GWIPS-viz: 2018 update

The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome

Repetitive mild traumatic brain injury causes optic nerve and retinal damage in a mouse model

There is increasing evidence that long-lasting morphologic and functional consequences can be present in the human visual system after repetitive mild traumatic brain injury (r-mTBI). The exact lo- cation and extent of the damage in this condition are not well un- derstood. Using a recently developed mouse model of r-mTBI, we assessed the effects on the retina and optic nerve using histology and immunohistochemistry, electroretinography (ERG), and spectral- domain optical coherence tomography (SD-OCT) at 10 and 13 weeks after injury. Control mice received repetitive anesthesia alone (r-sham). We observed decreased optic nerve diameters and increased cellularity and areas of demyelination in optic nerves in r-mTBI versus r-sham mice. There were concomitant areas of decreased cellularity in the retinal ganglion cell layer and approximately 67% decrease in brain- specific homeobox/POU domain protein 3AYpositive retinal ganglion cells in retinal flat mounts. Furthermore, SD-OCT demonstrated a de- tectable thinning of the inner retina; ERG demonstrated a decrease in the amplitude of the photopic negative response without any change in a- or b-wave amplitude or timing. Thus, the ERG and SD-OCT data correlated well with changes detected by morphometric, histologic, and immunohistochemical methods, thereby supporting the use of these noninvasive methods in the assessment of visual function and morphology in clinical cases of mTBI

Regionalizing healthcare: a vision for transforming Lebanon into a regional academic hub

<p>Abstract</p> <p>Background</p> <p>Lebanon suffers from a large scale emigration of physicians coupled with an oversaturation of the physician job market. Lebanon is currently witnessing an expansion of its medical education capacity with the establishment of new private medical schools, raising the fears of a worsening market oversaturation.</p> <p>Discussion</p> <p>The neighboring Arabian Gulf countries are suffering from a serious shortage of clinicians and academicians. In spite of their enormous investments in educational, clinical and research collaborative initiatives with some of the most renowned North American medical schools and institutions, their ability to recruit and retain highly qualified clinicians and academicians remains a major challenge. Lebanese universities have the opportunity to establish triangular collaborations with the Gulf regional medical centers and their North American partners. They could achieve this goal by tapping into the globalized and high quality Lebanese physician workforce and consequently regionalize healthcare delivery in the Middle East.</p> <p>Summary</p> <p>By recruiting its globalized and high quality physician workforce to establish collaborations with the Gulf regional, Lebanon could become a regional "academic hub".</p

The migration of physicians from sub-Saharan Africa to the United States of America: measures of the African brain drain

BACKGROUND: The objective of this paper is to describe the numbers, characteristics, and trends in the migration to the United States of physicians trained in sub-Saharan Africa. METHODS: We used the American Medical Association 2002 Masterfile to identify and describe physicians who received their medical training in sub-Saharan Africa and are currently practicing in the USA. RESULTS: More than 23% of America's 771 491 physicians received their medical training outside the USA, the majority (64%) in low-income or lower middle-income countries. A total of 5334 physicians from sub-Saharan Africa are in that group, a number that represents more than 6% of the physicians practicing in sub-Saharan Africa now. Nearly 86% of these Africans practicing in the USA originate from only three countries: Nigeria, South Africa and Ghana. Furthermore, 79% were trained at only 10 medical schools. CONCLUSIONS: Physician migration from poor countries to rich ones contributes to worldwide health workforce imbalances that may be detrimental to the health systems of source countries. The migration of over 5000 doctors from sub-Saharan Africa to the USA has had a significantly negative effect on the doctor-to-population ratio of Africa. The finding that the bulk of migration occurs from only a few countries and medical schools suggests policy interventions in only a few locations could be effective in stemming the brain drain

The rapid rotation and complex magnetic field geometry of Vega

The recent discovery of a weak surface magnetic field on the normal intermediate-mass star Vega raises the question of the origin of this magnetism in a class of stars that was not known to host magnetic fields. We aim to confirm the field detection and provide additional observational constraints about the field characteristics, by modelling the magnetic geometry of the star and by investigating the seasonal variability of the reconstructed field. We analyse a total of 799 circularly-polarized spectra collected with the NARVAL and ESPaDOnS spectropolarimeters during 2008 and 2009. We employ a cross-correlation procedure to compute, from each spectrum, a mean polarized line profile with a signal-to-noise ratio of about 20,000. The technique of Zeeman-Doppler Imaging is then used to determine the rotation period of the star and reconstruct the large-scale magnetic geometry of Vega at two different epochs. We confirm the detection of circularly polarized signatures in the mean line profiles. The amplitude of the signatures is larger when spectral lines of higher magnetic sensitivity are selected for the analysis, as expected for a signal of magnetic origin. The short-term evolution of polarized signatures is consistent with a rotational period of 0.732 \pm 0.008 d. The reconstructed magnetic topology unveils a magnetic region of radial field orientation, closely concentrated around the rotation pole. This polar feature is accompanied by a small number of magnetic patches at lower latitudes. No significant variability in the field structure is observed over a time span of one year. The repeated observation of a weak photospheric magnetic field on Vega suggests that a previously unknown type of magnetic stars exists in the intermediate-mass domain. Vega may well be the first confirmed member of a much larger, as yet unexplored, class of weakly-magnetic stars.Comment: Accepted by Astronomy & Astrophysics. Abstract shortened to respect the arXiv limit of 1920 character

GWIPS-viz: development of a ribo-seq genome browser

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing

MOST detects corotating bright spots on the mid-O type giant {\xi} Persei

We have used the MOST (Microvariability and Oscillations of STars) microsatellite to obtain four weeks of contiguous high-precision broadband visual photometry of the O7.5III(n)((f)) star {\xi} Persei in November 2011. This star is well known from previous work to show prominent DACs (Discrete Absorption Components) on time-scales of about 2 d from UV spectroscopy and NRP (Non Radial Pulsation) with one (l = 3) p-mode oscillation with a period of 3.5 h from optical spectroscopy. Our MOST-orbit (101.4 min) binned photometry fails to reveal any periodic light variations above the 0.1 mmag 3-sigma noise level for periods of hours, while several prominent Fourier peaks emerge at the 1 mmag level in the two-day period range. These longer-period variations are unlikely due to pulsations, including gravity modes. From our simulations based upon a simple spot model, we deduce that we are seeing the photometric modulation of several co-rotating bright spots on the stellar surface. In our model, the starting times (random) and lifetimes (up to several rotations) vary from one spot to another yet all spots rotate at the same period of 4.18 d, the best-estimated rotation period of the star. This is the first convincing reported case of co-rotating bright spots on an O star, with important implications for drivers of the DACs (resulting from CIRs - Corotating Interaction Regions) with possible bright-spot generation via a breakout at the surface of a global magnetic field generated by a subsurface convection zone.Comment: 9 pages, 4 figures, 2 tables, MNRAS in pres

Task Shifting for Scale-up of HIV Care: Evaluation of Nurse-Centered Antiretroviral Treatment at Rural Health Centers in Rwanda

Fabienne Shumbusho and colleagues evaluate a task-shifting model of nurse-centered antiretroviral treatment prescribing in rural primary health centers in Rwanda and find that nurses can effectively and safely prescribe ART when given adequate training, mentoring, and support

Educating a New Generation of Doctors to Improve the Health of Populations in Low- and Middle-Income Countries

Francesca Celletti and colleagues from WHO argue that a transformation in the scale-up of medical education in low- and middle-income countries is needed, and detail what this might look like