Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Neither Bad Apple nor Bad Barrel: How the Societal Context Impacts Unethical Behavior in Organizations

Every time another corporate scandal captures media headlines, the 'bad apple vs. bad barrel' discussion starts anew. Yet this debate overlooks the influence of the broader societal context on organizational behavior. In this article, we argue that misbehaviors of organizations (the 'barrels') and their members (the 'apples') cannot be addressed properly without a clear understanding of their broader context (the 'larder'). Whereas previously, a strong societal framework dampened the practical application of the Homo economicus concept (business actors as perfectly rational and egocentric utility-maximizing agents without any moral concern), specialization, individualization and globalization led to a business world disembedded from broader societal norms. This emancipated business world promotes a literal interpretation of Homo economicus among business organizations and their members. Consequently, we argue that the first step toward 'healthier' apples and barrels is to sanitize the larder, that is, adapt the framework in which organizations and their members evolve.Chaque fois qu'un nouveau scandale fait la une des médias, la question de savoir si le problème se situe au niveau des individus (des 'pommes isolées') ou au niveau des organisations (les 'caisses de pommes') refait surface. Ce débat tend néanmoins à sous-estimer l'influence du contexte sociétal plus large sur le comportement dans les organisations. Dans cet article, nous soutenons l'idée que les scandales éthiques dans les organisations ou parmi leurs membres ne peuvent être compris correctement sans une vision plus précise de leur contexte plus large (la 'cave à pommes'). Si dans le passé un contexte sociétal fort permettait d'adoucir les applications pratiques de l'Homo economicus (qui considère l'acteur économique comme un agent parfaitement rationnel et égocentrique cherchant à maximiser son utilité sans réflexion morale), l'individualisation et la globalisation ont conduit à un monde économique désencastré et déconnecté des normes sociales plus larges. Ce monde économique autonome promouvoit une interprétation littérale de l'Homo economicus parmi les entreprises et leurs employés. Il en résulte que le premier pas vers des pommes moins pourries passe par un assainissement de la cave, c'est-à-dire l'adoption d'un cadre socio-normatif qui permet un recadrage du contexte dans lequel les organisations économiques et leurs acteurs agissent.

Implantación CRM en un club deportivo

La propuesta CRM que se pretende ofrecer consiste en una herramienta estratégica de negocio para gestionar las relaciones con los clientes. La aplicación está desarrollada bajo un prisma Siebel para un determinado club deportivo. Esta herramienta ha de permitir estudiar todas las posibles oportunidades de negocio cubriendo la necesidad de saber en cualquier momento la circunstancia personalizada de cada cliente (socio o no socio) y de sus trámites. El objetivo fundamental del CRM es lograr la fidelización del cliente maximizando los recursos utilizados, mejorar los servicios ofrecidos en un grado óptimo y aumentar la cuenta de resultados. Para ello se plantea implantar una aplicación totalmente configurada y adaptada a las necesidades de un club deportivo.

Reducing the Risk: A Strategic Approach - The Report of the Task Force on Sudden Cardiac Death

The Minister for Health and Children established the Task Force on Sudden Cardiac Death (SCD) in the Autumn of 2004, with the following terms of reference:1) Define SCD and describe its incidence and underlying causes in Ireland.2) Advise on the detection and assessment of those at high risk of SCD and their relatives.3) Advise on the systematic assessment of those engaged in sports and exercise for risk of SCD.4) Advise on maximizing access to basic life support (BLS) and automated external defibrillators (AEDs) and on:- appropriate levels of training in BLS and use of AEDs, and on the maintenance of that training- priority individuals and priority groups for such training- geographic areas and functional locations of greatest need- best practice models of first responder scheme and public access defibrillation, and- integration of such training services.5) Advise on the establishment and maintenance of surveillance systems, including a registry of SCD and information systems to monitor risk assessment, and training and equipment programmes.6) Advise and make recommendations on other priority issues relevant to SCD in Ireland.7) Outline a plan for implementation and advise on monitoring the implementation of recommendations made in the Task Force’s report. In undertaking its work the Task Force was mindful of national health policy, relevant national strategies and of the recently reformed structures for health service delivery in Ireland. Read the Report (PDF, 1.66mb)

Is (1→3)-β-D-glucan the missing link from bedside assessment to pre-emptive therapy of invasive candidiasis?

