Mid-infrared Variability from the Spitzer Deep Wide-field Survey

We use the multi-epoch, mid-infrared Spitzer Deep Wide-Field Survey to investigate the variability of objects in 8.1 deg^2 of the NOAO Deep Wide Field Survey Boötes field. We perform a Difference Image Analysis of the four available epochs between 2004 and 2008, focusing on the deeper 3.6 and 4.5 μm bands. Out of 474, 179 analyzed sources, 1.1% meet our standard variability selection criteria that the two light curves are strongly correlated (r > 0.8) and that their joint variance (σ_(12)) exceeds that for all sources with the same magnitude by 2σ. We then examine the mid-IR colors of the variable sources and match them with X-ray sources from the XBoötes survey, radio catalogs, 24 μm selected active galactic nucleus (AGN) candidates, and spectroscopically identified AGNs from the AGN and Galaxy Evolution Survey (AGES). Based on their mid-IR colors, most of the variable sources are AGNs (76%), with smaller contributions from stars (11%), galaxies (6%), and unclassified objects, although most of the stellar, galaxy, and unclassified sources are false positives. For our standard selection criteria, 11%-12% of the mid-IR counterparts to X-ray sources, 24 μm AGN candidates, and spectroscopically identified AGNs show variability. The exact fractions depend on both the search depth and the selection criteria. For example, 12% of the 1131 known z>1 AGNs in the field and 14%-17% of the known AGNs with well-measured fluxes in all four Infrared Array Camera bands meet our standard selection criteria. The mid-IR AGN variability can be well described by a single power-law structure function with an index of γ ≈ 0.5 at both 3.6 and 4.5 μm, and an amplitude of S _0 ≃ 0.1 mag on rest-frame timescales of 2 yr. The variability amplitude is higher for shorter rest-frame wavelengths and lower luminosities

The Spitzer Deep, Wide-Field Survey

The Spitzer Deep, Wide-Field Survey (SDWFS) is a four-epoch infrared survey of ten square degrees in the Bootes field of the NOAO Deep Wide-Field Survey using the IRAC instrument on the Spitzer Space Telescope. SDWFS, a Cycle four Spitzer Legacy project, occupies a unique position in the area-depth survey space defined by other Spitzer surveys. The four epochs that make up SDWFS permit -- for the first time -- the selection of infrared-variable and high proper motion objects over a wide field on timescales of years. Because of its large survey volume, SDWFS is sensitive to galaxies out to z~3 with relatively little impact from cosmic variance for all but the richest systems. The SDWFS datasets will thus be especially useful for characterizing galaxy evolution beyond z~1.5. This paper explains the SDWFS observing strategy and data processing, presents the SDWFS mosaics and source catalogs, and discusses some early scientific findings. The publicly-released, full-depth catalogs contain 6.78, 5.23, 1.20, and 0.96 x 10e5 distinct sources detected to the average 5-sigma, 4" diameter, aperture-corrected limits of 19.77, 18.83, 16.50, and 15.82 Vega mag at 3.6, 4.5, 5.8, and 8.0 micron, respectively. The SDWFS number counts and color-color distribution are consistent with other, earlier Spitzer surveys. At the 6 min integration time of the SDWFS IRAC imaging, more than 50% of isolated FIRST radio sources and more than 80% of on-axis XBootes sources are detected out to 8.0 micron. Finally, we present the four highest proper motion IRAC-selected sources identified from the multi-epoch imaging, two of which are likely field brown dwarfs of mid-T spectral class.Comment: 71 pages, 18 figures, accepted for publication in the Astrophysical Journa

Constraining Exoplanet Metallicities and Aerosols with ARIEL: An Independent Study by the Contribution to ARIEL Spectroscopy of Exoplanets (CASE) Team

