Genetic polymorphisms in chronic hyperplastic sinusitis with nasal polyposis

Objectives/Hypothesis: Although many proinflammatory cytokines have been identified in nasal polyp tissue, the initial trigger that causes this inflammation characterized by edema, lymphocytosis, and eosinophilia, is still unknown. The purpose of the present study is to identify the presence of genetic polymorphisms in proinflammatory, anti-inflammatory, and chemokine genes that might contribute to genetic susceptibility to chronic hyperplastic sinusitis with nasal polyposis (CHSwNP). Study Design: Case control study. Methods: Buccal swabs were taken from the left and right oral mucosal surfaces from 179 patients with CHSwNP and 153 nonpolyposis controls with the Purgene DNA purification protocol (Gentra). Genotyping assays for cytokine gene loci were performed on 14 cytokine genes using the iPlex Gold and the Mass Array Compact system (Sequenom, San Diego, CA). Tests of Hardy-Weinberg equilibrium proportions were performed separately in the cases and controls. Tests for evidence of association between alleles at each single-nucleotide polymorphism (SNP) and case-control status were performed using unconditional logistic regression. Results: The frequency of the A allele in a SNP located in tumor necrosis factor (TNF)-Α (rs1800629) is significantly different in patients with nasal polyposis versus controls without nasal polyposis, 18.6% and 11.5%, respectively with an individuals' odds of susceptibility to nasal polyps increasing almost two-fold (odds ratio, 1.86; confidence interval, 1.4–3.09) given at least one copy of the A allele at this SNP. All other cytokine gene polymorphisms of both inflammatory, anti-inflammatory, and chemokine genes were not statistically different between the two groups. Conclusions: TNF-Α-308, a SNP in the promoter region of this cytokine gene is associated with increased odds of developing nasal polyposis. TNF-Α is a potent immuno-mediator and proinflammatory cytokine that has been implicated in the pathogenesis of a large number of human diseases. The location of this gene on the short arm of chromosome 6, with the major histocompatibility complex genes and complement, has raised the probability that polymorphism within this locus may contribute to a genetic association of this region of the genome with a wide variety of infectious and autoimmune diseases. Laryngoscope, 2009Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63071/1/20239_ftp.pd

Seroprevalence of Zika virus in wild African green monkeys and baboons

ABSTRACT Zika virus (ZIKV) has recently spread through the Americas and has been associated with a range of health effects, including birth defects in children born to women infected during pregnancy. Although the natural reservoir of ZIKV remains poorly defined, the virus was first identified in a captive “sentinel” macaque monkey in Africa in 1947. However, the virus has not been reported in humans or nonhuman primates (NHPs) in Africa outside Gabon in over a decade. Here, we examine ZIKV infection in 239 wild baboons and African green monkeys from South Africa, the Gambia, Tanzania, and Zambia using combinations of unbiased deep sequencing, quantitative reverse transcription-PCR (qRT-PCR), and an antibody capture assay that we optimized using serum collected from captive macaque monkeys exposed to ZIKV, dengue virus, and yellow fever virus. While we did not find evidence of active ZIKV infection in wild NHPs in Africa, we found variable ZIKV seropositivity of up to 16% in some of the NHP populations sampled. We anticipate that these results and the methodology described within will help in continued efforts to determine the prevalence, natural reservoir, and transmission dynamics of ZIKV in Africa and elsewhere. IMPORTANCE Zika virus (ZIKV) is a mosquito-borne virus originally discovered in a captive monkey living in the Zika Forest of Uganda, Africa, in 1947. Recently, an outbreak in South America has shown that ZIKV infection can cause myriad health effects, including birth defects in the children of women infected during pregnancy. Here, we sought to investigate ZIKV infection in wild African primates to better understand its emergence and spread, looking for evidence of active or prior infection. Our results suggest that up to 16% of some populations of nonhuman primate were, at some point, exposed to ZIKV. We anticipate that this study will be useful for future studies that examine the spread of infections from wild animals to humans in general and those studying ZIKV in primates in particular. Podcast: A podcast concerning this article is available

aCGHViewer: A Generic Visualization Tool For aCGH data

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/

The DEEP2 Galaxy Redshift Survey: Probing the Evolution of Dark Matter Halos around Isolated Galaxies at z ~ 1

