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.

A polymorphism in the dysbindin gene (DTNBP1) associated with multiple psychiatric disorders including schizophrenia

Background A number of studies have found associations between dysbindin (DTNBP1) polymorphisms and schizophrenia. Recently we identified a DTNBP1 SNP (rs9370822) that is strongly associated with schizophrenia. Individuals diagnosed with schizophrenia were nearly three times as likely to carry the CC genotype compared to the AA genotype. Methods To investigate the importance of this SNP in the function of DTNBP1, a number of psychiatric conditions including addictive behaviours and anxiety disorders were analysed for association with rs9370822. Results The DTNBP1 polymorphism was significantly associated with post-traumatic stress disorder (PTSD) as well as nicotine and opiate dependence but not alcohol dependence. Individuals suffering PTSD were more than three times as likely to carry the CC genotype compared to the AA genotype. Individuals with nicotine or opiate dependence were more than twice as likely to carry the CC genotype compared to the AA genotype. Conclusions This study provides further support for the importance of DTNBP1 in psychiatric conditions and suggests that there is a common underlying molecular defect involving DTNBP1 that contributes to the development of several anxiety and addictive disorders that are generally recognised as separate clinical conditions. These disorders may actually be different expressions of a single metabolic pathway perturbation. As our participant numbers are limited our observations should be viewed with caution until they are independently replicated.

The severity of chorioamnionitis in pregnant sheep is associated with in vivo variation of the surface-exposed multiple-banded antigen/gene of ureaplasma parvum

Ureaplasma species are the bacteria most frequently isolated from human amniotic fluid in asymptomatic pregnancies and placental infections. Ureaplasma parvum serovars 3 and 6 are the most prevalent serovars isolated from men and women. We hypothesized that the effects on the fetus and chorioamnion of chronic ureaplasma infection in amniotic fluid are dependent on the serovar, dose, and variation of the ureaplasma multiple banded antigen (MBA) and mba gene. We injected high- or low dose U. parvum serovar 3, serovar 6, or vehicle intra-amniotically into pregnant ewes at 55 days of gestation (term = 150 days) and examined the chorioamnion, amniotic fluid, and fetal lung tissue of animals delivered by cesarean section at 125 days of gestation. Variation of the multiple banded antigen/mba generated by serovar 3 and serovar 6 ureaplasmas in vivo were compared by PCR assay and Western blot. Ureaplasma inoculums demonstrated only one (serovar 3) or two (serovar 6) MBA variants in vitro, but numerous antigenic variants were generated in vivo: serovar 6 passage 1 amniotic fluid cultures contained more MBA size variants than serovar 3 (P = 0.005),and ureaplasma titers were inversely related to the number of variants (P = 0.025). The severity of chorioamnionitis varied between animals. Low numbers of mba size variants (five or fewer) within amniotic fluid were associated with severe inflammation, whereas the chorioamnion from animals with nine or more mba variants showed little or no inflammation. These differences in chorioamnion inflammation may explain why not all women with in utero Ureaplasma spp. experience adverse pregnancy outcomes.

Maternal administration of erythromycin fails to eradicate intrauterine ureaplasma infection in an ovine model

