A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.

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.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Background: Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results: Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion: Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.

Long-term decomposition of sugarcane harvest residues in Sao Paulo state, Brazil

Crop residues returned to the soil are important to preserve fertility and sustainability. This research addressed the long-term decomposition of sugarcane post-harvest residues (trash) under reduced tillage, therefore field renewal was performed with herbicide followed by subsoiling and ratoons were deprived of interrow scarification. The trial was conducted in the northern Sao Paulo State, Brazil during four consecutive crops (2005-2008) where litter bags containing N-15-labeled trash were disposed in the field attempting to simulate two distinct situations: the previous crop trash (PCT) or residues incorporated in the field after tillage, and post-harvest trash (PHT) or the remains of plant-cane harvest. Decomposition rates regarding dry matter (DM), carbon (C), root growth, plant nutrients (N, P, K, Ca, Mg and S), lignin (LIG) cellulose (CEL) and hemicellulose (HCEL) contents were assessed for PCT (2005 ndash;2008) and for PHT (2006-2008). There were significant reductions on DM and C:N ratio due to C losses and root growth within the litter bags over time. The DM from PCT and PHT decreased 96% and 73% after four and three crops, respectively, and the higher nutrients release were found for K, Ca and N. The LIG, CEL and HCEL concentrations in PCT decreased 60%, 29%, 70% after four crops and 47%, 35%, 70% from PHT after three crops, respectively. Trash decomposition was driven mainly by residues biochemical composition, root growth within the trash blanket and the climatic conditions during the crop cycles. (C) 2012 Elsevier Ltd. All rights reserved.

Ochratoxin A in wines from 2002 to 2008 harvest marketed in Rio de Janeiro, Brazil

The occurrence of ochratoxin A (OTA) in wine from 2002 to 2008 harvest, traded in Rio de Janeiro State, was evaluated by analysing 43 national and 37 imported wines from Argentina (32) and Chile (5), adding up to 80 samples in total. OTA determination was performed using immunoaffinity columns and high-performance liquid chromatography. In 80 wine samples analysed, 25 (31.3%) were positive, presenting levels greater than 0.020 ng OTA mL(-1). It was not detected in imported wines. Within national wines, 58.1% of the samples were contaminated, with levels ranging from 0.020 to 0.050 ng mL(-1). The toxin was detected in 18 (69.2%) of 26 samples analysed of red table wine. Wines from 2008 harvest presented 84.6% of samples contaminated in 13 samples analysed. Despite the levels found in this study, they are below Brazilian tolerance limits. Nevertheless, the presence of OTA as found contributes to the human exposure to this toxin.

Comparison of 3 modes of automated weaning from mechanical ventilation: A bench study

Purpose: Automated weaning modes are available in some mechanical ventilators, but no studies compared them hitherto. We compared the performance of 3 automated modes under standard and challenging situations. Methods: We used a lung simulator to compare 3 automated modes, adaptive support ventilation (ASV), mandatory rate ventilation (MRV), and Smartcare, in 6 situations, weaning success, weaning failure, weaning success with extreme anxiety, weaning success with Cheyne-Stokes, weaning success with irregular breathing, and weaning failure with ineffective efforts. Results: The 3 modes correctly recognized the situations of weaning success and failure, even when anxiety or irregular breathing were present but incorrectly recognized weaning success with Cheyne-Stokes. MRV incorrectly recognized weaning failure with ineffective efforts. Time to pressure support (PS) stabilization was shorter for ASV (1-2 minutes for all situations) and MRV (1-7 minutes) than for Smartcare (8-78 minutes). ASV had higher rates of PS oscillations per 5 minutes (4-15), compared with Smartcare (0-1) and MRV (0-12), except when extreme anxiety was present. Conclusions: Smartcare, ASV, and MRV were equally able to recognize weaning success and failure, despite the presence of anxiety or irregular breathing but performed incorrectly in the presence of Cheyne-Stokes. PS behavior over the time differs among modes, with ASV showing larger and more frequent PS oscillations over the time. Clinical studies are needed to confirm our results. (C) 2012 Elsevier Inc. All rights reserved.

EEG amplitude modulation analysis for semi-automated diagnosis of Alzheimer's disease

Recent experimental evidence has suggested a neuromodulatory deficit in Alzheimer's disease (AD). In this paper, we present a new electroencephalogram (EEG) based metric to quantitatively characterize neuromodulatory activity. More specifically, the short-term EEG amplitude modulation rate-of-change (i.e., modulation frequency) is computed for five EEG subband signals. To test the performance of the proposed metric, a classification task was performed on a database of 32 participants partitioned into three groups of approximately equal size: healthy controls, patients diagnosed with mild AD, and those with moderate-to-severe AD. To gauge the benefits of the proposed metric, performance results were compared with those obtained using EEG spectral peak parameters which were recently shown to outperform other conventional EEG measures. Using a simple feature selection algorithm based on area-under-the-curve maximization and a support vector machine classifier, the proposed parameters resulted in accuracy gains, relative to spectral peak parameters, of 21.3% when discriminating between the three groups and by 50% when mild and moderate-to-severe groups were merged into one. The preliminary findings reported herein provide promising insights that automated tools may be developed to assist physicians in very early diagnosis of AD as well as provide researchers with a tool to automatically characterize cross-frequency interactions and their changes with disease.

