Lossless filter for multiple repeats with bounded edit distance

Background: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. Results: The filter TUIUIU that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several strong necessary conditions that can be checked in a fast way. We implemented three versions of the filter. The first is simply a straightforward extension to the case of multiple sequences of an application of conditions already existing in the literature. The second uses a stronger condition which, as our results show, enable to filter sensibly more with negligible (if any) additional time. The third version uses an additional condition and pushes the sensibility of the filter even further with a non negligible additional time in many circumstances; our experiments show that it is particularly useful with large error rates. The latter version was applied as a preprocessing of a multiple alignment tool, obtaining an overall time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment), with in most cases a better quality alignment. Conclusion: To the best of our knowledge, TUIUIU is the first filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.

Polarity-Dependent Transcranial Direct Current Stimulation Effects on Central Auditory Processing

Given the polarity dependent effects of transcranial direct current stimulation (tDCS) in facilitating or inhibiting neuronal processing, and tDCS effects on pitch perception, we tested the effects of tDCS on temporal aspects of auditory processing. We aimed to change baseline activity of the auditory cortex using tDCS as to modulate temporal aspects of auditory processing in healthy subjects without hearing impairment. Eleven subjects received 2mA bilateral anodal, cathodal and sham tDCS over auditory cortex in a randomized and counterbalanced order. Subjects were evaluated by the Random Gap Detection Test (RGDT), a test measuring temporal processing abilities in the auditory domain, before and during the stimulation. Statistical analysis revealed a significant interaction effect of time vs. tDCS condition for 4000 Hz and for clicks. Post-hoc tests showed significant differences according to stimulation polarity on RGDT performance: anodal improved 22.5% and cathodal decreased 54.5% subjects' performance, as compared to baseline. For clicks, anodal also increased performance in 29.4% when compared to baseline. tDCS presented polarity-dependent effects on the activity of the auditory cortex, which results in a positive or negative impact in a temporal resolution task performance. These results encourage further studies exploring tDCS in central auditory processing disorders.

Direct evidence of singlet molecular oxygen generation from peroxynitrate, a decomposition product of peroxynitrite

The decomposition of peroxynitrite to nitrite and dioxygen at neutral pH follows complex kinetics, compared to its isomerization to nitrate at low pH. Decomposition may involve radicals or proceed by way of the classical peracid decomposition mechanism. Peroxynitrite (ONOOH/ONOO(-)) decomposition has been proposed to involve formation of peroxynitrate (O(2)NOOH/O(2)NOO(-)) at neutral pH (D. Gupta, B. Harish, R. Kissner and W. H. Koppenol, Dalton Trans., 2009, DOI: 10.1039/b905535e, see accompanying paper in this issue). Peroxynitrate is unstable and decomposes to nitrite and dioxygen. This study aimed to investigate whether O(2)NOO(-) formed upon ONOOH/ONOO(-) decomposition generates singlet molecular oxygen [O(2) ((1)Delta(g))]. As unequivocally revealed by the measurement of monomol light emission in the near infrared region at 1270 nm and by chemical trapping experiments, the decomposition of ONOO(-) or O(2)NOOH at neutral to alkaline pH generates O(2) ((1)Delta(g)) at a yield of ca. 1% and 2-10%, respectively. Characteristic light emission, corresponding to O(2) ((1)Delta(g)) monomolecular decay was observed for ONOO(-) and for O(2)NOOH prepared by reaction of H(2)O(2) with NO(2)BF(4) and of H(2)O(2) with NO(2)(-) in HClO(4). The generation of O(2) ((1)Delta(g)) from ONOO(-) increased in a concentration-dependent manner in the range of 0.1-2.5 mM and was dependent on pH, giving a sigmoid pro. le with an apparent pK(a) around pD 8.1 (pH 7.7). Taken together, our results clearly identify the generation of O(2) ((1)Delta(g)) from peroxynitrate [O(2)NOO(-) -> NO(2)(-) + O(2) ((1)Delta(g))] generated from peroxynitrite and also from the reactions of H(2)O(2) with either NO(2)BF(4) or NO(2)(-) in acidic media.

