Evolutionary comparisons of chelonid alphaherpesvirus 5 (ChHV5) genomes from fibropapillomatosis-afflicted green (chelonia mydas), Ooive ridley (lepidochelys olivacea) and kemp’s ridley (lepidochelys kempii) sea turtles

peer-reviewedThe spreading global sea turtle fibropapillomatosis (FP) epizootic is threatening some of Earth’s ancient reptiles, adding to the plethora of threats faced by these keystone species. Understanding this neoplastic disease and its likely aetiological pathogen, chelonid alphaherpesvirus 5 (ChHV5), is crucial to understand how the disease impacts sea turtle populations and species and the future trajectory of disease incidence. We generated 20 ChHV5 genomes, from three sea turtle species, to better understand the viral variant diversity and gene evolution of this oncogenic virus. We revealed previously underappreciated genetic diversity within this virus (with an average of 2035 single nucleotide polymorphisms (SNPs), 1.54% of the ChHV5 genome) and identified genes under the strongest evolutionary pressure. Furthermore, we investigated the phylogeny of ChHV5 at both genome and gene level, confirming the propensity of the virus to be interspecific, with related variants able to infect multiple sea turtle species. Finally, we revealed unexpected intra-host diversity, with up to 0.15% of the viral genome varying between ChHV5 genomes isolated from different tumours concurrently arising within the same individual. These findings offer important insights into ChHV5 biology and provide genomic resources for this oncogenic viru

For U.S. Black women, shift of hysterectomy to outpatient settings may have lagged behind White women: a claims-based analysis, 2011–2013

Abstract Background Hysterectomy is among the most common surgeries performed on U.S. women. For benign conditions, minimally invasive hysterectomy is recommended, whenever permitted by clinical indication and previous surgery history. No study has examined whether the use of less invasive hysterectomy spread more slowly for Black women. Methods We used the hysterectomy that occurs in outpatient settings as a proxy for minimally invasive hysterectomy. Using claims-based surgery data and census denominators, we calculated age-standardized rates of all hysterectomies in North Carolina from 2011 to 2013. Study participants were 41,899 women (64.6% non-Hispanic White, 28.3% non-Hispanic Black) who underwent hysterectomy for non-malignant indications. We fit Poisson models to determine whether changes in outpatient hysterectomy rates differed by Black-White race. We employed a difference-in-difference approach to control for racial differences in the severity of clinical indication. Further, we restricted to one state to minimize confounding from geographic differences in where Black and White women live. Results From 2011 to 2013, the overall hysterectomy rate decreased from 42.3 per 10,000 women (n = 14,648) to 37.9 per 10,000 (n = 13,241) (p < 0.0001). Most hysterectomy (67.6%) occurred in outpatient settings. The inpatient rate decreased 35.2% (p < 0.0001), to 10.3 per 10,000, while the outpatient rate increased 4.6% (p < 0.01), to 27.5 per 10,000. From 2011 to 2013, Black women’s outpatient rate increased 22% (p < 0.0001): from 25.8 per 10,000 to 31.5. In contrast, among White women, outpatient rates remained stable (p = 0.79): at 28.3 per 10,000 in 2013. Conclusions Rapid increases in outpatient hysterectomy among Black women compared to stable rates among White women indicate a race-specific catch-up phenomenon in the spread of minimally invasive hysterectomy. These results are consistent with the hypothesis that minimally invasive hysterectomy may have been adopted more slowly for Black women than their White counterparts after its introduction in the early 2000s. The persistently high rates of hysterectomy among young Black women and potentially slower adoption of minimally invasive procedures among these women highlight a potential racial disparity in women’s healthcare

Warm and Dense Molecular Gas in the N159 Region: 12CO J=4-3 and 13CO J=3-2 Observations with NANTEN2 and ASTE