ABSTRACT: Invasive candidiasis is a frequent life-threatening complication in critically ill patients. Early diagnosis followed by prompt treatment aimed at improving outcome by minimizing unnecessary antifungal use remains a major challenge in the ICU setting. Timely patient selection thus plays a key role for clinically efficient and cost-effective management. Approaches combining clinical risk factors and Candida colonization data have improved our ability to identify such patients early. While the negative predictive value of scores and predicting rules is up to 95 to 99%, the positive predictive value is much lower, ranging between 10 and 60%. Accordingly, if a positive score or rule is used to guide the start of antifungal therapy, many patients may be treated unnecessarily. Candida biomarkers display higher positive predictive values; however, they lack sensitivity and are thus not able to identify all cases of invasive candidiasis. The (1→3)-β-D-glucan (BG) assay, a panfungal antigen test, is recommended as a complementary tool for the diagnosis of invasive mycoses in high-risk hemato-oncological patients. Its role in the more heterogeneous ICU population remains to be defined. More efficient clinical selection strategies combined with performant laboratory tools are needed in order to treat the right patients at the right time by keeping costs of screening and therapy as low as possible. The new approach proposed by Posteraro and colleagues in the previous issue of Critical Care meets these requirements. A single positive BG value in medical patients admitted to the ICU with sepsis and expected to stay for more than 5 days preceded the documentation of candidemia by 1 to 3 days with an unprecedented diagnostic accuracy. Applying this one-point fungal screening on a selected subset of ICU patients with an estimated 15 to 20% risk of developing candidemia is an appealing and potentially cost-effective approach. If confirmed by multicenter investigations, and extended to surgical patients at high risk of invasive candidiasis after abdominal surgery, this Bayesian-based risk stratification approach aimed at maximizing clinical efficiency by minimizing health care resource utilization may substantially simplify the management of critically ill patients at risk of invasive candidiasis.

Life history analysis of integrative and conjugative element activation in growing microcolonies of Pseudomonas.

Integrative and conjugative elements (ICE) are in some ways parasitic mobile DNA that propagate vertically through replication with the bacterial host chromosome but at low frequencies can excise and invade new recipient cells through conjugation and reintegration (horizontal propagation). The factors that contribute to successful horizontal propagation are not very well understood. Here, we study the influence of host cell life history on the initiation of transfer of a model ICE named ICEclc in bacteria of the genus Pseudomonas. We use time-lapse microscopy of growing and stationary-phase microcolonies of ICEclc bearing cells in combination with physiological staining and gene reporter analysis in stationary-phase suspended cells. We provide evidence that cell age and cell lineage are unlikely to play a role in the decision to initiate the ICEclc transfer program. In contrast, cells activating ICEclc show more often increased levels of reactive oxygen species and membrane damage than nonactivating cells, suggesting that some form of biochemical damage may make cells more prone to ICEclc induction. Finally, we find that ICEclc active cells appear spatially at random in a microcolony, which may have been a selective advantage for maximizing ICEclc horizontal transmission to new recipient species.

Older people's views of falls-prevention interventions in six European countries.

PURPOSE: Our study identified factors common to a variety of populations and settings that may promote or inhibit uptake and adherence to falls-related interventions. DESIGN AND METHODS: Semistructured interviews to assess perceived advantages and barriers to taking part in falls-related interventions were carried out in six European countries with 69 people aged 68 to 97 years. The sample was selected to include people with very different experiences of participation or nonparticipation in falls-related interventions, but all individuals were asked about interventions that included strength and balance training. RESULTS: Attitudes were similar in all countries and contexts. People were motivated to participate in strength and balance training by a wide range of perceived benefits (interest and enjoyment, improved health, mood, and independence) and not just reduction of falling risk. Participation also was encouraged by a personal invitation from a health practitioner and social approval from family and friends. Barriers to participation included denial of falling risk, the belief that no additional falls-prevention measures were necessary, practical barriers to attendance at groups (e.g., transport, effort, and cost), and a dislike of group activities. IMPLICATIONS: Because many older people reject the idea that they are at risk of falling, the uptake of strength and balance training programs may be promoted more effectively by maximizing and emphasizing their multiple positive benefits for health and well-being. A personal invitation from a health professional to participate is important, and it also may be helpful to provide home-based programs for those who dislike or find it difficult to attend groups.

