Statistical Workflow for Feature Selection in Human Metabolomics Data.

High-throughput metabolomics investigations, when conducted in large human cohorts, represent a potentially powerful tool for elucidating the biochemical diversity underlying human health and disease. Large-scale metabolomics data sources, generated using either targeted or nontargeted platforms, are becoming more common. Appropriate statistical analysis of these complex high-dimensional data will be critical for extracting meaningful results from such large-scale human metabolomics studies. Therefore, we consider the statistical analytical approaches that have been employed in prior human metabolomics studies. Based on the lessons learned and collective experience to date in the field, we offer a step-by-step framework for pursuing statistical analyses of cohort-based human metabolomics data, with a focus on feature selection. We discuss the range of options and approaches that may be employed at each stage of data management, analysis, and interpretation and offer guidance on the analytical decisions that need to be considered over the course of implementing a data analysis workflow. Certain pervasive analytical challenges facing the field warrant ongoing focused research. Addressing these challenges, particularly those related to analyzing human metabolomics data, will allow for more standardization of as well as advances in how research in the field is practiced. In turn, such major analytical advances will lead to substantial improvements in the overall contributions of human metabolomics investigations

Proof-of-Concept Studies Directed toward the Formation of Metallic Ag Nanostructures from Ag3PO4 Induced by Electron Beam and Femtosecond Laser

In this work, for the first time, the instantaneous nucleation and growth processes of Ag nanoparticles on Ag3PO4 mediated by femtosecond laser pulses are reported and analyzed. The investigated samples are pure Ag3PO4sample, electron-irradiated Ag3PO4 sample, and laser-irradiated sample. Complete characterization of the samples is performed using X-ray diffraction (XRD), Rietveld refinements, field emission scanning electron microscopy, and energy dispersive spectroscopy (EDS). XRD confirms that the irradiated surface layer remains crystalline, and according to EDS analysis, the surface particles are composed primarily of Ag nanoparticles. This method not only offers a one-step route to synthesize Ag nanoparticles using laser-assisted irradiation with particle size control, but also reports a complex process involving the formation and subsequent growth of Ag nanoparticles through an unexpected additive-free in situ fabrication process

Payments for ecosystem services in the tropics: a closer look at effectiveness and equity

We undertake a review of academic literature that examines the effectiveness and equity-related performance of PES initiatives targeting biodiversity conservation in tropical and sub-tropical countries. We investigate the key features of such analyses as regards their analytical and methodological approach and we identify emerging lessons from PES practice, leading to a new suggested research agenda. Our results indicate that analyses of PES effectiveness have to date focused on either ecosystem service provision or habitat proxies, with only half of them making explicit assessment of additionality and most describing that payments have been beneficial for land cover and biodiversity. Studies evaluating the impact of PES on livelihoods suggest more negative outcomes, with an uneven treatment of the procedural and distributive considerations of scheme design and payment distribution, and a large heterogeneity of evaluative frameworks. We propose an agenda for future PES research based on the emerging interest in assessing environmental outcomes more rigorously and documenting social impacts in a more comparative and contextually situated form

Promoting Healthy Choices in Workplace Cafeterias: A Qualitative Study

Objectives: To develop 3 point-of-choice campaigns to influence food choice in workplace cafeterias. Design: Eight focus groups were conducted to guide campaign development. Setting: Focus groups were conducted in the workplace. Participants: University employees (n ¼ 36) aged 23–58 years (mean, 33.8 years). Phenomenon of Interest: To explore ways to prompt changes in behavior. Analysis: Transcripts were analyzed using thematic analysis. Results: This study identified calories and saturated fat as information that would have the greatest influence on food selection. Participants want this information at the time the choice is made. Participants reported limited time to eat at work, so converting nutrient density per 100 g or per serving to per portion consumed from point-of-choice labels was not a priority. Participants said that they have more time to read information in places where they line up for food, so at this point they are more open to persuasive messages. Effective messages urge the reader to take immediate action, which explains why they should chose the behavior and how it will help them achieve health. Conclusions and Implications: Point-of-choice campaigns were well received, but factors such as cost, time, and availability of healthy food at work may shape choices to a greater extent than will nutrition information

Reciprocal Regulation of Cephalosporin Resistance in Enterococcus faecalis

Antibiotic-resistant enterococci are major causes of hospital-acquired infections and therefore represent a serious public health problem. One well-known risk factor for the acquisition of hospital-acquired enterococcal infections is prior therapy with broad-spectrum cephalosporin antibiotics. Enterococci can proliferate in patients undergoing cephalosporin therapy due to intrinsic cephalosporin resistance, a characteristic of the genus Enterococcus. However, the molecular basis for cephalosporin resistance in E. faecalis has yet to be adequately elucidated. Previously we determined that a putative Ser/Thr kinase, IreK (formerly PrkC), is required for intrinsic cephalosporin resistance in E. faecalis. Here we show that kinase activity is required for cephalosporin resistance and, further, that resistance in E. faecalis is reciprocally regulated by IreK and IreP, a PP2C-type protein phosphatase encoded immediately upstream of IreK. Mutants of two divergent lineages of E. faecalis lacking IreP exhibit remarkable hyperresistance to cephalosporins but not to antibiotics targeting other cellular processes. Further genetic analyses indicate that hyperresistance of the IreP mutant is mediated by the IreK kinase. Additionally, competition experiments reveal that hyperresistant ΔireP mutants exhibit a substantial fitness defect in the absence of antibiotics, providing an evolutionary rationale for the use of a complex signaling system to control intrinsic cephalosporin resistance. These results support a model in which IreK and IreP act antagonistically via protein phosphorylation and dephosphorylation as part of a signal transduction circuit to regulate cellular adaptation to cephalosporin-induced stress

