Data dictionary services in XNAT and the Human Connectome Project

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software.We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g. textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as RDF, JSON, and XML. It also facilitates the conversion of XNAT’s native data schema into standard neuroimaging ontology structures and provenances.<br/

Metabolic diversity of aromatic hydrocarbon-degrading bacteria from a petroleum-contaminated aquifer

We characterized bacteria from contaminated aquifers for their ability to utilize aromatic hydrocarbons under hypoxic (oxygen-limiting) conditions (initial dissolved oxygen concentration about 2 mg/l) with nitrate as an alternate electron acceptor. This is relevant to current intense efforts to establish favorable conditions for in situ bioremediation. Using samples of granular activated carbon slurries from an operating groundwater treatment system, we isolated bacteria that are able to use benzene, toluene, ethylbenzene, or p -xylene as their sole source of carbon under aerobic or hypoxic-denitrifying conditions. Direct isolation on solid medium incubated aerobically or hypoxically with the substrate supplied as vapor yielded 10 3 to 10 5 bacteria ml −1 of slurry supernatant, with numbers varying little with respect to isolation substrate or conditions. More than sixty bacterial isolates that varied in colony morphology were purified and characterized according to substrate utilization profiles and growth condition (i.e., aerobic vs. hypoxic) specificity. Strains with distinct characteristics were obtained using benzene compared with those isolated on toluene or ethylbenzene. In general, isolates obtained from direct selection on benzene minimal medium grew well under aerobic conditions but poorly under hypoxic conditions, whereas many ethylbenzene isolates grew well under both incubation conditions. We conclude that the conditions of isolation, rather than the substrate used, will influence the apparent characteristic substrate utilization range of the isolates obtained. Also, using an enrichment culture technique, we isolated a strain of Pseudomonas fluorescens , designated CFS215, which exhibited nitrate dependent degradation of aromatic hydrocarbons under hypoxic conditions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42470/1/10532_2004_Article_BF00695973.pd

Professional Credentials -What Associated Schools of Construction (ASC) Members Are Doing

Professional Credentials have long been a part of the construction industry and many different credentials are available to the construction professional. Due to the number and variety of professional credentials it is often times difficult for individuals to decide which credentials are most advantageous to their career. ASC member schools with construction management programs have been conservative in the number and variety of professional credentials supported by their respective schools. ASC member schools have also not mirrored the construction industry in their support for certain professional credentials. This paper surveys the department heads of ASC member schools to decipher how they are incorporating professional credentials into their programs

Enumeration and characterization of BTEX-degrading bacteria from hypoxic environments functional with mixed electron acceptors

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31866/1/0000816.pd

An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein

Campylobacter jejuni is a Gram-negative food-borne pathogen associated with gastroenteritis in humans as well as cases of the autoimmune disease Guillain Barre syndrome. C. jejuni is asaccharolytic because it lacks an active glycolytic pathway for the use of sugars as a carbon source. This suggests an increased reliance on amino acids as nutrients and indeed the genome sequence of this organism indicates the presence of a number of amino acid uptake systems. Cj0982, also known as CjaA, is a putative extracytoplasmic solute receptor for one such uptake system as well as a major surface antigen and vaccine candidate. The crystal structure of Cj0982 reveals a two-domain protein with density in the enclosed cavity between the domains that clearly defines the presence of a bound cysteine ligand. Fluorescence titration experiments were used to demonstrate that Cj0982 binds cysteine tightly and specifically with a K-d of similar to 10(-7) M consistent with a role as a receptor for a high- affinity transporter. These data imply that Cj0982 is the binding protein component of an ABC-type cysteine transporter system and that cysteine uptake is important in the physiology of C. jejuni

The Global Structure of UTLS Ozone in GEOS-5: A Multi-Year Assimilation of EOS Aura Data

Eight years of ozone measurements retrieved from the Ozone Monitoring Instrument (OMI) and the Microwave Limb Sounder, both on the EOS Aura satellite, have been assimilated into the Goddard Earth Observing System version 5 (GEOS-5) data assimilation system. This study thoroughly evaluates this assimilated product, highlighting its potential for science. The impact of observations on the GEOS-5 system is explored by examining the spatial distribution of the observation-minus-forecast statistics. Independent data are used for product validation. The correlation coefficient of the lower-stratospheric ozone column with ozonesondes is 0.99 and the bias is 0.5%, indicating the success of the assimilation in reproducing the ozone variability in that layer. The upper-tropospheric assimilated ozone column is about 10% lower than the ozonesonde column but the correlation is still high (0.87). The assimilation is shown to realistically capture the sharp cross-tropopause gradient in ozone mixing ratio. Occurrence of transport-driven low ozone laminae in the assimilation system is similar to that obtained from the High Resolution Dynamics Limb Sounder (HIRDLS) above the 400 K potential temperature surface but the assimilation produces fewer laminae than seen by HIRDLS below that surface. Although the assimilation produces 5 - 8 fewer occurrences per day (up to approximately 20%) during the three years of HIRDLS data, the interannual variability is captured correctly. This data-driven assimilated product is complementary to ozone fields generated from chemistry and transport models. Applications include study of the radiative forcing by ozone and tracer transport near the tropopause

sígame v3: Gas Fragmentation in Postprocessing of Cosmological Simulations for More Accurate Infrared Line Emission Modeling

We present an update to the framework called Simulator of Galaxy Millimeter/submillimeter Emission (SÍGAME). SÍGAME derives line emission in the far-infrared (FIR) for galaxies in particle-based cosmological hydrodynamics simulations by applying radiative transfer and physics recipes via a postprocessing step after completion of the simulation. In this version, a new technique is developed to model higher gas densities by parameterizing the probability distribution function (PDF) of the gas density in higher-resolution simulations run with the pseudoLagrangian, Voronoi mesh code AREPO. The parameterized PDFs are used as a look-up table, and reach higher densities than in previous work. SÍGAME v3 is tested on redshift z = 0 galaxies drawn from the SIMBA cosmological simulation for eight FIR emission lines tracing vastly different phases of the interstellar medium. This version of SÍGAME includes dust radiative transfer with SKIRT and high-resolution photoionization models with CLOUDY, the latter sampled according to the density PDF of the AREPO simulations to augment the densities in the cosmological simulation. The quartile distributions of the predicted line luminosities overlap with the observed range for nearby galaxies of similar star formation rate (SFR) for all but two emission lines: [O I]63 and CO(3–2), which are overestimated by median factors of 1.3 and 1.0 dex, respectively, compared to the observed line–SFR relation of mixed-type galaxies. We attribute the remaining disagreement with observations to the lack of precise attenuation of the interstellar light on sub-grid scales (200 pc) and differences in sample selection

Challenges and Techniques for Simulating Line Emission

Modeling emission lines from the millimeter to the UV and producing synthetic spectra is crucial for a good understanding of observations, yet it is an art filled with hazards. This is the proceedings of “Walking the Line”, a 3-day conference held in 2018 that brought together scientists working on different aspects of emission line simulations, in order to share knowledge and discuss the methodology. Emission lines across the spectrum from the millimeter to the UV were discussed, with most of the focus on the interstellar medium, but also some topics on the circumgalactic medium. The most important quality of a useful model is a good synergy with observations and experiments. Challenges in simulating line emission are identified, some of which are already being worked upon, and others that must be addressed in the future for models to agree with observations. Recent advances in several areas aiming at achieving that synergy are summarized here, from micro-physical to galactic and circum-galactic scale

ISS Space Plasma Laboratory: An ISS instrument package for investigating the opening/closing of solar and heliospheric magnetic fields

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140428/1/6.2014-1422.pd