Yeast expression vectors using RNA polymerase III promoters

A series of Saccharomyces cerevisiae -- Escherichia coli shuttle vectors is described in which small RNAs can be stably expressed in yeast from two different promoters for RNA polymerase III transcription. The vectors are available in either high- or low-copy-number forms with either URA3, HIS3, or TRP1 selection markers, and are based on a previously described set of plasmid vectors [Sikorski and Hieter, Genetics 122 (1989) 19-27]. Transcripts have structured pre-tRNA or RPR1 leaders fused to RNA corresponding to inserted sequences. Levels of RNA accumulation are dependent on plasmid copy number and the type of transcript.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31111/1/0000007.pd

On Writ of Certiorari to the United States Court of Appeals for the Ninth Circuit, Brief of Product Liability Advisory Council, Inc., National Association of Manufacturers, Business Roundtable, and Chemical Manufacturers Association as Amici Curiae in Support of Respondent, William Daubert and Joyce Daubert, Individually and as Guardians Ad Litem for Jason Daubert, and Anita De Young, Individually and as Gaurdian Ad Litem for Eric Schuller v. Merrell Dow Pharmaceuticals, Inc.

The Federal Rules of Evidence exclude expert scientific testimony when it has been developed without regard for accepted scientific methods. This case focuses on expert scientific evidence. Such evidence plays a vital and often dispositive role in modern litigation. For scientific evidence to be helpful to the factfinder it must meet some minimal threshold of reliability. To hold otherwise would be to allow a system of adjudication based more on chance than on reason

A Global Health Research Checklist for clinicians.

Global health research has become a priority in most international medical projects. However, it is a difficult endeavor, especially for a busy clinician. Navigating the ethics, methods, and local partnerships is essential yet daunting.To date, there are no guidelines published to help clinicians initiate and complete successful global health research projects. This Global Health Research Checklist was developed to be used by clinicians or other health professionals for developing, implementing, and completing a successful research project in an international and often low-resource setting. It consists of five sections: Objective, Methodology, Institutional Review Board and Ethics, Culture and partnerships, and Logistics. We used individual experiences and published literature to develop and emphasize the key concepts. The checklist was trialed in two workshops and adjusted based on participants\u27 feedback

Tissue quality assessment using a novel direct elasticity assessment device (the E-finger): a cadaveric study of prostatectomy dissection.

INTRODUCTION: Minimally invasive radical prostatectomy (RP) (robotic and laparoscopic), have brought improvements in the outcomes of RP due to improved views and increased degrees of freedom of surgical devices. Robotic and laparoscopic surgeries do not incorporate haptic feedback, which may result in complications secondary to inadequate tissue dissection (causing positive surgical margins, rhabdosphincter damage, etc). We developed a micro-engineered device (6 mm2 sized) [E-finger]) capable of quantitative elasticity assessment, with amplitude ratio, mean ratio and phase lag representing this. The aim was to assess the utility of the device in differentiating peri-prostatic tissue types in order to guide prostate dissection. MATERIAL AND METHODS: Two embalmed and 2 fresh frozen cadavers were used in the study. Baseline elasticity values were assessed in bladder, prostate and rhabdosphincter of pre-dissected embalmed cadavers using the micro-engineered device. A measurement grid was created to span from the bladder, across the prostate and onto the rhabdosphincter of fresh frozen cadavers to enable a systematic quantitative elasticity assessment of the entire area by 2 independent assessors. Tissue was sectioned along each row of elasticity measurement points, and stained with haematoxylin and eosin (H&E). Image analysis was performed with Image Pro Premier to determine the histology at each measurement point. RESULTS: Statistically significant differences in elasticity were identified between bladder, prostate and sphincter in both embalmed and fresh frozen cadavers (p = < 0.001). Intra-class correlation (ICC) reliability tests showed good reliability (average ICC = 0.851). Sensitivity and specificity for tissue identification was 77% and 70% respectively to a resolution of 6 mm2. CONCLUSIONS: This cadaveric study has evaluated the ability of our elasticity assessment device to differentiate bladder, prostate and rhabdosphincter to a resolution of 6 mm2. The results provide useful data for which to continue to examine the use of elasticity assessment devices for tissue quality assessment with the aim of giving haptic feedback to surgeons performing complex surgery

Quantitative mechanical assessment of the whole prostate gland ex vivo using dynamic instrumented palpation