Erythromycin is the standard antibiotic used for treatment of Ureaplasma species during 3 pregnancy; however, maternally administered erythromycin may be ineffective at eliminating 4 intra-amniotic ureaplasma infections. We asked if erythromycin would eradicate intra-amniotic 5 ureaplasma infections in pregnant sheep. At 50 days of gestation (d, term=150d) pregnant ewes 6 received intra-amniotic injections of erythromycin-sensitive U. parvum serovar 3 (n=16) or 10B 7 medium (n=16). At 100d, amniocentesis was performed; five fetal losses (ureaplasma group: 8 n=4; 10B group: n=1) had occurred by this time. Remaining ewes were allocated into treatment 9 subgroups: medium only (M, n=7); medium and erythromycin (M/E, n=8); ureaplasma only (Up, 10 n=6) or ureaplasma and erythromycin (Up/E, n=6). Erythromycin was administered intra11 muscularly (500 mg), eight-hourly for four days (100d-104d). Amniotic fluid samples were 12 collected at 105d. At 125d preterm fetuses were surgically delivered and specimens were 13 collected for culture and histology. Erythromycin was quantified in amniotic fluid by liquid 14 chromatography-mass spectrometry. Ureaplasmas were isolated from the amniotic fluid, 15 chorioamnion and fetal lung of animals from the Up and Up/E groups, however, the numbers of 16 U. parvum recovered were not different between these groups. Inflammation in the 17 chorioamnion, cord and fetal lung was increased in ureaplasma-exposed animals compared to 18 controls, but was not different between the Up and Up/E groups. Erythromycin was detected in 19 amniotic fluid samples, although concentrations were low (<10-76 ng/mL). This study 20 demonstrates that maternally administered erythromycin does not eradicate chronic, intra- amniotic ureaplasma infections or improve fetal outcomes in an ovine model, potentially due to 22 the poor placental passage of erythromycin.

Modeling circulation of train-set with multiple routing

Planning on utilization of train-set is one of the key tasks of transport organization for passenger dedicated railway in China. It also has strong relationships with timetable scheduling and operation plans at a station. To execute such a task in a railway hub pooling multiple railway lines, the characteristics of multiple routing for train-set is discussed in term of semicircle of train-sets' turnover. In programming the described problem, the minimum dwell time is selected as the objectives with special derive constraints of the train-set's dispatch, the connecting conditions, the principle of uniqueness for train-sets, and the first plus for connection in the same direction based on time tolerance σ. A compact connection algorithm based on time tolerance is then designed. The feasibility of the model and the algorithm is proved by the case study. The result indicates that the circulation model and algorithm about multiple routing can deal with the connections between the train-sets of multiple directions, and reduce the train's pulling in or leaving impact on the station's throat.

Ecological aspects of biosecurity surveillance design for the detection of multiple invasive animal species

Complex surveillance problems are common in biosecurity, such as prioritizing detection among multiple invasive species, specifying risk over a heterogeneous landscape, combining multiple sources of surveillance data, designing for specified power to detect, resource management, and collateral effects on the environment. Moreover, when designing for multiple target species, inherent biological differences among species result in different ecological models underpinning the individual surveillance systems for each. Species are likely to have different habitat requirements, different introduction mechanisms and locations, require different methods of detection, have different levels of detectability, and vary in rates of movement and spread. Often there is a further challenge of a lack of knowledge, literature, or data, for any number of the above problems. Even so, governments and industry need to proceed with surveillance programs which aim to detect incursions in order to meet environmental, social and political requirements. We present an approach taken to meet these challenges in one comprehensive and statistically powerful surveillance design for non-indigenous terrestrial vertebrates on Barrow Island, a high conservation nature reserve off the Western Australian coast. Here, the possibility of incursions is increased due to construction and expanding industry on the island. The design, which includes mammals, amphibians and reptiles, provides a complete surveillance program for most potential terrestrial vertebrate invaders. Individual surveillance systems were developed for various potential invaders, and then integrated into an overall surveillance system which meets the above challenges using a statistical model and expert elicitation. We discuss the ecological basis for the design, the flexibility of the surveillance scheme, how it meets the above challenges, design limitations, and how it can be updated as data are collected as a basis for adaptive management.

Observational assessment and maternal reports of motivation in children and adolescents with Down Syndrome

Despite a lack of consistent empirical evidence, there has been an ongoing assumption that intellectual disability is associated with reduced levels of motivation. The participants in this study were 33 children with Down syndrome ages 10–15 years and 33 typically developing 3–8-year-old children. Motivation was measured through observational assessments of curiosity, preference for challenge, and persistence, as well as maternal reports. There were no significant group differences on motivation tasks, but mothers of children with Down syndrome rated their children significantly lower on motivation than did parents of typically developing children. There were some intriguing group differences in the pattern of correlations among observations and parent reports. The findings challenge long-held views that individuals with intellectual disability are invariably deficient in motivation.

