Bandt-Pompe symbolization dynamics for time series with tied values: A data-driven approach

In 2002, Bandt and Pompe [Phys. Rev. Lett. 88, 174102 (2002)] introduced a successfully symbolic encoding scheme based on the ordinal relation between the amplitude of neighboring values of a given data sequence, from which the permutation entropy can be evaluated. Equalities in the analyzed sequence, for example, repeated equal values, deserve special attention and treatment as was shown recently by Zunino and co-workers [Phys. Lett. A 381, 1883 (2017)]. A significant number of equal values can give rise to false conclusions regarding the underlying temporal structures in practical contexts. In the present contribution, we review the different existing methodologies for treating time series with tied values by classifying them according to their different strategies. In addition, a novel data-driven imputation is presented that proves to outperform the existing methodologies and avoid the false conclusions pointed by Zunino and co-workers.Fil: Traversaro Varela, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Lanús; ArgentinaFil: Redelico, Francisco Oscar. Hospital Italiano; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Risk, Marcelo. Hospital Italiano; Argentina. Instituto Tecnológico de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Frery, Alejandro César. Universidade Federal de Alagoas; BrasilFil: Rosso, Osvaldo Aníbal. Hospital Italiano; Argentina. Universidade Federal de Alagoas; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Los Andes; Chil

JHK Observations of Faint Standard Stars in the Mauna Kea Near-Infrared Photometric System

JHK photometry in the Mauna Kea Observatory (MKO) near-IR system is presented for 115 stars. Of these, 79 are UKIRT standards and 42 are LCO standards. The average brightness is 11.5 mag, with a range of 10 to 15. The average number of nights each star was observed is 4, and the average of the internal error of the final results is 0.011 mag. These JHK data agree with those reported by other groups to 0.02 mag. The measurements are used to derive transformations between the MKO JHK photometric system and the UKIRT, LCO and 2MASS systems. The 2MASS-MKO data scatter by 0.05 mag for redder stars: 2MASS-J includes H2O features in dwarfs and MKO-K includes CO features in giants. Transformations derived for stars whose spectra contain only weak features cannot give accurate transformations for objects with strong absorption features within a filter bandpasses. We find evidence of systematic effects at the 0.02 mag level in the photometry of stars with J<11 and H,K<10.5. This is due to an underestimate of the linearity correction for stars observed with the shortest exposure times; very accurate photometry of stars approaching the saturation limits of infrared detectors which are operated in double-read mode is difficult to obtain. Four stars in the sample, GSPC S705-D, FS 116 (B216-b7), FS 144 (Ser-EC84) and FS 32 (Feige 108), may be variable. 84 stars in the sample have 11< J< 15 and 10.5<H,K<15, are not suspected to be variable, and have magnitudes with an estimated error <0.027 mag; 79 of these have an error of <0.020 mag. These represent the first published high-accuracy JHK stellar photometry in the MKO photometric system; we recommend these objects be employed as primary standards for that system [abridged].Comment: Accepted for publication in MNRAS, 14 pages, 5 Figure

Methods for reliability and uncertainty assessment and for applicability evaluations of classification- and regression-based QSARs

This article provides an overview of methods for reliability assessment of quantitative structure–activity relationship (QSAR) models in the context of regulatory acceptance of human health and environmental QSARs. Useful diagnostic tools and data analytical approaches are highlighted and exemplified. Particular emphasis is given to the question of how to define the applicability borders of a QSAR and how to estimate parameter and prediction uncertainty. The article ends with a discussion regarding QSAR acceptability criteria. This discussion contains a list of recommended acceptability criteria, and we give reference values for important QSAR performance statistics. Finally, we emphasize that rigorous and independent validation of QSARs is an essential step toward their regulatory acceptance and implementation. Key words: QSAR acceptability criteria, QSAR applicability domain, QSAR reliability, QSAR uncertainty estimation, QSAR validation

