Texas A&M University

About: Texas A&M University is a education organization based out in College Station, Texas, United States. It is known for research contribution in the topics: Population & Finite element method. The organization has 72169 authors who have published 164372 publications receiving 5764236 citations.

Revised standards for statistical evidence

Abstract: Recent advances in Bayesian hypothesis testing have led to the development of uniformly most powerful Bayesian tests, which represent an objective, default class of Bayesian hypothesis tests that have the same rejection regions as classical significance tests. Based on the correspondence between these two classes of tests, it is possible to equate the size of classical hypothesis tests with evidence thresholds in Bayesian tests, and to equate P values with Bayes factors. An examination of these connections suggest that recent concerns over the lack of reproducibility of scientific studies can be attributed largely to the conduct of significance tests at unjustifiably high levels of significance. To correct this problem, evidence thresholds required for the declaration of a significant finding should be increased to 25–50:1, and to 100–200:1 for the declaration of a highly significant finding. In terms of classical hypothesis tests, these evidence standards mandate the conduct of tests at the 0.005 or 0.001 level of significance.

Prognostic value of an RNA expression signature derived from cell cycle proliferation genes in patients with prostate cancer: a retrospective study.

Abstract: Summary Background Optimum management of clinically localised prostate cancer presents unique challenges because of the highly variable and often indolent natural history of the disease. To predict disease aggressiveness, clinicians combine clinical variables to create prognostic models, but the models have limited accuracy. We assessed the prognostic value of a predefined cell cycle progression (CCP) score in two cohorts of patients with prostate cancer. Methods We measured the expression of 31 genes involved in CCP with quantitative RT-PCR on RNA extracted from formalin-fixed paraffin-embedded tumour samples, and created a predefined score and assessed its usefulness in the prediction of disease outcome. The signature was assessed retrospectively in a cohort of patients from the USA who had undergone radical prostatectomy, and in a cohort of randomly selected men with clinically localised prostate cancer diagnosed by use of a transurethral resection of the prostate (TURP) in the UK who were managed conservatively. The primary endpoint was time to biochemical recurrence for the cohort of patients who had radical prostatectomy, and time to death from prostate cancer for the TURP cohort. Findings After prostatectomy, the CCP score was useful for predicting biochemical recurrence in the univariate analysis (hazard ratio for a 1-unit change [doubling] in CCP 1·89; 95% CI 1·54–2·31; p=5·6×10 −9 ) and the best multivariate analysis (1·77, 1·40–2·22; p=4·3×10 −6 ). In the best predictive model (final multivariate analysis), the CCP score and prostate-specific antigen (PSA) concentration were the most important variables and were more significant than any other clinical variable. In the TURP cohort, the CCP score was the most important variable for prediction of time to death from prostate cancer in both univariate analysis (2·92, 2·38–3·57, p=6·1×10 −22 ) and the final multivariate analysis (2·57, 1·93–3·43; p=8·2×10 −11 ), and was stronger than all other prognostic factors, although PSA concentration also added useful information. Heterogeneity in the hazard ratio for the CCP score was not noted in any case for any clinical variables. Interpretation The results of this study provide strong evidence that the CCP score is a robust prognostic marker, which, after additional validation, could have an essential role in determining the appropriate treatment for patients with prostate cancer. Funding Cancer Research UK, Queen Mary University of London, Orchid Appeal, US National Institutes of Health, and Koch Foundation.

Milky Way Cepheid Standards for Measuring Cosmic Distances and Application to Gaia DR2: Implications for the Hubble Constant

