Modelagem do crescimento, maturação sexual e produção de ovos como ferramenta para estimar as exigências nutricionais de matrizes pesadas

Pós-graduação em Zootecnia - FCAV

Barriers to green buildings at two Brazilian engineering schools

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

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Symptom-based subtypes of depression and their psychosocial correlates: A person-centered approach focusing on the influence of sex

BACKGROUND: Reducing the complexity of major depressive disorder by symptom-based subtypes constitutes the basis of more specific treatments. To date, few studies have empirically derived symptom subtypes separated by sex, although the impact of sex has been widely accepted in depression research. METHODS: The community-based sample included 373 males and 443 females from the Zurich Program for Sustainable Development of Mental Health Services (ZInEP) manifesting depressive symptoms in the past 12 months. Latent Class Analysis (LCA) was performed separately by sex to extract sex-related depression subtypes. The subtypes were characterized by psychosocial characteristics. RESULTS: Three similar subtypes were found in both sexes: a severe typical subtype (males: 22.8%; females: 35.7%), a severe atypical subtype (males: 17.4%; females: 22.6%), and a moderate subtype (males: 25.2%; females: 41.8%). In males, two additional subgroups were identified: a severe irritable/angry-rejection sensitive (IARS) subtype (30%) comprising the largest group, and a small psychomotor retarded subtype (4%). Males belonging to the severe typical subtype exhibited the lowest masculine gender role orientation, while females of the typical subtype showed more anxiety disorders. The severe atypical subtype was associated with eating disorders in both sexes and with alcohol/drug abuse/dependence in females. In contrast, alcohol/drug abuse/dependence was associated with the severe IARS subtype in males. LIMITATIONS:The study had a cross-sectional design, allowing for no causal inferences. CONCLUSIONS:This study contributes to a better understanding of sex-related depression subtypes, which can be well distinguished on the basis of symptom profiles. This provides the base for future research investigating the etiopathogenesis and effective treatment of the heterogeneous depression disorder.

Architectural design and construction costs, tools towards territorial sustainability

This paper is presented in CIB: Management and Innovation Sustainable Built Environment 2011, as the study and analysis of the residential model of a rural area from the Iberian Peninsula, specifically applied to the case of the province of Cáceres, in the autonomous region of Extremadura, in Spain. To this end, from a database made up of building projects whose real costs are known, it is intended to establish the links of the different parameters studied through the corresponding functions of statistical analysis. One of the main objectives of this process is constituted by the possibility of establishing those design variables of higher economic importance, so as to keep an economic control of these parameters, generally geometrical and typological, from the very start of the project. And, in general, a higher optimization of resources in the construction of dwellings in the rural environment from their design is intended.

Modelos de análisis econométrico espacial aplicados al desarrollo económico

Los modelos de desarrollo regional, rural y urbano arrancaron en la década de los 90 en Estados Unidos, modelando los factores relacionados con la economía que suministran información y conocimiento acerca de cómo los parámetros geográficos y otros externos influencian la economía regional. El desarrollo regional y en particular el rural han seguido diferentes caminos en Europa y España, adoptando como modelo los programas estructurales de la UE ligados a la PAC. El Programa para el Desarrollo Rural Sostenible, recientemente lanzado por el Gobierno de España (2010) no profundiza en los modelos económicos de esta economía y sus causas. Este estudio pretende encontrar pautas de comportamiento de las variables de la economía regional-rural, y como el efecto de distribución geográfica de la población condiciona la actividad económica. Para este propósito, y utilizando datos espaciales y económicos de las regiones, se implementaran modelos espaciales que permitan evaluar el comportamiento económico, y verificar hipótesis de trabajo sobre la geografía y la economía del territorio. Se utilizarán modelos de análisis espacial como el análisis exploratorio espacial y los modelos econométricos de ecuaciones simultáneas, y dentro de estas los modelos ampliamente utilizados en estudios regionales de Carlino-Mills- Boarnet. ABSTRACT The regional development models for rural and urban areas started in USA in the ´90s, modeling the economy and the factors involved to understand and collect the knowledge of how the external parameters influenced the regional economy. Regional development and in particular rural development has followed different paths in Europe and Spain, adopting structural programs defined in the EU Agriculture Common Policy. The program for Sustainable Rural Development recently implemented in Spain (2010) is short sighted considering the effects of the regional economy. This study endeavors to underline models of behavior for the rural and regional economy variables, and how the regional distribution of population conditions the economic activities. For that purpose using current spatial regional economic data, this study will implement spatial economic models to evaluate the behavior of the regional economy, including the evaluation of working hypothesis about geography and economy in the territory. The approach will use data analysis models, like exploratory spatial data analysis, and spatial econometric models, and in particular for its wide acceptance in regional analysis, the Carlino-Mills-Boarnet equations model.

