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In this article, we discuss methods to select three different types of genes (treatment related, response related, or both) and investigate whether they can serve as biomarkers for a binary outcome variable. We consider an extension of the joint model introduced by Lin et al. (2010) and Tilahun et al. (2010) for a continuous response. As the model has certain drawbacks in a binary setting, we also present a way to use classical selection methods to identify subgroups of genes, which are treatment and/or response related. We evaluate their potential to serve as biomarkers by applying DLDA to predict the response level. [ABSTRACT FROM PUBLISHER]

It is well established in the literature that certain disease-associated gene signatures can be identified as a source for predicting the classification of samples or cell lines into diagnostic groups - for example, healthy and diseased. Using standard techniques for the selection of significant genes may lead to many highly correlated genes to be chosen, which may be an issue if we are limited in the number of genes we can select. This article therefore aims to investigate methods for selecting genes with the application of a correlation threshold. The methods are applied to two high-dimensional microarray datasets, one to aid the prediction of the presence or absence of Irritable Bowel Syndrome, and one to predict whether the oestrogen-receptor class of a given breast cancer cell line is positive or negative. Our results suggest that the effectiveness of the correlation threshold as a gene selection parameter depends on the particular microarray dataset and classification problem. While the correlation threshold may be beneficial in some specific scenarios where the number of required genes is restrictively small, it may also have no or even detrimental effect on the classification accuracy. [ABSTRACT FROM AUTHOR]

Abstract: Inhibition of conditioned avoidance behavior in rats is generally considered predictive for antipsychotic activity in man. The present study investigated the mGlu2-mediated modulation of conditioned avoidance and compared mGlu2 agonists with available antipsychotics for their relative effects on conditioned avoidance behavior and locomotion. The mGlu2/3 orthosteric agonist 4-amino-2-thiabicyclo[3.1.0]hexane-4,6-dicarboxylic acid 2,2-dioxide (LY-404039) and mGlu2 positive allosteric modulator (PAM) 3-(cyclopropylmethyl)-7-(4-phenylpiperidin-1-yl)-8-(trifluoromethyl)[1,2,4]triazolo[4,3-a]pyridine (JNJ-42153605) inhibited avoidance and blocked escape behavior. The mGlu2/3 negative allosteric modulators (NAMs) 7-(dimethylamino)-4-(3-pyridin-3-ylphenyl)-8-(trifluoromethyl)-1,3-dihydro-2 H-1,5-benzodiazepin-2-one (JNJ-42112265) and 4-[3-(2,6-dimethylpyridin-4-yl)phenyl]-7-methyl-8-(trifluoromethyl)-1,3-dihydro-2H-1,5-benzodiazepin-2-one (RO-4491533) reversed the LY-404039-induced impairment of avoidance and escape. JNJ-42112265 also reversed the impairment of avoidance and escape induced by the mGlu2-specific PAM JNJ-42153605, suggesting that the effects on conditioned avoidance are specifically mGlu2-mediated. The mGlu2/3 antagonist (2-(2-carboxycyclopropyl)-3-(9H-xanthen-9-yl)-d-alanine (LY-341495; s.c.) reversed the LY-404039-induced escape impairment but failed to restore avoidance, suggesting interfering side effects. Like the tested antipsychotics, mGlu2/3 orthosteric and allosteric agonists inhibited avoidance behavior and locomotion at similar doses. Hence no clear-cut differences between mGlu2 modulators and currently available antipsychotics in the way they interfere with avoidance behavior in relation to inhibition of locomotion could be established. [Copyright &y& Elsevier]

Although much is known about the terrestrial locomotion of great apes, their arboreal locomotion has been studied less extensively. This study investigates arboreal locomotion in bonobos (Pan paniscus), focusing on the gait characteristics and spatio-temporal variables associated with locomotion on a pole. These features are compared across different substrate inclinations (0°, 30°, 45°, 60°, and 90°), and horizontal quadrupedal walking is compared between an arboreal and a terrestrial substrate. Our results show greater variation in footfall patterns with increasing incline, resulting in more lateral gait sequences. During climbing on arboreal inclines, smaller steps and strides but higher stride frequencies and duty factors are found compared to horizontal arboreal walking. This may facilitate better balance control and dynamic stability on the arboreal substrate. We found no gradual change in spatio-temporal variables with increasing incline; instead, the results for all inclines were clustered together. Bonobos take larger strides at lower stride frequencies and lower duty factors on a horizontal arboreal substrate than on a flat terrestrial substrate. We suggest that these changes are the result of the better grip of the grasping feet on an arboreal substrate. Speed modulation of the spatio-temporal variables is similar across substrate inclinations and between substrate types, suggesting a comparable underlying motor control. Finally, we contrast these variables of arboreal inclined climbing with those of terrestrial bipedal locomotion, and briefly discuss the results with respect to the origin of habitual bipedalism. Am. J. Primatol. 78:1165-1177, 2016. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

During drug discovery and development, the early identification of adverse effects is expected to reduce costly late-stage failures of candidate drugs. As risk/safety assessment takes place rather late during the development process and due to the limited ability of animal models to predict the human situation, modern unbiased high-dimensional biology readouts are sought, such as molecular signatures predictive for in vivo response using high-throughput cell-based assays. In this theoretical proof of concept, we provide findings of an in-depth exploration of a single chemical core structure. Via transcriptional profiling, we identified a subset of close analogues that commonly downregulate multiple tubulin genes across cellular contexts, suggesting possible spindle poison effects. Confirmation via a qualified toxicity assay (in vitro micronucleus test) and the identification of a characteristic aggregate-formation phenotype via exploratory high-content imaging validated the initial findings. SAR analysis triggered the synthesis of a new set of compounds and allowed us to extend the series showing the genotoxic effect. We demonstrate the potential to flag toxicity issues by utilizing data from exploratory experiments that are typically generated for target evaluation purposes during early drug discovery. We share our thoughts on how this approach may be incorporated into drug development strategies.

High-density oligonucleotide microarrays are commonly used for GWAS studies as well as for tumor genome alteration identifications. The recent Affymetrix Genome-Wide SNP 6.0 microarray generation has two major advantages: (1) showing high genome coverage and (2) starting with very small amount of DNA material. The hybridization protocol needs to be standardized and highly reproducible, as DNA is first digested by restriction enzymes and then PCR-amplified to reduce genome complexity. Especially the restriction digestion step is highly sensitive to degradation of the initial material. The stronger the sample is degraded, the lower the number of restriction sites still present in the genome, and hence the less-efficient amplification step.Paraffin-embedded material generally only allows to extract partially degraded DNA, and therefore is difficult to analyze using SNP array technology. We and others (Jacobs et al., Cancer Res 67:2544-2551, 2007; Tuefferd et al., Genes Chromosomes Cancer 47:957-964, 2008) have shown that target preparation protocol can be adjusted to improve hybridization performances. The final in silico data analysis procedure should be modified accordingly to extract most of the biological information from the signal measured. By optimizing these crucial steps, it is possible to use Affymetrix SNP array 6.0 -technology in the context of genome variation, even for FFPE partially degraded material. This opens a lot of potential for large retrospective series of samples.