Abstract: We present HST photometry of a selected sample of 50 long-period, low-extinction Milky Way Cepheids measured on the same WFC3 F555W, F814W, and F160W-band photometric system as extragalactic Cepheids in SN Ia hosts. These bright Cepheids were observed with the WFC3 spatial scanning mode in the optical and near-infrared to mitigate saturation and reduce pixel-to-pixel calibration errors to reach a mean photometric error of 5 millimags per observation. We use the new Gaia DR2 parallaxes and HST photometry to simultaneously constrain the cosmic distance scale and to measure the DR2 parallax zeropoint offset appropriate for Cepheids. We find a value for the zeropoint offset of -46 +/- 13 muas or +/- 6 muas for a fixed distance scale, higher than found from quasars, as expected, for these brighter and redder sources. The precision of the distance scale from DR2 has been reduced by a factor of 2.5 due to the need to independently determine the parallax offset. The best fit distance scale is 1.006 +/- 0.033, relative to the scale from Riess et al 2016 with H0=73.24 km/s/Mpc used to predict the parallaxes photometrically, and is inconsistent with the scale needed to match the Planck 2016 CMB data combined with LCDM at the 2.9 sigma confidence level (99.6%). At 96.5% confidence we find that the formal DR2 errors may be underestimated as indicated. We identify additional error associated with the use of augmented Cepheid samples utilizing ground-based photometry and discuss their likely origins. Including the DR2 parallaxes with all prior distance ladder data raises the current tension between the late and early Universe route to the Hubble constant to 3.8 sigma (99.99 %). With the final expected precision from Gaia, the sample of 50 Cepheids with HST photometry will limit to 0.5% the contribution of the first rung of the distance ladder to the uncertainty in the Hubble constant.

The Herschel view of the dominant mode of galaxy growth from z = 4 to the present day

Abstract: We present an analysis of the deepest Herschel images in four major extragalactic fields GOODS–North, GOODS–South, UDS, and COSMOS obtained within the GOODS–Herschel and CANDELS–Herschel key programs. The star formation picture provided by a total of 10 497 individual far-infrared detections is supplemented by the stacking analysis of a mass complete sample of 62 361 star-forming galaxies from the Hubble Space Telescope (HST) H band-selected catalogs of the CANDELS survey and from two deep ground-based Ks band-selected catalogs in the GOODS–North and the COSMOS-wide field to obtain one of the most accurate and unbiased understanding to date of the stellar mass growth over the cosmic history. We show, for the first time, that stacking also provides a powerful tool to determine the dispersion of a physical correlation and describe our method called “scatter stacking”, which may be easily generalized to other experiments. The combination of direct UV and far-infrared UV-reprocessed light provides a complete census on the star formation rates (SFRs), allowing us to demonstrate that galaxies at z = 4 to 0 of all stellar masses (M∗) follow a universal scaling law, the so-called main sequence of star-forming galaxies. We find a universal close-to-linear slope of the log 10(SFR)–log 10(M∗) relation, with evidence for a flattening of the main sequence at high masses (log 10(M∗/M⊙) > 10.5) that becomesless prominent with increasing redshift and almost vanishes by z ≃ 2. This flattening may be due to the parallel stellar growth of quiescent bulges in star-forming galaxies, which mostly happens over the same redshift range. Within the main sequence, we measure a nonvarying SFR dispersion of 0.3 dex: at a fixed redshift and stellar mass, about 68% of star-forming galaxies form stars at a universal rate within a factor 2. The specific SFR (sSFR = SFR/M∗) of star-forming galaxies is found to continuously increase from z = 0 to 4. Finally we discuss the implications of our findings on the cosmic SFR history and on the origin of present-day stars: more than two-thirds of present-day stars must have formed in a regime dominated by the “main sequence” mode. As a consequence we conclude that, although omnipresent in the distant Universe, galaxy mergers had little impact in shaping the global star formation history over the last 12.5 billion years.

A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum.

Abstract: Crop yields are significantly reduced by aluminum toxicity on highly acidic soils, which comprise up to 50% of the world's arable land. Candidate aluminum tolerance proteins include organic acid efflux transporters, with the organic acids forming non-toxic complexes with rhizosphere aluminum. In this study, we used positional cloning to identify the gene encoding a member of the multidrug and toxic compound extrusion (MATE) family, an aluminum-activated citrate transporter, as responsible for the major sorghum (Sorghum bicolor) aluminum tolerance locus, Alt(SB). Polymorphisms in regulatory regions of Alt(SB) are likely to contribute to large allelic effects, acting to increase Alt(SB) expression in the root apex of tolerant genotypes. Furthermore, aluminum-inducible Alt(SB) expression is associated with induction of aluminum tolerance via enhanced root citrate exudation. These findings will allow us to identify superior Alt(SB) haplotypes that can be incorporated via molecular breeding and biotechnology into acid soil breeding programs, thus helping to increase crop yields in developing countries where acidic soils predominate.