Methods for prediction of peptide binding to MHC molecules: A comparative study

Background: A variety of methods for prediction of peptide binding to major histocompatibility complex (MHC) have been proposed. These methods are based on binding motifs, binding matrices, hidden Markov models (HMM), or artificial neural networks (ANN). There has been little prior work on the comparative analysis of these methods. Materials and Methods: We performed a comparison of the performance of six methods applied to the prediction of two human MHC class I molecules, including binding matrices and motifs, ANNs, and HMMs. Results: The selection of the optimal prediction method depends on the amount of available data (the number of peptides of known binding affinity to the MHC molecule of interest), the biases in the data set and the intended purpose of the prediction (screening of a single protein versus mass screening). When little or no peptide data are available, binding motifs are the most useful alternative to random guessing or use of a complete overlapping set of peptides for selection of candidate binders. As the number of known peptide binders increases, binding matrices and HMM become more useful predictors. ANN and HMM are the predictive methods of choice for MHC alleles with more than 100 known binding peptides. Conclusion: The ability of bioinformatic methods to reliably predict MHC binding peptides, and thereby potential T-cell epitopes, has major implications for clinical immunology, particularly in the area of vaccine design.

Comparative surface accessibility of a pore-lining threonine residue (T6') in the glycine and GABA(A) receptors

The substituted cysteine accessibility method was used to probe the surface exposure of a pore-lining threonine residue (T6') common to both the glycine receptor (GlyR) and gamma-aminobutyric acid, type A receptor (GABAAR) chloride channels. This residue lies close to the channel activation gate, the ionic selectivity filter, and the main pore blocker binding site. Despite their high amino acid sequence homologies and common role in conducting chloride ions, recent studies have suggested that the GlyRs and GABA(A)Rs have divergent open state pore structures at the 6' position. When both the human alpha1(T6'C) homomeric GlyR and the rat alpha1(T6'C)beta1(T6'C) heteromeric GABA(A)R were expressed in human embryonic kidney 293 cells, their 6' residue surface accessibilities differed significantly in the closed state. However, when a soluble cysteine-modifying compound was applied in the presence of saturating agonist concentrations, both receptors were locked into the open state. This action was not induced by oxidizing agents in either receptor. These results provide evidence for a conserved pore opening mechanism in anion-selective members of the ligand-gated ion channel family. The results also indicate that the GABA(A)R pore structure at the 6' level may vary between different expression systems.

Comparative surface accessibility of a pore-lining threonine residue (T6') in the glycine and GABA(A) receptors

The substituted cysteine accessibility method was used to probe the surface exposure of a pore-lining threonine residue (T6’) common to both the glycine receptor (GlyR) and GABAA receptor (GABAAR) chloride channels. This residue lies close to the channel activation gate, the ionic selectivity filter and the main pore blocker binding site. Recent studies have suggested that the GlyRs and GABAARs have divergent open state pore structures at the 6’ position. When both the human a1T6’C homomeric GlyR and the rat a1T6’Cb1T6’C heteromeric GABAAR were expressed in HEK293 cells, their 6’ residue surface accessibilities differed significantly in the closed state. However, when a soluble cysteine-modifying compound was applied in the presence of saturating agonist concentrations, both receptors were locked into the open state. This action was not induced by oxidising agents in either receptor. These results provide evidence for a conserved pore opening mechanism in anion-selective members of the ligand-gated ion channel family. The results also indicate that the GABAAR pore structure at the 6’ level may vary between different expression systems.

CHARACTERIZATION OF AGROINDUSTRIAL SYSTEMS: A COMPARATIVE STUDY OF THE SUCRO-ENERGETIC SECTORS OF BRASIL AND COLOMBIA

Concern about the growing demand of food and fuel has focused the attention on countries with conditions to provide for global requirements. Also, the build-up of an environmental awareness has compelled several governments to implement programs for the addition of biofuels to oil derivatives. Considering their relevance as world and South American producers, this study makes a characterization of the sucro-energetic sectors of Brazil and Colombia, based on a view of agro-industrial systems, industrial organization and transaction cost economy. The approach followed considered of a secondary information survey and in-depth interviews. The main differences found are centered on institutional development level and production volumes. However, the use of the same raw material, sugarcane, trade opening policies, cultural approaches and regional integration, are factors that could generate links of commercial exchange and technological cooperation between the two countries.

