Conservation status of New Zealand freshwater invertebrates, 2013

The conservation status of 644 freshwater invertebrate taxa, across five Phyla, 28 Orders and 75 Families, was assessed using the New Zealand Threat Classification System (NZTCS) criteria. Forty-six species were ranked Nationally Critical, 11 Nationally Endangered and 16 Nationally Vulnerable. One hundred and seventy-two taxa were listed as Data Deficient. A full list is presented, along with summaries and brief notes on the most important changes. This list replaces all previous NZTCS lists for freshwater invertebrates

The SWIRE/Chandra Survey: The X-ray Sources

We report a moderate-depth (70 ks), contiguous 0.7 deg^2 Chandra survey in the Lockman Hole Field of the Spitzer/SWIRE Legacy Survey coincident with a completed, ultra-deep VLA survey with deep optical and near-infrared imaging in-hand. The primary motivation is to distinguish starburst galaxies and active galactic nuclei (AGNs), including the significant, highly obscured (log N_H > 23) subset. Chandra has detected 775 X-ray sources to a limiting broadband (0.3-8 keV) flux ~4 × 10^(–16) erg cm^(–2) s^(–1). We present the X-ray catalog, fluxes, hardness ratios, and multi-wavelength fluxes. The log N versus log S agrees with those of previous surveys covering similar flux ranges. The Chandra and Spitzer flux limits are well matched: 771 (99%) of the X-ray sources have infrared (IR) or optical counterparts, and 333 have MIPS 24 μm detections. There are four optical-only X-ray sources and four with no visible optical/IR counterpart. The very deep (~2.7 μJy rms) VLA data yield 251 (>4σ) radio counterparts, 44% of the X-ray sources in the field. We confirm that the tendency for lower X-ray flux sources to be harder is primarily due to absorption. As expected, there is no correlation between observed IR and X-ray fluxes. Optically bright, type 1, and red AGNs lie in distinct regions of the IR versus X-ray flux plots, demonstrating the wide range of spectral energy distributions in this sample and providing the potential for classification/source selection. Many optically bright sources, which lie outside the AGN region in the optical versus X-ray plots (f_r /f_x >10), lie inside the region predicted for red AGNs in IR versus X-ray plots, consistent with the presence of an active nucleus. More than 40% of the X-ray sources in the VLA field are radio-loud using the classical definition, R_L . The majority of these are red and relatively faint in the optical so that the use of R_L to select those AGNs with the strongest radio emission becomes questionable. Using the 24 μm to radio flux ratio (q_(24)) instead results in 13 of the 147 AGNs with sufficient data being classified as radio-loud, in good agreement with the ~10% expected for broad-lined AGNs based on optical surveys. We conclude that q_(24) is a more reliable indicator of radio-loudness. Use of R_L should be confined to the optically selected type 1 AGN

The Metallicity Distribution Functions of SEGUE G and K dwarfs: Constraints for Disk Chemical Evolution and Formation

We present the metallicity distribution function (MDF) for 24,270 G and 16,847 K dwarfs at distances from 0.2 to 2.3 kpc from the Galactic plane, based on spectroscopy from the Sloan Extension for Galactic Understanding and Exploration (SEGUE) survey. This stellar sample is significantly larger in both number and volume than previous spectroscopic analyses, which were limited to the solar vicinity, making it ideal for comparison with local volume-limited samples and Galactic models. For the first time, we have corrected the MDF for the various observational biases introduced by the SEGUE target selection strategy. The SEGUE sample is particularly notable for K dwarfs, which are too faint to examine spectroscopically far from the solar neighborhood. The MDF of both spectral types becomes more metal-poor with increasing |Z|, which reflects the transition from a sample with small [alpha/Fe] values at small heights to one with enhanced [alpha/Fe] above 1 kpc. Comparison of our SEGUE distributions to those of two different Milky Way models reveals that both are more metal-rich than our observed distributions at all heights above the plane. Our unbiased observations of G and K dwarfs provide valuable constraints over the |Z|-height range of the Milky Way disk for chemical and dynamical Galaxy evolution models, previously only calibrated to the solar neighborhood, with particular utility for thin- and thick-disk formation models.Comment: 70 pages, 25 figures, 7 tables. Accepted by The Astrophysical Journa

Development and validation of the Crohn’s disease patient-reported outcomes signs and symptoms (CD-PRO/SS) diary

