Clustering climate and management practices to define environmental challenges affecting gastrointestinal parasitism in Katahdin sheep

Gastrointestinal nematodes (GIN) negatively affect the performance and well-being of sheep. Due to anthelmintic resistance, GIN are difficult to control leading producers to choose breeds that can exhibit resistance to parasitism. An example is Katahdin sheep. Katahdins are raised in various climates and management systems in the United States. These environmental factors can be combined to form eco-management groupings or clusters. We hypothesized that GIN challenge varies predictably based on the characteristics of these environmental clusters. Forty Katahdin producers from across the United States were surveyed for management information, with body weights (BW), fecal egg counts (FEC), and FAMACHA scores (FAM) available from 17 of the 40 flocks. The performance data included 3,426 lambs evaluated around 90 d of age. Management and climate data were combined into clusters using multiple correspondence and principal component (PC) analysis. Performance data were aligned with their corresponding cluster. Depending on the trait, eco-management cluster, birth-rearing type, sex, and, as a covariate, dam age, were fitted as systematic effects with ANOVA. Clusters also were formed based on climate or management data alone. When compared with fitting the eco-management clusters, they defined less variation in each of the traits based on Akaike and Bayesian information criterion, and adjusted r2 values. To further examine variation defined by eco-management clusters, residuals from an ANOVA model excluding eco-management cluster were retained, and their correlation with PC loadings calculated. All PC loadings were included as potential independent variables and tested for significance using backward stepwise regression. The PC loadings with a correlation |≥0.49| explained significant variation in each trait and were included in the final models chosen; adjusted r2 values for BW, FEC, and FAM were 0.90, 0.81, and 0.97, respectively. When analyzing GIN challenge, eco-management clusters corresponding with hotter temperatures and greater rainfall, and with pasture-born lambs, suffered greater parasitism. Conversely, the eco-management clusters with lambs turned out to pasture at older ages benefited from reduced parasitism. Through the formation of eco-management clusters, an environmental variable can be defined to study interactions of genotypes to their environment, providing a potentially useful tool for identifying parasite-resistant sheep

The Global Emerging Infection Surveillance and Response System (GEIS), a U.S. government tool for improved global biosurveillance: a review of 2009

The Armed Forces Health Surveillance Center, Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) has the mission of performing surveillance for emerging infectious diseases that could affect the United States (U.S.) military. This mission is accomplished by orchestrating a global portfolio of surveillance projects, capacity-building efforts, outbreak investigations and training exercises. In 2009, this portfolio involved 39 funded partners, impacting 92 countries. This article discusses the current biosurveillance landscape, programmatic details of organization and implementation, and key contributions to force health protection and global public health in 2009

NICMOS Observations of the Transiting Hot Jupiter XO-1b

We refine the physical parameters of the transiting hot Jupiter planet XO-1b and its stellar host XO-1 using HST NICMOS observations. XO-1b has a radius Rp=1.21+/-0.03 RJup, and XO-1 has a radius Rs=0.94+/-0.02 RSun, where the uncertainty in the mass of XO-1 dominates the uncertainty of Rp and Rs. There are no significant differences in the XO-1 system properties between these broad-band NIR observations and previous determinations based upon ground-based optical observations. We measure two transit timings from these observations with 9 s and 15 s precision. As a residual to a linear ephemeris model, there is a 2.0 sigma timing difference between the two HST visits that are separated by 3 transit events (11.8 days). These two transit timings and additional timings from the literature are sufficient to rule out the presence of an Earth mass planet orbiting in 2:1 mean motion resonance coplanar with XO-1b. We identify and correct for poorly understood gain-like variations present in NICMOS time series data. This correction reduces the effective noise in time series photometry by a factor of two, for the case of XO-1.Comment: 13 pages, 8 figures, submitted to Ap

Movement of deep-sea coral populations on climatic timescales

During the past 40,000 years, global climate has moved into and out of a full glacial period, with the deglaciation marked by several millennial-scale rapid climate change events. Here we investigate the ecological response of deep-sea coral communities to both glaciation and these rapid climate change events. We find that the deep-sea coral populations of Desmophyllum dianthus in both the North Atlantic and the Tasmanian seamounts expand at times of rapid climate change. However, during the more stable Last Glacial Maximum, the coral population globally retreats to a more restricted depth range. Holocene populations show regional patterns that provide some insight into what causes these dramatic changes in population structure. The most important factors are likely responses to climatically driven changes in productivity, [O_2] and [CO_3^(2–)]

Fundamental Properties of Kepler Planet-Candidate Host Stars using Asteroseismology

We have used asteroseismology to determine fundamental properties for 66 Kepler planet-candidate host stars, with typical uncertainties of 3% and 7% in radius and mass, respectively. The results include new asteroseismic solutions for four host stars with confirmed planets (Kepler-4, Kepler-14, Kepler-23 and Kepler-25) and increase the total number of Kepler host stars with asteroseismic solutions to 77. A comparison with stellar properties in the planet-candidate catalog by Batalha et al. shows that radii for subgiants and giants obtained from spectroscopic follow-up are systematically too low by up to a factor of 1.5, while the properties for unevolved stars are in good agreement. We furthermore apply asteroseismology to confirm that a large majority of cool main-sequence hosts are indeed dwarfs and not misclassified giants. Using the revised stellar properties, we recalculate the radii for 107 planet candidates in our sample, and comment on candidates for which the radii change from a previously giant-planet/brown-dwarf/stellar regime to a sub-Jupiter size, or vice versa. A comparison of stellar densities from asteroseismology with densities derived from transit models in Batalha et al. assuming circular orbits shows significant disagreement for more than half of the sample due to systematics in the modeled impact parameters, or due to planet candidates which may be in eccentric orbits. Finally, we investigate tentative correlations between host-star masses and planet candidate radii, orbital periods, and multiplicity, but caution that these results may be influenced by the small sample size and detection biases.Comment: 19 pages, 10 figures, 4 tables; accepted for publication in ApJ; machine-readable versions of tables 1-3 are available as ancillary files or in the source code; v2: minor changes to match published versio

