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.

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.

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.

Fault section estimation in automated distribution substations

In this paper, a methodology based on Unconstrained Binary Programming (UBP) model and Genetic Algorithms (GAs) is proposed for estimating fault sections in automated distribution substations. The UBP model, established by using the parsimonious set covering theory, looks for the match between the relays' protective alarms informed by the SCADA system and their expected states. The GA is developed to minimize the UBP model and estimate the fault sections in a swift and reliable manner. The proposed methodology is tested by utilizing a real-life automated distribution substation. Control parameters of the GA are tuned to achieve maximum computational efficiency and reduction of processing time. Results show the potential and efficiency of the methodology for estimating fault section in real-time at Distribution Control Centers. ©2009 IEEE.

Automated determination of the orientation of dust devil tracks in mars orbiter images

The paper presents and evaluates three methods for automatically estimating the main orientation of Martian dust devil tracks in MOC and HiRISE images. Inferring such information about dust devils from their tracks is important to better understand the near surface wind. The methods considered were based on gradient direction, directional openings and morphological granulometry. The accuracy of the methods was asserted by comparing the results to a set of directions estimated visually and assumed to be the ground truth. The higher accuracy was reached using directional openings. Besides, the directions inferred by this method were compared to those predicted by the GCM and the results agreed. © 2013 COSPAR.

Automated diagnosis of human intestinal parasites using optical microscopy images

Intestinal parasitosis constitutes a serious health problem in most tropical countries. The diagnosis of enteroparasites in laboratory routine relies on the examination of stool samples using optical microscopy and the error rates usually range from moderate to high. Approaches based on automatic image analysis have been proposed, but the methods are usually specific for some species, some of them are computationally expensive, and image acquisition and focus are manual. We present a solution to automate the diagnosis of the 15 most common species of enteroparasites in Brazil, using a sensitive parasitological technique, a motorized microscope with digital camera for automatic image acquisition and focus, and fast image analysis methods. The results indicate that our solution is effective and suitable for laboratory routine, in which the exam must be concluded in a few minutes. © 2013 IEEE.

Cryopreservation of bovine spermatozoa from the epididymal tail using conventional and automated methods

Cryopreservation of sperm is important to preserve the gerrnplasm from animals of genetic value, which can die unexpectedly. This study compares conventional and automated methods of cryopreservation of spermatozoa obtained from the epididymis of bulls post-mortem. Twenty-two epididymides were obtained from a commercial slaughterhouse. Spermatozoa were collected from the tail of the epididymis using the retrograde flow technique. Thus, the samples, which were diluted in 10 ml of extender without glycerol (Botubov (R) I, Botupharma, Botucatu, SP, Brazil), were evaluated on motility, sperm vigor, structural and functional (swelling hypoosmotic test) membrane integrity, mitochondrial activity, sperm viability and ADN fragmentation. The samples were divided into two aliquots and diluted in extender with glycerol (Botubov (R) II, Botupharma, Botucatu, SP, Brazil) at a concentration of 50x10(6) motile sperm/0.5 French straws. One sample was frozen by the conventional method (4 hours at 5 degrees C, in a refrigerator and 20 min in nitrogen vapor) and the other by the automated method (Cryogen (R) Dualflex, Neovet, Uberaba, MG, Brazil). The parameters were higher in all the tests of fresh sperm samples, with the exception of the swelling hypoosmotic test, which showed no significant difference when the results were compared with sperm frozen by the conventional method. The average motility of fresh spermatozoa was 74%, and conventional and automated averages were 29 and 25%, respectively. Therefore, although cryopreservation techniques reduce sperm quality parameters, the viability of the sperm is maintained, and these methods can be used to preserve sperm.

A novel automated alternating current biosusceptometry method to characterization of controlled-release magnetic floating tablets of metronidazole

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

A reference model as automated process for software adaptation at runtime

The development of self-adaptive software (SaS) has specific characteristics compared to traditional one, since it allows that changes to be incorporated at runtime. Automated processes have been used as a feasible solution to conduct the software adaptation at runtime. In parallel, reference model has been used to aggregate knowledge and architectural artifacts, since capture the systems essence of specific domains. However, there is currently no reference model based on reflection for the development of SaS. Thus, the main contribution of this paper is to present a reference model based on reflection for development of SaS that have a need to adapt at runtime. To present the applicability of this model, a case study was conducted and good perspective to efficiently contribute to the area of SaS has been obtained.

