Why democratize bioinformatics?

Network bioinformatics and web-based data collection instruments have the capacity to improve the efficiency of the UK’s appropriately high levels of investment into cardiovascular research. A very large proportion of scientific data falls into the long-tail of the cardiovascular research distribution curve, with numerous small independent research efforts yielding a rich variety of specialty data sets. The merging of such myriad datasets and the eradication of data silos, plus linkage with outcomes could be greatly facilitated through the provision of a national set of standardised data collection instruments—a shared-cardioinformatics library of tools designed by and for clinical academics active in the long-tail of biomedical research. Across the cardiovascular research domain, like the rest of medicine, the national aggregation and democratization of diverse long-tail data is the best way to convert numerous small but expensive cohort data sources into big data, expanding our knowledge-base, breaking down translational barriers, improving research efficiency and with time, improving patient outcomes

Signatures of recent asteroid disruptions in the formation and evolution of solar system dust bands

We have performed detailed dynamical modeling of the structure of a faint dust band observed in coadded InfraRed Astronomical Satellite data at an ecliptic latitude of 17 degrees that convincingly demonstrates that it is the result of a relatively recent (significantly less than 1Ma) disruption of an asteroid and is still in the process of forming. We show here that young dust bands retain information on the size distribution and cross-sectional area of dust released in the original asteroid disruption, before it is lost to orbital and collisional decay. We find that the Emilkowalski cluster is the source of this partial band and that the dust released in the disruption would correspond to a regolith layer similar to 3 m deep on the similar to 10 km diameter source body's surface. The dust in this band is described by a cumulative size-distribution inverse power-law index with a lower bound of 2.1 (implying domination of cross-sectional area by small particles) for dust particles with diameters ranging from a few mu m up to a few cm. The coadded observations show that the thermal emission of the dust band structure is dominated by large (mm-cm size) particles. We find that dust particle ejection velocities need to be a few times the escape velocity of the Emilkowalski cluster source body to provide a good fit to the inclination dispersion of the observations. We discuss the implications that such a significant release of material during a disruption has for the temporal evolution of the structure, composition, and magnitude of the zodiacal cloud

The ROTSE-III Robotic Telescope System

The observation of a prompt optical flash from GRB990123 convincingly demonstrated the value of autonomous robotic telescope systems. Pursuing a program of rapid follow-up observations of gamma-ray bursts, the Robotic Optical Transient Search Experiment (ROTSE) has developed a next-generation instrument, ROTSE-III, that will continue the search for fast optical transients. The entire system was designed as an economical robotic facility to be installed at remote sites throughout the world. There are seven major system components: optics, optical tube assembly, CCD camera, telescope mount, enclosure, environmental sensing & protection and data acquisition. Each is described in turn in the hope that the techniques developed here will be useful in similar contexts elsewhere.Comment: 19 pages, including 4 figures. To be published in PASP in January, 2003. PASP Number IP02-11

Observations of the Optical Counterpart to XTE J1118+480 During Outburst by the ROTSE-I Telescope

The X-ray nova XTE J1118+480 exhibited two outbursts in the early part of 2000. As detected by the Rossi X-ray Timing Explorer (RXTE), the first outburst began in early January and the second began in early March. Routine imaging of the northern sky by the Robotic Optical Transient Search Experiment (ROTSE) shows the optical counterpart to XTE J1118+480 during both outbursts. These data include over 60 epochs from January to June 2000. A search of the ROTSE data archives reveal no previous optical outbursts of this source in selected data between April 1998 and January 2000. While the X-ray to optical flux ratio of XTE J1118+480 was low during both outbursts, we suggest that they were full X-ray novae and not mini-outbursts based on comparison with similar sources. The ROTSE measurements taken during the March 2000 outburst also indicate a rapid rise in the optical flux that preceded the X-ray emission measured by the RXTE by approximately 10 days. Using these results, we estimate a pre-outburst accretion disk inner truncation radius of 1.2 x 10^4 Schwarzschild radii.Comment: 9 pages, 1 table, 2 figure

