Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Schooling and the intergenerational transmission of values

We present a model of the evolution of identity via dynamic interaction between the choice of education and the transmission of values in a community from parents to children, when parents care about the preservation of their traditional community values, different from the values of the host society. We compare the educational and socioeconomic outcomes in different scenarios (melting pot versus multiculturalism). If schooling shifts children’s identity away from their parents’ values, parents may choose lower levels of education for their children, at the cost of reducing their future earnings. We show how this effect can be attenuated and reversed when the school or, indeed, the host society are willing to accommodate the values of the community and/or to adjust to these values; otherwise the community gradually becomes alienated. This approach may be applied to the analysis of temporal changes in values and attitudes in a community of immigrants, as well as ethnic, religious, or other minority groups.

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the extensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on ""Joint Research Using Small Tokamaks"". (C) 2010 Elsevier B.V. All rights reserved.

The program and treatment effect of summer jobs on girls’ post-schooling incomes

Public programs (of disputed effect) offering summer jobs or work while in high school to smooth the transition from school to work is commonplace. In this paper, 1447 girls in their first grade of high school between 1997-2003 and randomly allotted summer jobs via a program in Falun (Sweden) are followed 5-12 years after graduation. The program led to a substantially larger accumulation of income while in high school. The causal effect of the high school income on post-schooling incomes was substantial and statistically significant. The implied elasticity of 0.4 is however potentially inflated dueto heterogeneous effects.

The Key Role of the School Principal’s Leadership in the Schooling of Newly Arrived Immigrant Pupils in Sweden : Experiences from an Interactive Action Research Project

When newly immigrated children and young people begin school in Sweden, certain challengesarise. These may result from weak Swedish-language skills and different schooling backgrounds,as well as organizational and pedagogical limitations in the schools. This generates demands onschool leaders to lead and develop the organization and teachers competences to meet these pupils’needs. This situation was behind the initiation of the project “New Immigrants and Learning—Competence Development for Teachers and School Principals.” The project ran in schools infour Swedish municipalities, its aim was to develop leadership, organizational and pedagogicalskills that would facilitate the schooling and integration of newly arrived pupils. This article aimsto describe and discuss a Participant Action Research (PAR) based on a think tank and researchcircles, drawing special attention to the role of the school leaders. It will also examine whether theresearch circles and the project overall served to develop educational and intercultural leadership,organizational conditions, collegial learning, pedagogical methods and competence in terms ofschooling for this pupil group.

Income composition, endogenous fertility and schooling investments in children

This paper studies how the eomposition of ineome between mothers and fathers affeets fertility and sehooling investments in ehildren, using data from the 1976 and 1996 PNAD, a Brazilian household survey. Ineome composition affeets the time eost of fertility because mothers and fathers alloeate different amounts of time to child-rearing. These effects are in turn transmitted to investments in ehildren through a tradeoffbetween quantity and quality of ehildren. The main contribution of this paper is twofold. First, it derives new implications about the relationship between household ineome composition and schooling investments in ehildren. Seeond, this paper devises and implements an empirieal approaeh to assess these implieations, using two eross-seetions of fertility and schooling data from Brazil. The main empirical findings of the paper ean be summarized as follows. First, the empirical analysis shows that a larger negative effect of the mother's labor in come on fertility in 1996 is associated with a larger positive effect on the adult child's schooling, refleeting the interaction between quantity and quality of children. Second, the larger negative effect of the mother's labor income on fertility in 1996 is associated with a reduction in the effect of other determinants of number of children. This suggests that an increase in the relative importanee of time costs of fertility may be an important determinant of variations in fertility over time in Brazil and other developing countries .

Conditional cash transfers, schooling and child labor : micro-simulating bolsa escola

Cash transfers targeted to poor people, but conditional on some behavior on their part, such as school attendance or regular visits to health care facilities, are being adopted in a growing number of developing countries. Even where ex-post impact evaluations have been conducted, a number of policy-relevant counterfactual questions have remained unanswered. These are questions about the potential impact of changes in program design, such as benefit levels or the choice of the means-test, on both the current welfare and the behavioral response of household members. This paper proposes a method to simulate the effects of those alternative program designs on welfare and behavior, based on microeconometrically estimated models of household behavior. In an application to Brazil’s recently introduced federal Bolsa Escola program, we find a surprisingly strong effect of the conditionality on school attendance, but a muted impact of the transfers on the reduction of current poverty and inequality levels.

Schooling and swimming behaviors of Hyla semilineata tadpoles (Anura, Hylidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Parmodel: a web server for automated comparative modeling of proteins

Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models ford a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools/parmodel. (C) 2004 Elsevier B.V. All rights reserved.

Schooling behavior of Mugil curema (Perciformes: Mugilidae) in an estuary in southeastern Brazil

Schools of mullets, Mugilidae, are abundant in estuaries and shallow marine waters. We report on the schooling behavior of juvenile white mullet, Mugil curema, in the estuary of the Canto da Paciência stream, in Ubatuba, southeastern Brazil. Schools of small fish (15 to 35 mm TL) were composed of a larger number of individuals (up to a hundred individuals), and were found feeding mainly in shallow nearshore waters, whereas schools of larger fish (40 to 100 mm TL) were observed only in deeper waters. Three patterns of swimming were observed for the schools: stationary feeding, slow movement while searching for food, and rapid displacement. The variations observed in school structure and behavior seem to be related to the balance between predation risk and increasing food intake. Copyright © 2007 Sociedade Brasileira de Ictiologia.