Standing together for reproducibility in large-scale computing: report on reproducibility@XSEDE

This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda focused on reproducibility in large-scale computational research. Two important themes capture the spirit of the workshop submissions and discussions: (1) organizational stakeholders, especially supercomputer centers, are in a unique position to promote, enable, and support reproducible research; and (2) individual researchers should conduct each experiment as though someone will replicate that experiment. Participants documented numerous issues, questions, technologies, practices, and potentially promising initiatives emerging from the discussion, but also highlighted four areas of particular interest to XSEDE: (1) documentation and training that promotes reproducible research; (2) system-level tools that provide build- and run-time information at the level of the individual job; (3) the need to model best practices in research collaborations involving XSEDE staff; and (4) continued work on gateways and related technologies. In addition, an intriguing question emerged from the day's interactions: would there be value in establishing an annual award for excellence in reproducible research? Overvie

Anti-Epithelial Cell Adhesion Molecule Antibodies and the Detection of Circulating Normal-Like Breast Tumor Cells

Identification of specific subtypes of circulating tumor cells in peripheral blood of cancer patients can provide information about the biology of metastasis and improve patient management. However, to be effective, the method used to identify circulating tumor cells must detect all tumor cell types. We investigated whether the five subtypes of human breast cancer cells that have been defined by global gene expression profiling—normal-like, basal, HER2-positive, and luminal A and B—were identified by CellSearch, a US Food and Drug Administration–approved test that uses antibodies against the cell surface–expressed epithelial cell adhesion molecule (EpCAM) to isolate circulating tumor cells. We used global gene expression profiling to determine the subtypes of a well-defined panel of 34 human breast cancer cell lines (15 luminal, nine normal-like, five basal-like, and five Her2-positive). We mixed 50-150 cells from 10 of these cell lines with 7.5 mL of blood from a single healthy human donor, and the mixtures were subjected to the CellSearch test to isolate the breast cancer cells. We found that the CellSearch isolation method, which uses EpCAM on the surface of circulating tumor cells for cell isolation, did not recognize, in particular, normal-like breast cancer cells, which in general have aggressive features. New tests that include antibodies that specifically recognize normal-like breast tumor cells but not cells of hematopoietic origin are needed

Low-risk susceptibility alleles in 40 human breast cancer cell lines

Background: Low-risk breast cancer susceptibility alleles or SNPs confer only modest breast cancer risks ranging from just over 1.0 to 1.3 fold. Yet, they are common among most populations and therefore are involved in the development of essentially all breast cancers. The mechanism by which the low-risk SNPs confer breast cancer risks is currently unclear. The breast cancer association consortium BCAC has hypothesized that the low-risk SNPs modulate expression levels of nearby located genes. Methods: Genotypes of five low-risk SNPs were determined for 40 human breast cancer cell lines, by direct sequencing of PCR-amplified genomic templates. We have analyzed expression of the four genes that are located nearby the low-risk SNPs, by using real-time RT-PCR and Human Exon microarrays. Results: The SNP genotypes and additional phenotypic data on the breast cancer cell lines are presented. We did not detect any effect of the SNP genotypes on expression levels of the nearby-located genes MAP3K1, FGFR2, TNRC9 and LSP1. Conclusion: The SNP genotypes provide a base line for functional studies in a well-characterized cohort of 40 human breast cancer cell lines. Our expression analyses suggest that a putative disease mechanism through gene expression modulation is not operative in breast cancer cell lines

Adhesion of Escherichia coli on to a series of poly(methacrylates) differing in charge and hydrophobicity

The adhesion of three Escherichia coli strains on to six poly(methacrylates) differing in hydrophobicity and surface charge was measured as a function of time under laminar flow conditions. Polymers used were poly(methy) methacrylate) (PMMA), poly(hydroxyethy) methacrylate) (PHEMA) and copolymers of MMA or HEMA with either 15% methacrylic acid (MAA) or 15% trimethylaminoethyl methacrylate-HCl salt (TMAEMA-CI). Bacterial and polymer surfaces were characterized by means of water contact angles and zeta potentials. Both the sessile drop contact angles and the zeta potentials of the bacterial surfaces were significantly different. No significant differences in the sessile drop contact angles of the polymer surfaces were observed. Using the Wilhelmy plate technique large contact angle hysteresis was observed for the different polymer surfaces. Surfaces of copolymers with MAA had more negative zeta potentials than those of the corresponding homopolymers. Surfaces of copolymers with TMAEMA-CI had positive zeta potentials. The highest numbers of adherent bacteria were found on materials with positive zeta potentials, irrespective of the bacterial strain used. Bacterial adhesion on to copolymers with MAA was less than on to the corresponding homopolymers. Bacterial equilibrium adhesion values correlate with the zeta potentials of the polymer surfaces (r > 0.85). On substrates with less negative zeta potentials high numbers of adhered bacteria were observed. Additionally, the equilibrium bacterial adhesion values could be related with receding contact angles of polymer surfaces with negative zeta potentials (r > 0.86). High equilibrium adhesion values were obtained for polymers with high contact angles. No correlation between the zeta potentials and contact angles of the bacteria with the adhesion values was found