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PDBeCIF: an open-source mmCIF/CIF parsing and processing package

Glen van Ginkel, Lukáš Pravda, José M. Dana, Mihaly Varadi, Peter Keller, Stephen Anyango, Sameer Velankar
2021 BMC Bioinformatics  
Background Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Information File format (PDBx/mmCIF) is still not widespread. Perhaps one of the reasons is the availability of easy to use tools that only support the legacy format, but also the inherent difficulties of processing mmCIF files correctly, given the number of edge cases that make
more » ... ient parsing problematic. Nevertheless, to fully exploit macromolecular structure data and their associated annotations such as multiscale structures from integrative/hybrid methods or large macromolecular complexes determined using traditional methods, it is necessary to fully adopt the new format as soon as possible. Results To this end, we developed PDBeCIF, an open-source Python project for manipulating mmCIF and CIF files. It is part of the official list of mmCIF parsers recorded by the wwPDB and is heavily employed in the processes of the Protein Data Bank in Europe. The package is freely available both from the PyPI repository (http://pypi.org/project/pdbecif) and from GitHub (https://github.com/pdbeurope/pdbecif) along with rich documentation and many ready-to-use examples. Conclusions PDBeCIF is an efficient and lightweight Python 2.6+/3+ package with no external dependencies. It can be readily integrated with 3rd party libraries as well as adopted for broad scientific analyses.
doi:10.1186/s12859-021-04271-9 pmid:34301175 pmcid:PMC8299628 fatcat:vsufapo3bzeppeyvadnvn2z4ey

Effectiveness of sanitation policy instruments in Mavoko Municipality of Machakos County, Kenya

Juliana Kamanthe Muia Mutua, Jones F. Agwata, Stephen Anyango, Thaddeus Nzeadibe
2017 Cogent Environmental Science  
Improved sanitation leads to better environmental quality however threatened environments, population densities and inadequate finances are some of the challenges facing proper sanitation management. This paper sought to establish the effectiveness of policy, legal and institutional frameworks on promotion of sanitation management in Mavoko Municipality. Resident's awareness and compliance with policy instruments, role and responsibilities of Mavoko Municipality Residents and Service Providers
more » ... nd Political Champions were used to gauge the effectiveness of these policy instruments. Mavoko Municipality has low sewer network coverage with a deficit of 86% in sewerage treatment capacity as its existing sewerage treatment capacity stands at 192,000 m 3 against a required capacity of 1,407,000 m 3 . The study site covered the urbanizing areas within the Municipality. A cross-sectional study design was chosen and both primary and secondary data were collected. 385 house hold respondents were interviewed. Simple random and purposive sampling methods were used to administer questionnaires to standalone houses and comprehensive housing schemes. Key informant interviews with County and National Officials mandated with sanitation management related services were conducted using structured forms and interview guides. Findings
doi:10.1080/23311843.2017.1339387 fatcat:tgryqrrxozfqrpfmi76wfelpji

Compensating Toxic Torts in Kenya: Overcoming the Causation Dilemma

Hannah Wamuyu, Collins Odote, Stephen Anyango
2021 Journal of Sustainable Development Law and Policy  
No Abstract
doi:10.4314/jsdlp.v12i2.5 fatcat:iclsmfgayzfctggpmes26ekafy

Computer Assisted Learning For Enhancing Mastery Of Concepts In Science

Sharon Anyango Onditi, Stephen Oloo Ajwang
2020 International Journal on Research in STEM Education  
Onditi, Stephen Oloo Ajwang  ...  0.003 E1 v/s E2 -0.75 0.723 International Journal of Research in STEM Education (IJRSE), Vol. 2 (2), 134-142 Computer Assisted Learning For Enhancing Mastery Of Concepts In Science Sharon Anyango  ... 
doi:10.31098/ijrse.v2i2.382 fatcat:3d6tll3aufcqxikdbpve5gbpli

Towards Sustainable Livelihood Practices in the Indigenous Forests of Zambia's Central Province: Barriers and Opportunities

