Highlights of the BioTM 2010 workshop on advances in bio text mining

This meeting report gives an overview of the keynote lectures, the panel discussion and a selection of the contributed presentations. The workshop was held in Gent, Belgium on May 10-11. It featured a tutorial aimed towards a broad audience of (computational) biologists, (computational) linguists and researchers working purely on text mining

Towards a concept for a Planetary Science Data Library based on a Spatial Data Infrastructure Model

International audienc

Long-term change and spatial variation in butterfly communities over an elevation gradient: driven by climate, buffered by habitat

AcceptedArticleThis is the accepted version of the following article: Nieto-Sánchez, S., Gutiérrez, D., Wilson, R. J. (2015), Long-term change and spatial variation in butterfly communities over an elevational gradient: driven by climate, buffered by habitat. Diversity and Distributions. doi: 10.1111/ddi.12316, which has been published in final form at doi: 10.1111/ddi.12316.(A) Abstract (B) Aim Efforts to adapt conservation to climate change are hampered by a scarcity of studies of community-level ecological responses. We examined temporal (40 years) and spatial (1700 m elevation gradient) variation in butterfly communities, aiming to test whether the composition of communities in terms of species’ thermal envelopes tracked regional warming, and whether local habitat influenced community responses to climate variation. (B) Location Sierra de Guadarrama (central Spain). (B) Methods Butterfly assemblages were sampled at sites between 550 m and 2250 m elevation, in 1967-1973 and 2006-2012. Changes in community composition over time and space were evaluated using the community temperature index, or CTI, which reflects for local assemblages the balance between species whose geographic ranges occupy regions of low versus high temperatures. We used multiple regressions and an information-theoretic approach to test: 1) whether relationships of CTI with elevation or temperature remained consistent after an estimated 1.78 °C regional warming; and 2) how spatial variation in CTI was related to air temperature and land cover. (B) Results CTI decreased consistently with increasing elevation, and increased after 40 years of warming, as communities were increasingly composed by species with warmer geographic ranges. Long-term CTI change represented a c. 160 m uphill shift in community thermal composition, whereas isotherms shifted 307 m upwards. In 2006-2012, CTI was influenced positively by temperature, and negatively by forest and meadow cover. (B) Main Conclusions Variation in community composition over space and time suggested a role of climate in structuring butterfly assemblages. Despite this, changing spatial patterns of community composition (CTI) did not appear to keep pace with climate change. In addition, lower values of CTI recorded for sites with greater forest and meadow/pasture cover suggested a role for local habitat in buffering the effects of climate change on community composition

Statewide Molecular Epidemiology of Mycobacterium tuberculosis Transmission in a Moderate- to Low-Incidence State: Are Contact Investigations Enough?

To assess the circumstances of recent transmission of tuberculosis (TB) (progression to active disease <2 years after infection), we obtained DNA fingerprints for 1,172 (99%) of 1,179 Mycobacterium tuberculosis isolates collected from Maryland TB patients from 1996 to 2000. We also reviewed medical records and interviewed patients with genetically matching M. tuberculosis strains to identify epidemiologic links (cluster investigation). Traditional settings for transmission were defined as households or close relatives and friends; all other settings were considered nontraditional. Of 436 clustered patients, 114 had recently acquired TB. Cluster investigations were significantly more likely than contact investigations to identify patients who recently acquired TB in nontraditional settings (33/42 vs. 23/72, respectively; p<0.001). Transmission from a foreign-born person to a U.S.-born person was rare and occurred mainly in public settings. The time from symptom onset to diagnosis was twice as long for transmitters as for nontransmitters (16.8 vs. 8.5 weeks, respectively; p<0.01). Molecular epidemiologic studies showed that eliminating diagnostic delays can prevent TB transmission in nontraditional settings, which elude contact investigations

Interacting Effects of Phenotypic Plasticity and Evolution on Population Persistence in a Changing Climate

Climate change affects individual organisms by altering development, physiology, behavior, and fitness, and populations by altering genetic and phenotypic composition, vital rates, and dynamics. We sought to clarify how selection, phenotypic plasticity, and demography are linked in the context of climate change. On the basis of theory and results of recent empirical studies of plants and animals, we believe the ecological and evolutionary issues relevant to population persistence as climate changes are the rate, type, magnitude, and spatial pattern of climate-induced abiotic and biotic change; generation time and life history of the organism; extent and type of phenotypic plasticity; amount and distribution of adaptive genetic variation across space and time; dispersal potential; and size and connectivity of subpopulations. An understanding of limits to plasticity and evolutionary potential across traits, populations, and species and feedbacks between adaptive and demographic responses is lacking. Integrated knowledge of coupled ecological and evolutionary mechanisms will increase understanding of the resilience and probabilities of persistence of populations and species

