Pragmatism old and new

Elektronische Version der gedr. Ausg. 199

ValiDichro: a website for validating and quality control of protein circular dichroism spectra

Circular dichroism (CD) spectroscopy is widely used in structural biology as a technique for examining the structure, folding and conformational changes of proteins. A new server, ValiDichro, has been developed for checking the quality and validity of CD spectral data and metadata, both as an aid to data collection and processing and as a validation procedure for spectra to be included in publications. ValiDichro currently includes 25 tests for data completeness, consistency and quality. For each test that is done, not only is a validation report produced, but the user is also provided with suggestions for correcting or improving the data. The ValiDichro server is freely available at http://valispec.cryst.bbk.ac.uk/circularDichroism/ValiDichro/upload.html

The Simons Observatory Large Aperture Telescope Receiver

The Simons Observatory (SO) Large Aperture Telescope Receiver (LATR) will be coupled to the Large Aperture Telescope located at an elevation of 5,200 m on Cerro Toco in Chile. The resulting instrument will produce arcminute-resolution millimeter-wave maps of half the sky with unprecedented precision. The LATR is the largest cryogenic millimeter-wave camera built to date with a diameter of 2.4 m and a length of 2.6 m. It cools 1200 kg of material to 4 K and 200 kg to 100 mk, the operating temperature of the bolometric detectors with bands centered around 27, 39, 93, 145, 225, and 280 GHz. Ultimately, the LATR will accommodate 13 40 cm diameter optics tubes, each with three detector wafers and a total of 62,000 detectors. The LATR design must simultaneously maintain the optical alignment of the system, control stray light, provide cryogenic isolation, limit thermal gradients, and minimize the time to cool the system from room temperature to 100 mK. The interplay between these competing factors poses unique challenges. We discuss the trade studies involved with the design, the final optimization, the construction, and ultimate performance of the system

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample

A prospective, multi-method, multi-disciplinary, multi-level, collaborative, social-organisational design for researching health sector accreditation [LP0560737]

BACKGROUND: Accreditation has become ubiquitous across the international health care landscape. Award of full accreditation status in health care is viewed, as it is in other sectors, as a valid indicator of high quality organisational performance. However, few studies have empirically demonstrated this assertion. The value of accreditation, therefore, remains uncertain, and this persists as a central legitimacy problem for accreditation providers, policymakers and researchers. The question arises as to how best to research the validity, impact and value of accreditation processes in health care. Most health care organisations participate in some sort of accreditation process and thus it is not possible to study its merits using a randomised controlled strategy. Further, tools and processes for accreditation and organisational performance are multifaceted. METHODS/DESIGN: To understand the relationship between them a multi-method research approach is required which incorporates both quantitative and qualitative data. The generic nature of accreditation standard development and inspection within different sectors enhances the extent to which the findings of in-depth study of accreditation process in one industry can be generalised to other industries. This paper presents a research design which comprises a prospective, multi-method, multi-level, multi-disciplinary approach to assess the validity, impact and value of accreditation. DISCUSSION: The accreditation program which assesses over 1,000 health services in Australia is used as an exemplar for testing this design. The paper proposes this design as a framework suitable for application to future international research into accreditation. Our aim is to stimulate debate on the role of accreditation and how to research it.Jeffrey Braithwaite, Johanna Westbrook, Marjorie Pawsey, David Greenfield, Justine Naylor, Rick Iedema, Bill Runciman, Sally Redman, Christine Jorm, Maureen Robinson, Sally Nathan and Robert Gibber

The Responsibility of Presidents: Remembering Harry Truman and the Atomic Bomb

Paper presented at Conference on Memory and History, Northeast Missouri State University (now Truman State University), 11 April 1996

Torturing the Conventions

Contribution to Human Rights Week Symposium sponsored by the Students for Social Justice, University of Rochester, 7 December 2005

Jesse Moore Retirement Minute

Tribute to an esteemed colleague on the occasion of his retirement, 11 May 2000

Democratic Hope: Response to My Critics

Paper delivered at the Annual Meeting of the American Philosophical Association, Western Division, Portland, 24 March 2006. Consists of my response to four critics of my book, DEMOCRATIC HOPE