Stephen Obiero Anyango, Biston Mbewe, Velice Shizia Nangavo, Maurine Mwal
2018 Energy and Environment Research  
This study was designed with the aim of establishing a comprehensive picture of the problems and needs of local communities in upholding sustainable livelihoods in the face of forest degradation and recommending how their livelihoods may be improved in the short and long term.  Thus make them self-reliant by enhancing their resilience.  Study Methodology: included a literature review and a household survey for a total of 443 household interviews. In addition, Focus Group Discussions
more » ... GDs) and Key Informant Interviews (KIIs) were conducted with the rural population and other stakeholders respectively. Field visits were made to all the 8 sites in the two districts Serenje and Chitambo. The main constrain of sustainable livelihood in the communities, included, low levels of education and skills, low levels of asset holding, weak local institutions and unfavorable legal and institutional frameworks. But the respondents registered a wide variety of NTFPs based livelihoods obtained from forests resources (15). Most important usage includes land for cultivation, fuelwood, poles for construction, charcoal production and use of NTFPs (collection of mushrooms, wild fruits and nuts, caterpillars, honey production and medicinal plants). The livelihood activities remains largely subsistence and for safety net functions. Trade resulting into incomes generation is minimal, unstructured and therefore unsustainable. In conclusion: commercialization of NTFPS and PES activities may be the solution to sustainable livelihood and forest conservation. A range of specifically forest sector elements would also need to be addressed, including, entrepreneurship, market and skill development for forest product and services delivery; embracing these elements will also require new kinds of enhanced institutional arrangement.
doi:10.5539/eer.v8n2p1 fatcat:phcdvq4vzzbx7caiglt4tprbou

Political Economy and Stakeholder Perspectives on Inclusive Low-Carbon Energy Transition: Case of Kenyan Rangelands

Angela Mungai, Richard Mulwa, Stephen Anyango
2018 International Journal of Sustainable Energy and Environmental Research  
Article History Keywords Off-grid Low-carbon Energy Actors Household Political economy Policy Kenya. Kenya, among other developing countries, is challenged by low access to clean power, particularly among households located in remote rangelands of the country. This study sought to evaluate the role and perspectives of energy sector actors in the transition of low-carbon off-grid technologies to households in Kenya as an alternative to the national grid for powering isolated low-income
more » ... s. To this end a key informant survey was conducted, involving State and non-state energy sector actors to assess the level of capacity, policy inclusiveness, constraints and delivery of clean offgrid energy technologies to rural households. Key findings revealed that County Government and non-state actors are largely excluded from clean energy planning for off-grid communities. In addition, women, within the framework of women's groups are strong players in this sector and have a high potential to expand clean energy access to off-grid areas. It was also found that despite the Kenyan Government commitment towards a green economy, a change in policy direction would be necessary to ensure a multi-stakeholder planning approach for increased private investment and inclusive access to clean energy. Contribution/Originality: This study is one of the very few studies investigating stakeholder perspectives and policy gaps constraining clean energy transitions into remote Kenyan rangelands, indicating that key constraints are economic, cultural and under-inclusion of local government and indigenous communities, particularly women, in national off-grid clean energy planning and implementation.
doi:10.18488/journal.13.2018.71.35.43 fatcat:ligsfijbyjct7fohnhuoc6o3xe

Relationship between Family Cohesion and Teenage Sexual Behavior in Public Secondary Schools in Kajiado County, Kenya

Juliana Anyango Nyaguti, Stephen Asatsa (PhD), Josephine Muthami
2021 International journal of research and innovation in social science  
This research aimed at examining the relationship between family functioning and teenagers' sexual behavioral patterns amongst students in public secondary schools in Kajiado West sub-county, Kajiado County, Kenya. The research used survey design with a target population of 6085 students from public secondary schools. Based on Yamane's formula, the sample size of 375 students was selected by simple random sampling to participate in the study. Data were collected from this sample using
more » ... ed questionnaires; the Family Assessment Device (FAD) and the Adolescent Clinical Sexual Behavior Inventory (ACSBI-S). Data were analyzed using descriptive analysis, Analysis of Variance (ANOVA), Independent t-Test and Correlation analysis. The findings indicated that there was statistically significant positive correlation between family cohesion and teenagers' sexual behavior. Family cohesion had a positive correlation with sexual knowledge at r=.200; p-value= .000. Therefore an increase in family cohesion has a corresponding positive influence on the student sexual knowledge. Family cohesion on the other hand had a positive and significant correlation with sexual interests (r=0.135; p= 0.11). The findings imply that family cohesion could be used in regulating some of the sexual behavior domains of teenagers.
doi:10.47772/ijriss.2021.5921 fatcat:w7zmdcum2ncfpgtsvnysmtijo4

Diarrhea Risk Factors Associated with Water, Sanitation and Hygiene Among the Under Five in Kasarani, Nairobi County

