Transition-transversion encoding and genetic relationship metric in ReliefF feature selection improves pathway enrichment in GWAS.

BACKGROUND: ReliefF is a nearest-neighbor based feature selection algorithm that efficiently detects variants that are important due to statistical interactions or epistasis. For categorical predictors, like genotypes, the standard metric used in ReliefF has been a simple (binary) mismatch difference. In this study, we develop new metrics of varying complexity that incorporate allele sharing, adjustment for allele frequency heterogeneity via the genetic relationship matrix (GRM), and physicochemical differences of variants via a new transition/transversion encoding. METHODS: We introduce a new two-dimensional transition/transversion genotype encoding for ReliefF, and we implement three ReliefF attribute metrics: 1.) genotype mismatch (GM), which is the ReliefF standard, 2.) allele mismatch (AM), which accounts for heterozygous differences and has not been used previously in ReliefF, and 3.) the new transition/transversion metric. We incorporate these attribute metrics into the ReliefF nearest neighbor calculation with a Manhattan metric, and we introduce GRM as a new ReliefF nearest-neighbor metric to adjust for allele frequency heterogeneity. RESULTS: We apply ReliefF with each metric to a GWAS of major depressive disorder and compare the detection of genes in pathways implicated in depression, including Axon Guidance, Neuronal System, and G Protein-Coupled Receptor Signaling. We also compare with detection by Random Forest and Lasso as well as random/null selection to assess pathway size bias. CONCLUSIONS: Our results suggest that using more genetically motivated encodings, such as transition/transversion, and metrics that adjust for allele frequency heterogeneity, such as GRM, lead to ReliefF attribute scores with improved pathway enrichment.

Synthesis and anticonvulsant activity of 3-aryl-5H-2,3-benzodiazephine AMPA antagonists.

A novel series of 3-aryl-5H-2,3-benzodiazepines with N-3 aromatic substituents has been synthesized. Good in vivo anticonvulsant activity of the new compounds has been demonstrated employing the maximal electroshock seizure test in mice. Evaluation of a subset of the compounds in the cortical wedge assay confirmed the new structures to be AMPA antagonists.

Synthesis, pharmacological characterization, and molecular modeling of heterobicyclic amino acids related to (+)-2-aminobicyclo[3.1.0] hexane-2,6-dicarboxylic acid (LY354740): identification of two new potent, selective, and systemically active agonists for group II metabotropic glutamate receptors.

As part of our ongoing research program aimed at the identification of highly potent, selective, and systemically active agonists for group II metabotropic glutamate (mGlu) receptors, we have prepared novel heterobicyclic amino acids (-)-2-oxa-4-aminobicyclo[3.1. 0]hexane-4,6-dicarboxylate (LY379268, (-)-9) and (-)-2-thia-4-aminobicyclo[3.1.0]hexane-4,6-dicarboxylate (LY389795, (-)-10). Compounds (-)-9 and (-)-10 are structurally related to our previously described nanomolar potency group II mGlu receptor agonist, (+)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylate monohydrate (LY354740 monohydrate, 5), with the C4-methylene unit of 5 being replaced with either an oxygen atom (as in (-)-9) or a sulfur atom (as in (-)-10). Compounds (-)-9 and (-)-10 potently and stereospecifically displaced specific binding of the mGlu2/3 receptor antagonist ([3H]LY341495) in rat cerebral cortical homogenates, displaying IC50 values of 15 +/- 4 and 8.4 +/- 0.8 nM, respectively, while having no effect up to 100 000 nM on radioligand binding to the glutamate recognition site on NMDA, AMPA, or kainate receptors. Compounds (-)-9 and (-)-10 also potently displaced [3H]LY341495 binding from membranes expressing recombinant human group II mGlu receptor subtypes: (-)-9, Ki = 14.1 +/- 1.4 nM at mGlu2 and 5.8 +/- 0.64 nM at mGlu3; (-)-10, Ki = 40.6 +/- 3.7 nM at mGlu2 and 4.7 +/- 1.2 nM at mGlu3. Evaluation of the functional effects of (-)-9 and (-)-10 on second-messenger responses in nonneuronal cells expressing human mGlu receptor subtypes demonstrated each to be a highly potent agonist for group II mGlu receptors: (-)-9, EC50 = 2.69 +/- 0.26 nM at mGlu2 and 4.58 +/- 0.04 nM at mGlu3; (-)-10, EC50 = 3.91 +/- 0.81 nM at mGlu2 and 7.63 +/- 2. 08 nM at mGlu3. In contrast, neither compound (up to 10 000 nM) displayed either agonist or antagonist activity in cells expressing recombinant human mGlu1a, mGlu5a, mGlu4a, or mGlu7a receptors. The agonist effects of (-)-9 and (-)-10 at group II mGlu receptors were not totally specific, however, as mGlu6 agonist activity was observed at high nanomolar concentrations for (-)-9 (EC50 = 401 +/- 46 nM) and at micromolar concentrations (EC50 = 2 430 +/- 600 nM) for (-)-10; furthermore, each activated mGlu8 receptors at micromolar concentrations (EC50 = 1 690 +/- 130 and 7 340 +/- 2 720 nM, respectively). Intraperitoneal administration of either (-)-9 or (-)-10 in the mouse resulted in a dose-related blockade of limbic seizure activity produced by the nonselective group I/group II mGluR agonist (1S,3R)-ACPD ((-)-9 ED50 = 19 mg/kg, (-)-10 ED50 = 14 mg/kg), indicating that these molecules effectively cross the blood-brain barrier following systemic administration and suppress group I mGluR-mediated limbic excitation. Thus, heterobicyclic amino acids (-)-9 and (-)-10 are novel pharmacological tools useful for exploring the functions of mGlu receptors in vitro and in vivo.

