A reaction norm model for genomic selection using high-dimensional genomic and environmental data

In most agricultural crops the effects of genes on traits are modulated by environmental conditions, leading to genetic by environmental interaction (G × E). Modern genotyping technologies allow characterizing genomes in great detail and modern information systems can generate large volumes of environmental data. In principle, G × E can be accounted for using interactions between markers and environmental covariates (ECs). However, when genotypic and environmental information is high dimensional, modeling all possible interactions explicitly becomes infeasible. In this article we show how to model interactions between high-dimensional sets of markers and ECs using covariance functions. The model presented here consists of (random) reaction norm where the genetic and environmental gradients are described as linear functions of markers and of ECs, respectively. We assessed the proposed method using data from Arvalis, consisting of 139 wheat lines genotyped with 2,395 SNPs and evaluated for grain yield over 8 years and various locations within northern France. A total of 68 ECs, defined based on five phases of the phenology of the crop, were used in the analysis. Interaction terms accounted for a sizable proportion (16 %) of the within-environment yield variance, and the prediction accuracy of models including interaction terms was substantially higher (17–34 %) than that of models based on main effects only. Breeding for target environmental conditions has become a central priority of most breeding programs. Methods, like the one presented here, that can capitalize upon the wealth of genomic and environmental information available, will become increasingly important

Procalcitonin levels in acute exacerbation of COPD admitted in ICU: a prospective cohort study

<p>Abstract</p> <p>Background</p> <p>Antibiotics are recommended for severe acute exacerbation of chronic obstructive pulmonary disease (AECOPD) admitted to intensive care units (ICU). Serum procalcitonin (PCT) could be a useful tool for selecting patients with a lower probability of developing bacterial infection, but its measurement has not been investigated in this population.</p> <p>Methods</p> <p>We conducted a single center prospective cohort study in consecutive COPD patients admitted to the ICU for AECOPD between September 2005 and September 2006. Sputum samples or tracheal aspirates were tested for the presence of bacteria and viruses. PCT levels were measured at the time of admittance, six hours, and 24 hours using a sensitive immunoassay.</p> <p>Results</p> <p>Thirty nine AECOPD patients were included, 31 of which (79%) required a ventilator support at admission. The median [25%–75% interquartile range] PCT level, assessed in 35/39 patients, was: 0.096 μg/L [IQR, 0.065 to 0.178] at the time of admission, 0.113 μg/L [IQR, 0.074 to 0.548] at six hours, and 0.137 μg/L [IQR, 0.088 to 0.252] at 24 hours. The highest PCT (PCTmax) levels were less than 0.1 μg/L in 14/35 (40%) patients and more than 0.25 μg/L in 10/35 (29%) patients, suggesting low and high probability of bacterial infection, respectively. Five species of bacteria and nine species of viruses were detected in 12/39 (31%) patients. Among the four patients positive for <it>Pseudomonas aeruginosa</it>, one had a PCTmax less than 0.25 μg/L and three had a PCTmax less than 0.1 μg/L. The one patient positive for <it>Haemophilus influenzae </it>had a PCTmax more than 0.25 μg/L. The presence or absence of viruses did not influence PCT at time of admission (0.068 vs 0.098 μg/L respectively, <it>P </it>= 0.80).</p> <p>Conclusion</p> <p>The likelihood of bacterial infection is low among COPD patients admitted to ICU for AECOPD (40% with PCT < 0.1 μg/L) suggesting a possible inappropriate use of antibiotics. Further studies are necessary to assess the impact of a procalcitonin-based therapeutic strategy in critically ill COPD patients.</p

Renal replacement therapy in acute kidney injury: controversy and consensus

Renal replacement therapies (RRTs) represent a cornerstone in the management of severe acute kidney injury. This area of intensive care and nephrology has undergone significant improvement and evolution in recent years. Continuous RRTs have been a major focus of new technological and treatment strategies. RRT is being used increasingly in the intensive care unit, not only for renal indications but also for other organ-supportive strategies. Several aspects related to RRT are now well established, but others remain controversial. In this review, we review the available RRT modalities, covering technical and clinical aspects. We discuss several controversial issues, provide some practical recommendations, and where possible suggest a research agenda for the future

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]