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In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 F1 dams, and 246 F2 progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F1 bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F2 progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production.

Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A + T content equals two at their immediate adjacent sites; and (3) C ↔ T and A ↔ G transitions have reverse complementary neighborhood patterns and so do A ↔ C and G ↔ T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C ↔ T/A ↔ G and A ↔ C/G ↔ T, the true neighborhood patterns for A ↔ T and C ↔ G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A + T and G + C was quite different. The ratio was lowest for C ↔ G, but increased for C ↔ T/A ↔ G, further for A ↔ C/G ↔ T, and the most for A ↔ T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A ↔ G and C ↔ T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for ∼20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.

Contributions of the emissions from a U.K. regulated fossil-fuel power station to regional air pollution and deposition are estimated using four air quality modeling systems for the year 2003. The modeling systems vary in complexity and emphasis in the way they treat atmospheric and chemical processes, and include the Community Multiscale Air Quality (CMAQ) modeling system in its versions 4.6 and 4.7, a nested modeling system that combines long- and short-range impacts (referred to as TRACK-ADMS [Trajectory Model with Atmospheric Chemical Kinetics-Atmospheric Dispersion Modelling System]), and the Fine Resolution Atmospheric Multi-pollutant Exchange (FRAME) model. An evaluation of the baseline calculations against U.K. monitoring network data is performed. The CMAQ modeling system version 4.6 data set is selected as the reference data set for the model footprint comparison. The annual mean air concentration and total deposition footprints are summarized for each modeling system. The footprints of the power station emissions can account for a significant fraction of the local impacts for some species (e.g., more than 50% for SO 2 air concentration and non-sea-salt sulfur deposition close to the source) for 2003. The spatial correlation and the coefficient of variation of the root mean square error (CVRMSE) are calculated between each model footprint and that calculated by the CMAQ modeling system version 4.6. The correlation coefficient quantifies model agreement in terms of spatial patterns, and the CVRMSE measures the magnitude of the difference between model footprints. Possible reasons for the differences between model results are discussed. Finally, implications and recommendations for the regulatory assessment of the impact of major industrial sources using regional air quality modeling systems are discussed in the light of results from this case study. IMPLICATIONS Modeling tools are required to assess the contribution of industrial sources to ambient levels of air pollution, acid deposition, and eutrophication. This study evaluates the performance characteristics of regional air quality modeling systems in predicting contributions of the emissions from a U.K. regulated fossil-fuel power station to regional air pollution and deposition. It contrasts acid deposition modeling approaches used in the United Kingdom and demonstrates the sensitivity of the modeling systems to large emission changes. This work suggests considering an ensemble average of model calculations to provide an estimate of the uncertainty associated with an industrial source footprint.

Candidate gene approaches provide tools for exploring and localizing causative genes affecting quantitative traits and the underlying variation may be better understood by determining the relative magnitudes of effects of their polymorphisms. Diacyglycerol O-acyltransferase 1 (DGAT1), fatty acid binding protein (heart) 3 (FABP3), growth hormone 1 (GH1), leptin (LEP) and thyroglobulin (TG) have been previously identified as genes contributing to genetic control of subcutaneous fat thickness (SFT) in beef cattle. In the present research, Bayesian model selection was used to evaluate effects of these five candidate genes by comparing competing non-nested models and treating candidate gene effects as either random or fixed. The analyses were implemented in SAS to simplify the programming and computation. Phenotypic data were gathered from a F2 population of Wagyu x Limousin cattle. The five candidate genes had significant but varied effects on SFT in this population. Bayesian model selection identified the DGAT1 model as the one with the greatest model probability, whether candidate gene effects were considered random or fixed, and DGAT1 had the greatest additive effect on SFT. The SAS codes developed in the study are freely available and can be downloaded at: http://www.ansci.wsu.edu/programs/.