A comparative study of similarity measures for manufacturing cell formation

We introduced a spectral clustering algorithm based on the bipartite graph model for the Manufacturing Cell Formation problem in [Oliveira S, Ribeiro JFF, Seok SC. A spectral clustering algorithm for manufacturing cell formation. Computers and Industrial Engineering. 2007 [submitted for publication]]. It constructs two similarity matrices; one for parts and one for machines. The algorithm executes a spectral clustering algorithm on each separately to find families of parts and cells of machines. The similarity measure in the approach utilized limited information between parts and between machines. This paper reviews several well-known similarity measures which have been used for Group Technology. Computational clustering results are compared by various performance measures. (C) 2008 The Society of Manufacturing Engineers. Published by Elsevier Ltd. All rights reserved.

Comparative analysis of population structure of endemic Western Atlantic hermit crab Loxopagurus loxochelis (Decapoda, Anomura) in two regions of state of Sao Paulo, Brazil

This work characterized the population structure of the hermit crab Loxopagurus loxochelis (Moreira, 1901) in terms of size frequency distribution and sex ratio. Specimens were collected monthly, over a period of one year (from July 2002 to June 2003), in seven transects (from 5 to 35 m of depth) using fishing boat equipped with two double-rig trawl nets, in Caraguatatuba and Ubatuba regions (state of Sao Paulo, Brazil). A total of 366 hermit crabs were collected in Caraguatatuba [222 males (60.65%), 114 non-ovigerous females (31.15%) and 30 ovigerous females (8.20%)] and 126 hermit crabs in Ubatuba [81 males (64.28%), 38 non-ovigerous females (30.16%) and seven ovigerous females (5.56%)]. In Caraguatatuba the highest incidence of ovigerous females occurred during winter (July 2002), whereas in Ubatuba, the number was incipient. The cephalothoracic shield length ranged from 2.0 to 7.9mm (5.29 +/- 0.96mm) in Caraguatatuba, and from 2.7 to 7.5mm (5.32 +/- 0.95mm) in Ubatuba. The mean size of males was significantly larger than the mean size of females in both regions. Overall sex ratio was in favor of males (1.54:1 in Caraguatatuba and 1.9:1 in Ubatuba). Sexual dimorphism was recorded to L. loxochelis by the presence of males in the largest size classes, following the standard pattern observed in Decapoda. There was an unimodal size distribution for both sexes, with normal distributions in both regions. The higher number of males in relation to females may indicate the existence of different growth and mortality rates between the sexes. Despite of the different geomorphologic characteristics between Caraguatatuba and Ubatuba regions, the dynamics of development was similar for both populations.

Comparative reproductive biology of two southwestern Atlantic populations of the hermit crab Pagurus exilis (Crustacea: Anomura: Paguridae)

Pagurus exilis (Benedict, 1892) is an endemic South Atlantic hermit crab with a distribution ranging from Rio de Janeiro State, Brazil, to Buenos Aires Province, Argentina. The present study analyzed the reproduction of two populations at the extremes of this geographical distribution, and compared their reproductive period, fecundity, and changes in egg size and egg volume during the incubation period in order to assess the variability over this latitudinal range. Hermit crabs were collected monthly over a 2-year period. In total, 108 females were analyzed for Brazil (44 non-ovigerous and 64 ovigerous), and 141 for Argentina (87 non-ovigerous and 54 ovigerous). Reproduction in Brazil occurs year-round, with peaks in the fall and winter seasons; in Argentina reproduction occurs only in spring and summer. The Brazilian ovigerous females were significantly larger than the Argentina ones (Brazil: SL = 5.33 +/- 1.45 mm; Argentina: SL = 4.15 +/- 0.52 mm; P < 0.001). The fecundity was 1447 +/- 831 eggs (317 to 2885) in Brazil and 987 +/- 711 eggs (114 to 2665) in Argentina, with a trend towards higher fecundity in Brazil. Eggs in the Argentina population were larger than those in Brazil for all the three stages investigated, and no changes in egg volume were found during egg development for both populations. The reproductive traits of the two populations showed some important differences, which may reflect adaptations to local environmental conditions, demonstrating a high plasticity of reproductive features of the species in Brazilian and Argentine waters. The strategy adopted by the Argentina population involves a lower production of larger eggs compared to the population in Brazil; this lower production is associated with reproduction in cold-water regions.

