Extraction of chemical-induced diseases using prior knowledge and textual information

We describe our approach to the chemical-disease relation (CDR) task in the BioCreative V challenge. The CDR task consists of two subtasks: Automatic disease-named entity recognition and normalization (DNER), and extraction of chemical-induced diseases (CIDs) from Medline abstracts. For the DNER subtask, we used our concept recognition tool Peregrine, in combination with several optimization steps. For the CID subtask, our system, which we named RELigator, was trained on a rich feature set, comprising features derived from a graph database containing prior knowledge about chemicals and diseases, and linguistic and statistical features derived from the abstracts in the CDR training corpus. We describe the systems that were developed and present evaluation results for both subtasks on the CDR test set. For DNER, our Peregrine system reached an F-score of 0.757. For CID, the system achieved an F-score of 0.526, which ranked second among 18 participating teams. Several post-challenge modifications of the systems resulted in substantially improved F-scores (0.828 for DNER and 0.602 for CID)

Is there a silver lining to the Zika virus epidemic in the Americas?

It is hard to find anything positive to say about an epidemic of an emerging virus that infects pregnant women, targets developing fetuses’ neural progenitor cells, and disrupts the sequence of neural development to cause a devastating syndrome resulting in lifelong disabilities. Infants with microcephaly became the faces of the Zika virus epidemic in the Americas, which affected almost all countries in the western hemisphere in 2014–17. By the end of 2017, Zika virus has nearly disappeared from the Americas as quickly as it emerged. Now that the dust is settling, what have the scientific and public health communities learned? Is there a silver lining to Zika’s devastation

Role of carbon dioxide and ion transport in the formation of sub-embryonic fluid by the blastoderm of the Japanese quail

1. The explanted blastoderm of the Japanese quail was used to explore the role of ions and carbon dioxide in determining the rate of sub-embryonic fluid (SEF) production between 54 and 72 h of incubation. 2. Amiloride, an inhibitor of Na+/H+ exchange, at concentrations of 10-3 to 10-6 M substantially decreased the rate of SEF production when added to the albumen culture medium. N-ethylmaleimide, an inhibitor of V type H+ ATPase, also decreased this rate but only to a small extent at the highest dose applied, 10-3 M. Both inhibitors had no effect on SEF production when added to the SEF. 3. The inhibitors of cellular bicarbonate and chloride exchange, 4-acetamido-4-'isothiocyano-2, 2-'disulphonic acid (SITS) and 4,4'diisothiocyanostilbene-2,2-'disulphonic acid (DIDS), had no effect upon SEF production. 4. Ouabain, an inhibitor of Na+/K+ ATPase, decreased SEF production substantially at all concentrations added to the SEF (10-3 to 10-6 M). Three sulphonamide inhibitors of carbonic anhydrase, acetazolamide, ethoxzolamide and benzolamide, decreased SEF production when added to the SEF at concentrations of 10-3 to 10-6 M. Benzolamide was by far the most potent. Neither ouabain nor the sulphonamides altered SEF production when added to the albumen culture medium. 5. Using a cobalt precipitation method, carbonic anhydrase activity was localised to the endodermal cells of the area vasculosa. The carbonic anhydrase activity was primarily associated with the lateral plasma membranes, which together with the potent inhibitory effect of benzolamide, suggests the carbonic anhydrase of these cells is the membrane-associated form, CA IV. 6. The changes in SEF composition produced by inhibitors were consistent with the production of SEF by local osmotic gradients. 7. It is concluded that a Na+/K+ ATPase is located on the basolateral membranes of the endodermal cells of the area vasculosa , and that a sodium ion/hydrogen ion exchanger is located on their apical surfaces. Protons for this exchanger would be provided by the hydration of CO2 catalysed by the membrane-associated carbonic anhydrase. Furthermore, it is proposed that the prime function of the endodermal cells of the area vasculosa is the production of SEF

Hydrodynamic Synchronisation of Model Microswimmers

We define a model microswimmer with a variable cycle time, thus allowing the possibility of phase locking driven by hydrodynamic interactions between swimmers. We find that, for extensile or contractile swimmers, phase locking does occur, with the relative phase of the two swimmers being, in general, close to 0 or pi, depending on their relative position and orientation. We show that, as expected on grounds of symmetry, self T-dual swimmers, which are time-reversal covariant, do not phase-lock. We also discuss the phase behaviour of a line of tethered swimmers, or pumps. These show oscillations in their relative phases reminiscent of the metachronal waves of cilia.Comment: 17 pages, 8 figure

Displaced but not replaced: the impact of e-learning on academic identities in higher education.

