Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

BackgroundPopulus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.ResultsWe identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others.ConclusionsSNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies

Globalization, domestic politics, and transatlantic relations

For two decades after the fall of the Berlin Wall, globalization functioned as a unifying force in the West. In the absence of a common security threat, the United States and Europe found common ground in a neoliberal agenda calling for the freer movements of capital, goods, services, and peoples across national boundaries. Today, support for that neoliberal agenda has been rapidly weakening across the West. Drawing on a variety of quantitative measures, we show that Western support for globalization has declined, both at the level of national policy and at the level of party politics. We argue that this erosion of domestic support for globalization is closely linked to the rise of populist parties in Europe and the USA. We consider the implications of this shift in the West’s domestic politics for the future of transatlantic cooperation and leadership

Measurement of Volumetric Flow

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135278/1/jum200625101305.pd

Human Performance Contributions to Safety in Commercial Aviation

In the commercial aviation domain, large volumes of data are collected and analyzed on the failures and errors that result in infrequent incidents and accidents, but in the absence of data on behaviors that contribute to routine successful outcomes, safety management and system design decisions are based on a small sample of non- representative safety data. Analysis of aviation accident data suggests that human error is implicated in up to 80% of accidents, which has been used to justify future visions for aviation in which the roles of human operators are greatly diminished or eliminated in the interest of creating a safer aviation system. However, failure to fully consider the human contributions to successful system performance in civil aviation represents a significant and largely unrecognized risk when making policy decisions about human roles and responsibilities. Opportunities exist to leverage the vast amount of data that has already been collected, or could be easily obtained, to increase our understanding of human contributions to things going right in commercial aviation. The principal focus of this assessment was to identify current gaps and explore methods for identifying human success data generated by the aviation system, from personnel and within the supporting infrastructure

The problem of shot selection in basketball

In basketball, every time the offense produces a shot opportunity the player with the ball must decide whether the shot is worth taking. In this paper, I explore the question of when a team should shoot and when they should pass up the shot by considering a simple theoretical model of the shot selection process, in which the quality of shot opportunities generated by the offense is assumed to fall randomly within a uniform distribution. I derive an answer to the question "how likely must the shot be to go in before the player should take it?", and show that this "lower cutoff" for shot quality $f$ depends crucially on the number $n$ of shot opportunities remaining (say, before the shot clock expires), with larger $n$ demanding that only higher-quality shots should be taken. The function $f(n)$ is also derived in the presence of a finite turnover rate and used to predict the shooting rate of an optimal-shooting team as a function of time. This prediction is compared to observed shooting rates from the National Basketball Association (NBA), and the comparison suggests that NBA players tend to wait too long before shooting and undervalue the probability of committing a turnover.Comment: 7 pages, 2 figures; comparison to NBA data adde

AI solutions for human problems

Abstract Background Bronchiectasis is a chronic respiratory condition. Persistent bacterial colonisation in the stable state with increased and sometimes altered bacterial burden during exacerbations are accepted as key features in the pathophysiology. The extent to which respiratory viruses are present during stable periods and in exacerbations is less well understood. Methods This study aimed to determine the incidence of respiratory viruses within a cohort of bronchiectasis patients with acute exacerbations at a teaching hospital and, separately, in a group of patients with stable bronchiectasis. In the group of stable patients, a panel of respiratory viruses were assayed for using real time quantitative PCR in respiratory secretions and exhaled breath. The Impact of virus detection on exacerbation rates and development of symptomatic infection was evaluated. Results Routine hospital-based viral PCR testing was only requested in 28% of admissions for an exacerbation. In our cohort of stable bronchiectasis patients, viruses were detected in 92% of patients during the winter season, and 33% of patients during the summer season. In the 2-month follow up period, 2 of 27 patients presented with an exacerbation. Conclusions This pilot study demonstrated that respiratory viruses are commonly detected in patients with stable bronchiectasis. They are frequently detected during asymptomatic viral periods, and multiple viruses are often present concurrently

HerMES: the rest-frame UV emission and a lensing model for the z= 6.34 luminous dusty starburst galaxy HFLS3

We discuss the rest-frame ultraviolet emission from the starbursting galaxy HFLS3 at a redshift of 6.34. The galaxy was discovered in Herschel/SPIRE data due to its red color in the submillimeter wavelengths from 250 to 500 μm. Keck/NIRC2 K s -band adaptive optics imaging data showed two potential near-IR counterparts near HFLS3. Previously, the northern galaxy was taken to be in the foreground at z = 2.1, while the southern galaxy was assumed to be HFLS3's near-IR counterpart. The recently acquired Hubble/WFC3 and Advanced Camera for Surveys (ACS) imaging data show conclusively that both optically bright galaxies are in the foreground at z < 6. A new lensing model based on the Hubble imaging data and the millimeter-wave continuum emission yields a magnification factor of 2.2 ± 0.3, with a 95% confidence upper limit on the magnification of 3.5. When corrected for lensing, the instantaneous star formation rate is 1320 M ☉ yr–1, with the 95% confidence lower limit around 830 M ☉ yr–1. The dust and stellar masses of HFLS3 from the same spectral energy distribution (SED) models are at the level of 3 × 108 M ☉ and ~5 × 1010 M ☉, respectively, with large systematic uncertainties on assumptions related to the SED model. With Hubble/WFC3 images, we also find diffuse near-IR emission about 0.5 arcsec (~3 kpc) to the southwest of HFLS3 that remains undetected in the ACS imaging data. The emission has a photometric redshift consistent with either z ~ 6 or a dusty galaxy template at z ~ 2