PI and PID controllers continue to be popular methods in industrial applications. It is well known that linear PI and PID controllers result from the application of model‐based controller design methods to linear first‐ and second‐order systems. It is shown that nonlinear PI and PID controllers result from the application of nonlinear controller design methods to nonlinear first‐ and second‐order systems. As a result, the controllers resulting from nonlinear model‐based control theory are put in a convenient form, more amenable to industrial implementation. Additionally, the quantities used in the controller are useful for monitoring the process and quantifying modeling error. Chemical engineering examples are used to illustrate the resulting control laws. A simulation example further demonstrates the performance of the nonlinear controllers, as well as their useful process monitoring quantities.

A gene-based approach was used to annotate 322 168 cattle expressed sequence tags (ESTs) based on human genes in order to census the transcriptomes, analyze their expression similarities, and identify genes preferentially expressed in different bovine tissues and (or) organs. Of the 34 157 human coding genes used in a standalone BLAST search, 14 928 could be matched with provisional orthologous sequences in a total of 230 135 bovine ESTs. The remaining 92 033 bovine ESTs were estimated to represent an additional 5970 genes in cattle. On average, approximately 8600 genes were estimated to be expressed in a single tissue and (or) organ and 13 000 in a pooled tissue library. On the basis of the estimated numbers of genes, no more than 3% of genes would be missed when approximately 34 000 ESTs were sequenced from a single tissue and (or) organ library and approximately 40 000 ESTs from a pooled source, respectively. Cluster analyses of the gene expression patterns among 12 single tissues and (or) organs in cattle revealed that their expression similarities would depend on physiological functions. In addition, a total of 1502 genes were identified as preferentially expressed genes in these 12 single tissues and (or) organs with LOD (logarithm of the odds, base 10) greater than or equal to 3.0. Therefore, our study provides some insights for further investigating the developmental and functional relations of various tissues and organs in mammals.

Biomagnification of methylmercury in aquatic systems can cause elevated tissue mercury (Hg) and physiological stress in top predators. Mercury is known to affect stress hormone levels in mammals, birds and fish. In this study, the effects of maternally-transferred methylmercury on the stress physiology of Northern Water Snake ( Nerodia sipedon ) neonates were tested. Gravid females were dosed via force-fed capsules during late gestation with 0, 0.01, or 10 µg methylmercury per gram of body mass. Plasma corticosterone levels and leukocyte differentials were analyzed in baseline and confinement-stressed neonates from all dose levels. Neither Hg nor confinement stress had a significant effect on leukocyte differentials nor was Hg related to corticosterone levels. However, stress group neonates showed lower heterophil/lymphocyte ratios and this study was the first to show that neonate N. sipedon can upregulate CORT in response to stress. These results indicate that N. sipedon may be somewhat tolerant to Hg contamination.

Purpose Early reports of 30-day mortality in COVID-positive patients with hip fracture were often over 30% and were higher than historical rates of 10% in pre-COVID studies. We conducted a multi-institutional retrospective cohort study to determine whether the incidence of 30-day mortality and complications in COVID-positive patients undergoing hip fracture surgery is as high as initially reported. Methods A retrospective chart review was performed at 11 level I trauma centers from January 1, 2020 to May 1, 2022. Patients 50 years or older undergoing hip fracture surgery with a positive COVID test at the time of surgery were included. The primary outcome measurements were the incidence of 30-day mortality and complications. Post-operative outcomes were reported using proportions with 95% confidence interval (C.I.). Results Forty patients with a median age of 71.5 years (interquartile range, 50–87 years) met the criteria. Within 30-days, four patients (10%; 95% C.I. 3–24%) died, four developed pneumonia, three developed thromboembolism, and three remained intubated post-operatively. Increased age was a statistically significant predictor of 30-day mortality ( p  = 0.01), with all deaths occurring in patients over 80 years. Conclusion In this multi-institutional analysis of COVID-positive patients undergoing hip fracture surgery, 30-day mortality was 10%. The 95% C.I. did not include 30%, suggesting that survival may be better than initially reported. While COVID-positive patients with hip fractures have high short-term mortality, the clinical situation may not be as dire as initially described, which may reflect initial publication bias, selection bias introduced by testing, or other issues. Levels of Evidence Therapeutic Level III.