A growing global network’s role in outbreak response: AFHSC-GEIS 2008-2009

A cornerstone of effective disease surveillance programs comprises the early identification of infectious threats and the subsequent rapid response to prevent further spread. Effectively identifying, tracking and responding to these threats is often difficult and requires international cooperation due to the rapidity with which diseases cross national borders and spread throughout the global community as a result of travel and migration by humans and animals. From Oct.1, 2008 to Sept. 30, 2009, the United States Department of Defense’s (DoD) Armed Forces Health Surveillance Center Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) identified 76 outbreaks in 53 countries. Emerging infectious disease outbreaks were identified by the global network and included a wide spectrum of support activities in collaboration with host country partners, several of which were in direct support of the World Health Organization’s (WHO) International Health Regulations (IHR) (2005). The network also supported military forces around the world affected by the novel influenza A/H1N1 pandemic of 2009. With IHR (2005) as the guiding framework for action, the AFHSC-GEIS network of international partners and overseas research laboratories continues to develop into a far-reaching system for identifying, analyzing and responding to emerging disease threats

Planetary Candidates Observed by Kepler V: Planet Sample from Q1-Q12 (36 Months)

The Kepler mission discovered 2842 exoplanet candidates with 2 years of data. We provide updates to the Kepler planet candidate sample based upon 3 years (Q1-Q12) of data. Through a series of tests to exclude false-positives, primarily caused by eclipsing binary stars and instrumental systematics, 855 additional planetary candidates have been discovered, bringing the total number known to 3697. We provide revised transit parameters and accompanying posterior distributions based on a Markov Chain Monte Carlo algorithm for the cumulative catalogue of Kepler Objects of Interest. There are now 130 candidates in the cumulative catalogue that receive less than twice the flux the Earth receives and more than 1100 have a radius less than 1.5 Rearth. There are now a dozen candidates meeting both criteria, roughly doubling the number of candidate Earth analogs. A majority of planetary candidates have a high probability of being bonafide planets, however, there are populations of likely false-positives. We discuss and suggest additional cuts that can be easily applied to the catalogue to produce a set of planetary candidates with good fidelity. The full catalogue is publicly available at the NASA Exoplanet Archive.Comment: Accepted for publication, ApJ

Planetary Candidates Observed by Kepler IV: Planet Sample From Q1-Q8 (22 Months)

We provide updates to the Kepler planet candidate sample based upon nearly two years of high-precision photometry (i.e., Q1-Q8). From an initial list of nearly 13,400 Threshold Crossing Events (TCEs), 480 new host stars are identified from their flux time series as consistent with hosting transiting planets. Potential transit signals are subjected to further analysis using the pixel-level data, which allows background eclipsing binaries to be identified through small image position shifts during transit. We also re-evaluate Kepler Objects of Interest (KOI) 1-1609, which were identified early in the mission, using substantially more data to test for background false positives and to find additional multiple systems. Combining the new and previous KOI samples, we provide updated parameters for 2,738 Kepler planet candidates distributed across 2,017 host stars. From the combined Kepler planet candidates, 472 are new from the Q1-Q8 data examined in this study. The new Kepler planet candidates represent ~40% of the sample with Rp~1 Rearth and represent ~40% of the low equilibrium temperature (Teq<300 K) sample. We review the known biases in the current sample of Kepler planet candidates relevant to evaluating planet population statistics with the current Kepler planet candidate sample.Comment: 12 pages, 8 figures, Accepted ApJ Supplemen

An Automated Method for Rapid Identification of Putative Gene Family Members in Plants

BACKGROUND: Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences following duplication (adaptive selection) appears to be a common mechanism of evolution in plants and can be accompanied by purifying selection on the coding region. Such negative selection can be detected by a bias toward synonymous over nonsynonymous substitutions. However, the process of identifying this bias requires many steps usually employing several different software programs. We have simplified the process and significantly shortened the time required by condensing many steps into a few scripts or programs to rapidly identify putative gene family members beginning with a single query sequence. RESULTS: In this report we 1) describe the software tools (SimESTs, PCAT, and SCAT) developed to automate the gene family identification, 2) demonstrate the validity of the method by correctly identifying 3 of 4 PAL gene family members from Arabidopsis using EST data alone, 3) identify 2 to 6 CAD gene family members from Glycine max (previously unidentified), and 4) identify 2 members of a putative Glycine max gene family previously unidentified in any plant species. CONCLUSION: Gene families in plants, particularly that subset where purifying selection has occurred in the coding region, can be identified quickly and easily by integrating our software tools and commonly available contig assembly and ORF identification programs