Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations

Background: Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both.Results: Here, we present and demonstrate a theory to split the knowledge-based potentials in scoring terms biologically meaningful and to combine them in new scores to predict near-native structures. Our strategy allows circumventing the problem of defining the reference state. In this approach we give the proof for a simple and linear application that can be further improved by optimizing the combination of Zscores. Using the simplest composite score () we obtained predictions similar to state-of-the-art methods. Besides, our approach has the advantage of identifying the most relevant terms involved in the stability of the protein structure. Finally, we also use the composite Zscores to assess the conformation of models and to detect local errors.Conclusion: We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations.

Eliciting and fostering learners' metacognitive knowledge about language learning in self-directed learning programs: a review of data collection methods and procedures

Són molts els estudis que avui en dia incideixen en la necessitat d’oferir un suport metodològic i psicològic als aprenents que treballen de manera autònoma. L’objectiu d’aquest suport és ajudar-los a desenvolupar les destreses que necessiten per dirigir el seu aprenentatge així com una actitud positiva i una major conscienciació envers aquest aprenentatge. En definitiva, aquests dos tipus de preparació es consideren essencials per ajudar els aprenents a esdevenir més autònoms i més eficients en el seu propi aprenentatge. Malgrat això, si bé és freqüent trobar estudis que exemplifiquen aplicacions del suport metodològic dins els seus programes, principalment en la formació d’estratègies o ajudant els aprenents a desenvolupar un pla de treball, aquest no és el cas quan es tracta de la seva preparació psicològica. Amb rares excepcions, trobem estudis que documentin com s’incideix en les actituds i en les creences dels aprenents, també coneguts com a coneixement metacognitiu (CM), en programes que fomenten l’autonomia en l’aprenentatge. Els objectius d’aquest treball son dos: a) oferir una revisió d’estudis que han utilitzat diferents mitjans per incidir en el CM dels aprenents i b) descriure les febleses i avantatges dels procediments i instruments que utilitzen, tal com han estat valorats en estudis de recerca, ja que ens permetrà establir criteris objectius sobre com i quan utilitzar-los en programes que fomentin l’aprenentatge autodirigit.

Testing Cayley graph densities

We present a computer-assisted analysis of combinatorial properties of the Cayley graphs of certain finitely generated groups: Given a group with a finite set of generators, we study the density of the corresponding Cayley graph, that is, the least upper bound for the average vertex degree (= number of adjacent edges) of any finite subgraph. It is known that an m-generated group is amenable if and only if the density of the corresponding Cayley graph equals to 2m. We test amenable and non-amenable groups, and also groups for which amenability is unknown. In the latter class we focus on Richard Thompson’s group F.

Human capital in a global and knowledge-based economy. Part 2. Asssessment at the EU country level.

This report is an extension and partial update of de la Fuente and Ciccone (2002). It constructs estimates of the private and social rates of return on schooling for fourteen EU countries using microeconometric estimates of Mincerian wage equations, the results of cross-country growth regressions and OECD data on educational expenditures, tax rates and social benefits. The results are used to draw some tentative conclusions regarding the optimality of observed investment patterns and educational subsidy levels.

Human capital in a global and knowledge-based economy

This document is a report prepared for the DG for Employment and Social Affairs of the European Commission. It surveys the available evidence on the contribution of investment in human capital to aggregate productivity growth and on its impact on wages and other labour outcomes at the individual level. It also draws some tentative policy conclusions for an average European country.

Knowledge, networks of cities and growth in regional urban systems

The objective of this paper is to measure the impact of different kinds of knowledge and external economies on urban growth in an intraregional context. The main hypothesis is that knowledge leads to growth, and that this knowledge is related to the existence of agglomeration and network externalities in cities. We develop a three-tage methodology: first, we measure the amount and growth of knowledge in cities using the OCDE (2003) classification and employment data; second, we identify the spatial structure of the area of analysis (networks of cities); third, we combine the Glaeser - Henderson - De Lucio models with spatial econometric specifications in order to contrast the existence of spatially static (agglomeration) and spatially dynamic (network) external economies in an urban growth model. Results suggest that higher growth rates are associated to higher levels of technology and knowledge. The growth of the different kinds of knowledge is related to local and spatial factors (agglomeration and network externalities) and each knowledge intensity shows a particular response to these factors. These results have implications for policy design, since we can forecast and intervene on local knowledge development paths.

