Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Classical and quantum general relativity: a new paradigm

We argue that recent developments in discretizations of classical and quantum gravity imply a new paradigm for doing research in these areas. The paradigm consists in discretizing the theory in such a way that the resulting discrete theory has no constraints. This solves many of the hard conceptual problems of quantum gravity. It also appears as a useful tool in some numerical simulations of interest in classical relativity. We outline some of the salient aspects and results of this new framework.Comment: 8 pages, one figure, fifth prize of the Gravity Research Foundation 2005 essay competitio

A glance beyond the quantum model

One of the most important problems in Physics is how to reconcile Quantum Mechanics with General Relativity. Some authors have suggested that this may be realized at the expense of having to drop the quantum formalism in favor of a more general theory. However, as the experiments we can perform nowadays are far away from the range of energies where we may expect to observe non-quantum effects, it is difficult to theorize at this respect. Here we propose a fundamental axiom that we believe any reasonable post-quantum theory should satisfy, namely, that such a theory should recover classical physics in the macroscopic limit. We use this principle, together with the impossibility of instantaneous communication, to characterize the set of correlations that can arise between two distant observers. Although several quantum limits are recovered, our results suggest that quantum mechanics could be falsified by a Bell-type experiment if both observers have a sufficient number of detectors

A window into the neutron star: Modelling the cooling of accretion heated neutron star crusts

In accreting neutron star X-ray transients, the neutron star crust can be substantially heated out of thermal equilibrium with the core during an accretion outburst. The observed subsequent cooling in quiescence (when accretion has halted) offers a unique opportunity to study the structure and thermal properties of the crust. Initially crust cooling modelling studies focussed on transient X-ray binaries with prolonged accretion outbursts (> 1 year) such that the crust would be significantly heated for the cooling to be detectable. Here we present the results of applying a theoretical model to the observed cooling curve after a short accretion outburst of only ~10 weeks. In our study we use the 2010 outburst of the transiently accreting 11 Hz X-ray pulsar in the globular cluster Terzan 5. Observationally it was found that the crust in this source was still hot more than 4 years after the end of its short accretion outburst. From our modelling we found that such a long-lived hot crust implies some unusual crustal properties such as a very low thermal conductivity (> 10 times lower than determined for the other crust cooling sources). In addition, we present our preliminary results of the modelling of the ongoing cooling of the neutron star in MXB 1659-298. This transient X-ray source went back into quiescence in March 2017 after an accretion phase of ~1.8 years. We compare our predictions for the cooling curve after this outburst with the cooling curve of the same source obtained after its previous outburst which ended in 2001.Comment: 4 pages, 1 figure, to appear in the proceedings of "IAUS 337: Pulsar Astrophysics - The Next 50 Years" eds: P. Weltevrede, B.B.P. Perera, L. Levin Preston & S. Sanida

Can black holes and naked singularities be detected in accelerators?

We study the conditions for the existence of black holes that can be produced in colliders at TeV-scale if the space-time is higher dimensional. On employing the microcanonical picture, we find that their life-times strongly depend on the details of the model. If the extra dimensions are compact (ADD model), microcanonical deviations from thermality are in general significant near the fundamental TeV mass and tiny black holes decay more slowly than predicted by the canonical expression, but still fast enough to disappear almost instantaneously. However, with one warped extra dimension (RS model), microcanonical corrections are much larger and tiny black holes appear to be (meta)stable. Further, if the total charge is not zero, we argue that naked singularities do not occur provided the electromagnetic field is strictly confined on an infinitely thin brane. However, they might be produced in colliders if the effective thickness of the brane is of the order of the fundamental length scale (~1/TeV).Comment: 6 pages, RevTeX 3, 1 figure and 1 table, important changes and addition

Prospects of Detecting Baryon and Quark Superfluidity from Cooling Neutron Stars

Baryon and quark superfluidity in the cooling of neutron stars are investigated. Observations could constrain combinations of the neutron or Lambda-hyperon pairing gaps and the star's mass. However, in a hybrid star with a mixed phase of hadrons and quarks, quark gaps larger than a few tenths of an MeV render quark matter virtually invisible for cooling. If the quark gap is smaller, quark superfluidity could be important, but its effects will be nearly impossible to distinguish from those of other baryonic constituents.Comment: 4 pages, 3 ps figures, uses RevTex(aps,prl). Submitted to Phys. Rev. Let

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

The platinum nuclei: concealed configuration mixing and shape coexistence

The role of configuration mixing in the Pt region is investigated. For this chain of isotopes, the nature of the ground state changes smoothly, being spherical around mass $A\sim 174$ and $A\sim 192$ and deformed around the mid-shell N=104 region. This has a dramatic effect on the systematics of the energy spectra as compared to the systematics in the Pb and Hg nuclei. Interacting Boson Model with configuration mixing calculations are presented for gyromagnetic factors, $\alpha$-decay hindrance factors, and isotope shifts. The necessity of incorporating intruder configurations to obtain an accurate description of the latter properties becomes evident.Comment: Accepted in Physical Review

Entropy bounds for charged and rotating systems

It was shown in a previous work that, for systems in which the entropy is an extensive function of the energy and volume, the Bekenstein and the holographic entropy bounds predict new results. In this paper, we go further and derive improved upper bounds to the entropy of {\it extensive} charged and rotating systems. Furthermore, it is shown that for charged and rotating systems (including non-extensive ones), the total energy that appear in both the Bekenstein entropy bound (BEB) and the causal entropy bound (CEB) can be replaced by the {\it internal} energy of the system. In addition, we propose possible corrections to the BEB and the CEB.Comment: 12 pages, revte