Does it pay to be socially responsible? Evidence from spanish retail banking sector

This paper presents a theoretical and empirical analysis of strategic competition in retail banking when some of the financial firms are non-profit organisations that invest in social activities. Banking literature about competition is fairly large, but the strategic interaction between profit maximizing and non profit maximizers has not been extensively analysed except for Purroy and Salas (1999). In this paper, a completely different approach is taken. An adaptation of Hotelling’s two stage model of spatial competition is developed to take into account consumer perceptions respect to the two different types of financial institutions. The empirical analysis confirms that consumers take into account other features different from the price, such as social contribution or closer service to make a deposit or mortgage decision. These conclusions are of interest in the debate about a firm’s social or ethical activities. It is shown that if consumers value social activities, firms can improv

Interpreting social enterprises

Institutional and organizational variety is increasingly characterizing advanced economic systems. While traditional economic theories have focused almost exclusively on profit-maximizing (i.e., for-profit) enterprises and on publicly-owned organizations, the increasing relevance of non-profit organizations, and especially of social enterprises, requires scientists to reflect on a new comprehensive economic approach for explaining this organizational variety. This paper examines the main limitations of the orthodox and institutional theories and asserts the need for creating and testing a new theoretical framework, which considers the way in which diverse enterprises pursue their goals, the diverse motivations driving actors and organizations, and the different learning patterns and routines within organizations. The new analytical framework proposed in the paper draws upon recent developments in the theories of the firm, mainly of an evolutionary and behavioral kind. The firm is interpreted as a coordination mechanism of economic activity, and one whose objectives need not coincide with profit maximization. On the other hand, economic agents driven by motivational complexity and intrinsic, non-monetary motivation play a crucial role in forming firm activity over and above purely monetary and financial objectives. The new framework is thought to be particularly suitable to correctly interpret the emergence and role of nontraditional organizational and ownership forms that are not driven by the profit motive (non-profit organizations), mainly recognized in the legal forms of cooperative firms, non-profit organizations and social enterprises. A continuum of organizational forms ranging from profit making activities to public benefit activities, and encompassing mutual benefit organizations as its core constituent, is envisaged and discussed.

Fitness, inclusive fitness, and optimization

Individual-as-maximizing agent analogies result in a simple understanding of the functioning of the biological world. Identifying the conditions under which individuals can be regarded as fitness maximizing agents is thus of considerable interest to biologists. Here, we compare different concepts of fitness maximization, and discuss within a single framework the relationship between Hamilton's (J Theor Biol 7: 1-16, 1964) model of social interactions, Grafen's (J Evol Biol 20: 1243-1254, 2007a) formal Darwinism project, and the idea of evolutionary stable strategies. We distinguish cases where phenotypic effects are additive separable or not, the latter not being covered by Grafen's analysis. In both cases it is possible to define a maximand, in the form of an objective function phi(z), whose argument is the phenotype of an individual and whose derivative is proportional to Hamilton's inclusive fitness effect. However, this maximand can be identified with the expression for fecundity or fitness only in the case of additive separable phenotypic effects, making individual-as-maximizing agent analogies unattractive (although formally correct) under general situations of social interactions. We also feel that there is an inconsistency in Grafen's characterization of the solution of his maximization program by use of inclusive fitness arguments. His results are in conflict with those on evolutionary stable strategies obtained by applying inclusive fitness theory, and can be repaired only by changing the definition of the problem.

Extremal principle of entropy production in the climate system

Paltridge found reasonable values for the most significant climatic variables through maximizing the material transport part of entropy production by using a simple box model. Here, we analyse Paltridge's box model to obtain the energy and the entropy balance equations separately. Derived expressions for global entropy production, which is a function of the radiation field, and even its material transport component, are shown to be different from those used by Paltridge. Plausible climatic states are found at extrema of these parameters. Feasible results are also obtained by minimizing the radiation part of entropy production, in agreement with one of Planck's results, Finally, globally averaged values of the entropy flux of radiation and material entropy production are obtained for two dynamical extreme cases: an earth with uniform temperature, and an earth in radiative equilibrium at each latitudinal point

Stochastic stability and the evolution of coordination in spatially structured populations.