Comparison of Visual Acuity and Automated Perimetry Findings in Patients With Neuromyelitis Optica or Multiple Sclerosis After Single or Multiple Attacks of Optic Neuritis

Objective: To review the clinical characteristics of patients with neuromyelitis optica (NMO) and to compare their visual outcome with those of patients with optic neuritis (ON) and multiple sclerosis (MS). Methods: Thirty-three patients with NMO underwent neuro-ophthalmic evaluation, including automated perimetry along with 30 patients with MS. Visual function in both groups was compared overall and specifically for eyes after a single episode of ON. Results: Visual function and average visual field (VF) mean deviation were significantly worse in eyes of patients with NMO. After a single episode of ON, the VF was normal in only 2 of 36 eyes of patients with NMO compared to 17 of 35 eyes with MS (P < 0.001). The statistical analysis indicated that after a single episode of ON, the odds ratio for having NMO was 6.0 (confidence interval [CI]: 1.6-21.9) when VF mean deviation was worse than -20.0 dB while the odds ratio for having MS was 16.0 (CI: 3.6-68.7) when better than -3.0 dB. Conclusion: Visual outcome was significantly worse in NMO than in MS. After a single episode of ON, suspicion of NMO should be raised in the presence of severe residual VF deficit with automated perimetry and lowered in the case of complete VF recovery.

Structure-function Relationships Using the Cirrus Spectral Domain Optical Coherence Tomograph and Standard Automated Perimetry

Purpose: To evaluate the relationship between glaucomatous structural damage assessed by the Cirrus Spectral Domain OCT (SDOCT) and functional loss as measured by standard automated perimetry (SAP). Methods: Four hundred twenty-two eyes (78 healthy, 210 suspects, 134 glaucomatous) of 250 patients were recruited from the longitudinal Diagnostic Innovations in Glaucoma Study and from the African Descent and Glaucoma Evaluation Study. All eyes underwent testing with the Cirrus SDOCT and SAP within a 6-month period. The relationship between parapapillary retinal nerve fiber layer thickness (RNFL) sectors and corresponding topographic SAP locations was evaluated using locally weighted scatterplot smoothing and regression analysis. SAP sensitivity values were evaluated using both linear as well as logarithmic scales. We also tested the fit of a model (Hood) for structure-function relationship in glaucoma. Results: Structure was significantly related to function for all but the nasal thickness sector. The relationship was strongest for superotemporal RNFL thickness and inferonasal sensitivity (R(2) = 0.314, P < 0.001). The Hood model fitted the data relatively well with 88% of the eyes inside the 95% confidence interval predicted by the model. Conclusions: RNFL thinning measured by the Cirrus SDOCT was associated with correspondent visual field loss in glaucoma.

Clinical Efficacy of a New Automated Hemoencefalographic Neurofeedback Protocol

Among the ongoing attempts to enhance cognitive performance, an emergent and yet underrepresented venue is brought by hemoencefalographic neurofeedback (HEG). This paper presents three related advances in HEG neurofeedback for cognitive enhancement: a) a new HEG protocol for cognitive enhancement, as well as b) the results of independent measures of biological efficacy (EEG brain maps) extracted in three phases, during a one year follow up case study; c) the results of the first controlled clinical trial of HEG, designed to assess the efficacy of the technique for cognitive enhancement of an adult and neurologically intact population. The new protocol was developed in the environment of a software that organizes digital signal algorithms in a flowchart format. Brain maps were produced through 10 brain recordings. The clinical trial used a working memory test as its independent measure of achievement. The main conclusion of this study is that the technique appears to be clinically promising. Approaches to cognitive performance from a metabolic viewpoint should be explored further. However, it is particularly important to note that, to our knowledge, this is the world's first controlled clinical study on the matter and it is still early for an ultimate evaluation of the technique.

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

The development of new procedures for quickly obtaining accurate information on the physiological potential of seed lots is essential for developing quality control programs for the seed industry. In this study, the effectiveness of an automated system of seedling image analysis (Seed Vigor Imaging System - SVIS) in determining the physiological potential of sun hemp seeds and its relationship with electrical conductivity tests, were evaluated. SVIS evaluations were performed three and four days after sowing and data on the vigor index and the length and uniformity of seedling growth were collected. The electrical conductivity test was made on 50 seed replicates placed in containers with 75 mL of deionised water at 25 ºC and readings were taken after 1, 2, 4, 8 and 16 hours of imbibition. Electrical conductivity measurements at 4 or 8 hours and the use of the SVIS on 3-day old seedlings can effectively detect differences in vigor between different sun hemp seed lots.

Adaptação cultural e confiabilidade para o Brasil do Automated Telephone Disease Management: resultados preliminares

OBJETIVOS: Traduzir, adaptar culturalmente para o Brasil o ATDM Satisfaction Scales e avaliar a confiabilidade da versão adaptada em adultos brasileiros com DM. MÉTODOS: Estudo metodológico, cujo processo de adaptação cultural incluiu: tradução, comitê de juízes, retrotradução, análise semântica e pré-teste. Este estudo incluiu uma amostra de 39 adultos brasileiros com DM cadastrados em um programa educativo do interior paulista. RESULTADOS: A versão adaptada do instrumento mostrou boa aceitação com fácil compreensão dos itens pelos participantes, com confiabilidade variando entre 0,30 e 0,43. CONCLUSÃO: Após a análise das propriedades psicométricas e finalização do processo de validação no País, o instrumento poderá ser utilizado por pesquisadores brasileiros, possibilitando ser comparado com outras culturas.