New 12CO J=4-3 and 13CO J=3-2 observations of the N159 region in the Large Magellanic Cloud have been made. The 12CO J=4-3 distribution is separated into three clumps. These new measurements toward the three clumps are used in coupled calculations of molecular rotational excitation and line radiation transfer, along with other transitions of the 12CO as well as the isotope transitions of 13CO. The temperatures and densities are determined to be ~70-80K and ~3x10^3 cm-3 in N159W and N159E and ~30K and ~1.6x10^3 cm-3 in N159S. These results are compared with the star formation activity. The N159E clump is associated with embedded cluster(s) as observed at 24 micron and the derived high temperature is explained as due to the heating by these sources. The N159E clump is likely responsible for a dark lane in a large HII region by the dust extinction. The N159W clump is associated with embedded clusters mainly toward the eastern edge of the clump only. These clusters show offsets of 20"-40" from the 12CO J=4-3 peak and are probably responsible for heating indicated by the derived high temperature. The N159W clump exhibits no sign of star formation toward the 12CO J=4-3 peak position and its western region. We suggest that the N159W peak represents a pre-star-cluster core of ~105M_sol which deserves further detailed studies. Note that recent star formation took place between N159W and N159E as indicated by several star clusters and HII regions, while the natal molecular gas toward the stars have already been dissipated by the ionization and stellar winds of the OB stars. The N159S clump shows little sign of star formation as is consistent with the lower temperature and somewhat lower density. The N159S clump is also a candidate for future star formation

Supernova Remnants and Star Formation in the Large Magellanic Cloud

It has often been suggested that supernova remnants (SNRs) can trigger star formation. To investigate the relationship between SNRs and star formation, we have examined the known sample of 45 SNRs in the Large Magellanic Cloud to search for associated young stellar objects (YSOs) and molecular clouds. We find seven SNRs associated with both YSOs and molecular clouds, three SNRs associated with YSOs but not molecular clouds, and eight SNRs near molecular clouds but not associated with YSOs. Among the 10 SNRs associated with YSOs, the association between the YSOs and SNRs can be either rejected or cannot be convincingly established for eight cases. Only two SNRs have YSOs closely aligned along their rims; however, the time elapsed since the SNR began to interact with the YSOs' natal clouds is much shorter than the contraction timescales of the YSOs, and thus we do not see any evidence of SNR-triggered star formation in the LMC. The 15 SNRs that are near molecular clouds may trigger star formation in the future when the SNR shocks have slowed down to <45 km/s. We discuss how SNRs can alter the physical properties and abundances of YSOs.Comment: 24 pages, 5 figures, 1 table, Accepted for publication in the August 2010 edition of the Astronomical Journa

Development and initial testing of a computer-based patient decision aid to promote colorectal cancer screening for primary care practice

BACKGROUND: Although colorectal cancer screening is recommended by major policy-making organizations, rates of screening remain low. Our aim was to develop a patient-directed, computer-based decision aid about colorectal cancer screening and investigate whether it could increase patient interest in screening. METHODS: We used content from evidence-based literature reviews and our previous decision aid research to develop a prototype. We performed two rounds of usability testing with representative patients to revise the content and format. The final decision aid consisted of an introductory segment, four test-specific segments, and information to allow comparison of the tests across several key parameters. We then conducted a before-after uncontrolled trial of 80 patients 50–75 years old recruited from an academic internal medicine practice. RESULTS: Mean viewing time was 19 minutes. The decision aid improved patients' intent to ask providers for screening from a mean score of 2.8 (1 = not at all likely to ask, 4 = very likely to ask) before viewing the decision aid to 3.2 afterwards (difference, 0.4; p < 0.0001, paired t-test). Most found the aid useful and reported that it improved their knowledge about screening. Sixty percent said they were ready to be tested, 18% needed more information, and 22% were not ready to be screened. Within 6 months of viewing, 43% of patients had completed screening tests. CONCLUSION: We conclude that a computer-based decision aid can increase patient intent to be screened and increase interest in screening. Practice Implications: This decision aid can be viewed by patients prior to provider appointments to increase motivation to be screened and to help them decide about which modality to use for screening. Further work is required to integrate the decision aid with other practice change strategies to raise screening rates to target levels

The Magellanic Mopra Assessment (MAGMA). I. The Molecular Cloud Population of the Large Magellanic Cloud

