Structure of Disk Dominated Galaxies I. Bulge/Disk Parameters, Simulations, and Secular Evolution

(Abridged) A robust analysis of galaxy structural parameters, based on the modeling of bulge and disk brightnesses in the BVRH bandpasses, is presented for 121 face-on and moderately inclined late-type spirals. Each surface brightness (SB) profile is decomposed into a sum of a generalized Sersic bulge and an exponential disk. The reliability and limitations of our bulge-to-disk (B/D) decompositions are tested with extensive simulations of galaxy brightness profiles (1D) and images (2D). Galaxy types are divided into 3 classes according to their SB profile shapes; Freeman Type-I and Type-II, and a third ``Transition'' class for galaxies whose profiles change from Type-II in the optical to Type-I in the infrared. We discuss possible interpretations of Freeman Type-II profiles. The Sersic bulge shape parameter for nearby Type-I late-type spirals shows a range between n=0.1-2 but, on average, the underlying surface density profile for the bulge and disk of these galaxies is adequately described by a double-exponential distribution. We confirm a coupling between the bulge and disk with a scale length ratio r_e/h=0.22+/-0.09, or h_bulge/h_disk=0.13+/-0.06 for late-type spirals, in agreement with recent N-body simulations of disk formation and models of secular evolution. This ratio increases from ~0.20 for late-type spirals to ~0.24 for earlier types. The similar scaling relations for early and late-type spirals suggest comparable formation and/or evolution scenarios for disk galaxies of all Hubble types.Comment: 78 pages with 23 embedded color figures + tables of galaxy structural parameters. Accepted for publication in the Astrophysical Journal. The interested reader is strongly encouraged to ignore some of the low res figures within; instead, download the high resolution version from http://www.astro.ubc.ca/people/courteau/public/macarthur02_disks.ps.g

The effects of anthropogenic noise and urban habitats on song structure in a vocal mimic; the gray catbird (Dumetella carolinensis) sings higher frequencies in noisier habitats

In urban and human-modified landscapes, animals face novel selection pressures resulting from differences in habitat structure and increased anthropogenic noise. Urban noise pollution can negatively impact songbirds because low-frequency noise often masks portions of birds’ mating signals and reduces signal transmission. Previous research has demonstrated that the songs of birds in more urban habitats have structural differences that can enhance signal transmission when noise is present. The majority of these studies have focused on species that deliver short, stereotyped songs and have limited repertoires. Gray catbirds (Dumetella carolinensis, family: Mimidae) sing long bouts containing imitated, improvised, and invented song elements, and therefore may have an increased ability to vary songs in response to noise. We hypothesized that aspects of developed habitats including loud anthropogenic noise and changes to land cover would impact catbirds’ song structural parameters, including song minimum, peak, and maximum frequency, frequency bandwidth, and entropy. We recorded and processed songs from 42 male catbirds and analyzed over 18,000 song elements from sites along an urban gradient from western Virginia to the Washington, DC metropolitan region. We quantified the urban intensity at each site-centroid based on percent canopy cover, percent impervious surface, and noise level. Song features such as minimum, maximum, and peak frequency increased significantly as noise levels increased, demonstrating that catbirds in noisier areas sing higher frequency songs compared to individuals in quieter habitats. Land cover variables also significantly predicted certain song features such as maximum frequency (impervious surface) or entropy (canopy cover). These structural differences in catbird song can limit the negative effects of environmental noise-masking, even for their long song bouts, and suggest that vocal mimics respond to anthropogenic noise. Future studies could investigate repertoire size and composition along an urban gradient and if these structural differences lead to functional consequences for the songs of vocal mimics

Taking the steps towards sustainable livestock: our multidisciplinary global farm platform journey

Implications The Global Farm Platform was conceived and established to explore multidisciplinary strategies for optimising the sustainability of ruminant livestock systems around the world. International sustainability issues are common, but the solutions are often region-specific; therefore, our farms, situated across all major agroclimatic zones, are a unique resource worldwide. Each farm is following ?steps to sustainable livestock? to improve their production system(s), thereby developing robust metrics to progress economic, environmental and social viability. The consortium works collaboratively to improve the sustainability of ruminants, which we argue are a vital component of global food systems, delivering both human and planetary health

A method for comparing multiple imputation techniques: A case study on the U.S. national COVID cohort collaborative.

Healthcare datasets obtained from Electronic Health Records have proven to be extremely useful for assessing associations between patients’ predictors and outcomes of interest. However, these datasets often suffer from missing values in a high proportion of cases, whose removal may introduce severe bias. Several multiple imputation algorithms have been proposed to attempt to recover the missing information under an assumed missingness mechanism. Each algorithm presents strengths and weaknesses, and there is currently no consensus on which multiple imputation algorithm works best in a given scenario. Furthermore, the selection of each algorithm’s pa- rameters and data-related modeling choices are also both crucial and challenging

Outer membrane protein a conservation among Orientia tsutsugamushi isolates suggests its potential as a protective antigen and diagnostic target

