Evolutionary Inference via the Poisson Indel Process

We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classical evolutionary process, the TKF91 model, is a continuous-time Markov chain model comprised of insertion, deletion and substitution events. Unfortunately this model gives rise to an intractable computational problem---the computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a new stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The new model is closely related to the TKF91 model, differing only in its treatment of insertions, but the new model has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared to separate inference of phylogenies and alignments.Comment: 33 pages, 6 figure

EMPREENDEDORISMO DIGITAL: UM ESTUDO SOBRE O USO DA TECNOLOGIA COMO GERAÇÃO DE NEGÓCIOS NAS STARTUPS EDUCACIONAIS

Este artigo  versa sobre como  a tecnologia da informação  (TI) influência no  aumento da qualidade da atividade empreendedora. Devido à nova realidade brasileira que se apresenta em um universo complexo e multifacetado, acaba exigindo grande flexibilidade do empreendedor para se conectar com o cliente através de aplicativos e dispositivos móveis que passam a ser acessíveis à sociedade brasileira, garantindo flexibilidade e novas relações de negócios em atividades tradicionais como a educação ou outras atividades do terceiro setor . Neste sentido o estudo objetiva explicar como a política de tecnologia da informação auxilia na  melhoria  dos  serviços  em  uma  organização  educacional.  Com  base  em  pesquisa quantitativa como método um “Startup” foi utilizado como objeto de estudo e validou o aumento  da  produção  dos  serviços  educacionais  através  da  publicação  de  aplicativos propostos na ESPEDUC, desta forma a meta de divulgação para oferta e demanda de publico foi atingida através de uma política de geração de produtos e acessos móveis digitais a futuros e atuais clientes

GOVERNANÇA DE TECNOLOGIA DA INFORMAÇÃO: ESTUDO SOBRE A RELAÇÃO ENTRE A TI E A GOVERNANÇA CORPORATIVA NAS ORGANIZAÇÕES

O artigo reflete sobre a aplicação da tecnologia da informação ao setor estratégico das organizações, em especial aos conselhos administrativos de organizações “S.A” e a evolução deste segmento como fator competitivo de mercado. Neste contexto a t.i acaba obrigatoriamente a se adaptar a códigos de conduta como o “Código das Boas Práticas” de Governança Corporativa.   Neste sentido o desenvolvimento de mecanismos e sistemas de informação rápida e acessível ao nível de conselho (Board) tende a gerar decisões mais assertivas podendo aumentar de maneira considerável o lucro das organizações de capital privado, esta é uma tendência que pode se consolidar no Brasil futuramente

Protecting a quantum state from environmental noise by an incompatible finite-time measurement

We show that measurements of finite duration performed on an open two-state system can protect the initial state from a phase-noisy environment, provided the measured observable does not commute with the perturbing interaction. When the measured observable commutes with the environmental interaction, the finite-duration measurement accelerates the rate of decoherence induced by the phase noise. For the description of the measurement of an observable that is incompatible with the interaction between system and environment, we have found an approximate analytical expression, valid at zero temperature and weak coupling with the measuring device. We have tested the validity of the analytical predictions against an exact numerical approach, based on the superoperator-splitting method, that confirms the protection of the initial state of the system. When the coupling between the system and the measuring apparatus increases beyond the range of validity of the analytical approximation, the initial state is still protected by the finite-time measurement, according with the exact numerical calculations.Comment: REVISED VERSION: 37 pages, 3 figure

Light is more important than nutrient ratios of fertilization for cymodocea nodosa seedling development

