Normalization And Matching Of Chemical Compound Names

We have developed ChemHits (http://sabio.h-its.org/chemHits/), an application which detects and matches synonymic names of chemical compounds. The tool is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Subsequently, matching of synonymous names is achieved by comparison of the normalized name forms. The tool is capable of normalizing a given name of a chemical compound and matching it against names in (bio-)chemical databases, like SABIO-RK, PubChem, ChEBI or KEGG, even when there is no exact name-to-name-match

Spin-wave Talbot effect in thin ferromagnetic film

The Talbot effect has been known in optics since XIX century and found various technological applications. In this paper, we demonstrate with the help of micromagnetic simulations this self-imaging phenomenon for spin waves propagating in a thin ferromagnetic film magnetized out-of-plane. We show that the main features of the obtained Talbot carpets for spin waves can be described, to a large extent, by the approximate analytical formulas yielded by the general analysis of the wave phenomena. Our results indicate a route to a feasible experimental realisation of the Talbot effect at low and high frequencies and offer interesting effects and possible applications in magnonics.Comment: 10 pages, 10 figure

Ureteroscopic lithotripsy for ureteral stones in children using holmium: yag laser energy: results of a multicentric survey

BACKGROUND: Holmium:YAG (Ho:YAG) laser lithotripsy has broadened the indications for ureteroscopic stone managements in adults, but few evidence are currently available in the pediatric population. OBJECTIVE: This article aimed to assess the outcome of Ho:YAG laser lithotripsy during retrograde ureteroscopic management of ureteral stones in different locations in children. STUDY DESIGN: The medical records of 149 patients (71 boys and 78 girls; median age 9.2 years) treated with Ho:YAG laser ureteroscopic lithotripsy in five international pediatric urology units over the last 5 years were retrospectively reviewed. Exclusion criteria included patients with renal calculi and/or with a history of ipsilateral stricture, renal failure, active urinary tract infection, or coagulation disorder. RESULTS: Stones were treated with dusting technique in all cases. The median stone size was 10.3 mm (range 5-17). Stones were located in the distal ureter in 77 cases (51.7%), in the middle ureter in 23 cases (15.4%), and in the proximal ureter in 49 cases (32.9%). The median operative time was 29.8 min (range 20-95). Intra-operative complications included five bleedings (3.3%) and seven stone retropulsions (4.7%). Overall stone-free rate was 97.3%. Overall postoperative complications rate was 4.0% and included two cases of stent migration (1.3%) (Clavien II) and four residual stone fragments (2.7%) that were successfully treated using the same technique (Clavien IIIb). On multivariate analysis, re-operation rate was significantly dependent on the proximal stone location and presence of residual fragments >2 mm (P = 0.001). DISCUSSION: This study is one of the largest pediatric series among those published until now. The study series reported a shorter operative time, a higher success rate, and a lower postoperative complications rate compared with previous series. A limitation of this study is that stone-free rates may be somewhat inaccurate using ultrasonography and plain X-ray compared with computed tomography (CT); the study's 97.3% success rate may be overestimated because no CT scan was done postoperatively to check the stone-free rate. Other limitations of this article include its retrospective nature, the multi-institutional participation, and the heterogeneous patient collective. CONCLUSION: The Ho:YAG laser ureteroscopic lithotripsy seems to be an excellent first-line treatment for children with ureteral stones, independently from primary location and size. However, patients with proximal ureteral stones and residual fragments >2 mm reported a higher risk to require a secondary procedure to become stone-free. Combination of techniques as well as appropriate endourologic tools are key points for the success of the procedure regardless of stones' size and location

Near-Complete Genome Sequences of Vesicular Stomatitis Virus Indiana Laboratory Strains HR and T1026R1 and Plaque Isolates 22-20 and 22-25

We report four near-complete genome sequences of vesicular stomatitis virus (VSV) Indiana obtained with Sanger and Illumina next-generation sequencing, namely, laboratory strains HR (heat resistant) and T1026R1 and isolates 22-20 and 22-25. Previously, only the M gene of these viruses had been sequenced, and these sequences were not deposited in GenBank

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them

Specifications of standards in systems and synthetic biology: status and developments in 2021

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards: CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Language (SBOL) Version 3.1.0. This document can also be used to identify the latest specifications for all COMBINE standards. In addition, this editorial provides a brief overview of the COMBINE 2022 meeting in Berlin

SBML2LaTEX: Conversion of SBML files into human-readable reports

Summary: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTEX and PDF, and provides many settings for customization

Specifications of standards in systems and synthetic biology: Status and developments in 2020

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology