Radiative interactions of electrons with matter Final report

Electron interaction with matter and differential cross section measurements for bremsstrahlung produced in coincidence with inelastically scattered electron

X-ray analysis of fatigue damage in copper

X-ray analysis of copper deformed in fatigue for average coherently diffracting domain size and root mean square strain distributio

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

High-throughput biological assays such as microarrays let us ask very detailed questions about how diseases operate, and promise to let us personalize therapy. Data processing, however, is often not described well enough to allow for exact reproduction of the results, leading to exercises in "forensic bioinformatics" where aspects of raw data and reported results are used to infer what methods must have been employed. Unfortunately, poor documentation can shift from an inconvenience to an active danger when it obscures not just methods but errors. In this report we examine several related papers purporting to use microarray-based signatures of drug sensitivity derived from cell lines to predict patient response. Patients in clinical trials are currently being allocated to treatment arms on the basis of these results. However, we show in five case studies that the results incorporate several simple errors that may be putting patients at risk. One theme that emerges is that the most common errors are simple (e.g., row or column offsets); conversely, it is our experience that the most simple errors are common. We then discuss steps we are taking to avoid such errors in our own investigations.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS291 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Transcriptome analysis of response to drought in poplar interspecific hybrids.

To investigate the response of poplar hybrids to drought, leaves were collected from plants to which water was suspended for 8 and 13 days. After measuring the respective relative water content, RNAs were isolated from leaves of moderately and severely droughted plants and from control plants, and Illumina RNA sequencing was performed to analyze RNA synthesis in these tissues. Our data provide a resource (available at Gene Expression Omnibus database under GSE64044) to be employed for comparative analyses of drought response in different poplar species, with the long-term aim of developing strategies to improve plant productivity under drought

Investigations of electron interactions with matter. Part 1 - Bremsstrahlung production in aluminum and iron. Part 2 - Electron scattering in aluminum

Bremsstrahlung production in aluminum and iron - electron scattering in aluminu

Integrated MicroRNA-mRNA Profiling Identifies Oncostatin M as a Marker of Mesenchymal-Like ER-Negative/HER2-Negative Breast Cancer

MicroRNAs (miRNAs) simultaneously modulate different oncogenic networks, establishing a dynamic system of gene expression and pathway regulation. In this study, we analyzed global miRNA and messenger RNA (mRNA) expression profiles of 17 cell lines representing different molecular breast cancer subtypes. Spearman's rank correlation test was used to evaluate the correlation between miRNA and mRNA expression. Hierarchical clustering and pathway analysis were also performed. Publicly available gene expression profiles (n = 699) and tumor tissues (n = 80) were analyzed to assess the relevance of key miRNA-regulated pathways in human breast cancer. We identified 39 significantly deregulated miRNAs, and the integration between miRNA and mRNA data revealed the importance of immune-related pathways, particularly the Oncostatin M (OSM) signaling, associated with mesenchymal-like breast cancer cells. OSM levels correlated with genes involved in the inflammatory response, epithelial-to-mesenchymal transition (EMT), and epidermal growth factor (EGF) signaling in human estrogen receptor (ER)-negative/human epidermal growth factor receptor 2 (HER2)-negative breast cancer. Our results suggest that the deregulation of specific miRNAs may cooperatively impair immune and EMT pathways. The identification of the OSM inflammatory pathway as an important mediator of EMT in triple-negative breast cancer (TNBC) may provide a novel potential opportunity to improve therapeutic strategies

Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data

The availability of large quantities of transcriptomic data in the form of RNA-seq count data has necessitated the development of methods to identify genes differentially expressed between experimental conditions. Many existing approaches apply a parametric model of gene expression and so place strong assumptions on the distribution of the data. Here we explore an alternate nonparametric approach that applies an empirical likelihood framework, allowing us to define likelihoods without specifying a parametric model of the data. We demonstrate the performance of our method when applied to gold standard datasets, and to existing experimental data. Our approach outperforms or closely matches performance of existing methods in the literature, and requires modest computational resources. An R package, EmpDiff implementing the methods described in the paper is available from: http://homepages.inf.ed.ac.uk/tthorne/software/packages/EmpDiff_0.99.tar.gz

The Importance of Reproducible Research in High-Throughput Biology

December 12, 2024 Keith Baggerly, Ph.D.ProfessorDepartment of Bioinformatics and Computational Biology, (retired)https://openworks.mdanderson.org/igct_workshops/1004/thumbnail.jp