Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle

Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the wellbeing and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study aimed to utilize multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the genetic and molecular mechanisms of BRD infection. Blood samples of 143 cattle (80 BRD; 63 non-BRD animals) were collected for genotyping, RNA sequencing, and metabolite profiling. Firstly, a genome-wide association study (GWAS) was performed for BRD susceptibility using 207,038 SNPs. Two SNPs (Chr5:25858264 and BovineHD1800016801) were identified as associated (p-value 2, logCPM>2, and FDR<0.01), 101 differentially expressed (DE) genes were identified. These DE genes significantly (p-value <0.05) enriched several immune responses related functions such as inflammatory response. Additionally, we performed expression quantitative trait loci (eQTL) analysis and identified 420 cis-eQTLs and 144 trans-eQTLs significantly (FDR <0.05) associated with the expression of DE genes. Interestingly, eQTL results indicated the most significant SNP (Chr5:25858264) identified via GWAS was a cis-eQTL for DE gene GPR84. This analysis also demonstrated that an important SNP (rs209419196) located in the promoter region of the DE gene BPI significantly influenced the expression of this gene. Finally, the abundance of 31 metabolites was significantly (FDR <0.05) different between BRD and non-BRD animals, and 17 of them showed correlations with multiple DE genes, which shed light on the interactions between immune response and metabolism. This study identified associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools

A Census of Star-Forming Galaxies in the z~9-10 Universe based on HST+Spitzer Observations Over 19 CLASH clusters: Three Candidate z~9-10 Galaxies and Improved Constraints on the Star Formation Rate Density at z~9

We utilise a two-color Lyman-Break selection criterion to search for z~9-10 galaxies over the first 19 clusters in the CLASH program. A systematic search yields three z~9-10 candidates. While we have already reported the most robust of these candidates, MACS1149-JD, two additional z~9 candidates are also found and have H_{160}-band magnitudes of ~26.2-26.9. A careful assessment of various sources of contamination suggests <~1 contaminants for our z~9-10 selection. To determine the implications of these search results for the LF and SFR density at z~9, we introduce a new differential approach to deriving these quantities in lensing fields. Our procedure is to derive the evolution by comparing the number of z~9-10 galaxy candidates found in CLASH with the number of galaxies in a slightly lower redshift sample (after correcting for the differences in selection volumes), here taken to be z~8. This procedure takes advantage of the fact that the relative volumes available for the z~8 and z~9-10 selections behind lensing clusters are not greatly dependent on the details of the lensing models. We find that the normalization of the UV LF at z~9 is just 0.28_{-0.20}^{+0.39}\times that at z~8, ~1.4_{-0.8}^{+3.0}x lower than extrapolating z~4-8 LF results. While consistent with the evolution in the UV LF seen at z~4-8, these results marginally favor a more rapid evolution at z>8. Compared to similar evolutionary findings from the HUDF, our result is less insensitive to large-scale structure uncertainties, given our many independent sightlines on the high-redshift universe.Comment: 22 pages, 11 figures, 5 tables, accepted for publication in the Astrophysical Journal, updated to include the much deeper Spitzer/IRAC observations over our three z~9-10 candidate

Towards an online-coupled chemistry-climate model: evaluation of trace gases and aerosols in COSMO-ART

Peer reviewe

Comparative Outcomes of Lung Volume Reduction Surgery and Lung Transplantation: A Systematic Review and Meta-Analysis

Background: Lung volume reduction (LVR) and lung transplantation (LTx) have been used in different populations of chronic obstructive pulmonary disease (COPD) patients. To date, comparative study of LVR and LTx has not been performed. We sought to address this gap by pooling the existing evidence in the literature. Methods: An electronic search was performed to identify all prospective studies on LVR and LTx published since 2000. Baseline characteristics, perioperative variables, and clinical outcomes were extracted and pooled for meta-analysis. Results: The analysis included 65 prospective studies comprising 3,671 patients [LTx: 15 studies (n=1,445), LVR: 50 studies (n=2,226)]. Mean age was 60 [95% confidence interval (CI): 58–62] years and comparable between the two groups. Females were 51% (95% CI: 30–71%) in the LTx group vs. 28% (95% CI: 21–36%) in LVR group (P=0.05). Baseline 6-minute walk test (6MWT) and pulmonary function tests were comparable except for the forced expiratory volume in 1 second (FEV1), which was lower in the LTx group [21.8% (95% CI: 16.8–26.7%) vs. 27.3% (95% CI: 25.5–29.2%), P=0.04]. Postoperatively, both groups experienced improved FEV1, however post-LTx FEV1 was significantly higher than post-LVR FEV1 [54.9% (95% CI: 41.4–68.4%) vs. 32.5% (95% CI: 30.1–34.8%), P\u3c0.01]. 6MWT was also improved after both procedures [LTx: 212.9 (95% CI: 119.0–306.9) to 454.4 m (95% CI: 334.7–574.2), P\u3c0.01; LVR: 286 (95% CI: 270.2–301.9) to 409.1 m (95% CI: 392.1–426.0), P\u3c0.01], however, with no significant difference between the groups. Pooled survival over time showed no significant difference between the groups. Conclusions: LTx results in better FEV1 but otherwise has comparable outcomes to LVR

