MIMAS 3.0 is a Multiomics Information Management and Annotation System.

BACKGROUND: DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. DESCRIPTION: MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. CONCLUSION: We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.

El camino hacia la integración de sistemas de gestión de la información científica : el TCD (Trinity College Dublin) como estudio de caso. CERIF y euroCRIS

Pablo de Castro, Director de GrandIR, describió la visión que el Grupo euroCRIS tiene de la infraestructura integrada de gestión de la información científica, compuesta por un sistema CRIS institucional, un repositorio de publicaciones y un repositorio de datos y software, y presentó el modelo de infraestructura integrada del Trinity College Dublin (TCD) como estudio de caso internacional. El sistema CRIS del TCD (TCD Research Support System o RSS), desde su primera versión en 2002, está basado en el estándar CERIF, un modelo de descripción de la actividad científica que está adquiriendo una progresiva relevancia como base de los sistemas CRIS en Europa, particularmente en el Reino Unido. Se citaron en la presentación los ensayos para incorporar CERIF al modelo de datos del software ePrints de repositorios, habilitándolo así para soportar parte de las tareas de recolección de información que realiza un CRIS, y la progresiva cobertura de CERIF a ámbitos tales como la gestión de datos de investigación.

What’s in it for me? Incentivizing the use of institutional repositories

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Factores de riesgo del comportamiento y readiness de aficionados inscritos a carreras atléticas de fondo de 18-64 años en Bogotá D.C., 2014”

La participación en carreras atléticas de calle ha aumentado; esto requiere detectar riesgos previos al esfuerzo físico. Objetivo. Identificar factores de riesgo del comportamiento y readiness de inscritos a una carrera. Método. Estudio transversal en aficionados de 18-64 años. Encuesta digital con módulos de IPAQ, PARQ+ y STEP. Muestreo aleatorio sistemático con n=510, para una inactividad física esperada de 35% (±5%). Se evaluó nivel de actividad física, consumo de alcohol (peligroso), de fruta, verdura, tabaco y sal, y readiness. Resultados. El cumplimiento de actividad física fue 97,4%; 2,4% consume nivel óptimo de fruta o verdura (diferencias por edad, sexo y estrato), 3,7% fuma y 44,1% consumo peligroso de alcohol. El 19,8% reportó PARQ+ positivo y 5,7% requiere supervisión. Hay diferencias por trabajo y estudio. Discusión. Los aficionados cumplen el nivel de actividad física; pero no de otros factores. Una estrategia de seguridad en el atletismo de calle es evaluar los factores de riesgo relacionados con el estilo de vida así como el readiness.

Fetal testosterone influences sexually dimorphic gray matter in the human brain

In nonhuman species, testosterone is known to have permanent organizing effects early in life that predict later expression of sex differences in brain and behavior. However, in humans, it is still unknown whether such mechanisms have organizing effects on neural sexual dimorphism. In human males, we show that variation in fetal testosterone (FT) predicts later local gray matter volume of specific brain regions in a direction that is congruent with sexual dimorphism observed in a large independent sample of age-matched males and females from the NIH Pediatric MRI Data Repository. Right temporoparietal junction/posterior superior temporal sulcus (RTPJ/pSTS), planum temporale/parietal operculum (PT/PO), and posterior lateral orbitofrontal cortex (plOFC) had local gray matter volume that was both sexually dimorphic and predicted in a congruent direction by FT. That is, gray matter volume in RTPJ/pSTS was greater for males compared to females and was positively predicted by FT. Conversely, gray matter volume in PT/PO and plOFC was greater in females compared to males and was negatively predicted by FT. Subregions of both amygdala and hypothalamus were also sexually dimorphic in the direction of Male > Female, but were not predicted by FT. However, FT positively predicted gray matter volume of a non-sexually dimorphic subregion of the amygdala. These results bridge a long-standing gap between human and nonhuman species by showing that FT acts as an organizing mechanism for the development of regional sexual dimorphism in the human brain.