We present the properties of an extensive sample of molecular clouds in the Large Magellanic Cloud (LMC) mapped at 11 pc resolution in the CO(1-0) line. We identify clouds as regions of connected CO emission, and find that the distributions of cloud sizes, fluxes and masses are sensitive to the choice of decomposition parameters. In all cases, however, the luminosity function of CO clouds is steeper than dN/dL \propto L^{-2}, suggesting that a substantial fraction of mass is in low-mass clouds. A correlation between size and linewidth, while apparent for the largest emission structures, breaks down when those structures are decomposed into smaller structures. We argue that the correlation between virial mass and CO luminosity is the result of comparing two covariant quantities, with the correlation appearing tighter on larger scales where a size-linewidth relation holds. The virial parameter (the ratio of a cloud's kinetic to self-gravitational energy) shows a wide range of values and exhibits no clear trends with the CO luminosity or the likelihood of hosting young stellar object (YSO) candidates, casting further doubt on the assumption of virialization for molecular clouds in the LMC. Higher CO luminosity increases the likelihood of a cloud harboring a YSO candidate, and more luminous YSOs are more likely to be coincident with detectable CO emission, confirming the close link between giant molecular clouds and massive star formation.Comment: Accepted by ApJS; 22 pages in emulateapj format; full-resolution version and data tables available at http://mmwave.astro.illinois.edu/magma

Blood Signature of Pre-Heart Failure: A Microarrays Study

International audienceBACKGROUND: The preclinical stage of systolic heart failure (HF), known as asymptomatic left ventricular dysfunction (ALVD), is diagnosed only by echocardiography, frequent in the general population and leads to a high risk of developing severe HF. Large scale screening for ALVD is a difficult task and represents a major unmet clinical challenge that requires the determination of ALVD biomarkers. METHODOLOGY/PRINCIPAL FINDINGS: 294 individuals were screened by echocardiography. We identified 9 ALVD cases out of 128 subjects with cardiovascular risk factors. White blood cell gene expression profiling was performed using pangenomic microarrays. Data were analyzed using principal component analysis (PCA) and Significant Analysis of Microarrays (SAM). To build an ALVD classifier model, we used the nearest centroid classification method (NCCM) with the ClaNC software package. Classification performance was determined using the leave-one-out cross-validation method. Blood transcriptome analysis provided a specific molecular signature for ALVD which defined a model based on 7 genes capable of discriminating ALVD cases. Analysis of an ALVD patients validation group demonstrated that these genes are accurate diagnostic predictors for ALVD with 87% accuracy and 100% precision. Furthermore, Receiver Operating Characteristic curves of expression levels confirmed that 6 out of 7 genes discriminate for left ventricular dysfunction classification. CONCLUSIONS/SIGNIFICANCE: These targets could serve to enhance the ability to efficiently detect ALVD by general care practitioners to facilitate preemptive initiation of medical treatment preventing the development of HF

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies

CSI 2264: Simultaneous optical and infrared light curves of young disk-bearing stars in NGC 2264 with CoRoT and Spitzer-- evidence for multiple origins of variability

Anne Marie Cody, et al, 'CSI 2264: SIMULTANEOUS OPTICAL AND INFRARED LIGHT CURVES OF YOUNG DISK-BEARING STARS IN NGC 2264 WITH CoRoT and SPITZER—EVIDENCE FOR MULTIPLE ORIGINS OF VARIABILITY', The Astronomical Journal, 147:82 (47pp), 2014 April doi:10.1088/0004-6256/147/4/82 © 2014. The American Astronomical Society.We present the Coordinated Synoptic Investigation of NGC 2264, a continuous 30-day multi-wavelength photometric monitoring campaign on more than 1000 young cluster members using 16 telescopes. The unprecedented combination of multi-wavelength, high-precision, high-cadence, and long-duration data opens a new window into the time domain behavior of young stellar objects. Here we provide an overview of the observations, focusing on results from Spitzer and CoRoT. The highlight of this work is detailed analysis of 162 classical T Tauri stars for which we can probe optical and mid-infrared flux variations to 1% amplitudes and sub-hour timescales. We present a morphological variability census and then use metrics of periodicity, stochasticity, and symmetry to statistically separate the light curves into seven distinct classes, which we suggest represent different physical processes and geometric effects. We provide distributions of the characteristic timescales and amplitudes, and assess the fractional representation within each class. The largest category (>20%) are optical "dippers" having discrete fading events lasting ~1-5 days. The degree of correlation between the optical and infrared light curves is positive but weak; notably, the independently assigned optical and infrared morphology classes tend to be different for the same object. Assessment of flux variation behavior with respect to (circum)stellar properties reveals correlations of variability parameters with H$\alpha$ emission and with effective temperature. Overall, our results point to multiple origins of young star variability, including circumstellar obscuration events, hot spots on the star and/or disk, accretion bursts, and rapid structural changes in the inner disk.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead