The effect of breed and diet type on the global transcriptome of hepatic tissue in beef cattle divergent for feed efficiency

peer-reviewedBackground Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar production levels but decreased feed intake, while also emitting less methane. RFI is difficult and expensive to measure and is not widely adopted in beef production systems. However, development of DNA-based biomarkers for RFI may facilitate its adoption in genomic-assisted breeding programmes. Cattle have been shown to re-rank in terms of RFI across diets and age, while also RFI varies by breed. Therefore, we used RNA-Seq technology to investigate the hepatic transcriptome of RFI-divergent Charolais (CH) and Holstein-Friesian (HF) steers across three dietary phases to identify genes and biological pathways associated with RFI regardless of diet or breed. Results Residual feed intake was measured during a high-concentrate phase, a zero-grazed grass phase and a final high-concentrate phase. In total, 322 and 33 differentially expressed genes (DEGs) were identified across all diets for CH and HF steers, respectively. Three genes, GADD45G, HP and MID1IP1, were differentially expressed in CH when both the high-concentrate zero-grazed grass diet were offered. Two canonical pathways were enriched across all diets for CH steers. These canonical pathways were related to immune function. Conclusions The absence of common differentially expressed genes across all dietary phases and breeds in this study supports previous reports of the re-ranking of animals in terms of RFI when offered differing diets over their lifetime. However, we have identified biological processes such as the immune response and lipid metabolism as potentially associated with RFI divergence emphasising the previously reported roles of these biological processes with respect to RFI

Born-Oppenheimer Approximation near Level Crossing

We consider the Born-Oppenheimer problem near conical intersection in two dimensions. For energies close to the crossing energy we describe the wave function near an isotropic crossing and show that it is related to generalized hypergeometric functions 0F3. This function is to a conical intersection what the Airy function is to a classical turning point. As an application we calculate the anomalous Zeeman shift of vibrational levels near a crossing.Comment: 8 pages, 1 figure, Lette

The Born Oppenheimer wave function near level crossing

The standard Born Oppenheimer theory does not give an accurate description of the wave function near points of level crossing. We give such a description near an isotropic conic crossing, for energies close to the crossing energy. This leads to the study of two coupled second order ordinary differential equations whose solution is described in terms of the generalized hypergeometric functions of the kind 0F3(;a,b,c;z). We find that, at low angular momenta, the mixing due to crossing is surprisingly large, scaling like \mu^(1/6), where \mu is the electron to nuclear mass ratio.Comment: 21 pages, 7 figure

The pneumococcal alpha-glycerophosphate oxidase enhances nasopharyngeal colonization through binding to host glycoconjugates

Streptococcus pneumoniae (the pneumococcus) is a major human pathogen, causing a broad spectrum of diseases including otitis media, pneumonia, bacteraemia and meningitis. Here we examined the role of a potential pneumococcal meningitis vaccine antigen, alpha-glycerophosphate oxidase (SpGlpO), in nasopharyngeal colonization. We found that serotype 4 and serotype 6A strains deficient in SpGlpO have significantly reduced capacity to colonize the nasopharynx of mice, and were significantly defective in adherence to human nasopharyngeal carcinoma cells in vitro. We also demonstrate that intranasal immunization with recombinant SpGlpO significantly protects mice against subsequent nasal colonization by wild type serotype 4 and serotype 6A strains. Furthermore, we show that SpGlpO binds strongly to lacto/neolacto/ganglio host glycan structures containing the GlcNAcβ1-3Galβ disaccharide, suggesting that SpGlpO enhances colonization of the nasopharynx through its binding to host glycoconjugates. We propose that SpGlpO is a promising vaccine candidate against pneumococcal carriage, and warrants inclusion in a multi-component protein vaccine formulation that can provide robust, serotype-independent protection against all forms of pneumococcal disease

GRADE Guidelines: 18. How ROBINS-I and other tools to assess risk of bias in nonrandomized studies should be used to rate the certainty of a body of evidence

To provide guidance on how systematic review authors, guideline developers, and health technology assessment practitioners should approach the use of the risk of bias in non-randomized studies of interventions (ROBINS-I) tool as part of GRADE's certainty rating process. Iterative discussions, testing in systematic reviews, presentation at GRADE working group meetings with feedback from the GRADE Working Group. We describe where to start the initial assessment of a body of evidence with the use of ROBINS-I, and where one would anticipate the final rating would end up. GRADE accounted for issues that mitigate concerns about confounding and selection bias by introducing the upgrading domains: large effects, dose-effect relations, and when plausible residual confounders or other biases increase certainty. They will need to be considered in an assessment of a body of evidence when using ROBINS-I. The use of ROBINS-I in GRADE assessments may allow for a better comparison of evidence from RCTs and NRS because they are placed on a common metric for risk of bias. Challenges remain that include appropriate presentation of evidence from RCTs and NRS for decision-making and how to optimally integrate RCTs and NRS in an evidence assessment

Dealing with missing standard deviation and mean values in meta-analysis of continuous outcomes: a systematic review