Method for cadmium and lead longitudinal profiles determination in hair by solid sampling graphite furnace atomic absorption spectrometry

This paper describes methods for the direct determination of Cd and Pb in hair segments (c.a. 5 mm similar to 80 mu g) by solid sampling graphite furnace atomic absorption spectrometry, becoming possible longitudinal profiles in a single strand of hair. To distinguish endogenous and exogenous content. strands of hair were washed by using two different procedures: IAEA protocol (acetone + water + acetone) and the combination of IAEA protocol with HCl washing (acetone + water + acetone + 0.1 mol l(-1) HCl). The concentration of Cd and Pb increased from the root Until the tip of hair washed according to IAEA protocol. However, when the strand of hair was washed using the combination of IAEA protocol and 0.1 mol l(-1) HCl, Cd concentrations decreased in all segments, and Pb concentrations decreased drastically near to the root (5 to 12 mm) and was systematically higher ill the end. The proposed method showed to be useful to assess the temporal variation to Cd and Pb exposure and call be Used for toxicological and environmental investigations. The limits of detection were 2.8 ng g(-1) for Cd and 40 ng g(-1) for Pb. The characteristic masses based oil integrated absorbance were 2.4 pg for Cd and 22 pg for Pb.

Validation of dot blot hybridization and denaturing high performance liquid chromatography as reliable methods for TP53 codon 72 genotyping in molecular epidemiologic studies

Background: Mutations in TP53 are common events during carcinogenesis. In addition to gene mutations, several reports have focused on TP53 polymorphisms as risk factors for malignant disease. Many studies have highlighted that the status of the TP53 codon 72 polymorphism could influence cancer susceptibility. However, the results have been inconsistent and various methodological features can contribute to departures from Hardy-Weinberg equilibrium, a condition that may influence the disease risk estimates. The most widely accepted method of detecting genotyping error is to confirm genotypes by sequencing and/or via a separate method. Results: We developed two new genotyping methods for TP53 codon 72 polymorphism detection: Denaturing High Performance Liquid Chromatography (DHPLC) and Dot Blot hybridization. These methods were compared with Restriction Fragment Length Polymorphism (RFLP) using two different restriction enzymes. We observed high agreement among all methodologies assayed. Dot-blot hybridization and DHPLC results were more highly concordant with each other than when either of these methods was compared with RFLP. Conclusions: Although variations may occur, our results indicate that DHPLC and Dot Blot hybridization can be used as reliable screening methods for TP53 codon 72 polymorphism detection, especially in molecular epidemiologic studies, where high throughput methodologies are required.

Evaluation of grinding methods for pellets preparation aiming at the analysis of plant materials by laser induced breakdown spectrometry

It has been demonstrated that laser induced breakdown spectrometry (LIBS) can be used as an alternative method for the determination of macro (P, K. Ca, Mg) and micronutrients (B, Fe, Cu, Mn, Zn) in pellets of plant materials. However, information is required regarding the sample preparation for plant analysis by LIBS. In this work, methods involving cryogenic grinding and planetary ball milling were evaluated for leaves comminution before pellets preparation. The particle sizes were associated to chemical sample properties such as fiber and cellulose contents, as well as to pellets porosity and density. The pellets were ablated at 30 different sites by applying 25 laser pulses per site (Nd:YAG@1064 nm, 5 ns, 10 Hz, 25J cm(-2)). The plasma emission collected by lenses was directed through an optical fiber towards a high resolution echelle spectrometer equipped with an ICCD. Delay time and integration time gate were fixed at 2.0 and 4.5 mu s, respectively. Experiments carried out with pellets of sugarcane, orange tree and soy leaves showed a significant effect of the plant species for choosing the most appropriate grinding conditions. By using ball milling with agate materials, 20 min grinding for orange tree and soy, and 60 min for sugarcane leaves led to particle size distributions generally lower than 75 mu m. Cryogenic grinding yielded similar particle size distributions after 10 min for orange tree, 20 min for soy and 30 min for sugarcane leaves. There was up to 50% emission signal enhancement on LIBS measurements for most elements by improving particle size distribution and consequently the pellet porosity. (C) 2011 Elsevier B.V. All rights reserved.

