bcp: An R Package for Performing a Bayesian Analysis of Change Point Problems

Barry and Hartigan (1993) propose a Bayesian analysis for change point problems. We provide a brief summary of selected work on change point problems, both preceding and following Barry and Hartigan. We outline Barry and Hartigan's approach and offer a new R package, pkgbcp (Erdman and Emerson 2007), implementing their analysis. We discuss two frequentist alternatives to the Bayesian analysis, the recursive circular binary segmentation algorithm (Olshen and Venkatraman 2004) and the dynamic programming algorithm of (Bai and Perron 2003). We illustrate the application of bcp with economic and microarray data from the literature.

bcp: An R Package for Performing a Bayesian Analysis of Change Point Problems

Barry and Hartigan (1993) propose a Bayesian analysis for change point problems. We provide a brief summary of selected work on change point problems, both preceding and following Barry and Hartigan. We outline Barry and Hartigan's approach and offer a new R package, bcp (Erdman and Emerson 2007), implementing their analysis. We discuss two frequentist alternatives to the Bayesian analysis, the recursive circular binary segmentation algorithm (Olshen and Venkatraman 2004) and the dynamic programming algorithm of (Bai and Perron 2003). We illustrate the application of bcp with economic and microarray data from the literature

Validated Sandwich ELISA for the Quantification of von Willebrand Factor in Rabbit Plasma

von Willebrand Factor (vWF) is a multimeric plasma protein important for platelet plug formation. As part of its haemostatic role, it is released from endothelial cells during vascular stress or injury and is considered an excellent biomarker of endothelial function. Currently, there are no validated kits available to measure vWF in rabbits. We developed a sensitive and reproducible sandwich enzyme-linked immunosorbent assay (ELISA) for detection of vWF in rabbit plasma using commercially available antibodies and reagents. Purified human vWF was used as a calibrator standard with a dynamic range of 1.56–100 ng/mL. The Minimum Required Dilution for rabbit plasma was 1:100. When plasma was spiked with 3.76 or 10 ng/mL vWF, recovery was 108 ± 2% and 93 ± 2%, respectively. Intra- and inter-assay precision for 8 rabbit plasma samples were 3% and 4%, respectively. The Minimum Detectable Concentration was 254 pg/mL for purified human vWF and 1:10,700 dilution of cholesterol-fed rabbit plasma, and the Reliable Detection Limits were 457 pg/mL and 1:5940. Three freeze-thaw cycles significantly decreased vWF concentrations for purified human vWF and 2 of 3 plasma samples assayed. This ELISA provides sensitive and reproducible measurements of rabbit plasma vWF, which is an important biomarker for cardiovascular research

Bioactive nutrients - Time for tolerable upper intake levels to address safety.

There is increasing interest by consumers, researchers, and regulators into the roles that certain bioactive compounds, derived from plants and other natural sources, can play in health maintenance and promotion, and even prolonging a productive quality of life. Research has rapidly emerged suggesting that a wide range of compounds and mixtures in and from plants (such as fruits and vegetables, tea and cocoa) and animals (such as fish and probiotics) may exert substantial health benefits. There is interest in exploring the possibility of establishing recommended intakes or dietary guidance for certain bioactive substances to help educate consumers. A key aspect of establishing dietary guidance is the assessment of safety/toxicity of these substances. Toxicologists need to be involved in both the development of the safety framework and in the evaluation of the science to establish maximum intake/upper limits

Are Dietary Bioactives Ready for Recommended Intakes?12

Research has shown that numerous dietary bioactive components that are not considered essential may still be beneficial to health. The dietary reference intake (DRI) process has been applied to nonessential nutrients, such as fiber, yet the majority of bioactive components await a recommended intake. Despite a plethora of new research over the past several years on the health effects of bioactives, it is possible that the field may never reach a point where the current DRI framework is suitable for these food components. If bioactives are to move toward dietary guidance, they will likely require an alternative path to get there

CODE-1 : moored array and large-scale data report

The Coastal Ocean Dynamics Experiment (CODE) was undertaken to identify and study the important dynamical processes which govern the wind-driven motion of coastal water over the continental shelf. The initial effort in this multi-year, multi-institutional research program was to obtain high-quality data sets of all the relevant physical variables needed to construct accurate kinematic and dynamic descriptions of the response of shelf water to strong wind forcing in the 2 to 10 day band. A series of two small-scale, densely-instrumented field experiments of approximately four months duration (called CODE-1 and CODE-2) were designed to explore and to determine the kinematics and momentum and heat balances of the local wind-driven flow over a region of the northern California shelf which is characterized by both relatively simple bottom topography and large wind stress events in both winter and summer. A more lightly instrumented, long-term, large-scale component was designed to help separate the local wind-driven response in the region of the small-scale experiments from motions generated either offshore by the California Current system or in some distant region along the coast, and also to help determine the seasonal cycles of the atmospheric forcing, water structure, and coastal currents over the northern California shelf. The first small-scale experiment (CODE-1) was conducted between April and August, 1981 as a pilot study in which primary emphasis was placed on characterizing the wind-driven "signal" and the "noise" from which this signal must be extracted. In particular, CODE-1 was designed to identify the key features of the circulation and its variability over the northern California shelf and to determine the important time and length scales of the wind-driven response. This report presents a basic description of the moored array data and some other Eulerian data collected during CODE-1. A brief description of the CODE-1 field program is presented first, followed by a description of the common data analysis procedures used to produce the various data sets presented here. Then basic descriptions of the following data sets are presented: (a) the coastal and moored meteorological measurements, (b) the moored current measurements, (c) the moored temperature and conductivity observations, (d) the bottom pressure measurements, and (e) the wind and adjusted coastal sea level observations obtained as part of the CODE-1 large-scale component.Prepared for the National Science Foundation under Grant OCE 80-14941

Does wage rank affect employees' well-being?

How do workers make wage comparisons? Both an experimental study and an analysis of 16,000 British employees are reported. Satisfaction and well-being levels are shown to depend on more than simple relative pay. They depend upon the ordinal rank of an individual's wage within a comparison group. “Rank” itself thus seems to matter to human beings. Moreover, consistent with psychological theory, quits in a workplace are correlated with pay distribution skewness

SARS Surveillance during Emergency Public Health Response, United States, March–July 2003

In response to the emergence of severe acute respiratory syndrome (SARS), the United States established national surveillance using a sensitive case definition incorporating clinical, epidemiologic, and laboratory criteria. Of 1,460 unexplained respiratory illnesses reported by state and local health departments to the Centers for Disease Control and Prevention from March 17 to July 30, 2003, a total of 398 (27%) met clinical and epidemiologic SARS case criteria. Of these, 72 (18%) were probable cases with radiographic evidence of pneumonia. Eight (2%) were laboratory-confirmed SARS-coronavirus (SARS-CoV) infections, 206 (52%) were SARS-CoV negative, and 184 (46%) had undetermined SARS-CoV status because of missing convalescent-phase serum specimens. Thirty-one percent (124/398) of case-patients were hospitalized; none died. Travel was the most common epidemiologic link (329/398, 83%), and mainland China was the affected area most commonly visited. One case of possible household transmission was reported, and no laboratory-confirmed infections occurred among healthcare workers. Successes and limitations of this emergency surveillance can guide preparations for future outbreaks of SARS or respiratory diseases of unknown etiology