Using the first 25% of DEEP2 Redshift Survey data, we probe the line-of-sight velocity dispersion profile for isolated galaxies with absolute B-band magnitude -22<M_B-5log(h)<-21 at z=0.7-1.0, using satellite galaxies as luminous tracers of the underlying velocity distribution. Measuring the velocity dispersion beyond a galactocentric radius of ~200 kpc/h (physical) permits us to determine the total mass, including dark matter, around these bright galaxies. We find a line-of-sight velocity dispersion (sigma_los) of 162^{+44}_{-30} km/s at ~110 kpc/h, 136^{+26}_{-20} km/s at ~230 kpc/h, and 150^{+55}_{-38} km/s at ~320 kpc/h. Assuming an NFW model for the dark matter density profile, this corresponds to a mass within r_{200} of M_200=5.5^{+2.5}_{-2.0} x 10^12 M_Sun/h for our sample of satellite hosts with mean luminosity ~2.5L*. Roughly $~60% of these host galaxies have early-type spectra and are red in restframe (U-B) color, consistent with the overall DEEP2 sample in the same luminosity and redshift range. The halo mass determined for DEEP2 host galaxies is consistent with that measured in the Sloan Digital Sky Survey for host galaxies within a similar luminosity range relative to M*_B. This comparison is insensitive to the assumed halo mass profile, and implies an increase in the dynamical mass-to-light ratio (M_200/L_B) of isolated galaxies which host satellites by a factor of ~2.5 from z ~ 1 to z ~ 0. Our results are consistent with scenarios in which galaxies populate dark matter halos similarly from z ~ 0 to z ~ 1, except for ~1 magnitude of evolution in the luminosity of all galaxies.Comment: 8 pages, 5 figures, ApJ accepte

Kepler Eclipsing Binary Stars. VI. Identification of Eclipsing Binaries in the K2 Campaign 0 Data-set

The original {\it Kepler} mission observed and characterized over 2400 eclipsing binaries in addition to its prolific exoplanet detections. Despite the mechanical malfunction and subsequent non-recovery of two reaction wheels used to stabilize the instrument, the {\it Kepler} satellite continues collecting data in its repurposed {\it K2} mission surveying a series of fields along the ecliptic plane. Here we present an analysis of the first full baseline {\it K2} data release: the Campaign 0 data-set. In the 7761 light curves, we have identified a total of 207 eclipsing binaries. Of these, 97 are new discoveries that were not previously identified. Our pixel-level analysis of these objects has also resulted in identification of several false positives (observed targets contaminated by neighboring eclipsing binaries), as well as the serendipitous discovery of two short period exoplanet candidates. We provide catalog cross-matched source identifications, orbital periods, morphologies and ephemerides for these eclipsing systems. We also describe the incorporation of the K2 sample into the Kepler Eclipsing Binary Catalog\footnote{\url{keplerebs.villanova.edu/k2}}, present spectroscopic follow-up observations for a limited selection of nine systems, and discuss prospects for upcoming {\it K2} campaigns.Comment: Accepted for publication in MNRAS. 51 pages [20 figures, 8 tables]. Results available online in the Kepler Eclipsing Binary Star Catalog http://keplerebs.villanova.edu/k

Common Genetic Variants Are Associated with Accelerated Bone Mineral Density Loss after Hematopoietic Cell Transplantation

BACKGROUND: Bone mineral density (BMD) loss commonly occurs after hematopoietic cell transplantation (HCT). Hypothesizing that genetic variants may influence post-HCT BMD loss, we conducted a prospective study to examine the associations of single nucleotide polymorphisms (SNP) in bone metabolism pathways and acute BMD loss after HCT. METHODS AND FINDINGS: We genotyped 122 SNPs in 45 genes in bone metabolism pathways among 121 autologous and allogeneic HCT patients. BMD changes from pre-HCT to day +100 post-HCT were analyzed in relation to these SNPs in linear regression models. After controlling for clinical risk factors, we identified 16 SNPs associated with spinal or femoral BMD loss following HCT, three of which have been previously implicated in genome-wide association studies of bone phenotypes, including rs2075555 in COL1A1, rs9594738 in RANKL, and rs4870044 in ESR1. When multiple SNPs were considered simultaneously, they explained 5-35% of the variance in post-HCT BMD loss. There was a significant trend between the number of risk alleles and the magnitude of BMD loss, with patients carrying the most risk alleles having the greatest loss. CONCLUSION: Our data provide the first evidence that common genetic variants play an important role in BMD loss among HCT patients similar to age-related BMD loss in the general population. This infers that the mechanism for post-HCT bone loss is a normal aging process that is accelerated during HCT. A limitation of our study comes from its small patient population; hence future larger studies are warranted to validate our findings

The DEEP2 Galaxy Redshift Survey: The Evolution of Void Statistics from z~1 to z~0

We present measurements of the void probability function (VPF) at z~1 using data from the DEEP2 Redshift Survey and its evolution to z~0 using data from the Sloan Digital Sky Survey (SDSS). We measure the VPF as a function of galaxy color and luminosity in both surveys and find that it mimics trends displayed in the two-point correlation function, $\xi$; namely that samples of brighter, red galaxies have larger voids (i.e. are more strongly clustered) than fainter, blue galaxies. We also clearly detect evolution in the VPF with cosmic time, with voids being larger in comoving units at z~0. We find that the reduced VPF matches the predictions of a `negative binomial' model for galaxies of all colors, luminosities, and redshifts studied. This model lacks a physical motivation, but produces a simple analytic prediction for sources of any number density and integrated two-point correlation function, \bar{\xi}. This implies that differences in the VPF across different galaxy populations are consistent with being due entirely to differences in the population number density and \bar{\xi}. The robust result that all galaxy populations follow the negative binomial model appears to be due to primarily to the clustering of dark matter halos. The reduced VPF is insensitive to changes in the parameters of the halo occupation distribution, in the sense that halo models with the same \bar{\xi} will produce the same VPF. For the wide range of galaxies studied, the VPF therefore does not appear to provide useful constraints on galaxy evolution models that cannot be gleaned from studies of \bar{\xi} alone. (abridged)Comment: 17 pages, 15 figures, ApJ accepte

