Comparing non-stationary and irregularly spaced time series

In this paper, we present approximate distributions for the ratio of the cumulative wavelet periodograms considering stationary and non-stationary time series generated from independent Gaussian processes. We also adapt an existing procedure to use this statistic and its approximate distribution in order to test if two regularly or irregularly spaced time series are realizations of the same generating process. Simulation studies show good size and power properties for the test statistic. An application with financial microdata illustrates the test usefulness. We conclude advocating the use of these approximate distributions instead of the ones obtained through randomizations, mainly in the case of irregular time series. (C) 2012 Elsevier B.V. All rights reserved.

Solar-Terrestrial Signal Record in Tree Ring Width Time Series from Brazil

This work investigates the behavior of the sunspot number and Southern Oscillation Index (SOI) signal recorded in the tree ring time series for three different locations in Brazil: Humaita in Amaznia State, Porto Ferreira in So Paulo State, and Passo Fundo in Rio Grande do Sul State, using wavelet and cross-wavelet analysis techniques. The wavelet spectra of tree ring time series showed signs of 11 and 22 years, possibly related to the solar activity, and periods of 2-8 years, possibly related to El Nio events. The cross-wavelet spectra for all tree ring time series from Brazil present a significant response to the 11-year solar cycle in the time interval between 1921 to after 1981. These tree ring time series still have a response to the second harmonic of the solar cycle (5.5 years), but in different time intervals. The cross-wavelet maps also showed that the relationship between the SOI x tree ring time series is more intense, for oscillation in the range of 4-8 years.

Structure- and Ligand-Based Structure-Activity Relationships for a Series of Inhibitors of Aldolase

Aldolase has emerged as a promising molecular target for the treatment of human African trypanosomiasis. Over the last years, due to the increasing number of patients infected with Trypanosoma brucei, there is an urgent need for new drugs to treat this neglected disease. In the present study, two-dimensional fragment-based quantitative-structure activity relationship (QSAR) models were generated for a series of inhibitors of aldolase. Through the application of leave-one-out and leave-many-out cross-validation procedures, significant correlation coefficients were obtained (r(2) = 0.98 and q(2) = 0.77) as an indication of the statistical internal and external consistency of the models. The best model was employed to predict pK(i) values for a series of test set compounds, and the predicted values were in good agreement with the experimental results, showing the power of the model for untested compounds. Moreover, structure-based molecular modeling studies were performed to investigate the binding mode of the inhibitors in the active site of the parasitic target enzyme. The structural and QSAR results provided useful molecular information for the design of new aldolase inhibitors within this structural class.

The Banhado Alkaline Complex, Southeastern Brazil: source and evolution of potassic SiO2-undersaturated high-Ca and low-Ca magmatic series

The Cretaceous Banhado alkaline complex in southeastern Brazil presents two potassic SiO2-undersaturated series. The high-Ca magmatic series consist of initially fractionated olivine (Fo(92-91)) + diopside (Wo(48-43)En(49-35)Ae(0-7)), as evidenced by the presence of xenocrysts and xenoliths. In that sequence, diopside (Wo(47-38)En(46-37)Ae(0-8)) + phlogopite + apatite + perovskite (Prv(> 92)) crystallized to form the phlogopite melteigite and led to the Ca enrichment of the magma. Diopside (Wo(47-41)En(32-24) Ae(3-14)) continued to crystallize as an early mafic mineral, followed by nepheline (Ne(74.8-70.1)Ks(26.3-21.2)Qz(7.6-0.9)) and leucite (Lc(65-56)) and subsequently by melanite and potassic feldspar (Or(85-99)Ab(1-7)) to form melanite ijolites, wollastonite-melanite urtites and melanite-nepheline syenites. Melanite-pseudoleucite-nepheline syenites are interpreted to be a leucite accumulation. Melanite nephelinite dykes are believed to represent some of the magmatic differentiation steps. The low-Ca magmatic series is representative of a typical fractionation of aegirine-augite (Wo(36-29)En(25-4)Ae(39-18)) + alkali feldspar (Or(57-96)Ab(3-43)) + nepheline (Ne(76.5-69.0)Ks(19.9-14.4)Qz(15.1-7.7)) + titanite from phonolite magma. The evolution of this series from potassic nepheline syenites to sodic sodalite syenites and sodalitolites is attributed to an extensive fractionation of potassic feldspar, which led to an increase of the NaCl activity in the melt during the final stages forming sodalite-rich rocks. Phonolite dykes followed a similar evolutionary process and also registered some crustal assimilation. The mesocratic nepheline syenites showed interactions with phlogopite melteigites, such as compatible trace element enrichments and the presence of diopside xenocrysts, which were interpreted to be due to a mixing/mingling process of phonolite and nephelinite magmas. The geochemical data show higher TiO2 and P2O5 contents and lower SiO2 contents for the high-Ca series and different LILE evolution trends and REE chondrite-normalized patterns as compared to the low-Ca series. The Sr-87/Sr-86, Nd-143/Nd-144, Pb-206/Pb-204 and Pb-208/Pb-204 initial ratios for the high-Ca series (0.70407-0.70526, 0.51242-0.51251, 17.782-19.266 and 38.051-39.521, respectively) were slightly different from those of the low-Ca series (0.70542-0.70583, 0.51232-0.51240, 17.758-17.772 and 38.021-38.061, respectively). For both series, a CO2-rich potassic metasomatized lithospheric mantle enriched the source with rutile-bearing phlogopite clinopyroxenite veins. Kamafugite-like parental magma is attributed to the high-Ca series with major contributions from the melting of the veins. Potassic nephelinite-like parental magma is assigned to the low-Ca series, where the metasomatized wall-rock played a more significant role in the melting process.

