Explaining Evolution via Constrained Persistent Perfect Phylogeny

BACKGROUND: The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. RESULTS: We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. CONCLUSIONS: A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not conform with the classical perfect phylogeny model

SRBench: A streaming RDF/SPARQL benchmark

We introduce SRBench, a general-purpose benchmark primarily designed for streaming RDF/SPARQL engines, completely based on real-world data sets from the Linked Open Data cloud. With the increasing problem of too much streaming data but not enough tools to gain knowledge from them, researchers have set out for solutions in which Semantic Web technologies are adapted and extended for publishing, sharing, analysing and understanding streaming data. To help researchers and users comparing streaming RDF/SPARQL (strRS) engines in a standardised application scenario, we have designed SRBench, with which one can assess the abilities of a strRS engine to cope with a broad range of use cases typically encountered in real-world scenarios. The data sets used in the benchmark have been carefully chosen, such that they represent a realistic and relevant usage of streaming data. The benchmark defines a concise, yet omprehensive set of queries that cover the major aspects of strRS processing. Finally, our work is complemented with a functional evaluation on three representative strRS engines: SPARQLStream, C-SPARQL and CQELS. The presented results are meant to give a first baseline and illustrate the state-of-the-art

Global endometrial ablation: A modern day solution to an age‐old problem

Menorrhagia remains a significant health issue for women worldwide. Traditionally hysterectomy has been the treatment of choice when excessive menstrual bleeding remains unresolved by hormonal manipulation. In an attempt to provide a less invasive alternative to hysterectomy, traditional techniques such as rollerball endometrial ablation were developed 20 years ago. Although extremely effective, they possessed the potential of significant intra‐operative risks and their success depended on high technical proficiency of the surgeon. As surgery and technology evolved, second generation endometrial ablation devices were developed which demonstrated improved safety and efficacy rates that paralleled traditional treatments. Since 1997, the Food and Drug Administration (FDA) has approved five such devices for use in the United States. Each possesses a unique technology profile with supporting level I evidence that allows for the treatment of a wide variety of uterine anatomy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135279/1/ijgo156.pd

Neuroprotective properties of marrow-isolated adult multilineage-inducible cells in rat hippocampus following global cerebral ischemia are enhanced when complexed to biomimetic microcarriers

Cell-based therapies for global cerebral ischemia represent promising approaches for neuronal damage prevention and tissue repair promotion. We examined the potential of marrow-isolated adult multilineage-inducible (MIAMI) cells, a homogeneous subpopulation of immature human mesenchymal stromal cell, injected into the hippocampus to prevent neuronal damage induced by global ischemia using rat organotypic hippocampal slices exposed to oxygen-glucose deprivation and rats subjected to asphyxial cardiac arrest. We next examined the value of combining fibronectin-coated biomimetic microcarriers (FN-BMMs) with epidermal growth factor (EGF)/basic fibroblast growth factor (bFGF) pre-treated MIAMI compared to EGF/bFGF pre-treated MIAMI cells alone, for their in vitro and in vivo neuroprotective capacity. Naive and EGF/bFGF pre-treated MIAMI cells significantly protected the Cornu Ammonis layer 1 (CA1) against ischemic death in hippocampal slices and increased CA1 survival in rats. MIAMI cells therapeutic value was significantly increased when delivering the cells complexed with FN-BMMs, probably by increasing stem cell survival and paracrine secretion of pro-survival and/or anti-inflammatory molecules as concluded from survival, differentiation and gene expression analysis. Four days after oxygen and glucose deprivation and asphyxial cardiac arrest, few transplanted cells administered alone survived in the brain whereas stem cell survival improved when injected complexed with FN-BMMs. Interestingly, a large fraction of the transplanted cells administered alone or in complexes expressed betaIII-tubulin suggesting that partial neuronal transdifferentiation may be a contributing factor to the neuroprotective mechanism of MIAMI cells

SN 2012ec: mass of the progenitor from PESSTO follow-up of the photospheric phase

