A novel forward gene selection algorithm for microarray data

This paper investigates the gene selection problem for microarray data with small samples and variant correlation. Most existing algorithms usually require expensive computational effort, especially under thousands of gene conditions. The main objective of this paper is to effectively select the most informative genes from microarray data, while making the computational expenses affordable. This is achieved by proposing a novel forward gene selection algorithm (FGSA). To overcome the small samples' problem, the augmented data technique is firstly employed to produce an augmented data set. Taking inspiration from other gene selection methods, the L2-norm penalty is then introduced into the recently proposed fast regression algorithm to achieve the group selection ability. Finally, by defining a proper regression context, the proposed method can be fast implemented in the software, which significantly reduces computational burden. Both computational complexity analysis and simulation results confirm the effectiveness of the proposed algorithm in comparison with other approaches

Species-level selection reduces selfishness through competitive exclusion

Adaptation does not necessarily lead to traits which are optimal for the population. This is because selection is often the strongest at the individual or gene level. The evolution of selfishness can lead to a 'tragedy of the commons', where traits such as aggression or social cheating reduce population size and may lead to extinction. This suggests that species-level selection will result whenever species differ in the incentive to be selfish. We explore this idea in a simple model that combines individual-level selection with ecology in two interacting species. Our model is not influenced by kin or trait-group selection. We find that individual selection in combination with competitive exclusion greatly increases the likelihood that selfish species go extinct. A simple example of this would be a vertebrate species that invests heavily into squabbles over breeding sites, which is then excluded by a species that invests more into direct reproduction. A multispecies simulation shows that these extinctions result in communities containing species that are much less selfish. Our results suggest that species-level selection and community dynamics play an important role in regulating the intensity of conflicts in natural populations.

Metsän erirakenteisuutta edistävien hakkuiden kannattavuustarkastelu metsäaluetasolla

Tutkimuksessa vertailtiin metsän erirakenteisuutta edistävien poimintahakkuiden ja pienaukkohakkuiden kannattavuutta metsänhoitosuositusten mukaiseen metsänkasvatukseen Keski-Suomessa. Poimintahakkuut ja pienaukkohakkuut ovat menetelmiä, joilla voidaan lisätä luonnonmetsän häiriödynamiikan mukaista pienipiirteistä elinympäristöjen vaihtelua ja siksi ne sopivat etenkin erityiskohteisiin monimuotoisuuden, maiseman tai metsien monikäytön vuoksi. Ne johtavat yleensä vähitellen eri-ikäisrakenteiseen metsään, jossa puuston läpimittaluokkajakauma muistuttaa käänteistä J-kirjainta. Eri-ikäisrakenteisen metsänkäsittelyn taloudellista kannattavuutta puoltavat uudistumiskustannusten poisjäänti ja tukkipuihin painottuvat säännöllisin väliajoin toteutuvat hakkuut. Menetelmän soveltumista Suomen olosuhteisiin pidetään kuitenkin epävarmana. Tässä tutkimuksessa tarkasteltiin tasaikäisrakenteisen metsän muuttamista eri-ikäisrakenteiseksi 40 vuoden siirtymäaikana Metsähallituksen hallinnoimassa Isojäven ympäristöarvometsässä Kuhmoisissa. Tutkimusaineisto koostui 405 kuusivaltaisesta tasaikäisestä kuviosta, joiden pinta-alasta metsämaata on 636 hehtaaria. Metsän kehitystä simuloitiin puutason kasvumalleja käyttäen ja käsittelytoimenpiteet simuloitiin viisivuotiskausittain SIMO-metsäsuunnitteluohjelmistolla. Simulointien avulla selvitettiin jokaisen käsittelyskenaarion hakkuumäärät puutavaralajeittain, diskontatut kassavirrat ja puustopääoman muutos tarkasteluajanjakson aikana. Puunkorjuun yksikkökustannusten laskennan apuna käytettiin automatisoitua seurantajärjestelmää, jossa metsäkoneisiin asennettuilla matkapuhelimilla kerättiin MobiDoc2-sovelluksella metsäkoneiden käytöstä kiihtyvyystiedot, GPS-paikkatiedot ja syötetiedot. Lopulta jokaiselle käsittelyskenaariolle laskettiin metsän puuntuotannollista arvoa kuvaavalla tuottoarvon yhtälöllä nettonykyarvot, josta vähennettiin diskontatut puunkorjuun kustannukset. Tutkimuksen tulosten mukaan poimintahakkuun NPV oli 3 prosentin korkokannalla noin 91 % (7420 €/ha) ja pienaukkohakkuiden noin 99 % (8076 €/ha) metsänhoitosuositusten mukaisesta käsittelystä (8176 €/ha). Komparatiivinen statiikka osoitti, että korkokannan kasvattaminen 5 prosenttiin ei olennaisesti lisännyt nettonykyarvojen eroja. Poimintahakkuiden puunkorjuun yksikkökustannukset olivat 0,8 €/m3 harvennushakkuita pienemmät ja 7,2 €/m3 uudistushakkuita suuremmat. Pienaukkohakkuiden yksikkökustannukset olivat 0,7 €/m3 uudistushakkuita suuremmat.Tulosten perusteella on väistämätöntä että siirtymävaihe tasaikäisrakenteisesta eri-ikäisrakenteiseksi metsäksi aiheuttaa taloudellisia tappioita siitäkin huolimatta, että hakkuut ovat voimakkaita ja tehdään varttuneeseen kasvatusmetsään. Tappion määrä on metsän peitteisyyden ylläpidosta aiheutuva vaihtoehtoiskustannus.

