Formal Derivation of Concurrent Garbage Collectors

Concurrent garbage collectors are notoriously difficult to implement correctly. Previous approaches to the issue of producing correct collectors have mainly been based on posit-and-prove verification or on the application of domain-specific templates and transformations. We show how to derive the upper reaches of a family of concurrent garbage collectors by refinement from a formal specification, emphasizing the application of domain-independent design theories and transformations. A key contribution is an extension to the classical lattice-theoretic fixpoint theorems to account for the dynamics of concurrent mutation and collection.Comment: 38 pages, 21 figures. The short version of this paper appeared in the Proceedings of MPC 201

Assessing the influence of land-use change on the variability of soil chemical properties in semi-arid zone of Ghana

The study aimed at providing basis to consider spatial variability in soil fertility to inform effective decision making in mineral fertilizer recommendations. The study area was classified into six land-use categories using a rural rapid appraisal technique with the aid of the farmers in the community, and by remote sensing satellite imagery (Quick bird). Land-use categories varied significantly in their nutrient, organic carbon content, and stock with coefficient of determination ranging from 0.14 to 0.46. This is reflected in decline in soil nutrient, organic carbon content, and stock with increasing number of years the land was put under cultivation except for permanently cultivated fields. Permanantly cultivated fields were located in the homestead and benefited from nutrient imports from the bush fields. The two farm types also differed significantly with respect to soil nutrients, organic carbon and stock. Soil organic carbon content was 8.2 and 4.5 g kg-1 for the homestead and bushfields, respectively. Soil organic carbon stock estimated for the two farm types were 125 and 74 t ha-1 for the homestead and bush fields, respectively. The study shows a distinct zone of nutrient enhancement within the homestead and bushfields that should be sampled separately when sampling the zone for fertilizer recommendations

AID Overlapping and Polη Hotspots Are Key Features of Evolutionary Variation Within the Human Antibody Heavy Chain (IGHV) Genes

© Copyright © 2020 Tang, Bagnara, Chiorazzi, Scharff and MacCarthy. Somatic hypermutation (SHM) of the immunoglobulin variable (IgV) loci is a key process in antibody affinity maturation. The enzyme activation-induced deaminase (AID), initiates SHM by creating C → U mismatches on single-stranded DNA (ssDNA). AID has preferential hotspot motif targets in the context of WRC/GYW (W = A/T, R = A/G, Y = C/T) and particularly at WGCW overlapping hotspots where hotspots appear opposite each other on both strands. Subsequent recruitment of the low-fidelity DNA repair enzyme, Polymerase eta (Polη), during mismatch repair, creates additional mutations at WA/TW sites. Although there are more than 50 functional immunoglobulin heavy chain variable (IGHV) segments in humans, the fundamental differences between these genes and their ability to respond to all possible foreign antigens is still poorly understood. To better understand this, we generated profiles of WGCW hotspots in each of the human IGHV genes and found the expected high frequency in complementarity determining regions (CDRs) that encode the antigen binding sites but also an unexpectedly high frequency of WGCW in certain framework (FW) sub-regions. Principal Components Analysis (PCA) of these overlapping AID hotspot profiles revealed that one major difference between IGHV families is the presence or absence of WGCW in a sub-region of FW3 sometimes referred to as “CDR4.” Further differences between members of each family (e.g., IGHV1) are primarily determined by their WGCW densities in CDR1. We previously suggested that the co-localization of AID overlapping and Polη hotspots was associated with high mutability of certain IGHV sub-regions, such as the CDRs. To evaluate the importance of this feature, we extended the WGCW profiles, combining them with local densities of Polη (WA) hotspots, thus describing the co-localization of both types of hotspots across all IGHV genes. We also verified that co-localization is associated with higher mutability. PCA of the co-localization profiles showed CDR1 and CDR2 as being the main contributors to variance among IGHV genes, consistent with the importance of these sub-regions in antigen binding. Our results suggest that AID overlapping (WGCW) hotspots alone or in conjunction with Polη (WA/TW) hotspots are key features of evolutionary variation between IGHV genes

Evaluation of soil properties of the Sudan Savannah ecological zone of Ghana for crop production

