Statistical Modeling of Epistasis and Linkage Decay using Logic Regression

Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction for vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of conjugate operators

Statistical Modeling of Epistasis and Linkage Decay using Logic Regression

Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction of vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of conjugate
operators

The HR 4796A Debris System: Discovery of Extensive Exo-Ring Dust Material

The optically and IR bright, and starlight-scattering, HR 4796A ring-like debris disk is one of the most (and best) studied exoplanetary debris systems. The presence of a yet-undetected planet has been inferred (or suggested) from the narrow width and inner/outer truncation radii of its r = 1.05" (77 au) debris ring. We present new, highly sensitive, Hubble Space Telescope (HST) visible-light images of the HR 4796A circumstellar debris system and its environment over a very wide range of stellocentric angles from 0.32" (23 au) to ~ 15" (1100 au). These very high contrast images were obtained with the Space Telescope Imaging Spectrograph (STIS) using 6-roll PSF-template subtracted coronagraphy suppressing the primary light of HR 4796A and using three image plane occulters and simultaneously subtracting the background light from its close angular proximity M2.5V companion. The resulting images unambiguously reveal the debris ring embedded within a much larger, morphologically complex, and bi-axially asymmetric exoring scattering structure. These images at visible wavelengths are sensitive to, and map, the spatial distribution, brightness, and radial surface density of micron size particles over 5 dex in surface brightness. These particles in the exo-ring environment may be unbound from the system and interacting with the local ISM. Herein we present a new morphological and photometric view of the larger than prior seen HR 4796A exoplanetary debris system with sensitivity to small particles at stellocentric distances an order of magnitude greater than has previously been observed.Comment: 28 pages, 17 figures, accepted for publication in the Astronomical Journal 21 December 201

Massive Protoplanetary Disks in the Trapezium Region

(abridged) We determine the disk mass distribution around 336 stars in the young Orion Nebula cluster by imaging a 2.5' x 2.5' region in 3 mm continuum emission with the Owens Valley Millimeter Array. For this sample of 336 stars, we observe 3 mm emission above the 3-sigma noise level toward ten sources, six of which have also been detected optically in silhouette against the bright nebular background. In addition, we detect 20 objects that do not correspond to known near-IR cluster members. Comparisons of our measured fluxes with longer wavelength observations enable rough separation of dust emission from thermal free-free emission, and we find substantial dust emission toward most objects. For the ten objects detected at both 3 mm and near-IR wavelengths, eight exhibit substantial dust emission. Excluding the high-mass stars and assuming a gas-to-dust ratio of 100, we estimate circumstellar masses ranging from 0.13 to 0.39 Msun. For the cluster members not detected at 3 mm, images of individual objects are stacked to constrain the mean 3 mm flux of the ensemble. The average flux is detected at the 3-sigma confidence level, and implies an average disk mass of 0.005 Msun, comparable to the minimum mass solar nebula. The percentage of stars in Orion surrounded by disks more massive than ~0.1 Msun is consistent with the disk mass distribution in Taurus, and we argue that massive disks in Orion do not appear to be truncated through close encounters with high-mass stars. Comparison of the average disk mass and number of massive dusty structures in Orion with similar surveys of the NGC 2024 and IC 348 clusters constrains the evolutionary timescales of massive circumstellar disks in clustered environments.Comment: 27 pages, including 7 figures. Accepted by Ap