Testing the entrepreneurial intention model on a two-country sample

This paper tests the Entrepreneurial Intention Model -which is adapted from the Theory of Planned Behavior- on a sample of 533 individuals from two quite different countries: one of them European (Spain) and the other South Asian (Taiwan). A newly developed Entrepreneurial Intention Questionnaire (EIQ) has being used which tries to overcome some of the limitations of previous instruments. Structural equations techniques were used in the empirical analysis. Results are generally satisfactory, indicating that the model is probably adequate for studying entrepreneurship. Support for the model was found not only in the combined sample, but also in each of the national ones. However, some differences arose that may indicate demographic variables contribute differently to the formation of perceptions in each culture.

Testing of stair climbing point-of-choice prompts in Barcelona at an outdoor set of stairs and scalators on the Montjuïc site

Regular stair climbing has well-documented health dividends, such as increased fitness and strength, weight loss and reduced body fat, improved lipid profiles and reduced risk of osteoporosis. The general absence of barriers to participation makes stair climbing an ideal physical activity (PA) for health promotion. Studies in the US and the UK have consistently shown that interventions to increase the accumulation of lifestyle PA by climbing stairs rather than using the escalators are effective. However, there are no previous in Catalonia. This project tested one message for their ability to prompt travelers on the Montjuïc site to choose the stairs rather than the escalator when climbing up the Monjuïc hill. One standard message, " Take the stairs! 7 minutes of stair climbing a day protects your heart" provided a comparison with previous research done in the UK. Translated into Catalan and Spanish, it was presented on a poster positioned at the point of choice between the stairs and the escalator. The study used a quasi-experimental, interrupted time series design. Travelers, during several and specific hours on two days of the week, were coded for stair or escalator use, gender, age, ethnic status, presence of accompanying children or bags by one observer. Overall, the intervention resulted in a 81% increase in stair climbing. In the follow-up period without messages, stair climbing dropped out to baseline levels. This preliminary study showed a significant effect on stair use. However, caution is needed since results are based on a small sample and, only a low percentage of the sample took the stairs at baseline or the intervention phase . Future research on stair use in Catalonia should focus on using bigger samples, different sites (metro stations, airports, shopping centers, etc) , different messages and techniques to promote stair climbing.

Trials, tricks and transparency: how disclosure rules affect clinical knowledge

Scandals of selective reporting of clinical trial results by pharmaceutical firms have underlined the need for more transparency in clinical trials. We provide a theoretical framework which reproduces incentives for selective reporting and yields three key implications concerning regulation. First, a compulsory clinical trial registry complemented through a voluntary clinical trial results database can implement full transparency (the existence of all trials as well as their results is known). Second, full transparency comes at a price. It has a deterrence effect on the incentives to conduct clinical trials, as it reduces the firms'gains from trials. Third, in principle, a voluntary clinical trial results database without a compulsory registry is a superior regulatory tool; but we provide some qualified support for additional compulsory registries when medical decision-makers cannot anticipate correctly the drug companies' decisions whether to conduct trials. Keywords: pharmaceutical firms, strategic information transmission, clinical trials, registries, results databases, scientific knowledge JEL classification: D72, I18, L15

Efficient knowledge retrieval to calibrate input variables in forest fire prediction

Forest fires are a serious threat to humans and nature from an ecological, social and economic point of view. Predicting their behaviour by simulation still delivers unreliable results and remains a challenging task. Latest approaches try to calibrate input variables, often tainted with imprecision, using optimisation techniques like Genetic Algorithms. To converge faster towards fitter solutions, the GA is guided with knowledge obtained from historical or synthetical fires. We developed a robust and efficient knowledge storage and retrieval method. Nearest neighbour search is applied to find the fire configuration from knowledge base most similar to the current configuration. Therefore, a distance measure was elaborated and implemented in several ways. Experiments show the performance of the different implementations regarding occupied storage and retrieval time with overly satisfactory results.

