A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed

A comparative analysis by means of quantum molecular similarity measures of density distributions derived from conventional ab initio and density functional methods

A procedure based on quantum molecular similarity measures (QMSM) has been used to compare electron densities obtained from conventional ab initio and density functional methodologies at their respective optimized geometries. This method has been applied to a series of small molecules which have experimentally known properties and molecular bonds of diverse degrees of ionicity and covalency. Results show that in most cases the electron densities obtained from density functional methodologies are of a similar quality than post-Hartree-Fock generalized densities. For molecules where Hartree-Fock methodology yields erroneous results, the density functional methodology is shown to yield usually more accurate densities than those provided by the second order Møller-Plesset perturbation theory

Suitability of GRIND-based principal properties for the description of molecular similarity and ligand-based virtual screening

The information provided by the alignment-independent GRid Independent Descriptors (GRIND) can be condensed by the application of principal component analysis, obtaining a small number of principal properties (GRIND-PP), which is more suitable for describing molecular similarity. The objective of the present study is to optimize diverse parameters involved in the obtention of the GRIND-PP and validate their suitability for applications, requiring a biologically relevant description of the molecular similarity. With this aim, GRIND-PP computed with a collection of diverse settings were used to carry out ligand-based virtual screening (LBVS) on standard conditions. The quality of the results obtained was remarkable and comparable with other LBVS methods, and their detailed statistical analysis allowed to identify the method settings more determinant for the quality of the results and their optimum. Remarkably, some of these optimum settings differ significantly from those used in previously published applications, revealing their unexplored potential. Their applicability in large compound database was also explored by comparing the equivalence of the results obtained using either computed or projected principal properties. In general, the results of the study confirm the suitability of the GRIND-PP for practical applications and provide useful hints about how they should be computed for obtaining optimum results.

Prediction of enzyme function by combining sequence similarity and protein interactions

Background: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners. Results: The method has been tested against the PSI-BLAST program using a set of 3,890 protein sequences from which interaction data was available. For protein sequences that align with at least 40% sequence identity to a known enzyme, the specificity of our method in predicting the first three EC digits increased from 80% to 90% at 80% coverage when compared to PSI-BLAST. Conclusion: Our method can also be used in proteins for which homologous sequences with known interacting partners can be detected. Thus, our method could increase 10% the specificity of genome-wide enzyme predictions based on sequence matching by PSI-BLAST alone.

Chroma binary similarity and local alignment applied to cover song identification

We present a new technique for audio signal comparison based on tonal subsequence alignment and its application to detect cover versions (i.e., different performances of the same underlying musical piece). Cover song identification is a task whose popularity has increased in the Music Information Retrieval (MIR) community along in the past, as it provides a direct and objective way to evaluate music similarity algorithms.This article first presents a series of experiments carried outwith two state-of-the-art methods for cover song identification.We have studied several components of these (such as chroma resolution and similarity, transposition, beat tracking or Dynamic Time Warping constraints), in order to discover which characteristics would be desirable for a competitive cover song identifier. After analyzing many cross-validated results, the importance of these characteristics is discussed, and the best-performing ones are finally applied to the newly proposed method. Multipleevaluations of this one confirm a large increase in identificationaccuracy when comparing it with alternative state-of-the-artapproaches.

Range-Wide Sex-Chromosome Sequence Similarity Supports Occasional XY Recombination in European Tree Frogs (Hyla arborea).

In contrast with mammals and birds, most poikilothermic vertebrates feature structurally undifferentiated sex chromosomes, which may result either from frequent turnovers, or from occasional events of XY recombination. The latter mechanism was recently suggested to be responsible for sex-chromosome homomorphy in European tree frogs (Hyla arborea). However, no single case of male recombination has been identified in large-scale laboratory crosses, and populations from NW Europe consistently display sex-specific allelic frequencies with male-diagnostic alleles, suggesting the absence of recombination in their recent history. To address this apparent paradox, we extended the phylogeographic scope of investigations, by analyzing the sequences of three sex-linked markers throughout the whole species distribution. Refugial populations (southern Balkans and Adriatic coast) show a mix of X and Y alleles in haplotypic networks, and no more within-individual pairwise nucleotide differences in males than in females, testifying to recurrent XY recombination. In contrast, populations of NW Europe, which originated from a recent postglacial expansion, show a clear pattern of XY differentiation; the X and Y gametologs of the sex-linked gene Med15 present different alleles, likely fixed by drift on the front wave of expansions, and kept differentiated since. Our results support the view that sex-chromosome homomorphy in H. arborea is maintained by occasional or historical events of recombination; whether the frequency of these events indeed differs between populations remains to be clarified.