Definitions of Urinary Tract Infection in Current Research: A Systematic Review

Defining urinary tract infection (UTI) is complex, as numerous clinical and diagnostic parameters are involved. In this systematic review, we aimed to gain insight into how UTI is defined across current studies. We included 47 studies, published between January 2019 and May 2022, investigating therapeutic or prophylactic interventions in adult patients with UTI. Signs and symptoms, pyuria, and a positive urine culture were required in 85%, 28%, and 55% of study definitions, respectively. Five studies (11%) required all 3 categories for the diagnosis of UTI. Thresholds for significant bacteriuria varied from 103 to 105 colony-forming units/mL. None of the 12 studies including acute cystitis and 2 of 12 (17%) defining acute pyelonephritis used identical definitions. Complicated UTI was defined by both host factors and systemic involvement in 9 of 14 (64%) studies. In conclusion, UTI definitions are heterogeneous across recent studies, highlighting the need for a consensus-based, research reference standard for UTI

The DEEP2 Galaxy Redshift Survey: The Voronoi-Delaunay Method Catalog of Galaxy Groups

We present a public catalog of galaxy groups constructed from the spectroscopic sample of galaxies in the fourth data release from the Deep Extragalactic Evolutionary Probe 2 (DEEP2) Galaxy Redshift Survey, including the Extended Groth Strip (EGS). The catalog contains 1165 groups with two or more members in the EGS over the redshift range 0 0.6 in the rest of DEEP2. Twenty-five percent of EGS galaxies and fourteen percent of high-z DEEP2 galaxies are assigned to galaxy groups. The groups were detected using the Voronoi-Delaunay method (VDM) after it has been optimized on mock DEEP2 catalogs following similar methods to those employed in Gerke et al. In the optimization effort, we have taken particular care to ensure that the mock catalogs resemble the data as closely as possible, and we have fine-tuned our methods separately on mocks constructed for the EGS and the rest of DEEP2. We have also probed the effect of the assumed cosmology on our inferred group-finding efficiency by performing our optimization on three different mock catalogs with different background cosmologies, finding large differences in the group-finding success we can achieve for these different mocks. Using the mock catalog whose background cosmology is most consistent with current data, we estimate that the DEEP2 group catalog is 72% complete and 61% pure (74% and 67% for the EGS) and that the group finder correctly classifies 70% of galaxies that truly belong to groups, with an additional 46% of interloper galaxies contaminating the catalog (66% and 43% for the EGS). We also confirm that the VDM catalog reconstructs the abundance of galaxy groups with velocity dispersions above ~300 km s^(–1) to an accuracy better than the sample variance, and this successful reconstruction is not strongly dependent on cosmology. This makes the DEEP2 group catalog a promising probe of the growth of cosmic structure that can potentially be used for cosmological tests

Evolution in the Halo Masses of Isolated Galaxies between z~1 and z~0: From DEEP2 to SDSS

We measure the evolution in the virial mass-to-light ratio (M_{200}/L_B) and virial-to-stellar mass ratio (M_{200}/M_\ast) for isolated ~ L* galaxies between z~1 and z~0 by combining data from the DEEP2 Galaxy Redshift Survey and the Sloan Digital Sky Survey. Utilizing the motions of satellite galaxies around isolated galaxies, we measure line-of-sight velocity dispersions and derive dark matter halo virial masses for these host galaxies. At both epochs the velocity dispersion of satellites correlates with host galaxy stellar mass, \sigma\propto M_\ast^{0.4+/-0.1}, while the relation between satellite velocity dispersion and host galaxy B-band luminosity may grow somewhat shallower from \sigma\propto L_B^{0.6+/-0.1} at z~1 to \sigma\propto L_B^{0.4+/-0.1} at z~0. The evolution in M_200/M_\ast from z~1 to z~0 displays a bimodality insofar as host galaxies with stellar mass below M_\ast ~10^{11} M_Sun/h maintain a constant ratio (the intrinsic increase is constrained to a factor of 1.1+/-0.7) while host galaxies above M_\ast ~10^{11} M_Sun/h experience a factor of 4+/-3 increase in their virial-to-stellar mass ratio. This result can be easily understood if galaxies below this stellar mass scale continue to form stars while star formation in galaxies above this scale is quenched and the dark matter halos of galaxies both above and below this scale grow in accordance with LCDM cosmological simulations. Host galaxies that are red in U-B color have larger satellite dispersions and hence reside on average in more massive halos than blue galaxies at both z~1 and z~0. The redshift and host galaxy stellar mass dependence of M_200/M_\ast agrees qualitatively with the Millennium Run semi-analytic model of galaxy formation. (ABRIDGED)Comment: 20 pages, 8 figures, submitted to Ap