Innovation, R&D spillovers and productivity: the role of knowledge-intensive services

This paper analyses the performance of companies’ R&D and innovation and the effects of intra- and inter-industry R&D spillover on firms’ productivity in Catalonia. The paper deals simultaneously with the performance of manufacturing and service firms, with the aim of highlighting the growing role of knowledge-intensive services in promoting innovation and productivity gains. We find that intra-industry R&D spillovers have an important effect on the productivity level of manufacturing firms, and the inter-industrial R&D spillovers related to computer and software services also play an important role, especially in high-tech manufacturing industries. The main conclusion is that the traditional classification of manufactured goods and services no longer makes sense in the ‘knowledge economy’ and in Catalonia the regional policy makers will have to design policies that favour inter-industrial R&D flows, especially from high-tech services.

Testing for poverty dominance: an application to Canada

The paper proposes and applies statistical tests for poverty dominance that check for whether poverty comparisons can be made robustly over ranges of poverty lines and classes of poverty indices. This helps provide both normative and statistical confidence in establishing poverty rankings across distributions. The tests, which can take into account the complex sampling procedures that are typically used by statistical agencies to generate household-level surveys, are implemented using the Canadian Survey of Labour and Income Dynamics (SLID) for 1996, 1999 and 2002. Although the yearly cumulative distribution functions cross at the lower tails of the distributions, the more recent years tend to dominate earlier years for a relatively wide range of poverty lines. Failing to take into account SLID's sampling variability (as is sometimes done) can inflate significantly one's confidence in ranking poverty. Taking into account SLID's complex sampling design (as has not been done before) can also decrease substantially the range of poverty lines over which a poverty ranking can be inferred.

Testing low-altitude infrared digital photography from a mini-UAV to retrieve information for biological conservation

Satellite remote sensing imagery is used for forestry, conservation and environmental applications, but insufficient spatial resolution, and, in particular, unavailability of images at the precise timing required for a given application, often prevent achieving a fully operational stage. Airborne remote sensing has the advantage of custom-tuned sensors, resolution and timing, but its price prevents using it as a routine technique for the mentioned fields. Some Unmanned Aerial Vehicles might provide a “third way” solution as low-cost techniques for acquiring remotely sensed information, under close control of the end-user, albeit at the expense of lower quality instrumentation and instability. This report evaluates a light remote sensing system based on a remotely-controlled mini-UAV (ATMOS-3) equipped with a color infra-red camera (VEGCAM-1) designed and operated by CATUAV. We conducted a testing mission over a Mediterranean landscape dominated by an evergreen woodland of Aleppo pine (Pinus halepensis) and (Holm) oak (Quercus ilex) in the Montseny National Park (Catalonia, NE Spain). We took advantage of state-of-the-art ortho-rectified digital aerial imagery (acquired by the Institut Cartogràfic de Catalunya over the area during the previous year) and used it as quality reference. In particular, we paid attention to: 1) Operationality of flight and image acquisition according to a previously defined plan; 2) Radiometric and geometric quality of the images; and 3) Operational use of the images in the context of applications. We conclude that the system has achieved an operational stage regarding flight activities, although with meteorological limits set by wind speed and turbulence. Appropriate landing areas can be sometimes limiting also, but the system is able to land on small and relatively rough terrains such as patches of grassland or short matorral, and we have operated the UAV as far as 7 km from the control unit. Radiometric quality is sufficient for interactive analysis, but probably insufficient for automated processing. A forthcoming camera is supposed to greatly improve radiometric quality and consistency. Conventional GPS positioning through time synchronization provides coarse orientation of the images, with no roll information.