Structural requirement for PPAR gamma binding revealed by a meta analysis of holo-crystal structures

PPAR gamma is a ligand regulated transcriptional factor that modulates the transcription of several genes involved in fat and sugar metabolism. Due to its easy bacterial expression and crystallization, several crystal structures of holo-PPAR gamma have been reported and deposited in the Protein Data Bank. Here, we investigated the three-dimensional electrostatic properties of 55 PPAR gamma ligands and used this information for clustering them through principal component analysis. We found out that, according to their electrostatic potential, these ligands can be separated in three groups, with different binding features. We also observed that non-selective and selective ligands show different 3D electrostatic properties and are separated in different clusters. The relevance of this analysis for the development of new binders is discussed. (C) 2010 Elsevier Masson SAS. All rights reserved.

Multivariate Analysis for the Classification Differentiation of Brazilian Sugarcane Spirits by Analysis of Organic and Inorganic Compounds

Brazilian sugarcane spirits were analyzed to elucidate similarities and dissimilarities by principal component analysis. Nine aldehydes, six alcohols, and six metal cations were identified and quantified. Isobutanol (LD 202.9 mu gL-1), butiraldehyde (0.08-0.5 mu gL-1), ethanol (39-47% v/v), and copper (371-6068 mu gL-1) showed marked similarities, but the concentration levels of n-butanol (1.6-7.3 mu gL-1), sec-butanol (LD 89 mu gL-1), formaldehyde (0.1-0.74 mu gL-1), valeraldehyde (0.04-0.31 mu gL-1), iron (8.6-139.1 mu gL-1), and magnesium (LD 1149 mu gL-1) exhibited differences from samples.

Digital spiral analysis for objective assessment of fine motor timing variability in Parkinson's disease

OBJECTIVES: To develop a method for objective assessment of fine motor timing variability in Parkinson’s disease (PD) patients, using digital spiral data gathered by a touch screen device. BACKGROUND: A retrospective analysis was conducted on data from 105 subjects including65 patients with advanced PD (group A), 15 intermediate patients experiencing motor fluctuations (group I), 15 early stage patients (group S), and 10 healthy elderly subjects (HE) were examined. The subjects were asked to perform repeated upper limb motor tasks by tracing a pre-drawn Archimedes spiral as shown on the screen of the device. The spiral tracing test was performed using an ergonomic pen stylus, using dominant hand. The test was repeated three times per test occasion and the subjects were instructed to complete it within 10 seconds. Digital spiral data including stylus position (x-ycoordinates) and timestamps (milliseconds) were collected and used in subsequent analysis. The total number of observations with the test battery were as follows: Swedish group (n=10079), Italian I group (n=822), Italian S group (n = 811), and HE (n=299). METHODS: The raw spiral data were processed with three data processing methods. To quantify motor timing variability during spiral drawing tasks Approximate Entropy (APEN) method was applied on digitized spiral data. APEN is designed to capture the amount of irregularity or complexity in time series. APEN requires determination of two parameters, namely, the window size and similarity measure. In our work and after experimentation, window size was set to 4 and similarity measure to 0.2 (20% of the standard deviation of the time series). The final score obtained by APEN was normalized by total drawing completion time and used in subsequent analysis. The score generated by this method is hence on denoted APEN. In addition, two more methods were applied on digital spiral data and their scores were used in subsequent analysis. The first method was based on Digital Wavelet Transform and Principal Component Analysis and generated a score representing spiral drawing impairment. The score generated by this method is hence on denoted WAV. The second method was based on standard deviation of frequency filtered drawing velocity. The score generated by this method is hence on denoted SDDV. Linear mixed-effects (LME) models were used to evaluate mean differences of the spiral scores of the three methods across the four subject groups. Test-retest reliability of the three scores was assessed after taking mean of the three possible correlations (Spearman’s rank coefficients) between the three test trials. Internal consistency of the methods was assessed by calculating correlations between their scores. RESULTS: When comparing mean spiral scores between the four subject groups, the APEN scores were different between HE subjects and three patient groups (P=0.626 for S group with 9.9% mean value difference, P=0.089 for I group with 30.2%, and P=0.0019 for A group with 44.1%). However, there were no significant differences in mean scores of the other two methods, except for the WAV between the HE and A groups (P<0.001). WAV and SDDV were highly and significantly correlated to each other with a coefficient of 0.69. However, APEN was not correlated to neither WAV nor SDDV with coefficients of 0.11 and 0.12, respectively. Test-retest reliability coefficients of the three scores were as follows: APEN (0.9), WAV(0.83) and SD-DV (0.55). CONCLUSIONS: The results show that the digital spiral analysis-based objective APEN measure is able to significantly differentiate the healthy subjects from patients at advanced level. In contrast to the other two methods (WAV and SDDV) that are designed to quantify dyskinesias (over-medications), this method can be useful for characterizing Off symptoms in PD. The APEN was not correlated to none of the other two methods indicating that it measures a different construct of upper limb motor function in PD patients than WAV and SDDV. The APEN also had a better test-retest reliability indicating that it is more stable and consistent over time than WAV and SDDV.

