BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Multiple indicators of ambient and personal ultraviolet radiation exposure and risk of non-Hodgkin lymphoma (United States)

Recent epidemiologic studies have suggested that ultraviolet radiation (UV) may protect against non-Hodgkin lymphoma (NHL), but few, if any, have assessed multiple indicators of ambient and personal UV exposure. Using the US Radiologic Technologists study, we examined the association between NHL and self-reported time outdoors in summer, as well as average year-round and seasonal ambient exposures based on satellite estimates for different age periods, and sun susceptibility in participants who had responded to two questionnaires (1994–1998, 2003–2005) and who were cancer-free as of the earlier questionnaire. Using unconditional logistic regression, we estimated the odds ratio (OR) and 95% confidence intervals for 64,103 participants with 137 NHL cases. Self-reported time outdoors in summer was unrelated to risk. Lower risk was somewhat related to higher average year-round and winter ambient exposure for the period closest in time, and prior to, diagnosis (ages 20–39). Relative to 1.0 for the lowest quartile of average year-round ambient UV, the estimated OR for successively higher quartiles was 0.68 (0.42–1.10); 0.82 (0.52–1.29); and 0.64 (0.40–1.03), p-trend = 0.06), for this age period. The lower NHL risk associated with higher year-round average and winter ambient UV provides modest additional support for a protective relationship between UV and NHL.

Performance optimization for parallel processing on a multiple-CPU server

Symmetric multi-processor (SMP) systems, or multiple-CPU servers, are suitable for implementing parallel algorithms because they employ dedicated communication devices to enhance the inter-processor communication bandwidth, so that a better performance can be obtained. However, the cost for a multiple-CPU server is high and therefore, the server is usually shared among many users. The work-load due to other users will certainly affect the performance of the parallel programs so it is desirable to derive a method to optimize parallel programs under different loading conditions. In this paper, we present a simple method, which can be applied in SPMD type parallel programs, to improve the speedup by controlling the number of threads within the programs.

Multiple Health Behavior Changes and Co-variation in a Telephone Counseling Trial

Background Delivering effective multiple health behavior interventions to large numbers of adults with chronic conditions via primary care settings is a public health priority. Purpose Within a 12-month, telephone-delivered diet and physical activity intervention with multiple behavioral outcomes, we examined the extent and co-variation of multiple health behavior change. Methods A cluster-randomized trial with 434 patients with type 2 diabetes or hypertension were recruited from 10 general practices, which were randomized to receive telephone counseling or usual care. Results Those receiving telephone counseling were significantly more likely than those in usual care to make greater reductions in multiple behaviors after adjusting for baseline risk behaviors (OR 2.42; 95%CI 1.43, 4.11). Controlling for baseline risk and group allocation, making changes to either physical activity, fat, vegetable, or fiber intake was associated with making significantly more improvements in other behaviors. Conclusions For patients with chronic conditions, telephone counseling can significantly improve multiple health behaviors, with behavioral changes tending to co-vary.

Directional earth fault relay operation in mutually coupled multiple circuit distribution lines

Many of the power utilities around the world experienced spurious tripping of directional earth fault relays in their mesh distribution networks due to induced circulating currents. This circulating current is zero sequence and induced in the healthy circuit due to the zero sequence current flow resulting from a ground fault of a parallel circuit. This paper quantitatively discusses the effects of mutual coupling on earth fault protection of distribution systems. An actual spurious tripping event is analyzed to support the theory and to present options for improved resilience to spurious tripping.

Measuring export readiness using a multiple-item index

Since the 1970s the internationalisation process of firms has attracted wide research interest. One of the dominant explanations of firm internationalisation resulting from this research activity is the Uppsala stages model. In this paper, a pre-internationalisation phase is incorporated into the traditional Uppsala model to address the question: What are the antecedents of this model? Four concepts are proposed as the key components that define the experiential learning process underlying a firm’s pre-export phase: export stimuli, attitudinal/psychological commitment, resources and lateral rigidity. Through a survey of 290 Australian exporting and non-exporting small-medium sized firms, data relating to the four pre-internationalisation concepts is collected and an Export Readiness Index (ERI) is constructed through factor analysis. Using logistic regression, the ERI is tested as a tool for analysing export readiness among Australian SMEs.

Queensland Aborigines, multiple realities and the social sources of suffering. Part 2: Suicide, spirits and symbolism

This is the second part of a paper that explores a range of magico-religious experiences such as immaterial voices and visions, in terms of local cultural, moral and socio-political circumstances in an Aboriginal town in rural Queensland. This part of the paper explores the political and cultural symbolism and meaning of suicide. It charts the saliency of suicide amongst two groups of kin and cohorts and the social meaningfulness and problematic of the voices and visions in relation to suicide, to identity and family forms and to funerals and a heavily drinking lifestyle. I argue that voices and visions are used to reinterpret social experience and to establish meaning and that tragically suicide evokes connectivity rather than anomie and here cannot be understood merely as an individualistic act or evidence of individual pathology. Rather it is about transformation and crossing a threshold to join an enduring domain of Aboriginality. In this life world, where family is the highest social value and where a relational view of persons holds sway, the individualistic practice of psychiatric and other helping professions, is a considerable problem.

