MouseMine: a new data warehouse for MGI.

MouseMine (www.mousemine.org) is a new data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Based on the InterMine software framework, MouseMine supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. Through MouseMine, users can access a significant portion of MGI data in new and useful ways. Importantly, MouseMine is also a member of a growing community of online data resources based on InterMine, including those established by other model organism databases. Adopting common interfaces and collaborating on data representation standards are critical to fostering cross-species data analysis. This paper presents a general introduction to MouseMine, presents examples of its use, and discusses the potential for further integration into the MGI interface.

A unified gene catalog for the laboratory mouse reference genome.

We report here a semi-automated process by which mouse genome feature predictions and curated annotations (i.e., genes, pseudogenes, functional RNAs, etc.) from Ensembl, NCBI and Vertebrate Genome Annotation database (Vega) are reconciled with the genome features in the Mouse Genome Informatics (MGI) database (http://www.informatics.jax.org) into a comprehensive and non-redundant catalog. Our gene unification method employs an algorithm (fjoin--feature join) for efficient detection of genome coordinate overlaps among features represented in two annotation data sets. Following the analysis with fjoin, genome features are binned into six possible categories (1:1, 1:0, 0:1, 1:n, n:1, n:m) based on coordinate overlaps. These categories are subsequently prioritized for assessment of annotation equivalencies and differences. The version of the unified catalog reported here contains more than 59,000 entries, including 22,599 protein-coding coding genes, 12,455 pseudogenes, and 24,007 other feature types (e.g., microRNAs, lincRNAs, etc.). More than 23,000 of the entries in the MGI gene catalog have equivalent gene models in the annotation files obtained from NCBI, Vega, and Ensembl. 12,719 of the features are unique to NCBI relative to Ensembl/Vega; 11,957 are unique to Ensembl/Vega relative to NCBI, and 3095 are unique to MGI. More than 4000 genome features fall into categories that require manual inspection to resolve structural differences in the gene models from different annotation sources. Using the MGI unified gene catalog, researchers can easily generate a comprehensive report of mouse genome features from a single source and compare the details of gene and transcript structure using MGI's mouse genome browser.

The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data.

The Mouse Tumor Biology Database (MTB) is designed to provide an electronic data storage, search, and analysis system for information on mouse models of human cancer. The MTB includes data on tumor frequency and latency, strain, germ line, and somatic genetics, pathologic notations, and photomicrographs. The MTB collects data from the primary literature, other public databases, and direct submissions from the scientific community. The MTB is a community resource that provides integrated access to mouse tumor data from different scientific research areas and facilitates integration of molecular, genetic, and pathologic data. Current status of MTB, search capabilities, data types, and future enhancements are described in this article.

A non-coding plastid DNA phylogeny of Asian Begonia (Begoniaceae): evidence for morphological homoplasy and sectional polyphyly.

Maximum likelihood and Bayesian analyses of non-coding plastid DNA sequence data based on a broad sampling of all major Asian Begonia sections (ndhA intron, ndhF-rpl32 spacer, rpl32-trnL spacer, 3977 aligned characters, 84 species) were used to reconstruct the phylogeny of Asian Begonia and to test the monophyly of major Asian Begonia sections. Ovary and fruit characters which are crucial in current sectional circumscriptions were mapped on the phylogeny to assess their utility in infrageneric classifications. The results indicate that the strong systematic emphasis placed on single, homoplasious characters such as undivided placenta lamellae (section Reichenheimia) and fleshy pericarps (section Sphenanthera), and the recognition of sections primarily based on a suite of plesiomorphic characters including three-locular ovaries with axillary, bilamellate placentae and dry, dehiscent pericarps (section Diploclinium), has resulted in the circumscription of several polyphyletic sections. Moreover, sections Platycentrum and Petermannia were recovered as paraphyletic. Because of the homoplasy of systematically important characters, current classifications have a certain diagnostic, but only poor predictive value. The presented phylogeny provides for the first time a reasonably resolved and supported phylogenetic framework for Asian Begonia which has the power to inform future taxonomic, biogeographic and evolutionary studies.

Rapid diversification of a species-rich genus of neotropical rain forest trees.