Automatic spiral analysis for objective assessment of motor symptoms in Parkinson's disease

Objective: To develop a method for objective quantification of PD motor symptoms related to Off episodes and peak dose dyskinesias, using spiral data gathered by using a touch screen telemetry device. The aim was to objectively characterize predominant motor phenotypes (bradykinesia and dyskinesia), to help in automating the process of visual interpretation of movement anomalies in spirals as rated by movement disorder specialists. Background: A retrospective analysis was conducted on recordings from 65 patients with advanced idiopathic PD from nine different clinics in Sweden, recruited from January 2006 until August 2010. In addition to the patient group, 10 healthy elderly subjects were recruited. Upper limb movement data were collected using a touch screen telemetry device from home environments of the subjects. Measurements with the device were performed four times per day during week-long test periods. On each test occasion, the subjects were asked to trace pre-drawn Archimedean spirals, using the dominant hand. The pre-drawn spiral was shown on the screen of the device. The spiral test was repeated three times per test occasion and they were instructed to complete it within 10 seconds. The device had a sampling rate of 10Hz and measured both position and time-stamps (in milliseconds) of the pen tip. Methods: Four independent raters (FB, DH, AJ and DN) used a web interface that animated the spiral drawings and allowed them to observe different kinematic features during the drawing process and to rate task performance. Initially, a number of kinematic features were assessed including ‘impairment’, ‘speed’, ‘irregularity’ and ‘hesitation’ followed by marking the predominant motor phenotype on a 3-category scale: tremor, bradykinesia and/or choreatic dyskinesia. There were only 2 test occasions for which all the four raters either classified them as tremor or could not identify the motor phenotype. Therefore, the two main motor phenotype categories were bradykinesia and dyskinesia. ‘Impairment’ was rated on a scale from 0 (no impairment) to 10 (extremely severe) whereas ‘speed’, ‘irregularity’ and ‘hesitation’ were rated on a scale from 0 (normal) to 4 (extremely severe). The proposed data-driven method consisted of the following steps. Initially, 28 spatiotemporal features were extracted from the time series signals before being presented to a Multilayer Perceptron (MLP) classifier. The features were based on different kinematic quantities of spirals including radius, angle, speed and velocity with the aim of measuring the severity of involuntary symptoms and discriminate between PD-specific (bradykinesia) and/or treatment-induced symptoms (dyskinesia). A Principal Component Analysis was applied on the features to reduce their dimensions where 4 relevant principal components (PCs) were retained and used as inputs to the MLP classifier. Finally, the MLP classifier mapped these components to the corresponding visually assessed motor phenotype scores for automating the process of scoring the bradykinesia and dyskinesia in PD patients whilst they draw spirals using the touch screen device. For motor phenotype (bradykinesia vs. dyskinesia) classification, the stratified 10-fold cross validation technique was employed. Results: There were good agreements between the four raters when rating the individual kinematic features with intra-class correlation coefficient (ICC) of 0.88 for ‘impairment’, 0.74 for ‘speed’, 0.70 for ‘irregularity’, and moderate agreements when rating ‘hesitation’ with an ICC of 0.49. When assessing the two main motor phenotype categories (bradykinesia or dyskinesia) in animated spirals the agreements between the four raters ranged from fair to moderate. There were good correlations between mean ratings of the four raters on individual kinematic features and computed scores. The MLP classifier classified the motor phenotype that is bradykinesia or dyskinesia with an accuracy of 85% in relation to visual classifications of the four movement disorder specialists. The test-retest reliability of the four PCs across the three spiral test trials was good with Cronbach’s Alpha coefficients of 0.80, 0.82, 0.54 and 0.49, respectively. These results indicate that the computed scores are stable and consistent over time. Significant differences were found between the two groups (patients and healthy elderly subjects) in all the PCs, except for the PC3. Conclusions: The proposed method automatically assessed the severity of unwanted symptoms and could reasonably well discriminate between PD-specific and/or treatment-induced motor symptoms, in relation to visual assessments of movement disorder specialists. The objective assessments could provide a time-effect summary score that could be useful for improving decision-making during symptom evaluation of individualized treatment when the goal is to maximize functional On time for patients while minimizing their Off episodes and troublesome dyskinesias.