The organisation of physiotherapy for people with multiple sclerosis across Europe: a multicentre questionnaire survey

Background Understanding the organisational set-up of physiotherapy services across different countries is increasingly important as clinicians around the world use evidence to improve their practice. This also has to be taken into consideration when multi-centre international clinical trials are conducted. This survey aimed to systematically describe organisational aspects of physiotherapy services for people with multiple sclerosis (MS) across Europe. Methods Representatives from 72 rehabilitation facilities within 23 European countries completed an online web-based questionnaire survey between 2013 and 2014. Countries were categorised according to four European regions (defined by United Nations Statistics). Similarities and differences between regions were examined. Results Most participating centres specialized in rehabilitation (82 %) and neurology (60 %), with only 38 % specialising in MS. Of these, the Western based Specialist MS centres were predominately based on outpatient services (median MS inpatient ratio 0.14), whilst the Eastern based European services were mostly inpatient in nature (median MS inpatient ratio 0.5). In almost all participating countries, medical doctors - specialists in neurology (60 %) and in rehabilitation (64 %) - were responsible for referral to/prescription of physiotherapy. The most frequent reason for referral to/prescription of physiotherapy was the worsening of symptoms (78 % of centres). Physiotherapists were the most common members of the rehabilitation team; comprising 49 % of the team in Eastern countries compared to approximately 30 % in the rest of Europe. Teamwork was commonly adopted; 86 % of centres based in Western countries utilised the interdisciplinary model, whilst the multidisciplinary model was utilised in Eastern based countries (p = 0.046). Conclusion This survey is the first to provide data about organisational aspects of physiotherapy for people with MS across Europe. Overall, care in key organisational aspects of service provision is broadly similar across regions, although some variations, for example the models of teamwork utilised, are apparent. Organisational framework specifics should be considered anytime a multi-centre study is conducted and results from such studies are applied.PubMedWoSScopu

Atmospheric effects on extensive air showers observed with the Surface Detector of the Pierre Auger Observatory

Atmospheric parameters, such as pressure (P), temperature (T) and density, affect the development of extensive air showers initiated by energetic cosmic rays. We have studied the impact of atmospheric variations on extensive air showers by means of the surface detector of the Pierre Auger Observatory. The rate of events shows a ~10% seasonal modulation and ~2% diurnal one. We find that the observed behaviour is explained by a model including the effects associated with the variations of pressure and density. The former affects the longitudinal development of air showers while the latter influences the Moliere radius and hence the lateral distribution of the shower particles. The model is validated with full simulations of extensive air showers using atmospheric profiles measured at the site of the Pierre Auger Observatory.Comment: 24 pages, 9 figures, accepted for publication in Astroparticle Physic

Update on the correlation of the highest energy cosmic rays with nearby extragalactic matter

Data collected by the Pierre Auger Observatory through 31 August 2007 showed evidence for anisotropy in the arrival directions of cosmic rays above the Greisen-Zatsepin-Kuz'min energy threshold, \nobreak{$6\times 10^{19}$eV}. The anisotropy was measured by the fraction of arrival directions that are less than $3.1^\circ$ from the position of an active galactic nucleus within 75 Mpc (using the V\'eron-Cetty and V\'eron $12^{\rm th}$ catalog). An updated measurement of this fraction is reported here using the arrival directions of cosmic rays recorded above the same energy threshold through 31 December 2009. The number of arrival directions has increased from 27 to 69, allowing a more precise measurement. The correlating fraction is $(38^{+7}_{-6})$, compared with $21$ expected for isotropic cosmic rays. This is down from the early estimate of $(69^{+11}_{-13})$. The enlarged set of arrival directions is examined also in relation to other populations of nearby extragalactic objects: galaxies in the 2 Microns All Sky Survey and active galactic nuclei detected in hard X-rays by the Swift Burst Alert Telescope. A celestial region around the position of the radiogalaxy Cen A has the largest excess of arrival directions relative to isotropic expectations. The 2-point autocorrelation function is shown for the enlarged set of arrival directions and compared to the isotropic expectation.Comment: Accepted for publication in Astroparticle Physics on 31 August 201