Database construction and Peptide identification strategies for proteogenomic studies on sequenced genomes.

Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene product( s). Mass-spectrometry based proteomics provides the necessary high throughput technology to show evidences of protein presence and, from the identified sequences, confirmation or invalidation of predicted annotations. We review here different strategies used to perform a MS-based proteogenomics experiment with a bottom-up approach. We start from the strengths and weaknesses of the different database construction strategies, based on different genomic information (whole genome, ORF, cDNA, EST or RNA-Seq data), which are then used for matching mass spectra to peptides and proteins. We also review the important points to be considered for a correct statistical assessment of the peptide identifications. Finally, we provide references for tools used to map and visualize the peptide identifications back to the original genomic information.

The credit ratings game

The collapse of so many AAA-rated structured finance products in 2007-2008has brought renewed attention to the causes of ratings failures and the conflicts of interestin the Credit Ratings Industry. We provide a model of competition among Credit RatingsAgencies (CRAs) in which there are three possible sources of conflicts: 1) the CRA conflictof interest of understating credit risk to attract more business; 2) the ability of issuersto purchase only the most favorable ratings; and 3) the trusting nature of some investorclienteles who may take ratings at face value. We show that when combined, these give riseto three fundamental equilibrium distortions. First, competition among CRAs can reducemarket efficiency, as competition facilitates ratings shopping by issuers. Second, CRAs aremore prone to inflate ratings in boom times, when there are more trusting investors, andwhen the risks of failure which could damage CRA reputation are lower. Third, the industrypractice of tranching of structured products distorts market efficiency as its role is to deceivetrusting investors. We argue that regulatory intervention requiring: i) upfront paymentsfor rating services (before CRAs propose a rating to the issuer), ii) mandatory disclosure ofany rating produced by CRAs, and iii) oversight of ratings methodology can substantiallymitigate ratings inflation and promote efficiency.

Appraising and selecting strategies to combat and mitigate desertification based on stakeholder knowledge and globalbest practices in Cape Verde Archipelago

Cape Verde is considered part of Sahelian Africa, where drought and desertification are common occurrences. The main activity of the rural population is rain-fed agriculture, which over time has been increasingly challenged by high temporal and spatial rainfall variability, lack of inputs, limited land area, fragmentation of land, steep slopes, pests, lack of mechanization and loss of top soil by water erosion. Human activities, largely through poor farming practices and deforestation (Gomez, 1989) have accelerated natural erosion processes, shifting the balance between soil erosion and soil formation (Norton, 1987). According to previous studies, vegetation cover is one of the most important factors in controlling soil loss (Cyr et al., 1995; Hupy, 2004; Zhang et al., 2004; Zhou et al., 2006). For this reason, reforestation is a touchstone of the Cape Verdean policy to combat desertification. After Independence in 1975, the Cape Verde government had pressing and closely entangled environmental and socio-economic issues to address, as long-term desertification had resulted in a lack of soil cover, severe soil erosion and a scarcity of water resources and fuel wood. Across the archipelago, desertification was resulting from a variety of processes including poor farming practices, soil erosion by water and wind, soil and water salinity in coastal areas due to over pumping and seawater intrusion, drought and unplanned urbanization (DGA-MAAP, 2004). All these issues directly affected socio-economic vulnerability in rural areas, where about 70% of people depended directly or indirectly on agriculture in 1975. By becoming part of the Inter- State Committee for the Fight against Drought in the Sahel in 1975, the government of Cape Verde gained structured support to address these issues more efficiently. Presentday policies and strategies were defined on the basis of rational use of resources and human efforts and were incorporated into three subsequent national plans: the National Action Plan for Development (NDP) (1982–1986), the NDP (1986–1990) and the NDP (1991–1995) (Carvalho

The impact of gender composition on team performance and decision-making: Evidence from the field

We investigate whether the gender composition of teams affect theireconomic performance. We study a large business game, played in groups ofthree, where each group takes the role of a general manager. There are twoparallel competitions, one involving undergraduates and the other involvingMBAs. Our analysis shows that teams formed by three women aresignificantly outperformed by any other gender combination, both at theundergraduate and MBA levels. Looking across the performancedistribution, we find that for undergraduates, three women teams areoutperformed throughout, but by as much as 10pp at the bottom and by only1pp at the top. For MBAs, at the top, the best performing group is two menand one woman. The differences in performance are explained bydifferences in decision-making. We observe that three women teams are lessaggressive in their pricing strategies, invest less in R&D, and invest more insocial sustainability initiatives, than any other gender combination teams.Finally, we find support for the hypothesis that it is poor work dynamicsamong the three women teams that drives the results.

