Automated system of seedling image analysis (SVIS) and electrical conductivity to assess sun hemp seed vigor

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

Candida spp.: manual identification (reference method) and automated identification (Vitek system platform)

Yeasts are becoming a common cause of nosocomial fungal infections that affect immunocompromised patients. Such infections can evolve into sepsis, whose mortality rate is high. This study aimed to evaluate the viability of Candida species identification by the automated system Vitek-Biomerieux (Durham, USA). Ninety-eight medical charts referencing the Candida spp. samples available for the study were retrospectively analyzed. The system Vitek-Biomerieux with Candida identification card is recommended for laboratory routine use and presents 80.6% agreement with the reference method. By separate analysis of species, 13.5% of C. parapsilosis samples differed from the reference method, while the Vitek system wrongly identified them as C. tropicalis, C. lusitaneae or as Candida albicans. C. glabrata presented a discrepancy of only one sample (25%), and was identified by Vitek as C. parapsilosis. C. guilliermondii also differed in only one sample (33.3%), being identified as Candida spp. All C. albicans, C. tropicalis and C. lusitaneae samples were identified correctly.

Ethyl Carbamate Analysis in German Fruit Spirits and Brazilian Sugarcane Spirits (Cachaca): Improved Sample Cleanup with Automated Parallel Evaporation

The analysis of alcoholic beverages for the important carcinogenic contaminant ethyl carbamate is very time-consuming and expensive. Due to possible matrix interferences, sample cleanup using diatomaceous earth (Extrelut) column is required prior to gas chromatographic and mass spectrometric measurement. A limiting step in this process is the rotary evaporation of the eluate containing the analyte in organic solvents, which is currently conducted manually and requires approximately 20-30 min per sample. This paper introduces the use of a parallel evaporation device for ethyl carbamate analysis, which allows for the simultaneous evaporation of 12 samples to a specified residual volume without manual intervention. A more efficient and, less expensive analysis is therefore possible. The method validation showed no differences between the fully-automated parallel evaporation and the manual operation. The applicability was proven by analyzing authentic spirit samples from Germany, Canada and Brazil. It is interesting to note that Brazilian cachacas had a relatively high incidence for ethyl carbamate contamination (55% of all samples were above 0.15 mg/l), which may be of public health relevance and requires further evaluation.

Automated Nuclear Analysis of Leishmania major Telomeric Clusters Reveals Changes in Their Organization during the Parasite's Life Cycle

Parasite virulence genes are usually associated with telomeres. The clustering of the telomeres, together with their particular spatial distribution in the nucleus of human parasites such as Plasmodium falciparum and Trypanosoma brucei, has been suggested to play a role in facilitating ectopic recombination and in the emergence of new antigenic variants. Leishmania parasites, as well as other trypanosomes, have unusual gene expression characteristics, such as polycistronic and constitutive transcription of protein-coding genes. Leishmania subtelomeric regions are even more unique because unlike these regions in other trypanosomes they are devoid of virulence genes. Given these peculiarities of Leishmania, we sought to investigate how telomeres are organized in the nucleus of Leishmania major parasites at both the human and insect stages of their life cycle. We developed a new automated and precise method for identifying telomere position in the three-dimensional space of the nucleus, and we found that the telomeres are organized in clusters present in similar numbers in both the human and insect stages. While the number of clusters remained the same, their distribution differed between the two stages. The telomeric clusters were found more concentrated near the center of the nucleus in the human stage than in the insect stage suggesting reorganization during the parasite's differentiation process between the two hosts. These data provide the first 3D analysis of Leishmania telomere organization. The possible biological implications of these findings are discussed.