Low soil fertility and limited ability of farmers to purchase fertilizers in the Sudan savannah zone of Ghana has resulted in the decline in the yield of cereals over the years. There is, therefore, the need to identify soil parameters that are critical to crop production, to manage them effectively and improve fertilizer use efficiency to increase crop yield. To achieve this, an area of about 1.5 km2 was divided into grid cells (100m2) and characterised for their soil properties (organic carbon, pH, and soil texture). Data collected was used in a pedo-transfer function to estimate additional soil parameters that were not measured (i.e. wilting point, field capacity, available water and saturation). These were used as input to the crop simulation model (APSIM- Agriculture Productions Systems sIMulator) to simulate sorghum grain yield for each grid cell. Linear regression and factor analysis were also employed in explaining the data. Grain yield ranged from 402 to 1092 kg ha-1 with a mean of 673 kg ha-1 using 2005 weather data and 228 to 907 kg ha-1 with a mean of 427 kg ha-1 using 2000 weather data without fertilizer application. The model was sensitive to all input parameters. Soil texture and organic carbon were identified to have significant effect on crop yield. Soil organic carbon is, therefore, to be managed for the development of a good tilth and hence sustainable yields of sorghum at the study site

The polycystic kidney disease 1 gene encodes a 14 kb transcript and lies within a duplicated region on chromosome 16

Autosomal dominant polycystic kidney disease (ADPKD) is a common genetic disorder that frequently results in renal fallure due to progressive cyst development. The major locus, PKD1, maps to 16p13.3. We identified a chromosome translocation associated with ADPKD that disrupts a gene (PBP) encoding a 14 kb transcript in the PKD1 candidate region. Further mutations of the PBP gene were found in PKD1 patients, two deletions (one a de novo event) and a splicing defect, confirming that PBP is the PKD1 gene. This gene is located adjacent to the TSC2 locus in a genomic region that is reiterated more proximally on 16p. The duplicate area encodes three transcripts substantially homologous to the PKD1 transcript. Partial sequence analysis of the PKD1 transcript shows that it encodes a novel protein whose function is at present unknown

How are gender equality and human rights interventions included in sexual and reproductive health programmes and policies: A systematic review of existing research foci and gaps

The importance of promoting gender equality and human rights in sexual and reproductive health (SRH) programmes and policies has been affirmed in numerous international and regional agreements, most recently the 2030 Agenda for Sustainable Development. Given the critical role of research to determine what works, we aimed to identify research gaps as part of a broader priority setting exercise on integrating gender equality and human rights approaches in SRH programmes and policies. A systematic literature review of reviews was conducted to examine the question: what do we know about how research in the context of SRH programmes and policies has addressed gender equality and human rights and what are the current gaps in research. We searched three databases for reviews that addressed the research question, were published between 1994-2014, and met methodological standards for systematic reviews, qualitative meta-syntheses and other reviews of relevance to the research question. Additional grey literature was identified based on expert input. Articles were appraised by the primary author and examined by an expert panel. An abstraction and thematic analysis process was used to synthesize findings. Of the 3,073 abstracts identified, 56 articles were reviewed in full and 23 were included along with 10 from the grey literature. The majority focused on interventions addressing gender inequalities; very few reviews explicitly included human rights based interventions. Across both topics, weak study designs and use of intermediate outcome measures limited evidence quality. Further, there was limited evidence on interventions that addressed marginalized groups. Better quality studies, longer-term indicators, and measurement of unintended consequences are needed to better understand the impact of these types of interventions on SRH outcomes. Further efforts are needed to cover research on gender equality and human rights issues as they pertain to a broader set of SRH topics and populations.Scopu

Mode of Biochar Application to Vertisols Influences Water Balance Components and Water Use Efficiency of Maize (Zea mays L.)

Vertisols belong to a group of soils with high fertility but poor physical properties of swelling when wet and shrinking and cracking when dry. The swelling inhibits infiltration, resulting in flooding, limiting the production of upland crops. Biochar (<BC) application has been shown to reduce the shrink-swell behaviour of Vertisols. However, the mode of biochar application to these soils may affect the effectiveness of the amendment. This study investigated the water relations and maize (Zea mays L.) growth under two BC application modes: (i) biochar applied into cracks that develop with drying, C, and (ii) biochar that was surface broadcast and incorporated into the topsoil, FM. A control treatment did not receive any BC amendment. Maize was grown on the BC-amended Vertisols using the two modes of application in a greenhouse under two seasonal water regimes of 610 and 450 mm. The results showed that the proportion of total water application lost to runoff was 37%, 49% and 53% for C, FM and control treatments, respectively. Both maize yield and Water Use Efficiency (WUE), for the C treatments were significantly (p < 0.05) higher than those for FM treatments. The maize yield under the C treatments was 19% over the control. Similarly, the WUE for the C treatments was 28% above the control treatment. It is concluded that the application of biochar into cracks is a more effective way of improving the water relations and upland crop productivity and WUE in Vertisols than the traditional surface incorporation