Multivariate analysis for the classification and differentiation of Madeira wines according to main grape varieties

In order to differentiate and characterize Madeira wines according to main grape varieties, the volatile composition (higher alcohols, fatty acids, ethyl esters and carbonyl compounds) was determined for 36 monovarietal Madeira wine samples elaborated from Boal, Malvazia, Sercial and Verdelho white grape varieties. The study was carried out by headspace solid-phase microextraction technique (HS-SPME), in dynamic mode, coupled with gas chromatography–mass spectrometry (GC–MS). Corrected peak area data for 42 analytes from the above mentioned chemical groups was used for statistical purposes. Principal component analysis (PCA) was applied in order to determine the main sources of variability present in the data sets and to establish the relation between samples (objects) and volatile compounds (variables). The data obtained by GC–MS shows that the most important contributions to the differentiation of Boal wines are benzyl alcohol and (E)-hex-3-en-1-ol. Ethyl octadecanoate, (Z)-hex-3-en-1-ol and benzoic acid are the major contributions in Malvazia wines and 2-methylpropan-1-ol is associated to Sercial wines. Verdelho wines are most correlated with 5-(ethoxymethyl)-furfural, nonanone and cis-9-ethyldecenoate. A 96.4% of prediction ability was obtained by the application of stepwise linear discriminant analysis (SLDA) using the 19 variables that maximise the variance of the initial data set.

Ecomorfologia de dez espécies de peixes marinhos mais abundantes de Galinhos/RN

Ecomorphology is a science based on the idea that morphological differences among species could be associated with distinct biological and environmental pressures suffered by them. These differences can be studied employing morphological and biometric indexes denominated Ecomorphological attributes , representing standards that express characteristics of the individual in relation to its environment, and can be interpreted as indicators of life habits or adaptations suffered due its occupation of different habitats. This work aims to contribute for the knowledge of the ecomorphology of the Brazilian marine ichthyofauna, specifically from Galinhos, located at Rio Grande do Norte state. 10 different species of fish were studied, belonging the families Gerreidae (Eucinostomus argenteus), Haemulidae (Orthopristis ruber,Pomadasyscorvinaeformis,Haemulonaurolineatum,Haemulonplumieri,Haemulonsteindachneri), Lutjanidae (Lutjanus synagris), Paralichthyidae (Syaciummicrurum), Bothidae (Bothus ocellatus) and Tetraodontidae (Sphoeroidestestudineus), which were obtained during five collections, in the period time of September/2004 to April/2005, utilizing three special nets. The ecomorphological study was performed at the laboratory. Eight to ten samples of each fish specie were measured. Fifteen morphological aspects were considered to calculate twelve ecomorphological attributes. Multivariate statistical analysis methods such as Principal Component Analysis (PCA) and Cluster Analysis were done to identify ecmorphological patterns to describe the data set obtained. As results, H.aurolineatumwas the most abundant specie found (23,03%) and S.testudineusthe less one with 0,23%. The 1st Principal component showed variation of 60,03% with influence of the ecomorphological attribute related to body morphology, while the 2nd PC with 23,25% variation had influence of the ecomorphological attribute related to oral morphology. The Cluster Analiysis promoted the identification of three distinct groups Perciformes, Pleuronectiformes and Tetraodontiformes. Based on the obtained data, considering morphological characters differences among the species studied, we suggest that all of them live at the medium (E.argenteus,O.rubber, P.corvinaeformis,H.aurolineatum,H.plumieri,H.steindachneri,L.synagris) and bottom (S.micrurum,B.ocellatus,S.testudineus) region of column water.