Humphrey Mbuti Kimani, Daniel Nyagetiria Akunga, Stephen Obiero Anyango, Taratisio Ndwiga
2019 Central African Journal of Public Health  
Provision of quality water continues to be a challenge in the developing Counties particularly in the informal settlements and Kenya is not an exception. This study assessed diarrhea disease attributable to water, sanitation and hygiene (WASH) among the under five in Kasarani, Nairobi County. The main objective of this study was to establish the association between diarrhea among the under five and Water, Sanitation and hygiene. To achieve this goal Kasarani was categorized into four study
more » ... ons namely low density high income, Medium density middle income, high density low income and informal settlement low income. Structured questionnaire and hygiene checklist were used as data collection instruments. Association and significant differences between variables were determined using inferential statistics and Chi-square tests. To compare quantitative variables (ANOVA) test was preferred. This study determined that water consumed in Kasarani was a risk for childhood diarrhea (p=0.019). Tap water showed a significantly higher contamination 13.7% than household water container 7.2% for T. Coli Bacteria. The amount of water a household consumed per day was an important risk factor for childhood diarrhea (P=0.001). Overall, Age of a child (P=0.046), water treatment method (P=0.002), method of storage of solid waste P<0.001, quantity and frequencies of water supply (P<0.001) were also found to be the most important risk factors for childhood diarrhea. The study concluded that there was a relationship between childhood diarrhea and water, sanitation and hygiene in Kasarani. The study recommended that Nairobi water and Sewerage Company institute programs that will facilitate adequate and wholesome water supply to HDLI and ISLI residential environs respectively.
doi:10.11648/j.cajph.20190506.18 fatcat:uooatjxqc5a73p74fbq5iyptym

Appraising Policy, legal and Institutional Frameworks used in promoting Sustainable Sanitation Management Approaches in Mavoko Municipality within Machakos County

Juliana Kamanthe Mutua, Dr Jones Agwata, Stephen Anyango, Nicholas Oguge
2018 Advances in Social Sciences Research Journal  
., Anyango, S., & Oguge, N. (2018) .  ... 
doi:10.14738/assrj.510.5284 fatcat:nxqctmakojfmpmaj5qpahgqsqi

High fluoride water in Bondo-Rarieda area of Siaya County, Kenya: a hydro-geological implication on public health in the Lake Victoria Basin

Enos W Wambu, Stephen G Agong, Beatrice Anyango, Walter Akuno, Teresa Akenga
2014 BMC Public Health  
Only a few studies to evaluate groundwater fluoride in Eastern Africa have been undertaken outside the volcanic belt of the Great Eastern Africa Rift Valley. The extent and impact of water fluoride outside these regions therefore remain unclear. The current study evaluated fluoride levels in household water sources in Bondo-Rarieda Area in the Kenyan part of the Lake Victoria Basin (LVB) and highlighted the risk posed by water fluoride to the resident communities. The results, it was
more » ... , will contribute to in-depth understanding of the fluoride problem in the region. Methods: A total of 128 water samples were collected from different water sources from the entire study area and analyzed for fluoride content using ion-selective electrodes. Results: Lake Victoria was the main water source in the area but dams and open pans (39.5%), boreholes and shallow wells (23.5%), and streams (18.5%) were the principal water sources outside walking distances from the lake. The overall mean fluoride content of the water exceeded recommended limits for drinking water. The mean water fluoride was highest in Uyoma (1.39±0.84 ppm), Nyang'oma (1.00±0.59 ppm) and Asembo (0.92±0.46 ppm) and lowest in Maranda Division (0.69±0.42 ppm). Ponds (1.41±0.82 ppm), springs (1.25±0.43 ppm), dams and open pans (0.96±0.79 ppm), and streams (0.95±0.41 ppm) had highest fluoride levels but lake and river water did not have elevated fluoride levels. Groundwater fluoride decreased with increasing distance from the lake indicating that water fluoride may have hydro-geologically been translocated into the region from geochemical sources outside the area. Conclusions: Lake Victoria was the main water source for the residents of Bondo-Rarieda Area. Majority of in-land residents however used water from dams, open pans, boreholes, shallow wells, ponds and streams, which was generally saline and fluoridated. It was estimated that 36% of children living in this area, who consume water from ground sources from the area could be at the risk of dental fluorosis.
doi:10.1186/1471-2458-14-462 pmid:24884434 pmcid:PMC4049395 fatcat:s6zc5acfefeqbiqdnogfouqdxi

Field evaluation of near point of care Cepheid GeneXpert HIV-1 Qual for early infant diagnosis

