Gbrowse Moby: a Web-based browser for BioMoby Services

BACKGROUND: The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client – Gbrowse Moby – that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface. RESULTS: Gbrowse Moby is a low-throughput, exploratory tool specifically aimed at non-informaticians. It provides a straightforward, minimal interface that enables a researcher to query the BioMoby Central web service registry for data retrieval or analytical tools of interest, and then select and execute their chosen tool with a single mouse-click. The data is preserved at each step, thus allowing the researcher to manually "click" the data from one service to the next, with the Gbrowse Moby application managing all data formatting and interface interpretation on their behalf. The path of manual exploration is preserved and can be downloaded for import into automated, high-throughput tools such as Taverna. Gbrowse Moby also includes a robust data rendering system to ensure that all new data-types that appear in the BioMoby registry can be properly displayed in the Web interface. CONCLUSION: Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment

cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models

The increasing availability of sequencing data of cancer samples is fueling the development of algorithmic strategies to investigate tumor heterogeneity and infer reliable models of cancer evolution. We here build up on previous works on cancer progression inference from genomic alteration data, to deliver two distinct Cytoscape-based applications, which allow to produce, visualize and manipulate cancer evolution models, also by interacting with public genomic and proteomics databases. In particular, we here introduce cyTRON, a stand-alone Cytoscape app, and cyTRON/JS, a web application which employs the functionalities of Cytoscape/JS. cyTRON was developed in Java; the code is available at https://github.com/BIMIB-DISCo/cyTRON and on the Cytoscape App Store http://apps.cytoscape.org/apps/cytron. cyTRON/JS was developed in JavaScript and R; the source code of the tool is available at https://github.com/BIMIB-DISCo/cyTRON-js and the tool is accessible from https://bimib.disco.unimib.it/cytronjs/welcome

Prostaglandin insert dinoprostone versus trans-cervical balloon catheter for outpatient labour induction: a randomised controlled trial of feasibility (PROBIT-F)

Background The aim was to assess the feasibility of conducting a randomised controlled trial (RCT) of induction of labour comparing use of two methods in the outpatient setting. Methods An open-label feasibility RCT was conducted in two UK maternity units from October 2017 to March 2019. Women aged ≥ 16 years, undergoing induction of labour (IOL) at term, with intact membranes and deemed suitable for outpatient IOL according to local guidelines were considered eligible. They were randomised to cervical ripening balloon catheter (CRB) or vaginal dinoprostone (Propess). The participants completed a questionnaire and a sub-group underwent detailed interview. Service use and cost data were collected via the Adult Service Use Schedule (AD-SUS). Women who declined to participate were requested to complete a decliners’ questionnaire. Results During the study period, 274 eligible women were identified. Two hundred thirty (83.9%) were approached for participation of whom 84/230 (36.5%) agreed and 146 did not. Of these, 38 were randomised to Propess (n = 20) and CRB (n = 18). Decliner data were collected for 93 women. The reasons for declining were declining IOL (n = 22), preference for inpatient IOL (n = 22) and preference for a specific method, Propess (n = 19). The intended sample size of 120 was not reached due to restrictive criteria for suitability for outpatient IOL, participant preference for Propess and shortage of research staff. The intervention as randomised was received by 29/38 (76%) women. Spontaneous vaginal delivery was observed in 9/20 (45%) women in the dinoprostone group and 11/18 (61%) women in the CRB group. Severe maternal adverse events were recorded in one woman in each group. All babies were born with good condition and all except one (37/38, 97.4%) remained with the mother after delivery. No deaths were recorded. − 21% of women in the dinoprostone group were re-admitted prior to diagnosis of active labour compared to 12% in the CRB group. Conclusions A third of the approached eligible women agreed for randomisation. An RCT is not feasible in the current service context. Modifications to the eligibility criteria for outpatient IOL, better information provision and round the clock availability of research staff would be needed to reach sufficient numbers

Valence and Core Photoelectron Spectra of Aqueous I3− from Multi-Reference Quantum Chemistry

The I3− molecule is known to undergo substantial structural reorganization upon solvation by a protic solvent, e.g., water. However, the details of this process are still controversially discussed in the literature. In the present study, we combined experimental and theoretical efforts to disentangle this controversy. The valence (5p), N4,5 (4d), and M4,5 (3d) edge photoelectron spectra were measured in an aqueous solution and computed using high-level multi-reference methods. Our previous publication mainly focused on obtaining reliable experimental evidence, whereas in the present article, we focused primarily on theoretical aspects. The complex electronic structure of I3− requires the inclusion of both static and dynamic correlation, e.g., via the multi-configurational perturbation theory treatment. However, the resulting photoelectron spectra appear to be very sensitive to problems with variational stability and intruder states. We attempted to obtain artifact-free spectra, allowing for a more reliable interpretation of experiments. Finally, we concluded that the 3d Photoelectron Spectrum (PES) is particularly informative, evidencing an almost linear structure with a smaller degree of bond asymmetry than previously reported.Deutsche ForschungsgemeinschaftPeer Reviewe

No Detectable Fertility Benefit from a Single Additional Mating in Wild Stalk-Eyed Flies

Background: Multiple mating by female insects is widespread, and the explanation(s) for repeated mating by females has been the subject of much discussion. Females may profit from mating multiply through direct material benefits that increase their own reproductive output, or indirect genetic benefits that increase offspring fitness. One particular direct benefit that has attracted significant attention is that of fertility assurance, as females often need to mate multiply to achieve high fertility. This hypothesis has never been tested in a wild insect population.Methodology/Principal Findings: Female Malaysian stalk-eyed flies (Teleopsis dalmanni) mate repeatedly during their lifetime, and have been shown to be sperm limited under both laboratory and field conditions. Here we ask whether receiving an additional mating alleviates sperm limitation in wild females. In our experiment one group of females received a single additional mating, while a control group received an interrupted, and therefore unsuccessful, mating. Females that received an additional mating did not lay more fertilised eggs in total, nor did they lay proportionately more fertilised eggs. Female fertility declined significantly through time, demonstrating that females were sperm limited. However, receipt of an additional mating did not significantly alter the rate of this decline.Conclusions/Significance: Our data suggest that the fertility consequences of a single additional mating were small. We discuss this effect (or lack thereof), and suggest that it is likely to be attributed to small ejaculate size, a high proportion of failed copulations, and the presence of X-linked meiotic drive in this species

Challenges in Chagas Disease Drug Development.

The protozoan parasite Trypanosoma cruzi causes Chagas disease, an important public health problem throughout Latin America. Current therapeutic options are characterised by limited efficacy, long treatment regimens and frequent toxic side-effects. Advances in this area have been compromised by gaps in our knowledge of disease pathogenesis, parasite biology and drug activity. Nevertheless, several factors have come together to create a more optimistic scenario. Drug-based research has become more systematic, with increased collaborations between the academic and commercial sectors, often within the framework of not-for-profit consortia. High-throughput screening of compound libraries is being widely applied, and new technical advances are helping to streamline the drug development pipeline. In addition, drug repurposing and optimisation of current treatment regimens, informed by laboratory research, are providing a basis for new clinical trials. Here, we will provide an overview of the current status of Chagas disease drug development, highlight those areas where progress can be expected, and describe how fundamental research is helping to underpin the process