The Australian Universities Teaching Committee project in 'Learning Outcomes and Curriculum Development in Psychology'

The Australian Universities Teaching Committee (AUTC) funds projects intended to improve the quality of teaching and learning in specific disciplinary areas. The project brief for 'Learning Outcomes and Curriculum Development in Psychology' for 2004/2005 was to 'produce an evaluative overview of courses ... with a focus on the specification and assessment of learning outcomes and ... identify strategic directions for universities to enhance teaching and learning'. This project was awarded to a consortium from The University of Queensland, University of Tasmania, and Southern Cross University. The starting point for this project is an analysis of the scientist-practitioner model and its role in curriculum design, a review of current challenges at a conceptual level, and consideration of the implications of recent changes to universities relating to such things as intemationalisation of programs and technological advances. The project will seek to bring together stakeholders from around the country in order to survey the widest possible range of perspectives on the project brief requirements. It is hoped also to establish mechanisms for fiiture scholarly discussion of these issues, including the establishment of an Australian Society for the Teaching of Psychology and an annual conference.

HISTORIOGRAPHY OF PSYCHOLOGY IN BRAZIL: Pioneer Works, Recent Developments

The evolution of the historiography of psychology in Brazil is surveyed, to describe how the field has evolved from the seminal works of the pioneer, mostly self-taught, psychologists, to the now professional historians working from a variety of theoretical models and methods of inquiry. The first accounts of the history of psychology written by Brazilians and by foreigners are surveyed, as well as the recent works made by researchers linked to the Work Group on the History of Psychology of the Brazilian Association of Research and Graduate Education in Psychology and published in periodicals such as Memorandum and Mnemosine. The present historiography focuses mainly the relationship of psychological knowledge to specific social and cultural conditions, emphasizing themes such as women`s participation in the construction of the field, the development of psychology as a science and as a profession in education and health, and the development of psychology as an expression of Brazilian culture and of the experience of resistance of local communities to domination. To reveal this process of identity construction, a cultural historiography is an important tool, coupled with methodological pluralism.

Comparative Study of Analgesic Effectiveness Using Three Different Anesthetic Techniques for Intravitreal Injection of Bevacizumab

BACKGROUND AND OBJECTIVE: To compare the analgesic effectiveness and aesthetic appearance associated with topical, subconjunctival, and peribulbar anesthesia for intravitreal bevacizumab injection. PATIENTS AND METHODS: Sixty consecutive patients undergoing their first intravitreal bevacizumab injection were randomized to receive one of three forms of anesthesia: proxymetacaine eye drops, subconjunctival injection of 2% xylocaine, and peribulbar injection of 2% xylocaine. Pain associated with the intravitreal injection and with the entire procedure (including anesthesia administration) was recorded using a Visual Analog Scale 15 minutes after intravitreal injection. Anterior segment evaluation was performed 24 hours after injection to measure the number of clock hours of subconjunctival hemorrhage. RESULTS: Median injection-related pain score was significantly lower in the peribulbar group compared with the topical and subconjunctival groups (P < .05). Median entire procedure pain score was significantly higher In the peribulbar group compared with the topical and subconjunctival groups (P < .05). The median extent of subconjunctival hemorrhage was significantly lower in the topical group compared with the other groups (P < .05). CONCLUSION: Among the three anesthetic techniques, peribulbar anesthesia was associated with greater effectiveness in controlling injection-related pain but was least effective in controlling entire procedure pain. There was no significant difference in pain scores between the topical and subconjunctival groups, and topical anesthesia was associated with less subconjunctival hemorrhage.

A comparative study of population traits between two South American populations of the striped-legged hermit crab Clibanarius vittatus

The striped-legged hermit Crab Clibanarius vittatus, with a geographical distribution covering a wide range Of latitudes in the western Atlantic, was selected for a comparative study on population features between two different areas of the Brazilian coast that are separated by approximately 3000 km. The two populations Were sampled concurrently for nine months. The populations in northern and southeastern Brazil showed different profiles in terms of size of specimens, sex ratio, and shell occupation. The observed plasticity of these life-cycle traits of C. vittatus in relation to local environmental conditions is discussed. (C) 2009 Elsevier Masson SAS. All rights reserved