Outcomes of Surgical Treatment for Carcinoid Heart Disease: A Systematic Review and Meta-Analysis

Introduction and Objective: Carcinoid Heart Disease (CaHD) develops from vasoactive substances released by neuroendocrine tumors causing significant patient morbidity and mortality necessitating surgical intervention. We performed a systematic review and meta-analysis to elucidate granular perioperative details and long-term outcomes in these patients. Methods: Electronic search of Ovid, Scopus, Cumulative Index of Nursing and Allied Health Literature, and Cochrane Controlled Trials Register was performed. Nine articles comprising 416 patients who received surgery were selected. Primary outcomes investigated included patient characteristics, surgical characteristics and survival data. Study-level data were extracted and pooled for meta-analysis. Results: Primary outcomes consisted of survival, length of stay and thirty-day mortality. Secondary outcomes included presence of right heart failure pre-operatively and type of valve replaced. Right heart failure was present in 48%. Moderate or severe regurgitation was present in 97% of tricuspid and 72% of pulmonary valves. 99% of tricuspid and 59% of pulmonary valves were replaced. Mean hospital length of stay was 16 days. Thirty-day mortality was 9%. Mean follow up was 25 months. Median survival was 3 years. Conclusion: Surgical treatment of CaHD can be performed with acceptable short-term outcomes. However, overall survival appears to suffer from ongoing effects of the primary disease. Surgery is often performed after patients have extensive right-sided heart involvement. Overall, onset and duration of symptoms of carcinoid heart disease should be closely monitored to properly identify and refer patients who would most benefit from valvular surgery

European Red List of Habitats Part 1. Marine habitats

The European Red List of Habitats provides an overview of the risk of collapse (degree of endangerment) of marine, terrestrial and freshwater habitats in the European Union (EU28) and adjacent regions (EU28+), based on a consistent set of categories and criteria, and detailed data and expert knowledge from involved countries1. A total of 257 benthic marine habitat types were assessed. In total, 19% (EU28) and 18% (EU28+) of the evaluated habitats were assessed as threatened in categories Critically Endangered, Endangered and Vulnerable. An additional 12% were Near Threatened in the EU28 and 11% in the EU28+. These figures are approximately doubled if Data Deficient habitats are excluded. The percentage of threatened habitat types differs across the regional seas. The highest proportion of threatened habitats in the EU28 was found in the Mediterranean Sea (32%), followed by the North-East Atlantic (23%), the Black Sea (13%) and then the Baltic Sea (8%). There was a similar pattern in the EU28+. The most frequently cited pressures and threats were similar across the four regional seas: pollution (eutrophication), biological resource use other than agriculture or forestry (mainly fishing but also aquaculture), natural system modifications (e.g. dredging and sea defence works), urbanisation and climate change. Even for habitats where the assessment outcome was Data Deficient, the Red List assessment process has resulted in the compilation of a substantial body of useful information to support the conservation of marine habitats

Why Do Borrowers Pledge Collateral? New Empirical Evidence on the Role of Asymmetric Information

An important theoretical literature motivates collateral as a mechanism that mitigates adverse selection, credit rationing, and other inefficiencies that arise when borrowers hold ex ante private information. There is no clear empirical evidence regarding the central implication of this literature - that a reduction in asymmetric information reduces the incidence of collateral. We exploit exogenous variation in lender information related to the adoption of an information technology that reduces ex ante private information, and compare collateral outcomes before and after adoption. Our results are consistent with this central implication of the private-information models and support the empirical importance of this theory