Background: Rigorous, informative meta-analyses rely on availability of appropriate summary statistics or individual participant data. For continuous outcomes, especially those with naturally skewed distributions, summary information on the mean or variability often goes unreported. While full reporting of original trial data is the ideal, we sought to identify methods for handling unreported mean or variability summary statistics in meta-analysis. Methods: We undertook two systematic literature reviews to identify methodological approaches used to deal with missing mean or variability summary statistics. Five electronic databases were searched, in addition to the Cochrane Colloquium abstract books and the Cochrane Statistics Methods Group mailing list archive. We also conducted cited reference searching and emailed topic experts to identify recent methodological developments. Details recorded included the description of the method, the information required to implement the method, any underlying assumptions and whether the method could be readily applied in standard statistical software. We provided a summary description of the methods identified, illustrating selected methods in example meta-analysis scenarios. Results: For missing standard deviations (SDs), following screening of 503 articles, fifteen methods were identified in addition to those reported in a previous review. These included Bayesian hierarchical modelling at the meta-analysis level; summary statistic level imputation based on observed SD values from other trials in the meta-analysis; a practical approximation based on the range; and algebraic estimation of the SD based on other summary statistics. Following screening of 1124 articles for methods estimating the mean, one approximate Bayesian computation approach and three papers based on alternative summary statistics were identified. Illustrative meta-analyses showed that when replacing a missing SD the approximation using the range minimised loss of precision and generally performed better than omitting trials. When estimating missing means, a formula using the median, lower quartile and upper quartile performed best in preserving the precision of the meta-analysis findings, although in some scenarios, omitting trials gave superior results. Conclusions: Methods based on summary statistics (minimum, maximum, lower quartile, upper quartile, median) reported in the literature facilitate more comprehensive inclusion of randomised controlled trials with missing mean or variability summary statistics within meta-analyses

Effect of increasing the time between slurry application and first rainfall event on phosphorus concentrations in runoff

Publication history: Accepted - 26 May 2021; Published online - 12 August 2021.Minimizing slurry phosphorus (P) losses in runoff requires careful management in the context of both soil P surpluses and changing patterns in rainfall. Increasing the time interval between slurry application and the first rainstorm event is known to reduce P loss in runoff although the risk period for elevated P concentrations in runoff can extend for weeks. This study investigated the impact of increasing the time interval between slurry application and first rainstorm event on P concentrations in runoff. Simulated rainfall (40 mm h−1) was applied at 2, 4, 10, 18, 30 and 49 days after dairy slurry was surface-applied to a grassland sward in Ireland. Increasing time to runoff resulted in a decrease in dissolved reactive P concentrations from 5.0 to 1.0 mg P L−1 and a P signal in runoff for 18 days. Beyond 18 days, elevated P concentrations were observed in runoff collected from natural rainfall that preceded the day 49 rainstorm event. A published surface phosphorus and runoff model (SurPhos) was used to understand the slurry P dynamics controlling P interactions with runoff. Dissolved reactive P in runoff was predicted with accuracy by SurPhos, R2 = .89. The SurPhos model implied thatslurry P mineralization occurred during the experimental period that resulted in a small spike in P concentrations beyond the defined risk period. This study shows that the experimental data have the potential to be extrapolated to different weather scenarios using SurPhos and could test when and where slurry P could be most safely spread.Open access funding provided by IReL. WOA Institution: University College Dublin Blended DEAL: IReL

Global changes in extreme daily temperature since 1950

Copyright 2008 by the American Geophysical UnionExtreme value analysis of observed daily temperature anomalies from a new quasi-global data set indicates that extreme daily maximum and minimum temperatures (>98.5 or <1.5 percentile) have warmed for most regions since 1950. Changes in extreme anomalous daily temperatures are determined by fitting extreme value distributions with time-varying parameters. Changes in the distribution of anomaly exceedances above a high threshold are found to be statistically significant at the 10% level for most land areas when compared with a time-invariant distribution and with the unforced natural variability produced by a coupled climate model. The largest positive trends in the location parameter of the extreme distribution are found in Canada and Eurasia where daily maximum temperatures have typically warmed by 1 to 3 degrees C since 1950. The total area exhibiting positive trends is significantly greater than can be attributed to unforced natural variability. For most regions, positive trend magnitudes are larger and cover a greater area for daily minimum temperatures than for maximum temperatures. The comparatively small areas of cooling are found to be consistent with unforced natural climate variability. The North Atlantic Oscillation (NAO) is found to have a significant influence on extreme winter daily temperatures for many areas, with a negative NAO of one standard deviation reducing expected extreme winter daily temperatures by similar to 2 degrees C over Eurasia but increasing temperatures over northeastern North America

Outcome of ATP-based tumor chemosensitivity assay directed chemotherapy in heavily pre-treated recurrent ovarian carcinoma

BACKGROUND: We wished to evaluate the clinical response following ATP-Tumor Chemosensitivity Assay (ATP-TCA) directed salvage chemotherapy in a series of UK patients with advanced ovarian cancer. The results are compared with that of a similar assay used in a different country in terms of evaluability and clinical endpoints. METHODS: From November 1998 to November 2001, 46 patients with pre-treated, advanced ovarian cancer were given a total of 56 courses of chemotherapy based on in-vitro ATP-TCA responses obtained from fresh tumor samples or ascites. Forty-four patients were evaluable for results. Of these, 18 patients had clinically platinum resistant disease (relapse < 6 months after first course of chemotherapy). There was evidence of cisplatin resistance in 31 patients from their first ATP-TCA. Response to treatment was assessed by radiology, clinical assessment and tumor marker level (CA 125). RESULTS: The overall response rate was 59% (33/56) per course of chemotherapy, including 12 complete responses, 21 partial responses, 6 with stable disease, and 15 with progressive disease. Two patients were not evaluable for response having received just one cycle of chemotherapy: if these were excluded the response rate is 61%. Fifteen patients are still alive. Median progression free survival (PFS) was 6.6 months per course of chemotherapy; median overall survival (OAS) for each patient following the start of TCA-directed therapy was 10.4 months (95% confidence interval 7.9-12.8 months). CONCLUSION: The results show similar response rates to previous studies using ATP-TCA directed therapy in recurrent ovarian cancer. The assay shows high evaluability and this study adds weight to the reproducibility of results from different centre