Spin orbit alignment for KELT-7b and HAT-P-56b via Doppler tomography with TRES

We present Doppler tomographic analyses for the spectroscopic transits of KELT-7b and HAT-P-56b, two hot-Jupiters orbiting rapidly rotating F-dwarf host stars. These include analyses of archival TRES observations for KELT-7b, and a new TRES transit observation of HAT-P-56b. We report spin-orbit aligned geometries for KELT-7b (2.7 +/- 0.6 deg) and HAT-P-56b (8 +/- 2 deg). The host stars KELT-7 and HAT-P-56 are among some of the most rapidly rotating planet-hosting stars known. We examine the tidal re-alignment model for the evolution of the spin-orbit angle in the context of the spin rates of these stars. We find no evidence that the rotation rates of KELT-7 and HAT-P-56 have been modified by star-planet tidal interactions, suggesting that the spin-orbit angle of systems around these hot stars may represent their primordial configuration. In fact, KELT-7 and HAT-P-56 are two of three systems in super-synchronous, spin-orbit aligned states, where the rotation periods of the host stars are faster than the orbital periods of the planets.Comment: 9 pages, accepted for publication in MNRA

Soil properties under different orchard floor management systems for organic apple production

Orchard floor management impacts soil conditions and thus tree performance. This research was initiated to investigate the effects of alternative orchard floor management systems compatible with organic production on soil parameters using the“Pacific Gala” apple cultivar (Malus × domestica Borkh.) on three rootstocks of varying vigor. Alfalfa hay mulch, propane flame burner, and Swiss sandwich system(combination of resident vegetation and tilled strips)were compared from 2001 to 2005. These treatments were applied to tree rows which provided different vegetation-free areas. Contrasting additions of organic matter were evaluated for their effect on soil organic matter (SOM), C content, nitrate and ammonium availability, moisture, and soil food web through nematode populations. Laboratory incubations to determine C and N mineralization potentials were performed. During this time period, SOM increased under the mulched soil and slightly less under the Swiss sandwich system (SSS) but in this last case without external inputs. Carbon and N pools were not impacted by flame burning (FL) but were enhanced by alfalfa hay mulch (MU) and to a lesser extent by SSS. Nitrate-N content in soil under MU increased between five and ten times compared to SSS and FL. Total number of nematodes was higher for SSS and MU compared with FL treatment; however, SSS had the most structured soil food web, an important sustainability trait, while MU had the leas

Grassland Resources and Protections in the Yellow River Source Zone on the Qinghai-Tibet Plateau

This paper summarises resources and protections of the Yellow River Source Zone on the Qinghai-Tibet Plateau. A concerted effort has been made to address concerns for overgrazing on the alpine steppe and alpine meadow landscapes in the source zone of the Yellow River. An assessment of the impacts of overgrazing includes consideration of the role of small mammals (on the one hand they are considered as a critical ecosystem engineer, on the other they are perceived as a major threatening pest). Analyzed in this paper are management options in the restoration of degraded grasslands

Performance of nonparametric species richness estimators in a high diversity plant community

The efficiency of four nonparametric species richness estimators - first-order Jackknife, second-order Jackknife, Chao2 and Bootstrap - was tested using simulated quadrat sampling of two field data sets (a sandy 'Dune' and adjacent 'Swale') in high diversity shrublands (kwongan) in south-western Australia. The data sets each comprised > 100 perennial plant species and < 10 000 individuals, and the explicit (x-y coordinate) location of every individual. We applied two simulated sampling strategies to these data sets based on sampling quadrats of unit sizes 1/400th and 1/100th of total plot area. For each site and sampling strategy we obtained 250 independent sample curves, of 250 quadrats each, and compared the estimators' performances by using three indices of bias and precision: MRE (mean relative error), MSRE (mean squared relative error) and OVER (percentage overestimation). The analysis presented here is unique in providing sample estimates derived from a complete, field-based population census for a high diversity plant community. In general the true reference value was approached faster for a comparable area sampled for the smaller quadrat size and for the swale field data set, which was characterized by smaller plant size and higher plant density. Nevertheless, at least 15-30% of the total area needed to be sampled before reasonable estimates of St (total species richness) were obtained. In most field surveys, typically less than 1% of the total study domain is likely to be sampled, and at this sampling intensity underestimation is a problem. Results showed that the second-order Jackknife approached the actual value of St more quickly than the other estimators. All four estimators were better than Sobs (observed number of species). However, the behaviour of the tested estimators was not as good as expected, and even with large sample size (number of quadrats sampled) all of them failed to provide reliable estimates. First- and second-order Jackknives were positively biased whereas Chao2 and Bootstrap were negatively biased. The observed limitations in the estimators' performance suggests that there is still scope for new tools to be developed by statisticians to assist in the estimation of species richness from sample data, especially in communities with high species richness