An instrumented palpation sensor, designed for measuring the dynamic modulus of tissue in vivo, has been developed and trialled on ex vivo whole prostate glands. The sensor consists of a flexible membrane sensor/actuator with an embedded strain gauge and is actuated using a dynamically varying airflow at frequencies of 1 and 5 Hz. The device was calibrated using an indentation stiffness measurement rig and gelatine samples with a range of static modulus similar to that reported in the literature for prostate tissue. The glands were removed from patients with diagnosed prostate cancer scheduled for radical prostatectomy, and the stiffness was measured within 30 min of surgical removal. Each prostate was later examined histologically in a column immediately below each indentation point and graded into one of the four groups; normal, benign prostatic hyperplasia, cancerous and mixed cancer and benign prostatic hyperplasia. In total, 11 prostates were assessed using multiple point probing, and the complex modulus at 1 and 5 Hz was calculated on a point-by-point basis. The device yielded values of quasi-static modulus of 15 ± 0.5 kPa and dynamic modulus of 20 ± 0.5 kPa for whole prostates, and a sensitivity of up to 80% with slightly lower specificity was achieved on diagnosis of prostate cancer using a combination of mechanical measures. This assessment did not take into account some obvious factors such as edge effects, overlap and clinical significance of the cancer, all of which would improve performance. The device, as currently configured, is immediately deployable in vivo. A number of improvements are also identified which could improve the sensitivity and specificity in future embodiments of the probe

Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes.

http://deepblue.lib.umich.edu/bitstream/2027.42/85738/1/Haeusler-Pratt-Hystt-Engelke-2008.pd

Seahawk: moving beyond HTML in Web-based bioinformatics analysis

<p>Abstract</p> <p>Background</p> <p>Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therfore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis.</p> <p>Results</p> <p>We have developed a program (Seahawk) that allows biologists to intuitively and seamlessly chain together Web Services using a data-centric, rather than the customary service-centric approach. The approach is illustrated with a ferredoxin mutation analysis. Seahawk concentrates on lowering entry barriers for biologists: no prior knowledge of the data ontology, or relevant services is required. In stark contrast to other MOBY-S clients, in Seahawk users simply load Web pages and text files they already work with. Underlying the familiar Web-browser interaction is an XML data engine based on extensible XSLT style sheets, regular expressions, and XPath statements which import existing user data into the MOBY-S format.</p> <p>Conclusion</p> <p>As an easily accessible applet, Seahawk moves beyond standard Web browser interaction, providing mechanisms for the biologist to concentrate on the analytical task rather than on the technical details of data formats and Web forms. As the MOBY-S protocol nears a 1.0 specification, we expect more biologists to adopt these new semantic-oriented ways of doing Web-based analysis, which empower them to do more complicated, <it>ad hoc </it>analysis workflow creation without the assistance of a programmer.</p

Multi-Messenger Gravitational Wave Searches with Pulsar Timing Arrays: Application to 3C66B Using the NANOGrav 11-year Data Set

When galaxies merge, the supermassive black holes in their centers may form binaries and, during the process of merger, emit low-frequency gravitational radiation in the process. In this paper we consider the galaxy 3C66B, which was used as the target of the first multi-messenger search for gravitational waves. Due to the observed periodicities present in the photometric and astrometric data of the source of the source, it has been theorized to contain a supermassive black hole binary. Its apparent 1.05-year orbital period would place the gravitational wave emission directly in the pulsar timing band. Since the first pulsar timing array study of 3C66B, revised models of the source have been published, and timing array sensitivities and techniques have improved dramatically. With these advances, we further constrain the chirp mass of the potential supermassive black hole binary in 3C66B to less than $(1.65\pm0.02) \times 10^9~{M_\odot}$ using data from the NANOGrav 11-year data set. This upper limit provides a factor of 1.6 improvement over previous limits, and a factor of 4.3 over the first search done. Nevertheless, the most recent orbital model for the source is still consistent with our limit from pulsar timing array data. In addition, we are able to quantify the improvement made by the inclusion of source properties gleaned from electromagnetic data to `blind' pulsar timing array searches. With these methods, it is apparent that it is not necessary to obtain exact a priori knowledge of the period of a binary to gain meaningful astrophysical inferences.Comment: 14 pages, 6 figures. Accepted by Ap

Low energy diet and intracranial pressure in women with idiopathic intracranial hypertension: prospective cohort study

Objective To observe intracranial pressure in women with idiopathic intracranial hypertension who follow a low energy diet