Self-organising management of Grid environments

This paper presents basic concepts, architectural principles and algorithms for efficient resource and security management in cluster computing environments and the Grid. The work presented in this paper is funded by BTExacT and the EPSRC project SO-GRM (GR/S21939)

Aeromonas-related Diarrhoea in Nasarawa, Nigeria

Background: Two hundred and fifty volunteer patients attending 5 major hospitals in Nasarawa town, Nasarawa State, Nigeria were involved in this study to determine the prevalence of Aeromonasspp in persons with diarrhoea. The study population consisted of 133 males and 117 females between the ages of 0-70 years. Methods: Stool samples (148 diarrhoeal and 102 non-diarrhoeal) were analysed for the presence of Aeromonas spp. using standard bacteriological methods. The isolates were also subjected to antimicrobial susceptibility testing using the disc diffusion method. Results: Four (1.60%) of the 250 stool samples were positive for Aeromonasspp. Three (2.03%) of the isolates were recovered from diarrhoeal specimens and 1 (0.98%) from non-diarrhoeal (control) samples. The difference was statistically significant (P<0.05). The highest numbers of isolates 3 (3.66%) were recovered from age group 0-10 years while age group 61-70 years yielded 1 (14.29%). All isolates were found to be Aeromonas hydrophilia. The isolates were all sensitive to tetracycline, gentamicin, chloramphenicol, cotrimoxazole and streptomycin but resistant to penicillin and ampicillin. Other enteropathogens isolated were Shigella spp 5 (2.0%) and Salmonella spp 2(0.8%). Conclusion: This study has shown that a small percentage of gastroenteritis can be attributed to Aeromonas hydrophilia.Introduction: Deux cents cinquante patients volontaaires qui consultent 5 h\uf4pitaux majeurs dans la ville de Nasarawa l'Etat de Nasarawa, Nig\ue9ria ont particip\ue9 dans cette \ue9tude pour d\ue9cider la fr\ue9quence d'aeromone spp chez des individus atteints de la diarrh\ue9e. La population d'\ue9tude se compose de 133 du sexe masculin et 117 du sexe f\ue9minin entre 0 \u2013 70 ans. M\ue9thodes: Echantillons des f\ue8ces (148 diarrh\ue9e et 102 non \u2013 diarrh\ue9e) ont \ue9t\ue9 analys\ue9s pour la pr\ue9sence d'aeromone spp \ue0 travers l'utilisation de la m\ue9thode bact\ue9riologique. Les isolates \ue9taient \ue9galement en butte d'examen de la susceptibilit\ue9 antimicrobiale \ue0 travers l'utilization de la m\ue9thode de diffusion de disque. R\ue9sultats: Quatre soit 1,60% de 250 \ue9chantillons de f\ue8ces \ue9taient positifs pour l'aeromone spp. Trois soit 2,03% des isolates ont \ue9t\ue9 soign\ue9s des sp\ue9cimens de la diarrh\ue9e et 1 soit 0,98% des \ue9chantillons non-diarrh\ue9e (contr\uf4le). La diff\ue9rence \ue9tait statistiquement importante (p<0,05). Nombre le plus \ue9lev\ue9 des isolates 3(3,66%) ont \ue9t\ue9 soign\ue9s d'une trance d'\ue2ge 0 -10 ans, tandis que groupe d'\ue2ge 61070 ans donnent 1 soit 14,29%. On avait trouv\ue9 que toutes les isolates \ue9taient arromone hydrophilie. Toutes les isolates \ue9taient sensibles \ue0 la t\ue9tracycline, gentamicine, chloramph\ue9nicol cotrimoxazole et str\ue9ptomycine mais r\ue9sistant \ue0 la p\ue9nicilline et ampicilline, Des autres isolates enteropathogens \ue9taient shigella spp 5 soit 2,0% et salmonella spp. 2(0,8%) Conclusion: A travers cette \ue9tude on peut conclure que un petit pourcentage de la gastroenterite peut \ueatre attribuable au aeromone hydrophlilie

