Wikipedia as an encyclopaedia of life

In his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia ("http://en.wikipedia.org/wiki/Main_Page":http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision

Black Hole Emission in String Theory and the String Phase of Black Holes

String theory properly describes black-hole evaporation. The quantum string emission by Black Holes is computed. The black-hole temperature is the Hawking temperature in the semiclassical quantum field theory (QFT) regime and becomes the intrinsic string temperature, T_s, in the quantum (last stage) string regime. The QFT-Hawking temperature T_H is upper bounded by the string temperature T_S. The black hole emission spectrum is an incomplete gamma function of (T_H - T_S). For T_H << T_S, it yields the QFT-Hawking emission. For T_H \to T_S, it shows highly massive string states dominate the emission and undergo a typical string phase transition to a microscopic `minimal' black hole of mass M_{\min} or radius r_{\min} (inversely proportional to T_S) and string temperature T_S. The string back reaction effect (selfconsistent black hole solution of the semiclassical Einstein equations) is computed. Both, the QFT and string black hole regimes are well defined and bounded.The string `minimal' black hole has a life time tau_{min} simeq (k_B c)/(G hbar [T_S]^3). The semiclassical QFT black hole (of mass M and temperature T_H) and the string black hole (of mass M_{min} and temperature T_S) are mapped one into another by a `Dual' transform which links classical/QFT and quantum string regimes.Comment: LaTex, 22 pages, Lectures delivered at the Chalonge School, Nato ASI: Phase Transitions in the Early Universe: Theory and Observations. To appear in the Proceedings, Editors H. J. de Vega, I. Khalatnikov, N. Sanchez. (Kluwer Pub

Cooling of Dark-Matter Admixed Neutron Stars with density-dependent Equation of State

We propose a dark-matter (DM) admixed density-dependent equation of state where the fermionic DM interacts with the nucleons via Higgs portal. Presence of DM can hardly influence the particle distribution inside neutron star (NS) but can significantly affect the structure as well as equation of state (EOS) of NS. Introduction of DM inside NS softens the equation of state. We explored the effect of variation of DM mass and DM Fermi momentum on the NS EOS. Moreover, DM-Higgs coupling is constrained using dark matter direct detection experiments. Then, we studied cooling of normal NSs using APR and DD2 EOSs and DM admixed NSs using dark-matter modified DD2 with varying DM mass and Fermi momentum. We have done our analysis by considering different NS masses. Also DM mass and DM Fermi momentum are varied for fixed NS mass and DM-Higgs coupling. We calculated the variations of luminosity and temperature of NS with time for all EOSs considered in our work and then compared our calculations with the observed astronomical cooling data of pulsars namely Cas A, RX J0822-43, 1E 1207-52, RX J0002+62, XMMU J17328, PSR B1706-44, Vela, PSR B2334+61, PSR B0656+14, Geminga, PSR B1055-52 and RX J0720.4-3125. It is found that APR EOS agrees well with the pulsar data for lighter and medium mass NSs but cooling is very fast for heavier NS. For DM admixed DD2 EOS, it is found that for all considered NS masses, all chosen DM masses and Fermi momenta agree well with the observational data of PSR B0656+14, Geminga, Vela, PSR B1706-44 and PSR B2334+61. Cooling becomes faster as compared to normal NSs in case of increasing DM mass and Fermi momenta. It is infered from the calculations that if low mass super cold NSs are observed in future that may support the fact that heavier WIMP can be present inside neutron stars.Comment: 24 Pages, 15 Figures and 2 Tables. Version accepted in The European Physical Journal

A model for selection of eyespots on butterfly wings

The development of eyespots on the wing surface of butterflies of the family Nympalidae is one of the most studied examples of biological pattern formation.However, little is known about the mechanism that determines the number and precise locations of eyespots on the wing. Eyespots develop around signaling centers, called foci, that are located equidistant from wing veins along the midline of a wing cell (an area bounded by veins). A fundamental question that remains unsolved is, why a certain wing cell develops an eyespot, while other wing cells do not. We illustrate that the key to understanding focus point selection may be in the venation system of the wing disc. Our main hypothesis is that changes in morphogen concentration along the proximal boundary veins of wing cells govern focus point selection. Based on previous studies, we focus on a spatially two-dimensional reaction-diffusion system model posed in the interior of each wing cell that describes the formation of focus points. Using finite element based numerical simulations, we demonstrate that variation in the proximal boundary condition is sufficient to robustly select whether an eyespot focus point forms in otherwise identical wing cells. We also illustrate that this behavior is robust to small perturbations in the parameters and geometry and moderate levels of noise. Hence, we suggest that an anterior-posterior pattern of morphogen concentration along the proximal vein may be the main determinant of the distribution of focus points on the wing surface. In order to complete our model, we propose a two stage reaction-diffusion system model, in which an one-dimensional surface reaction-diffusion system, posed on the proximal vein, generates the morphogen concentrations that act as non-homogeneous Dirichlet (i.e., fixed) boundary conditions for the two-dimensional reaction-diffusion model posed in the wing cells. The two-stage model appears capable of generating focus point distributions observed in nature. We therefore conclude that changes in the proximal boundary conditions are sufficient to explain the empirically observed distribution of eyespot focus points on the entire wing surface. The model predicts, subject to experimental verification, that the source strength of the activator at the proximal boundary should be lower in wing cells in which focus points form than in those that lack focus points. The model suggests that the number and locations of eyespot foci on the wing disc could be largely controlled by two kinds of gradients along two different directions, that is, the first one is the gradient in spatially varying parameters such as the reaction rate along the anterior-posterior direction on the proximal boundary of the wing cells, and the second one is the gradient in source values of the activator along the veins in the proximal-distal direction of the wing cell

TSR: A storage and cooling ring for HIE-ISOLDE

It is planned to install the heavy-ion, low-energy ring TSR, currently at the Max-Planck-Institute for Nuclear Physics in Heidelberg, at the HIE-ISOLDE facility in CERN, Geneva. Such a facility will provide a capability for experiments with stored, cooled secondary beams that is rich and varied, spanning from studies of nuclear ground-state properties and reaction studies of astrophysical relevance, to investigations with highly-charged ions and pure isomeric beams. In addition to experiments performed using beams recirculating within the ring, the cooled beams can be extracted and exploited by external spectrometers for high-precision measurements. The capabilities of the ring facility as well as some physics cases will be presented, together with a brief report on the status of the project

A soliton menagerie in AdS

We explore the behaviour of charged scalar solitons in asymptotically global AdS4 spacetimes. This is motivated in part by attempting to identify under what circumstances such objects can become large relative to the AdS length scale. We demonstrate that such solitons generically do get large and in fact in the planar limit smoothly connect up with the zero temperature limit of planar scalar hair black holes. In particular, for given Lagrangian parameters we encounter multiple branches of solitons: some which are perturbatively connected to the AdS vacuum and surprisingly, some which are not. We explore the phase space of solutions by tuning the charge of the scalar field and changing scalar boundary conditions at AdS asymptopia, finding intriguing critical behaviour as a function of these parameters. We demonstrate these features not only for phenomenologically motivated gravitational Abelian-Higgs models, but also for models that can be consistently embedded into eleven dimensional supergravity.Comment: 62 pages, 21 figures. v2: added refs and comments and updated appendice

Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library

Background: The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. Description: A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article locating service is exposed as a standard OpenURL resolver on the BioStor web site http://biostor.org/openurl/. This resolver can be used on the web, or called by bibliographic tools that support OpenURL. Conclusions: BioStor provides tools for extracting, annotating, and visualising articles from the Biodiversity Heritage Library. BioStor is available from http://biostor.org