AtPIN: Arabidopsis thaliana Protein Interaction Network

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets.</p> <p>Description</p> <p>All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C³) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening.</p> <p>Conclusions</p> <p>AtPIN is a friendly and easy-to-use tool that aggregates information on <it>Arabidopsis thaliana </it>PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at <url>http://bioinfo.esalq.usp.br/atpin</url>.</p

Ultrasonic Spectral Analysis for Nuclear Fuel Characterization

Ceramic materials have been widely used for various purposes in many different industries due to certain characteristics, such as high melting point and high resistance to corrosion. Concerning the areas of applications, automobile, aeronautics, naval and even nuclear, the characteristics of these materials should be strictly controlled. In the nuclear area, ceramics are of great importance once they are the nuclear fuel pellets and must have, among other features, a well controlled porosity due to mechanical strength and thermal conductivity required by the application. Generally, the techniques used to characterize nuclear fuel are destructive and require costly equipment and facilities. This paper aims to present a nondestructive technique for ceramic characterization using ultrasound. This technique differs from other ultrasonic techniques because it uses ultrasonic pulse in frequency domain instead of time domain, associating the characteristics of the analyzed material with its frequency spectrum. In the present work, 40 Alumina (Al2O3) ceramic pellets with porosities ranging from 5% to 37%, in absolute terms measured by Archimedes technique, were tested. It can be observed that the frequency spectrum of each pellet varies according to its respective porosity and microstructure, allowing a fast and non-destructive association of the same characteristics with the same spectra pellets

Exploring the Elastic Properties and Fracture Patterns of Me-Graphene Monolayers and Nanotubes through Reactive Molecular Dynamics Simulations

Me-graphene (MeG) is a novel two-dimensional (2D) carbon allotrope. Due to its attractive electronic and structural properties, it is important to study the mechanical behavior of MeG in its monolayer and nanotube topologies. In this work, we conducted fully atomistic reactive molecular dynamics simulations using the Tersoff force field to investigate their mechanical properties and fracture patterns. Our results indicate that Young's modulus of MeG monolayers is about 414 GPa and in the range of 421-483 GPa for the nanotubes investigated here. MeG monolayers and MeGNTs directly undergo from elastic to complete fracture under critical strain without a plastic regime.Comment: 10 pages, 01 table, and 05 figure

The Structure Of The Giant Haemoglobin From Glossoscolex Paulistus.

The sequences of all seven polypeptide chains from the giant haemoglobin of the free-living earthworm Glossoscolex paulistus (HbGp) are reported together with the three-dimensional structure of the 3.6 MDa complex which they form. The refinement of the full particle, which has been solved at 3.2 Å resolution, the highest resolution reported to date for a hexagonal bilayer haemoglobin composed of 12 protomers, is reported. This has allowed a more detailed description of the contacts between subunits which are essential for particle stability. Interpretation of features in the electron-density maps suggests the presence of metal-binding sites (probably Zn(2+) and Ca(2+)) and glycosylation sites, some of which have not been reported previously. The former appear to be important for the integrity of the particle. The crystal structure of the isolated d chain (d-HbGp) at 2.1 Å resolution shows different interchain contacts between d monomers compared with those observed in the full particle. Instead of forming trimers, as seen in the complex, the isolated d chains associate to form dimers across a crystallographic twofold axis. These observations eliminate the possibility that trimers form spontaneously in solution as intermediates during the formation of the dodecameric globin cap and contribute to understanding of the possible ways in which the particle self-assembles.711257-127

The BLue Amazon Brain (BLAB): A Modular Architecture of Services about the Brazilian Maritime Territory

We describe the first steps in the development of an artificial agent focused on the Brazilian maritime territory, a large region within the South Atlantic also known as the Blue Amazon. The "BLue Amazon Brain" (BLAB) integrates a number of services aimed at disseminating information about this region and its importance, functioning as a tool for environmental awareness. The main service provided by BLAB is a conversational facility that deals with complex questions about the Blue Amazon, called BLAB-Chat; its central component is a controller that manages several task-oriented natural language processing modules (e.g., question answering and summarizer systems). These modules have access to an internal data lake as well as to third-party databases. A news reporter (BLAB-Reporter) and a purposely-developed wiki (BLAB-Wiki) are also part of the BLAB service architecture. In this paper, we describe our current version of BLAB's architecture (interface, backend, web services, NLP modules, and resources) and comment on the challenges we have faced so far, such as the lack of training data and the scattered state of domain information. Solving these issues presents a considerable challenge in the development of artificial intelligence for technical domains

