Urine Specimens from Pregnant and Nonpregnant Women Inhibitory to Amplification of \u3cem\u3eChlamydia trachomatis\u3c/em\u3e Nucleic Acid by PCR, Ligase Chain Reaction, and Transcription-Mediated Amplification: Identification of Urinary Substances Associated with Inhibition and Removal of Inhibitory Activity

The presence of endogenous amplification inhibitors in urine may produce false-negative results for the detection of Chlamydia trachomatis nucleic acids by tests such as PCR, ligase chain reaction (LCR), and transcription-mediated amplification (TMA). Consecutive urine specimens from 101 pregnant women and 287 nonpregnant women submitted for urinalysis were processed for C. trachomatis detection. Aliquots were spiked with the equivalent of one C. trachomatis elementary body and were tested by three commercial assays: AMPLICOR CT/NG, Chlamydia LCX, and Chlamydia TMA. The prevalence of inhibitors resulting in complete inhibition of amplification was 4.9% for PCR, 2.6% for LCR, and 7.5% for TMA. In addition, all three assays were partially inhibited by additional urine specimens. Only PCR was more often inhibited by urine from pregnant women than by urine from nonpregnant women (9.9 versus 3.1%; P = 0.011). A complete urinalysis including dipstick and a microscopic examination was performed. Logistic regression analysis revealed that the following substances were associated with amplification inhibition: beta-human chorionic gonadotropin (odd ratio [OR], 3.3) and crystals (OR, 3.3) for PCR, nitrites for LCR (OR, 14.4), and hemoglobin (OR, 3.3), nitrites (OR, 3.3), and crystals (OR, 3.3) for TMA. Aliquots of each inhibitory urine specimen were stored at 4 and -70°C and a dilution of 1:10 (84% for PCR, 100% for LCR, and 92% for TMA). Five urine specimens (three for PCR and two for TMA) required phenol-chloroform extraction to remove inhibitors. The results indicate that the prevalence of nucleic acid amplification inhibitors in female urine is different for each technology, that this prevalence may be predicted by the presence of urinary factors, and that storage and dilution remove most of the inhibitors

Prediction and Generation of Binary Markov Processes: Can a Finite-State Fox Catch a Markov Mouse?

Understanding the generative mechanism of a natural system is a vital component of the scientific method. Here, we investigate one of the fundamental steps toward this goal by presenting the minimal generator of an arbitrary binary Markov process. This is a class of processes whose predictive model is well known. Surprisingly, the generative model requires three distinct topologies for different regions of parameter space. We show that a previously proposed generator for a particular set of binary Markov processes is, in fact, not minimal. Our results shed the first quantitative light on the relative (minimal) costs of prediction and generation. We find, for instance, that the difference between prediction and generation is maximized when the process is approximately independently, identically distributed.Comment: 12 pages, 12 figures; http://csc.ucdavis.edu/~cmg/compmech/pubs/gmc.ht

The TIGRE gamma-ray telescope

TIGRE is an advanced telescope for gamma-ray astronomy with a few arcmin resolution. From 0.3 to 10 MeV it is a Compton telescope. Above 1 MeV, its multi-layers of double sided silicon strip detectors allow for Compton recoil electron tracking and the unique determination for incident photon direction. From 10 to 100 MeV the tracking feature is utilized for gamma-ray pair event reconstruction. Here we present TIGRE energy resolutions, background simulations and the development of the electronics readout system

A comparative framework: how broadly applicable is a 'rigorous' critical junctures framework?

The paper tests Hogan and Doyle's (2007, 2008) framework for examining critical junctures. This framework sought to incorporate the concept of ideational change in understanding critical junctures. Until its development, frameworks utilized in identifying critical junctures were subjective, seeking only to identify crisis, and subsequent policy changes, arguing that one invariably led to the other, as both occurred around the same time. Hogan and Doyle (2007, 2008) hypothesized ideational change as an intermediating variable in their framework, determining if, and when, a crisis leads to radical policy change. Here we test this framework on cases similar to, but different from, those employed in developing the exemplar. This will enable us determine whether the framework's relegation of ideational change to a condition of crisis holds, or, if ideational change has more importance than is ascribed to it by this framework. This will also enable us determined if the framework itself is robust, and fit for the purposes it was designed to perform — identifying the nature of policy change

Focused Ion Beam Fabrication

Contains summary of research program and reports on four research projects.Charles Stark Draper Laboratory (Contract DL-H-225270)Hughes Research LaboratoriesInternational Business Machines, Inc. (Contract 456614)Nippon Telegraph and Telephone, Inc.U.S. Navy - Office of Naval Research (Contract N00014-84-K-0073)U.S. Department of Defense (Contract MDA903-85-C-0215)Hitachi Central Research Laborator

Religious Identity, Religious Attendance, and Parental Control

Using a national sample of adolescents aged 10–18 years and their parents (N = 5,117), this article examines whether parental religious identity and religious participation are associated with the ways in which parents control their children. We hypothesize that both religious orthodoxy and weekly religious attendance are related to heightened levels of three elements of parental control: monitoring activities, normative regulations, and network closure. Results indicate that an orthodox religious identity for Catholic and Protestant parents and higher levels of religious attendance for parents as a whole are associated with increases in monitoring activities and normative regulations of American adolescents

Supply Chain Logistics and Business Ecosystems Needed for the Development of Natural Vaccines with Novel, Safer, and Noninvasive Delivery Mechanisms

The success of natural, non-invasive vaccines is dependent not only on their efficacy and safety but also on the logistics and business ecosystems required to develop and distribute them. This chapter discusses the challenges and opportunities associated with developing and implementing a supply chain for such vaccines as well as different scenarios that a similar new business could encounter on its path to the market. We examine options for vertical coordination within the value chain in areas such as product manufacturing, packaging, and distribution. Market and stakeholder analysis is also provided, which focuses on contracting strategies, while keeping in mind the importance of an efficient and equitable distribution of vaccines. Lastly, we will explain our most probable road map, how we arrived at that decision, and how this information can be used by natural vaccine producers to develop supply chains

Observations of convective and dynamical instabilities in tropopause folds and their contribution to stratosphere-troposphere exchange

With aircraft-mounted in situ and remote sensing instruments for dynamical, thermal, and chemical measurements we studied two cases of tropopause folding. In both folds we found Kelvin-Helmholtz billows with horizontal wavelength of ∼900 m and thickness of ∼120 m. In one case the instability was effectively mixing the bottomside of the fold, leading to the transfer of stratospheric air into the troposphere. Also, we discovered in both cases small-scale secondary ozone maxima shortly after the aircraft ascended past the topside of the fold that corresponded to regions of convective instability. We interpreted this phenomenon as convectively breaking gravity waves. Therefore we posit that convectively breaking gravity waves acting on tropopause folds must be added to the list of important irreversible mixing mechanisms leading to stratosphere-troposphere exchange.United States. National Aeronautics and Space Administration (Grant NAG2-1105)United States. National Aeronautics and Space Administration (Grant NAGl-1758)United States. National Aeronautics and Space Administration (Grant NAGl-1901

Focused Ion Beam Fabrication

Contains reports on five research projects.DARPA/Naval Electronic Systems Command (Contract MDA-903-85-C-0215)Charles Stark Draper Laboratory (Contract DL-H-261827)U.S. Navy - Office of Naval Research (Contract N00014-84-K-0073)Nippon Telephone and TelegraphHitachi Central Research Laborator