BioMAJ: a flexible framework for databanks synchronization and processing

Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks

Effect of powdered seed of Nigella sativa administration on sub-chronic and chronic lead acetate induced hemato-biochemical and histopathological changes in Sprague Dawley rats

Lead acetate (PbAC) toxicity can occur by either ingestion or inhalation from contaminated surfaces or from the environment. Nigella sativa is a natural product with immense pharmacological properties, which include antioxidant, antibacterial, and antianemia properties. It has been showed to counter the effect of PbAC-induced hematological and biochemical changes in short-term studies. This study hypothesized that the N. sativa (NS) administration will ameliorate the deleterious effects of chronic PbAC toxicity in rats. A total of 75 Sprague Dawley rats were divided into three groups of 25 rats, and each group was further sub-divided into five groups of five rats each. Group 1 rats (negative control) were given distilled water, group 2 (positive control; PC) were given 10 mg/kg of lead acetate (PbAC) daily, and groups 3 (T1), 4 (T2), and 5 (T3) were each given 10 mg/kg of PbAC followed by graded concentrations of powdered seeds of NS; 100, 150, and 200 mg/kg, respectively. Five rats in each group were euthanized at 30, 60, and 90 days for collection of whole blood and selected organs. Whole blood was collected after euthanized via cardio puncture and used to evaluate the complete blood profile, while plasma was used for biochemical analysis. Tissue samples of the liver and kidney were fixed with 10% buffered formalin, processed, and stained with H&E and periodic acid–Schiff (PAS) for the liver. Aggression and fear were increased in the PbAC-exposed group and absent in the T3 group. There was a lower (p < 0.05) red blood cell count (RBC), packed cell volume (PCV), mean corpuscular hemoglobin concentration (MCHC), and lymphocyte count in the PC and T1 groups only. Biochemical analysis revealed elevated (p < 0.05) liver enzyme and creatinine levels in the PC and T1 groups on day 90 for AST and day 30 for ALT and creatinine. The level of alkaline phosphatase (ALP) was higher (p < 0.05) in the PC at 30 and 60 days of sampling. Other parameters, such as WBCs, prothrombin, urea, and cholesterol, were not significant in all groups. Histopathological lesions in the liver and kidneys were more severe in the PC and T1 groups, while the T2 and T3 groups showed mild lesions resulting from N. sativa administration. There was a decrease (p < 0.05) in the total PAS-stained area signifying glycogen depletion in the PC, T1, and T2 groups at 60 days and a higher distribution of the PAS-stained areas (p < 0.05) in the T3 group. At 90 days, the PC group had a lower (p < 0.05) distribution of PAS-stained areas in comparison to the other groups. The results showed the therapeutic potential of N. sativa extract in modulating both hematological and biochemical alterations induced by chronic lead acetate administration in rats

Heat Treated NiP–SiC Composite Coatings: Elaboration and Tribocorrosion Behaviour in NaCl Solution

Tribocorrosion behaviour of heat-treated NiP and NiP–SiC composite coatings was investigated in a 0.6 M NaCl solution. The tribocorrosion tests were performed in a linear sliding tribometer with an electrochemical cell interface. It was analyzed the influence of SiC particles dispersion in the NiP matrix on current density developed, on coefficient of friction and on wear volume loss. The results showed that NiP–SiC composite coatings had a lower wear volume loss compared to NiP coatings. However, the incorporation of SiC particles into the metallic matrix affects the current density developed by the system during the tribocorrosion test. It was verified that not only the volume of co-deposited particles (SiC vol.%) but also the number of SiC particles per coating area unit (and consequently the SiC particles size) have made influence on the tribocorrosion behaviour of NiP–SiC composite coatings

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