Species richness in the tropics has been attributed to the gradual accumulation of species over a long geological period in stable equatorial climates or, conversely, to speciation in response to late Tertiary geological events and unstable Pleistocene climates. DNA sequence data are consistent with recent diversification in Inga, a species-rich neotropical tree genus. We estimate that speciation was concentrated in the past 10 million years, with many species arising as recently as 2 million years ago. This coincides with the more recent major uplifts of the Andes, the bridging of the Isthmus of Panama, and Quaternary glacial cycles. Inga may be representative of other species-rich neotropical genera with rapid growth and reproduction, which contribute substantially to species numbers in the world's most diverse flora.

Hemispheric Differences in Leukoaraiosis in Patients with Carotid Artery Stenosis: A Systematic Review.

PURPOSE: Despite the prevalence of leukoaraiosis in neuroimaging and its link to dementia, stroke, and death, the exact pathogenesis is still unclear. While some have postulated a link between carotid artery disease and leukoaraiosis, the exact relationship between the two common clinical findings is unknown. To determine the link between carotid disease and leukoaraiosis, we performed a systematic review of interhemispheric differences in white matter disease in patients with carotid artery disease. METHODS: We performed a comprehensive literature search in multiple electronic databases evaluating the association of carotid artery and white matter disease using both subjective and volumetric assessment of white matter burden. The included studies examined patients with at least 30 % carotid artery stenosis for white matter burden both ipsilateral and contralateral to the site of carotid artery disease. RESULTS: Of the 2920 manuscripts screened, five were included in the systematic review. One study used a volumetric analysis of the white matter burden and the others used various subjective methods. Four studies found no statistically significant relationship between carotid artery disease and ipsilateral white matter burden and one study found a significantly higher amount of white matter disease ipsilateral to carotid artery stenosis. CONCLUSIONS: The mixed results in degree of hemispheric leukoaraiosis in patients with carotid artery disease indicate that no definite relationship can be established based on the existing literature. Given the complex nature of carotid artery disease, including increased risk with certain plaque components, the exact relationship requires further investigation with more rigorous research design.

The Mouse Genome Database (MGD): integration nexus for the laboratory mouse.

The Mouse Genome Database (MGD) is the community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology and disease (http://www.informatics.jax.org). MGD provides standard nomenclature and consensus map positions for mouse genes and genetic markers; it provides a curated set of mammalian homology records, user-defined chromosomal maps, experimental data sets and the definitive mouse 'gene to sequence' reference set for the research community. The integration and standardization of these data sets facilitates the transition between mouse DNA sequence, gene and phenotype annotations. A recent focus on allele and phenotype representations enhances the ability of MGD to organize and present data for exploring the relationship between genotype and phenotype. This link between the genome and the biology of the mouse is especially important as phenotype information grows from large mutagenesis projects and genotype information grows from large-scale sequencing projects.

The Mouse Gene Expression Database (GXD).

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD's utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu. shtml.

Physiological responses of firefighters wearing level 3 chemical protective suits while working in controlled hot environments.

Firefighters in Queensland are exposed to hot, humid weather conditions that contribute to the overall workload encountered during emergency operations. Responding to certain hazardous material incidents requires firefighters to wear fully encapsulated chemical protective suits for a maximum period of 20 minutes. The nature of these suits, combined with workload and environmental conditions, poses a potential heat stress problem for firefighters. This study evaluates the heat-induced physiological responses of firefighters while wearing fully encapsulated chemical protective suits in a series of controlled thermal environments. Heart rate, body (aural) temperature, blood pressure, fluid loss, and a rating of perceived exertion were measured to evaluate the effect of increasing ambient air temperature during the performance of standard tasks. The results of the study indicated that the significant increase in heart rate, body temperature, and blood pressure was directly related to the increase in air temperature. The research indicates that the recommended suit wearing time of 20 minutes provided adequate physiological protection under the research conditions.

Traumatic wound of the heart: value of intraoperative colour Doppler flow imaging.

A patient who sustained a traumatic ventricular septal defect from a stab wound is presented. Intraoperative echo-Doppler imaging provided an additional diagnosis of avulsion of anterior papillary muscle of the tricuspid valve prior to cardiotomy. It was concluded that intraoperative echo-Doppler imaging proves a useful guide for cardiac surgery following penetrating trauma.