Predicting the spatial and temporal dynamics of species interactions in Fagus sylvatica and Pinus sylvestris forests across Europe

The productivity and functioning of mixed-species forests often differs from that of monocultures. However, the magnitude and direction of these differences are difficult to predict because species interactions can be modified by many potentially interacting climatic and edaphic conditions, stand structure and previous management. Process-based forest growth models could potentially be used to disentangle the effects of these factors and thereby improve our understanding of mixed forest functioning while facilitating their design and silvicultural management. However, to date, the predicted mixing effects of forest growth models have not been compared with measured mixing effects. In this study, 26 sites across Europe, each containing a mixture and monocultures of Fagus sylvatica and Pinus sylvestris, were used to calculate mixing effects on growth and yield and compare them with the mixing effects predicted by the forest growth model 3-PGmix. The climate and edaphic conditions, stand structures and ages varied greatly between sites. The model performed well when predicting the stem mass and total mass (and mixing effects on these components), with model efficiency that was usually >0.7. The model efficiency was lower for growth or smaller components such as foliage mass and root mass. The model was also used to predict how mixing effects would change along gradients in precipitation, temperature, potential available soil water, age, thinning intensity and soil fertility. The predicted patterns were consistent with measurements of mixing effects from published studies. The 3-PG model is a widely used management tool for monospecific stands and this study shows that 3-PGmix can be used to examine the dynamics of mixed-species stands and determine how they may need to be managed.This article is based upon work from COST Action EuMIXFOR, supported by COST (European Cooperation in Science and Technology). Funding for the Czech Republic site was provided by the MŠMT projects COST CZ – LD14063 and LD14074. All contributors thank their national funding institutions and the forest owners for agreeing to establish the plots and to measure and analyse data from the plots. The first author was funded by a Heisenberg Fellowship (FO 791/4-1) from the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). Mário Pereira was supported by European Investment Funds by FEDER/COMPETE/POCI– Operacional Competitiveness and Internacionalization Programme, under Project POCI-01-0145-FEDER-006958 and National Funds by FCT – Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013 as well as by project Interact-Integrative Research in Environment, Agro-Chain and Technology, NORTE-01-0145-FEDER-000017, research line BEST, co-financed by FEDER/NORTE 2020

Qualitative characteristics of meat from confined crossbred heifers fed with lipid sources

Lipids have been used in ruminant feed to replace high amounts of grain for increasing the diet energy density, performance and meat quality. This study evaluated the qualitative characteristics of meat from feedlot heifers fed with sources of lipid supplements. Twenty-one crossbred heifers (1/4Nelore × 1/4Santa Gertrudis × 1/2Braunvieh) were used. Each heifer received 60 % forage with a base of corn silage and 40 % concentrate, resulting in 5.8 % lipid content in the total diet. The following sources of lipids were used: soybeans, protected fat and soybean oil. There were no differences on physical characteristics of meat samples from heifers fed with the lipid sources. Soybeans increased the concentration of linoleic acid, content of polyunsaturated fatty acid and activity of the Δ9-desaturase C16 enzyme in the Longissimus muscle. The use of soybean oil in the diet increased the oleic acid, monounsaturated fatty acid, total cis- and trans-fatty acids (C18:0) and the activity of the Δ9-desaturase C16 enzyme in the subcutaneous fat. Diets with soybean grain had greater deposition of linoleic and linolenic acids than diets with fat protected and greater presence of these essential fatty acids are associated to a better composition and meat quality

Bioactive compounds recovery optimization from vine pruning residues using conventional heating and microwave-assisted extraction methods

Polyphenol compounds from vine pruning residue (VPR) were extracted by conventional heating and microwave-assisted treatments. For each treatment, total phenolic compounds and their antioxidant activity were optimized by experimental design. Maximal extraction of polyphenolic compounds (2.17g/100g VPR) was obtained at 80°C, 120min and 45% of ethanol by conventional heating, and 2.37g/100g of VPR were extracted by microwave-assisted process at 120°C, 5min and 60% of ethanol. Ellagic acid and apigenin were the predominant polyphenolic compounds in the extracts, achieving concentration of 68.65 and 208.23mg/100g VPR, respectively for conventional heating and 185.15 and 118.84mg/100g of VPR for microwave-assisted treatment. The results showed reduction of extraction time and energy consumption for microwave-assisted treatment leading to cost-effective technology for the extraction of polyphenol compounds. Furthermore, the results hereby compiled allow for the tailor-made extraction of specific high-value compounds from a renewable biomass as vine pruning residue.Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unitBioTecNorte operation(NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do NorteInternational Cooperation Program CNPq/CSFinfo:eu-repo/semantics/publishedVersio