Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum.

The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In fivefold cross-validation, prediction accuracies ranged from 0.46 (PBN) to 0.49 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.75 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4-52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits

Continuous bioreactor leaching of nickel sulfide concentrates with moderately thermophilic bacteria and archaea

This is the final version. Available on open access from Elsevier via the DOI in this recordData availability: No data was used for the research described in the article.A commercial process for bioreactor leaching of a nickel concentrate by-product of talc mining has been described previously. It was developed and operated (2016–2018) at about 45–46 °C. Further features of bioleaching that concentrate have now been investigated in laboratory-scale reactors with continuous feeds of up to 10% (w/v) solids and an emphasis on temperatures at and a few degrees above that of the commercial process. The sulfur-oxidizing At. caldus was more abundant than the sulfide mineral-oxidizing S. thermosulfidooxidans and Atm. siderophilum at 48 °C but was essentially lost with a 3 °C temperature rise, simultaneously with a rise in pH and in iron precipitation from solution, without adversely affecting nickel leaching. The relative abundance among bacteria was similar between two reactors operated in series but there was more than a fourfold increase in the relative abundance of the ferrous-iron oxidizing, heterotrophic archaeon Ac. cupricumulans in the secondary reactor, most likely in response to an increase in the acidity as the sulfide concentrate oxidation proceeded

Evaluation of objective and subjective indicators of death in a period of one year in a sample of prevalent patients under regular hemodialysis

<p>Abstract</p> <p>Background</p> <p>To identify objective and subjective indicators of death in prevalent hemodialysis (HD) patients in a follow-up study of 12 months.</p> <p>Methods</p> <p>The study included end-stage renal disease patients undergoing HD and analyzed demographic and laboratory data from the dialysis unit's records. Baseline data concerning socioeconomic status, comorbidity, quality of life level, coping style and depression were also assessed. For variables that differed in the comparison between survivors and non-survivors, Cox proportional hazards for death were calculated.</p> <p>Results</p> <p>The mortality rate was 13.0%. Non-survivors differed in age, comorbidity, inclusion on the transplant waiting list and physical functioning score. The hazard ratios of death were 8.958 (2.843-28.223; <it>p </it>< 0.001) for comorbidity, 3.992 (1.462-10.902; <it>p </it>= 0.007) for not being on the transplant waiting list, 1.038 (1.012-1.066; <it>p </it>= 0.005) for age, and 0.980 (0.964-0.996; <it>p </it>= 0.014) for physical functioning.</p> <p>Conclusions</p> <p>Comorbidity, not being on the transplant waiting list, age and physical functioning, which reflects physical status, must be seen as risk indicators of death among patients undergoing HD.</p

Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs

© 2015 Wyrsch et al. Background: Enterotoxigenic Escherichia coli (ETEC) are a major economic threat to pig production globally, with serogroups O8, O9, O45, O101, O138, O139, O141, O149 and O157 implicated as the leading diarrhoeal pathogens affecting pigs below four weeks of age. A multiple antimicrobial resistant ETEC O157 (O157 SvETEC) representative of O157 isolates from a pig farm in New South Wales, Australia that experienced repeated bouts of pre- and post-weaning diarrhoea resulting in multiple fatalities was characterized here. Enterohaemorrhagic E. coli (EHEC) O157:H7 cause both sporadic and widespread outbreaks of foodborne disease, predominantly have a ruminant origin and belong to the ST11 clonal complex. Here, for the first time, we conducted comparative genomic analyses of two epidemiologically-unrelated porcine, disease-causing ETEC O157; E. coli O157 SvETEC and E. coli O157:K88 734/3, and examined their phylogenetic relationship with EHEC O157:H7. Results: O157 SvETEC and O157:K88 734/3 belong to a novel sequence type (ST4245) that comprises part of the ST23 complex and are genetically distinct from EHEC O157. Comparative phylogenetic analysis using PhyloSift shows that E. coli O157 SvETEC and E. coli O157:K88 734/3 group into a single clade and are most similar to the extraintestinal avian pathogenic Escherichia coli (APEC) isolate O78 that clusters within the ST23 complex. Genome content was highly similar between E. coli O157 SvETEC, O157:K88 734/3 and APEC O78, with variability predominantly limited to laterally acquired elements, including prophages, plasmids and antimicrobial resistance gene loci. Putative ETEC virulence factors, including the toxins STb and LT and the K88 (F4) adhesin, were conserved between O157 SvETEC and O157:K88 734/3. The O157 SvETEC isolate also encoded the heat stable enterotoxin STa and a second allele of STb, whilst a prophage within O157:K88 734/3 encoded the serum survival gene bor. Both isolates harbor a large repertoire of antibiotic resistance genes but their association with mobile elements remains undetermined. Conclusions: We present an analysis of the first draft genome sequences of two epidemiologically-unrelated, pathogenic ETEC O157. E. coli O157 SvETEC and E. coli O157:K88 734/3 belong to the ST23 complex and are phylogenetically distinct to EHEC O157 lineages that reside within the ST11 complex

COVID-19 Mortality and Case-Fatality Rates in Sergipe State, Northeast Brazil, From April to June 2020