Differential convergence of self-report and informant data for multidimensional personality questionnaire traits: implications for the construct of negative emotionality.

Construct validation work on Tellegen's (1982) Multidimensional Personality Questionnaire (MPQ) resulted in further inferences about Negative Emotionality. Two hundred thirty-two students were rated by three knowledgeable informants, yielding a total of 928 participants. The median monotrait correlation of MPQ primary scores with summed observer ratings was .48, and all were significant, p < .01. These data show higher self-report to informant rating convergences in the Positive Emotionality (Extroversion) domain than in the Negative Emotionality (Neuroticism) domain. Furthermore, in the Negative Emotionality domain, peers, mothers, and fathers were not equivalent as classes of raters. Stress Reaction ratings showed uniformly lower levels of convergence with self-report (relative to Positive Emotionality traits) across all rater classes. For Alienation, peer and maternal ratings were comparable, but paternal ratings correlated significantly less with self-report scores than did maternal ratings. And finally, with Aggression, peer ratings correlated significantly higher with self-report than either maternal or paternal ratings. These findings, taken in the context of the literature, have implications for a hierarchical model of Negative Emotionality, support inferences about the display of cues of Negative Emotionality, and offer new cautions for rating-based assessment.

Structures of personality and their relevance to psychopathology.

Trait concepts are used extensively in psychopathology research, but much of this research has failed to consider recent advances in the dimensional structure of personality. Many investigators have discounted the importance of this structural research, arguing that (a) little progress has been made in this area, (b) structural models have little direct relevance for psychopathology research, and (c) the principal methodological tool of structural research--factor analysis--is too subjective to yield psychologically meaningful results. We dispute each of these objections. Specifically, we offer an integrative hierarchical model--composed of four higher order traits--that is congruent with each of the major structural subtraditions within personality. We also discuss the implications of this integrative scheme for basic trait research, for the conceptualization and assessment of psychopathology, and for the etiology of disorder.

Structural models of captivity trauma, resilience, and trauma response among former prisoners of war 20 to 40 years after release.

Long-term responses to captivity trauma were measured in a national sample of American former prisoners of war. Their responses included negative affect, positive affect, and somatic symptoms as assessed by the Cornell Medical Index in 1967 and the Center for Epidemiological Study Depression Scale in 1985. These responses were strongly associated with captivity trauma (as indexed by captivity weight loss, torture, and disease) and resilience (as indexed by age and education at capture). Symptoms reported in 1967 were related to symptoms reported in 1985, suggesting symptom stability. These results are consistent with a model of trauma response that incorporates both trauma exposure and individual resilience. The findings are interpreted within a theoretical view of trauma response as adaptive when viewed from an evolutionary perspective.

The natural history of change in intellectual performance: who changes? How much? Is it meaningful?

A prerequisite step for studying the magnitude and meaning of IQ change is to distinguish between true IQ change that is a researchable phenomenon and IQ "change" that can be accounted for by measurement error. We studied the reliability, magnitude and meaning of IQ change using scores on the WISC--R obtained from a representative sample of 794 children at ages 7, 9, 11 and 13. The findings suggest that, in the majority of children, IQ change is either negligible in amount, unreliably measured or both. In a nontrivial minority of children, naturalistic IQ change is marked and real, but this change is variable in its timing, idiosyncratic in its source and transient in its course. We discuss the implications of these findings for interventions that aspire to improve IQ scores.