The Five Factor Model of personality and evaluation of drug consumption risk

The problem of evaluating an individual's risk of drug consumption and misuse is highly important. An online survey methodology was employed to collect data including Big Five personality traits (NEO-FFI-R), impulsivity (BIS-11), sensation seeking (ImpSS), and demographic information. The data set contained information on the consumption of 18 central nervous system psychoactive drugs. Correlation analysis demonstrated the existence of groups of drugs with strongly correlated consumption patterns. Three correlation pleiades were identified, named by the central drug in the pleiade: ecstasy, heroin, and benzodiazepines pleiades. An exhaustive search was performed to select the most effective subset of input features and data mining methods to classify users and non-users for each drug and pleiad. A number of classification methods were employed (decision tree, random forest, $k$-nearest neighbors, linear discriminant analysis, Gaussian mixture, probability density function estimation, logistic regression and na{\"i}ve Bayes) and the most effective classifier was selected for each drug. The quality of classification was surprisingly high with sensitivity and specificity (evaluated by leave-one-out cross-validation) being greater than 70\% for almost all classification tasks. The best results with sensitivity and specificity being greater than 75\% were achieved for cannabis, crack, ecstasy, legal highs, LSD, and volatile substance abuse (VSA).Comment: Significantly extended report with 67 pages, 27 tables, 21 figure

For Pity’s Sake: Comparative Conceptions of Inclusion in England and India

This paper offers a critique of transnational aspects of ‘inclusion,’ one of those global education buzzwords that as Slee (2009) puts it, say everything but say nothing. It starts off by trying to compare Indian and English usages and attitudes at the level of teacher discourse, and notes the impossibility of any ‘authentic’ translation, given the very different cultural contexts and histories. In response to these divergences, the authors undertake a much more genealogical and ‘forensic’ examination of values associated with ‘inclusion,’ focussing especially on a key notion of ‘pity.’ The Eurocentric tradition is traced from its Platonic origins through what is claimed to be the ‘industrialization of pity’ and its rejection as a virtue in favour of more apparently egalitarian measures of fairness. The Indian tradition relates rather to religious traditions across a number of different belief systems, most of which centre on some version of a karmic notion of pity. The authors both criticise and reject ‘inclusion’ as a colonisation of the global and call for a new understanding of notions like ‘pity’ as affective commitment rather than ‘fair’ dispensation of equality

For pity’s sake: comparative conceptions of inclusion in England and India.

Hodkinson, A., & Devarakonda, C., For pity’s sake: comparative conceptions of inclusion in England and India., International Review of Qualitative Research (4,2) pp. 253-270. Copyright © [2011] (The Authors). DOI: [10.1525/irqr.2011.4.2.253].This paper offers a critique of transnational aspects of ‘inclusion,’ one of those global education buzzwords that as Slee (2009) puts it, say everything but say nothing. It starts off by trying to compare Indian and English usages and attitudes at the level of teacher discourse, and notes the impossibility of any ‘authentic’ translation, given the very different cultural contexts and histories. In response to these divergences, the authors undertake a much more genealogical and ‘forensic’ examination of values associated with ‘inclusion,’ focussing especially on a key notion of ‘pity.’ The Eurocentric tradition is traced from its Platonic origins through what is claimed to be the ‘industrialization of pity’ and its rejection as a virtue in favour of more apparently egalitarian measures of fairness. The Indian tradition relates rather to religious traditions across a number of different belief systems, most of which centre on some version of a karmic notion of pity. The authors both criticise and reject ‘inclusion’ as a colonisation of the global and call for a new understanding of notions like ‘pity’ as affective commitment rather than ‘fair’ dispensation of equality

Human Well-being: Concepts and Conceptualizations

well-being, welfare, happiness, objective, subjective, measurement

Specifications and programs for computer software validation

Three software products developed during the study are reported and include: (1) FORTRAN Automatic Code Evaluation System, (2) the Specification Language System, and (3) the Array Index Validation System

