BEAT: An Open-Source Web-Based Open-Science Platform

With the increased interest in computational sciences, machine learning (ML), pattern recognition (PR) and big data, governmental agencies, academia and manufacturers are overwhelmed by the constant influx of new algorithms and techniques promising improved performance, generalization and robustness. Sadly, result reproducibility is often an overlooked feature accompanying original research publications, competitions and benchmark evaluations. The main reasons behind such a gap arise from natural complications in research and development in this area: the distribution of data may be a sensitive issue; software frameworks are difficult to install and maintain; Test protocols may involve a potentially large set of intricate steps which are difficult to handle. Given the raising complexity of research challenges and the constant increase in data volume, the conditions for achieving reproducible research in the domain are also increasingly difficult to meet. To bridge this gap, we built an open platform for research in computational sciences related to pattern recognition and machine learning, to help on the development, reproducibility and certification of results obtained in the field. By making use of such a system, academic, governmental or industrial organizations enable users to easily and socially develop processing toolchains, re-use data, algorithms, workflows and compare results from distinct algorithms and/or parameterizations with minimal effort. This article presents such a platform and discusses some of its key features, uses and limitations. We overview a currently operational prototype and provide design insights.Comment: References to papers published on the platform incorporate

The effect of dietary calcium inclusion on broiler gastrointestinal pH: quantification and method optimization

There is little consensus as to the most appropriate methodology for the measurement of gastrointestinal pH in chickens. An experiment was conducted to establish the optimum sampling method for the determination of broiler digesta pH in birds fed differing levels of dietary calcium. Ross 308 broilers (n = 60) were fed one of two experimental diets, one containing 0.8% monocalcium phosphate and 2% limestone and one containing 0.4% monocalcium phosphate and 1% limestone. Four factors were investigated to determine the most appropriate method of measuring broiler gastrointestinal digesta pH: removal from the tract, prolonged air exposure, altering the temperature of the assay, and controlling the water content of the digesta. The conditions were assessed at bird ages from 7 to 42 d post hatch. Dietary Ca content had no significant effect on in situ pH, but it contributed towards variance in ex situ pH of both gizzard and duodenum digesta

Targeted sequencing identifies genetic polymorphisms of flavin-containing monooxygenase genes contributing to susceptibility of nicotine dependence in European American and African American

BACKGROUND: Smoking is a leading cause of preventable death. Early studies based on samples of twins have linked the lifetime smoking practices to genetic predisposition. The flavin‐containing monooxygenase (FMO) protein family consists of a group of enzymes that metabolize drugs and xenobiotics. Both FMO1 and FMO3 were potentially susceptible genes for nicotine metabolism process. METHODS: In this study, we investigated the potential of FMO genes to confer risk of nicotine dependence via deep targeted sequencing in 2,820 study subjects comprising 1,583 nicotine dependents and 1,237 controls from European American and African American. Specifically, we focused on the two genomic segments including FMO1,FMO3, and pseudo gene FMO6P, and aimed to investigate the potential association between FMO genes and nicotine dependence. Both common and low‐frequency/rare variants were analyzed using different algorithms. The potential functional significance of SNPs with association signal was investigated with relevant bioinformatics tools. RESULTS: We identified different clusters of significant common variants in European (with most significant SNP rs6674596, p = .0004, OR = 0.67, MAF_EA = 0.14, FMO1) and African Americans (with the most significant SNP rs6608453, p = .001, OR = 0.64, MAF_AA = 0.1, FMO6P). No significant signals were identified through haplotype‐based analyses. Gene network investigation indicated that both FMO1 and FMO3 have a strong relation with a variety of genes belonging to CYP gene families (with combined score greater than 0.9). Most of the significant variants identified were SNPs located within intron regions or with unknown functional significance, indicating a need for future work to understand the underlying functional significance of these signals. CONCLUSIONS: Our findings indicated significant association between FMO genes and nicotine dependence. Replications of our findings in other ethnic groups were needed in the future. Most of the significant variants identified were SNPs located within intronic regions or with unknown functional significance, indicating a need for future work to understand the underlying functional significance of these signals

Effect of varying ratios of dietary calcium and phosphorus on performance, phytate P and mineral retention in Japanese quail (Coturnix cotnurnix Japonica).

The effect of different ratios of dietary calcium (Ca) to total phosphorus (tP) on the performances and retention of minerals and phytate phosphorus (pP) by quails were studied using 600 unsexed broiler quails from 1 to 21 days of age. Treatments consist of five corn and soybean meal (CSM) based diets with variable ratios of Ca:tP (1.96, 1.81, 1.66, 1.53 and 1.39) with four replicate of 30 birds each. Diets contained 3g chromium oxide (Cr2O3)/kg as marker. All ratios of Ca and P had no significant effect on feed consumption of birds. There were pronounced differences (P < 0.05) in body weight gain of chicks among treatments at second and third week of age. Improved (P < 0.05) feed conversion ratio was observed at 3 wk of age. Higher ratios of Ca:tP (1.96 and 1.81) increased (P < 0.05) the retention of P compared to other treatments while ratio of 1.96 decreased (P < 0.05) the retention of Ca and phytate. In conclusion, Ca:tP ratio of 1.81 showed positive effect on most of parameters measured in this study

Gender, economics and culture: diversity and the international evolution of smoking prevalence

