| 1. |
- Abraham, Mark James, et al.
(author)
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Sharing Data from Molecular Simulations
- 2019
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In: Journal of Chemical Information and Modeling. - : AMER CHEMICAL SOC. - 1549-9596 .- 1549-960X. ; 59:10, s. 4093-4099
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Journal article (peer-reviewed)abstract
- Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 (https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.
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| 2. |
- Ahlberg, Sara, et al.
(author)
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A Risk Assessment of Aflatoxin M1 Exposure in Low and Mid-Income Dairy Consumers in Kenya
- 2018
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In: Toxins. - : MDPI. - 2072-6651. ; 10:9
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Journal article (peer-reviewed)abstract
- Aflatoxin M-1 (AFM(1)), a human carcinogen, is found in milk products and may have potentially severe health impacts on milk consumers. We assessed the risk of cancer and stunting as a result of AFM(1) consumption in Nairobi, Kenya, using worst case assumptions of toxicity and data from previous studies. Almost all (99.5%) milk was contaminated with AFM(1). Cancer risk caused by AFM(1) was lower among consumers purchasing from formal markets (0.003 cases per 100,000) than for low-income consumers (0.006 cases per 100,000) purchasing from informal markets. Overall cancer risk (0.004 cases per 100,000) from AFM(1) alone was low. Stunting is multifactorial, but assuming only AFM(1) consumption was the determinant, consumption of milk contaminated with AFM(1) levels found in this study could contribute to 2.1% of children below three years in middle-income families, and 2.4% in low-income families, being stunted. Overall, 2.7% of children could hypothetically be stunted due to AFM(1) exposure from milk. Based on our results AFM(1) levels found in milk could contribute to an average of -0.340 height for age z-score reduction in growth. The exposure to AFM(1) from milk is 46 ng/day on average, but children bear higher exposure of 3.5 ng/kg bodyweight (bw)/day compared to adults, at 0.8 ng/kg bw/day. Our paper shows that concern over aflatoxins in milk in Nairobi is disproportionate if only risk of cancer is considered, but that the effect on stunting children might be much more significant from a public health perspective; however, there is still insufficient data on the health effects of AFM(1).
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| 3. |
- Ahlberg, Sara, et al.
(author)
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Aflatoxin Binders in Foods for Human Consumption-Can This be Promoted Safely and Ethically?
- 2019
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In: Toxins. - : MDPI. - 2072-6651. ; 11:7
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Journal article (peer-reviewed)abstract
- Aflatoxins continue to be a food safety problem globally, especially in developing regions. A significant amount of effort and resources have been invested in an attempt to control aflatoxins. However, these efforts have not substantially decreased the prevalence nor the dietary exposure to aflatoxins in developing countries. One approach to aflatoxin control is the use of binding agents in foods, and lactic acid bacteria (LAB) have been studied extensively for this purpose. However, when assessing the results comprehensively and reviewing the practicality and ethics of use, risks are evident, and concerns arise. In conclusion, our review suggests that there are too many issues with using LAB for aflatoxin binding for it to be safely promoted. Arguably, using binders in human food might even worsen food safety in the longer term.
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| 4. |
- Alonso, Silvia, et al.
(author)
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Prevalence of tuberculosis, brucellosis and trypanosomiasis in cattle in Tanzania : a systematic review and meta-analysis.
- 2016
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In: Animal Health Research Reviews. - 1466-2523 .- 1475-2654. ; 17:1, s. 16-27
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Journal article (peer-reviewed)abstract
- A meta-analysis was performed to derive prevalence estimates for Brucella spp., Mycobacterium spp. and Trypanosoma spp. in cattle in Tanzania using data derived from a systematic review of zoonotic hazards in cattle production systems. Articles published before 2012 reporting prevalence and considered at least moderate in quality were included in the analysis. Results showed high heterogeneity between studies, with wide ranges in the reported prevalence: Brucella (0.3-60.8%), Mycobacterium (0.1-13.2%) and Trypanosoma (0.82-33.3%). Overall meta-analytic mean prevalence estimates were 8.2% (95% CI 6.5-10.2), 1.28% (95% CI 0.35-4.58) and 10.3% (95% CI 6.20-16.70) respectively, for Brucella spp., Mycobacterium spp. and Trypanosoma spp. Time and region were predictors of variability of Brucella spp. prevalence, while diagnostic test was a strong predictor of Mycobacterium spp. prevalence, with higher prevalence estimates given by skin tests compared with post-mortem inspection. None of the studied factors were associated with prevalence of Trypanosoma spp. The small sample sizes, range of study locations, study designs and diagnostics used, contributed to high variability among prevalence estimates. Larger and more robust prevalence studies are needed to adequately support risk assessment and management of animal and public health threats.
