The Open-Source Neuroimaging Research Enterprise

While brain imaging in the clinical setting is largely a practice of looking at images, research neuroimaging is a quantitative and integrative enterprise. Images are run through complex batteries of processing and analysis routines to generate numeric measures of brain characteristics. Other measures potentially related to brain function – demographics, genetics, behavioral tests, neuropsychological tests – are key components of most research studies. The canonical scanner – PACS – viewing station axis used in clinical practice is therefore inadequate for supporting neuroimaging research. Here, we model the neuroimaging research enterprise as a workflow. The principal components of the workflow include data acquisition, data archiving, data processing and analysis, and data utilization. We also describe a set of open-source applications to support each step of the workflow and the transitions between these steps. These applications include DIGITAL IMAGING AND COMMUNICATIONS IN MEDICINE viewing and storage tools, the EXTENSIBLE NEUROIMAGING ARCHIVE TOOLKIT data archiving and exploration platform, and an engine for running processing/analysis pipelines. The overall picture presented is aimed to motivate open-source developers to identify key integration and communication points for interoperating with complimentary applications

Optical and Near-Infrared Observations of the Peculiar Type Ia Supernova 1999ac

We present 39 nights of optical photometry, 34 nights of infrared photometry, and 4 nights of optical spectroscopy of the Type Ia SN 1999ac. This supernova was discovered two weeks before maximum light, and observations were begun shortly thereafter. At early times its spectra resembled the unusual SN 1999aa and were characterized by very high velocities in the Ca II H and K lines, but very low velocities in the Si II 6355 A line. The optical photometry showed a slow rise to peak brightness but, quite peculiarly, was followed by a more rapid decline from maximum. Thus, the B- and V-band light curves cannot be characterized by a single stretch factor. We argue that the best measure of the nature of this object is not the decline rate parameter Delta m_15 (B). The B-V colors were unusual from 30 to 90 days after maximum light in that they evolved to bluer values at a much slower rate than normal Type Ia supernovae. The spectra and bolometric light curve indicate that this event was similar to the spectroscopically peculiar slow decliner SN 1999aa.Comment: 42 pages, 14 figures, accepted for publication in the Astronomical Journal (January 28, 2006

Engaging Undergraduates in Science Research: Not Just About Faculty Willingness.

Despite the many benefits of involving undergraduates in research and the growing number of undergraduate research programs, few scholars have investigated the factors that affect faculty members' decisions to involve undergraduates in their research projects. We investigated the individual factors and institutional contexts that predict faculty members' likelihood of engaging undergraduates in their research project(s). Using data from the Higher Education Research Institute's 2007-2008 Faculty Survey, we employ hierarchical generalized linear modeling to analyze data from 4,832 science, technology, engineering, and mathematics (STEM) faculty across 194 institutions to examine how organizational citizenship behavior theory and social exchange theory relate to mentoring students in research. Key findings show that faculty who work in the life sciences and those who receive government funding for their research are more likely to involve undergraduates in their research project(s). In addition, faculty at liberal arts or historically Black colleges are significantly more likely to involve undergraduate students in research. Implications for advancing undergraduate research opportunities are discussed

Chasing Jenner's Vaccine: Revisiting Cowpox Virus Classification

Cowpox virus (CPXV) is described as the source of the first vaccine used to prevent the onset and spread of an infectious disease. It is one of the earliest described members of the genus Orthopoxvirus, which includes the viruses that cause smallpox and monkeypox in humans. Both the historic and current literature describe “cowpox” as a disease with a single etiologic agent. Genotypic data presented herein indicate that CPXV is not a single species, but a composite of several (up to 5) species that can infect cows, humans, and other animals. The practice of naming agents after the host in which the resultant disease manifests obfuscates the true taxonomic relationships of “cowpox” isolates. These data support the elevation of as many as four new species within the traditional “cowpox” group and suggest that both wild and modern vaccine strains of Vaccinia virus are most closely related to CPXV of continental Europe rather than the United Kingdom, the homeland of the vaccine

Spitzer Survey of the Large Magellanic Cloud, Surveying the Agents of a Galaxy's Evolution (SAGE) I: Overview and Initial Results