QoS-oriented resource allocation and scheduling of multiple composite Web services in a hybrid cloud using a random-key genetic algorithm

In cloud computing resource allocation and scheduling of multiple composite web services is an important challenge. This is especially so in a hybrid cloud where there may be some free resources available from private clouds but some fee-paying resources from public clouds. Meeting this challenge involves two classical computational problems. One is assigning resources to each of the tasks in the composite web service. The other is scheduling the allocated resources when each resource may be used by more than one task and may be needed at different points of time. In addition, we must consider Quality-of-Service issues, such as execution time and running costs. Existing approaches to resource allocation and scheduling in public clouds and grid computing are not applicable to this new problem. This paper presents a random-key genetic algorithm that solves new resource allocation and scheduling problem. Experimental results demonstrate the effectiveness and scalability of the algorithm.

Perturbation solutions for flow through symmetrical hoppers with inserts and asymmetrical wedge hoppers

Under certain circumstances, an industrial hopper which operates under the "funnel-flow" regime can be converted to the "mass-flow" regime with the addition of a flow-corrective insert. This paper is concerned with calculating granular flow patterns near the outlet of hoppers that incorporate a particular type of insert, the cone-in-cone insert. The flow is considered to be quasi-static, and governed by the Coulomb-Mohr yield condition together with the non-dilatant double-shearing theory. In two dimensions, the hoppers are wedge-shaped, and as such the formulation for the wedge-in-wedge hopper also includes the case of asymmetrical hoppers. A perturbation approach, valid for high angles of internal friction, is used for both two-dimensional and axially symmetric flows, with analytic results possible for both leading order and correction terms. This perturbation scheme is compared with numerical solutions to the governing equations, and is shown to work very well for angles of internal friction in excess of 45 degree.

Trajectory design and implementation for multiple autonomous underwater vehicles based on ocean model predictions

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The nature of caregiving in children of a parent with multiple sclerosis from multiple sources and the associations between caregiving activities and youth adjustment overtime

This study explored youth caregiving for a parent with multiple sclerosis (MS) from multiple perspectives, and examined associations between caregiving and child negative (behavioural emotional difficulties, somatisation) and positive (life satisfaction, positive affect, prosocial behaviour) adjustment outcomes overtime. A total of 88 families participated; 85 parents with MS, 55 partners and 130 children completed questionnaires at Time 1. Child caregiving was assessed by the Youth Activities of Caregiving Scale (YACS). Child and parent questionnaire data were collected at Time 1 and child data were collected 12 months later (Time 2). Factor analysis of the child and parent YACS data replicated the four factors (instrumental, social-emotional, personal-intimate, domestic-household care), all of which were psychometrically sound. The YACS factors were related to parental illness and caregiving context variables that reflected increased caregiving demands. The Time 1 instrumental and social-emotional care domains were associated with poorer Time 2 adjustment, whereas personal-intimate was related to better adjustment and domestic-household care was unrelated to adjustment. Children and their parents exhibited highest agreement on personal-intimate, instrumental and total caregiving, and least on domestic-household and social-emotional care. Findings delineate the key dimensions of young caregiving in MS and the differential links between caregiving activities and youth adjustment.

Decentralised particle filtering for multiple target tracking in wireless sensor networks

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Low frequency of CHEK2 1100delC allele in Australian multiple-case breast cancer families : functional analysis in heterozygous individuals

A protein-truncating variant of CHEK2, 1100delC, is associated with a moderate increase in breast cancer risk. We have determined the prevalence of this allele in index cases from 300 Australian multiple-case breast cancer families, 95% of which had been found to be negative for mutations in BRCA1 and BRCA2. Only two (0.6%) index cases heterozygous for the CHEK2 mutation were identified. All available relatives in these two families were genotyped, but there was no evidence of co-segregation between the CHEK2 variant and breast cancer. Lymphoblastoid cell lines established from a heterozygous carrier contained approximately 20% of the CHEK2 1100delC mRNA relative to wild-type CHEK2 transcript. However, no truncated CHK2 protein was detectable. Analyses of expression and phosphorylation of wild-type CHK2 suggest that the variant is likely to act by haploinsufficiency. Analysis of CDC25A degradation, a downstream target of CHK2, suggests that some compensation occurs to allow normal degradation of CDC25A. Such compensation of the 1100delC defect in CHEK2 might explain the rather low breast cancer risk associated with the CHEK2 variant, compared to that associated with truncating mutations in BRCA1 or BRCA2.

Multiple human single-stranded DNA binding proteins function in genome maintenance : structural, biochemical and functional analysis

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two singlestranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein–protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.

Model and prototype for querying multiple linked scientific datasets

Scientists need to transfer semantically similar queries across multiple heterogeneous linked datasets. These queries may require data from different locations and the results are not simple to combine due to differences between datasets. A query model was developed to make it simple to distribute queries across different datasets using RDF as the result format. The query model, based on the concept of publicly recognised namespaces for parts of each scientific dataset, was implemented with a configuration that includes a large number of current biological and chemical datasets. The configuration is flexible, providing the ability to transparently use both private and public datasets in any query. A prototype implementation of the model was used to resolve queries for the Bio2RDF website, including both Bio2RDF datasets and other datasets that do not follow the Bio2RDF URI conventions.