Information on how coronavirus disease 2019 (COVID-19) mortality is related to population characteristics in low- and middle-income countries is still limited. We described the deaths from COVID-19 in Sergipe state, Northeast Brazil, from April 2 to June 27, 2020. For this purpose, we conducted a study composed of (i) a case series study of all deaths due to COVID-19 and (ii) a population-based study to verify the behavior of the mortality and case-fatality rates (CFR) related to COVID-19. Data from 605 deaths due to COVID-19 were used to describe the characteristics of individuals with the disease, as well as the differences in gender, age, and comorbidities. Additionally, population data were extracted to estimate the mortality and CFR by population stratum. We also performed an adjusted CFR analysis including a time lag of 14 days between the onset of symptoms and reporting deaths. Of the 605 patients included in this study, 321 (53.1%) were males and the median age was 67.0 years. Most patients (n = 447, 73.9%) who died from COVID-19 had at least one pre-existing clinical condition. The mortality rate was 29.3 deaths per 100,000 inhabitants and the crude CRF was 2.6% (95% CI 2.4–2.8). CFR was higher in males (3.1%, 95% CI 2.8–3.4; p < 0.001) and people aged =60 years (14.2%, 95% CI 13.0–15.6; p = 0.042). About 25% of patients died during the first 24-h post-hospital admission. The adjusted CFR for a 14-day time lag was ~2-fold higher than the crude CFR over the study period.We dedicated this article to all health professionals who are facing COVID-19. This study was part of the EpiSERGIPE project. NM thanks the Portuguese Foundation for Science and Technology under the Horizon 2020 Program (PTDC/PSI-GER/280 76/2017)

Experimental investigation of the air-fuel charging process in a four-valve supercharged two-stroke cycle GDI engine

Fuel consumption standards imposed in several countries for the next years have prompted the development of hybrid passenger cars with ever smaller internal combustion engines. In such powertrain, fuel consumption is as important as engine packaging and power density, so two-stroke engines may be an option due to their higher combustion frequency compared to four-stroke engines. Therefore, the present research investigates the air–fuel charging process of an overhead four-valve direct injection supercharged engine operating in the two-stroke cycle. The optimum start of fuel injection was evaluated for commercial gasoline by means of indicated and combustion efficiencies where a trade-off was found between early and late fuel injections. By advancing the injection timing, more fuel was prone to short circuit to the exhaust during the valve overlap, while late injections resulted in poor charge preparation. The gas exchange parameters, i.e. charging and trapping efficiencies, were obtained from seventy operating points running at fuel-rich conditions. The Benson–Brandham mixing-displacement scavenging model was then fit to the experimental data with a coefficient of determination better than 0.95. With such model, the air trapping and charging efficiencies could be estimated solely based on the scavenge ratio and exhaust lambda, regardless of the engine load, speed, or air/fuel ratio employed. Further twenty-five different lean-burn testing points were tested to certify the proposed methodology applied to the poppet valve two-stroke engine. The in-cylinder lambda was calculated and found different from the exhaust lambda due to mixing between burned gases and intake air during the scavenging process

Tracking Holocene palaeostratification and productivity changes in the Western Irish Sea: A multi-proxy record

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.The Western Irish Sea preserves an exceptionally thick (ca. 40 m) Holocene succession that is ideally suited to understanding the pattern of palaeostratification and water mass productivity changes in the region, and their relationship with sea level, sedimentation, and biota. Additionally, the presence of shallow-buried methane provides an opportunity to explore its potential impact on the local pattern of Holocene marine environmental change. Multi-proxy investigation of a cored borehole succession through the Holocene interval tracks changes from mixed to seasonally stratified conditions. In the earliest Holocene (11.2–10 ka), high productivity, mixed water conditions prevailed, with abundant and diverse foraminifera and dominant heterotrophic dinoflagellate cysts. Productivity was probably driven by high nutrient fluxes related to high rates of sedimentation (>1600 cm/kyr), in turn influenced by relatively low sea level and restricted sediment accommodation space across shelf areas to the east of the borehole site (eastern Irish Sea Basin). With rising sea level in the later part of the Early Holocene, the region evolved into a relatively lower productivity mixed water mass system, with significant changes in ecology revealed by dinoflagellate cysts and foraminifera. In the latest Early Holocene and earliest Mid Holocene (ca. 8.4–8.2 ka) a return to higher productivity is signalled by dinoflagellate cyst data; a result of seasonal stratification becoming established, evidenced by sharply increased summer sea surface temperature estimates (typically 16–17 °C) that contrast with an opposite (more positive) trend in δ18O values for benthic foraminifera. Reductions in turbulent mixing associated with stratification might have exacerbated the palaeoecological impact of shallow-buried methane associated with the borehole site, potentially evidenced by a significant change in dominant benthic foraminifera and strong, localised excursions in the benthic δ13C/δ18O record

Lactate signalling regulates fungal β-glucan masking and immune evasion

AJPB: This work was supported by the European Research Council (STRIFE, ERC- 2009-AdG-249793), The UK Medical Research Council (MR/M026663/1), the UK Biotechnology and Biological Research Council (BB/K017365/1), the Wellcome Trust (080088; 097377). ERB: This work was supported by the UK Biotechnology and Biological Research Council (BB/M014525/1). GMA: Supported by the CNPq-Brazil (Science without Borders fellowship 202976/2014-9). GDB: Wellcome Trust (102705). CAM: This work was supported by the UK Medical Research Council (G0400284). DMM: This work was supported by UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC/K000306/1). NARG/JW: Wellcome Trust (086827, 075470,101873) and Wellcome Trust Strategic Award in Medical Mycology and Fungal Immunology (097377). ALL: This work was supported by the MRC Centre for Medical Mycology and the University of Aberdeen (MR/N006364/1).Peer reviewedPostprin