Pareto-optimal phylogenetic tree reconciliation

Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies.National Science Foundation (U.S.) (CAREER award 0644282)University of Connecticut (Startup funds)Harvey Mudd College (R. Michael Shanahan Endowment

Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny

Supplementary sections 1–13, tables S1–S10, and figures S1–S9 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene families, and thus, any comprehensive study of gene evolution in these species will need to account for such events. Here, we present a new computational model and algorithm for reconstructing gene evolution at the domain level. We develop a method for detecting homologous domains between genes and present a phylogenetic algorithm for reconstructing maximum parsimony evolutionary histories that include domain generation, duplication, loss, merge (fusion), and split (fission) events. Using this method, we find that genes involved in fusion and fission are enriched in signaling and development, suggesting that domain rearrangements and reuse may be crucial in these processes. We also find that fusion is more abundant than fission, and that fusion and fission events occur predominantly alongside duplication, with 92.5% and 34.3% of fusion and fission events retaining ancestral architectures in the duplicated copies. We provide a catalog of ∼9,000 genes that undergo domain rearrangement across nine sequenced species, along with possible mechanisms for their formation. These results dramatically expand on evolution at the subgene level and offer several insights into how new genes and functions arise between species.National Science Foundation (U.S.) (Graduate Research Fellowship)National Science Foundation (U.S.) (CAREER award NSF 0644282

The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard

The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics

Interactions Between Reinforcement Corrosion and Chloride Ion Diffusion in Mortar

This study explored the diffusion of the chloride ions influenced by the reinforcement corrosion in the mortar. It is believed that, during the corroding process, a small current is generated at the surface of the reinforcement. Such current is supposed to influence the diffusion of the chloride ions, but the relationship between both was not well studied in the literature. In this study, the corroded reinforcements were prepared by applied currents. Reinforced mortar specimens with w/c of 0.6 were then prepared and cured by either salt or fresh water. Results showed that the chloride ion distribution was likely associated with the reinforcement corrosion. During the early hydration, the chloride ions were attracted by the reinforcement corrosion in the specimens prepared with fresh water and cured in salt water. The concentration of the chloride ions near the surface of the reinforcement was increased with the increases of the charging time during the preparation for the corroded reinforcement. On the contrary, the chloride ions were likely bound in those specimens prepared with salt water and cured by saturated lime water. The concentration of the chloride ions near the surface of the reinforcement was higher than those near the outer surface. However, such influencing effects were not clear in the long term, possibly due to the hydration. The results of this study show that the reinforcement corrosion have influences on the diffusion of the chloride ions and such effect should be considered during the refinement of the traditional chloride ion diffusion models

Knowledge Sharing in Virtual Community: The Comparison between Contributors and Lurkers

Internet-based virtual communities are growing with an unprecedented rate. Virtual communities have been viewed as platforms for sharing knowledge. The present study proposed an integrated model by investigating social capital and motivational factors that would influence the knowledge sharing attitude of members. Data were collected from 207 professional virtual community users (including 53 contributors and 154 lurkers). The results showed that trust and pro-sharing norms mediate the relationship between shared understanding and knowledge sharing attitude. Enjoy helping, commitment, and community-related outcome expectations enhance contributors’ attitudes toward knowledge sharing. When lurkers perceived more reciprocity in their communities and expect more community-related outcome, they incline to sharing knowledge with others. The implications of these results are discussed

The Impact of IT Governance on Organizational Performance

IT governance, as a subset of corporate governance, consists of organizational structures and processes that ensure theorganization’s IT can sustain and extend the organization’s strategies and objectives. In previous research, different types ofIT governance have been proposed. However, it is not clear how different governance types affect firm performance andwhat are the theories underlying the causal relationships. Drawing from strategic alignment and coordination theories, aresearch model is proposed for investigating how intra-organizational coordination could help build goal congruence throughstrategic alignment and hence achieve higher organizational performance. The purpose of this research is to examine therelationship between IT governance, strategic alignment, and organizational performance. Data collected from 167Taiwanese firms were used to empirically evaluate the theoretical relationships proposed in the research model, and theresults show that strategic alignment is a major factor that mediates the effect of IT governance on firm performance

The Impacts Of Presentation Modes And Product Involvements On “Line” Short Message Service (SMS) Advertising Effectiveness

In today’s ubiquitous commerce (UC) era, short message service (SMS) advertisement has played an important role in the world of marketing. Convenience and economical reasons influence SMS usage frequency along with social involvement to influence attitudes towards SMS advertising. SMS advertising creates numerous opportunities for the marketers in promoting their products effectively. Adopting the competition for attention theory as the theoretical framework, we developed hypotheses to investigate the influences of presentation mode and involvement on SMS advertising performance (recall of advertising information). An experiment was conducted to examine the effects of three types of information presentation modes (text-only, image-text, and emoji-text) in the contexts of two product types (high- versus low-involvement products) in the “LINE” SMS environment. Specifically, in this current study, we allocate participants to six experimental environments (text-only for high-involvement products, text-only for low-involvement products, image-text for high-involvement products, image-text for low-involvement products, emoji-text for high-involvement products and emoji-text for low-involvement products) randomly to collected empirical data to examine the proposed hypotheses. The research findings are expected to provide instrumental guidelines for the practitioners to better achieve the goals of ads in the “LINE” SMS environment. Also, the empirical results may provide insights into the research of advertising interface design of SMS and integrating efforts from cognitive science and vision research to understand users’ involvement of SMS advertising processes

Analysis and practical considerations of linear and nonlinear piezoelectric energy conversion and harvesting techniques