On p-beauty contest integer games

In this paper we provide a full characterization of the pure-strategyNash Equilibria for the p-Beauty Contest Game when we restrict player schoices to integer numbers. Opposed to the case of real number choices,equilibrium uniqueness may be lost depending on the value of p and thenumber of players: in particular, as p approaches 1 any symmetric profileconstitutes a Nash Equilibrium. We also show that any experimental p-BeautyContest Game can be associated to a game with the integer restriction andthus multiplicity of equilibria becomes an issue. Finally, we show thatin these games the iterated deletion of weakly dominated strategies maynot lead to a single outcome while the iterated best-reply process alwaysdoes (though the outcome obtained depends on the initial conditions).

Impact of a board-game approach on current smokers: a randomized controlled trial.

ABSTRACT: BACKGROUND: The main objective of our study was to assess the impact of a board game on smoking status and smoking-related variables in current smokers. To accomplish this objective, we conducted a randomized controlled trial comparing the game group with a psychoeducation group and a waiting-list control group. METHODS: The following measures were performed at participant inclusion, as well as after a 2-week and a 3-month follow-up period: "Attitudes Towards Smoking Scale" (ATS-18), "Smoking Self-Efficacy Questionnaire" (SEQ-12), "Attitudes Towards Nicotine Replacement Therapy" scale (ANRT-12), number of cigarettes smoked per day, stages of change, quit attempts, and smoking status. Furthermore, participants were assessed for concurrent psychiatric disorders and for the severity of nicotine dependence with the Fagerström Test for Nicotine Dependence (FTND). RESULTS: A time × group effect was observed for subscales of the ANRT-12, ATS-18 and SEQ-12, as well as for the number of cigarettes smoked per day. At three months follow-up, compared to the participants allocated to the waiting list group, those on Pick-Klop group were less likely to remain smoker.Outcomes at 3 months were not predicted by gender, age, FTND, stage of change, or psychiatric disorders at inclusion. CONCLUSIONS: The board game seems to be a good option for smokers. The game led to improvements in variables known to predict quitting in smokers. Furthermore, it increased smoking-cessation rates at 3-months follow-up. The game is also an interesting alternative for smokers in the precontemplation stage.

Soil and Water Conservation Strategies in Cape Verde (Cabo Verde in Portuguese) and Their Impacts on Livelihoods - An Overview from the Ribeira Seca Watershed

Severe land degradation has strongly affected both people’s livelihood and the environment in Cape Verde (Cabo Verde in Portuguese), a natural resource poor country. Despite the enormous investment in soil and water conservation measures (SWC or SLM), which are visible throughout the landscape, and the recognition of their benefits, their biophysical and socioeconomic impacts have been poorly assessed and scientifically documented. This paper contributes to filling this gap, by bringing together insights from literature and policy review, field survey and participatory assessment in the Ribeira Seca Watershed through a concerted approach devised by the DESIRE project (the “Desire approach”). Specifically, we analyze government strategies towards building resilience against the harsh conditions, analyze the state of land degradation and its drivers, survey and map the existing SWC measures, and assess their effectiveness against land degradation, on crop yield and people’s livelihood. We infer that the relative success of Cape Verde in tackling desertification and rural poverty owes to an integrated governance strategy that comprises raising awareness, institutional framework development, financial resource allocation, capacity building, and active participation of rural communities. We recommend that specific, scientific-based monitoring and assessment studies be carried out on the biophysical and socioeconomic impact of SLM and that the “Desire approach” be scaled-up to other watersheds in the country.

