OrChem - An open source chemistry search engine for Oracle®

<p>Abstract</p> <p>Background</p> <p>Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world.</p> <p>Results</p> <p>Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets.</p> <p>Availability</p> <p>OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via <url>http://orchem.sourceforge.net</url>.</p

The effects of estradiol on mood and behavior in human female adolescents: a systematic review

Mood disorders and health risk behaviors increase in adolescence. Puberty is considered to contribute to these events. However, the precise impact of pubertal hormone changes to the emergence of mood disorders and risk behaviors is relatively unclear. It is important that inappropriate attribution is not made. Our aim was to determine what is known about the effect of endogenous estradiol on human adolescent girls’ mood and behavior. The databases searched were MEDLINE, Embase, PsycINFO, Education Resources Information Center (ERIC), Pre-MEDLINE, Web of Science, and Scopus for all dates to October 2014. For inclusion, contemporaneous hormone and mood or behavioral assessment was required. Data were extracted following a template created by the authors. Fourteen studies met our inclusion criteria. There was some consistency in findings for mood and estradiol levels, with associations between estradiol and depression and emotional tone and risk taking. Results were less consistent for studies assessing other mood and behavioural outcomes. Most studies were cross-sectional in design; assay methodologies used in older studies may lack the precision to detect early pubertal hormone levels. Conclusion: Three longitudinal and several cross-sectional studies indicate potential associations between estradiol and certain mood or affective states, especially depression and mood variability though there are insufficient data to confirm that the rise in estradiol during puberty is causative. We believe that it is important for health professionals to take care when attributing adolescent psychopathology to puberty hormones, as the current data supporting these assertions are limited.Australian National Health and Medical Research Council (NHMRC

Swimming into peptidomimetic chemical space using pepMMsMIMIC

pepMMsMIMIC is a novel web-oriented peptidomimetic compound virtual screening tool based on a multi-conformers three-dimensional (3D)-similarity search strategy. Key to the development of pepMMsMIMIC has been the creation of a library of 17 million conformers calculated from 3.9 million commercially available chemicals collected in the MMsINC® database. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein–protein recognition of this natural peptide using both pharmacophore and shape similarity techniques. We hope that the accessibility of pepMMsMIMIC (freely available at http://mms.dsfarm.unipd.it/pepMMsMIMIC) will encourage medicinal chemists to de-peptidize protein–protein recognition processes of biological interest, thus increasing the potential of in silico peptidomimetic compound screening of known small molecules to expedite drug development

Requirement for specific gravity and creatinine adjustments for urinary steroids and luteinizing hormone concentrations in adolescents

Objectives: Urinary hormone concentrations are often adjusted to correct for hydration status. We aimed to determine whether first morning void urine hormones in growing adolescents require adjustments and, if so, whether urinary creatinine or specific gravity (SG) are better adjustments. Design and Methods: The study population was adolescents aged 10.1 to 14.3 years initially who provided fasting morning blood samples at 0 and 12 months (n=343) and first morning urine every three months (n=644). Unadjusted, creatinine and SG-adjusted hormonal concentrations were compared by Deming regression and Bland-Altman analysis and grouped according to self-rated Tanner stage or chronological age. F-ratios for self-rated Tanner stages and age groups were used to compare unadjusted and adjusted hormonal changes in growing young adolescents. Correlations of paired serum and urinary hormonal concentration of unadjusted and creatinine and SG adjusted were also compared. Results: Fasting first morning void hormone concentrations correlated well and were unbiased between unadjusted or adjusted by either creatinine or SG. Urine creatinine concentration increases with Tanner stages, age and male gender whereas, urine SG was not influenced by Tanner stage, age or gender. Adjustment by creatinine or SG of urinary luteinizing hormone, estradiol, testosterone, dihydrotestosterone and dehydroepiandrosterone concentrations did not improve correlation with paired serum concentrations. Conclusions: Urine steroid and LH concentrations in first morning void samples of adolescents are not significantly influenced by hydration status and may not require adjustments; however, if desired, both creatinine and SG adjustments are equally suitable

Real Time Global Tests of the ALICE High Level Trigger Data Transport Framework

The High Level Trigger (HLT) system of the ALICE experiment is an online event filter and trigger system designed for input bandwidths of up to 25 GB/s at event rates of up to 1 kHz. The system is designed as a scalable PC cluster, implementing several hundred nodes. The transport of data in the system is handled by an object-oriented data flow framework operating on the basis of the publisher-subscriber principle, being designed fully pipelined with lowest processing overhead and communication latency in the cluster. In this paper, we report the latest measurements where this framework has been operated on five different sites over a global north-south link extending more than 10,000 km, processing a ``real-time'' data flow.Comment: 8 pages 4 figure