TRY: a global database of plant traits

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

A reconstruction of atmospheric carbon dioxide and its stable carbon isotopic composition from the penultimate glacial maximum to the last glacial inception

The reconstruction of the stable carbon isotope evolution in atmospheric CO2 (δ13Catm), as archived in Antarctic ice cores, bears the potential to disentangle the contributions of the different carbon cycle fluxes causing past CO2 variations. Here we present a new record of δ13Catm before, during and after the Marine Isotope Stage 5.5 (155 000 to 105 000 yr BP). The dataset is archived on the data repository PANGEA® (www.pangea.de) under 10.1594/PANGAEA.817041. The record was derived with a well established sublimation method using ice from the EPICA Dome C (EDC) and the Talos Dome ice cores in East Antarctica. We find a 0.4‰ shift to heavier values between the mean δ13Catm level in the Penultimate (~ 140 000 yr BP) and Last Glacial Maximum (~ 22 000 yr BP), which can be explained by either (i) changes in the isotopic composition or (ii) intensity of the carbon input fluxes to the combined ocean/atmosphere carbon reservoir or (iii) by long-term peat buildup. Our isotopic data suggest that the carbon cycle evolution along Termination II and the subsequent interglacial was controlled by essentially the same processes as during the last 24 000 yr, but with different phasing and magnitudes. Furthermore, a 5000 yr lag in the CO2 decline relative to EDC temperatures is confirmed during the glacial inception at the end of MIS5.5 (120 000 yr BP). Based on our isotopic data this lag can be explained by terrestrial carbon release and carbonate compensation.

UNDERSTANDING NURSE CREATED COGNITIVE ARTIFACTS: PERSONALLY-CREATED-COGNITIVE-ARTIFACTS AS EXTERNAL REPRESENTATIONS OF DISTRIBUTED COGNITION

Manuscript 1: “Conceptual Analysis: Externalizing Nursing Knowledge” We use concept analysis to establish that the report tool nurses prepare, carry, reference, amend, and use as a temporary data repository are examples of cognitive artifacts. This tool, integrally woven throughout the work and practice of nurses, is important to cognition and clinical decision-making. Establishing the tool as a cognitive artifact will support new dimensions of study. Such studies can characterize how this report tool supports cognition, internal representation of knowledge and skills, and external representation of knowledge of the nurse. Manuscript 2: “Research Methods: Exploring Cognitive Work” The purpose of this paper is to describe a complex, cross-sectional, multi-method approach to study of personal cognitive artifacts in the clinical environment. The complex data arrays present in these cognitive artifacts warrant the use of multiple methods of data collection. Use of a less robust research design may result in an incomplete understanding of the meaning, value, content, and relationships between personal cognitive artifacts in the clinical environment and the cognitive work of the user. Manuscript 3: “Making the Cognitive Work of Registered Nurses Visible” Purpose: Knowledge representations and structures are created and used by registered nurses to guide patient care. Understanding is limited regarding how these knowledge representations, or cognitive artifacts, contribute to working memory, prioritization, organization, cognition, and decision-making. The purpose of this study was to identify and characterize the role a specific cognitive artifact knowledge representation and structure as it contributed to the cognitive work of the registered nurse. Methods: Data collection was completed, using qualitative research methods, by shadowing and interviewing 25 registered nurses. Data analysis employed triangulation and iterative analytic processes. Results: Nurse cognitive artifacts support recall, data evaluation, decision-making, organization, and prioritization. These cognitive artifacts demonstrated spatial, longitudinal, chronologic, visual, and personal cues to support the cognitive work of nurses. Conclusions: Nurse cognitive artifacts are an important adjunct to the cognitive work of nurses, and directly support patient care. Nurses need to be able to configure their cognitive artifact in ways that are meaningful and support their internal knowledge representations.

Oxygen isotope composition of benthic and planktonic foraminifera from ODP Holes 146-893A and 167-1017B

The detailed structure and timing of the penultimate deglaciation are insufficiently defined yet critical for understanding mechanisms responsible for abrupt climate change. Here we present oxygen isotope records (from planktonic and benthic foraminifera) at unprecedented resolution encompassing late marine oxygen isotope stage (MIS) 6 and Termination II (ca. 150-120 ka) from the Santa Barbara Basin, supported by additional southern California margin records, a region highly sensitive to millennial-scale climate oscillations during the last deglaciation. These records reveal millennial- and centennial-scale climate variability throughout the interval, including an interstadial immediately preceding the deglaciation, a brief warm event near the beginning of Termination II, and a Bølling-Allerød-Younger Dryas-like climate oscillation midway through the deglaciation. Recognition of these events in an oxygen isotope record from a 230Th-dated stalagmite allows the adoption of this radiometric chronology for the California margin records. This chronology supports the Milankovitch theory of deglaciation. The suborbital history of climate variability during Termination II may account for records of early deglaciation.