I like the floors

The use of wood in architectural design and the sustainable built environment

Coastal regulation zone rules in coastal panchayats (villages) of Kerala, India vis-a` -vis socio-economic impacts from the recently introduced peoples’ participatory program for local self-governance and sustainable development

Coastal Regulation Zone (CRZ) notification was issued by the Ministry of Environment and Forest of Government of India in February 1991 as a part of the Environmental Protection Act of 1986 to protect the coast from eroding and to preserve its natural resources. The initial notification did not distinguish the variability and diversity of various coastal states before enforcing it on the various states and Union Territories. Impact assessments were not carried out to assess its impact on socio-economic life of the coastal population. For the very same reason, it was unnoticed or rather ignored till 1994 when the Supreme Court of India made a land mark judgment on the fate of the coastal aquaculture which by then had established as an economically successful industry in many South Indian States. Coastal aquaculture in its modern form was a prohibited activity within CRZ. Lately, only various stakeholders of the coast realized the real impact of the CRZ rules on their property rights andbusiness. To overcome the initial drawbacks several amendments were made in the regulation to suit regional needs. In 1995, another great transformation took place in the State of Kerala as a part of the reorganization of the local self government institutions into a decentralized three tier system called ‘‘Panchayathi Raj System’’. In 1997, the state government also decided to transfer the power with the required budget outlay to the grass root level panchayats (villages) and municipalities to plan and implement the various projects in their localities with the full participation of the local people by constituting Grama Sabhas (Peoples’ Forum). It is called the ‘‘Peoples’ Planning Campaign’’(Peoples’ Participatory Programme—PPP for Local Level Self-Governance). The management of all the resources including the local natural resources was largely decentralized to the level of local communities and villages. Integrated, sustainable coastal zone management has become the concern of the local population. The paper assesses the socio-economic impact of the centrally enforced CRZ and the state sponsored PPP on the coastal community in Kerala and suggests measures to improve the system and living standards of the coastal people within the framework of CRZ.

Forest-related partnerships in Brazilian Amazonia: There is more to sustainable forest management than reduced impact logging

There is more to sustainable forest management than reduced impact logging. Partnerships between multiple actors are needed in order to create the institutional context for good forest governance and sustainable forest management and stimulate the necessary local community involvement. The idea behind this is that the parties would be able to achieve more jointly than on their own by combining assets, knowledge, skills and political power of actors at different levels of scale. This article aims to demonstrate by example the nature and variety of forest-related partnerships in Brazilian Amazonia. Based on the lessons learned from these cases and the authors` experience, the principal characteristics of successful partnerships are described, with a focus on political and socioeconomic aspects. These characteristics include fairly negotiated partnership objectives, the active involvement of the public sector as well as impartial brokers, equitable and cost-effective institutional arrangements, sufficient and equitably shared benefits for all the parties involved, addressing socioeconomic drawbacks, and taking measures to maintain sustainable exploitation levels. The authors argue that, in addition to product-oriented partnerships which focus on sustainable forest management, there is also a need for politically oriented partnerships based on civil society coalitions. The watchdog function of these politically oriented partnerships, their awareness-raising campaigns regarding detrimental policies and practices, and advocacy for good forest governance are essential for the creation of the appropriate legal and political framework for sustainable forest management. (C) 2008 Elsevier B.V. All rights reserved.

Modelling basin level allocation of water in the Murray-Darling Basin in a world of uncertainty, Murray-Darling Program Working Papers WPM05-1, Risk and Sustainable Management Group, 8 February 2005

Abstract: The Murray-Darling Basin comprises over 1 million km2; it lies within four states and one territory; and over 12, 800 GL of irrigation water is used to produce over 40% of the nation's gross value of agricultural production. This production is used by a diverse collection of some-times mutually exclusive commodities (e.g. pasture; stone fruit; grapes; cotton and field crops). The supply of water for irrigation is subject to climatic and policy uncertainty. Variable inflows mean that water property rights do not provide a guaranteed supply. With increasing public scrutiny and environmental issues facing irrigators, greater pressure is being placed on this finite resource. The uncertainty of the water supply, water quality (salinity), combined with where water is utilised, while attempting to maximising return for investment makes for an interesting research field. The utilisation and comparison of a GAMS and Excel based modelling approach has been used to ask: where should we allocate water?; amongst what commodities?; and how does this affect both the quantity of water and the quality of water along the Murray-Darling river system?