Icodextrin reduces insulin resistance in non-diabetic patients undergoing automated peritoneal dialysis: results of a randomized controlled trial (STARCH)

Insulin resistance is a common risk factor in chronic kidney disease patients contributing to the high cardiovascular burden, even in the absence of diabetes. Glucose-based peritoneal dialysis (PD) solutions are thought to intensify insulin resistance due to the continuous glucose absorption from the peritoneal cavity. The aim of our study was to analyse the effect of the substitution of glucose for icodextrin on insulin resistance in non-diabetic PD patients in a multicentric randomized clinical trial. This was a multicenter, open-label study with balanced randomization (1:1) and two parallel-groups. Inclusion criteria were non-diabetic adult patients on automated peritoneal dialysis (APD) for at least 3 months on therapy prior to randomization. Patients assigned to the intervention group were treated with 2L of icodextrin 7.5%, and the control group with glucose 2.5% during the long dwell and, at night in the cycler, with a prescription of standard glucose-based PD solution only in both groups. The primary end-point was the change in insulin resistance measured by homeostatic model assessment (HOMA) index at 90 days. Sixty patients were included in the intervention (n = 33) or the control (n = 27) groups. There was no difference between groups at baseline. After adjustment for pre-intervention HOMA index levels, the group treated with icodextrin had the lower post-intervention levels at 90 days in both intention to treat [1.49 (95% CI: 1.23-1.74) versus 1.89 (95% CI: 1.62-2.17)], (F = 4.643, P = 0.03, partial η(2) = 0.078); and the treated analysis [1.47 (95% CI: 1.01-1.84) versus 2.18 (95% CI: 1.81-2.55)], (F = 7.488, P = 0.01, partial η(2) = 0.195). The substitution of glucose for icodextrin for the long dwell improved insulin resistance measured by HOMA index in non-diabetic APD patients.

Automated peritoneal dialysis is associated with better survival rates compared to continuous ambulatory peritoneal dialysis: a propensity score matching analysis

The impact of peritoneal dialysis modality on patient survival and peritonitis rates is not fully understood, and no large-scale randomized clinical trial (RCT) is available. In the absence of a RCT, the use of an advanced matching procedure to reduce selection bias in large cohort studies may be the best approach. The aim of this study is to compare automated peritoneal dialysis (APD) and continuous ambulatory peritoneal dialysis (CAPD) according to peritonitis risk, technique failure and patient survival in a large nation-wide PD cohort. This is a prospective cohort study that included all incident PD patients with at least 90 days of PD recruited in the BRAZPD study. All patients who were treated exclusively with either APD or CAPD were matched for 15 different covariates using a propensity score calculated with the nearest neighbor method. Clinical outcomes analyzed were overall mortality, technique failure and time to first peritonitis. For all analysis we also adjusted the curves for the presence of competing risks with the Fine and Gray analysis. After the matching procedure, 2,890 patients were included in the analysis (1,445 in each group). Baseline characteristics were similar for all covariates including: age, diabetes, BMI, Center-experience, coronary artery disease, cancer, literacy, hypertension, race, previous HD, gender, pre-dialysis care, family income, peripheral artery disease and year of starting PD. Mortality rate was higher in CAPD patients (SHR1.44 CI95%1.21-1.71) compared to APD, but no difference was observed for technique failure (SHR0.83 CI95%0.69-1.02) nor for time till the first peritonitis episode (SHR0.96 CI95%0.93-1.11). In the first large PD cohort study with groups balanced for several covariates using propensity score matching, PD modality was not associated with differences in neither time to first peritonitis nor in technique failure. Nevertheless, patient survival was significantly better in APD patients.

Towards automated first-order abduction: the cut-based approach

Traditional abduction imposes as a precondition the restriction that the background information may not derive the goal data. In first-order logic such precondition is, in general, undecidable. To avoid such problem, we present a first-order cut-based abduction method, which has KE-tableaux as its underlying inference system. This inference system allows for the automation of non-analytic proofs in a tableau setting, which permits a generalization of traditional abduction that avoids the undecidable precondition problem. After demonstrating the correctness of the method, we show how this method can be dynamically iterated in a process that leads to the construction of non-analytic first-order proofs and, in some terminating cases, to refutations as well.

Automated analysis of lidocaine and its metabolite in plasma by in-tube solid-phase microextraction coupled with LC-UV for pharmacokinetic study

A sensitive, selective, and reproducible in-tube solid-phase microextraction and liquid chromatographic (in-tube SPME/LC-UV) method for determination of lidocaine and its metabolite monoethylglycinexylidide (MEGX) in human plasma has been developed, validated, and further applied to pharmacokinetic study in pregnant women with gestational diabetes mellitus (GDM) subjected to epidural anesthesia. Important factors in the optimization of in-tube SPME performance are discussed, including the draw/eject sample volume, draw/eject cycle number, draw/eject flow rate, sample pH, and influence of plasma proteins. The limits of quantification of the in-tube SPME/LC method were 50 ng/mL for both metabolite and lidocaine. The interday and intraday precision had coefficients of variation lower than 8%, and accuracy ranged from 95 to 117%. The response of the in-tube SPME/LC method for analytes was linear over a dynamic range from 50 to 5000 ng/mL, with correlation coefficients higher than 0.9976. The developed in-tube SPME/LC method was successfully used to analyze lidocaine and its metabolite in plasma samples from pregnant women with GDM subjected to epidural anesthesia for pharmacokinetic study.