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| 5. |
- Alonso, Silvia, et al.
(author)
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Where literature is scarce : observations and lessons learnt from four systematic reviews of zoonoses in African countries.
- 2016
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In: Animal Health Research Reviews. - 1466-2523 .- 1475-2654. ; 17:1, s. 28-38
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Journal article (peer-reviewed)abstract
- The success of a systematic review depends on the availability, accessibility and quality of literature related to the review question. This paper presents the literature found in four systematic reviews conducted for a selection of zoonotic hazards in four livestock value chains in Africa, as well as setting out the challenges in conducting the reviews. The protocol was designed following international standards, and addressed four questions around prevalence, risk factors, control options and impact of various hazards and populations. Searches were conducted in four online databases. Articles were screened for relevance, and quality was assessed before data extraction. Literature on zoonotic hazards was in general scarce and access to full articles was limited. Overall, 25-40% of papers were considered poor quality. The diversity of approaches and designs in the studies compromised the ability to generate summarized estimates. We found that the emphasis of veterinary research has been on livestock problems rather than public health issues, although this seems to be shifting in the last decade; we also found there are limited studies on impact and control. While increasing literature is being published around zoonoses in Africa, this is still inadequate to appropriately inform policy and guide research efforts.
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| 6. |
- Anyango, Gladys, et al.
(author)
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A survey of aflatoxin M1 contamination in raw milk produced in urban and peri-urban areas of Kisumu County, Kenya
- 2018
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In: Infection Ecology & Epidemiology. - : Taylor & Francis. - 2000-8686. ; 8:1
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Journal article (peer-reviewed)abstract
- ABSTRACTBackground: Food safety is of increasing global concern, and a OneHealth issue requiring attention of many disciplines. Aflatoxins are toxins produced by fungi and found in foods and feeds, and exposure causes negative health effects in humans and animals. When lactating animals consume aflatoxin B1, the metabolite (AFM1) is transferred to milk.Methods: A cross-sectional study was designed to determine characteristics of smallholder dairy farming in urban and peri-urban areas of Kisumu and quantify AFM1 in milk. Data was collected from 97 randomly selected dairy farms on farming practices, milk production, and awareness about aflatoxins. Collected milk samples were analyzed using enzyme-linked immunosorbent assay for AFM1.Results: Average milk produced was 13 liters per day per household and mainly used for household consumption and sold to neighbours. Farmers mainly fed cows on forage and concentrates (62.9%). Levels of AFM1 ranged from below the detection limit to 151 ppt, with a mean of 29.67 p...
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| 7. |
- Bett, B, et al.
(author)
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Association between Rift Valley fever virus seroprevalences in livestock and humans and their respective intra-cluster correlation coefficients, Tana River County, Kenya
- 2019
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In: Epidemiology and Infection. - 0950-2688 .- 1469-4409. ; 147
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Journal article (peer-reviewed)abstract
- We implemented a cross-sectional study in Tana River County, Kenya, a Rift Valley fever (RVF)-endemic area, to quantify the strength of association between RVF virus (RVFv) seroprevalences in livestock and humans, and their respective intra-cluster correlation coefficients (ICCs). The study involved 1932 livestock from 152 households and 552 humans from 170 households. Serum samples were collected and screened for anti-RVFv immunoglobulin G (IgG) antibodies using inhibition IgG enzyme-linked immunosorbent assay (ELISA). Data collected were analysed using generalised linear mixed effects models, with herd/household and village being fitted as random variables. The overall RVFv seroprevalences in livestock and humans were 25.41% (95% confidence interval (CI) 23.49-27.42%) and 21.20% (17.86-24.85%), respectively. The presence of at least one seropositive animal in a household was associated with an increased odds of exposure in people of 2.23 (95% CI 1.03-4.84). The ICCs associated with RVF virus seroprevalence in livestock were 0.30 (95% CI 0.19-0.44) and 0.22 (95% CI 0.12-0.38) within and between herds, respectively. These findings suggest that there is a greater variability of RVF virus exposure between than within herds. We discuss ways of using these ICC estimates in observational surveys for RVF in endemic areas and postulate that the design of the sentinel herd surveillance should consider patterns of RVF clustering to enhance its effectiveness as an early warning system for RVF epidemics.
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| 8. |
- Bett, Bernard, et al.
