The Reactome BioMart

Reactome is an open source, expert-authored, manually curated and peer-reviewed database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Reactome BioMart provides biologists and bioinformaticians with a single web interface for performing simple or elaborate queries of the Reactome database, aggregating data from different sources and providing an opportunity to integrate experimental and computational results with information relating to biological pathways. Database URL: http://www.reactome.org

Market intelligence for informing crop-breeding decisions by CGIAR and NARES

Crop breeding by the Consultative Group on International Agricultural Research (CGIAR), in partnership with national agricultural research and extension systems (NARES) and privately owned seed companies, forms the backbone of the research and development (R&D) effort needed to ensure future food security in developing regions. Over the past decades, varieties derived from CGIAR germplasm have helped provide food for hundreds of millions living in harsh and vulnerable environments. However, the capacity to deliver increased benefits from crop breeding will depend on effective strategies to address the stubbornly slow rate of uptake of improved varieties. Meeting the challengewill require, among other inputs, deeper insights on the evolving preferences and requirements of farmers, processors and consumers. In short, breeding will need to be led more by demand. Key to the success of demand-led breeding will be the availability of reliable and timely intelligence on the current and future preferences and requirements of farmers, processors and consumers. Although ‘market intelligence’ has existed in various forms in CGIAR’s social science research agenda, an opportunity exists for increased relevance based on shared approaches and tools and new partnerships, both within CGIAR and between CGIAR and its partners. Beginning in 2022, a coordinated effort through the CGIAR Initiative on Market Intelligence looks to build cross-functional and transdisciplinary teams to provide market intelligence in support of crop breeding and seed-system development

Building democracy from below : lessons from Western Uganda

How to achieve democratisation in the neopatrimonial and agrarian environments that predominate in sub-Saharan Africa continues to present a challenge for both development theory and practice. Drawing on intensive fieldwork in Western Uganda, this paper argues that Charles Tilly’s ‘democratisation as process’ provides us with the framework required to explain the ways in which particular kinds of association can advance democratisation from below. Moving beyond the current focus on how elite-bargaining and certain associational forms may contribute to liberal forms of democracy, this approach helps identify the intermediate mechanisms involved in building democracy from below, including the significance of challenging categorical inequalities, notably through the role of producer groups, and of building trust networks, cross-class alliances and synergistic relations between civil and political society. The evidence and mode of analysis deployed here help suggest alternative routes for supporting local efforts to build democracy from below in sub-Saharan Africa

ECONOMIC INTEGRATION FOR DEVELOPMENT IN EASTERN AND SOUTHERN AFRICA: ASSESSMENT AND PROSPECTS

Summary Eastern and Southern Africa has a long history of efforts to achieve operational economic integration and a complex set of overlapping institutional frames. The gains from successful cooperation are agreed ? the basic issues turn on how to attain them. In this context the experiences of the two key actors, PTA (Preferential Trade Area) and SADC (Southern African Development Community), offer insights into the strengths and weaknesses of a broad, secretariat?led trade barrier reducing organization and a narrower (geographically), key sector production coordination, country?led one (SADC). The divergences ? as well as history ? have hampered attempts to coordinate or to merge them and their responses to the opportunities and challenges posed by the re?entry of South Africa into Africa. The latter raises rather more complex issues (and ones less threatening ? or promising in some respects ? to its Eastern and Southern African region potential partners) than is sometimes supposed. Resumé efforts pour d'obtenir l'intégration économique et de rendre celle?ci opérationnelle dans le contexte d'une série complexe de cadres institutionnels parfois superposés. Les gains résultant des réussites dans la coopération ne sont pas contestés: les questions fondamentales tournent autour des moyens d'y parvenir. Dans ce contexte l'expérience de deux acteurs principaux (la PTA – Preferential Trade Area ou Zone commerciale privilégiée et la SADC – Southern African Development Community ou Communauté de développement de l'Afrique australe) offrent des aperçus quant aux avantages et désavantages de l'existence d'une organisation de grande envergure et fondée sur secrétariat, consacrée à la réduction des barrières douannières, et d'une autre organisation, cette fois limitée en termes de sa superficie géographique et menée par des pays, qui cherche à coordiner la production dans les secteurs clef: la SADC. Leurs divergences, et l'histoire même, ont servi d'entrave aux efforts de les coordiner ou de les faire fusionner, surtout en ce qui concerne les nouvelles possibilités et le challenge même de la réintégration de l'Afrique du Sud dans la grande Afrique. Cette réintégration soulève des questions un peu plus complexes (et moins menaçantes) et aussi, moins promettrices sous certains jours pour ses éventuels partenaires dans les régions orientales et australes de l'Afrique) qu'on ne le supposerait parfois. Resumen El Africa oriental y el Africa austral tienen un largo historial de esfuerzos para alcanzar la integración económica operacional y un complejo grupo de estructuras institucionales superpuestas. Los beneficios de una cooperación exitosa no están en discusión ? el punto básico es cómo obtenerlos. En este contexto las experiencias de dos actores clave, (la PTA?Preferential Trade Area o Zona de Comercio Privilegiado, y la SADC ? Southern Africa Development Community o Comunidad para el Desarrollo de Africa Austral), ofrecen interesantes revelaciones sobre los puntos fuertes y débiles de una amplia y burocrática barrera comercial que reduce la organización, y la coordinación de la producción en sectores clave de un área geográfica más reducida, de orientación nacional. Las divergenias ? así como la historia ? han estorbado intentos de combinar o coordinar estos dos aspectos y sus respuestas a las oportunidades o desafíos que presenta el reingreso de Sudafrica al Africa. Esto último plantea más asuntos complejos de los que a veces se suponen (y menos amenazantes ? más prometedores en alugunos aspectos) para sus socios comerciales en potencia en Africa oriental y Africa del sur