Abordagem multivariada envolvendo características físicas e morfológicas do sêmen bovino, idade dos touros e época de colheita de sêmen

Avaliaram-se as relações entre características físicas e morfológicas do sêmen de bovinos das subespécies Bos taurus taurus e Bos taurus indicus com a idade dos touros e a época de colheita do sêmen. Utilizaram-se observações feitas durante o período de 1993 a 1999, em 42 touros com 12 a 174 meses de idade, divididos em cinco classes: Bos taurus taurus - 12 a 36 meses; 37 a 60 meses; 61 a 84 meses; 85 a 108 meses; e 109 a 138 meses; e Bos taurus indicus - 12 a 42 meses; 43 a 72 meses; 73 a 102 meses; 103 a 132 meses; e 133 a 174 meses. As características analisadas foram: volume, turbilhonamento espermático, concentração espermática, motilidade espermática, vigor espermático, anormalidades espermáticas e integridade do acrossoma. No processamento das análises, utilizaram-se as médias das características em cada classe de idade e o mês de colheita de sêmen durante o período de 1993 a 1999. As técnicas estatísticas multivariadas de componentes principais e de agrupamento hierárquico mostraram resultados que podem contribuir na escolha de sêmen de melhor qualidade. As classes 103 a 132 meses e 133 a 174 meses para a subespécie Bos taurus indicus e a classe de idade 109 a 138 meses para a subespécie Bos taurus taurus foram as mais contrastantes. Para ambas as subespécies, nos meses mais úmidos, o sêmen apresentou menor qualidade, principalmente na subespécie Bos taurus taurus. As características do sêmen mais contrastantes no estudo por classes e no período de coleta de sêmen foram: vigor espermático, motilidade espermática, concentração espermática, integridade do acrossoma e anormalidades terciárias no sêmen.

Multivariate analysis of fresh-cut carambola slices stored under different temperatures

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

Ingredient classification according to the digestible amino acid profile: an exploratory analysis

This study aimed: 1) to classify ingredients according to the digestible amino acid (AA) profile; 2) to determine ingredients with AA profile closer to the ideal for broiler chickens; and 3) to compare digestible AA profiles from simulated diets with the ideal protein profile. The digestible AA levels of 30 ingredients were compiled from the literature and presented as percentages of lysine according to the ideal protein concept. Cluster and principal component analyses (exploratory analyses) were used to compose and describe groups of ingredients according to AA profiles. Four ingredient groups were identified by cluster analysis, and the classification of the ingredients within each of these groups was obtained from a principal component analysis, showing 11 classes of ingredients with similar digestible AA profiles. The ingredients with AA profiles closer to the ideal protein were meat and bone meal 45, fish meal 60 and wheat germ meal, all of them constituting Class 1; the ingredients from the other classes gradually diverged from the ideal protein. Soybean meal, which is the main protein source for poultry, showed good AA balance since it was included in Class 3. on the contrary, corn, which is the main energy source in poultry diets, was classified in Class 8. Dietary AA profiles were improved when corn and/or soybean meal were partially or totally replaced in the simulations by ingredients with better AA balance.

Discrimination of geomorphic surfaces with multivariate analysis of soil attributes in sandstone - basalt lithosequence

O conceito de superfície geomórfica permite uma interligação entre os diferentes ramos da ciência do solo, tais como geologia, geomorfologia e pedologia. Esta associação favorece a compreensão da distribuição espacial dos solos na paisagem, e torna possível compreender o comportamento dos atributos do solo, que estão principalmente relacionadas com a estratigrafia e formas do relevo. Assim, este estudo visa à aplicação da estatística multivariada para categorizar superfícies geomórficas em uma litossequência arenito-basalto, de modo a fornecer uma base para a avaliação do solo em áreas afins. A área de estudo está localizada no município de Pereira Barreto, São Paulo, Brasil. A área escolhida possui 530 hectares, onde foram localizadas e mapeadas três superfícies geomórficas (I, II e III). Na área, 134 amostras foram coletadas nas profundidades de 0,0-0,2 m e 0,8-1,0 m, foram determinados os conteúdos de areia, silte e argila, pH em CaCl2, conteúdo de MO, P, Ca, Mg, K, Al e H+Al. Com base nos resultados, foram realizadas a análise univariada e multivariada de variância, clusters e principal componente, a fim de comparar as três superfícies geomórficas. A análise estatística univariada dos atributos do solo não foi eficiente na identificação das três superfícies geomórficas. Utilizando-se os atributos físicos e químicos do solo, as técnicas estatísticas multivariada permitiram à separação dos três grupos de corpos naturais do solo que foram equivalentes as três superfícies geomórficas mapeadas. Estes resultados são interessantes, pois demonstram a viabilidade da utilização de classificação numérica das superfícies geomórficas para ajudar no mapeamento de solo.