Comparative growth of trichoderma strains in different nutritional sources, using bioscreen c automated system

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Case-based reasoning in offshore well design

Petroleum well drilling is an expensive and risky operation. In this context, well design presents itself as a fundamental key to decrease costs and risks involved. Experience acquired by engineers is notably an important factor in good drilling design elaborations. Therefore, the loss of this knowledge may entail additional problems and costs. In this way, this work represents an initiative to model a petroleum well design case-based architecture. Tests with a prototype showed that the system built with this architecture may help in a well design and enable corporate knowledge preservation. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Cholinesterase measurements with an automated kit

Background the Test-mate kit determines acetylcholinesterase (AChE, EC 3.1.1.7) and hemoglobin content of a drop of blood, displaying enzyme activities normalized to 25degreesC. Previous models produced inconsistent results at different temperatures. This report focuses on the current model, ChE 400, and two instruments of a previous OP model.Methods AChE activities were determined by the Ellman assay, using the three kits and a 96-well microplate reader Temperatures ranged from 10 to 37degreesC. Fetal bovine serum was the source of AChE.Results Normalized activities decreased below 20degreesC in the ChE model and below 25 C in the OP models. Activities of the same serum sample differed between the three Test-mate kits, ranging from 1.03 to 1.49 mumoles/min/ml. Percent errors were greater than with the microplate reader at all temperatures.Conclusions Neither we nor the manufacturer recommend the current Test-mate model for fieldwork. Nevertheless, there have been field measurements with Test-Mate kits, and we recommend that an enzyme activity standard be run in parallel with their use. (C) 2002 Wiley-Liss, Inc.

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.

Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus

Crotamine is one of four major components of the venom of the South American rattlesnake Crotalus durissus terrificus. Similar to its counterparts in the family of the myotoxins, it induces myonecrosis of skeletal muscle cells. This paper describes a new NMR structure determination of crotamine in aqueous solution at pH 5.8 and 20 degrees C, using standard homonuclear (1)H NMR spectroscopy at 900 MHz and the automated structure calculation software ATNOS/CANDID/DYANA. The automatic NOESY spectral analysis included the identification of a most likely combination of the six cysteines into three disulfide bonds, i.e. Cys4-Cys36, Cys11-Cys30 and Cys18-Cys37; thereby a generally applicable new computational protocol is introduced to determine unknown disulfide bond connectivities in globular proteins. A previous NMR structure determination was thus confirmed and the structure refined. Crotamine contains an alpha-helix with residues 1-7 and a two-stranded anti-parallel beta-sheet with residues 9-13 and 34-38 as the only regular secondary structures. These are connected with each other and the remainder of the polypeptide chain by the three disulfide bonds, which also form part of a central hydrophobic core. A single conformation was observed, with Pro13 and Pro21 in the trans and Pro20 in the cis-form. The global fold and the cysteine-pairing pattern of crotamine are similar to the beta-defensin fold, although the two proteins have low sequence homology, and display different biological activities. (c) 2005 Elsevier Ltd. All rights reserved.

Parentage testing in alpacas (Vicugna pacos) using semi-automated fluorescent multiplex PCRs with 10 microsatellite markers

The aim of this study was to assess and apply a microsatellite multiplex system for parentage determination in alpacas. An approach for parentage testing based on 10 microsatellites was evaluated in a population of 329 unrelated alpacas from different geographical zones in Peru. All microsatellite markers, which amplified in two multiplex reactions, were highly polymorphic with a mean of 14.5 alleles per locus (six to 28 alleles per locus) and an average expected heterozygosity (H-E) of 0.8185 (range of 0.698-0.946). The total parentage exclusion probability was 0.999456 for excluding a candidate parent from parentage of an arbitrary offspring, given only the genotype of the offspring, and 0.999991 for excluding a candidate parent from parentage of an arbitrary offspring, given the genotype of the offspring and the other parent. In a case test of parentage assignment, the microsatellite panel assigned 38 (from 45 cases) offspring parentage to 10 sires with LOD scores ranging from 2.19 x 10(+13) to 1.34 x 10(+15) and Delta values ranging from 2.80 x 10(+12) to 1.34 x 10(+15) with an estimated pedigree error rate of 15.5%. The performance of this multiplex panel of markers suggests that it will be useful in parentage testing of alpacas.