Epidemiology and outcomes of non-cardiac surgical patients in Brazilian intensive care units

OBJECTIVES: Due to the dramatic medical breakthroughs and an increasingly ageing population, the proportion of patients who are at risk of dying following surgery is increasing over time. The aim of this study was to evaluate the outcomes and the epidemiology of non-cardiac surgical patients admitted to the intensive care unit. METHODS: A multicenter, prospective, observational, cohort study was carried out in 21 intensive care units. A total of 885 adult surgical patients admitted to a participating intensive care unit from April to June 2006 were evaluated and 587 patients were enrolled. Exclusion criteria were trauma, cardiac, neurological, gynecologic, obstetric and palliative surgeries. The main outcome measures were postoperative complications and intensive care unit and 90-day mortality rates. RESULTS: Major and urgent surgeries were performed in 66.4% and 31.7% of the patients, respectively. The intensive care unit mortality rate was 15%, and 38% of the patients had postoperative complications. The most common complication was infection or sepsis (24.7%). Myocardial ischemia was diagnosed in only 1.9% of the patients. A total of 94 % of the patients who died after surgery had co-morbidities at the time of surgery (3.4 ± 2.2). Multiple organ failure was the main cause of death (53%). CONCLUSION: Sepsis is the predominant cause of morbidity in patients undergoing non-cardiac surgery. In this patient population, multiple organ failure prevailed as the most frequent cause of death in the hospital.OBJETIVO: Devido aos avanços da medicina e ao envelhecimento da população, a proporção de pacientes em risco de morte após cirurgias está aumentando. Nosso objetivo foi avaliar o desfecho e a epidemiologia de cirurgias não cardíacas em pacientes admitidos em unidade de terapia intensiva. MÉTODOS: Estudo prospectivo, observacional, de coorte, realizado em 21 unidades de terapia intensiva. Um total de 885 pacientes adultos, cirúrgicos, consecutivamente admitidos em unidades de terapia intensiva no período de abril a junho de 2006 foi avaliado e destes, 587 foram incluídos. Os critérios de exclusão foram; trauma, cirurgias cardíacas, neurológicas, ginecológicas, obstétricas e paliativas. Os principais desfechos foram complicações pós-cirúrgicas e mortalidade na unidade de terapia intensiva e 90 dias após a cirurgia. RESULTADOS: Cirurgias de grande porte e de urgência foram realizadas em 66,4% e 31,7%, dos pacientes, respectivamente. A taxa de mortalidade na unidade de terapia intensiva foi de 15%, e 38% dos pacientes tiveram complicações no pós-operatório. A complicação mais comum foi infecção ou sepse (24,7%). Isquemia miocárdica foi diagnosticada em apenas 1,9%. Um total de 94 % dos pacientes que morreram após a cirurgia tinha co-morbidades associadas (3,4 ± 2,2). A principal causa de óbito foi disfunção de múltiplos órgãos (53%). CONCLUSÃO: Sepse é a causa predominante de morbidade em pacientes submetidos a cirurgias não cardíacas. A grande maioria dos óbitos no pós-operatório ocorreu por disfunção de múltiplos órgãos.Faculdade de Medicina de São José do Rio PretoServidor Público Estadual Serviço de Terapia IntensivaHospital São Lucas Unidade Coronariana IntensivaHospital Moinhos de Vento Centro de Terapia IntensivaClínica Sorocaba Centro de Terapia IntensivaClínica São Vicente Centro de Terapia IntensivaUniversidade Federal da Paraíba Hospital Universitário Unidade de Terapia Intensiva de AdultosUniversidade Federal de São Paulo (UNIFESP)Hospital Pró-Cardíaco Centro de Terapia IntensivaUniversidade Federal do Mato Grosso do Sul Hospital Universitário Centro de Terapia Intensiva AdultoUniversidade Estadual de LondrinaHospital de Terapia IntensivaUniversidade Estadual do PiauíHospital Santa Luzia Centro de Terapia IntensivaUniversidade Estadual do Oeste do ParanáFaculdade de Medicina de São José do Rio Preto Hospital de BaseHospital do Servidor Público EstadualHospital Cardiotrauma IpanemaSanta Casa de Misericórdia Centro de Terapia IntensivaUNIFESPSciEL