Measurement of the local Jahn-Teller distortion in LaMnO_3.006

The atomic pair distribution function (PDF) of stoichiometric LaMnO_3 has been measured. This has been fit with a structural model to extract the local Jahn-Teller distortion for an ideal Mn(3+)O_6 octahedron. These results are compared to Rietveld refinements of the same data which give the average structure. Since the local structure is being measured in the PDF there is no assumption of long-range orbital order and the real, local, Jahn-Teller distortion is measured directly. We find good agreement both with published crystallographic results and our own Rietveld refinements suggesting that in an accurately stoichiometric material there is long range orbital order as expected. The local Jahn-Teller distortion has 2 short, 2 medium and 2 long bonds.Comment: 5 pages, 3 postscript figures, minor change

MetaFIND: A feature analysis tool for metabolomics data

<p>Abstract</p> <p>Background</p> <p>Metabolomics, or metabonomics, refers to the quantitative analysis of all metabolites present within a biological sample and is generally carried out using NMR spectroscopy or Mass Spectrometry. Such analysis produces a set of peaks, or <it>features</it>, indicative of the metabolic composition of the sample and may be used as a basis for sample classification. Feature selection may be employed to improve classification accuracy or aid model explanation by establishing a subset of class discriminating features. Factors such as experimental noise, choice of technique and threshold selection may adversely affect the set of selected features retrieved. Furthermore, the high dimensionality and multi-collinearity inherent within metabolomics data may exacerbate discrepancies between the set of features retrieved and those required to provide a complete explanation of metabolite signatures. Given these issues, the latter in particular, we present the MetaFIND application for 'post-feature selection' correlation analysis of metabolomics data.</p> <p>Results</p> <p>In our evaluation we show how MetaFIND may be used to elucidate metabolite signatures from the set of features selected by diverse techniques over two metabolomics datasets. Importantly, we also show how MetaFIND may augment standard feature selection and aid the discovery of additional significant features, including those which represent novel class discriminating metabolites. MetaFIND also supports the discovery of higher level metabolite correlations.</p> <p>Conclusion</p> <p>Standard feature selection techniques may fail to capture the full set of relevant features in the case of high dimensional, multi-collinear metabolomics data. We show that the MetaFIND 'post-feature selection' analysis tool may aid metabolite signature elucidation, feature discovery and inference of metabolic correlations.</p

VISIR/VLT mid-infrared imaging of Seyfert nuclei: Nuclear dust emission and the Seyfert-2 dichotomy

Half of the Seyfert-2 galaxies escaped detection of broad lines in their polarised spectra observed so far. Some authors have suspected that these non-HBLRs contain real Sy2 nuclei without intrinsic broad line region hidden behind a dust torus. If this were true, then their nuclear structure would fundamentally differ from that of Sy2s with polarised broad lines: in particular, they would not be explained by orientation-based AGN unification. Further arguments for two physically different Sy2 populations have been derived from the warm and cool IRAS F25/F60 ratios. These ratios, however, refer to the entire host galaxies and are unsuitable to conclusively establish the absence of a nuclear dust torus. Instead, a study of the Seyfert-2 dichotomy should be performed on the basis of nuclear properties only. Here we present the first comparison between [OIII] 5007A and mid-infrared imaging at matching spatial resolution. Exploring the Seyfert-2 dichotomy we find that the distributions of nuclear mid-infrared/[OIII] luminosity ratios are indistinguishable for Sy1s and Sy2s with and without detected polarised broad lines and irrespective of having warm or cool IRAS F25/F60 ratios. We find no evidence for the existence of a population of real Sy2s with a deficit of nuclear dust emission. Our results suggest 1) that all Seyfert nuclei possess the same physical structure including the putative dust torus and 2) that the cool IRAS colours are caused by a low contrast of AGN to host galaxy. Then the Seyfert-2 dichotomy is explained in part by unification of non-HBLRs with narrow-line Sy1s and to a larger rate by observational biases caused by a low AGN/host contrast and/or an unfavourable scattering geometry.Comment: 11 pages, 6 figures, accepted by A&

Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques

<p>Abstract</p> <p>Background</p> <p>Protein kinases play crucial roles in cell growth, differentiation, and apoptosis. Abnormal function of protein kinases can lead to many serious diseases, such as cancer. Kinase inhibitors have potential for treatment of these diseases. However, current inhibitors interact with a broad variety of kinases and interfere with multiple vital cellular processes, which causes toxic effects. Bioinformatics approaches that can predict inhibitor-kinase interactions from the chemical properties of the inhibitors and the kinase macromolecules might aid in design of more selective therapeutic agents, that show better efficacy and lower toxicity.</p> <p>Results</p> <p>We applied proteochemometric modelling to correlate the properties of 317 wild-type and mutated kinases and 38 inhibitors (12,046 inhibitor-kinase combinations) to the respective combination's interaction dissociation constant (K_d). We compared six approaches for description of protein kinases and several linear and non-linear correlation methods. The best performing models encoded kinase sequences with amino acid physico-chemical z-scale descriptors and used support vector machines or partial least- squares projections to latent structures for the correlations. Modelling performance was estimated by double cross-validation. The best models showed high predictive ability; the squared correlation coefficient for new kinase-inhibitor pairs ranging P²= 0.67-0.73; for new kinases it ranged P²_kin= 0.65-0.70. Models could also separate interacting from non-interacting inhibitor-kinase pairs with high sensitivity and specificity; the areas under the ROC curves ranging AUC = 0.92-0.93. We also investigated the relationship between the number of protein kinases in the dataset and the modelling results. Using only 10% of all data still a valid model was obtained with P²= 0.47, P²_kin= 0.42 and AUC = 0.83.</p> <p>Conclusions</p> <p>Our results strongly support the applicability of proteochemometrics for kinome-wide interaction modelling. Proteochemometrics might be used to speed-up identification and optimization of protein kinase targeted and multi-targeted inhibitors.</p

Functional traits of hyporheic and benthic invertebrates reveal importance of wood-driven geomorphological processes to rivers

1.Large wood (LW) is a natural element of river environments and an integral component of many river restoration schemes to promote biodiversity. It is an important habitat in itself, but it also induces a wide range of hydraulic, hydrological, geomorphological, and chemical conditions that influence the ecological community. However, the effects of hydro‐geomorphological processes induced by LW on local benthic and hyporheic invertebrates have not been well characterized. 2.A functional approach was applied to invertebrate data collected in a field survey at sites with LW and without LW (control), to investigate the response of hyporheic and benthic invertebrates’ trait profiles in response to local LW‐induced processes. 3.We hypothesized LW sites to be associated with different trait modalities than control sites in relation to wood‐induced processes and conditions (i.e. hyporheic exchange flow, oxygen availability, temporal stability, organic matter, denitrification, hydraulic conductivity). Multivariate analyses and Partial Least Squares (PLS) Path Modelling were used to detect the differences in trait profiles between LW and control sites and to study the variation of traits as a function of hydrological, sedimentological, physical and chemical variables. 4.Biological (i.e. aquatic stages, reproduction), physiological (i.e. dispersal, feeding habits) and behavioural (i.e. substrate preferences) trait utilization by the hyporheic meiofauna differed between LW and control sites. At LW sites, the hyporheic meiofaunal assemblage was significantly associated with aquatic active dispersal, aquatic eggs and hard substrate preferences. This trait category selection was linked to changes in physical‐sedimentological processes at LW sites when compared to control sites. Macrofaunal benthic and hyporheic functional traits did not differ significasignificantly between wood and control sites, suggesting similar functioning of these assemblages at the surface‐subsurface interface. 5.This study found that LW affects invertebrate traits by altering fluvial processes to produce, locally, a mosaic of habitats. Hyporheic meiofauna trait responses to LW‐processes have suggested (i) the crucial role of LW in supporting river benthic zone functioning, and thus (ii) a possible benefit to river restoration by enhancing functional interactions among different ecological niches