Novel bioinformatics programs for taxonomical classification and functional analysis of the whole genome sequencing data of arbuscular mycorrhizal fungi

Résumé [TITRE] Classification taxonomique et analyse fonctionnelle spécifique àla position des séquences génomique des champignons mycorhiziens arbusculaires et les microorganismes qui leurs sont associés [PROBLÉMATIQUE ET CADRE CONCEPTUEL] Les champignons mycorhiziens arbusculaires (CMA) sont des symbiotes obligatoires des racines de la majoritédes plantes vasculaires. Les CMA appartiennent au phylum Glomeromycota et ils sont considérés comme une lignée fongique primitive qui a conservé la structure coenocytique des hyphes et la production des spores asexuées multinucléées. De nombeuses études ont démontréque plusieurs microorganismes sont associés avec les mycélia des CMA soit àla surface des hyphes et des spores mais aussi àl'intérieurs de celles-ci. Le séquençage des génomes des CMA cultivés in-vivo représente un défi considérable car il s’agit d’un métagénome constituédu génome du CMA lui-même et les génomes des microbes qui lui sont associés. Par conséquence, l’identification de l'origine taxonomique de chaque séquence représente une tâche extrêmement ardue. Dans mon projet, j’ai développédeux nouveaux programmes bioinformatiques qui permettent de classer les séquences selon groupe taxonomique et d’identifier les fonctions de celles-ci. J’ai crééune base de données avec 444 génomes d'espèces appartenant à54 genres. Le choix de ces espèces des bactéries et des champignons a étébasésur leur abondance dans les sols). [MÉTHODOLOGIE] Le programme bioinformatique utilise le tableau des références des microorganismes et des méthodes statistiques pour la classification taxonomique des séquences. Par la suite, des tableaux des codons synonymes étaient créés àpartir des structures secondaires (SS) des bases de données de protéines (PDB) pour les séquences codantes (SC) et des motifs de composition pour les séquences non-codantes (SNC). Chaque tableau est composéde 3 niveaux - les caractéristiques d'acides aminés; l'utilisation des acides aminés synonymes correspondants, et l'utilisation des codons synonymes correspondants. En comparant les méthodes existantes qui utilisent les taux de substitution moyenne globale quelle que soit les spécificités des acides aminés dans diverses structures, mon programme fournit une classification àhaute résolution pour des séquences courtes (150-300 pb) parce que les biais dans l'utilisation des codons synonymes àpartir d'environ 8000 trimères d'acides aminés spécifiques des sous-unités de structure secondaire, ont étéextraits avec des substitutions d'acides aminés pris en considération dans chaque trimère spécifique. Pour l'analyse fonctionnelle, le programme crée dynamiquement des données comparatives de 54 genres microbiens basés sur leurs biais dans l'utilisation des codons synonymes d'appariement de trois codons d’ADN (9-mères) identifiés dans une séquence de requête. Le programme applique une analyse en composantes principales basée sur la matrice de corrélation en association avec le partitionnement en k-moyennes aux données comparatives. [RETOMBÉES] Les taux de prédiction correcte de la CDS et les non-CDS étaient de 50 à71% pour les bactéries, et 65 à73% pour les champignons, respectivement. Pour les CMA, 49% des CDS et 72% des non-CDS ont étécorrectement classés. Ce programme nous permet d'estimer les abondances approximatives des communautés microbiennes associées au CMA. Les résultats de l'analyse fonctionnelle peuvent fournir des informations sur des sites d'interaction moléculaire importants impliqués dans la diversification des séquences et l’évolution des gènes. Les programmes sont disponibles gratuitement sur www.fungalsesame.org. Mots-clés: sesame, sesame PS function, les caractéristiques d'acides aminés, trois codons ADN 9-mères, structure secondaire, classification taxonomique, analyse fonctionnelle spécifique àla position; Code génétique; Étude Comparative; Génome MitochondrialAbstract Arbuscular Mycorrhizal Fungi (AMF) are obligate plant-root symbionts belonging to the phylum Glomeromycota. They form coenocytic hyphae and reproduce through large multinucleated asexual spores. Numerous studies have shown that AMF interact closely or loosely with a myriad of microorganisms, particularly bacteria and fungi that live on the surface of or inside of their mycelia and spores. Whole genome sequencing (WGS) data of the AMF grown in-vivo (typically grown in root of a host plant in pot filled with soil) contain a large amount of sequences from microorganisms inhabiting in their spore along with their own genome sequences, resulting in a metagenome. The goal of my study was to develop bioinformatics programs for taxonomical classification and for functional analysis of the WGS data of the AMF. In the area of metagenomics, there are mainly two approaches for taxonomical classification: similarity-based (i.e., homology search) and composition-based (i.e., k-mers) methods. Similarity-based method solely depends on bioinformatics