Direct Solid-Phase Optical Measurements in Flow Systems: A Review

Measurements based on absorption, reflectance, or luminescence of molecular species or complex ions can be carried out directly on a solid support simultaneously to the retention of the analyte. The use of this strategy in flow-based systems is advantageous in view of the reproducible handling of solutions in retention and elution steps of the analyte. This approach can be exploited to increase sensitivity, minimize reagent consumption as well as waste generation, improve selectivity or for simultaneous determination based on selective retention or differences in sorption rates of the analytes. This review focuses on the main characteristics of direct solid-phase measurements in flow systems, including the discussion of advantages and limitations and practical guidelines to the successful implementation of this approach. Selected applications in diverse fields, such as pharmaceutical, food, and environmental analysis are discussed.

Comparison of univariate and multivariate calibration for the determination of micronutrients in pellets of plant materials by laser induced breakdown spectrometry

The application of laser induced breakdown spectrometry (LIBS) aiming the direct analysis of plant materials is a great challenge that still needs efforts for its development and validation. In this way, a series of experimental approaches has been carried out in order to show that LIBS can be used as an alternative method to wet acid digestions based methods for analysis of agricultural and environmental samples. The large amount of information provided by LIBS spectra for these complex samples increases the difficulties for selecting the most appropriated wavelengths for each analyte. Some applications have suggested that improvements in both accuracy and precision can be achieved by the application of multivariate calibration in LIBS data when compared to the univariate regression developed with line emission intensities. In the present work, the performance of univariate and multivariate calibration, based on partial least squares regression (PLSR), was compared for analysis of pellets of plant materials made from an appropriate mixture of cryogenically ground samples with cellulose as the binding agent. The development of a specific PLSR model for each analyte and the selection of spectral regions containing only lines of the analyte of interest were the best conditions for the analysis. In this particular application, these models showed a similar performance. but PLSR seemed to be more robust due to a lower occurrence of outliers in comparison to the univariate method. Data suggests that efforts dealing with sample presentation and fitness of standards for LIBS analysis must be done in order to fulfill the boundary conditions for matrix independent development and validation. (C) 2009 Elsevier B.V. All rights reserved.

Methods of imagetic information representation

The aim of this paper is to highlight some of the methods of imagetic information representation, reviewing the literature of the area and proposing a model of methodology adapted to Brazilian museums. An elaboration of a methodology of imagetic information representation is developed based on Brazilian characteristics of information treatment in order to adapt it to museums. Finally, spreadsheets that show this methodology are presented.

Prevalence, magnitude, and methods of rapid weight loss among judo competitors

ARTIOLI, G. G., B. GUALANO, E. FRANCHINI, F. B. SCAGLIUSI, M. TAKESIAN, M. FUCHS, and A. H. LANCHA. Prevalence, Magnitude, and Methods of Rapid Weight Loss among Judo Competitors. Med. Sci. Sports Exerc., Vol. 42, No. 3, pp. 436-442, 2010. Purpose: To identify the prevalence, magnitude, and methods of rapid weight loss among judo competitors. Methods: Athletes (607 males and 215 females; age = 19.3 +/- 5.3 yr, weight = 70 +/- 7.5 kg, height = 170.6 +/- 9.8 cm) completed a previously validated questionnaire developed to evaluate rapid weight loss in judo athletes, which provides a score. The higher the score obtained, the more aggressive the weight loss behaviors. Data were analyzed using descriptive statistics and frequency analyses. Mean scores obtained in the questionnaire were used to compare specific groups of athletes using, when appropriate, Mann-Whitney U-test or general linear model one-way ANOVA followed by Tamhane post hoc test. Results: Eighty-six percent of athletes reported that have already lost weight to compete. When heavyweights are excluded, this percentage rises to 89%. Most athletes reported reductions of up to 5% of body weight (mean +/- SD: 2.5 +/- 2.3%). The most weight ever lost was 2%-5%, whereas a great part of athletes reported reductions of 5%-10% (mean +/- SD: 6 +/- 4%). The number of reductions underwent in a season was 3 +/- 5. The reductions usually occurred within 7 +/- 7 d. Athletes began cutting weight at 12.6 +/- 6.1 yr. No significant differences were found in the score obtained by male versus female athletes as well as by athletes from different weight classes. Elite athletes scored significantly higher in the questionnaire than nonelite. Athletes who began cutting weight earlier also scored higher than those who began later. Conclusions: Rapid weight loss is highly prevalent in judo competitors. The level of aggressiveness in weight management behaviors seems to not be influenced by the gender or by the weight class, but it seems to be influenced by competitive level and by the age at which athletes began cutting weight.