Animals can often coordinate their actions to achieve mutually beneficial outcomes. However, this can result in a social dilemma when uncertainty about the behavior of partners creates multiple fitness peaks. Strategies that minimize risk ("risk dominant") instead of maximizing reward ("payoff dominant") are favored in economic models when individuals learn behaviors that increase their payoffs. Specifically, such strategies are shown to be "stochastically stable" (a refinement of evolutionary stability). Here, we extend the notion of stochastic stability to biological models of continuous phenotypes at a mutation-selection-drift balance. This allows us to make a unique prediction for long-term evolution in games with multiple equilibria. We show how genetic relatedness due to limited dispersal and scaled to account for local competition can crucially affect the stochastically-stable outcome of coordination games. We find that positive relatedness (weak local competition) increases the chance the payoff dominant strategy is stochastically stable, even when it is not risk dominant. Conversely, negative relatedness (strong local competition) increases the chance that strategies evolve that are neither payoff nor risk dominant. Extending our results to large multiplayer coordination games we find that negative relatedness can create competition so extreme that the game effectively changes to a hawk-dove game and a stochastically stable polymorphism between the alternative strategies evolves. These results demonstrate the usefulness of stochastic stability in characterizing long-term evolution of continuous phenotypes: the outcomes of multiplayer games can be reduced to the generic equilibria of two-player games and the effect of spatial structure can be analyzed readily.

GeneID in "Drosophila"

GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the log-likelihood ratio of a Markov model for coding DNA. In the last step, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. In this paper we describe the obtention of PWMs for sites, and the Markov model of coding DNA in Drosophila melanogaster. We also compare other models of coding DNA with the Markov model. Finally, we present and discuss the results obtained when GeneID is used to predict genes in the Adh region. These results show that the accuracy of GeneID predictions compares currently with that of other existing tools but that GeneID is likely to be more efficient in terms of speed and memory usage.

What can spike train distances tell us about the neural code?

Time scale parametric spike train distances like the Victor and the van Rossum distancesare often applied to study the neural code based on neural stimuli discrimination.Different neural coding hypotheses, such as rate or coincidence coding,can be assessed by combining a time scale parametric spike train distance with aclassifier in order to obtain the optimal discrimination performance. The time scalefor which the responses to different stimuli are distinguished best is assumed to bethe discriminative precision of the neural code. The relevance of temporal codingis evaluated by comparing the optimal discrimination performance with the oneachieved when assuming a rate code.We here characterize the measures quantifying the discrimination performance,the discriminative precision, and the relevance of temporal coding. Furthermore,we evaluate the information these quantities provide about the neural code. Weshow that the discriminative precision is too unspecific to be interpreted in termsof the time scales relevant for encoding. Accordingly, the time scale parametricnature of the distances is mainly an advantage because it allows maximizing thediscrimination performance across a whole set of measures with different sensitivitiesdetermined by the time scale parameter, but not due to the possibility toexamine the temporal properties of the neural code.

Correlations between imatinib pharmacokinetics, pharmacodynamics, adherence, and clinical response in advanced metastatic gastrointestinal stromal tumor (GIST): An emerging role for drug blood level testing?

Imatinib is the standard of care for patients with advanced metastatic gastrointestinal stromal tumors (GIST), and is also approved for adjuvant treatment in patients at substantial risk of relapse. Studies have shown that maximizing benefit from imatinib depends on long-term administration at recommended doses. Pharmacokinetic (PK) and pharmacodynamic factors, adherence, and drug-drug interactions can affect exposure to imatinib and impact clinical outcomes. This article reviews the relevance of these factors to imatinib's clinical activity and response in the context of what has been demonstrated in chronic myelogenous leukemia (CML), and in light of new data correlating imatinib exposure to response in patients with GIST. Because of the wide inter-patient variability in drug exposure with imatinib in both CML and GIST, blood level testing (BLT) may play a role in investigating instances of suboptimal response, unusually severe toxicities, drug-drug interactions, and suspected non-adherence. Published clinical data in CML and in GIST were considered, including data from a PK substudy of the B2222 trial correlating imatinib blood levels with clinical responses in patients with GIST. Imatinib trough plasma levels <1100ng/mL were associated with lower rates of objective response and faster development of progressive disease in patients with GIST. These findings have been supported by other analyses correlating free imatinib (unbound) levels with response. These results suggest a future application for imatinib BLT in predicting and optimizing therapeutic response. Nevertheless, early estimates of threshold imatinib blood levels must be confirmed prospectively in future studies and elaborated for different patient subgroups.