Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range

Prey Coat Color Selection and Bioenergetics of Captive Screech Owls

Author Institution: The Institute of Environmental Sciences and Department of Zoology, Miami Universit

Dietary Patterns and Cognitive Function among Older Community-Dwelling Adults.

Diet may be an important modifiable risk factor for maintenance of cognitive health in later life. This study aimed at examining associations between common dietary indices and dietary patterns defined by factor analysis and cognitive function in older community-dwelling adults. Dietary information for 1499 participants from the Rancho Bernardo Study was collected in 1988⁻1992 and used to calculate the alternate Mediterranean diet score, Alternate Healthy Eating Index (AHEI)-2010 score and factor scores derived from factor analysis of nutrients. Global cognitive function, executive function, verbal fluency and episodic memory were assessed at approximate four-year intervals from 1988⁻2016. Linear mixed models were used to examine associations between dietary patterns and cognitive trajectories. Estimates for the highest vs. lowest tertile in models adjusting for age, sex, education, energy intake, lifestyle variables and retest effect showed greater adherence to the Mediterranean score was associated with better baseline global cognitive function (β (95% CI) = 0.33 (0.11, 0.55)). The AHEI-2010 score was not significantly associated with cognitive performance. Higher loading on a plant polyunsaturated fatty acid (PUFA)/vitamin E factor was associated with better baseline global cognitive function and executive function (β = 0.22 (0.02, 0.42) and β = -7.85 (-13.20, -2.47)). A sugar/low protein factor was associated with poorer baseline cognitive function across multiple domains. Dietary patterns were not associated with cognitive decline over time. Adherence to a healthy diet with foods high in PUFA and vitamin E and a low sugar to protein ratio, as typified by a Mediterranean diet, may be beneficial for cognitive health in late life

Poor transferability of a distribution model for a widespread coastal marsh bird in the southeastern United States

Species distribution models have been applied across a wide range of spatial scales to generate information for conservation planning. Understanding how well models transfer through space and time is important to promote effective species–habitat conservation. Here, we assess model transferability in coastal tidal marshes of the southeastern United States using count data of a widespread marsh bird: the Clapper Rail (Rallus crepitans). We developed species–habitat models at a state level in both South Carolina and Georgia, and then assessed how well top models from each state predicted abundance in the other state. Internally (locally) validated models performed well with reasonable fit (SC: R2 = 0.35, GA: R2 = 0.14), and high significance (P = 0.0005); however, both models performed poorly when predicting abundance from the other state (R2 = 0.03 and 0.003). To assess the consequences of this lack of transferability, we applied the South Carolina‐ and Georgia‐derived parameter estimates to habitat features in South Carolina and identified the top 25% of tidal marsh habitat that each model predicted within the state. There was minimal overlap between model habitat quality predictions (\u3c5%). Our results address the predictive power and uncertainties that arise from using habitat associations and climate models to predict species distributions or abundance in locations without training data. We discuss potential reasons model transferability was not successful and address the need for better regional datasets and the importance of intraspecific variability in response to environmental gradients

The spatial distribution of galaxies of different spectral types in the massive intermediate-redshift cluster MACSJ0717.5+3745

We present the results of a wide-field spectroscopic analysis of the galaxy population of the massive cluster MACSJ0717.5+3745 and the surrounding filamentary structure (z=0.55), as part of our systematic study of the 12 most distant clusters in the MACS sample. Of 1368 galaxies spectroscopically observed in this field, 563 are identified as cluster members; of those, 203 are classified as emission-line galaxies, 260 as absorption-line galaxies, and 17 as E+A galaxies (defined by $\frac{H_{\delta}+H_{\gamma}}{2}>6$\AA and no detection of [OII] and $H_{\beta}$ in emission). The variation of the fraction of emission- and absorption-line galaxies as a function of local projected galaxy density confirms the well-known morphology-density relation, and becomes flat at projected galaxy densities less than $\sim 20Mpc^{-2}. Interestingly, 16 out of 17 E+A galaxies lie (in projection) within the ram-pressure stripping radius around the cluster core, which we take to be direct evidence of ram-pressure stripping being the primary mechanism that terminates star-formation in the E+A population of galaxy clusters. This conclusion is supported by the rarity of E+A galaxies in the filament which rules out galaxy mergers as the dominant driver of evolution for E+A galaxies in clusters. In addition, we find the 42 e(a) and 27 e(b) member galaxies, i.e., the dusty-starburst and starburst galaxies respectively, to be spread out across almost the entire study area. Their spatial distribution, which shows a strong preference for the filament region, suggests that starbursts are triggered in relatively low-density environments as galaxies are accreted from the field population.Comment: 16 pages, 15 figures, accepted by Ap

Association of lung function with coronary heart disease and cardiovascular disease outcomes in elderly: The Rancho Bernardo study

