measurements collected at locations close to each other and over time tend to be correlated because of common exposures such as environmental or climatic conditions. Non- spatial statistical methods, when applied to analyze such data, may lead to biased estimates. We developed rigorous methods for analyzing sparse and spatially correlated data. We applied Bayesian variable selection to identify the most important predictors as well as the elapsing time between climate suitability and changes in entomological indices.; Bayesian geostatistical zero-inflated binomial and negative binomial models including harmonic seasonal terms, temporal trends and climatic remotely sensed proxies were applied to assess spatio-temporal variation of sporozoite rate and mosquito density in the study area. Bayesian variable selection was employed to determine the most important climatic predictors and elapsing (lag) time between climatic suitability and malaria transmission. Bayesian kriging was used to predict mosquito density and sporozoite rate at unsampled locations. These estimates were converted to covariate and season-adjusted maps of entomological inoculation rates. Models were fitted using Markov chain Monte Carlo simulation. The results show that Anophele. gambiae is the most predominant vector (79.29%) and is more rain-dependant than its sibling Anophele. funestus (20.71%). Variable selection suggests that the two species react differently to different climatic conditions. Prediction maps of entomological inoculation rate (EIR) depict a strong spatial and temporal heterogeneity in malaria transmission risk despite the relatively small geographical extend of the study area. CONCLUSION: Malaria transmission is very heterogeneous over the study area. The EIR maps clearly depict a strong spatial and temporal heterogeneity despite the relatively small geographical extend of the study area. Model based estimates of transmission can be used to identify high transmission areas in order to prioritise interventions and support research in malaria epidemiology
A tool box for operational mosquito larval control: preliminary results and early lessons from the Urban Malaria Control Programme in Dar es Salaam, Tanzania.
No full textBACKGROUND\ud
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As the population of Africa rapidly urbanizes, large populations could be protected from malaria by controlling aquatic stages of mosquitoes if cost-effective and scalable implementation systems can be designed.\ud
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METHODS\ud
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A recently initiated Urban Malaria Control Programme in Dar es Salaam delegates responsibility for routine mosquito control and surveillance to modestly-paid community members, known as Community-Owned Resource Persons (CORPs). New vector surveillance, larviciding and management systems were designed and evaluated in 15 city wards to allow timely collection, interpretation and reaction to entomologic monitoring data using practical procedures that rely on minimal technology. After one year of baseline data collection, operational larviciding with Bacillus thuringiensis var. israelensis commenced in March 2006 in three selected wards.\ud
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RESULTS\ud
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The procedures and staff management systems described greatly improved standards of larval surveillance relative to that reported at the outset of this programme. In the first year of the programme, over 65,000 potential Anopheles habitats were surveyed by 90 CORPs on a weekly basis. Reaction times to vector surveillance at observations were one day, week and month at ward, municipal and city levels, respectively. One year of community-based larviciding reduced transmission by the primary malaria vector, Anopheles gambiae s.l., by 31% (95% C.I. = 21.6-37.6%; p = 0.04).\ud
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CONCLUSION\ud
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This novel management, monitoring and evaluation system for implementing routine larviciding of malaria vectors in African cities has shown considerable potential for sustained, rapidly responsive, data-driven and affordable application. Nevertheless, the true programmatic value of larviciding in urban Africa can only be established through longer-term programmes which are stably financed and allow the operational teams and management infrastructures to mature by learning from experience
Atlas of human cranial macromorphoscopic traits /
No full textAtlas of Human Cranial Macromorphoscopic Traits synthesizes macromorphoscopic traits and their analysis in an accessible manner, providing detailed descriptions and examples of the various character state manifestations intended for use in classrooms, laboratories, and in the field. The volume begins with an outline of the macromorphoscopic dataset, its history, recent modifications to the historical approach, and recent technological and analytical advances. Additional sections cover Nomenclature, Gross Anatomy, Function, Methodology, Line Drawings, Detailed Definitions, Multiple High-resolution Photographs, and Population Variation Data from the Macromorphoscopic Databank (MaMD). The volume concludes with a chapter outlining the statistical analysis of macromorphoscopic data and a summary of the computer programs and reference databases available to forensic anthropologists for the analysis of these