A scalable machine-learning approach to recognize chemical names within large text databases

MOTIVATION: The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. RESULTS: A first-order Markov Model (MM) was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid

RAPTOR observations of delayed explosive activity in the high-redshift gamma-ray burst GRB 060206

The RAPid Telescopes for Optical Response (RAPTOR) system at Los Alamos National Laboratory observed GRB 060206 starting 48.1 minutes after gamma-ray emission triggered the Burst Alert Telescope (BAT) on-board the Swift satellite. The afterglow light curve measured by RAPTOR shows a spectacular re-brightening by ~1 mag about 1 h after the trigger and peaks at R ~ 16.4 mag. Shortly after the onset of the explosive re-brightening the OT doubled its flux on a time-scale of about 4 minutes. The total R-band fluence received from GRB 060206 during this episode is 2.3e-9 erg/cm2. In the rest frame of the burst (z = 4.045) this yields an isotropic equivalent energy release of ~0.7e50 erg in just a narrow UV band 130 +/- 22 nm. We discuss the implications of RAPTOR observations for untriggered searches for fast optical transients and studies of GRB environments at high redshift.Comment: Submitted to ApJ Letter

CO2 induced seawater acidification impacts sea urchin larval development I: Elevated metabolic rates decrease scope for growth and induce developmental delay

Anthropogenic CO(2) emissions are acidifying the world's oceans. A growing body of evidence is showing that ocean acidification impacts growth and developmental rates of marine invertebrates. Here we test the impact of elevated seawater pCO(2) (129Pa, 1271 atm) on early development, larval metabolic and feeding rates in a marine model organism, the sea urchin Strongylocentrotus purpuratus. Growth and development was assessed by measuring total body length, body rod length, postoral rod length and posterolateral rod length. Comparing these parameters between treatments suggests that larvae suffer from a developmental delay (by ca. 8%) rather than from the previously postulated reductions in size at comparable developmental stages. Further, we found maximum increases in respiration rates of +100% under elevated pCO(2), while body length corrected feeding rates did not differ between larvae from both treatments. Calculating scope for growth illustrates that larvae raised under high pCO(2) spent an average of 39 to 45% of the available energy for somatic growth, while control larvae could allocate between 78 and 80% of the available energy into growth processes. Our results highlight the importance of defining a standard frame of reference when comparing a given parameter between treatments, as observed differences can be easily due to comparison of different larval ages with their specific set of biological characters

ROTSE All Sky Surveys for Variable Stars I: Test Fields

The ROTSE-I experiment has generated CCD photometry for the entire Northern sky in two epochs nightly since March 1998. These sky patrol data are a powerful resource for studies of astrophysical transients. As a demonstration project, we present first results of a search for periodic variable stars derived from ROTSE-I observations. Variable identification, period determination, and type classification are conducted via automatic algorithms. In a set of nine ROTSE-I sky patrol fields covering about 2000 square degrees we identify 1781 periodic variable stars with mean magnitudes between m_v=10.0 and m_v=15.5. About 90% of these objects are newly identified as variable. Examples of many familiar types are presented. All classifications for this study have been manually confirmed. The selection criteria for this analysis have been conservatively defined, and are known to be biased against some variable classes. This preliminary study includes only 5.6% of the total ROTSE-I sky coverage, suggesting that the full ROTSE-I variable catalog will include more than 32,000 periodic variable stars.Comment: Accepted for publication in AJ 4/00. LaTeX manuscript. (28 pages, 11 postscript figures and 1 gif

The Bioactivity and Ion Release of Titanium-Containing Glass Polyalkenoate Cements for Medical Applications

The ion release profiles and bioactivity of a series of Ti containing glass polyalkenoate cements. Characterization revealed each material to be amorphous with a Tg in the region of 650-660°C. The network connectivity decreased (1.83-1.35) with the addition of TiO2 which was also evident with analysis by X-ray photoelectron spectroscopy. Ion release from cements were determined using atomic absorption spectroscopy for zinc (Zn2+), calcium (Ca2+), strontium (Sr2+), Silica (Si4+) and titanium (Ti4+). Ions such as Zn2+ (0.1-2.0 mg/l), Ca2+ (2.0-8.3 mg/l,) Sr2+ (0.1-3.9 mg/l), and Si4+ (14-90 mg/l) were tested over 1-30 days. No Ti4+ release was detected. Simulated body fluid revealed a CaP surface layer on each cement while cell culture testing of cement liquid extracts with TW-Z (5 mol% TiO2) produced the highest cell viability (161%) after 30 days. Direct contact testing of discs resulted in a decrease in cell viability of the each cement tested. © 2010 Springer Science+Business Media, LLC

Haptic Guidance and Haptic Error Amplification in a Virtual Surgical Robotic Training Environment

Teleoperated robotic systems have introduced more intuitive control for minimally invasive surgery, but the optimal method for training remains unknown. Recent motor learning studies have demonstrated that exaggeration of errors helps trainees learn to perform tasks with greater speed and accuracy. We hypothesized that training in a force field that pushes the operator away from a desired path would improve their performance on a virtual reality ring-on-wire task. Forty surgical novices trained under a no-force, guidance, or error-amplifying force field over five days. Completion time, translational and rotational path error, and combined error-time were evaluated under no force field on the final day. The groups significantly differed in combined error-time, with the guidance group performing the worst. Error-amplifying field participants showed the most improvement and did not plateau in their performance during training, suggesting that learning was still ongoing. Guidance field participants had the worst performance on the final day, confirming the guidance hypothesis. Participants with high initial path error benefited more from guidance. Participants with high initial combined error-time benefited more from guidance and error-amplifying force field training. Our results suggest that error-amplifying and error-reducing haptic training for robot-assisted telesurgery benefits trainees of different abilities differently.Comment: 11 pages, 7 Figure, Under Revie