Methods of quantification of training load in exercise performed at maximal lactate steady state

The aim of the present study was to compare and correlate training impulse (TRIMP) estimates proposed by Banister (TRIMP(Banister)), Stagno (TRIMP(Stagno)) and Manzi (TRIMP(Manzi)). The subjects were submitted to an incremental test on cycle ergometer with heart rate and blood lactate concentration measurements. In the second occasion, they performed 30 min. of exercise at the intensity corresponding to maximal lactate steady state, and TRIMP(Banister), TRIMP(Stagno) and TRIMP(Manzi) were calculated. The mean values of TRIMP(Banister) (56.5 +/- 8.2 u.a.) and TRIMP(Stagno) (51.2 +/- 12.4 u.a.) were not different (P > 0.05) and were highly correlated (r = 0.90). Besides this, they presented a good agreement level, which means low bias and relatively narrow limits of agreement. On the other hand, despite highly correlated (r = 0.93), TRIMP(Stagno) and TRIMP(Manzi) (73.4 +/- 17.6 u.a.) were different (P < 0.05), with low agreement level. The TRIMP(Banister) e TRIMP(Manzi) estimates were not different (P = 0.06) and were highly correlated (r = 0.82), but showed low agreement level. Thus, we concluded that the investigated TRIMP methods are not equivalent. In practical terms, it seems prudent monitor the training process assuming only one of the estimates.

Preparation and characterization of Mo/W bimetallic carbides by using different synthesis methods

Molybdenum and tungsten bimetallic oxides were synthetized according to the following methods: Pechini, coprecipitation and solid state reaction (SSR). After the characterization, those solids were carbureted at programmed temperature. The carburation process was monitored by checking the consumption of carburant hydrocarbon and CO produced. The monitoring process permits to avoid or to diminish the formation of pirolytic carbon.

Identification and Validation of Brazilian Chronic Pain Descriptors

Appropriate pain assessment is very important for managing chronic pain. Given the cultural differences in verbally expressing pain and in psychosocial problems, specific tools are needed. The goal of this study was to identify and validate Brazilian pain descriptors. A purposive sample of health professionals and chronic pain patients was recruited. Four studies were conducted using direct and indirect psychophysical methods: category estimation, magnitude estimation, and magnitude estimation and tine-length. Results showed the descriptors which best describe chronic pain in Brazilian culture and demonstrated that there is not a significant correlation between patients and health professionals and that the psychophysical scale of judgment of pain descriptors is valid, stable, and consistent. Results reinforced that the translations of word descriptors and research tools into another language may be inappropriate, owing to differences in perception and communication and the inadequacy of exact translations to reflect the intended meaning. Given the complexity of the chronic pain, personal suffering involved, and the need for accurate assessment of chronic pain using descriptors stemming from Brazilian culture and language, it is essential to investigate the most adequate words to describe chronic pain. Although it requires more refinement, the Brazilian chronic pain descriptors can be used further to develop a multidimensional pain assessment tool that is culturally sensitive. (C) 2009 by the American Society for Pain Management Nursing

Ecodesign methods focused on remanufacturing

Understanding the product`s `end-of-life` is important to reduce the environmental impact of the products` final disposal. When the initial stages of product development consider end-of-life aspects, which can be established by ecodesign (a proactive approach of environmental management that aims to reduce the total environmental impact of products), it becomes easier to close the loop of materials. The `end-of-life` ecodesign methods generally include more than one `end-of-life` strategy. Since product complexity varies substantially, some components, systems or sub-systems are easier to be recycled, reused or remanufactured than others. Remanufacture is an effective way to maintain products in a closed-loop, reducing both environmental impacts and costs of the manufacturing processes. This paper presents some ecodesign methods focused on the integration of different `end-of-life` strategies, with special attention to remanufacturing, given its increasing importance in the international scenario to reduce the life cycle impacts of products. (C) 2009 Elsevier Ltd. All rights reserved.

A Study on Unconditionally Stable FDTD Methods for the Modeling of Metamaterials

We assess the performance of three unconditionally stable finite-difference time-domain (FDTD) methods for the modeling of doubly dispersive metamaterials: 1) locally one-dimensional FDTD; 2) locally one-dimensional FDTD with Strang splitting; and (3) alternating direction implicit FDTD. We use both double-negative media and zero-index media as benchmarks.