The dust, planetesimals and planets of HD 38529

HD 38529 is a post-main sequence G8III/IV star (3.5 Gyr old) with a planetary system consisting of at least two planets having Msin(i) of 0.8 MJup and 12.2 MJup, semimajor axes of 0.13 AU and 3.74 AU, and eccentricities of 0.25 and 0.35, respectively. Spitzer observations show that HD 38529 has an excess emission above the stellar photosphere, with a signal-to-noise ratio (S/N) at 70 micron of 4.7, a small excess at 33 micron (S/N=2.6) and no excess <30 micron. We discuss the distribution of the potential dust-producing planetesimals from the study of the dynamical perturbations of the two known planets, considering in particular the effect of secular resonances. We identify three dynamically stable niches at 0.4-0.8 AU, 20-50 AU and beyond 60 AU. We model the spectral energy distribution of HD 38529 to find out which of these niches show signs of harboring dust-producing plantesimals. The secular analysis, together with the SED modeling resuls, suggest that the planetesimals responsible for most of the dust emission are likely located within 20-50 AU, a configuration that resembles that of the Jovian planets + Kuiper Belt in our Solar System. Finally, we place upper limits (8E-6 lunar masses of 10 micron particles) to the amount of dust that could be located in the dynamically stable region that exists between the two planets (0.25--0.75 AU).Comment: 23 pages, including 1 table and 5 figures. Accepted for publication in Ap

Reply to ''Comments on 'Why Hasn't Earth Warmed as much as Expected?'''

In response to our article, Why Hasnt Earth Warmed as Much as Expected? (2010), Knutti and Plattner (2012) wrote a rebuttal. The term climate sensitivity is usually defined as the change in global mean surface temperature that is produced by a specified change in forcing, such as a change in solar heating or greenhouse gas concentrations. We had argued in the 2010 paper that although climate models can reproduce the global mean surface temperature history over the past century, the uncertainties in these models, due primarily to the uncertainty in climate forcing by airborne particles, mean that the models lack the confidence to actually constrain the climate sensitivity within useful limits for climate prediction. Knutti and Plattner are climate modelers, and they argued essentially that because the models could reproduce the surface temperature history, the issue we raised was moot. Our response amounts to straightening out this confusion; for the models to be constraining, they must be able to reproduce the surface temperature history with sufficient confidence, not just to match the measurements, but to exclude alternative histories. As before, we concluded that if we can actually make the aerosol measurements using currently available, state-of-the-art techniques, we can determine the aerosol climate forcing to the degree required to constrain that aspect of model climate sensitivity. A technical issue relating to the timescale over which a change in CO2 emissions would be equilibrated in the environmental energy balance was also discussed, again, a matter of differences in terminology

Qatar Exoplanet Survey : Qatar-3b, Qatar-4b and Qatar-5b

We report the discovery of Qatar-3b, Qatar-4b, and Qatar-5b, three new transiting planets identified by the Qatar Exoplanet Survey (QES). The three planets belong to the hot Jupiter family, with orbital periods of $P_{Q3b}$=2.50792 days, $P_{Q4b}$=1.80539 days, and $P_{Q5b}$=2.87923 days. Follow-up spectroscopic observations reveal the masses of the planets to be $M_{Q3b}$=4.31$\pm0.47$ $M_{\rm J}$, $M_{Q4b}$=6.10$\pm0.54$ $M_{\rm J}$, and $M_{Q5b}$ = 4.32$\pm0.18$ $M_{\rm J}$, while model fits to the transit light curves yield radii of $R_{Q3b}$ = 1.096$\pm0.14$ $R_{\rm J}$, $R_{Q4b}$ = 1.135$\pm0.11$ $R_{\rm J}$, and $R_{Q5b}$ = 1.107$\pm0.064$ $R_{\rm J}$. The host stars are low-mass main sequence stars with masses and radii $M_{Q3}$ = 1.145$\pm0.064$ $M_{\odot}$, $M_{Q4}$ = 0.896$\pm0.048$ $M_{\odot}$, $M_{Q5}$ = 1.128$\pm0.056$ $M_{\odot}$ and $R_{Q3}$ = 1.272$\pm0.14$ $R_{\odot}$, $R_{Q4}$ = 0.849$\pm0.063$ $R_{\odot}$ and $R_{Q5}$ = 1.076$\pm0.051$ $R_{\odot}$ for Qatar-3, 4 and 5 respectively. The V magnitudes of the three host stars are $V_{Q3}$=12.88, $V_{Q4}$=13.60, and $V_{Q5}$=12.82. All three new planets can be classified as heavy hot Jupiters (M > 4 $M_{J}$).Comment: 13Pages, 8Figure