Photo- and electroluminescence in a series of PPV type terpolymers containing fluorene, thiophene and phenylene units

The emissive properties of terpolymers with fluorene, thiophene and phenylene groups, forming alternating PPV type structures, are discussed in terms of their composition, photo- and electroluminescence properties. The fluorene groups were inserted in each phenylene-vinylene and thiophene-vinylene units, and their concentration did not vary, representing 50% of the molar composition. The ratio of thiophene-vinylene/phenylene-vinylene varied in the range 25,50 and 75%. Photo- and electroluminescence properties were strongly dependent on the thiophene-vinylene content and were compared with the fluorene-vinylene-thiophene and fluorene-vinylene-phenylene parent copolymers. (C) 2012 Elsevier B.V. All rights reserved.

Constraint-based analysis of gene interactions using restricted boolean networks and time-series data

Abstract Background A popular model for gene regulatory networks is the Boolean network model. In this paper, we propose an algorithm to perform an analysis of gene regulatory interactions using the Boolean network model and time-series data. Actually, the Boolean network is restricted in the sense that only a subset of all possible Boolean functions are considered. We explore some mathematical properties of the restricted Boolean networks in order to avoid the full search approach. The problem is modeled as a Constraint Satisfaction Problem (CSP) and CSP techniques are used to solve it. Results We applied the proposed algorithm in two data sets. First, we used an artificial dataset obtained from a model for the budding yeast cell cycle. The second data set is derived from experiments performed using HeLa cells. The results show that some interactions can be fully or, at least, partially determined under the Boolean model considered. Conclusions The algorithm proposed can be used as a first step for detection of gene/protein interactions. It is able to infer gene relationships from time-series data of gene expression, and this inference process can be aided by a priori knowledge available.

Neural coding tools, based on Information Theory, applied to discrete time series: from electrophysiology to neuroethology

This work is supported by Brazilian agencies Fapesp, CAPES and CNPq

Two series of new semisynthetic triterpene derivatives: differences in anti-malarial activity, cytotoxicity and mechanism of action

Background The discovery and development of anti-malarial compounds of plant origin and semisynthetic derivatives thereof, such as quinine (QN) and chloroquine (CQ), has highlighted the importance of these compounds in the treatment of malaria. Ursolic acid analogues bearing an acetyl group at C-3 have demonstrated significant anti-malarial activity. With this in mind, two new series of betulinic acid (BA) and ursolic acid (UA) derivatives with ester groups at C-3 were synthesized in an attempt to improve anti-malarial activity, reduce cytotoxicity, and search for new targets. In vitro activity against CQ-sensitive Plasmodium falciparum 3D7 and an evaluation of cytotoxicity in a mammalian cell line (HEK293T) are reported. Furthermore, two possible mechanisms of action of anti-malarial compounds have been evaluated: effects on mitochondrial membrane potential (ΔΨm) and inhibition of β-haematin formation. Results Among the 18 derivatives synthesized, those having shorter side chains were most effective against CQ-sensitive P. falciparum 3D7, and were non-cytotoxic. These derivatives were three to five times more active than BA and UA. A DiOC6(3) ΔΨm assay showed that mitochondria are not involved in their mechanism of action. Inhibition of β-haematin formation by the active derivatives was weaker than with CQ. Compounds of the BA series were generally more active against P. falciparum 3D7 than those of the UA series. Conclusions Three new anti-malarial prototypes were obtained from natural sources through an easy and relatively inexpensive synthesis. They represent an alternative for new lead compounds for anti-malarial chemotherapy.

Functional clustering of time series gene expression data by Granger causality

Background: A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results: In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions: This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them.