Mouse alarm pheromone shares structural similarity with predator scents.

Sensing the chemical warnings present in the environment is essential for species survival. In mammals, this form of danger communication occurs via the release of natural predator scents that can involuntarily warn the prey or by the production of alarm pheromones by the stressed prey alerting its conspecifics. Although we previously identified the olfactory Grueneberg ganglion as the sensory organ through which mammalian alarm pheromones signal a threatening situation, the chemical nature of these cues remains elusive. We here identify, through chemical analysis in combination with a series of physiological and behavioral tests, the chemical structure of a mouse alarm pheromone. To successfully recognize the volatile cues that signal danger, we based our selection on their activation of the mouse olfactory Grueneberg ganglion and the concomitant display of innate fear reactions. Interestingly, we found that the chemical structure of the identified mouse alarm pheromone has similar features as the sulfur-containing volatiles that are released by predating carnivores. Our findings thus not only reveal a chemical Leitmotiv that underlies signaling of fear, but also point to a double role for the olfactory Grueneberg ganglion in intraspecies as well as interspecies communication of danger.

Small-area estimation with spatial similarity

A class of composite estimators of small area quantities that exploit spatial (distancerelated)similarity is derived. It is based on a distribution-free model for the areas, but theestimators are aimed to have optimal design-based properties. Composition is applied alsoto estimate some of the global parameters on which the small area estimators depend.It is shown that the commonly adopted assumption of random effects is not necessaryfor exploiting the similarity of the districts (borrowing strength across the districts). Themethods are applied in the estimation of the mean household sizes and the proportions ofsingle-member households in the counties (comarcas) of Catalonia. The simplest version ofthe estimators is more efficient than the established alternatives, even though the extentof spatial similarity is quite modest.

External morphology of the adult of Dynamine postverta (Cramer) (Lepidoptera, Nymphalidae, Biblidinae) and patterns of morphological similarity among species from eight tribes of Nymphalidae

External morphology of the adult of Dynamine postverta (Cramer) (Lepidoptera, Nymphalidae, Biblidinae) and patterns of morphological similarity among species from eight tribes of Nymphalidae. The external structure of the integument of Dynamine postverta postverta (Cramer, 1779) is based on detailed morphological drawings and scanning electron microscopy. The data are compared with other species belonging to eight tribes of Nymphalidae, to assist future studies on the taxonomy and systematics of Neotropical Biblidinae.

Comparative testing of a miniature diffusion size classifier to assess airborne ultrafine particles under field conditions

Miniature diffusion size classifiers (miniDiSC) are novel handheld devices to measure ultrafine particles (UFP). UFP have been linked to the development of cardiovascular and pulmonary diseases; thus, detection and quantification of these particles are important for evaluating their potential health hazards. As part of the UFP exposure assessments of highwaymaintenance workers in western Switzerland, we compared a miniDiSC with a portable condensation particle counter (P-TRAK). In addition, we performed stationary measurements with a miniDiSC and a scanning mobility particle sizer (SMPS) at a site immediately adjacent to a highway. Measurements with miniDiSC and P-TRAK correlated well (correlation of r = 0.84) but average particle numbers of the miniDiSC were 30%âeuro"60% higher. This difference was significantly increased for mean particle diameters below 40 nm. The correlation between theminiDiSC and the SMPSduring stationary measurements was very high (r = 0.98) although particle numbers from the miniDiSC were 30% lower. Differences between the three devices were attributed to the different cutoff diameters for detection. Correction for this size dependent effect led to very similar results across all counters.We did not observe any significant influence of other particle characteristics. Our results suggest that the miniDiSC provides accurate particle number concentrations and geometric mean diameters at traffic-influenced sites, making it a useful tool for personal exposure assessment in such settings.

DNA fingerprinting of glioma cell lines and considerations on similarity measurements.