Local perceptions of intermittent screening and treatment for malaria in school children on the south coast of Kenya.

BACKGROUND: The intermittent screening and treatment (IST) of school children for malaria is one possible intervention strategy that could help reduce the burden of malaria among school children. Future implementation of IST will not only depend on its efficacy and cost-effectiveness but also on its acceptability to parents of the children who receive IST, as well as those responsible for its delivery. This study was conducted alongside a cluster-randomized trial to investigate local perceptions of school-based IST among parents and other stakeholders on the Kenyan south coast. METHODS: Six out of the 51 schools receiving the IST intervention were purposively sampled, based on the prevalence of Plasmodium infection, to participate in the qualitative study. Twenty-two focus group discussions and 17 in-depth interviews were conducted with parents and other key stakeholders involved in the implementation of school health programmes in the district. Data analysis was guided by the framework analysis method. RESULTS: High knowledge of the burden of clinical malaria on school children, the perceived benefits of preventing clinical disease through IST and previous positive experiences and interactions with other school health programmes facilitated the acceptability of IST. However, lack of understanding of the consequences of asymptomatic parasitaemia for apparently healthy school children could potentially contribute to non-adherence to treatment, and use of alternative anti-malarial drugs with simpler regimens was generally preferred. The general consensus of stakeholders was that health workers were best placed to undertake the screening and provide treatment, and although teachers' involvement in the programme is critical, most participants were opposed to teachers taking finger-prick blood samples from children. There was also a strong demand for the distribution of mosquito nets to augment IST. CONCLUSION: School-based malaria control through IST was acceptable to most parents and other stakeholders, but careful consideration of the various roles of teachers, community health workers, and health workers, and the use of anti-malarial drugs with simpler regimens are critical to its future implementation

Reactome: a database of reactions, pathways and biological processes

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice

The role of public involvement in the design of the first SARS-CoV-2 human challenge study during an evolving pandemic

High quality health care research must involve patients and the public. This ensures research is important, relevant and acceptable to those it is designed to benefit. The world’s first human challenge study with SARS-CoV-2 undertook detailed public involvement to inform study design despite the urgency to review and establish the study. The work was integral to the UK Research Ethics Committee review and approval of the study. Discussion with individuals from ethnic minorities within the UK population supported decision-making around the study exclusion criteria. Public review of study materials for consent processes led to the addition of new information, comparisons and visual aids to help volunteers consider the practicalities and risks involved in participating. A discussion exploring the acceptability of a human challenge study with SARS-CoV-2 taking place in the UK, given the current context of the pandemic, identified overall support for the study. Public concern for the wellbeing of trial participants, as a consequence of isolation, was identified. We outline our approach to public involvement and its impact on study design

Greenhouse gas emissions from agricultural food production to supply Indian diets: Implications for climate change mitigation

Agriculture is a major source of greenhouse gas (GHG) emissions globally. The growing global population is putting pressure on agricultural production systems that aim to secure food production while minimising GHG emissions. In this study, the GHG emissions associated with the production of major food commodities in India are calculated using the Cool Farm Tool. GHG emissions, based on farm management for major crops (including cereals like wheat and rice, pulses, potatoes, fruits and vegetables) and livestock-based products (milk, eggs, chicken and mutton meat), are quantified and compared. Livestock and rice production were found to be the main sources of GHG emissions in Indian agriculture with a country average of 5.65 kg CO2eq kg-1 rice, 45.54 kg CO2eq kg-1 mutton meat and 2.4 kg CO2eq kg-1 milk. Production of cereals (except rice), fruits and vegetables in India emits comparatively less GHGs with <1 kg CO2eq kg-1 product. These findings suggest that a shift towards dietary patterns with greater consumption of animal source foods could greatly increase GHG emissions from Indian agriculture. A range of mitigation options are available that could reduce emissions from current levels and may be compatible with increased future food production and consumption demands in India

BioMart Central Portal: an open database network for the biological community

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities