UTOPIA—User-Friendly Tools for Operating Informatics Applications

Bioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of an ad hoc collection of data manipulation tools, scripting languages and visualization systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of current databases and the scale of the analyses necessary, routine bioinformatics tasks are often automated, but many still require the unique experience and intuition of human researchers: this requires tools that support real-time interaction with complex datasets. Many existing tools have poor user interfaces and limited real-time performance when applied to realistically large datasets; much of the user's cognitive capacity is therefore focused on controlling the tool rather than on performing the research. The UTOPIA project is addressing some of these issues by building reusable software components that can be combined to make useful applications in the field of bioinformatics. Expertise in the fields of human computer interaction, high-performance rendering, and distributed systems is being guided by bioinformaticians and end-user biologists to create a toolkit that is both architecturally sound from a computing point of view, and directly addresses end-user and application-developer requirements

Perceptions Of School By Two Teenage Boys With Asperger Syndrome And Their Mothers: A Qualitative Study

This qualitative study aimed to develop an understanding of the challenges faced by teenage boys with Asperger syndrome and their mothers. A case study approach was used to collect data from two 13-year-old boys who have Asperger syndrome and their mothers in Queensland, Australia. Data were collected through the use of semi¬structured interviews. The words of the boys and their mothers provide a valuable insight into the personal experiences and feelings of the par¬ticipants. An inductive approach to data analysis identified four themes: (1) developmental differences; (2) problems associated with the general characteristics of Asperger syndrome (i.e. communication and social difficulties, restricted range of interests, a need for routine); (3) stress; and (4) 'masquerading'. The first three themes relate strongly to the current literature, but the emergence of masquerading is of particular interest in developing a fuller understanding of the experiences of individuals with Asperger syndrome at school

METIS: multiple extraction techniques for informative sentences

Summary: METIS is a web-based integrated annotation tool. From single query sequences, the PRECIS component allows users to generate structured protein family reports from sets of related Swiss-Prot entries. These reports may then be augmented with pertinent sentences extracted from online biomedical literature via support vector machine and rule-based sentence classification systems. Availability: Contact: [email protected] Supplementary informatio

An active registry for bioinformatics web services

Summary: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks

Comparing laparoscopic antireflux surgery with esomeprazole in the management of patients with chronic gastro-oesophageal reflux disease: a 3-year interim analysis of the LOTUS trial

BACKGROUND: With the introduction of laparoscopic antireflux surgery (LARS) for gastro-oesophageal reflux disease (GORD) along with the increasing efficacy of modern medical treatment, a direct comparison is warranted. The 3-year interim results of a randomised study comparing both the efficacy and safety of LARS and esomeprazole (ESO) are reported. METHODS: LOTUS is an open, parallel-group multicentre, randomised and controlled trial conducted in dedicated centres in 11 European countries. LARS was completed according to a standardised protocol, comprising a total fundoplication and a crural repair. Medical treatment comprised ESO 20 mg once daily, which could be increased stepwise to 40 mg once daily and then 20 mg twice daily in the case of incomplete GORD control. The primary outcome variable was time to treatment failure (Kaplan-Meier analysis). Treatment failure was defined on the basis of symptomatic relapse requiring treatment beyond that stated in the protocol. RESULTS: 554 patients were randomised, of whom 288 were allocated to LARS and 266 to ESO. The two study arms were well matched. The proportions of patients who remained in remission after 3 years were similar for the two therapies: 90% of surgical patients compared with 93% medically treated for the intention to treat population, p = 0.25 (90% vs 95% per protocol). No major unexpected postoperative complications were experienced and ESO was well tolerated. However, postfundoplication complaints remain a problem after LARS. CONCLUSIONS: Over the first 3 years of this long-term study, both laparoscopic total fundoplication and continuous ESO treatment were similarly effective and well-tolerated therapeutic strategies for providing effective control of GORD

Spatial coherence measurement of a high average power table-top soft X-ray laser

Includes bibliographical references (page 126).An extraordinarily high degree of spatial coherence from a high average power tabletop 46.9 nm laser was observed in two-pinhole interference experiments. Refractive anti-guiding and gain guiding along a capillary discharge-produced plasma column causes a rapid increase of the spatial coherence with amplifier length. Full spatial coherence was approached with a 36 cm long plasma of very high axial uniformity and a length to diameter ratio exceeding 1000: 1

Spatial coherence measurements of a 13.2 nm transient Nickel-like Cadmium soft x-ray laser pumped at grazing incidence

Includes bibliographical references (pages [12872-12873]).The spatial coherence of a 13.2 nm transient collisional Ni-like Cd soft X-ray laser pumped at 23 degrees grazing incidence was measured in a series of Young's double-slit experiments. We observed pronounced fringe visibility variations associated with microstructures in the beam's intensity profile. The transverse coherence length was measured to be about 1/20 of the beam diameter and did not significantly improve with longer plasma columns. The equivalent incoherent source size is determined to be 10 μm and the laser's peak spectral brightness ~ 3 × 1023 photons/sec/mm2/mrad2 within less than 0.01% spectral bandwidth

Utopia documents: linking scholarly literature with research data

Motivation: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged

DNA methylation and the regulation of gene transcription

The regulation of gene transcription is not simply dependent on the presence or absence of DNA-binding transcription factors that turn genes on or off, but also involves processes determining the ability of transcription factors to gain access to and bind their target DNA. Methylation of DNA cytosine bases leads to the inaccessibility of DNA regulatory elements to their transcription factors by a number of mechanisms. Our understanding of DNA methylation has advanced rapidly in recent years with the identification of an increasingly large number of novel proteins involved in this process. These include methylcytosine-binding proteins as well as additional members of the DNA methyltransferase family. The creation of mice with targeted deletions in a number of genes involved in DNA methylation has further elucidated the functions of many of these proteins. The characterization of complexes that contain proteins known to be involved in DNA methylation has led to the identification of additional proteins, especially those involved in histone deacetylation, indicating that DNA methylation and histone deacetylation very likely act in a synergistic fashion to regulate gene transcription. Finally, the implication of DNA methylation in tumorigenesis and the realization that some congenital diseases are caused by deficiency of proteins involved in DNA methylation has confirmed the importance of this process in regulating gene expression.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41835/1/18-59-2-241_20590241.pd

DNA-Sequence Variation Among Schistosoma mekongi Populations and Related Taxa; Phylogeography and the Current Distribution of Asian Schistosomiasis

Schistosomiasis is a disease caused by parasitic worms of the genus Schistosoma. In the lower Mekong river, schistosomiasis in humans is called Mekong schistosomiasis and is caused by Schistosoma mekongi. In the past, Mekong schistosomiasis was known only from the lower Mekong river. Here DNA-sequence variation is used to study the relationships and history of populations of S. mekongi. Populations from other rivers are compared and shown to be S. mekongi, thus confirming that this species is not restricted to only a small section of one river. The dates of divergence among populations are also estimated. Prior to this study it was assumed that S. mekongi originated in Yunnan, China, migrated southwards across Laos and into Cambodia, later becoming extinct in Laos (due to conditions unsuitable for transmission). In contrast, the dates estimated here indicate that S. mekongi entered Cambodia from Vietnam, 2.5–1 Ma. The pattern of genetic variation fits better with a more recent, and ongoing, northwards migration from Cambodia into Laos. The implications are that Mekong schistosomiasis is more widespread than once thought and that the human population at risk is up to 10 times greater than originally estimated. There is also an increased possibility of the spread of Mekong schistosomiasis across Laos