Strontium Isotopic Composition of Paleozoic Carbonate Rocks in the Nevada Test Site Vicinity, Clark, Lincoln, and Nye Counties, Nevada and Inyo County, California.

Ground water moving through permeable Paleozoic carbonate rocks represents the most likely pathway for migration of radioactive contaminants from nuclear weapons testing at the Nevada Test Site, Nye County, Nevada. The strontium isotopic composition (87Sr/86Sr) of ground water offers a useful means of testing hydrochemical models of regional flow involving advection and reaction. However, reaction models require knowledge of 87Sr/86Sr data for carbonate rock in the Nevada Test Site vicinity, which is scarce. To fill this data gap, samples of core or cuttings were selected from 22 boreholes at depth intervals from which water samples had been obtained previously around the Nevada Test Site at Yucca Flat, Frenchman Flat, Rainier Mesa, and Mercury Valley. Dilute acid leachates of these samples were analyzed for a suite of major- and trace-element concentrations (MgO, CaO, SiO2, Al2O3, MnO, Rb, Sr, Th, and U) as well as for 87Sr/86Sr. Also presented are unpublished analyses of 114 Paleozoic carbonate samples from outcrops, road cuts, or underground sites in the Funeral Mountains, Bare Mountain, Striped Hills, Specter Range, Spring Mountains, and ranges east of the Nevada Test Site measured in the early 1990's. These data originally were collected to evaluate the potential for economic mineral deposition at the potential high-level radioactive waste repository site at Yucca Mountain and adjacent areas (Peterman and others, 1994). Samples were analyzed for a suite of trace elements (Rb, Sr, Zr, Ba, La, and Ce) in bulk-rock powders, and 87Sr/86Sr in partial digestions of carbonate rock using dilute acid or total digestions of silicate-rich rocks. Pre-Tertiary core samples from two boreholes in the central or western part of the Nevada Test Site also were analyzed. Data are presented in tables and summarized in graphs; however, no attempt is made to interpret results with respect to ground-water flow paths in this report. Present-day 87Sr/86Sr values are compared to values for Paleozoic seawater present at the time of deposition. Many of the samples have 87Sr/86Sr compositions that remain relatively unmodified from expected seawater values. However, rocks underlying the northern Nevada Test Site as well as rocks exposed at Bare Mountain commonly have elevated 87Sr/86Sr values derived from post-depositional addition of radiogenic Sr most likely from fluids circulating through rubidium-rich Paleozoic strata or Precambrian basement rocks

LL-37 and HMGB1 induce alveolar damage and reduce lung tissue regeneration via RAGE

The receptor for advanced glycation end-products (RAGE) has been implicated in the pathophysiology of chronic obstructive pulmonary disease (COPD). However, it is still unknown whether RAGE directly contributes to alveolar epithelial damage and abnormal repair responses. We hypothesize that RAGE activation not only induces lung tissue damage but also hampers alveolar epithelial repair responses. The effects of the RAGE ligands LL-37 and HMGB1 were examined on airway inflammation and alveolar tissue damage in wild-type and RAGE-deficient mice and on lung damage and repair responses using murine precision cut lung slices (PCLS) and organoids. In addition, their effects were studied on the repair response of human alveolar epithelial A549 cells, using siRNA knockdown of RAGE and treatment with the RAGE inhibitor FPS-ZM1. We observed that intranasal installation of LL-37 and HMGB1 induces RAGE-dependent inflammation and severe alveolar tissue damage in mice within 6 h, with stronger effects in a mouse strain susceptible for emphysema compared with a nonsusceptible strain. In PCLS, RAGE inhibition reduced the recovery from elastaseinduced alveolar tissue damage. In organoids, RAGE ligands reduced the organoid-forming efficiency and epithelial differentiation into pneumocyte-organoids. Finally, in A549 cells, we confirmed the role of RAGE in impaired repair responses upon exposure to LL-37. Together, our data indicate that activation of RAGE by its ligands LL-37 and HMGB1 induces acute lung tissue damage and that this impedes alveolar epithelial repair, illustrating the therapeutic potential of RAGE inhibitors for lung tissue repair in emphysema