Microwave Spectroscopy

Contains reports on three research projects

Microwave Spectroscopy

Contains reports on three research projects

Microwave Spectroscopy

Contains reports on four research projects

The GNAT library for local and remote gene mention normalization

Summary: Identifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987

Microwave Spectroscopy

Contains reports on four research projects

Computer-assisted curation of a human regulatory core network from the biological literature

Motivation: A highly interlinked network of transcription factors (TFs) orchestrates the context-dependent expression of human genes. ChIP-chip experiments that interrogate the binding of particular TFs to genomic regions are used to reconstruct gene regulatory networks at genome-scale, but are plagued by high false-positive rates. Meanwhile, a large body of knowledge on high-quality regulatory interactions remains largely unexplored, as it is available only in natural language descriptions scattered over millions of scientific publications. Such data are hard to extract and regulatory data currently contain together only 503 regulatory relations between human TFs. Results: We developed a text-mining-assisted workflow to systematically extract knowledge about regulatory interactions between human TFs from the biological literature. We applied this workflow to the entire Medline, which helped us to identify more than 45 000 sentences potentially describing such relationships. We ranked these sentences by a machine-learning approach. The top-2500 sentences contained ∼900 sentences that encompass relations already known in databases. By manually curating the remaining 1625 top-ranking sentences, we obtained more than 300 validated regulatory relationships that were not present in a regulatory database before. Full-text curation allowed us to obtain detailed information on the strength of experimental evidences supporting a relationship. Conclusions: We were able to increase curated information about the human core transcriptional network by >60% compared with the current content of regulatory databases. We observed improved performance when using the network for disease gene prioritization compared with the state-of-the-art. Availability and implementation: Web-service is freely accessible athttp://fastforward.sys-bio.net/.FWN – Publicaties zonder aanstelling Universiteit Leide

Regulation of Expression of Citrate Synthase by the Retinoic Acid Receptor-Related Orphan Receptor α (RORα)

The retinoic acid receptor-related orphan receptor α (RORα) is a member of the nuclear receptor superfamily of transcription factors that plays an important role in regulation of the circadian rhythm and metabolism. Mice lacking a functional RORα display a range of metabolic abnormalities including decreased serum cholesterol and plasma triglycerides. Citrate synthase (CS) is a key enzyme of the citric acid cycle that provides energy for cellular function. Additionally, CS plays a critical role in providing citrate derived acetyl-CoA for lipogenesis and cholesterologenesis. Here, we identified a functional RORα response element (RORE) in the promoter of the CS gene. ChIP analysis demonstrates RORα occupancy of the CS promoter and a putative RORE binds to RORα effectively in an electrophoretic mobility shift assay and confers RORα responsiveness to a reporter gene in a cotransfection assay. We also observed a decrease in CS gene expression and CS enzymatic activity in the staggerer mouse, which has a mutation of in the Rora gene resulting in nonfunctional RORα protein. Furthermore, we found that SR1001 a RORα inverse agonist eliminated the circadian pattern of expression of CS mRNA in mice. These data suggest that CS is a direct RORα target gene and one mechanism by which RORα regulates lipid metabolism is via regulation of CS expression

Octupolar ordering of Gamma8 ions in magnetic field

We study f-electron lattice models which are capable of supporting octupolar, as well dipolar and quadrupolar, order. Analyzing the properties of the Gamma8 ground state quartet, we find that (111)-type combinations of the Gamma5 octupoles Tbeta(111)=Tbeta(x)+Tbeta(y)+Tbeta(z) are the best candidates for octupolar order parameters. Octupolar ordering induces Gamma5-type quadrupoles as secondary order parameter. Octupolar order is to some extent assisted, but in its basic nature unchanged, by allowing for the presence of quadrupolar interactions. In the absence of an external magnetic field, equivalent results hold antiferro-octupolar ordering on the fcc lattice. In this sense, the choice of our model is motivated by the recent suggestion of octupolar ordering in NpO2. The bulk of our paper is devoted to a study of the effect of an external magnetic field on ferro-octupolar ordering. We found that octupolar order survives up to a critical magnetic field if the field is lying in specific directions, while for general field directions, the underlying symmetry of the model is destroyed and therefore the phase transition suppressed even in weak fields. Field-induced multipoles and field-induced couplings between various order parameters are discussed on the basis of a group theoretical analysis of the Helmholtz potential. We also studied the effect of octupolar ordering on the non-linear magnetic susceptibility which satisfies Ehrenfest-type relations at continuous octupolar transitions.Comment: 29 pages, 10 figures LaTeX In its contents, the present version agrees with the published one (see Journal Reference below). Essential additions to the text in Sec. III, otherwise some change of wording, and minor correction

The IDvIP Trial: A two-centre randomised double-blind controlled trial comparing intramuscular diamorphine and intramuscular pethidine for labour analgesia

<p>Abstract</p> <p>Background</p> <p>Intramuscular pethidine is routinely used throughout the UK for labour analgesia. Studies have suggested that pethidine provides little pain relief in labour and has a number of side effects affecting mother and neonate. It can cause nausea, vomiting and dysphoria in mothers and can cause reduced fetal heart rate variability and accelerations. Neonatal effects include respiratory depression and impaired feeding. There are few large studies comparing the relative side effects and efficacy of different opioids in labour. A small trial comparing intramuscular pethidine with diamorphine, showed diamorphine to have some benefits over pethidine when used for labour analgesia but the study did not investigate the adverse effects of either opioid.</p> <p>Methods</p> <p>The Intramuscular Diamorphine versus Intramuscular Pethidine (IDvIP) trial is a randomised double-blind two centre controlled trial comparing intramuscular diamorphine and pethidine regarding their analgesic efficacy in labour and their side effects in mother, fetus and neonate. Information about the trial will be provided to women in the antenatal period or in early labour. Consent and recruitment to the trial will be obtained when the mother requests opioid analgesia. The sample size requirement is 406 women with data on primary outcomes. The maternal primary outcomes are pain relief during the first 3 hours after trial analgesia and specifically pain relief after 60 minutes. The neonatal primary outcomes are need for resuscitation and Apgar Score <7 at 1 minute. The secondary outcomes are an additional measure of pain relief, maternal sedation, nausea and vomiting, maternal oxygen saturation, satisfaction with analgesia, whether method of analgesia would be used again, use of Entonox, umbilical arterial and venous pH, fetal heart rate, meconium staining, time from delivery to first breath, Apgar scores at 5 mins, naloxone requirement, transfer to neonatal intensive care unit, neonatal haemoglobin oxygen saturation at 30, 60, 90, and 120 mins after delivery, and neonatal sedation and feeding behaviour during first 2 hours.</p> <p>Discussion</p> <p>If the trial demonstrates that diamorphine provides better analgesia with fewer side effects in mother and neonate this could lead to a change in national practice and result in diamorphine becoming the preferred intramuscular opioid for analgesia in labour.</p> <p>Trial Registration</p> <p><a href="http://www.controlled-trials.com/ISRCTN14898678">ISRCTN14898678</a></p> <p>Eudra No: 2006-003250-18, REC Reference No: 06/Q1702/95, MHRA Authorisation No: 1443/0001/001-0001, NIHR UKCRN reference 6895, RfPB grant PB-PG-0407-13170_IR5</p