We are performing a uniform and unbiased, ~7x7 degrees imaging survey of the Large Magellanic Cloud (LMC), using the IRAC and MIPS instruments on board the Spitzer Space Telescope in order to survey the agents of a galaxy's evolution (SAGE), the interstellar medium (ISM) and stars in the LMC. The detection of diffuse ISM with column densities >1.2x10^21 H cm^-2 permits detailed studies of dust processes in the ISM. SAGE's point source sensitivity enables a complete census of newly formed stars with masses >3 solar masses that will determine the current star formation rate in the LMC. SAGE's detection of evolved stars with mass loss rates >1x10^-8 solar masses per year will quantify the rate at which evolved stars inject mass into the ISM of the LMC. The observing strategy includes two epochs in 2005, separated by three months, that both mitigate instrumental artifacts and constrain source variability. The SAGE data are non-proprietary. The data processing includes IRAC and MIPS pipelines and a database for mining the point source catalogs, which will be released to the community in support of Spitzer proposal cycles 4 and 5. We present initial results on the epoch 1 data with a special focus on the N79 and N83 region. The SAGE epoch 1 point source catalog has ~4 million sources. The point source counts are highest for the IRAC 3.6 microns band and decrease dramatically towards longer wavelengths consistent with the fact that stars dominate the point source catalogs and that the dusty objects, e.g. young stellar objects and dusty evolved stars that detected at the longer wavelengths, are rare in comparison. We outline a strategy for identifying foreground MW stars, that may comprise as much as 18% of the source list, and background galaxies, that may comprise ~12% of the source list.Comment: Accepted by the Astronomical Journa

Spatially Explicit Network Analysis Reveals Multi‐Species Annual Cycle Movement Patterns of Sea Ducks

Conservation of long‐distance migratory species poses unique challenges. Migratory connectivity, that is, the extent to which groupings of individuals at breeding sites are maintained in wintering areas, is frequently used to evaluate population structure and assess use of key habitat areas. However, for species with complex or variable annual cycle movements, this traditional bimodal framework of migratory connectivity may be overly simplistic. Like many other waterfowl, sea ducks often travel to specific pre‐ and post‐breeding sites outside their nesting and wintering areas to prepare for migration by feeding extensively and, in some cases, molting their flight feathers. These additional migrations may play a key role in population structure, but are not included in traditional models of migratory connectivity. Network analysis, which applies graph theory to assess linkages between discrete locations or entities, offers a powerful tool for quantitatively assessing the contributions of different sites used throughout the annual cycle to complex spatial networks. We collected satellite telemetry data on annual cycle movements of 672 individual sea ducks of five species from throughout eastern North America and the Great Lakes. From these data, we constructed a multi‐species network model of migratory patterns and site use over the course of breeding, molting, wintering, and migratory staging. Our results highlight inter‐ and intra‐specific differences in the patterns and complexity of annual cycle movement patterns, including the central importance of staging and molting sites in James Bay, the St. Lawrence River, and southern New England to multi‐species annual cycle habitat linkages, and highlight the value of Long‐tailed Ducks (Calengula haemalis) as an umbrella species to represent the movement patterns of multiple sea duck species. We also discuss potential applications of network migration models to conservation prioritization, identification of population units, and integrating different data streams

Implanted Satellite Transmitters Affect Sea Duck Movement Patterns at Short and Long Timescales

Studies of the effects of transmitters on wildlife often focus on survival. However, sublethal behavioral changes resulting from radio-marking have the potential to affect inferences from telemetry data and may vary based on individual and environmental characteristics. We used a long-term, multi-species tracking study of sea ducks to assess behavioral patterns at multiple temporal scales following implantation of intracoelomic satellite transmitters. We applied state-space models to assess short-term behavioral patterns in 476 individuals with implanted satellite transmitters, as well as comparing breeding site attendance and migratory phenology across multiple years after capture. In the short term, our results suggest an increase in dispersive behavior immediately following capture and transmitter implantation; however, behavior returned to seasonally average patterns within ~5 days after release. Over multiple years, we found that breeding site attendance by both males and females was depressed during the first breeding season after radio-marking relative to subsequent years, with larger relative decreases in breeding site attendance among males than females. We also found that spring and breeding migrations occurred later in the first year after radio-marking than in subsequent years. Across all behavioral effects, the severity of behavioral change often varied by species, sex, age, and capture season. We conclude that, although individuals appear to adjust relatively quickly (i.e. within 1 week) to implanted satellite transmitters, changes in breeding phenology may occur over the longer term and should be considered when analyzing and reporting telemetry data

Spitzer survey of the Large Magellanic Cloud, surveying the agents of a galaxy's evolution (SAGE). IV. Dust properties in the interstellar medium