Comparative effectiveness of enalapril, lisinopril, and ramipril in the treatment of patients with chronic heart failure: a propensity score-matched cohort study

Background: Angiotensin converting enzyme inhibitors (ACEIs) are recommended as first-line therapy in patients with heart failure with reduced ejection fraction (HFrEF). The comparative effectiveness of different ACEIs is not known. Methods and results: 4,723 out-patients with stable HFrEF prescribed either enalapril, lisinopril, or ramipril were identified from three registries in Norway, England, and Germany. In three separate matching procedures, patients were individually matched with respect to both dose equivalents and their respective propensity scores for ACEI treatment. During a follow-up of 21,939 patient-years, 360 (49.5%), 337 (52.4%), and 1,119 (33.4%) patients died amongst those prescribed enalapril, lisinopril, and ramipril, respectively. In univariable analysis of the general sample, enalapril and lisinopril were both associated with higher mortality as compared with ramipril treatment (HR 1.46, 95% CI 1.30-1.65, p &lt; 0.001, and HR 1.38, CI 1.22-1.56, p &lt; 0.001, respectively). Patients prescribed enalapril or lisinopril had similar mortality (HR 1.06, 95% CI 0.92-1.24, p = 0.41). However, there was no significant association between ACEI choice and all-cause mortality in any of the matched samples (HR 1.07, 95% CI 0.91-1.25, p = 0.40; HR 1.12, 95% CI 0.96-1.32, p = 0.16; and HR 1.08, HR 1.10, 95% CI 0.93-1.31, p = 0.25 for enalapril vs. ramipril, lisinopril vs. ramipril, and enalapril vs. lisinopril, respectively). Results were confirmed in subgroup analyses with respect to age, sex, left ventricular ejection fraction, NYHA functional class, cause of HFrEF, rhythm, and systolic blood pressure. Conclusion: Our results suggest that enalapril, lisinopril and ramipril are equally effective in the treatment of patients with HFrEF when given at equivalent doses

Field-Based Estimates of Heritability and Genetic Correlations in Hop

Hop (Humulus lupulus L. var. lupulus) is grown worldwide for the production of the dried female inflorescence (strobulus), or cones, used principally for the bittering and flavoring of beer. Information is scant on the inheritance of traits of economic importance in hop, and present knowledge is based on historical data rather than designed experimental investigation. The objective of this study was to estimate the heritability of and genetic correlation among six traits: yield (YLD), α-acid (ALP) concentration, β-acid (BET) concentration, cohumulone (COH) percentage, colupulone (COL) percentage, and xanthohumol (XAN) concentration. Twenty-five full-sib families were developed by crossing five randomly chosen females and five randomly chosen males in a North Carolina Design II mating design. Plants were transplanted into the field in a randomized complete block (RCB) design with four replicates. Data were recorded for two years. Heritabilities for all traits were moderate to high using variance components estimated from males. With the exception of heritability estimates for YLD and ALP, all other traits were not significantly different from zero using female variance components as estimators. Pooled estimates of heritability yielded more reasonable estimates with lowest heritability for BET (h² = 0.57 ± 0.19) and highest for COL (h² = 0.89 ± 0.02). Pooled estimates of genetic correlations ranged from r = 0.28 (ALP and YLD) to r = 0.92 (YLD and XAN). Finally, correlations between coefficients of coancestry (COA) between pairs and their respective mean offspring data were significant for ALP, COL, and XAN suggesting that for these traits at least, COA values may be predictive of potential heterosis. On the basis of these data, selection for COL, ALP, and YLD would be successful using simple selection protocols such as phenotypic recurrent or mass selection. The likelihood of success when selecting for BET and XAN would be low, thus requiring one of the genotypic recurrent selection techniques. Selection against COH (a negative factor in brewing) appears problematic because of positive correlations with all other traits. The information presented in this study is the first published record of field-based estimates of narrow-sense heritability and genetic correlations in hop and will aid hop breeders working with these traits