Occurrence of hiatuses PH and NH 1 through NH 7 in DSDP holes

Miocene paleoceanographic evolution exhibits major changes resulting from the opening and closing of passages, the subsequent changes in oceanic circulation, and development of major Antarctic glaciation. The consequences and timing of these events can be observed in variations in the distribution of deep-sea hiatuses, sedimentation patterns, and biogeographic distribution of planktic organisms. The opening of the Drake Passage in the latest Oligocene to early Miocene (25-20 Ma) resulted in the establishment of the deep circumpolar current, which led to thermal isolation of Antarctica and increased global cooling. This development was associated with a major turnover in planktic organisms, resulting in the evolution of Neogene assemblages and the eventual extinction of Paleogene assemblages. The erosive patterns of two widespread hiatuses (PH, 23.0-22.5 Ma; and NH 1, 20-18 Ma) indicate that a deep circumequatorial circulation existed at this time, characterized by a broad band of carbonate-ooze deposition. Siliceous sedimentation was restricted to the North Atlantic and a narrow band around Antarctica. A major reorganization in deep-sea sedimentation and hiatus distribution patterns occurred near the early/middle Miocene boundary, apparently resulting from changes in oceanic circulation. Beginning at this time, deep-sea erosion occurred throughout the Caribbean (hiatus NH 2, 16-15 Ma), suggesting disruption of the deep circumequatorial circulation and northward deflection of deep currents, and/or intensification of the Gulf Stream. Sediment distribution patterns changed dramatically with the sudden appearance of siliceous-ooze deposition in the marginal and east equatorial North Pacific by 16.0 to 15.5 Ma, coincident with the decline of siliceous sedimentation in the North Atlantic. This silica switch may have been caused by the introduction of Norwegian Overflow Water into the North Atlantic acting as a barrier to outcropping of silica-rich Antarctic Bottom Water. The main aspects of the present oceanic circulation system and sediment distribution pattern were established by 13.5 to 12.5 Ma (hiatus NH 3), coincident with the establishment of a major East Antarctic ice cap. Antarctic glaciation resulted in a broadening belt of siliceous-ooze deposition around Antarctica, increased siliceous sedimentation in the marginal and east equatorial North Pacific and Indian Oceans, and further northward restriction of siliceous sediments in the North Atlantic. Periodic cool climatic events were accompanied by lower eustatic sea levels and widespread deep-sea erosion at 12 to 11 Ma (NH 4), 10 to 9 Ma (NH 5), 7.5 to 6.2 Ma (NH 6), and 5.2 to 4.7 Ma (NH 7).

(Table 1) Age model for ODP Site 175-1077 based on oxygen isotopes of Globigerinoides ruber pink

Palynological records from the Congo fan reveal environmental change in equatorial Africa occurring 1.05 Ma ago, 100 k.y. before the mid-Pleistocene climatic shift at 0.9 Ma. Prior to 1.05 Ma, a glacial-interglacial rhythm is not obvious in the African vegetation variation. Afterwards, Podocarpus spread in the mountains of central Africa mainly during glacials and Congo River discharge decreased. The sequence of vegetation variation associated with the mid-Pleistocene glacials and interglacials differed from that observed during the late Pleistocene. Between 0.9 and 0.6 Ma, interglacials were characterized by warm dry conditions and glacials were characterized by cool humid conditions, while during the past 0.2 Ma glacials were cold and dry and interglacials warm and humid. Our data indicate that before the Northern Hemisphere ice caps dramatically increased in size (0.9-0.6 Ma), low-latitude climate forcing and response in the tropics played an important role in the initiation of 100 k.y. ice-age cycles. During the mid to late Pleistocene, however, the climate conditions in the tropics were increasingly influenced by the glacial-interglacial variations of continental ice sheets.

Physical properties, pore water geochemistry, 210Pb-dating of sediment cores GeoB16426-1, GeoB16427-1, GeoB16429-1

We present differential bathymetry and sediment core data from the Japan Trench, sampled after the 2011 Tohoku-Oki (offshore Japan) earthquake to document that prominent bathymetric and structural changes along the trench axis relate to a large (~27.7 km**2) slump in the trench. Transient geochemical signals in the slump deposit and analysis of diffusive re-equilibration of disturbed SO4**2- profiles over time constrain the triggering of the slump to the 2011 earthquake. We propose a causal link between earthquake slip to the trench and rotational slumping above a subducting horst structure. We conclude that the earthquake-triggered slump is a leading agent for accretion of trench sediments into the forearc and hypothesize that forward growth of the prism and seaward advance of the deformation front by more than 2 km can occur, episodically, during a single-event, large mega-thrust earthquake.