Promoting the achievement of looked after children and young people in the City of Nottingham

As of March 2016, there were 70,440 children and young people in care in England. The number of looked after children has continued to increase steadily over the last eight years. Sixty per cent of these children are in care because of abuse or neglect and three-quarters are placed in foster care arrangements. Children and young people who are in or have experienced care remain one of the lowest performing groups in terms of educational outcomes. Last year, 14% of looked after children achieved five or more A*–C GCSEs or equivalent, including English and mathematics. As a consequence, they also experience poorer employment and health outcomes after leaving school compared to their peers. They are over-represented amongst the offender population and those who experience homelessness. However, research is emerging to show that children and young people in care can have very positive experiences of school and are supported effectively to reach their full potential academically and socially. The purpose of this report is to share practice in selected City of Nottingham schools that is contributing to improved outcomes and school experiences for children and young people in care. In July 2015, the City of Nottingham Virtual School (VS) commissioned UCL Institute of Education to run their Promoting the Achievement of Looked After Children (PALAC) programme with seven schools in the Local Authority (LA). This report presents an account of the programme, including the activities undertaken by the participants and the outcomes of the programme to date for pupils in care and staff in the participating schools

Patterns of ash (Fraxinus excelsior L.) colonization in mountain grasslands: the importance of management practices

International audienceWoody colonization of grasslands is often associated with changes in abiotic or biotic conditions or a combination of both. Widely used as fodder and litter in the past traditional agro-pastoral system, ash (Fraxinus excelsior L.) has now become a colonizing species of mountain grasslands in the French Pyrenees. Its present distribution is dependent on past human activities and it is locally controlled by propagule pressure and abiotic conditions. However, even when all favourable conditions are met, all the potentially colonizable grasslands are not invaded. We hypothesize that management practices should play a crucial role in the control of ash colonization. From empirical field surveys we have compared the botanical composition of a set of grasslands (present and former) differing in management practices and level of ash colonization. We have displayed a kind of successional gradient positively linked to both ash cover and height but not to the age of trees. We have tested the relationships between ash presence in grassland and management types i.e. cutting and/or grazing, management intensity and some grassland communities' features i.e. total and local specific richness and species heterogeneity. Mixed use (cutting and grazing) is negatively linked to ash presence in grassland whereas grazing alone positively. Mixed use and high grazing intensity are directly preventing ash seedlings establishment, when low grazing intensity is allowing ash seedlings establishment indirectly through herbaceous vegetation neglected by livestock. Our results show the existence of a limit between grasslands with and without established ashes corresponding to a threshold in the intensity of use. Under this threshold, when ash is established, the colonization process seems to become irreversible. Ash possesses the ability of compensatory growth and therefore under a high grazing intensity develops a subterranean vegetative reproduction. However the question remains at which stage of seedling development and grazing intensity these strategies could occur

Location and Land use effects on Soil Carbon Accretion and Productivity in the Coastal Savanna Agro-ecological Zone of Ghana

Land use type, climate and soil properties are major determinants of soil carbon storage and productivity, especially in low-input agriculture. In this study, we investigated the interactions among these factors at four (4) locations, namely Accra Metropolis, Ga West, Ga East and Shai Osudoku, within the Coastal-Savannah agro-ecological zone of Ghana. The land use types were maize-based cropping, cassava-based cropping, woodlot/plantations and natural forests. The impact of these on soil productivity at a given location was assessed in terms of soil carbon stocks and a Soil Productivity Index (SPI). The SPI is a composite value derived from routine soil properties such as: soil texture, available water capacity, pH, cation exchange capacity, soil organic carbon, available P, exchangeable K, potentially mineralizable nitrogen, and basic cations, among others. Principal component analysis was used to select soil properties that were used to estimate SPI. The results showed that the locations differed with respect to rainfall regimes and soil types. Locations with slightly heavier soil texture and relatively higher rainfall regimes (Ga East and Shai Osudoku) had significantly higher soil carbon storage and SPI values than the lighter soil textured locations (Accra Metropolis and Ga West). With regards to land use, forest had significantly higher soil carbon storage and SPI than all the other land use types, irrespective of location. The order of soil carbon storage and SPI were: forest > woodlot/plantation > cassava > maize. It was observed that though the Accra Metropolis location hosted the oldest forest, soil carbon was still low, apparently due to the lighter soil texture. We concluded that the soil productivity restorative ability is an interactive effect of carbon management (land use), soil texture and other properties. This interaction hitherto has not been adequately investigated, especially in low-input agriculture