La décroissance de la consommation électrique des dispositifs électroniques leur a permis une croissance sans précédent. Néanmoins, les éléments de stockage d énergie (piles et batteries), bien qu ayant initialement promus ce développement, sont devenus un frein à la prolifération des microsystèmes électroniques, de part leur durée de vie limitée ainsi que des considérations environnementales (recyclage). Pour palier à ce problème, la possibilité d exploiter l énergie de l environnement immédiat du dispositif a été proposée et a fait l objet de nombreuses recherches au cours des dernières années. En particulier, la récupération d énergie mécanique exploitant l effet piézoélectrique est l une des pistes les plus étudiées actuellement pour la conception de microgénérateurs autonomes capables d alimenter les dispositifs électroniques. Par ailleurs, dans ce domaine, il a été démontré qu un traitement non-linéaire de la tension de sortie de l élément actif permet d améliorer les capacités de récupération de l énergie vibratoire. L une de ces approches, nommée Synchronized Switch Harvesting on Inductor (récupération par commutation synchronisée sur inductance) et consistant en une inversion de la tension de manière synchrone avec le déplacement, s est montrée particulièrement efficace, pouvant augmenter la quantité d énergie récupérée par un facteur supérieur à 10. Cette dernière conduit à un processus cumulatif qui augmente artificiellement la tension de sortie de l élément piézoélectrique ainsi qu à une réduction du déphasage entre tension et vitesse de déplacement ; ces deux effets conduisant à l augmentation importante des capacités de conversion. Néanmoins, l étude des microgénérateurs d énergie s est quasiment toujours faite en considérant une excitation sinusoïdale, ce qui correspond rarement à la réalité. Peu de travaux expérimentaux, et encore moins théoriques, ont été menés en considérant une excitation large bande ; ceci étant d autant plus vrai pour les dispositifs incluant un élément non-linéaire. Ainsi l objectif de cette thèse est d étudier le comportement des récupérateurs d énergie piézoélectriques interfacés de manière non-linéaire. Pour ce faire, différentes approches seront envisagées, en considérant le processus de commutation comme un auto-échantillonnage du signal, ou en appliquant des théories d analyse stochastique pour quantifier les performances du dispositif. Ainsi, plusieurs formes d excitation appliquée au système pourront être analysées, permettant d étudier la réponse du système sous des conditions plus réalistes. Toujours dans l optique d une implémentation réaliste, un autre objectif de cette thèse consistera à évaluer l impact de la récupération d énergie par couplage sismique sur la structure hôte, démontrant la nécessité d envisager le système dans sa globalité afin de disposer de systèmes performants capables de convertir efficacement l énergie vibratoire sous forme électrique pour un usage ultérieur.A nonlinear interface consisting in a switching device has been proved to improve the piezoelectric harvester performance. Although existing works are usually done under single frequency excitation. practical cases are more likely broadband and random. In addition, the coupling effect due to the harvesting process is also an interesting issue to discuss. In terms of energy conversion process in seismic piezoelectric harvesters, mechanical interactions between host structure and harvester is an essential issue as well. The purpose of this work is to analysis seismic type piezoelectric harvesters from a practical perspective and to provide an optimal design of the latter. The broadband modeling based on the concepts of self-sampling and self-aliasing is described under broadband excitations for the nonlinear interface called "Periodic Switching Harvesting on Inductor" (PSHI). For this technique, the switching device is considered to be turned on at a fixed switching frequency. Then stochastic modeling is applied to have mathematical expressions that can describe broadband performance of the harvester with power spectral density (PSD) function of signals. As the switch is turned on at a given frequency, the modeling can be derived using cyclostationary theory. The effectiveness of stochastic modeling is validated with experimental measurements and time-domain iterative calculations, and the harvester performance under a band-limited noise excitation is discussed under bell-curved spectra excitations. An optimal switching frequency slightly less than twice the harvester resonant frequency is proved to have the optimal power output under the optimal resistive load. This switching frequency is however dependent on the electromechanical coupling factor of the harvester. Another part of this work discusses the interaction between the host structure and the harvester. The analysis is conducted with a Two-Degree-of-Freedom (TDOF) model. An energy conversion loop is therefore formed between the host structure and the harvester, within the harvester and the resistive load. The TDOF model is verified with Finite Element model and experimental work. An optimal mass ratio is proved to provide the maximal power output. The modeling is further applied to a practical self-powered Structural Health Monitoring system providing the best design of the harvester. A practical consideration of the broadband excitation is also introduced showing the effect of frequency detuning between the host structure and the harvester. Compared to constant force factor case, the harvester performance with a constant electromechanical coupling factor is surprisingly with very little decreases due to the mismatching of harvester and host structure resonant.VILLEURBANNE-DOC'INSA-Bib. elec. (692669901) / SudocSudocFranceF

Engulfing cells promote neuronal regeneration and remove neuronal debris through distinct biochemical functions of CED-1

Two important biological events happen coincidently soon after nerve injury in the peripheral nervous system in C. elegans: removal of axon debris and initiation of axon regeneration. But, it is not known how these two events are co-regulated. Mutants of ced-1, a homolog of Draper and MEGF10, display defects in both events. One model is that those events could be related. But our data suggest that they are actually separable. CED-1 functions in the muscle-type engulfing cells in both events and is enriched in muscle protrusions in close contact with axon debris and regenerating axons. Its two functions occur through distinct biochemical mechanisms; extracellular domain-mediated adhesion for regeneration and extracellular domain binding-induced intracellular domain signaling for debris removal. These studies identify CED-1 in engulfing cells as a receptor in debris removal but as an adhesion molecule in neuronal regeneration, and have important implications for understanding neural circuit repair after injury