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution

Physicochemical and mineralogical characterization datasets from oil drill cuttings in comparison with other cement types for cement partial-replacement in concrete

This article presents data on the physical/chemical and mineralogical characterizations of treated oil drill cuttings (ODC) in comparisons with other cement types, for suitabil- ity insight for partial-replacement of cement in concrete. The physical properties were compared for cement/cement fillers including Portland Cement (PC), Pulverized Fuel Ash (PFA), and Ground Granulated Blast-furnace Slag (GGBS). The particle size distribution of the ODC and the other cement/cementitious materials were also rendered to the extreme-value probability density models, with the Normal distribution employed as a reference, while the goodness-of-fit data-distribution compatibility was ascertained using Kolmogorov-Smirnov test-statistics. Characterized properties indicated treated ODC physic- ochemical and mineralogical properties compared well to the ranges exhibited by the other cement types, and requisite standards. The presented comparative results from the mea- sured/analyzed physicochemical and mineralogical data are useful information for further- ing research on the suitability of ODC, wastes from oil and gas explorations, as partial- replacement of cement in concret

Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms

The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parva. Over a million bovines die each year of ECF, with a tremendous economic burden to pastoralists in endemic countries. Comprehensive, accurate parasite genome annotation can facilitate the discovery of novel chemotherapeutic targets for disease treatment, as well as elucidate the biology of the parasite. However, genome annotation remains a significant challenge because of limitations in the quality and quantity of the data being used to inform the location and function of protein-coding genes and, when RNA data are used, the underlying biological complexity of the processes involved in gene expression. Here, we apply our recently published RNAseq dataset derived from the schizont life-cycle stage of T. parva to update structural and functional gene annotations across the entire nuclear genome.; The re-annotation effort lead to evidence-supported updates in over half of all protein-coding sequence (CDS) predictions, including exon changes, gene merges and gene splitting, an increase in average CDS length of approximately 50 base pairs, and the identification of 128 new genes. Among the new genes identified were those involved in N-glycosylation, a process previously thought not to exist in this organism and a potentially new chemotherapeutic target pathway for treating ECF. Alternatively-spliced genes were identified, and antisense and multi-gene family transcription were extensively characterized.; The process of re-annotation led to novel insights into the organization and expression profiles of protein-coding sequences in this parasite, and uncovered a minimal N-glycosylation pathway that changes our current understanding of the evolution of this post-translational modification in apicomplexan parasites

Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

Theileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle- and buffalo-associated T. parva populations. Here, we describe a capture-based target enrichment approach that enables, for the first time, de novo assembly of nearly complete T. parva genomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle- and buffalo-derived T. parva parasites. De novo genome assemblies generated for cattle genotypes differ from the reference by ~54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derived T. parva genome, which is ~20 kb larger than the genome from the reference, cattle-derived, Muguga strain, and contains 25 new potential genes. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derived T. parva and the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an average Wright’s fixation index (FST), genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle- and buffalo-derived T. parva parasites more commonly seen between, rather than within, species. These findings present clear implications for vaccine development, further demonstrated by the ability to assemble nearly all known antigens in the buffalo-derived strain, which will be critical in design of next generation vaccines. The DNA capture approach used provides a clear advantage in specificity over alternative T. parva DNA enrichment methods used previously, such as those that utilize schizont purification, is less labor intensive, and enables in-depth comparative genomics in this apicomplexan parasite

Neonatal inpatient dataset for small and sick newborn care in low- and middle-income countries: systematic development and multi-country operationalisation with NEST360.