Temporal Changes in a Tropical Nekton Assemblage and Performance of a Prawn Selective Gear

The temporal variation of components of a moderately diverse (H=1.46) tropical estuarine fish assemblage (long. 146°30'E, lat. 8°45'S) was directed by salinities that had been determined by local oceanographic and probably topographic conditions. For this assemblage, two types of intrayear component profiles are predicted. Pooled data (1988-91) reveal a large component of regular/resident species (43%) in an assemblage which has been under a narrow temperature regime «5T). These results facilitate a discussion on the relevance and usefulness of three hypotheses often cited in studies concerning species diversity and component characteristics of the subtropical/tropical coastal nonreef fish assemblages. Manifestations of the assemblage are reflected in catch composition and weights of 39 trials conducted for a selective prawning gear whose performance in bycatch reduction, mainly for finfishes, is judged by an index, E, we have previously proposed. This gear is capable of harvesting the prawn while conserving the demersal fish. Behavioral responses to netting of the prawns and the finfishes, especially the nearshore surface schoolers such as leiognathids, are discussed from several points of view. An adaptation in terms of group selection for leiognathids of their locking mechanism of median fin spines has been interpreted. For the purpose of bycatch reduction or E enhancement, suggestions for improvements in net design and trawl configuration by considering the behavioral features of fish are made. Our original formula of E is modified for general use. Bycatch problems in the regional prawn fisheries and their possible impacts on fishery planning and development in Papua New Guinea as a developing country are discussed. The gear tested may offer enormous ecological and economic benefits. The gear is multipurpose, extremely simple, and can also be used as a biological sampler.

Les origines biologiques de la musique.