sequence databases and homology search programs such as BLAST program. The similarity-based method may not be suitable for ancient fungi AMF, because bioinformatics databases represent only a small fraction of the diversity of existing microorganisms, and gene prediction programs are highly biased towards intensively studied microorganisms. Considering that AMF have high inter/ intra genome variations, in addition to coenocytic and multi-genomic characteristics, probably due to their adaptation via various kinds of symbioses, composition-based method alone is not an effective solution for AMF, because it relies on base composition biases and focuses on taxonomical classification for prokaryotic organisms. In the first project, I a developed novel bioinformatics program, called SeSaMe (Spore associated Symbiotic Microbes), for taxonomical classification of the WGS data of the AMF. I selected microorganisms that were dominant in soil environment and grouped them into 54 genera which were used as references. I created a reference sequence database with a variable called Three codon DNA 9-mer. They were created based on a large number of structure files from Protein Data Bank (PDB): approx. 224,000 Three codon DNA 9-mers encoding for subunits of protein secondary structures. Based on the reference sequence database, I created genus specific usage databases containing codon usage and amino acid usage per taxonomic rank- genus. The program distinguishes between coding sequence (CDS) and non-CDS, detects an open reading frame, and classifies a query sequence into a genus group out of 54 genera used as reference. The developed program enables us to estimate relative abundances of taxonomic groups and to assess symbiotic roles of taxonomic groups associated with AMF. The program can be applied to other microorganisms as well as soil metagenome data. The program has applications in applied environmental microbiology. The developed program is available for free of charge at www.fungalsesame.org. In the second project, I developed another bioinformatics program, called SeSaMe PS Function, for position specific functional analysis of the WGS data of the AMF. AMF may contain a large portion of genes with unknown functions for which we may not be able to find homologues in existing sequence databases. While existing motif annotation programs rely on sequence alignment and have limitations for inferring functionality of novel genes, the developed program identifies potentially important interaction sites that are structurally and functionally distinctive from other subsequences, within a query sequence with exploratory data analysis. The program identifies matching Three codon DNA 9-mers in a query sequence, and dynamically creates comparative dataset of 54 genera, based on codon usage bias information retrieved from the genus specific usage databases. The program applies correlation Principal Component Analysis in conjunction with K-means clustering method to the comparative dataset. The program identifies outliers; Three codon DNA 9-mers, assigned into a cluster with a single member or with only a few members, are often outliers with important structures that may play roles in molecular interaction. In the third project, I developed a novel bioinformatics program called Posts (POsition Specific genetic code Tables) that assigns a codon into an amino acid group according to the codon position. The standard genetic code table may be more readily applicable to the genes whose genetic codes comply with the standard biological coding rules obtained from model organisms grown under laboratory condition. However, it may be insufficient for studying evolutions of genetic codes that may provide important information about codon properties. The mainstream hypotheses of genetic code origin suggested that codon position played important roles in the evolution of genetic codes. As a case study, we investigated irregular codons in 187 mitochondrial genomes of plants, lichen-forming fungi, endophytic fungi, and AMF. Each column of the Post contains 16 codons and the amino acids encoded by these are called an amino acid characteristics group (A.A. Char Group). Based on A.A. Char Group, an irregular codon can be classified into within-column type or trans-column type. The majority of the identified irregular codons belonged to the within-column type. The Post may offer new perspectives on codon property and codon assignment. The developed program is freely available at www.codon.kr. Taken together, the developed programs, the SeSaMe, the SeSaMe PS Function, and the Post, provide important research tools for advancing our knowledge of AMF genomics and for studying their symbiotic relations with associated microorganisms. Keywords: Sesame; Spore associated Symbiotic Microbes; Symbiosis; Sesame PS function; Arbuscular mycorrhizal fungi; Three codon DNA 9-mer; Amino acid characteristics; Secondary structure; Taxonomical classification; Position specific functional analysis; Position specific genetic code tables; Post; Comparative study; Mitochondrial genom