Abstract Background The clinical course of Crohn’s disease (CD) and the effect of its treatment are monitored through patient-reported signs and symptoms (S&S), and endoscopic evidence of inflammation. The Crohn’s Disease Patient-reported Outcomes Signs and Symptoms (CD-PRO/SS) measure was developed to standardize the quantification of gastrointestinal S&S of CD through direct report from patient ratings. Methods The CD-PRO/SS was developed based on data from concept elicitation (focus groups, interviews; n = 29), then refined through cognitive interviews of CD patients (n = 20). Measurement properties, including item-level statistics, scaling structure, reliability, and validity, were examined using secondary analyses of baseline and two-week clinical trial data of adults with moderate-to-severe CD (n = 238). Results Findings from qualitative interviews identified nine S&S items covering bowel and abdominal symptoms. The final CD-PRO/SS daily diary includes two scales: Bowel S&S (three items) and Abdominal Symptoms (three items), each scored separately. Each scale showed evidence of adequate reliability (α = 0.74 and 0.67, respectively); reproducibility (intraclass correlation coefficient > 0.80), and validity, with the last including moderate correlations with the Inflammatory Bowel Disease Questionnaire bowel symptom score and select items (ranging from r = 0.43–0.54). Scores distinguished patients categorized by patient global ratings of disease severity (p < 0.0001). Conclusions Results suggest the CD-PRO/SS is a reliable and valid measure of gastrointestinal symptom severity in CD patients. Additional longitudinal data are needed to evaluate the ability of the CD-PRO/SS scores to detect responsiveness and inform the selection of responder definitions.https://deepblue.lib.umich.edu/bitstream/2027.42/143542/1/41687_2018_Article_44.pd

The Seventh Data Release of the Sloan Digital Sky Survey

This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11663 deg^2 of imaging data, with most of the roughly 2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry over 250 deg^2 along the Celestial Equator in the Southern Galactic Cap. A coaddition of these data goes roughly two magnitudes fainter than the main survey. The spectroscopy is now complete over a contiguous area of 7500 deg^2 in the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog (UCAC-2), reducing the rms statistical errors at the bright end to 45 milli-arcseconds per coordinate. A systematic error in bright galaxy photometr is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat-fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities. (Abridged)Comment: 20 pages, 10 embedded figures. Accepted to ApJS after minor correction

A population of gamma-ray emitting globular clusters seen with the Fermi Large Area Telescope

Globular clusters with their large populations of millisecond pulsars (MSPs) are believed to be potential emitters of high-energy gamma-ray emission. Our goal is to constrain the millisecond pulsar populations in globular clusters from analysis of gamma-ray observations. We use 546 days of continuous sky-survey observations obtained with the Large Area Telescope aboard the Fermi Gamma-ray Space Telescope to study the gamma-ray emission towards 13 globular clusters. Steady point-like high-energy gamma-ray emission has been significantly detected towards 8 globular clusters. Five of them (47 Tucanae, Omega Cen, NGC 6388, Terzan 5, and M 28) show hard spectral power indices $(0.7 < \Gamma <1.4)$ and clear evidence for an exponential cut-off in the range 1.0-2.6 GeV, which is the characteristic signature of magnetospheric emission from MSPs. Three of them (M 62, NGC 6440 and NGC 6652) also show hard spectral indices $(1.0 < \Gamma < 1.7)$, however the presence of an exponential cut-off can not be unambiguously established. Three of them (Omega Cen, NGC 6388, NGC 6652) have no known radio or X-ray MSPs yet still exhibit MSP spectral properties. From the observed gamma-ray luminosities, we estimate the total number of MSPs that is expected to be present in these globular clusters. We show that our estimates of the MSP population correlate with the stellar encounter rate and we estimate 2600-4700 MSPs in Galactic globular clusters, commensurate with previous estimates. The observation of high-energy gamma-ray emission from a globular cluster thus provides a reliable independent method to assess their millisecond pulsar populations that can be used to make constraints on the original neutron star X-ray binary population, essential for understanding the importance of binary systems in slowing the inevitable core collapse of globular clusters.Comment: Accepted for publication in A&A. Corresponding authors: J. Kn\"odlseder, N. Webb, B. Pancraz

CONQUER Scleroderma: Association of Gastrointestinal Tract Symptoms in Early Disease With Resource Utilization