Valarie Sarah Opollo, Alliance Nikuze, Jihane Ben-Farhat, Emily Anyango, Felix Humwa, Boaz Oyaro, Stephen Wanjala, Willis Omwoyo, Maxwel Majiwa, Victor Akelo, Clement Zeh, David Maman (+1 others)
2018 PLoS ONE  
Access to point-of-care HIV testing shortens turn-around times, time to diagnosis and reduces loss to follow-up hence minimizing barriers to early linkage to care and treatment among HIV infected infants. Currently samples for early infant HIV diagnosis are sent to centralized testing facilities which are few and located only at specific regions in Kenya. However, there are Point of Care (POC) early infant diagnosis [EID] technologies elsewhere such as SAMBA and ALERE-Q that are yet to be
more » ... ted in Kenya despite the urgent need for data to inform policy formulation regarding EID. The Cepheid GeneXpert HIV-1 Qual (GeneXpert) technology for POC EID offers a great opportunity to minimize HIV associated morbidity, mortality and loss to follow-up through decentralization of early infant HIV testing to the clinics. This technology also allows for same-day results thus facilitating prompt linkage to care.
doi:10.1371/journal.pone.0209778 pmid:30589900 pmcid:PMC6307732 fatcat:foa6pldc4jh5lihmdngvuz4y2u

Mainstreaming the Culture of Eco-Industrial Parks (EIPs) in Kenya for the Sustainable Realization of the Country's Vision 2030

Kelvin Khisa, Nicholas Oguge, Stephen Anyango Obiero
2018 Journal of International Business Research and Marketing  
Competitive and productive Special Economic Zones (SEZs)/ industrial Parks (IPs) of the future will be those that will abandon the wasteful linear development model and instead embrace a circular economy that is characterized with the circular flow of materials and energy. Doing this will not only lower pressure on the use of the country's virgin raw materials but also contribute to the reduced carbon footprint of the SEZs/IPs by helping to divert wastes from the landfill. T his paper
more » ... ed the spontaneous evolution of waste and by-product exchange at the agroprocessing and garment clusters of the Athi River SEZ. T hese cluster based material exchanges evolved on their own largely as a result of the prevailing forces of material supply and demand. T hough at its infancy, this emergency of industrial symbiosis at the economic zone has helped to demonstrate the social inclusion dimension of green growth through the creation of decent green jobs. T he practice has also enabled participating firms to reduce t heir GHG emissions and lower their operational costs. The economic zone's desire to fully embrace waste recovery, reuse and recycling as part of its deliberate efforts of advancing the ideals of a circular economy is currently being hampered by a lack of functional waste recovery, reuse, and recycling infrastructure. T he proposed strengthening of University-Industry-Government (U-I-G) collaboration at the Athi River SEZ, will help promote eco-innovation that forms the cornerstone of the economic zone's improved productivity and competitiveness. T he paper sought to unravel the enabling policy interventions that need to be put in place so as to accelerate the transformation of the country's economic zones into environmentally friendly Eco -Industrial Parks (EIP s) capable of attracting green foreign direct investments (FDIs). It also tackled the barriers that need to be overcome by key stakeholders so that the country's SEZs/ IPs can adopt a development trajectory that enjoys low-emission levels, efficiently uses its resources, and is socially inclusive through the creation of decent green jobs.
doi:10.18775/jibrm.1849-8558.2015.36.3001 fatcat:zfutxw73gzdfvb3zmzfs5b2l7m

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam (+10 others)
2017 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of
more » ... res solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
doi:10.1093/nar/gkx1070 pmid:29126160 pmcid:PMC5753225 fatcat:j6ocp5cauvau3d7jd4gw3htwiq

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Žídek, Tim Green (+15 others)
2021 Nucleic Acids Research  
The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted
more » ... ned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.
doi:10.1093/nar/gkab1061 pmid:34791371 pmcid:PMC8728224 fatcat:m3lwyaoecnbxnhegqu4arkqhs4

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources [article]

Mihaly Varadi, Sreenath S Nair, Ian Sillitoe, Gerardo Tauriello, Stephen Anyango, Stefan Bienert, Clemente Borges, Mandar Deshpande, Tim Green, Andras Hatos, Tamas Hegedus, Maarten L Hekkelman (+20 others)
2022 bioRxiv   pre-print
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated theoretical protein modelling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various data
more » ... and perform comparative analysis to identify what models best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. 3D-Beacons allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and the Protein Data Bank.
doi:10.1101/2022.08.01.501973 fatcat:7lij36comrfklicvhytg6akriy
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