Emergence of Cooperation on Static and Dynamic Networks

Game theory is a branch of applied mathematics used to analyze situation where two or more agents are interacting. Originally it was developed as a model for conflicts and collaborations between rational and intelligent individuals. Now it finds applications in social sciences, eco- nomics, biology (particularly evolutionary biology and ecology), engineering, political science, international relations, computer science, and philosophy. Networks are an abstract representation of interactions, dependencies or relationships. Net- works are extensively used in all the fields mentioned above and in many more. Many useful informations about a system can be discovered by analyzing the current state of a network representation of such system. In this work we will apply some of the methods of game theory to populations of agents that are interconnected. A population is in fact represented by a network of players where one can only interact with another if there is a connection between them. In the first part of this work we will show that the structure of the underlying network has a strong influence on the strategies that the players will decide to adopt to maximize their utility. We will then introduce a supplementary degree of freedom by allowing the structure of the population to be modified along the simulations. This modification allows the players to modify the structure of their environment to optimize the utility that they can obtain.

Stochastic evolution of rules for playing normal form games

The evolution of boundedly rational rules for playing normal form games is studied within stationary environments ofstochastically changing games. Rules are viewed as algorithms prescribing strategies for the different normal formgames that arise. It is shown that many of the folk results of evolutionary game theory typically obtained witha fixed game and fixed strategies carry over to the present case. The results are also related to recent experimentson rules and games.

Historical contingency affects signaling strategies and competitive abilities in evolving populations of simulated robots.

One of the key innovations during the evolution of life on earth has been the emergence of efficient communication systems, yet little is known about the causes and consequences of the great diversity within and between species. By conducting experimental evolution in 20 independently evolving populations of cooperatively foraging simulated robots, we found that historical contingency in the occurrence order of novel phenotypic traits resulted in the emergence of two distinct communication strategies. The more complex foraging strategy was less efficient than the simpler strategy. However, when the 20 populations were placed in competition with each other, the populations with the more complex strategy outperformed the populations with the less complex strategy. These results demonstrate a tradeoff between communication efficiency and robustness and suggest that stochastic events have important effects on signal evolution and the outcome of competition between distinct populations.

Social value orientation as a moral intuition: Decision-making in the dictator game

We studied the decision making process in the Dictator Game and showed that decisions are the result of a two-step process. In a first step, decision makers generate an automatic, intuitive proposal. Given sufficient motivation and cognitive resources, they adjust this in a second, more deliberated phase. In line with the social intuitionist model, we show that one s Social Value Orientation determines intuitive choice tendencies in the first step, and that this effect is mediated by the dictator s perceived interpersonal closeness with the receiver. Self-interested concerns subsequently leadto a reduction of donation size in step 2. Finally, we show that increasing interpersonal closeness can promote pro-social decision-making.

First price auctions: Monotonicity and uniqueness

I study monotonicity and uniqueness of the equilibrium strategies in a two-person first price auction with affiliated signals. I show thatwhen the game is symmetric there is a unique Nash equilibrium thatsatisfies a regularity condition requiring that the equilibrium strategies be{\sl piecewise monotone}. Moreover, when the signals are discrete-valued, the equilibrium is unique. The central part of the proof consists of showing that at any regular equilibrium the bidders' strategies must be monotone increasing within the support of winning bids. The monotonicity result derived in this paper provides the missing link for the analysis of uniqueness in two-person first price auctions. Importantly, this result extends to asymmetric auctions.

Complementarity between technology make and buy in innovation strategies: Evidence from Belgiam manufacturing firms

This paper characterizes the innovation strategy of manufacturing firms andexamines the relation between the innovation strategy and importantindustry-, firm- and innovation-specific characteristics using Belgiandata from the Eurostat Community Innovation Survey. In addition to importantsize effects explaining innovation, we find that high perceived risks andcosts and low appropriability of innovations do not discourage innovation,but rather determine how the innovation sourcing strategy is chosen. Withrespect to the determinants of the decision of the innovative firm toproduce technology itself (Make) or to source technology externally (Buy),we find that small firms are more likely restrict their innovation strategyto an exclusive make or buy strategy, while large firms are more likely tocombine both internal and external knowledge acquisition in their innovationstrategy. An interesting result that highlights the complementary nature ofthe Make and Buy decisions, is that, controlled for firm size, companies forwhich internal information is an important source for innovation are morelikely to combine internal and external sources of technology. We find thisto be evidence of the fact that in-house R&D generates the necessaryabsorptive capacity to profit from external knowledge acquisition. Also theeffectiveness of different mechanisms to appropriate the benefits ofinnovations and the internal organizational resistance against change areimportant determinants of the firm's technology sourcing strategy.