Aims: To examine whether the observed diversity between national patterns of smoking prevalence could require modification of the World Health Organization (WHO) linear model for an international `smoking pandemic' (a worldwide epidemic) to address data from non-western countries. Method: We conducted secondary research using current measures in three publicly available databases: Globalink, the International Labour Organization and the World Bank (all internetaccessible). The measures we used are the separate percentage data for men and women on: smoking and employment and national income per capita (US$) and percentage growth per annum. Results: Regression analysis showed that women smokers were more frequent in countries with higher national income, but women were less likely to smoke in countries of rapid growth. Men were less likely to smoke in countries with higher national income, but more likely to smoke in countries of rapid growth. Two principle components together explained 62% of all the variance in the international data. The largest factor was positively correlated with the percentage of employed females, the percentage of female smokers and national income per capita, but negatively correlated with the percentage of male smokers and percentage annual growth. The effect of female employment was not continuous, but above a threshold of 51%, was associated with a higher prevalence of female smoking. The smaller, second factor was only weakly correlated with any smoking variables. Conclusions: In his 1994 model (subsequently adopted by the WHO) Lopez looked at historical trends in `stages' of smoking prevalence. These have been associated with `stages' of economic development. We extended this analysis to look at a dynamic change (% annual growth) and a social indicator (employment). Male and female smoking is affected differentially by economic change and by level of income. These are also strongly related to the percentage of women in employment. This has implications for workplace policies on smoking

Growth performance, in vitro antioxidant properties and chemical composition of the halophyte Limonium algarvense Erben are strongly influenced by the irrigation salinity

Limonium algarvense Erben (sea lavender) is a halophyte species with potential to provide natural ingredients with in vitro antioxidant, anti-inflammatory, neuroprotective and antidiabetic properties. This study reports for the first time the 1) cultivation of sea lavender in greenhouse conditions under irrigation with freshwater (approx. 0 mM NaCl) and saline aquaculture wastewater (300 and 600 mM NaCl), and 2) the influence of the irrigation salinity on the plant performance (e.g growth, number of produced leaves and flowers), in vitro antioxidant properties [radical scavenging activity (DPPH and ABTS), ferric reducing antioxidant power (FRAP), metal chelating properties on copper (CCA) and iron (ICA)], toxicity (in vitro on three mammalian cell lines) and chemical composition (determined by LC-ESI-HRMS/MS). The freshwater-irrigated plants had better growth performance than those irrigated with saltwater. Extracts from wild plants, had the highest antioxidant activity, but those from cultivated ones kept high in vitro antioxidant properties and interesting chemical profile. The flowers' extracts of plants irrigated with 300 mM NaCl had the highest antioxidant activities against DPPH, whereas those from freshwater-irrigated plants were more active on ABTS, CCA and FRAP. Most of the extracts showed nil toxicity. The flowers' extracts displayed the highest diversity of compounds, mainly quercetin, apigenin, luteolin, naringenin and their glycoside derivatives. Moreover, their abundance varied with the irrigation salinity. These data indicate that sea lavender plants can be successfully cultivated in greenhouse conditions under fresh- and saltwater irrigation, maintaining interesting biological and chemical properties.Funding Agency Portuguese Foundation for Science and Technology Portuguese National Budget CCMAR/Multi/04326/2019 GreenVet project ALG-01-0145-FEDER-028876 XtrerneAquaCrops FA-05-2017-028 Lisboa-01-0145-FEDER-022125-RNEM-IST ID/QUI/00100/201 Portuguese Foundation for Science and Technology SFRH/BD/116604/2016 CEECIND/00425/2017info:eu-repo/semantics/publishedVersio

Harmful effects of endosulfan treatment on cyanobacterial distribution and some macromolecules of soybean plant

In a trial to evaluate the impact of one of the commonly used insecticides in Egypt, a plot area cultivated with soybean was sprayed with endosulfan. Some of the biochemical criteria of the treated soybean and the biodiversity and biochemical activity of its companion cyanobacteria were compared with those of the untreated ones. The results revealed that endosulfan application caused inhibition in the attendance and biodiversity of the soil cyanobacteria found in the rhizosphere of the treated soybean, specially the filamentous species. The treated soil showed a highly significant inhibition in their ARA (acetylene-reducing activity) and exopolysaccharides. The biochemical analysis showed a high significant decrease in all the carbohydrate fractions as well as DNA and RNA contents of the treated soybean plants compared with the untreated ones. However, the total soluble proteins significantly Increased, indicating some defense pattern against the lethal effects of endosulfan. From the results, it could be concluded that application of endosulfan has a significant potential to change ecosystems and soil biological processes and could potentially reduce future farm productivity and cause harmful impact to agriculture

ANTIMICROBIAL RESISTANCE PATTERNS OF PROTEUS ISOLATES FROM CLINICAL SPECIMENS

Total of 6840 clinical samples were collected from King Fahd Hospital at Medina, Kingdom of Saudi Arabia (KSA). Clinical samples were screened for Proteus spp. It is found that Proteus spp isolates representing about 3% of all positive samples isolated from different clinical sources. Males were found to be more vulnerable than females in acquiring Proteus infections. Results showed that the greatest number of Proteus spp. isolates from clinical specimens were isolated from wound and sputum swabs specimens representing about 88% of all clinical specimens.Thirteen different antibiotics representing different families of antibiotics were tested on Proteus spp. specimens for studying its antimicrobial sensitivity pattern. Results of antimicrobial sensitivity tests revealed that imipenem (IMP) antibiotic was the most effective antibiotic against Proteus spp. with 91% of antimicrobial sensitivity. Imipenem (Imp) was followed by amikacin (AK) with 61% of antimicrobial sensitivity.Results are recommending prescribing of imipenem (IMP) antibiotic in the treatment of Proteus spp infections. It is recommended also to prescribe amikacin (AK) in the case of sensitivity to imipenem (IMP). In acute cases, Proteus infections could require use of combined antimicrobial therapy (imipenem- amikacin). Results also demonstrated that percentage of Proteus spp. infections was highest during summer season representing about 40% of infections all year along. Summer season was followed by winter season with about 32% of infections