Restoration of seagrass beds through seedlings is an alternative to the transplantation of adult plants that reduces the impact over donor areas and increases the genetic variability of restored meadows. To improve the use of Cymodocea nodosa seedlings, obtained from seeds germinated in vitro, in restoration programs, we investigated the ammonium and phosphate uptake rates of seedlings, and the synergistic effects of light levels (20 and 200 mu mol quanta m(-2) s(-1)) and different nitrogen to phosphorus molar ratios (40 mu M N:10 mu M P, 25 mu M N:25 mu M P, and 10 mu N:40 mu M P) on the photosynthetic activity and growth of seedlings. The nutrient content of seedlings was also compared to the seed nutrient reserves to assess the relative importance of external nutrient uptake for seedling development. Eighty two percent of the seeds germinated after 48 days at a mean rate of 1.5 seeds per day. All seedlings under all treatments survived and grew during the 4 weeks of the experiment. Seedlings of C. nodosa acquired ammonium and phosphate from the incubation media while still attached to the seed, at rates of about twice of adult plants. The relevance of external nutrient uptake was further highlighted by the observation that seedlings' tissues were richer in nitrogen and phosphorus than non-germinated seeds. The uptake of ammonium followed saturation kinetics with a half saturation constant of 32 mu M whereas the uptake of phosphate increased linearly with nutrient concentration within the range tested (5 - 100 mu M). Light was more important than the nutrient ratio of fertilization for the successful development of the young seedlings. The seedlings' photosynthetic and growth rates were about 20% higher in the high light treatment, whereas different nitrogen to phosphorus ratios did not significantly affect growth. The photosynthetic responses of the seedlings to changes in the light level and their capacity to use external nutrient sources showed that seedlings of C. nodosa have the ability to rapidly acclimate to the surrounding light and nutrient environment while still attached to the seeds. C. nodosa seedlings experiencing fertilization under low light levels showed slightly enhanced growth if nourished with a balanced formulation, whereas a slight increase in growth was also observed with unbalanced formulations under a higher light level. Our results highlight the importance of high light availability at the seedling restoration sites.Department of the Environment, Heritage and Climate Change of Gibraltar; FCT, the Portuguese Foundation for Science and Technology [SFRH/BPD/91629/2012]; FCT [UID/Multi/04326/2013

How much time does a measurement take?

We consider the problem of measurement using the Lindblad equation, which allows the introduction of time in the interaction between the measured system and the measurement apparatus. We use analytic results, valid for weak system-environment coupling, obtained for a two-level system in contact with a measurer (Markovian interaction) and a thermal bath (non-Markovian interaction), where the measured observable may or may not commute with the system-environment interaction. Analysing the behavior of the coherence, which tends to a value asymptotically close to zero, we obtain an expression for the time of measurement which depends only on the system-measurer coupling, and which does not depend on whether the observable commutes with the system-bath interaction. The behavior of the coherences in the case of strong system-environment coupling, found numerically, indicates that an increase in this coupling decreases the measurement time, thus allowing our expression to be considered the upper limit for the duration of the process.Comment: REVISED VERSION: 17 pages, 2 figure

UCP2 Regulates the Glucagon Response to Fasting and Starvation

Glucagon is important for maintaining euglycemia during fasting/starvation, and abnormal glucagon secretion is associated with type 1 and type 2 diabetes; however, the mechanisms of hypoglycemia-induced glucagon secretion are poorly understood. We previously demonstrated that global deletion of mitochondrial uncoupling protein 2 (UCP2−/−) in mice impaired glucagon secretion from isolated islets. Therefore, UCP2 may contribute to the regulation of hypoglycemia-induced glucagon secretion, which is supported by our current finding that UCP2 expression is increased in nutrient-deprived murine and human islets. Further to this, we created α-cell–specific UCP2 knockout (UCP2AKO) mice, which we used to demonstrate that blood glucose recovery in response to hypoglycemia is impaired owing to attenuated glucagon secretion. UCP2-deleted α-cells have higher levels of intracellular reactive oxygen species (ROS) due to enhanced mitochondrial coupling, which translated into defective stimulus/secretion coupling. The effects of UCP2 deletion were mimicked by the UCP2 inhibitor genipin on both murine and human islets and also by application of exogenous ROS, confirming that changes in oxidative status and electrical activity directly reduce glucagon secretion. Therefore, α-cell UCP2 deletion perturbs the fasting/hypoglycemic glucagon response and shows that UCP2 is necessary for normal α-cell glucose sensing and the maintenance of euglycemia