Caracterização morfológica de espécies de trapoeraba (Commelina spp.) utilizando a análise multivariada

As espécies Commelina benghalensis, C. villosa, C. diffusa e C. erecta são conhecidas como trapoeraba e, freqüentemente, são confundidas entre si, dificultando o controle químico, o que pode provocar prejuízos econômicos e danos ambientais. O presente trabalho teve como objetivo selecionar características morfológicas que possibilitem facilitar a identificação dessas espécies, utilizando a técnica de análise multivariada. Foram avaliadas 12 características morfológicas descritivas e 13 quantitativas, utilizando-se os métodos de análise de agrupamento e análise de componentes principais. As espécies apresentaram alto grau de dissimilaridade, sobretudo em relação às características descritivas, destacando-se: hábito da planta, pilosidade do caule e da folha, entre outros. As características quantitativas também mostraram poder discriminatório. Características que apresentaram alto valor taxonômico foram selecionadas para compor a chave de identificação para as quatro espécies de Commelina.

Classification of Aristolochia species based on GC-MS and chemometric analyses of essential oils

Essential oils were obtained from roots of 10 Aristolochia species by hydrodistillation and analysed by GC MS. A total of 75 compounds were identified in the analysed oils. Multivariate analyses of the chemical constituents of the roots enabled classification of the species into four morphological groups. These forms of analysis represent an aid in identification of further specimens belonging to these species. (C) 2007 Elsevier Ltd. All rights reserved.

Características morfo-anatômicas e bromatológicas de folhas de amoreira em relação às preferências do bicho-da-seda

O objetivo deste trabalho foi avaliar, quantitativamente, as características morfo-anatômicas e bromatológicas das folhas de dez cultivares de amoreira, e estabelecer as relações de preferência do bicho-da-seda, por essas cultivares. Foram coletadas as folhas superior (5ª) e mediana (15ª) da planta, contadas a partir do ápice. As cultivares foram comparadas pelos métodos estatísticos multivariados de análise de agrupamento e análise de componentes principais. As cultivares Korin, Calabresa, IZ 5/2 e IZ 15/7 foram consideradas as mais recomendáveis para a alimentação das lagartas do bicho-da-seda, pois apresentaram valores altos de porcentagem de folha consumida, atribuídos à ocorrência de características desejáveis nas folhas, tais como menor teor de fibra bruta, menor quantidade de idioblastos de cistólito e de mucilagem, menor proporção de epiderme e maior de parênquima, comparativamente, às outras cultivares estudadas. As cultivares IZ 13/6 e IZ 57/2 foram consideradas as menos recomendáveis. As demais cultivares comportaram-se como intermediárias na preferência do bicho-da-seda.

Estatística multivariada na discriminação de raças amazônicas de pupunheiras (Bactris gasipaes Kunth) em Manaus (Brasil)

As raças e populações de pupunheiras ao longo dos rios Amazonas e Solimões apresentam grande variabilidade genética ainda não totalmente caracterizada. Neste estudo, foram aplicadas técnicas estatísticas multivariadas a 15 descritores morfológicos numa tentativa de caracterizar, morfometricamente, três raças existentes ao longo da Bacia desses rios. As três análises em conjunto permitiram uma discriminação das raças, mostrando também que os descritores mais importantes nessa seleção foram: número de espigas, comprimento da ráquis, peso do fruto, espessura das cascas, facilidade para descascar os frutos, peso das cascas, sabor dos frutos, espessura da polpa, distância morfológica dos frutos e peso da semente.

Analysis of floristic composition and structure as an aid to monitoring protected areas of dense rain forest in southeastern Brazil

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