174 research outputs found
On the hidden half: testing precision of techniques used in estimating below ground biomass in mangrove forests
Climate variability and change:perceptions, experiences and realities
Farming in the semi-arid tropics, where climatic conditions
are marginal and highly variable, is a risky
enterprise. The main source of this risk is the variability
in rainfall that occurs at many different timescales,
ranging from seasons to years to decades and beyond.
Farmers operating under these conditions make decisions
based on their perceptions and experiences gained from
several years of keen observation and practice in the field.
However, perceptions are influenced by many factors, both
real and subjective. For agriculture, factors like farm productivity,
crop, market and local preferences, capacity to invest,
willingness to take risks and soil quality play an important
role. While the role and significance of some of these
factors on productivity and profitability can be perceived
more easily due to their relative predictability, extreme variability
in climate and the random nature of that variability
makes it difficult for farmers to accurately perceive trends
in climate. In the absence of detailed measurements, perceptions
can be biased and unreliable. Climate information can
play an important role in helping farmers better understand
this variability and its associated risks, and enhancing their
decision-making for effective risk management
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
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
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations
The reversible phosphorylation of serine, threonine and tyrosine hydroxyl groups is an especially prominent form of post-translational modification (PTM) of proteins. It plays critical roles in the regulation of diverse processes, and mutations that directly or indirectly affect these phosphorylation events have been associated with many cancers and other pathologies. Here, we describe the development of a new BioMart tool that gathers data from three different biological resources to provide the user with an integrated view of phosphorylation events associated with a human protein of interest, the complexes of which the protein (modified or not) is a part, the reactions in which the protein and its complexes participate and the somatic mutations that might be expected to perturb those functions. The three resources used are the Reactome, PRIDE and COSMIC databases. The Reactome knowledgebase contains annotations of phosphorylated human proteins linked to the reactions in which they are phosphorylated and dephosphorylated, to the complexes of which they are parts and to the reactions in which the phosphorylated proteins participate as substrates, catalysts and regulators. The PRIDE database holds extensive mass spectrometry data from which protein phosphorylation patterns can be inferred, and the COSMIC database holds records of somatic mutations found in human cancer cells. This tool supports both flexible, user-specified queries and standard (‘canned’) queries to retrieve frequently used combinations of data for user-specified proteins and reactions. We demonstrate using the Wnt signaling pathway and the human c-SRC protein how the tool can be used to place somatic mutation data into a functional perspective by changing critical residues involved in pathway modulation, and where available, check for mass spectrometry evidence in PRIDE supporting identification of the critical residue
Characterization of Schistosome Tegumental Alkaline Phosphatase (SmAP)
Schistosomes are parasitic platyhelminths that currently infect over 200 million people globally. The parasites can live for years in a putatively hostile environment - the blood of vertebrates. We have hypothesized that the unusual schistosome tegument (outer-covering) plays a role in protecting parasites in the blood; by impeding host immunological signaling pathways we suggest that tegumental molecules help create an immunologically privileged environment for schistosomes. In this work, we clone and characterize a schistosome alkaline phosphatase (SmAP), a predicted ∼60 kDa glycoprotein that has high sequence conservation with members of the alkaline phosphatase protein family. The SmAP gene is most highly expressed in intravascular parasite life stages. Using immunofluorescence and immuno-electron microscopy, we confirm that SmAP is expressed at the host/parasite interface and in internal tissues. The ability of living parasites to cleave exogenous adenosine monophosphate (AMP) and generate adenosine is very largely abolished when SmAP gene expression is suppressed following RNAi treatment targeting the gene. These results lend support to the hypothesis that schistosome surface enzymes such as SmAP could dampen host immune responses against the parasites by generating immunosuppressants such as adenosine to promote their survival. This notion does not rule out other potential functions for the adenosine generated e.g. in parasite nutrition
Climate Variability and Change: Farmer Perceptions and Understanding of Intra-Seasonal Variability in Rainfall and Associated Risk in Semi-Arid Kenya
This study examines farmers’ perceptions of short- and long-term variability in climate, their ability to
discern trends in climate and how the perceived trends converge with actual weather observations in five
districts of Eastern Province in Kenya where the climate is semi-arid with high intra- and inter-annual
variability in rainfall. Field surveys to elicit farmers’ perceptions about climate variability and change
were conducted in Machakos, Makueni, Kitui, Mwingi and Mutomo districts. Long-term rainfall records
from five meteorological stations within a 10 km radius from the survey locations were obtained from the
Kenya Meteorological Department and were analysed to compare with farmers’ observations. Farmers’
responses indicate that they are well aware of the general climate in their location, its variability, the