La musique est un comportement humain incontestablement universel, elle demeure néanmoins peu abordée par l’anthropologie. Si les connaissances empiriques accumulées à ce jour ont permis de bien la caractériser à des niveaux proximaux d’analyse, la question de son origine évolutionniste est, en contrepartie, souvent délaissée. Or, toute tentative sérieuse de comprendre ce phénomène requiert une investigation de sa fonction adaptative et de sa phylogénèse. Le projet entrepris ici consiste en une tentative de définition du concept de musique en terme d’universaux, d’une comparaison interspécifique du phénomène et d’un résumé de l’histoire phylogénétique des comportements musicaux, ainsi que d’une analyse de deux modèles portant sur les origines de la musique (Miller, 2000; Mithen, 2006). De ces modèles sont extraites des prévisions qui sont confrontées à des données empiriques provenant de disciplines diverses afin d’évaluer leur valeur scientifique. L’analyse des données disponibles permet de produire un inventaire des universaux musicaux aux plans cognitif, structurel, émotionnel, fonctionnel et symbolique et d’identifier ainsi certaines des bases biologiques du phénomène. Plusieurs mécanismes évolutionnistes, dont la sélection naturelle, la sélection sexuelle, la sélection de groupe et la sélection parentale sont employés par les divers auteurs afin d’expliquer l’apparition du phénomène musical. Il appert que la musique a joué un rôle important dans la relation parent-enfant au cours de l’évolution humaine, de même que dans la cohésion sociale, la coordination des activités et la formation de l’identité de groupe. En ce qui a trait aux deux modèles analysés ici, chacun ne traite que d’une partie des invariants musicaux et leur comparaison permet d’établir qu’ils sont mutuellement exclusifs. En guise de conclusion, nous tentons de formuler un scénario évolutif qui concilie les différentes hypothèses abordées.

Revisión sistemática de estudios descriptivos : tratamiento de fracturas diafisarias antebrazo en niños entre 6 y 12 años

El tratamiento de las fracturas de tercio medio de antebrazo en niños de 6-12 años es controversial, debido a las diferentes opciones de manejo que existen en la actualidad. Objetivo: realizar una revisión sistemática de la literatura para determinar cuál es el mejor tratamiento de las fracturas diafisiarias del tercio medio del antebrazo en niños de 6-12 años. Materiales y métodos: se realizó una búsqueda sistemática y ampliada de estudios descriptivos comparativos sobre los diferentes tratamientos para fracturas tercio medio antebrazo en niños de 6-12 años de edad. Resultados: se identificaron en total 16 artículos, seis de los cuales cumplieron los criterios de inclusión, con cinco diferentes opciones de tratamiento. No se encontraron diferencias en los resultados funcionales de los diferentes tipos de tratamiento y se evidencio un mayor número de complicaciones por angulación de las fracturas en los grupos de tratamiento con clavos endomedulares. Los estudios presentan sesgos de selección y hay varias diferencias en la medición de sus respectivos desenlaces. Conclusiones: la evidencia evaluada en esta revisión sistemática no permite determinar cuál es el mejor tratamiento para este tipo de fracturas, sin importar el tipo de material de osteosíntesis utilizado. Se requieren ensayos clínicos controlados que evalúen los diferentes tipos de tratamiento para poder determinar el mejor manejo de estas.

The information capacity of hypercycles

Hypercycles are information integration systems which are thought to overcome the information crisis of prebiotic evolution by ensuring the coexistence of several short templates. For imperfect template replication, we derive a simple expression for the maximum number of distinct templates n(m). that can coexist in a hypercycle and show that it is a decreasing function of the length L of the templates. In the case of high replication accuracy we find that the product n(m)L tends to a constant value, limiting thus the information content of the hypercycle. Template coexistence is achieved either as a stationary equilibrium (stable fixed point) or a stable periodic orbit in which the total concentration of functional templates is nonzero. For the hypercycle system studied here we find numerical evidence that the existence of an unstable fixed point is a necessary condition for the presence of periodic orbits. (C) 2008 Elsevier Ltd. All rights reserved.

Package models and the information crisis of prebiotic evolution

The coexistence between different types of templates has been the choice solution to the information crisis of prebiotic evolution, triggered by the finding that a single RNA-like template cannot carry enough information to code for any useful replicase. In principle, confining d distinct templates of length L in a package or protocell, whose Survival depends on the coexistence of the templates it holds in, could resolve this crisis provided that d is made sufficiently large. Here we review the prototypical package model of Niesert et al. [1981. Origin of life between Scylla and Charybdis. J. Mol. Evol. 17, 348-353] which guarantees the greatest possible region of viability of the protocell population, and show that this model, and hence the entire package approach, does not resolve the information crisis. In particular, we show that the total information stored in a viable protocell (Ld) tends to a constant value that depends only on the spontaneous error rate per nucleotide of the template replication mechanism. As a result, an increase of d must be followed by a decrease of L, so that the net information gain is null. (C) 2008 Elsevier Ltd. All rights reserved.