BACKGROUND: Every Newborn Action Plan (ENAP) coverage target 4 necessitates national scale-up of Level-2 Small and Sick Newborn Care (SSNC) (with Continuous Positive Airway Pressure (CPAP)) in 80% of districts by 2025. Routine neonatal inpatient data is important for improving quality of care, targeting equity gaps, and enabling data-driven decision-making at individual, district, and national-levels. Existing neonatal inpatient datasets vary in purpose, size, definitions, and collection processes. We describe the co-design and operationalisation of a core inpatient dataset for use to track outcomes and improve quality of care for small and sick newborns in high-mortality settings. METHODS: A three-step systematic framework was used to review, co-design, and operationalise this novel neonatal inpatient dataset in four countries (Malawi, Kenya, Tanzania, and Nigeria) implementing with the Newborn Essential Solutions and Technologies (NEST360) Alliance. Existing global and national datasets were identified, and variables were mapped according to categories. A priori considerations for variable inclusion were determined by clinicians and policymakers from the four African governments by facilitated group discussions. These included prioritising clinical care and newborn outcomes data, a parsimonious variable list, and electronic data entry. The tool was designed and refined by > 40 implementers and policymakers during a multi-stakeholder workshop and online interactions. RESULTS: Identified national and international datasets (n = 6) contained a median of 89 (IQR:61-154) variables, with many relating to research-specific initiatives. Maternal antenatal/intrapartum history was the largest variable category (21, 23.3%). The Neonatal Inpatient Dataset (NID) includes 60 core variables organised in six categories: (1) birth details/maternal history; (2) admission details/identifiers; (3) clinical complications/observations; (4) interventions/investigations; (5) discharge outcomes; and (6) diagnosis/cause-of-death. Categories were informed through the mapping process. The NID has been implemented at 69 neonatal units in four African countries and links to a facility-level quality improvement (QI) dashboard used in real-time by facility staff. CONCLUSION: The NEST360 NID is a novel, parsimonious tool for use in routine information systems to inform inpatient SSNC quality. Available on the NEST360/United Nations Children's Fund (UNICEF) Implementation Toolkit for SSNC, this adaptable tool enables facility and country-level comparisons to accelerate progress toward ENAP targets. Additional linked modules could include neonatal at-risk follow-up, retinopathy of prematurity, and Level-3 intensive care

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Strengthening retinopathy of prematurity screening and treatment services in Nigeria: a case study of activities, challenges and outcomes 2017-2020.

OBJECTIVES: Retinopathy of prematurity (ROP) will become a major cause of blindness in Nigerian children unless screening and treatment services expand. This article aims to describe the collaborative activities undertaken to improve services for ROP between 2017 and 2020 as well as the outcome of these activities in Nigeria. DESIGN: Descriptive case study. SETTING: Neonatal intensive care units in Nigeria. PARTICIPANTS: Staff providing services for ROP, and 723 preterm infants screened for ROP who fulfilled screening criteria (gestational age <34 weeks or birth weight ≤2000 g, or sickness criteria). METHODS AND ANALYSIS: A WhatsApp group was initiated for Nigerian ophthalmologists and neonatologists in 2018. Members participated in a range of capacity-building, national and international collaborative activities between 2017 and 2018. A national protocol for ROP was developed for Nigeria and adopted in 2018; 1 year screening outcome data were collected and analysed. In 2019, an esurvey was used to collect service data from WhatsApp group members for 2017-2018 and to assess challenges in service provision. RESULTS: In 2017 only six of the 84 public neonatal units in Nigeria provided ROP services; this number had increased to 20 by 2018. Of the 723 babies screened in 10 units over a year, 127 (17.6%) developed any ROP; and 29 (22.8%) developed type 1 ROP. Only 13 (44.8%) babies were treated, most by intravitreal bevacizumab. The screening criteria were revised in 2020. Challenges included lack of equipment to regulate oxygen and to document and treat ROP, and lack of data systems. CONCLUSION: ROP screening coverage and quality improved after national and international collaborative efforts. To scale up and improve services, equipment for neonatal care and ROP treatment is urgently needed, as well as systems to monitor data. Ongoing advocacy is also essential