Glioma cell lines are an important tool for research in basic and translational neuro-oncology. Documentation of their genetic identity has become a requirement for scientific journals and grant applications to exclude cross-contamination and misidentification that lead to misinterpretation of results. Here, we report the standard 16 marker short tandem repeat (STR) DNA fingerprints for a panel of 39 widely used glioma cell lines as reference. Comparison of the fingerprints among themselves and with the large DSMZ database comprising 9 marker STRs for 2278 cell lines uncovered 3 misidentified cell lines and confirmed previously known cross-contaminations. Furthermore, 2 glioma cell lines exhibited identity scores of 0.8, which is proposed as the cutoff for detecting cross-contamination. Additional characteristics, comprising lack of a B-raf mutation in one line and a similarity score of 1 with the original tumor tissue in the other, excluded a cross-contamination. Subsequent simulation procedures suggested that, when using DNA fingerprints comprising only 9 STR markers, the commonly used similarity score of 0.8 is not sufficiently stringent to unambiguously differentiate the origin. DNA fingerprints are confounded by frequent genetic alterations in cancer cell lines, particularly loss of heterozygosity, that reduce the informativeness of STR markers and, thereby, the overall power for distinction. The similarity score depends on the number of markers measured; thus, more markers or additional cell line characteristics, such as information on specific mutations, may be necessary to clarify the origin.

Spouse similarity in recollections of parenting received : a study in a nonclinical sample

Rapport de synthèse : L'article constituant le présent travail de thèse décrit une recherche portant sur des couples adultes recrutés dans la population générale, décrivant rétrospectivement les attitudes de leurs parents respectifs envers eux au cours de leur enfance. Le rôle joué par les attitudes d'attachement dans les relations adultes, et notamment les relations de couples, est bien démontré. De même, il est établi que les relations établies avec les parents dans l'enfance influencent le type d'attitude d'attachement qui prédominera à l'âge adulte. Dès lors, nous avons investigué l'existence, au sein de ces couples adultes, de souvenirs similaires quant aux attitudes prodiguées par les parents. Pour réaliser cette recherche, nous avons contacté tous les parents des enfants scolarisés en 2e/3e années et en 6e/7e années au sein des écoles de plusieurs communes de la région lausannoise, permettant de constituer un échantillon de 563 couples de parents. Au moyen d'autoquestionnaires, nous avons évalué pour chaque membre du couple : 1) sa description rétrospective des attitudes de ses deux parents envers lui pendant son enfance ; 2) le degré de sa symptomatologie psychiatrique actuelle ; et 3) son évaluation du degré d'ajustement dyadique actuel au sein du couple. La comparaison des scores des époux respectifs sur « l'échelle de lien parental » (PBI : Parental Bonding Instrument) a montré une ressemblance, au sein des couples, concernant la c chaleur et affection » (« Care ») témoignée au cours de l'enfance parle parent de même sexe que le sujet. Les analyses complémentaires effectuées semblent exclure que cette similarité soit due à des facteurs confondant comme l'âge, l'origine culturelle, le niveau socio-économique, ou le degré de symptomatologie psychiatrique. De même, cette similarité ne semble pas être attribuable à une convergence de vue grandissante des conjoints au cours de leur union. Par ailleurs, le degré d'ajustement dyadique s'est révélé être dépendant du degré cumulé de chaleur et d'affection tel que remémoré par chaque conjoint, et non du degré de similarité dans le couple pour ce qui concerne le souvenir de la chaleur et de l'affection reçues. Bien que basée sur des évaluations rétrospectives des attitudes parentales, et ne disposant pas d'une investigation psychiatrique standardisée incluant les critères diagnostiques, cette étude repose néanmoins sur un grand échantillon, recruté dans la population générale. Nos résultats ont notamment des implications concernant la santé des enfants. En effet, en raison de la similarité mise en évidence dans nos résultats, un enfant dont un des parents a reçu peu de chaleur et d'affection dans son enfance a plus de chances que son autre parent aie lui-même également reçu moins de chaleur et d'affection. De ce fait, d'une part l'ajustement dyadique du couple parental sera particulièrement bas, ce qui peut se répercuter sur les enfants du couple. D'autre part, comme les attitudes parentales se transmettent en partie de génération en génération, le même enfant risque d'être exposé, de la part de ses deux parents, à une attitude comportant peu de chaleur et d'affection, ce qui représente un risque de développement ultérieur des pathologies psychiatriques chez cet enfant.