OBJECTIVES: SSc is associated with increased health-care resource utilization and economic burden. The Collaborative National Quality and Efficacy Registry (CONQUER) is a US-based collaborative that collects longitudinal follow-up data on SSc patients withparticipants. METHODS: CONQUER participants who had completed a baseline and 12-month Gastrointestinal Tract Questionnaire (GIT 2.0) and a Resource Utilization Questionnaire (RUQ) were included in this analysis. Patients were categorized by total GIT 2.0 severity: none-to-mild (0-0.49); moderate (0.50-1.00), and severe-to-very severe (1.01-3.00). Clinical features and medication exposures were examined in each of these categories. The 12-month RUQ responses were summarized by GIT 2.0 score categories at 12 months. RESULTS: Among the 211 CONQUER participants who met the inclusion criteria, most (64%) had mild GIT symptoms, 26% had moderate symptoms, and 10% severe GIT symptoms at 12 months. The categorization of GIT total severity score by RUQ showed that more upper endoscopy procedures and inpatient hospitalization occurred in the CONQUER participants with severe GIT symptoms. These patients with severe GIT symptoms also reported the use of more adaptive equipment. CONCLUSION: This report from the CONQUER cohort suggests that severe GIT symptoms result in more resource utilization. It is especially important to understand resource utilization in early disease cohorts when disease activity, rather than damage, primarily contributes to health-related costs of SSc

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

The Sloan Digital Sky Survey (SDSS) started a new phase in August 2008, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Ly alpha forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg^2 in the Southern Galactic Cap, bringing the total footprint of the SDSS imaging to 14,555 deg^2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Evolution (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameters pipeline, which has better determination of metallicity for high metallicity stars.Comment: Astrophysical Journal Supplements, in press (minor updates from submitted version

SDSS-IV/MaNGA: Spectrophotometric Calibration Technique

Mapping Nearby Galaxies at Apache Point Observatory (MaNGA), one of three core programs in the Sloan Digital Sky Survey-IV, is an integral-field spectroscopic survey of roughly 10,000 nearby galaxies. It employs dithered observations using 17 hexagonal bundles of 2'' fibers to obtain resolved spectroscopy over a wide wavelength range of 3600–10300 Å. To map the internal variations within each galaxy, we need to perform accurate spectral surface photometry, which is to calibrate the specific intensity at every spatial location sampled by each individual aperture element of the integral field unit. The calibration must correct only for the flux loss due to atmospheric throughput and the instrument response, but not for losses due to the finite geometry of the fiber aperture. This requires the use of standard star measurements to strictly separate these two flux loss factors (throughput versus geometry), a difficult challenge with standard single-fiber spectroscopy techniques due to various practical limitations. Therefore, we developed a technique for spectral surface photometry using multiple small fiber-bundles targeting standard stars simultaneously with galaxy observations. We discuss the principles of our approach and how they compare to previous efforts, and we demonstrate the precision and accuracy achieved. MaNGA's relative calibration between the wavelengths of Hα and Hβ has an rms of 1.7%, while that between [N ii] λ6583 and [O ii] λ3727 has an rms of 4.7%. Using extinction-corrected star formation rates and gas-phase metallicities as an illustration, this level of precision guarantees that flux calibration errors will be sub-dominant when estimating these quantities. The absolute calibration is better than 5% for more than 89% of MaNGA's wavelength range

Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function

The WHO estimates around a million children contract tuberculosis (TB) annually with over 80 000 deaths from dissemination of infection outside of the lungs. The insidious onset and association with skin test anergy suggests failure of the immune system to both recognise and respond to infection. To understand the immune mechanisms, we studied genome-wide whole blood RNA expression in children with TB meningitis (TBM). Findings were validated in a second cohort of children with TBM and pulmonary TB (PTB), and functional T-cell responses studied in a third cohort of children with TBM, other extrapulmonary TB (EPTB) and PTB. The predominant RNA transcriptional response in children with TBM was decreased abundance of multiple genes, with 140/204 (68%) of all differentially regulated genes showing reduced abundance compared to healthy controls. Findings were validated in a second cohort with concordance of the direction of differential expression in both TBM (r2 = 0.78 p = 2x10-16) and PTB patients (r2 = 0.71 p = 2x10-16) when compared to a second group of healthy controls. Although the direction of expression of these significant genes was similar in the PTB patients, the magnitude of differential transcript abundance was less in PTB than in TBM. The majority of genes were involved in activation of leucocytes (p = 2.67E-11) and T-cell receptor signalling (p = 6.56E-07). Less abundant gene expression in immune cells was associated with a functional defect in T-cell proliferation that recovered after full TB treatment (p<0.0003). Multiple genes involved in T-cell activation show decreased abundance in children with acute TB, who also have impaired functional T-cell responses. Our data suggest that childhood TB is associated with an acquired immune defect, potentially resulting in failure to contain the pathogen. Elucidation of the mechanism causing the immune paresis may identify new treatment and prevention strategies