UV/Optical Emission Accompanying Gamma-ray Burst

We discuss the possible simultaneously UV/optical emission accompanying Gamma-ray bursts (GRBs). We show that as long as the intrinsic spectrum of GRB can extend to $\sim$10 GeV or higher, there is a large amount of relativistic $e^\pm$ pairs generated due to the annihilation of the soft $\gamma-$rays with the very energetic photons, which dominates over the electrons/positrons associated with the fireball, no matter the fireball is highly magnetized or not (For the highly magnetized fireball, the magnetic field is ordered, the high linear polarization of the multi-wavelength emission is expected). We find that these $e^\pm$ pairs can power an UV flash with $m\simeq 12-13{\rm th}$ magnitude, and the corresponding optical emission can be up to $m_{\rm R}\simeq15-16{\rm th}$ magnitude. Such bright UV emission can be detected by the upcoming satellite Swift, planned for launch in early 2004. The behavior of the optical-UV spectrum ($F_{\nu}\propto \nu^{5/2}$) differs significantly from that of the reverse shock emission ($F_{\nu}\propto \nu^{-\beta/2}$, $\beta \simeq 2.2$), which is a signature of the emission accompanying with GRB. The mild optical emission can be detected with the ROTSE-IIIa telescope system, if the response to the GRB alert is fast enough.Comment: 5 pages, no figures. MNRAS in pres

Defensive insect symbiont leads to cascading extinctions and community collapse

This is the final version of the article. Available from Wiley via the DOI in this record.Animals often engage in mutualistic associations with microorganisms that protect them from predation, parasitism or pathogen infection. Studies of these interactions in insects have mostly focussed on the direct effects of symbiont infection on natural enemies without studying community-wide effects. Here, we explore the effect of a defensive symbiont on population dynamics and species extinctions in an experimental community composed of three aphid species and their associated specialist parasitoids. We found that introducing a bacterial symbiont with a protective (but not a non-protective) phenotype into one aphid species led to it being able to escape from its natural enemy and increase in density. This changed the relative density of the three aphid species which resulted in the extinction of the two other parasitoid species. Our results show that defensive symbionts can cause extinction cascades in experimental communities and so may play a significant role in the stability of consumer-herbivore communities in the field.The authors thank two anonymous reviewers for their helpful comments. This project was funded by the British Ecological Society (BES research grant #4682/5720 to EF), and by the Natural Environment Research Council (NERC grant #NE/K005650/1 to FJFvV). EF was funded by Marie Curie Intra-European Fellowship within the 7th European Community Framework Programme, FP7-PEOPLE-2012-IEF #329648

Using item response theory to explore the psychometric properties of extended matching questions examination in undergraduate medical education

BACKGROUND: As assessment has been shown to direct learning, it is critical that the examinations developed to test clinical competence in medical undergraduates are valid and reliable. The use of extended matching questions (EMQ) has been advocated to overcome some of the criticisms of using multiple-choice questions to test factual and applied knowledge. METHODS: We analysed the results from the Extended Matching Questions Examination taken by 4th year undergraduate medical students in the academic year 2001 to 2002. Rasch analysis was used to examine whether the set of questions used in the examination mapped on to a unidimensional scale, the degree of difficulty of questions within and between the various medical and surgical specialties and the pattern of responses within individual questions to assess the impact of the distractor options. RESULTS: Analysis of a subset of items and of the full examination demonstrated internal construct validity and the absence of bias on the majority of questions. Three main patterns of response selection were identified. CONCLUSION: Modern psychometric methods based upon the work of Rasch provide a useful approach to the calibration and analysis of EMQ undergraduate medical assessments. The approach allows for a formal test of the unidimensionality of the questions and thus the validity of the summed score. Given the metric calibration which follows fit to the model, it also allows for the establishment of items banks to facilitate continuity and equity in exam standards