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy

Background: Polyadenylation is a key regulatory step in eukaryotic gene expression and one of the major contributors of transcriptome diversity. Aberrant polyadenylation often associates with expression defects and leads to human diseases. Results: To better understand global polyadenylation regulation, we have developed a polyadenylation sequencing (PA-seq) approach. By profiling polyadenylation events in 13 human tissues, we found that alternative cleavage and polyadenylation (APA) is prevalent in both protein-coding and noncoding genes. In addition, APA usage, similar to gene expression profiling, exhibits tissue-specific signatures and is sufficient for determining tissue origin. A 3? untranslated region shortening index (USI) was further developed for genes with tandem APA sites. Strikingly, the results showed that different tissues exhibit distinct patterns of shortening and/or lengthening of 3? untranslated regions, suggesting the intimate involvement of APA in establishing tissue or cell identity. Conclusions: This study provides a comprehensive resource to uncover regulated polyadenylation events in human tissues and to characterize the underlying regulatory mechanism

Infant Vocal Development in a Dynamic Communication System: Vocal Exploration Activities in Various Social Settings

Pre-linguistic vocal productions are the manifestations of a unique capacity ofhuman infants.The uniqueness is characterized by voluntaryvocal play and systematic repetition which serveno fixed functions.Such pre-linguistic infant vocalizations are the product of complex processes of internal vocal exploration activities and external social interactions. However,very few studies have incorporated both aspects to understand the nature of early vocal development. Therefore, the current study aims to investigate the relationship between vocal category development and exploration activities in varying social communication circumstances, using a developmentally appropriate coding scheme for infant vocalization.The vocalizations of 7 infants at three different ages (approximately 4, 7, and 11 months) were used. The three vocal types (i.e., vocant, growl, and squeal), the three engagement types (i.e., symmetrical, asymmetrical, and unengaged), and two proximity types (i.e., immediate and distant) were included. Based on observation and reports from prior research, the current dissertation incorporates fundamental frequency (f0) and duration of utterances as parameters to measure vocal exploration activities in various social settings.The findings in this study provides that infants build their vocal categories, producing the three vocal categories distinctively in the acoustic domains of f0 and duration and showing systematic vocal repetition patterns among the categories. These results provide empirical evidence against Jakobson\u27s view that pre-linguistic vocal sounds are mere byproducts of biological functions, and presumably not affected by socialization.The current results seem to suggest that internally driven vocal activities might tend to be more active when social demands are low, indicating that vocal play is a cognitively intensive process requiring attentional resources.In terms of age effect on vocal exploration activities, at the earliest stage we see high exploration ( and thus repetition), and at the latest stage we see consolidated categories( and thus high discriminability). This result provides a significant new perspective on the sequential logic of the two domains in vocal category development.This research also showed infants\u27 systematic tendency to utilize the vocal categories differentially in various social settings early on, suggesting infants\u27 voluntary control efforts on their pre-linguistic vocal productions to respond to constantly changing social circumstances

An investigation into interest and its elicitation in Middle School Science lessons

I surveyed 193 Year 8 students in 50 high schools about their interest in science. Prior interest in science predicted general academic aptitude and lesson interest was inversely proportional to class size. Students with low prior interest in science responded differently from their peers. Novelty of visual teaching materials was the most influential factor in lesson interest. The study reinforced the significance of interest in education