SummaryIntroductionLung function is inversely associated with coronary heart disease (CHD) and cardiovascular disease (CVD). We evaluated the prospective association of reduced lung function by spirometry and CHD or CVD events in older community-dwelling adults.MethodsWe studied 1548 participants (mean age 73.6 ± 9.2 years, 42% males) from the Rancho Bernardo Study using age, sex, and risk-factor adjusted Cox regression to assess pulmonary function (FEV1, FVC, and FEV1/FVC ratio) as a predictor of CHD and CVD events followed for up to 22 years.ResultsOf CVD risk factors, older age, male sex, current/past smoking, physical exercise (<3× a week), and prevalent CVD predicted an increased risk of CHD and CVD. Higher FEV1 and FVC were each associated with a decreased risk of CHD [HR 0.80 (0.73–0.88) for both FEV1 and FVC, per SD, p < 0.01] and CVD [HR 0.82 (0.74–0.91) for both FEV1 and FVC, per SD, p < 0.01]. Those in the lowest quartiles of FEV1 and FVC had hazard ratios of 1.68 (1.33–2.13) and 1.55 (1.21–2.00) respectively for CHD and 1.74 (1.34–2.25) and 1.49 (1.13–1.96) respectively for CVD (all p < 0.01, relative to those in the highest quartile). Similar findings were observed for CHD and CVD mortality. Sex- and age-stratified analyses showed the strongest associations for CHD and CVD events in women and in the oldest participants.ConclusionsFEV1 and FVC are inversely associated with risk of future CHD and CVD events in older community-dwelling adults and may add to CVD risk stratification in the elderly

Genomic comparison of diverse Salmonella serovars isolated from swine.

Food animals act as a reservoir for many foodborne pathogens. Salmonella enterica is one of the leading pathogens that cause food borne illness in a broad host range including animals and humans. They can also be associated with a single host species or a subset of hosts, due to genetic factors associated with colonization and infection. Adult swine are often asymptomatic carriers of a broad range of Salmonella servoars and can act as an important reservoir of infections for humans. In order to understand the genetic variations among different Salmonella serovars, Whole Genome Sequences (WGS) of fourteen Salmonella serovars from swine products were analyzed. More than 75% of the genes were part of the core genome in each isolate and the higher fraction of gene assign to different functional categories in dispensable genes indicated that these genes acquired for better adaptability and diversity. High concordance (97%) was detected between phenotypically confirmed antibiotic resistances and identified antibiotic resistance genes from WGS. The resistance determinants were mainly located on mobile genetic elements (MGE) on plasmids or integrated into the chromosome. Most of known and putative virulence genes were part of the core genome, but a small fraction were detected on MGE. Predicted integrated phage were highly diverse and many harbored virulence, metal resistance, or antibiotic resistance genes. CRISPR (Clustered regularly interspaced short palindromic repeats) patterns revealed the common ancestry or infection history among Salmonella serovars. Overall genomic analysis revealed a great deal of diversity among Salmonella serovars due to acquired genes that enable them to thrive and survive during infection

Epidemiology of rib fractures in older men: Osteoporotic Fractures in Men (MrOS) prospective cohort study

Objective To study the causes and consequences of radiologically confirmed rib fractures (seldom considered in the context of osteoporosis) in community dwelling older men

Kinematic Evidence of Minor Mergers in Normal Sa Galaxies: NGC3626, NGC3900, NGC4772 and NGC5854

BVRI and H-alpha imaging and long-slit optical spectroscopic data are presented for four morphologically normal and relatively isolated Sa galaxies, NGC3626, NGC3900, NGC4772 and NGC5854. VLA HI synthesis imaging is presented for the first 3 objects. In all 4 galaxies, evidence of kinematic decoupling of ionized gas components is found; the degree and circumstances of the distinct kinematics vary from complete counterrotation of all of the gas from all of the stars (NGC3626) to nuclear gas disks decoupled from the stars (NGC5854) to anomalous velocity central gas components (NGC3900 and NGC4772). In the 3 objects mapped in HI, the neutral gas extends far beyond the optical radius, R_HI/R_25 > 2. In general, the HI surface density is very low and the outer HI is patchy and asymmetric or found in a distinct ring, exterior to the optical edge. While the overall HI velocity fields are dominated by circular motions, strong warps are suggested in the outer regions. Optical imaging is also presented for NGC 4138 previously reported by Jore et al. (1996) to show counterrotating stellar components. The multiwavelength evidence is interpreted in terms of the kinematic "memory" of past minor mergers in objects that otherwise exhibit no morphological signs of interaction.Comment: 26 pages, 15 figures, accepted for publication in Astron. J., postscript figures available at ftp://culebra.tn.cornell.edu/pub/haynes/figures.tar.g