Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing

We propose a flexible change-point model for inhomogeneous Poisson Processes, which arise naturally from next-generation DNA sequencing, and derive score and generalized likelihood statistics for shifts in intensity functions. We construct a modified Bayesian information criterion (mBIC) to guide model selection, and point-wise approximate Bayesian confidence intervals for assessing the confidence in the segmentation. The model is applied to DNA Copy Number profiling with sequencing data and evaluated on simulated spike-in and real data sets.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS517 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The Economic Impact of the Nevada Clean Indoor Air Act in Clark County, Nevada – Preliminary Findings

Objective. The primary purpose of this exploratory study was to quantitatively evaluate the economic impact of the Nevada Clean Indoor Air Act (NCIAA) on businesses in Clark County. Methods. The goal of this research was to assess economic indicators over a ten year period utilizing measurable data points, including restaurant and drinking establishment employment rates, taxable sales, openings and closings, as well as slot gaming revenues. This ten year time period consisted of a seven year span prior to the enactment of the NCIAA, and three years post enactment. Researchers conceived this study as a means to independently evaluate and address the potential economic impact of a smoke-free law in a region dependent upon tourism and gaming. Results. Economic indicators did in fact decrease after the NCIAA was enforced but most of the declining trends began prior to the passage of the smoke-free act and are consistent with downward trends in other, non-NCIAA affected segments of our economy. Conclusion. The overall findings of this study are consistent with similar non-tobacco industry supported economic studies showing little or no statistically significant downward economic trends after passage of smoke-free legislation

A hydrodynamic model for Galveston Bay and the shelf in the northern Gulf of Mexico

A 3-D unstructured-grid hydrodynamic model for the northern Gulf of Mexico was developed, with a hybrid s–z vertical grid and high-resolution horizontal grid for the main estuarine systems along the Texas–Louisiana coast. This model, based on the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), is driven by the observed river discharge, reanalysis atmospheric forcing, and open boundary conditions from global HYCOM output. The model reproduces the temporal and spatial variation of observed water level, salinity, temperature, and current velocity in Galveston Bay and on the shelf. The validated model was applied to examine the remote influence of neighboring large rivers, specifically the Mississippi–Atchafalaya River (MAR) system, on salinity, stratification, vertical mixing, and longshore transport along the Texas coast. Numerical experiments reveal that the MAR discharge could significantly decrease the salinity and change the stratification and vertical mixing on the inner Texas shelf. It would take about 25 and 50 d for the MAR discharge to reach the mouth of Galveston Bay and Port Aransas, respectively. The influence of the MAR discharge is sensitive to the wind field. Winter wind constrains the MAR freshwater to form a narrow lower-salinity band against the shore from the Mississippi Delta all the way to the southwestern Texas coast, while summer wind reduces the downcoast longshore transport significantly, weakening the influence of the MAR discharge on surface salinity along Texas coast. However, summer wind causes a much stronger stratification on the Texas shelf, leading to a weaker vertical mixing. The decrease in salinity of up to 10 psu at the mouth of Galveston Bay due to the MAR discharge results in a decrease in horizontal density gradient, a decrease in the salt flux, and a weakened estuarine circulation and estuarine–ocean exchange. We highlight the flexibility of the model and its capability to simulate not only estuarine dynamics and shelf-wide transport, but also the interactions between them

Pilot trial of paclitaxel-trastuzumab adjuvant therapy for early stage breast cancer: a trial of the ECOG-ACRIN cancer research group (E2198)

BACKGROUND: Blockade of human epidermal growth factor receptor type 2 (HER2) has dramatically improved outcome for patients with HER2-positive breast cancer. Trastuzumab, an anti-HER2 monoclonal antibody, has previously demonstrated improvement in overall survival (OS) in patients with metastatic and early stage HER2-positive breast cancer. However, trastuzumab can cause congestive heart failure (CHF) with an increased frequency for patients who have also received an anthracycline. The current trial was designed to evaluate the impact of the duration of trastuzumab on CHF. METHODS: E2198 included 227 eligible women with histologically confirmed stage II or IIIA HER2-positive breast cancer. The patients were randomised to receive 12 weeks of paclitaxel and trastuzumab followed by four cycles of doxorubicin and cyclophosphamide (abbreviated Arm) or the aforementioned treatment with additional 1 year of trastuzumab (conventional Arm). The primary end point was to evaluate the safety of this variable duration of trastuzumab therapy, particularly cardiac toxicity defined as CHF or left ventricular ejection fraction decrease >10%. Secondary end points included disease-free survival (DFS) and OS. RESULTS: Compared with 12-week treatment with trastuzumab, 1 year of trastuzumab-based therapy did not increase the frequency or severity of cardiac toxicity: three patients on the abbreviated Arm and four on the conventional Arm experienced CHF. The 5-year DFS was 76% and 73% for the abbreviated and conventional Arms, respectively, with a hazard ratio (HR) of 1.3 (95% CI: 0.8-2.1; P=0.3). There was also no statistically significance difference in OS (HR, 1.4; P=0.3). CONCLUSIONS: Compared with 12 weeks of treatment, 1 year of treatment with trastuzumab did not significantly increase the risk of cardiac toxicity. Although not powered for efficacy comparisons, the longer duration of trastuzumab therapy did not demonstrate a signal for marked superiority

Growth mixture modeling as an exploratory analysis tool in longitudinal quantitative trait loci analysis

