MetWAMer: eukaryotic translation initiation site prediction

<p>Abstract</p> <p>Background</p> <p>Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.</p> <p>Results</p> <p>MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the <it>k</it>-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.</p> <p>Conclusion</p> <p>We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.</p

Increasing health worker capacity through distance learning: a comprehensive review of programmes in Tanzania

<p>Abstract</p> <p>Background</p> <p>Tanzania, like many developing countries, faces a crisis in human resources for health. The government has looked for ways to increase the number and skills of health workers, including using distance learning in their training. In 2008, the authors reviewed and assessed the country's current distance learning programmes for health care workers, as well as those in countries with similar human resource challenges, to determine the feasibility of distance learning to meet the need of an increased and more skilled health workforce.</p> <p>Methods</p> <p>Data were collected from 25 distance learning programmes at health training institutions, universities, and non-governmental organizations throughout the country from May to August 2008. Methods included internet research; desk review; telephone, email and mail-in surveys; on-site observations; interviews with programme managers, instructors, students, information technology specialists, preceptors, health care workers and Ministry of Health and Social Welfare representatives; and a focus group with national HIV/AIDS care and treatment organizations.</p> <p>Results</p> <p>Challenges include lack of guidelines for administrators, instructors and preceptors of distance learning programmes regarding roles and responsibilities; absence of competencies for clinical components of curricula; and technological constraints such as lack of access to computers and to the internet. Insufficient funding resulted in personnel shortages, lack of appropriate training for personnel, and lack of materials for students.</p> <p>Nonetheless, current and prospective students expressed overwhelming enthusiasm for scale-up of distance learning because of the unique financial and social benefits offered by these programs. Participants were retained as employees in their health care facilities, and remained in their communities and supported their families while advancing their careers. Space in health training institutions was freed up for new students entering in-residence pre-service training.</p> <p>Conclusions</p> <p>A blended print-based distance learning model is most feasible at the national level due to current resource and infrastructure constraints. With an increase in staffing; improvement of infrastructure, coordination and curricula; and decentralization to the zonal or district level, distance learning can be an effective method to increase both the skills and the numbers of qualified health care workers capable of meeting the health care needs of the Tanzanian population.</p

Large-Area Balloon-Borne Polarized Gamma Ray Observer (PoGO)

We are developing a new balloon-borne instrument (PoGO), to measure polarization of soft gamma rays (30-200 keV) using asymmetry in azimuth angle distribution of Compton scattering. PoGO is designed to detect 10% polarization in 100mCrab sources in a 6-8 hour observation and bring a new dimension to studies on gamma ray emission/transportation mechanism in pulsars, AGNs, black hole binaries, and neutron star surface. The concept is an adaptation to polarization measurements of well-type phoswich counter consisting of a fast plastic scintillator (the detection part), a slow plastic scintillator (the active collimator) and a BGO scintillator (the bottom anti-counter). PoGO consists of close-packed array of 217 hexagonal well-type phoswich counters and has a narrow field-of-view ({approx} 5 deg{sup 2}) to reduce possible source confusion. A prototype instrument has been tested in the polarized soft gamma-ray beams at Advanced Photon Source (ANL) and at Photon Factory (KEK). On the results, the polarization dependence of EGS4 has been validated and that of Geant4 has been corrected

Genome sequence of the bioplastic-producing ‘‘Knallgas’’ bacterium Ralstonia eutropha H16

The H2-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically versatile organism capable of subsisting, in the absence of organic growth substrates, on H2 and CO2 as its sole sources of energy and carbon. R. eutropha H16 first attracted biotechnological interest nearly 50 years ago with the realization that the organism’s ability to produce and store large amounts of poly[R-(–)-3-hydroxybutyrate] and other polyesters could be harnessed to make biodegradable plastics. Here we report the complete genome sequence of the two chromosomes of R. eutropha H16. Together, chromosome 1 (4,052,032 base pairs (bp)) and chromosome 2 (2,912,490 bp) encode 6,116 putative genes. Analysis of the genome sequence offers the genetic basis for exploiting the biotechnological potential of this organism and provides insights into its remarkable metabolic versatility

Inequality in treatment use among elderly patients with acute myocardial infarction: USA, Belgium and Quebec

<p>Abstract</p> <p>Background</p> <p>Previous research has provided evidence that socioeconomic status has an impact on invasive treatments use after acute myocardial infarction. In this paper, we compare the socioeconomic inequality in the use of high-technology diagnosis and treatment after acute myocardial infarction between the US, Quebec and Belgium paying special attention to financial incentives and regulations as explanatory factors.</p> <p>Methods</p> <p>We examined hospital-discharge abstracts for all patients older than 65 who were admitted to hospitals during the 1993–1998 period in the US, Quebec and Belgium with a primary diagnosis of acute myocardial infarction. Patients' income data were imputed from the median incomes of their residential area. For each country, we compared the risk-adjusted probability of undergoing each procedure between socioeconomic categories measured by the patient's area median income.</p> <p>Results</p> <p>Our findings indicate that income-related inequality exists in the use of high-technology treatment and diagnosis techniques that is not justified by differences in patients' health characteristics. Those inequalities are largely explained, in the US and Quebec, by inequalities in distances to hospitals with on-site cardiac facilities. However, in both Belgium and the US, inequalities persist among patients admitted to hospitals with on-site cardiac facilities, rejecting the hospital location effect as the single explanation for inequalities. Meanwhile, inequality levels diverge across countries (higher in the US and in Belgium, extremely low in Quebec).</p> <p>Conclusion</p> <p>The findings support the hypothesis that income-related inequality in treatment for AMI exists and is likely to be affected by a country's system of health care.</p

Temporary techno-social gatherings? A (hacked) discussion about open practices

This paper is rooted in an experimental inquiry of issue-oriented temporary techno-social gatherings or TTGs, which are typically referred to as hackathons, workshops or pop-ups and employ rapid design and development practices to tackle technical challenges while engaging with social issues. Based on a collaboration between three digital practitioners (a producer, a researcher and a designer), qualitative and creative data was gathered across five different kinds of TTG events in London and in Tartu which were held in partnership with large institutions, including Art:Work at Tate Exchange within Tate Modern, the Mozilla Festival at Ravensbourne College and the 2017 Association of Internet Researchers conference hosted in Tartu. By analysing data using an open and discursive approach manifested in both text and visual formats, we reflect on the dynamic and generative characteristics of TTG gatherings while also arriving at our own conclusions as situated researchers and practitioners who are ourselves engaged in increasingly messy webs where new worlds of theory and practice are built

The Quasiparticle Puzzle: Reconciling ARPES and FTSTS Studies of Bi2212

Angle Resolved Photoemission Spectroscopy (ARPES) probes the momentum-space electronic structure of materials, and provides invaluable information about the high-temperature superconducting cuprates. Likewise, cuprates real-space, inhomogeneous electronic structure is elucidated by Scanning Tunneling Spectroscopy (STS). Recently, STS has exploited quasiparticle interference (QPI) - wave-like electrons scattering off impurities to produce periodic interference patterns - to infer properties of the QP in momentum-space. Surprisingly, some interference peaks in Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} (Bi-2212) are absent beyond the antiferromagnetic (AF) zone boundary, implying the dominance of particular scattering process. Here, we show that ARPES sees no evidence of quasiparticle (QP) extinction: QP-like peaks are measured everywhere on the Fermi surface, evolving smoothly across the AF zone boundary. This apparent contradiction stems from different natures of single-particle (ARPES) and two-particle (STS) processes underlying these probes. Using a simple model, we demonstrate extinction of QPI without implying the loss of QP beyond the AF zone boundary