data.Online resource; title from PDF title page (EBSCO, viewed August 9, 2018)Includes bibliographical references and index.Atlas of Human Cranial Macromorphoscopic Traits synthesizes macromorphoscopic traits and their analysis in an accessible manner, providing detailed descriptions and examples of the various character state manifestations intended for use in classrooms, laboratories, and in the field. The volume begins with an outline of the macromorphoscopic dataset, its history, recent modifications to the historical approach, and recent technological and analytical advances. Additional sections cover Nomenclature, Gross Anatomy, Function, Methodology, Line Drawings, Detailed Definitions, Multiple High-resolution Photographs, and Population Variation Data from the Macromorphoscopic Databank (MaMD). The volume concludes with a chapter outlining the statistical analysis of macromorphoscopic data and a summary of the computer programs and reference databases available to forensic anthropologists for the analysis of these data.Front Cover; Atlas of Human Cranial Macromorphoscopic Traits; Copyright Page; Abstract; Contents; List of Figures; List of Tables; Foreword; Quotes; Preface; Acknowledgements; 1 Introduction; Macromorphoscopic Data and Datasets; Historical Ties; Macromorphoscopic Data in the Modern Era; The Macromorphoscopic Databank; Cranial Samples; 2 Macromorphoscopic Traits; Anterior View; Inferior Nasal Aperture; Interorbital Breadth; Malar Tubercle; Nasal Aperture Shape; Nasal Aperture Width; Nasal Bone Contour; Nasal Bone Shape; Nasofrontal Suture; Orbital Shape; Supranasal SutureZygomaticomaxillary SutureLateral View; Anterior Nasal Spine; Nasal Overgrowth; Postbregmatic Depression; Posterior Zygomatic Tubercle; Inferior View; Palate Shape; Transverse Palatine Suture; 3 Anterior Nasal Spine; Nomenclature; Gross Anatomy; Growth and Development; Functional Morphology; Within Population Variation; Character States; Character States for Anterior Nasal Spine=1; Character States for Anterior Nasal Spine=2; Character States for Anterior Nasal Spine=3; 4 Inferior Nasal Aperture; Nomenclature; Gross Anatomy; Growth and Development; Functional MorphologyWithin Population VariationCharacter States; Character States for Inferior Nasal Aperture=1; Character States for Inferior Nasal Aperture=2; Character States for Inferior Nasal Aperture=3; Character States for Inferior Nasal Aperture=4; Character States for Inferior Nasal Aperture=5; 5 Interorbital Breadth; Nomenclature; Gross Anatomy; Growth and Development; Functional Morphology; Within Population Variation; Character States; Character States for Interorbital Breadth=1; Character States for Interorbital Breadth=2; Character States for Interorbital Breadth=3; 6 The Malar TubercleNomenclatureGross Anatomy; Growth and Development; Functional Morphology; Within Population Variation; Character States; Character States for Malar Tubercle=0; Character States for Malar Tubercle=1; Character States for Malar Tubercle=2; Character States for Malar Tubercle=3; 7 Nasal Aperture Shape; Nomenclature; Gross Anatomy; Growth and Development; Functional Morphology; Within Population Variation; Character States; Character States for Nasal Aperture Shape=1; Character States for Nasal Aperture Shape=2; Character States for Nasal Aperture Shape=3; 8 Nasal Aperture Width; NomenclatureGross AnatomyGrowth and Development; Functional Morphology; Within Population Variation; Character States; Character States for Nasal Aperture Width=1; Character States for Nasal Aperture Width=2; Character States for Nasal Aperture Width=3; 9 Nasal Bone Contour; Nomenclature; Gross Anatomy; Growth and Development; Functional Morphology; Within Population Variation; Character States; Character States for Nasal Bone Contour=0; Character States for Nasal Bone Contour=1; Character States for Nasal Bone Contour=2; Character States for Nasal Bone Contour=3Elsevie
Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina
No full textThe arbuscular mycorrhizal fungi (AMFs) are obligate root symbionts in the subphylum Glomeromycotina that can benefit land plants by increasing their soil nutrient uptake in exchange for photosynthetically fixed carbon sources. To date, annotated genome data from representatives of the AMF orders Glomerales, Diversisporales and Archaeosporales have shown that these organisms have large and highly repeated genomes, and no genes to produce sugars and fatty acids. This led to the hypothesis that the most recent common ancestor (MRCA) of Glomeromycotina was fully dependent on plants for nutrition. Here, we aimed to further test this hypothesis by obtaining annotated genome data from a member of the early diverging order Paraglomerales (Paraglomus occultum). Genome analyses showed this species carries a 39.6 Mb genome and considerably fewer genes and repeats compared to most AMF relatives with annotated genomes. Consistent with phylogenies based on ribosomal genes, our phylogenetic analyses suggest P. occultum as the earliest diverged branch within Glomeromycotina. Overall, our analyses support the view that the MRCA of Glomeromycotina carried hallmarks of obligate plant biotrophy. The small genome size and content of P. occultum could either reflect adaptive reductive processes affecting some early AMF lineages, or indicate that the high gene and repeat family diversity thought to drive AMF adaptability to host and environmental change was not an ancestral feature of these prominent plant symbionts
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