We examined the properties of growth mixture modeling in finding longitudinal quantitative trait loci in a genome-wide association study. Two software packages are commonly used in these analyses: Mplus and the SAS TRAJ procedure. We analyzed the 200 replicates of the simulated data with these programs using three tests: the likelihood-ratio test statistic, a direct test of genetic model coefficients, and the chi-square test classifying subjects based on the trajectory model's posterior Bayesian probability. The Mplus program was not effective in this application due to its computational demands. The distributions of these tests applied to genes not related to the trait were sensitive to departures from Hardy-Weinberg equilibrium. The likelihood-ratio test statistic was not usable in this application because its distribution was far from the expected asymptotic distributions when applied to markers with no genetic relation to the quantitative trait. The other two tests were satisfactory. Power was still substantial when we used markers near the gene rather than the gene itself. That is, growth mixture modeling may be useful in genome-wide association studies. For markers near the actual gene, there was somewhat greater power for the direct test of the coefficients and lesser power for the posterior Bayesian probability chi-square test

Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production

Background Lignocellulosic biomass is one of the most promising renewable and clean energy resources to reduce greenhouse gas emissions and dependence on fossil fuels. However, the resistance to accessibility of sugars embedded in plant cell walls (so-called recalcitrance) is a major barrier to economically viable cellulosic ethanol production. A recent report from the US National Academy of Sciences indicated that, “absent technological breakthroughs”, it was unlikely that the US would meet the congressionally mandated renewable fuel standard of 35 billion gallons of ethanol-equivalent biofuels plus 1 billion gallons of biodiesel by 2022. We here describe the properties of switchgrass (Panicum virgatum) biomass that has been genetically engineered to increase the cellulosic ethanol yield by more than 2-fold. Results We have increased the cellulosic ethanol yield from switchgrass by 2.6-fold through overexpression of the transcription factor PvMYB4. This strategy reduces carbon deposition into lignin and phenolic fermentation inhibitors while maintaining the availability of potentially fermentable soluble sugars and pectic polysaccharides. Detailed biomass characterization analyses revealed that the levels and nature of phenolic acids embedded in the cell-wall, the lignin content and polymer size, lignin internal linkage levels, linkages between lignin and xylans/pectins, and levels of wall-bound fucose are all altered in PvMYB4-OX lines. Genetically engineered PvMYB4-OX switchgrass therefore provides a novel system for further understanding cell wall recalcitrance. Conclusions Our results have demonstrated that overexpression of PvMYB4, a general transcriptional repressor of the phenylpropanoid/lignin biosynthesis pathway, can lead to very high yield ethanol production through dramatic reduction of recalcitrance. MYB4-OX switchgrass is an excellent model system for understanding recalcitrance, and provides new germplasm for developing switchgrass cultivars as biomass feedstocks for biofuel production. Keywords: Switchgrass; Bioenergy; Biofuel; Feedstock; Cellulosic ethanol; PvMYB4; Transcription factor; Cell wall; Recalcitrance; Lignin; Hemicellulose; Pecti

A causative relationship exists between eosinophils and the development of allergic pulmonary pathologies in the mouse

Asthma and mouse models of allergic respiratory inflammation are invariably associated with a pulmonary eosinophilia; however, this association has remained correlative. In this report, a causative relationship between eosinophils and allergen-provoked pathologies was established using eosinophil adoptive transfer. Eosinophils were transferred directly into the lungs of either naive or OVA-treated IL-5-/- mice. This strategy resulted in a pulmonary eosinophilia equivalent to that observed in OVA-treated wild-type animals. A concomitant consequence of this eosinophil transfer was an increase in Th2 bronchoalveolar lavage cytokine levels and the restoration of intracellular epithelial mucus in OVA-treated IL-5-/- mice equivalent to OVA-treated wild-type levels. Moreover, the transfer also resulted in the development of airway hyperresponsiveness. These pulmonary changes did not occur when eosinophils were transferred into naive IL-5-/- mice, eliminating nonspecific consequences of the eosinophil transfer as a possible explanation. Significantly, administration of OVA-treated IL-5-/- mice with GK1.5 (anti-CD4) Abs abolished the increases in mucus accumulation and airway hyperresponsiveness following adoptive transfer of eosinophils. Thus, CD4+ T cell-mediated inflammatory signals as well as signals derived from eosinophils are each necessary, yet alone insufficient, for the development of allergic pulmonary pathology. These data support an expanded view of T cell and eosinophil activities and suggest that eosinophil effector functions impinge directly on lung function

Light whole genome sequence for SNP discovery across domestic cat breeds

<p>Abstract</p> <p>Background</p> <p>The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- FeLV, feline coronavirus -- FECV, feline immunodeficiency virus - FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery.</p> <p>Description</p> <p>To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly available 2X cat whole genome sequence. All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs. To reduce potential false positive SNPs due to the low coverage assembly, a low upper-limit was placed on sequence coverage and a high lower-limit on the quality of the discrepant bases at a potential variant site. In all domestic cats of different breeds: female Abyssinian, female American shorthair, male Cornish Rex, female European Burmese, female Persian, female Siamese, a male Ragdoll and a female African wildcat were sequenced lightly. We report a total of 964 k common SNPs suitable for a domestic cat SNP genotyping array and an additional 900 k SNPs detected between African wildcat and domestic cats breeds. An empirical sampling of 94 discovered SNPs were tested in the sequenced cats resulting in a SNP validation rate of 99%.</p> <p>Conclusions</p> <p>These data provide a large collection of mapped feline SNPs across the cat genome that will allow for the development of SNP genotyping platforms for mapping feline diseases.</p