The changing face of major trauma in the UK

Aim Major trauma (MT) has traditionally been viewed as a disease of young men caused by high-energy transfer mechanisms of injury, which has been reflected in the configuration of MT services. With ageing populations in Western societies, it is anticipated that the elderly will comprise an increasing proportion of the MT workload. The aim of this study was to describe changes in the demographics of MT in a developed Western health system over the last 20 years. Methods The Trauma Audit Research Network (TARN) database was interrogated to identify all cases of MT (injury severity score >15) between 1990 and the end of 2013. Age at presentation, gender, mechanism of injury and use of CT were recorded. For convenience, cases were categorised by age groups of 25 years and by common mechanisms of injury. Longitudinal changes each year were recorded. Results Profound changes in the demographics of recorded MT were observed. In 1990, the mean age of MT patients within the TARN database was 36.1, the largest age group suffering MT was 0–24 years (39.3%), the most common causative mechanism was road traffic collision (59.1%), 72.7% were male and 33.6% underwent CT. By 2013, mean age had increased to 53.8 years, the single largest age group was 25–50 years (27.1%), closely followed by those >75 years (26.9%), the most common mechanism was low falls (39.1%), 68.3% were male and 86.8% underwent CT. Conclusions This study suggests that the MT population identified in the UK is becoming more elderly, and the predominant mechanism that precipitates MT is a fall from <2 m. Significant improvements in outcomes from MT may be expected if services targeting the specific needs of the elderly are developed within MT centres

Artificial nighttime light changes aphid-parasitoid population dynamics

This is the final version of the article. Available from Nature Publishing Group via the DOI in this record.Artificial light at night (ALAN) is recognized as a widespread and increasingly important anthropogenic environmental pressure on wild species and their interactions. Understanding of how these impacts translate into changes in population dynamics of communities with multiple trophic levels is, however, severely lacking. In an outdoor mesocosm experiment we tested the effect of ALAN on the population dynamics of a plant-aphid-parasitoid community with one plant species, three aphid species and their specialist parasitoids. The light treatment reduced the abundance of two aphid species by 20% over five generations, most likely as a consequence of bottom-up effects, with reductions in bean plant biomass being observed. For the aphid Megoura viciae this effect was reversed under autumn conditions with the light treatment promoting continuous reproduction through asexuals. All three parasitoid species were negatively affected by the light treatment, through reduced host numbers and we discuss induced possible behavioural changes. These results suggest that, in addition to direct impacts on species behaviour, the impacts of ALAN can cascade through food webs with potentially far reaching effects on the wider ecosystem.The research leading to this paper was funded by the European Research council under the European Union’s Seventh Framework programme (FP7/2007-2013)/ERC grant agreement no. 268504 to KJG, and by NERC (grant no. NE/K005650/1) to FJFvV

Observation of contemporaneous optical radiation from a gamma-ray burst

The origin of gamma-ray bursts (GRBs) has been enigmatic since their discovery. The situation improved dramatically in 1997, when the rapid availability of precise coordinates for the bursts allowed the detection of faint optical and radio afterglows - optical spectra thus obtained have demonstrated conclusively that the bursts occur at cosmological distances. But, despite efforts by several groups, optical detection has not hitherto been achieved during the brief duration of a burst. Here we report the detection of bright optical emission from GRB990123 while the burst was still in progress. Our observations begin 22 seconds after the onset of the burst and show an increase in brightness by a factor of 14 during the first 25 seconds; the brightness then declines by a factor of 100, at which point (700 seconds after the burst onset) it falls below our detection threshold. The redshift of this burst, approximately 1.6, implies a peak optical luminosity of 5 times 10^{49} erg per second. Optical emission from gamma-ray bursts has been generally thought to take place at the shock fronts generated by interaction of the primary energy source with the surrounding medium, where the gamma-rays might also be produced. The lack of a significant change in the gamma-ray light curve when the optical emission develops suggests that the gamma-rays are not produced at the shock front, but closer to the site of the original explosion.Comment: 10 pages, 2 figures. Accepted for publication in Nature. For additional information see http://www.umich.edu/~rotse