The incidence of childhood diabetes in certain parts of Scotland.

The incidence of diabetes in children under 12 years of age has been studied in three regions of Scotland from 1976 to 1986. These areas represent more than half of the Scottish population of that age group. The overall annual incidence is 17.6 per 100,000, ranging from 16.8 in densely populated areas to 23.4 in more rural areas. Earlier studies have concerned the age group 0-18 years so the present results from a younger age group are, as expected, slightly lower but show the same trends. After a rise to 1983 there appears to have been a drop, but not in all areas. The danger of drawing conclusions from areas of low population or from short periods of time is stressed.

A case report in health information exchange for inter-organizational patient transfers.

OBJECTIVE: To provide a case report of barriers and promoters to implementing a health information exchange (HIE) tool that supports patient transfers between hospitals and skilled nursing facilities. METHODS: A multi-disciplinary team conducted semi-structured telephone and in-person interviews in a purposive sample of HIE organizational informants and providers in New York City who implemented HIE to share patient transfer information. The researchers conducted grounded theory analysis to identify themes of barriers and promoters and took steps to improve the trustworthiness of the results including vetting from a knowledgeable study participant. RESULTS: Between May and October 2011, researchers recruited 18 participants: informaticians, healthcare administrators, software engineers, and providers from a skilled nursing facility. Subjects perceived the HIE tool's development a success in that it brought together stakeholders who had traditionally not partnered for informatics work, and that they could successfully share patient transfer information between a hospital and a skilled nursing facility. Perceived barriers included lack of hospital stakeholder buy-in and misalignment with clinical workflows that inhibited use of HIE-based patient transfer data. Participants described barriers and promoters in themes related to organizational, technical, and user-oriented issues. The investigation revealed that stakeholders could develop and implement health information technology that technically enables clinicians in both hospitals and skilled nursing facilities to exchange real-time information in support of patient transfers. User level barriers, particularly in the emergency department, should give pause to developers and implementers who plan to use HIE in support of patient transfers. CONCLUSIONS: Participants' experiences demonstrate how stakeholders may succeed in developing and piloting an electronic transfer form that relies on HIE to aggregate, communicate, and display relevant patient transfer data across health care organizations. Their experiences also provide insights for others seeking to develop HIE applications to improve patient transfers between emergency departments and skilled nursing facilities.

Evolution of syncarpy and other morphological characters in African Annonaceae: a posterior mapping approach.

The congenital fusion of carpels, or syncarpy, is considered a key innovation as it is found in more than 80% of angiosperms. Within the magnoliids however, syncarpy has rarely evolved. Two alternative evolutionary origins of syncarpy were suggested in order to explain the evolution of this feature: multiplication of a single carpel vs. fusion of a moderate number of carpels. The magnoliid family Annonaceae provides an ideal situation to test these hypotheses as two African genera, Isolona and Monodora, are syncarpous in an otherwise apocarpous family with multicarpellate and unicarpellate genera. In addition to syncarpy, the evolution of six other morphological characters was studied. Well-supported phylogenetic relationships of African Annonaceae and in particular those of Isolona and Monodora were reconstructed. Six plastid regions were sequenced and analyzed using maximum parsimony and Bayesian inference methods. The Bayesian posterior mapping approach to study character evolution was used as it accounts for both mapping and phylogenetic uncertainty, and also allows multiple state changes along the branches. Our phylogenetic analyses recovered a fully resolved clade comprising twelve genera endemic to Africa, including Isolona and Monodora, which was nested within the so-called long-branch clade. This is the largest and most species-rich clade of African genera identified to date within Annonaceae. The two syncarpous genera were inferred with maximum support to be sister to a clade characterized by genera with multicarpellate apocarpous gynoecia, supporting the hypothesis that syncarpy arose by fusion of a moderate number of carpels. This hypothesis was also favoured when studying the floral anatomy of both genera. Annonaceae provide the only case of a clear evolution of syncarpy within an otherwise apocarpous magnoliid family. The results presented here offer a better understanding of the evolution of syncarpy in Annonaceae and within angiosperms in general.

Do farmers reduce genetic diversity when they domesticate tropical trees? A case study from Amazonia.

Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high.