Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.

Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a "covarion-like" pattern of correlated changes in evolutionary rates, and switches in conserved residues ("conserved but different"). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than "constant but different," but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs

Polarizations of J/psi and psi(2S) Mesons Produced in ppbar Collisions at 1.96 TeV

We have measured the polarizations of \jpsi and \psiprime mesons as functions of their transverse momentum \pt when they are produced promptly in the rapidity range $|y|<0.6$ with \pt \geq 5 \pgev. The analysis is performed using a data sample with an integrated luminosity of about 800 \ipb collected by the CDF II detector. For both vector mesons, we find that the polarizations become increasingly longitudinal as \pt increases from 5 to 30 \pgev. These results are compared to the predictions of nonrelativistic quantum chromodynamics and other contemporary models. The effective polarizations of \jpsi and \psiprime mesons from $B$-hadron decays are also reported.Comment: 8 pages, 7 figures, published in Physical Review Letter

Prospects for observing and localizing gravitational-wave transients with Advanced LIGO, Advanced Virgo and KAGRA

We present possible observing scenarios for the Advanced LIGO, Advanced Virgo and KAGRA gravitational-wave detectors over the next decade, with the intention of providing information to the astronomy community to facilitate planning for multi-messenger astronomy with gravitational waves. We estimate the sensitivity of the network to transient gravitational-wave signals, and study the capability of the network to determine the sky location of the source. We report our findings for gravitational-wave transients, with particular focus on gravitational-wave signals from the inspiral of binary neutron star systems, which are the most promising targets for multi-messenger astronomy. The ability to localize the sources of the detected signals depends on the geographical distribution of the detectors and their relative sensitivity, and 90% credible regions can be as large as thousands of square degrees when only two sensitive detectors are operational. Determining the sky position of a significant fraction of detected signals to areas of 5– 20 deg2 requires at least three detectors of sensitivity within a factor of ∼2 of each other and with a broad frequency bandwidth. When all detectors, including KAGRA and the third LIGO detector in India, reach design sensitivity, a significant fraction of gravitational-wave signals will be localized to a few square degrees by gravitational-wave observations alone

Social disparities in exposures to bisphenol A and polyfluoroalkyl chemicals: a cross-sectional study within NHANES 2003-2006

<p>Abstract</p> <p>Background</p> <p>Bisphenol A (BPA) and polyfluoroalkyl chemicals (PFCs) are suspected endocrine disrupting compounds known to be ubiquitous in people's bodies. Population disparities in exposure to these chemicals have not been fully characterized.</p> <p>Methods</p> <p>We analyzed data from the 2003-2006 National Health and Nutrition Examination Survey. Using multivariable linear regression we examined the association between urinary concentrations of BPA, serum concentrations of four PFCs, and multiple measures of socioeconomic position (SEP): family income, education, occupation, and food security. We also examined associations with race/ethnicity.</p> <p>Results</p> <p>All four PFCs were positively associated with family income, whereas BPA was inversely associated with family income. BPA concentrations were higher in people who reported very low food security and received emergency food assistance than in those who did not. This association was particularly strong in children: 6-11 year-olds whose families received emergency food had BPA levels 54% higher (95% CI, 13 to 112%) than children of families who did not. For BPA and PFCs we saw smaller and less consistent associations with education and occupation. Mexican Americans had the lowest concentrations of any racial/ethnic group of both types of chemicals; for PFCs, Mexican Americans not born in the U.S. had much lower levels than those born in the U.S.</p> <p>Conclusions</p> <p>People with lower incomes had higher body burdens of BPA; the reverse was true for PFCs. Family income with adjustment for family size was the strongest predictor of chemical concentrations among the different measures of SEP we studied. Income, education, occupation, and food security appear to capture different aspects of SEP that may be related to exposure to BPA and PFCs and are not necessarily interchangeable as measures of SEP in environmental epidemiology studies. Differences by race/ethnicity were independent of SEP.</p

Why Rice Farmers Don't Sail: Coastal Subsistence Traditions and Maritime Trends in Early China

The Lower Yangtze River Valley is a key region for the early development of rice farming and the emergence of wet rice paddy field systems. Subsistence evidence from Neolithic sites in this area highlights the importance of freshwater wetlands for both plant and animal food resources. Early Neolithic rice cultivators looked inland, especially to wetlands and nearby woodlands, for their main protein sources. Links to the sea among these Neolithic populations are notably scarce. Due to the high yields of wet rice, compared with other staple crops as well as dryland rice, the wetland rice focused subsistence strategy of the Lower Yangtze would have supported high, and increasing, local population densities. Paddy agriculture demands labor input and water management on a large scale, which would have stimulated and reinforced trends towards more complex societies, such as that represented by Liangzhu in the lower Yangtze region. Population growth could have been largely absorbed locally, suggesting that population packing, not migration, was the dominant trend. Other case studies of agricultural dispersal, for the Korean Peninsula and Japan further illustrate the lack of correlation between the spread of rice agriculture and wet rice cultivation. Although wet rice cultivation was a pull factor that drew local populations towards increased density and increased social complexity, it did not apparently push groups to migrate outwards. Instead, the transition from wetland to rain fed rice cultivation systems and/or the integration of rice with rain fed millet crops are much more likely to have driven the demographic dynamics that underpin early farmer migrations and crop dispersal

Diabetic retinopathy: current and future methods for early screening from a retinal hemodynamic and geometric approach

Diabetic retinopathy (DR) is a major disease and is the number one cause of blindness in the UK. In England alone, 4200 new cases appear every year and 1280 lead to blindness. DR is a result of diabetes mellitus, which affects the retina of the eye and specifically the vessel structure. Elevated levels of glucose cause a malfunction in the cell structure, which affects the vessel wall and, in severe conditions, leads to their breakage. Much research has been carried out on detecting the different stages of DR but not enough versatile research has been carried out on the detection of early DR before the appearance of any lesions. In this review, the authors approach the topic from the functional side of the human eye and how hemodynamic factors that are impaired by diabetes affect the vascular structur

ICAR: endoscopic skull‐base surgery

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