CP asymmetry and branching ratio of B -> pi pi

We investigate the branching ratios and CP asymmetries of the B -> pi pi processes measured in B factory experiments. Fits to the experimental data of this process indicate a large ratio of color-suppressed (C) to color-allowed (T) tree contributions. We investigate whether the large C/T can be explained within the QCD based model computation with i) a large effect from the end-point singularity or with ii) large final-state-interaction phase between two different isospin amplitudes. We show that the current experimental data do not exclude either possibility but we may be able to distinguish these two effects in future measurements of direct CP asymmetry of B -> pi^0 pi^0.Comment: 8 pages, 10 figure

Screening of organically based fungicides for apple scab (Venturia inaequalis) control and a histopathological study of the mode of action of a resistance inducer.

A range of possible substitutes for copper-based fungicides for control of apple scab (Venturia inaequalis) in organic growing were tested in laboratory and growth chamber experiments in the Danish project StopScab (2002-2004). Eighteen crude plant extracts, 19 commercial plant-based products and 6 miscellaneous compounds were tested for their ability to reduce scab symptoms on apple seedlings. Most of the compounds were also tested for their effect on conidium germination on glass slides. Fourteen of the crude plant extracts, 13 of the commercial plant products and 5 of the miscellaneous compounds showed promising control efficacies when used either preventively or curatively in the plant assay. A histopathological study was carried out on the mode of action of the resistance inducer, acibenzolar-S-methyl (ASM), which reduced scab severity and sporulation on apple seedlings in several plant assays when applied as preventive treatment. The effect of the inducer on key pre- and post-penetration events of V. inaequalis was studied and compared to these events in water-treated control leaves. The histopathological study showed that the inducer had its strongest effect on post-penetration events indicated by delayed infection and reduced stroma development. In addition, a small but significant inhibition of conidial germination and a stimulation of germ tube length were observed. This investigation provides new histopathological evidence for the mode of action of ASM against V. inaequalis and serves as a model for evaluation of the mechanisms by which the organically based fungicides reduce infection of V. inaequalis

Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets

BACKGROUND: Genome-wide microarrays have been useful for predicting chemical-genetic interactions at the gene level. However, interpreting genome-wide microarray results can be overwhelming due to the vast output of gene expression data combined with off-target transcriptional responses many times induced by a drug treatment. This study demonstrates how experimental and computational methods can interact with each other, to arrive at more accurate predictions of drug-induced perturbations. We present a two-stage strategy that links microarray experimental testing and network training conditions to predict gene perturbations for a drug with a known mechanism of action in a well-studied organism. RESULTS: S. cerevisiae cells were treated with the antifungal, fluconazole, and expression profiling was conducted under different biological conditions using Affymetrix genome-wide microarrays. Transcripts were filtered with a formal network-based method, sparse simultaneous equation models and Lasso regression (SSEM-Lasso), under different network training conditions. Gene expression results were evaluated using both gene set and single gene target analyses, and the drug’s transcriptional effects were narrowed first by pathway and then by individual genes. Variables included: (i) Testing conditions – exposure time and concentration and (ii) Network training conditions – training compendium modifications. Two analyses of SSEM-Lasso output – gene set and single gene – were conducted to gain a better understanding of how SSEM-Lasso predicts perturbation targets. CONCLUSIONS: This study demonstrates that genome-wide microarrays can be optimized using a two-stage strategy for a more in-depth understanding of how a cell manifests biological reactions to a drug treatment at the transcription level. Additionally, a more detailed understanding of how the statistical model, SSEM-Lasso, propagates perturbations through a network of gene regulatory interactions is achieved.Published versio

Arithmetic results on orbits of linear groups

Let $p$ be a prime and $G$ a subgroup of $GL_d(p)$. We define $G$ to be $p$-exceptional if it has order divisible by $p$, but all its orbits on vectors have size coprime to $p$. We obtain a classification of $p$-exceptional linear groups. This has consequences for a well known conjecture in representation theory, and also for a longstanding question concerning 1/2-transitive linear groups (i.e. those having all orbits on nonzero vectors of equal length), classifying those of order divisible by $p$.Comment: slight revisions after referee's comment

Study of meta-analysis strategies for network inference using information-theoretic approaches

© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Reverse engineering of gene regulatory networks (GRNs) from gene expression data is a classical challenge in systems biology. Thanks to high-throughput technologies, a massive amount of gene-expression data has been accumulated in the public repositories. Modelling GRNs from multiple experiments (also called integrative analysis) has; therefore, naturally become a standard procedure in modern computational biology. Indeed, such analysis is usually more robust than the traditional approaches focused on individual datasets, which typically suffer from some experimental bias and a small number of samples. To date, there are mainly two strategies for the problem of interest: the first one (”data merging”) merges all datasets together and then infers a GRN whereas the other (”networks ensemble”) infers GRNs from every dataset separately and then aggregates them using some ensemble rules (such as ranksum or weightsum). Unfortunately, a thorough comparison of these two approaches is lacking. In this paper, we evaluate the performances of various metaanalysis approaches mentioned above with a systematic set of experiments based on in silico benchmarks. Furthermore, we present a new meta-analysis approach for inferring GRNs from multiple studies. Our proposed approach, adapted to methods based on pairwise measures such as correlation or mutual information, consists of two steps: aggregating matrices of the pairwise measures from every dataset followed by extracting the network from the meta-matrix.Peer ReviewedPostprint (author's final draft

Liquid droplet generation

A pre-prototype segment of a droplet sheet generator for a liquid droplet radiator was designed, constructed and tested. The ability to achieve a uniform, non-diverging droplet sheet is limited by manufacturing tolerances on nozzle parallelism. For an array of 100, 100 micrometer diameters nozzles spaced 5 stream diameters apart, typical standard deviations in stream alignment were plus or minus 10 mrad. The drop to drop fractional speed variations of the drops in typical streams were similar and independent of position in the array. The absolute value of the speed dispersion depended on the amplitude of the disturbance applied to the stream. A second generation preliminary design of a 5200 stream segment of a droplet sheet generator was completed. The design is based on information developed during testing of the pre-prototype segment, along with the results of an acoustical analysis for the stagnation cavity pressure fluctuations used to break-up the streams into droplets