Maternal exposure to ambient temperature and the risk of preterm birth and stillbirth in Brisbane, Australia

Almost 10% of all births are preterm and 2.2% are stillbirths globally. Recent research has suggested that environmental factors may be a contributory cause to these adverse birth outcomes. The authors examined the relationship between ambient temperature and preterm birth and stillbirth in Brisbane, Australia between 2005 and 2009 (n = 101,870). They used a Cox proportional hazard model with live birth and stillbirth as competing risks. They also examined if there were periods of the pregnancy where exposure to high temperatures had a greater effect. Exposure to higher ambient temperatures during pregnancy increased the risk of stillbirth. The hazard ratio for stillbirth was 0.3 at 12 °C relative to the reference temperature at 21 °C. The temperature effect was greatest for fetuses of less than 36 weeks of gestation. There was an association between higher temperature and shorter gestation, as the hazard ratio for live birth was 0.96 at 15 °C and 1.02 at 25 °C. This effect was greatest at later gestational ages. The results provide strong evidence of an association between increased temperature and increased risk of stillbirth and shorter gestations.

Sustainable assessment for large science classes : non-multiple choice, randomised assignments through a Learning Management System

This paper reports on the development of a tool that generates randomised, non-multiple choice assessment within the BlackBoard Learning Management System interface. An accepted weakness of multiple-choice assessment is that it cannot elicit learning outcomes from upper levels of Biggs’ SOLO taxonomy. However, written assessment items require extensive resources for marking, and are susceptible to copying as well as marking inconsistencies for large classes. This project developed an assessment tool which is valid, reliable and sustainable and that addresses the issues identified above. The tool provides each student with an assignment assessing the same learning outcomes, but containing different questions, with responses in the form of words or numbers. Practice questions are available, enabling students to obtain feedback on their approach before submitting their assignment. Thus, the tool incorporates automatic marking (essential for large classes), randomised tasks to each student (reducing copying), the capacity to give credit for working (feedback on the application of theory), and the capacity to target higher order learning outcomes by requiring students to derive their answers rather than choosing them. Results and feedback from students are presented, along with technical implementation details.

Multiple evolutionary rate classes in animal genome evolution

The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend on the difference between the distribution of genomewide evolutionary rates and that observed in a subset of sequences presumed to be neutrally evolving. Motivated by the widening gap between these estimates and experimental evidence of genome function, especially in mammals, we developed a sensitive technique for evaluating such distributions and found that they are much more complex than previously apparent. We found strong evidence for at least nine well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least seven classes in an alignment of four mammals, including human. We also identified at least three rate classes in human ancestral repeats. By positing that the largest of these ancestral repeat classes is neutrally evolving, we estimate that the proportion of nonneutrally evolving sequence is 30% of human ancestral repeats and 45% of the aligned portion of the genome. However, we also question whether any of the classes represent neutrally evolving sequences and argue that a plausible alternative is that they reflect variable structure-function constraints operating throughout the genomes of complex organisms.

Preferences of first-time expectant mothers for care of their child : 'I wouldn't leave them somewhere that made me feel insecure'

Australia has witnessed a continual increase in maternal employment over the past two decades, which places focus on both supply of childcare and a demand for high quality care. This study examined childcare preferences regarding the return to paid work of 124 Australian women who were expecting their first child. In contrast with most studies that have retrospective designs, the design of this study presents the perspectives of women prior to the birth of their first child-that is, before they have made a final decision about child care. This study found that the majority (78 per cent) of the women intended to re-commence work within the 12 months after the birth of their child. There were two factors that were the most salient features in their decision making-the quality of care and the personal satisfaction of engaging in paid work. The findings suggest that family friendly employment practices and access to secure, high-quality child care are key to women's secure participation in the paid workforce.