Extending the Functionality of Behavioural Change-Point Analysis with k-Means Clustering: A Case Study with the Little Penguin (Eudyptula minor)

We present a simple framework for classifying mutually exclusive behavioural states within the geospatial lifelines of animals. This method involves use of three sequentially applied statistical procedures: (1) behavioural change point analysis to partition movement trajectories into discrete bouts of same-state behaviours, based on abrupt changes in the spatiotemporal autocorrelation structure of movement parameters; (2) hierarchical multivariate cluster analysis to determine the number of different behavioural states; and (3) k-means clustering to classify inferred bouts of same-state location observations into behavioural modes. We demonstrate application of the method by analysing synthetic trajectories of known ‘artificial behaviours’ comprised of different correlated random walks, as well as real foraging trajectories of little penguins (Eudyptula minor) obtained by global-positioning-system telemetry. Our results show that the modelling procedure correctly classified 92.5% of all individual location observations in the synthetic trajectories, demonstrating reasonable ability to successfully discriminate behavioural modes. Most individual little penguins were found to exhibit three unique behavioural states (resting, commuting/active searching, arearestricted foraging), with variation in the timing and locations of observations apparently related to ambient light, bathymetry, and proximity to coastlines and river mouths. Addition of k-means clustering extends the utility of behavioural change point analysis, by providing a simple means through which the behaviours inferred for the location observations comprising individual movement trajectories can be objectively classified

Vaccinating the Young Calf with a Parenteral Adjuvanted Vaccine to Develop a Protective BRSV IgA nasal Response

Objective The purpose of this study was to evaluate the efficacy of an adjuvanted modified live virus (MLV) vaccine in the presence of well-defined maternal passive immunity.Study Description Calves were vaccinated at approximately 1 month of age and challenged ~90 days later when BRSV systemic antibodies were less than 1:4. Clinical signs, nasal secretions and blood samples for virus measurement [polymerase chain reaction (PCR) and virus isolation (VI)] and to measure for mucosal BRSV IgA antibodies were collected and the animals were euthanized and necropsied 8 days post infection. Body temperature and other clinical signs were lower at 6 and 7 days post challenge in the vaccinates. Nasal viral shed was 3–4 times lower in the vaccinated animals as measured by VI and PCR compared to the controls. On day 8 following challenge, animals were necropsied, and lung lobes were scored and tested for virus by PCR and indirect fluorescent assay (IFA). There was a 25-fold reduction in PCR virus detection in vaccinates and two of the vaccinated calves’ lungs were PCR negative. Only 29.4% of vaccinated calves were BRSV positive on IFA testing at necropsy, while 87.5% of control calves were BRSV positive. Vaccinated calves developed a mucosal BRSV IgA response with over 50% of the vaccinated calves having IgA prior to challenge and all vaccinated calves were positive following challenge

The Interactions of Change in Nutrition on Uterine Environment and Cholesterol Concentrations in Beef Cattle

The objective of this study was to evaluate the impact of nutritional changes prior to and after artificial insemination (AI) on uterine environment and plasma cholesterol concentrations

Use of Sperm In Vitro Capacitation and Flow Cytometry to Estimate Bull Fertility

Study Description: Frozen-thawed semen from five bulls previously identified as high (48.1% and 47.7%, bulls A and B, respectively), intermediary (45.5%, bull C) or low (43.1% and 40.7%, bulls D and E, respectively) fertility, based on pregnancy per AI, were evaluated with several laboratory measures. Measures included total motility, sperm plasma membrane integrity (viability), acrosome integrity, reactive oxygen species (ROS), mitochondrial membrane energy potential (mito-potential), zinc signatures (signatures 1 to 4), and CD9 protein populations at pre-wash, post-wash, h 0 (diluted with non-capacitation media), and at 0, 3, 6, and 24 h after dilution with capacitation media and incubation at 37 ºC. Data were analyzed using the GLIMMIX procedure of SAS for repeated measures with bull, time, and the interaction as fixed effects. Bull by time interaction was significant (P ≤ 0.01) for total motility and viability. There tended (P = 0.06) to be a bull by time interaction for zinc signatures 1 + 2 combined. There was a significant effect of bull (P ≤ 0.03) for viability, viable sperm with disrupted acrosome, zinc signatures 1, 2, and 1 + 2, viable CD9- (CD9 negative), and dead CD9+ (CD9 positive). High and intermediary field fertility bulls had greater (P ≤ 0.04) percentages of viable sperm, zinc signature 2, and zinc signature 1 + 2 compared to low fertility bulls. High and intermediary fertility bulls had decreased (P ≤ 0.05) percentage of dead CD9+ compared to low fertility bulls. There was or tended to be a positive correlation between pregnancy per AI and viability (P = 0.10; r = 0.81), zinc signature 2 (P = 0.04; r = 0.89), and zinc signature 1 + 2 (P = 0.10; r = 0.80)

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/