Effectiveness of insecticide-treated bednets in malaria prevention in Haiti: a case-control study

Background Insecticide-treated bednets (ITNs) are eff ective in preventing malaria where vectors primarily bite indoors and late at night, but their eff ectiveness is uncertain where vectors bite outdoors and earlier in the evening. We studied the eff ectiveness of ITNs following a mass distribution in Haiti from May to September, 2012, where the Anopheles albimanus vector bites primarily outdoors and often when people are awake. Methods In this case-control study, we enrolled febrile patients presenting to outpatient departments at 17 health facilities throughout Haiti from Sept 4, 2012, to Feb 27, 2014, who were tested with malaria rapid diagnostic tests (RDTs), and administered questionnaires on ITN use and other risk factors. Cases were defi ned by positive RDT and controls were febrile patients from the same clinic with a negative RDT. Our primary analysis retrospectively matched cases and controls by age, sex, location, and date, and used conditional logistic regression on the matched sample. A sensitivity analysis used propensity scores to match patients on ITN use propensity and analyse malaria among ITN users and non-users. Additional ITN bioeffi cacy and entomological data were collected. Findings We enrolled 9317 patients, including 378 (4%) RDT-positive cases. 1202 (13%) patients reported ITN use. Post-hoc matching of cases and controls yielded 362 cases and 1201 matched controls, 19% (333) of whom reported consistent campaign net use. After using propensity scores to match on consistent campaign ITN use, 2298 patients, including 138 (7%) RDT-positive cases, were included: 1149 consistent campaign ITN users and 1149 non-consistent campaign ITN users. Both analyses revealed that ITNs did not signifi cantly protect against clinical malaria (odds ratio [OR]=0·95, 95% CI 0·68–1·32, p=0·745 for case-control analysis; OR=0·95, 95% CI 0·45–1·97, p=0·884 for propensity score analysis). ITN and entomological data indicated good ITN physical integrity and bioeffi cacy, and no permethrin resistance among local mosquitoes. Interpretation We found no evidence that mass ITN campaigns reduce clinical malaria in this observational study in Haiti; alternative malaria control strategies should be prioritised

Probes of Lorentz Violation

Lorentz invariance is such an important principle of fundamental physics that it should constantly be subjected to experimental scrutiny as well as theoretical questioning. Distant astrophysical sources of energetic photons with rapid time variations, such as active galactic nuclei (AGNs) and gamma-ray bursters (GRBs), provide ideal experimental opportunities for testing Lorentz invariance. The Cherenkov Telescope Array (CTA) is an excellent experimental tool for making such tests with sensitivities exceeding those possible using other detectors.Comment: 17 pages, 2 figures, submitted to Astroparticle Physics Topical Issue: Cherenkov Telescope Arra

Decoherence and CPT Violation in a Stringy Model of Space-Time Foam

I discuss a model inspired from the string/brane framework, in which our Universe is represented as a three brane, propagating in a bulk space time punctured by D0-brane (D-particle) defects. As the D3-brane world moves in the bulk, the D-particles cross it, and from an effective observer on D3 the situation looks like a ``space-time foam'' with the defects ``flashing'' on and off (``D-particle foam''). The open strings, with their ends attached on the brane, which represent matter in this scenario, can interact with the D-particles on the D3-brane universe in a topologically non-trivial manner, involving splitting and capture of the strings by the D0-brane defects. Such processes are described by logarithmic conformal field theories on the world-sheet. Physically, they result in effective decoherence of the string matter on the D3 brane, and as a result, of CPT Violation, but of a type that implies an ill-defined nature of the effective CPT operator. Due to electric charge conservation, only electrically neutral (string) matter can exhibit such interactions with the D-particle foam. This may have unique, experimentally detectable, consequences for electrically-neutral entangled quantum matter states on the brane world, in particular the modification of the pertinent EPR Correlation of neutral mesons in a meson factory.Comment: 41 pages Latex, five eps figures incorporated. Uses special macro