Launching in 2028, ESA's Atmospheric Remote-sensing Exoplanet Large-survey (ARIEL) survey of $\sim$1000 transiting exoplanets will build on the legacies of Kepler and TESS and complement JWST by placing its high precision exoplanet observations into a large, statistically-significant planetary population context. With continuous 0.5--7.8~$\mu$m coverage from both FGS (0.50--0.55, 0.8--1.0, and 1.0--1.2~$\mu$m photometry; 1.25--1.95~$\mu$m spectroscopy) and AIRS (1.95--7.80~$\mu$m spectroscopy), ARIEL will determine atmospheric compositions and probe planetary formation histories during its 3.5-year mission. NASA's proposed Contribution to ARIEL Spectroscopy of Exoplanets (CASE) would be a subsystem of ARIEL's FGS instrument consisting of two visible-to-infrared detectors, associated readout electronics, and thermal control hardware. FGS, to be built by the Polish Academy of Sciences' Space Research Centre, will provide both fine guiding and visible to near-infrared photometry and spectroscopy, providing powerful diagnostics of atmospheric aerosol contribution and planetary albedo, which play a crucial role in establishing planetary energy balance. The CASE team presents here an independent study of the capabilities of ARIEL to measure exoplanetary metallicities, which probe the conditions of planet formation, and FGS to measure scattering spectral slopes, which indicate if an exoplanet has atmospheric aerosols (clouds and hazes), and geometric albedos, which help establish planetary climate. Our design reference mission simulations show that ARIEL could measure the mass-metallicity relationship of its 1000-planet single-visit sample to $>7.5\sigma$ and that FGS could distinguish between clear, cloudy, and hazy skies and constrain an exoplanet's atmospheric aerosol composition to $>5\sigma$ for hundreds of targets, providing statistically-transformative science for exoplanet atmospheres.Comment: accepted to PASP; 23 pages, 6 figure

Isolated Case of Bioterrorism-related Inhalational Anthrax, New York City, 2001

On October 31, 2001, in New York City, a 61-year-old female hospital employee who had acquired inhalational anthrax died after a 6-day illness. To determine sources of exposure and identify additional persons at risk, the New York City Department of Health, Centers for Disease Control and Prevention, and law enforcement authorities conducted an extensive investigation, which included interviewing contacts, examining personal effects, summarizing patient’s use of mass transit, conducting active case finding and surveillance near her residence and at her workplace, and collecting samples from co-workers and the environment. We cultured all specimens for Bacillus anthracis. We found no additional cases of cutaneous or inhalational anthrax. The route of exposure remains unknown. All environmental samples were negative for B. anthracis. This first case of inhalational anthrax during the 2001 outbreak with no apparent direct link to contaminated mail emphasizes the need for close coordination between public health and law enforcement agencies during bioterrorism-related investigations

Genes That Influence Swarming Motility and Biofilm Formation in Variovorax paradoxus EPS

Variovorax paradoxus is an aerobic soil bacterium associated with important biodegradative processes in nature. We use V. paradoxus EPS to study multicellular behaviors on surfaces.We recovered flanking sequence from 123 clones in a Tn5 mutant library, with insertions in 29 different genes, selected based on observed surface behavior phenotypes. We identified three genes, Varpa_4665, Varpa_4680, and Varpa_5900, for further examination. These genes were cloned into pBBR1MCS2 and used to complement the insertion mutants. We also analyzed expression of Varpa_4680 and Varpa_5900 under different growth conditions by qPCR.The 29 genes we identified had diverse predicted functions, many in exopolysaccharide synthesis. Varpa_4680, the most commonly recovered insertion site, encodes a putative N-acetyl-L-fucosamine transferase similar to WbuB. Expression of this gene in trans complemented the mutant fully. Several unique insertions were identified in Varpa_5900, which is one of three predicted pilY1 homologs in the EPS genome. No insertions in the two other putative pilY1 homologs present in the genome were identified. Expression of Varpa_5900 altered the structure of the wild type swarm, as did disruption of the chromosomal gene. The swarming phenotype was complemented by expression of Varpa_5900 from a plasmid, but biofilm formation was not restored. Both Varpa_4680 and Varpa_5900 transcripts were downregulated in biofilms and upregulated during swarming when compared to log phase culture. We identified a putative two component system (Varpa_4664-4665) encoding a response regulator (shkR) and a sensor histidine kinase (shkS), respectively. Biofilm formation increased and swarming was strongly delayed in the Varpa_4665 (shkS) mutant. Complementation of shkS restored the biofilm phenotype but swarming was still delayed. Expression of shkR in trans suppressed biofilm formation in either genetic background, and partially restored swarming in the mutant.The data presented here point to complex regulation of these surface behaviors