We present the results of a photometric and spectroscopic monitoring campaign of SN 2012ec, which exploded in the spiral galaxy NGC 1084, during the photospheric phase. The photometric light curve exhibits a plateau with luminosity L = 0.9 × 1042 erg s−1 and duration ∼90 d, which is somewhat shorter than standard Type II-P supernovae (SNe). We estimate the nickel mass M(56Ni) = 0.040 ± 0.015 M⊙ from the luminosity at the beginning of the radioactive tail of the light curve. The explosion parameters of SN 2012ec were estimated from the comparison of the bolometric light curve and the observed temperature and velocity evolution of the ejecta with predictions from hydrodynamical models. We derived an envelope mass of 12.6 M⊙, an initial progenitor radius of 1.6 × 1013 cm and an explosion energy of 1.2 foe. These estimates agree with an independent study of the progenitor star identified in pre-explosion images, for which an initial mass of M = 14-22 M⊙ was determined. We have applied the same analysis to two other Type II-P SNe (SNe 2012aw and 2012A), and carried out a comparison with the properties of SN 2012ec derived in this paper. We find a reasonable agreement between the masses of the progenitors obtained from pre-explosion images and masses derived from hydrodynamical models. We estimate the distance to SN 2012ec with the standardized candle method (SCM) and compare it with other estimates based on other primary and secondary indicators. SNe 2012A, 2012aw and 2012ec all follow the standard relations for the SCM for the use of Type II-P SNe as distance indicators

Search for Neutral Higgs Bosons of the Minimal Supersymmetric Standard Model in e+e- Interactions at \sqrt{s} = 189 GeV

A search for the lightest neutral scalar and neutral pseudoscalar Higgs bosons in the Minimal Supersymmetric Standard Model is performed using 176.4 pb^-1 of integrated luminosity collected by L3 at a center-of-mass energy of 189 GeV. No signal is observed, and the data are consistent with the expected Standard Model background. Lower limits on the masses of the lightest neutral scalar and pseudoscalar Higgs bosons are given as a function of tan(beta). Lower mass limits for tan(beta)>1 are set at the 95% confidence level to be m_h > 77.1 GeV and m_A > 77.1 GeV

Measurement of the Lifetime of the Tau Lepton

The tau lepton lifetime is measured with the L3 detector at LEP using the complete data taken at centre-of-mass energies around the Z pole resulting in tau_tau = 293.2 +/- 2.0 (stat) +/- 1.5 (syst) fs. The comparison of this result with the muon lifetime supports lepton universality of the weak charged current at the level of six per mille. Assuming lepton universality, the value of the strong coupling constant, alpha_s is found to be alpha_s(m_tau^2) = 0.319 +/- 0.015(exp.) +/- 0.014 (theory)

Search for Extra Dimensions in Boson and Fermion Pair Production in e+e- Interactions at LEP

Extra spatial dimensions are proposed by recent theories that postulate the scale of gravity to be of the same order as the electroweak scale. A sizeable interaction between gravitons and Standard Model particles is then predicted. Effects of these new interactions in boson and fermion pair production are searched for in the data sample collected at centre-of-mass energies above the Z pole by the L3 detector at LEP. In addition, the direct production of a graviton associated with a Z boson is investigated. No statistically significant hints for the existence of these effects are found and lower limits in excess of 1 TeV are derived on the scale of this new theory of gravity

Measurement of the Probability of Gluon Splitting into Charmed Quarks in Hadronic Z Decays

We have measured the probability, n(g->cc~), of a gluon splitting into a charm-quark pair using 1.7 million hadronic Z decays collected by the L3 detector. Two independent methods have been applied to events with a three-jet topology. One method relies on tagging charmed hadrons by identifying a lepton in the lowest energy jet. The other method uses a neural network based on global event shape parameters. Combining both methods, we measure n(g->cc~)= [2.45 +/- 0.29 +/- 0.53]%