Semantic Web integration of Cheminformatics resources with the SADI framework

<p>Abstract</p> <p>Background</p> <p>The diversity and the largely independent nature of chemical research efforts over the past half century are, most likely, the major contributors to the current poor state of chemical computational resource and database interoperability. While open software for chemical format interconversion and database entry cross-linking have partially addressed database interoperability, computational resource integration is hindered by the great diversity of software interfaces, languages, access methods, and platforms, among others. This has, in turn, translated into limited reproducibility of computational experiments and the need for application-specific computational workflow construction and semi-automated enactment by human experts, especially where emerging interdisciplinary fields, such as systems chemistry, are pursued. Fortunately, the advent of the Semantic Web, and the very recent introduction of RESTful Semantic Web Services (SWS) may present an opportunity to integrate all of the existing computational and database resources in chemistry into a machine-understandable, unified system that draws on the entirety of the Semantic Web.</p> <p>Results</p> <p>We have created a prototype framework of Semantic Automated Discovery and Integration (SADI) framework SWS that exposes the QSAR descriptor functionality of the Chemistry Development Kit. Since each of these services has formal ontology-defined input and output classes, and each service consumes and produces RDF graphs, clients can automatically reason about the services and available reference information necessary to complete a given overall computational task specified through a simple SPARQL query. We demonstrate this capability by carrying out QSAR analysis backed by a simple formal ontology to determine whether a given molecule is drug-like. Further, we discuss parameter-based control over the execution of SADI SWS. Finally, we demonstrate the value of computational resource envelopment as SADI services through service reuse and ease of integration of computational functionality into formal ontologies.</p> <p>Conclusions</p> <p>The work we present here may trigger a major paradigm shift in the distribution of computational resources in chemistry. We conclude that envelopment of chemical computational resources as SADI SWS facilitates interdisciplinary research by enabling the definition of computational problems in terms of ontologies and formal logical statements instead of cumbersome and application-specific tasks and workflows.</p

Discovery of high affinity inhibitors of Leishmania donovani N-myristoyltransferase

N-Myristoyltransferase (NMT) is a potential drug target in Leishmania parasites. Scaffold-hopping from published inhibitors yielded the serendipitous discovery of a chemotype selective for Leishmania donovani NMT; development led to high affinity inhibitors with excellent ligand efficiency. The binding mode was characterised by crystallography and provides a structural rationale for selectivity

Mephedrone in adolescent rats: residual memory impairment and acute but not lasting 5-HT depletion

Mephedrone (4-methylmethcathinone, MMC) is a popular recreational drug, yet its potential harms are yet to be fully established. The current study examined the impact of single or repeated MMC exposure on various neurochemical and behavioral measures in rats. In Experiment 1 male adolescent Wistar rats received single or repeated (once a day for 10 days) injections of MMC (30 mg/kg) or the comparator drug methamphetamine (METH, 2.5 mg/kg). Both MMC and METH caused robust hyperactivity in the 1 h following injection although this effect did not tend to sensitize with repeated treatment. Striatal dopamine (DA) levels were increased 1 h following either METH or MMC while striatal and hippocampal serotonin (5-HT) levels were decreased 1 h following MMC but not METH. MMC caused greater increases in 5-HT metabolism and greater reductions in DA metabolism in rats that had been previously exposed to MMC. Autoradiographic analysis showed no signs of neuroinflammation ([125I]CLINDE ligand used as a marker for translocator protein (TSPO) expression) with repeated exposure to either MMC or METH. In Experiment 2, rats received repeated MMC (7.5, 15 or 30 mg/kg once a day for 10 days) and were examined for residual behavioral effects following treatment. Repeated high (30 mg/kg) dose MMC produced impaired novel object recognition 5 weeks after drug treatment. However, no residual changes in 5-HT or DA tissue levels were observed at 7 weeks post-treatment. Overall these results show that MMC causes acute but not lasting changes in DA and 5-HT tissue concentrations. MMC can also cause long-term memory impairment. Future studies of cognitive function in MMC users are clearly warranted. © 2012 PLoS On

SADI, SHARE, and the in silico scientific method

<p>Abstract</p> <p>Background</p> <p>The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct <it>in silico</it> science. Web Service Workflows are already becoming first-class objects in “the new way”, and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies.</p> <p>Results</p> <p>Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to <it>ad hoc</it> user queries.</p> <p>Conclusions</p> <p>The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the “semantification” of those aspects of the <it>in silico</it> scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.</p