Conditional reasoning: A key to assessing computer-based knowledge-building communication processes

This article describes a methodological approach to conditional reasoning in online asynchronous learning environments such as Virtual-U VGroups, developed by SFU, BC, Canada, consistent with the notion of meaning implication: If part of a meaning C is embedded in B and a part of a meaning B is embedded in A, then A implies C in terms of meaning [Piaget 91]. A new transcript analysis technique was developed to assess the flows of conditional meaning implications and to identify the occurrence of hypotheses and connections among them in two human science graduate mixed-mode online courses offered in the summer/spring session of 1997 by SFU. Flows of conditional meaning implications were confronted with Virtual-U VGroups threads and results of the two courses were compared. Findings suggest that Virtual-U VGroups is a knowledge-building environment although the tree-like Virtual-U VGroups threads should be transformed into neuronal-like threads. Findings also suggest that formulating hypotheses together triggers a collaboratively problem-solving process that scaffolds knowledge-building in asynchronous learning environments: A pedagogical technique and an built-in tool for formulating hypotheses together are proposed. © Springer Pub. Co.

Automated extraction of road network from medium-and high-resolution images

This paper presents an automatic methodology for road network extraction from medium-and high-resolution aerial images. It is based on two steps. In the first step, the road seeds (i.e., road segments) are extracted using a set of four road objects and another set of connection rules among road objects. Each road object is a local representation of an approximately straight road fragment and its construction is based on a combination of polygons describing all relevant image edges, according to some rules embodying road knowledge. Each road seed is composed by a sequence of connected road objects in which each sequence of this type can be geometrically structured as a chain of contiguous quadrilaterals. In the second step, two strategies for road completion are applied in order to generate the complete road network. The first strategy is based on two basic perceptual grouping rules, i.e., proximity and collinearity rules, which allow the sequential reconstruction of gaps between every pair of disconnected road segments. This strategy does not allow the reconstruction of road crossings, but it allows the extraction of road centerlines from the contiguous quadrilaterals representing connected road segments. The second strategy for road completion aims at reconstructing road crossings. Firstly, the road centerlines are used to find reference points for road crossings, which are their approximate positions. Then these points are used to extract polygons representing the contours of road crossings. This paper presents the proposed methodology and experimental results. © Pleiades Publishing, Inc. 2006.

Abductive reasoning, information, and mechanical systems

We investigate, from a philosophical perspective, the relation between abductive reasoning and information in the context of biological systems. Emphasis is given to the organizational role played by abductive reasoning in practical activities of embodied embedded agency that involve meaningful information. From this perspective, meaningful information is provisionally characterized as a selforganizing process of pattern generation that constrains coherent action. We argue that this process can be considered as a part of evolutionarily developed learning abilities of organisms in order to help with their survival. We investigate the case of inorganic mechanical systems (like robots), which deal only with stable forms of habits, rather than with evolving learning abilities. Some difficulties are considered concerning the hypothesis that mechanical systems may operate with meaningful information, present in abductive reasoning. Finally, an example of hypotheses creation in the domain of medical sciences is presented in order to illustrate the complexity of abduction in practical reasoning concerning human activities. © 2007 Springer-Verlag Berlin Heidelberg.

Cone-beam computed tomography analysis of the apical third of curved roots after mechanical preparation with different automated systems

The present study evaluated by cone-beam computed tomography (CBCT) the apical canal transportation and centralizing ability of different automated systems after root canal preparation. The mesiobuccal canals of maxillary first molars (n=10 per group) were prepared with: GI - reciprocating system with K-Flexofile; GII - reciprocating system with NiTiFlex files; GIII - rotary system with K3 instruments; GIV - rotary system with RaCe instruments. CBCT scans were taken before and after biomechanical preparation up to a #40.02 diameter. Canal transportation was determined by measuring the smallest distance between the inner canal walls and the mesial and distal sides of the root. The centralization ability corresponded to the difference between the measurements from transportation evaluation, using the linear voxel to voxel method of analysis. The mean transportation was 0.06 ± 0.14 mm, with a tendency to deviate to the mesial side of the root (n=22), with no statistically significant difference among the groups (p=0.4153). The mean centralization index was 0.15 ± 0.65 also without statistically significant difference among the groups (p=0.0881). It may be concluded that apical canal transportation and centralization ability were not influenced by the type of mechanical movement and instruments used.