(author)
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Climate Change and Infectious Livestock Diseases : The Case of Rift Valley Fever and Tick-Borne Diseases
- 2019
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In: The Climate-Smart Agriculture Papers. - Cham : Springer. - 9783319927978 - 9783319927985 ; , s. 29-37
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Book chapter (peer-reviewed)abstract
- Climate change influences the occurrence and transmission of a wide range of livestock diseases through multiple pathways. Diseases caused by pathogens that spent part of their life cycle outside the host (e.g. in vectors or the environment) are more sensitive in this regard, compared to those caused by obligate pathogens. In this chapter, we use two well-studied vector-borne diseases—Rift Valley fever (RVF) and tick-borne diseases (TBDs)—as case studies to describe direct pathways through which climate change influences infectious disease-risk in East and southern Africa. The first case study demonstrates that changes in the distribution and frequency of above-normal precipitation increases the frequency of RVF epidemics. The second case study suggests that an increase in temperature would cause shifts in the spatial distribution of TBDs, with cooler and wetter areas expected to experience heightened risk with climate change. These diseases already cause severe losses in agricultural productivity, food security and socio-economic development wherever they occur, and an increase in their incidence or geographical coverage would intensify these losses. We further illustrate some of the control measures that can be used to manage these diseases and recommend that more research should be done to better understand the impacts of climate change on livestock diseases as well as on the effectiveness of the available intervention measures.
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| 9. |
- Bett, B, et al.
(author)
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Effects of climate change on the occurrence and distribution of livestock diseases.
- 2017
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In: Preventive Veterinary Medicine. - : Elsevier BV. - 0167-5877 .- 1873-1716. ; 137:Pt B, s. 119-129
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Journal article (peer-reviewed)abstract
- The planet's mean air and ocean temperatures have been rising over the last century because of increasing greenhouse gas (GHG) emissions. These changes have substantial effects on the epidemiology of infectious diseases. We describe direct and indirect processes linking climate change and infectious diseases in livestock with reference to specific case studies. Some of the studies are used to show a positive association between temperature and expansion of the geographical ranges of arthropod vectors (e.g. Culicoides imicola, which transmits bluetongue virus) while others are used to illustrate an opposite trend (e.g. tsetse flies that transmit a range of trypanosome parasites in sub-Saharan Africa). We further describe a positive association between extreme events: droughts and El Niño/southern oscillation (ENSO) weather patterns and Rift Valley fever outbreaks in East Africa and some adaptation practices used to mitigate the impacts of climate change that may increase risk of exposure to infectious pathogens. We conclude by outlining mitigation and adaptation measures that can be used specifically in the livestock sector to minimize the impacts of climate change-associated livestock diseases.
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| 10. |
- Bett, Bernard, et al.
(author)
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Effects of flood irrigation on the risk of selected zoonotic pathogens in an arid and semi-arid area in the eastern Kenya
- 2017
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In: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 12:5
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Journal article (peer-reviewed)abstract
- To investigate the effects of irrigation on land cover changes and the risk of selected zoonotic pathogens, we carried out a study in irrigated, pastoral and riverine areas in the eastern Kenya. Activities implemented included secondary data analyses to determine land use and land cover (LULC) changes as well as human, livestock and wildlife population trends; entomological surveys to characterize mosquitoes population densities and species distribution by habitat and season; and serological surveys in people to determine the risk of Rift Valley fever virus (RVFV), West Nile fever virus (WNV), dengue fever virus (DFV), Leptospira spp. and Brucella spp. Results demonstrate a drastic decline in vegetation cover over R approximate to 25 years particularly in the irrigated areas where cropland increased by about 1,400% and non-farm land (under closed trees, open to closed herbaceous vegetation, bushlands and open trees) reduced by 30-100%. The irrigated areas had high densities of Aedes mcintoshi, Culexspp. and Mansonia spp. (important vectors for multiple arboviruses) during the wet and dry season while pastoral areas had high densities of Ae. tricholabis specifically in the wet season. The seroprevalences of RVFV, WNV and DFV were higher in the irrigated compared to the pastoral areas while those for Leptospira spp and Brucella spp. were higher in the pastoral compared to the irrigated areas. It is likely that people in the pastoral areas get exposed to Leptospira spp by using water fetched from reservoirs that are shared with livestock and wildlife, and to Brucella spp. by consuming raw or partially cooked animal source foods such as milk and meat. This study suggests that irrigation increases the risk of mosquito-borne infections while at the same time providing a protective effect against zoonotic pathogens that thrive in areas with high livestock population densities.
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