Challenges facing universities are leading many to implement institutional strategies to incorporate e-learning rather than leaving its adoption up to enthusiastic individuals. Although there is growing understanding about the impact of e-learning on the student experience, there is less understanding of academics’ perceptions of e-learning and its impact on their identities. This paper explores the changing nature of academic identities revealed through case study research into the implementation of e-learning at one UK university. By providing insight into the lived experiences of academics in a university in which technology is not only transforming access to knowledge but also influencing the balance of power between academic and student in knowledge production and use, it is suggested that academics may experience a jolt to their ‘trajectory of self’ when engaging with e-learning. The potential for e-learning to prompt loss of teacher presence and displacement as knowledge expert may appear to undermine the ontological security of their academic identity

Three-sphere low-Reynolds-number swimmer with a passive elastic arm

One of the simplest model swimmers at low Reynolds number is the three-sphere swimmer by Najafi and Golestanian. It consists of three spheres connected by two rods which change their lengths periodically in non-reciprocal fashion. Here we investigate a variant of this model in which one rod is periodically actuated while the other is replaced by an elastic spring. We show that the competition between the elastic restoring force and the hydrodynamic drag produces a delay in the response of the passive elastic arm with respect to the active one. This leads to non-reciprocal shape changes and self-propulsion. After formulating the equations of motion, we study their solutions qualitatively and numerically. The leading-order term of the solution is computed analytically. We then address questions of optimization with respect to both actuation frequency and swimmer\u2019s geometry. Our results can provide valuable conceptual guidance in the engineering of robotic microswimmers

Homogeneous nucleation of quark-gluon plasma, finite size effects and long-lived metastable objects

The general formalism of homogeneous nucleation theory is applied to study the hadronization pattern of the ultra-relativistic quark-gluon plasma (QGP) undergoing a first order phase transition. A coalescence model is proposed to describe the evolution dynamics of hadronic clusters produced in the nucleation process. The size distribution of the nucleated clusters is important for the description of the plasma conversion. The model is most sensitive to the initial conditions of the QGP thermalization, time evolution of the energy density, and the interfacial energy of the plasma-hadronic matter interface. The rapidly expanding QGP is first supercooled by about $\Delta T = T - T_c = 4-6$. Then it reheats again up to the critical temperature T_c. Finally it breaks up into hadronic clusters and small droplets of plasma. This fast dynamics occurs within the first $5-10 fm/c$. The finite size effects and fluctuations near the critical temperature are studied. It is shown that a drop of longitudinally expanding QGP of the transverse radius below 4.5 fm can display a long-lived metastability. However, both in the rapid and in the delayed hadronization scenario, the bulk pion yield is emitted by sources as large as 3-4.5 fm. This may be detected experimentally both by a HBT interferometry signal and by the analysis of the rapidity distributions of particles in narrow p_T-intervals at small p_T on an event-by-event basis.Comment: 29 pages, incl. 12 figures and 1 table; to be published in Phys. Rev.

On the verge of Umdeutung in Minnesota: Van Vleck and the correspondence principle (Part One)

In October 1924, the Physical Review, a relatively minor journal at the time, published a remarkable two-part paper by John H. Van Vleck, working in virtual isolation at the University of Minnesota. Van Vleck combined advanced techniques of classical mechanics with Bohr's correspondence principle and Einstein's quantum theory of radiation to find quantum analogues of classical expressions for the emission, absorption, and dispersion of radiation. For modern readers Van Vleck's paper is much easier to follow than the famous paper by Kramers and Heisenberg on dispersion theory, which covers similar terrain and is widely credited to have led directly to Heisenberg's "Umdeutung" paper. This makes Van Vleck's paper extremely valuable for the reconstruction of the genesis of matrix mechanics. It also makes it tempting to ask why Van Vleck did not take the next step and develop matrix mechanics himself.Comment: 82 page

Pedicle Screw Surgery in the UK and Ireland: A Questionnaire Study

Pedicle screw (PS) malpositioning rates are high in spine surgery. This has resulted in the use of computed navigational aids to reduce the rate of malposition; but these are often expensive and limited in availability. A simple mechanical device to aid PS insertion might overcome some of these disadvantages. The purpose of this study was to determine the demand and design criteria for a simple device to aid PS placement, as well as to collect opinions and experiences on PS surgery in the UK and Ireland. A postal questionnaire was sent to 422 spinal surgeons in the UK and Ireland. 101 questionnaires were received; 67 of these (16% of total sent) contained useful information. 78% of surgeons experienced problems with PS placement. The need for a simple mechanical device to aid PS placement was expressed by 59% of respondent surgeons. The proportion of respondents that inserted PSs in the cervical spine was 14%; PSs are mainly inserted in the thoracic, lumbar and sacral spine, but potential exists for a PS placement aid for the cervical and thoracic spine. From the experiences of these 67 surgeons, there is evidence to suggest that surgeons would prefer a pedicle aid that is multiple use, one-piece, hand-held, radiolucent, unilateral and uses the line of sight principle in traditional open surgery. Based on the experiences of 67 surgeons, there is evidence to suggest that computed navigational aids are not readily used in PS surgery and that a simple mechanical device could be a better option. This paper provides useful data for improving the outcomes of spinal surgery

Active Galactic Nuclei at the Crossroads of Astrophysics

Over the last five decades, AGN studies have produced a number of spectacular examples of synergies and multifaceted approaches in astrophysics. The field of AGN research now spans the entire spectral range and covers more than twelve orders of magnitude in the spatial and temporal domains. The next generation of astrophysical facilities will open up new possibilities for AGN studies, especially in the areas of high-resolution and high-fidelity imaging and spectroscopy of nuclear regions in the X-ray, optical, and radio bands. These studies will address in detail a number of critical issues in AGN research such as processes in the immediate vicinity of supermassive black holes, physical conditions of broad-line and narrow-line regions, formation and evolution of accretion disks and relativistic outflows, and the connection between nuclear activity and galaxy evolution.Comment: 16 pages, 5 figures; review contribution; "Exploring the Cosmic Frontier: Astrophysical Instruments for the 21st Century", ESO Astrophysical Symposia Serie