Carbapenem-Resistant Acinetobacter baumannii in U.S. Hospitals: Diversification of Circulating Lineages and Antimicrobial Resistance

Carbapenem-resistant Acinetobacter baumannii (CRAb) is a major cause of health care-associated infections. CRAb is typically multidrug resistant, and infection is difficult to treat. Despite the urgent threat that CRAb poses, few systematic studies of CRAb clinical and molecular epidemiology have been conducted. The Study Network of Acinetobacter as a Carbapenem-Resistant Pathogen (SNAP) is designed to investigate the clinical characteristics and contemporary population structure of CRAb circulating in U.S. hospital systems using whole-genome sequencing (WGS). Analysis of the initial 120 SNAP patients from four U.S. centers revealed that CRAb remains a significant threat to hospitalized patients, affecting the most vulnerable patients and resulting in 24% all-cause 30-day mortality. The majority of currently circulating isolates belonged to ST2Pas, a part of clonal complex 2 (CC2), which is the dominant drug-resistant lineage in the United States and Europe. We identified three distinct sublineages within CC2, which differed in their antibiotic resistance phenotypes and geographic distribution. Most concerning, colistin resistance (38%) and cefiderocol resistance (10%) were common within CC2 sublineage C (CC2C), where the majority of isolates belonged to ST2Pas/ST281Ox. Additionally, we identified ST499Pas as the most common non-CC2 lineage in our study. Our findings suggest a shift within the CRAb population in the United States during the past 10 years and emphasize the importance of real-time surveillance and molecular epidemiology in studying CRAb dissemination and clinical impact

First Steps in Eukaryogenesis: Physical phenomena in the origin and evolution of chromosome structure

Our present understanding of the origin and evolution of chromosomes differs considerably from current understanding of the origin and evolution of the cell itself. Chromosome origins have been less prominent in research, as the emphasis has not shifted so far appreciably from the phenomenon of primeval nucleic acid encapsulation to that of the origin of gene organization, expression, and regulation. In this work we discuss some reasons why preliminary steps in this direction are being taken. We have been led to examine properties that have contributed to raise the ancestral prokaryotic programmes to a level where we can appreciate in eukaryotes a clear departure from earlier themes in the evolution of the cell from the last common ancestor. We shift our point of view from the evolution of cell morphology to the point of view of the genes. In particular, we focus attention on possible physical bases for the way transmission of information has evolved in eukaryotes, namely, the inactivation of whole chromosomes. The special case of the inactivation of the X chromosome in mammals is discussed, paying particular attention to the physical process of the spread of X inactivation in monotremes (platypus and echidna). When experimental data is unavailable some theoretical analysis is possible based on the idea that in certain cases collective phenomena in genetics, rather than chemical detail, are better correlates of complex chemical processes

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Chondroitin sulfates and their binding molecules in the central nervous system

Chondroitin sulfate (CS) is the most abundant glycosaminoglycan (GAG) in the central nervous system (CNS) matrix. Its sulfation and epimerization patterns give rise to different forms of CS, which enables it to interact specifically and with a significant affinity with various signalling molecules in the matrix including growth factors, receptors and guidance molecules. These interactions control numerous biological and pathological processes, during development and in adulthood. In this review, we describe the specific interactions of different families of proteins involved in various physiological and cognitive mechanisms with CSs in CNS matrix. A better understanding of these interactions could promote a development of inhibitors to treat neurodegenerative diseases