Hepatitis B revaccination for healthcare workers who are anti-HBs-negative after receiving a primary vaccination series

INTRODUCTION: This study aimed to evaluate the response to hepatitis B (HB) revaccination of healthcare workers (HCW) who are negative for antibodies to HB surface antigen (anti-HBs) after a complete vaccination series. METHODS: HCW whose anti-HBs test was performed > 90 days after a HB vaccination course were given a 4th dose. A post-vaccination test was done within 30 to 90 days. RESULTS: One hundred and seventy HCW were enrolled: 126 (74.1%) were anti-HBs-positive after the 4th dose. CONCLUSIONS: Rechecking anti-HBs after the 4th HB vaccine dose is a practical approach in case of post-vaccination tests performed >90 days after the full vaccination course.

Comparison between the complete Bayesian method and empirical Bayesian method for ARCH models using Brazilian financial time series

In this work we compared the estimates of the parameters of ARCH models using a complete Bayesian method and an empirical Bayesian method in which we adopted a non-informative prior distribution and informative prior distribution, respectively. We also considered a reparameterization of those models in order to map the space of the parameters into real space. This procedure permits choosing prior normal distributions for the transformed parameters. The posterior summaries were obtained using Monte Carlo Markov chain methods (MCMC). The methodology was evaluated by considering the Telebras series from the Brazilian financial market. The results show that the two methods are able to adjust ARCH models with different numbers of parameters. The empirical Bayesian method provided a more parsimonious model to the data and better adjustment than the complete Bayesian method.

CID: an efficient complexity-invariant distance for time series

The ubiquity of time series data across almost all human endeavors has produced a great interest in time series data mining in the last decade. While dozens of classification algorithms have been applied to time series, recent empirical evidence strongly suggests that simple nearest neighbor classification is exceptionally difficult to beat. The choice of distance measure used by the nearest neighbor algorithm is important, and depends on the invariances required by the domain. For example, motion capture data typically requires invariance to warping, and cardiology data requires invariance to the baseline (the mean value). Similarly, recent work suggests that for time series clustering, the choice of clustering algorithm is much less important than the choice of distance measure used.In this work we make a somewhat surprising claim. There is an invariance that the community seems to have missed, complexity invariance. Intuitively, the problem is that in many domains the different classes may have different complexities, and pairs of complex objects, even those which subjectively may seem very similar to the human eye, tend to be further apart under current distance measures than pairs of simple objects. This fact introduces errors in nearest neighbor classification, where some complex objects may be incorrectly assigned to a simpler class. Similarly, for clustering this effect can introduce errors by “suggesting” to the clustering algorithm that subjectively similar, but complex objects belong in a sparser and larger diameter cluster than is truly warranted.We introduce the first complexity-invariant distance measure for time series, and show that it generally produces significant improvements in classification and clustering accuracy. We further show that this improvement does not compromise efficiency, since we can lower bound the measure and use a modification of triangular inequality, thus making use of most existing indexing and data mining algorithms. We evaluate our ideas with the largest and most comprehensive set of time series mining experiments ever attempted in a single work, and show that complexity-invariant distance measures can produce improvements in classification and clustering in the vast majority of cases.

A system for classification of time-series data from industrial non-destructive device

This work proposes a system for classification of industrial steel pieces by means of magnetic nondestructive device. The proposed classification system presents two main stages, online system stage and off-line system stage. In online stage, the system classifies inputs and saves misclassification information in order to perform posterior analyses. In the off-line optimization stage, the topology of a Probabilistic Neural Network is optimized by a Feature Selection algorithm combined with the Probabilistic Neural Network to increase the classification rate. The proposed Feature Selection algorithm searches for the signal spectrogram by combining three basic elements: a Sequential Forward Selection algorithm, a Feature Cluster Grow algorithm with classification rate gradient analysis and a Sequential Backward Selection. Also, a trash-data recycling algorithm is proposed to obtain the optimal feedback samples selected from the misclassified ones.

Structure-based drug design studies on a series of aldolase inhibitors

Human African trypanosomiasis, also known as sleeping sickness, is a major cause of death in Africa, and for which there are no safe and effective treatments available. The enzyme aldolase from Trypanosoma brucei is an attractive, validated target for drug development. A series of alkyl‑glycolamido and alkyl-monoglycolate derivatives was studied employing a combination of drug design approaches. Three-dimensional quantitative structure-activity relationships (3D QSAR) models were generated using the comparative molecular field analysis (CoMFA). Significant results were obtained for the best QSAR model (r2 = 0.95, non-cross-validated correlation coefficient, and q2 = 0.80, cross-validated correlation coefficient), indicating its predictive ability for untested compounds. The model was then used to predict values of the dependent variables (pKi) of an external test set,the predicted values were in good agreement with the experimental results. The integration of 3D QSAR, molecular docking and molecular dynamics simulations provided further insight into the structural basis for selective inhibition of the target enzyme.