The goal of this paper is to present the results of a preliminary analysis of the extended infrared (IR) emission by dust in the interstellar medium (ISM) of the Large Magellanic Cloud (LMC). We combine Spitzer Surveying the Agents of Galaxy Evolution (SAGE) and Infrared Astronomical Satellite (IRAS) data and correlate the infrared emission with gas tracers of H I, CO, and Hα. We present a global analysis of the infrared emission as well as detailed modeling of the spectral energy distribution (SED) of a few selected regions. Extended emission by dust associated with the neutral, molecular, and diffuse ionized phases of the ISM is detected at all IR bands from 3.6 μm to 160 μm. The relative abundance of the various dust species appears quite similar to that in the Milky Way (MW) in all the regions we have modeled. We construct maps of the temperature of large dust grains. The temperature map shows variations in the range 12.1-34.7 K, with a systematic gradient from the inner to outer regions, tracing the general distribution of massive stars and individual H II regions as well as showing warmer dust in the stellar bar. This map is used to derive the far-infrared (FIR) optical depth of large dust grains. We find two main departures in the LMC with respect to expectations based on the MW: (1) excess mid-infrared (MIR) emission near 70 μm, referred to as the 70 μm excess, and (2) departures from linear correlation between the FIR optical depth and the gas column density, which we refer to as FIR excess emission. The 70 μm excess increases gradually from the MW to the LMC to the Small Magellanic Cloud (SMC), suggesting evolution with decreasing metallicity. The excess is associated with the neutral and diffuse ionized gas, with the strongest excess region located in a loop structure next to 30 Dor. We show that the 70 μm excess can be explained by a modification of the size distribution of very small grains with respect to that in the MW, and a corresponding mass increase of ≃13% of the total dust mass in selected regions. The most likely explanation is that the 70 μm excess is due to the production of large very small grains (VSG) through erosion of larger grains in the diffuse medium. This FIR excess could be due to intrinsic variations of the dust/gas ratio, which would then vary from 4.6 to 2.3 times lower than the MW values across the LMC, but X_(CO) values derived from the IR emission would then be about three times lower than those derived from the Virial analysis of the CO data. We also investigate the possibility that the FIR excess is associated with an additional gas component undetected in the available gas tracers. Assuming a constant dust abundance in all ISM phases, the additional gas component would have twice the known H I mass. We show that it is plausible that the FIR excess is due to cold atomic gas that is optically thick in the 21 cm line, while the contribution by a pure H_2 phase with no CO emission remains a possible explanation

A multi-decade record of high quality fCO2 data in version 3 of the Surface Ocean CO2 Atlas (SOCAT)

The Surface Ocean CO2 Atlas (SOCAT) is a synthesis of quality-controlled fCO2 (fugacity of carbon dioxide) values for the global surface oceans and coastal seas with regular updates. Version 3 of SOCAT has 14.7 million fCO2 values from 3646 data sets covering the years 1957 to 2014. This latest version has an additional 4.6 million fCO2 values relative to version 2 and extends the record from 2011 to 2014. Version 3 also significantly increases the data availability for 2005 to 2013. SOCAT has an average of approximately 1.2 million surface water fCO2 values per year for the years 2006 to 2012. Quality and documentation of the data has improved. A new feature is the data set quality control (QC) flag of E for data from alternative sensors and platforms. The accuracy of surface water fCO2 has been defined for all data set QC flags. Automated range checking has been carried out for all data sets during their upload into SOCAT. The upgrade of the interactive Data Set Viewer (previously known as the Cruise Data Viewer) allows better interrogation of the SOCAT data collection and rapid creation of high-quality figures for scientific presentations. Automated data upload has been launched for version 4 and will enable more frequent SOCAT releases in the future. High-profile scientific applications of SOCAT include quantification of the ocean sink for atmospheric carbon dioxide and its long-term variation, detection of ocean acidification, as well as evaluation of coupled-climate and ocean-only biogeochemical models. Users of SOCAT data products are urged to acknowledge the contribution of data providers, as stated in the SOCAT Fair Data Use Statement. This ESSD (Earth System Science Data) “living data” publication documents the methods and data sets used for the assembly of this new version of the SOCAT data collection and compares these with those used for earlier versions of the data collection (Pfeil et al., 2013; Sabine et al., 2013; Bakker et al., 2014). Individual data set files, included in the synthesis product, can be downloaded here: doi:10.1594/PANGAEA.849770. The gridded products are available here: doi:10.3334/CDIAC/OTG.SOCAT_V3_GRID