probabilistic nature of the variability and the impacts of this variability on crop production. However,
their ability to synthesize the knowledge they have gained from their observations and discern longterm
trends in the probabilistic distribution of seasonal conditions is more subjective, mainly due to the
compounding interactions between climate and other factors such as soil fertility, soil water and land use
change that determine the climate’s overall influence on crop productivity. There is a general tendency
among the farmers to give greater weight to negative impacts leading to higher risk perception. In relation
to long-term changes in the climate, farmer observations in our study that rainfall patterns are changing
corroborated well with reported perceptions from other places across the African continent but were not
supported by the observed trends in rainfall data from the five study locations. The main implication of
our findings is the need to be aware of and account for the risk during the development and promotion of
technologies involving significant investments by smallholder farmers and exercise caution in interpreting
farmers’ perceptions about long-term climate variability and change
Diagnostic criteria and symptom grading for delayed gastric conduit emptying after esophagectomy for cancer : international expert consensus based on a modified Delphi process
Delayed gastric conduit emptying (DGCE) after esophagectomy for cancer is associated with adverse outcomes and troubling symptoms. Widely accepted diagnostic criteria and a symptom grading tool for DGCE are missing. This hampers the interpretation and comparison of studies. A modified Delphi process, using repeated web-based questionnaires, combined with live interim group discussions was conducted by 33 experts within the field, from Europe, North America, and Asia. DGCE was divided into early DGCE if present within 14 days of surgery and late if present later than 14 days after surgery. The final criteria for early DGCE, accepted by 25 of 27 (93%) experts, were as follows: >500 mL diurnal nasogastric tube output measured on the morning of postoperative day 5 or later or>100% increased gastric tube width on frontal chest x-ray projection together with the presence of an air-fluid level. The final criteria for late DGCE accepted by 89% of the experts were as follows: the patient should have 'quite a bit' or 'very much' of at least two of the following symptoms; early satiety/fullness, vomiting, nausea, regurgitation or inability to meet caloric need by oral intake and delayed contrast passage on upper gastrointestinal water-soluble contrast radiogram or on timed barium swallow. A symptom grading tool for late DGCE was constructed grading each symptom as: 'not at all', 'a little', 'quite a bit', or 'very much', generating 0, 1, 2, or 3 points, respectively. For the five symptoms retained in the diagnostic criteria for late DGCE, the minimum score would be 0, and the maximum score would be 15. The final symptom grading tool for late DGCE was accepted by 27 of 31 (87%) experts. For the first time, diagnostic criteria for early and late DGCE and a symptom grading tool for late DGCE are available, based on an international expert consensus process.Peer reviewe
Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis
BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London
Composition, potential emissions and agricultural value of pig slurry from Spanish commercial farms
[EN] Pig slurry is a valuable fertilizer for crop
production but at the same time its management may
pose environmental risks. Slurry samples were collected
from 77 commercial farms of four animal categories
(gestating and lactating sows, nursery piglets and
growing pigs) and analyzed for macronutrients,
micronutrients, heavy metals and volatile fatty acids.
Emissions of ammonia (NH3) and biochemical methane
potential (BMP) were quantified. Slurry electrical
conductivity, pH, dry matter content and ash content
were also determined. Data analysis included an
analysis of correlations among variables, the development
of predictionmodels for gaseousemissions and the
analysis of nutritional content of slurries for crop
production. Descriptive information is provided in this
work and shows a wide range of variability in all studied
variables. Animal category affected some physicochemical
parameters, probably as a consequence of
different slurry management and use of cleaning water.
Slurries from gestating sows and growing pigs tended to
be more concentrated in nutrients, whereas the slurry
from lactating sows and nursery piglets tended to be
more diluted. Relevant relationships were found among
slurry characteristics expressed in fresh basis and gas
emissions. Predictivemodels using on-farmmeasurable
parameterswere obtained forNH3 (R2 = 0.51) andCH4
(R2 = 0.76), which suggests that BMP may be estimated
in commercial farms from easily determined
slurry characteristics. Finally, slurry nutrient composition
was highly variable. Therefore, complete analyses
of slurries should be performed for an effective and
environmental friendly land application.This project was funded by the Spanish Ministry of Science and Innovation (AGL2011-30023) and the Valencian Government (ACOMP/2013/118). We thank the BABEL Project, Building Academic Bonds between Europe and Latin America. Erasmus Mundus Programme Action 2 for PhD fellowships. The translation of this paper was funded by the Universitat Politecnica de Valencia, Spain.Antezana-Julian, WO.; Blas, CD.; García-Rebollar, P.; Rodríguez, C.; Beccaccia, A.; Ferrer Riera, P.; Cerisuelo, A.... (2016). Composition, potential emissions and agricultural value of pig slurry from Spanish commercial farms. Nutrient Cycling in Agroecosystems. 104(2):159-173. https://doi.org/10.1007/s10705-016-9764-3S1591731042Aarnink AJA, Verstegen MWA (2007) Nutrition, key factor to reduce environmental load from pig production. 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