Scrub typhus threatens one billion people in the Asia-Pacific area and cases have emerged outside this region. It is caused by infection with any of the multitude of strains of the bacterium; Orientia tsutsugamushi; . A vaccine that affords heterologous protection and a commercially-available molecular diagnostic assay are lacking. Herein, we determined that the nucleotide and translated amino acid sequences of outer membrane protein A (OmpA) are highly conserved among 51; O. tsutsugamushi; isolates. Molecular modeling revealed the predicted tertiary structure of; O. tsutsugamushi; OmpA to be very similar to that of the phylogenetically-related pathogen,; Anaplasma phagocytophilum; , including the location of a helix that contains residues functionally essential for; A. phagocytophilum; infection. PCR primers were developed that amplified; ompA; DNA from all; O. tsutsugamushi; strains, but not from negative control bacteria. Using these primers in quantitative PCR enabled sensitive detection and quantitation of; O. tsutsugamushi ompA; DNA from organs and blood of mice that had been experimentally infected with the Karp or Gilliam strains. The high degree of OmpA conservation among; O. tsutsugamushi; strains evidences its potential to serve as a molecular diagnostic target and justifies its consideration as a candidate for developing a broadly-protective scrub typhus vaccine

Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12

The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli. The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS (“sensitive” genes), and genes whose expression changes very little with the production of a little RpoS (“insensitive”). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS

Clinical Impact of Ceftriaxone Resistance in Escherichia coli Bloodstream Infections: A Multicenter Prospective Cohort Study

BACKGROUND: Ceftriaxone-resistant (CRO-R) Escherichia coli bloodstream infections (BSIs) are common. METHODS: This is a prospective cohort of patients with E coli BSI at 14 United States hospitals between November 2020 and April 2021. For each patient with a CRO-R E coli BSI enrolled, the next consecutive patient with a ceftriaxone-susceptible (CRO-S) E coli BSI was included. Primary outcome was desirability of outcome ranking (DOOR) at day 30, with 50% probability of worse outcomes in the CRO-R group as the null hypothesis. Inverse probability weighting (IPW) was used to reduce confounding. RESULTS: Notable differences between patients infected with CRO-R and CRO-S E coli BSI included the proportion with Pitt bacteremia score ≥4 (23% vs 15%, P = .079) and the median time to active antibiotic therapy (12 hours [interquartile range {IQR}, 1-35 hours] vs 1 hour [IQR, 0-6 hours]; P \u3c .001). Unadjusted DOOR analyses indicated a 58% probability (95% confidence interval [CI], 52%-63%) for a worse clinical outcome in CRO-R versus CRO-S BSI. In the IPW-adjusted cohort, no difference was observed (54% [95% CI, 47%-61%]). Secondary outcomes included unadjusted and adjusted differences in the proportion of 30-day mortality between CRO-R and CRO-S BSIs (-5.3% [95% CI, -10.3% to -.4%] and -1.8 [95% CI, -6.7% to 3.2%], respectively), postculture median length of stay (8 days [IQR, 5-13 days] vs 6 days [IQR, 4-9 days]; P \u3c .001), and incident admission to a long-term care facility (22% vs 12%, P = .045). CONCLUSIONS: Patients with CRO-R E coli BSI generally have poorer outcomes compared to patients infected with CRO-S E coli BSI, even after adjusting for important confounders

The PhanSST global database of Phanerozoic sea surface temperature proxy data

Paleotemperature proxy data form the cornerstone of paleoclimate research and are integral to understanding the evolution of the Earth system across the Phanerozoic Eon. Here, we present PhanSST, a database containing over 150,000 data points from five proxy systems that can be used to estimate past sea surface temperature. The geochemical data have a near-global spatial distribution and temporally span most of the Phanerozoic. Each proxy value is associated with consistent and queryable metadata fields, including information about the location, age, and taxonomy of the organism from which the data derive. To promote transparency and reproducibility, we include all available published data, regardless of interpreted preservation state or vital effects. However, we also provide expert-assigned diagenetic assessments, ecological and environmental flags, and other proxy-specific fields, which facilitate informed and responsible reuse of the database. The data are quality control checked and the foraminiferal taxonomy has been updated. PhanSST will serve as a valuable resource to the paleoclimate community and has myriad applications, including evolutionary, geochemical, diagenetic, and proxy calibration studies

A Loss of Function Screen of Identified Genome-Wide Association Study Loci Reveals New Genes Controlling Hematopoiesis

The formation of mature cells by blood stem cells is very well understood at the cellular level and we know many of the key transcription factors that control fate decisions. However, many upstream signalling and downstream effector processes are only partially understood. Genome wide association studies (GWAS) have been particularly useful in providing new directions to dissect these pathways. A GWAS meta-analysis identified 68 genetic loci controlling platelet size and number. Only a quarter of those genes, however, are known regulators of hematopoiesis. To determine function of the remaining genes we performed a medium-throughput genetic screen in zebrafish using antisense morpholino oligonucleotides (MOs) to knock down protein expression, followed by histological analysis of selected genes using a wide panel of different hematopoietic markers. The information generated by the initial knockdown was used to profile phenotypes and to position candidate genes hierarchically in hematopoiesis. Further analysis of brd3a revealed its essential role in differentiation but not maintenance and survival of thrombocytes. Using the from-GWAS-to-function strategy we have not only identified a series of genes that represent novel regulators of thrombopoiesis and hematopoiesis, but this work also represents, to our knowledge, the first example of a functional genetic screening strategy that is a critical step toward obtaining biologically relevant functional data from GWA study for blood cell traits