A quasispecies approach to the evolution of sexual replication in unicellular organisms

This study develops a simplified model describing the evolutionary dynamics of a population composed of obligate sexually and asexually reproducing, unicellular organisms. The model assumes that the organisms have diploid genomes consisting of two chromosomes, and that the sexual organisms replicate by first dividing into haploid intermediates, which then combine with other haploids, followed by the normal mitotic division of the resulting diploid into two new daughter cells. We assume that the fitness landscape of the diploids is analogous to the single-fitness-peak approach often used in single-chromosome studies. That is, we assume a master chromosome that becomes defective with just one point mutation. The diploid fitness then depends on whether the genome has zero, one, or two copies of the master chromosome. We also assume that only pairs of haploids with a master chromosome are capable of combining so as to produce sexual diploid cells, and that this process is described by second-order kinetics. We find that, in a range of intermediate values of the replication fidelity, sexually reproducing cells can outcompete asexual ones, provided the initial abundance of sexual cells is above some threshold value. The range of values where sexual reproduction outcompetes asexual reproduction increases with decreasing replication rate and increasing population density. We critically evaluate a common approach, based on a group selection perspective, used to study the competition between populations and show its flaws in addressing the evolution of sex problem.

Solvable model for template coexistence in protocells

Compartmentalization of self-replicating molecules (templates) in protocells is a necessary step towards the evolution of modern cells. However, coexistence between distinct template types inside a protocell can be achieved only if there is a selective pressure favoring protocells with a mixed template composition. Here we study analytically a group selection model for the coexistence between two template types using the diffusion approximation of population genetics. The model combines competition at the template and protocell levels as well as genetic drift inside protocells. At the steady state, we find a continuous phase transition separating the coexistence and segregation regimes, with the order parameter vanishing linearly with the distance to the critical point. In addition, we derive explicit analytical expressions for the critical steadystate probability density of protocell compositions.

Promoting Biodiversity in Forest Ecosystems Using Ecological Forestry

A subset of forest management techniques, termed ecological forestry, have been developed in order to produce timber and maintain the ecological integrity of forest communities through practices that more closely mirror natural disturbance regimes. Even though alternative methods have been described and tested, these approaches still need to be established and analyzed in a variety of geographic regions in order to calibrate and measure effectiveness across different forest types. The primary objective of this research project was to assess whether group selection combined with legacy-tree retention could enhance mid-tolerant tree recruitment in a late-successional northern hardwood forest. In order to evaluate a novel alternative regeneration technique, 49 group-selection openings in three size classes were created in 2003 with a biological legacy tree retained in the center of each opening. Twenty reference sites, managed using single-tree selection, were also analyzed for comparison. The specific goals of the project were to: 1) determine the fate and persistence of the openings and legacy trees 2) assess the understory response of the group-selection openings versus the single-tree selection reference sites, and 3) evaluate the spatial patterns of yellow birch (Betula alleghaniensis Britt.) and eastern hemlock (Tsuga canadensis (L.) Carr.) in the group-selection openings. The results from 8-9 years post-study implementation and the changes that have occurred between 2004/5 and 2011/12 are discussed. The alternative regeneration technique developed and assessed in this study has the potential to enrich biodiversity in a range of forest types. Projected group-selection opening persistence rates ranged from 41-91 years. Openings from 500-1500 m2 are predicted to persist long enough for mid-tolerant tree recruitment. The legacy trees responded well to release and experienced a low mortality rate. Yellow birch (the primary shade mid-tolerant tree in the study area) densities increased with opening size. Maples surpassed all other species in abundance. In the sapling layer, sugar maple (Acer saccharum Marsh.) was 2 to over 300 times more abundant in the group-selection openings and 2 to 3 times more abundant in the references sites than all other species present. Red maple (Acer rubrum L.) was the second most abundant species present in the openings and reference sites. Spatial patterns of yellow birch and eastern hemlock in the openings were mostly aggregated. The southern edges of the largest openings contained the highest magnitude of yellow birch and eastern hemlock per unit area. Continued monitoring and additional treatments will likely be necessary in order to ensure underrepresented species successfully reach maturity.