International Educators’ Perspectives on the Purpose of Science Education and the Relationship between School Science and Creativity

This is the author accepted manuscript. The final version is available from Taylor & Francis (Routledge) via the DOI in this record.Background: Creativity across all disciplines is increasingly viewed as a fundamental educational capability. Science can play a potentially important role in the nurturing of creativity. Research also suggests that creative pedagogy, including interdisciplinary teaching with Science and the Arts, can engage students with science. Previous studies into teachers’ attitudes to the relationship between science and creativity have been largely situated within national educational contexts. Purpose: This study, part of the large EU funded CREATIONs project, explores educators’ perspectives on the relationship between Science and Creativity across national contexts drawn from Europe and beyond. Sample and Methods: 270 educators, broadly defined to include primary (age 4-11) and secondary (age 11-18) teachers and trainee teachers, informal educators and teacher educators, responded to a survey designed to explore perceptions of the relationship between science and creativity. Respondents were a convenience sample recruited by project partners and through online media. The elements of the survey reported here included Likert-scale questions, open response questions, and ranking questions in the form of an electronic self-administered questionnaire. Exploratory factor analysis was used to develop a combined attitude scale labelled ‘science is creative’, with results compared across nationalities and phases of education. Open question responses were analysed thematically to allow more nuanced interpretation of the descriptive statistical findings. Results: The findings show broad agreement internationally and across phases that science is a creative endeavour, with a small number of educators disagreeing about the 3 relationship between science and creativity in the context of school science. Those who disagreed were usually secondary science teachers, from England, Malta or outside Europe (primarily from the United States). The role of scientific knowledge within creativity in science education was found to be contentious. Conclusions: That educators broadly see science as creative is unsurprising, but initial exploration of educators’ perspectives internationally shows some areas of difference. These were especially apparent for educators working in formal education, particularly relating to the role of knowledge with respect to creativity in science. With current interest in STEAM education, further investigation to understand potential mediating factors of national educational contexts on teachers’ perspectives with respect to the role of disciplinary knowledge(s) in creativity and their interaction in interdisciplinary teaching and learning, is recommended.European Commissio

A gauge model for quantum mechanics on a stratified space

In the Hamiltonian approach on a single spatial plaquette, we construct a quantum (lattice) gauge theory which incorporates the classical singularities. The reduced phase space is a stratified K\"ahler space, and we make explicit the requisite singular holomorphic quantization procedure on this space. On the quantum level, this procedure furnishes a costratified Hilbert space, that is, a Hilbert space together with a system which consists of the subspaces associated with the strata of the reduced phase space and of the corresponding orthoprojectors. The costratified Hilbert space structure reflects the stratification of the reduced phase space. For the special case where the structure group is $\mathrm{SU}(2)$, we discuss the tunneling probabilities between the strata, determine the energy eigenstates and study the corresponding expectation values of the orthoprojectors onto the subspaces associated with the strata in the strong and weak coupling approximations.Comment: 38 pages, 9 figures. Changes: comments on the heat kernel and coherent states have been adde

Access to Scientific Publications: The Scientist's Perspective

BACKGROUND: Scientific publishing is undergoing significant changes due to the growth of online publications, increases in the number of open access journals, and policies of funders and universities requiring authors to ensure that their publications become publicly accessible. Most studies of the impact of these changes have focused on the growth of articles available through open access or the number of open-access journals. Here, we investigated access to publications at a number of institutes and universities around the world, focusing on publications in HIV vaccine research--an area of biomedical research with special importance to the developing world. METHODS AND FINDINGS: We selected research papers in HIV vaccine research field, creating: 1) a first set of 50 most recently published papers with keywords "HIV vaccine" and 2) a second set of 200 articles randomly selected from those cited in the first set. Access to the majority (80%) of the recently published articles required subscription, while cited literature was much more accessible (67% freely available online). Subscriptions at a number of institutions around the world were assessed for providing access to subscription-only articles from the two sets. The access levels varied widely, ranging among institutions from 20% to 90%. Through the WHO-supported HINARI program, institutes in low-income countries had access comparable to that of institutes in the North. Finally, we examined the response rates for reprint requests sent to corresponding authors, a method commonly used before internet access became widespread. Contacting corresponding authors with requests for electronic copies of articles by email resulted in a 55-60% success rate, although in some cases it took up to 1.5 months to get a response. CONCLUSIONS: While research articles are increasingly available on the internet in open access format, institutional subscriptions continue to play an important role. However, subscriptions do not provide access to the full range of HIV vaccine research literature. Access to papers through subscriptions is complemented by a variety of other means, including emailing corresponding authors, joint affiliations, use of someone else's login information and posting requests on message boards. This complex picture makes it difficult to assess the real ability of scientists to access literature, but the observed differences in access levels between institutions suggest an unlevel playing field, in which some researchers have to spend more efforts than others to obtain the same information