Essays on robust mechanism design

Chapter 1: Under the average common value function, we select almost uniquely the mechanism that gives the seller the largest portion of the true value in the worst situation among all the direct mechanisms that are feasible, ex-post implementable and individually rational. Chapter 2: Strategy-proof, budget balanced, anonymous, envy-free linear mechanisms assign p identical objects to n agents. The efficiency loss is the largest ratio of surplus loss to efficient surplus, over all profiles of non-negative valuations. The smallest efficiency loss is uniquely achieved by the following simple allocation rule: assigns one object to each of the p−1 agents with the highest valuation, a large probability to the agent with the pth highest valuation, and the remaining probability to the agent with the (p+1)th highest valuation. When “envy freeness” is replaced by the weaker condition “voluntary participation”, the optimal mechanism differs only when p is much less than n. Chapter 3: One group is to be selected among a set of agents. Agents have preferences over the size of the group if they are selected; and preferences over size as well as the “stand-outside” option are single-peaked. We take a mechanism design approach and search for group selection mechanisms that are efficient, strategy-proof and individually rational. Two classes of such mechanisms are presented. The proposing mechanism allows agents to either maintain or shrink the group size following a fixed priority, and is characterized by group strategy-proofness. The voting mechanism enlarges the group size in each voting round, and achieves at least half of the maximum group size compatible with individual rationality.

Plano de intervenção para combater e evitar a obesidade infantil

A obesidade é uma doença crónica, reincidente e multifactorial, que apresenta grandes riscos para a saúde e que se torna bastante dispendiosa nas contas do estado. Tem-se verificado uma preocupação crescente sobre a relação de uma alimentação desequilibrada durante a infância e a manifestação de determinadas doenças na idade adulta. Na infância a criança passa por um período de grande desenvolvimento físico, marcado pelo gradual crescimento em altura e do peso e é também um período onde se desenvolve psicologicamente, envolvendo graduais mudanças no comportamento e na aquisição das bases da sua personalidade. A população alvo é constituída pelos indivíduos com ≤ 19 anos de idade, inscritos no Centro de Saúde de Mação, a selecção do grupo foi feita tendo em conta a acessibilidade dos dados. Então optou-se pela consulta e recolha dos 98 exames globais de saúde efectuados nos anos 2009 e 2010, tendo sido recolhidos os seguintes dados: género, idade, peso e altura. O presente estudo mostra que o IMC das crianças na sua grande maioria não é o desejado, ou porque se encontra abaixo ou acima do peso desejável. A problemática da obesidade é actual, com repercussões incalculáveis para o futuro, é tempo de agir. Como resultado desta vontade surge o Põe-te na linha, que é um projecto de combate à obesidade dos jovens, onde através de grupos de entre ajuda vão ser utilizadas dinâmicas de grupo.

La notion de l’explosion de la coopération et ses implications chez Kim Sterelny.

Le concept de coopération est souvent utilisé dans le domaine de l’éthique et de la politique pour illustrer et comprendre l’alignement des comportements associatifs entre les êtres humains. En lien avec ce concept, notre recherche portera sur la première question de savoir si Kim Sterelny (2003) réussit à produire un modèle théorique permettant d’expliquer les origines et les mécanismes de la coopération humaine. Notre recherche portera aussi sur la deuxième question de savoir s’il arrive à se servir de ce modèle pour infirmer la thèse de la modularité massive. Ainsi, ce mémoire traitera successivement du problème de la coopération, de la théorie de la sélection de groupe, du déclencheur écologique de la coopération des hominidés, des notions de coalition, d’exécution et d’engagement et finalement de la thèse de la modularité massive. Par l’examen de ces sujets, nous souhaitons démontrer que Sterelny n’arrive qu’à fournir une esquisse probable des origines et du développement de la coopération humaine et que sa critique de la thèse de la modularité massive n’arrive pas à infirmer cette dernière.