Barriers and Facilitators to Adoption of Genomic Services for Colorectal Care within the Veterans Health Administration.

We examined facilitators and barriers to adoption of genomic services for colorectal care, one of the first genomic medicine applications, within the Veterans Health Administration to shed light on areas for practice change. We conducted semi-structured interviews with 58 clinicians to understand use of the following genomic services for colorectal care: family health history documentation, molecular and genetic testing, and genetic counseling. Data collection and analysis were informed by two conceptual frameworks, the Greenhalgh Diffusion of Innovation and Andersen Behavioral Model, to allow for concurrent examination of both access and innovation factors. Specialists were more likely than primary care clinicians to obtain family history to investigate hereditary colorectal cancer (CRC), but with limited detail; clinicians suggested templates to facilitate retrieval and documentation of family history according to guidelines. Clinicians identified advantage of molecular tumor analysis prior to genetic testing, but tumor testing was infrequently used due to perceived low disease burden. Support from genetic counselors was regarded as facilitative for considering hereditary basis of CRC diagnosis, but there was variability in awareness of and access to this expertise. Our data suggest the need for tools and policies to establish and disseminate well-defined processes for accessing services and adhering to guidelines.

Responsiveness and clinical utility of the geriatric self-efficacy index for urinary incontinence

OBJECTIVES: To report on the responsiveness testing and clinical utility of the 12-item Geriatric Self-Efficacy Index for Urinary Incontinence (GSE-UI). DESIGN: Prospective cohort study. SETTING: Six urinary incontinence (UI) outpatient clinics in Quebec, Canada. PARTICIPANTS: Community-dwelling incontinent adults aged 65 and older. MEASUREMENTS: The abridged 12-item GSE-UI, measuring older adults' level of confidence for preventing urine loss, was administered to all new consecutive incontinent patients 1 week before their initial clinic visit, at baseline, and 3 months posttreatment. At follow-up, a positive rating of improvement in UI was ascertained from patients and their physicians using the Patient's and Clinician's Global Impression of Improvement scales, respectively. Responsiveness of the GSE-UI was calculated using Guyatt's change index. Its clinical utility was determined using receiver operating curves. RESULTS: Eighty-nine of 228 eligible patients (39.0%) participated (mean age 72.6+5.8, range 65–90). At 3-month follow-up, 22.5% of patients were very much better, and 41.6% were a little or much better. Guyatt's change index was 2.6 for patients who changed by a clinically meaningful amount and 1.5 for patients having experienced any level of improvement. An improvement of 14 points on the 12-item GSE-UI had a sensitivity of 75.1% and a specificity of 78.2% for detecting clinically meaningful changes in UI status. Mean GSE-UI scores varied according to improvement status (P<.001) and correlated with changes in quality-of-life scores (r=0.7, P<.001) and reductions in UI episodes (r=0.4, P=.004). CONCLUSION: The GSE-UI is responsive and clinically useful.

Aerodynamic Testing of Variable Message Signs

The increasing nationwide interest in intelligent transportation systems (ITS) and the need for more efficient transportation have led to the expanding use of variable message sign (VMS) technology. VMS panels are substantially heavier than flat panel aluminum signs and have a larger depth (dimension parallel to the direction of traffic). The additional weight and depth can have a significant effect on the aerodynamic forces and inertial loads transmitted to the support structure. The wind induced drag forces and the response of VMS structures is not well understood. Minimum design requirements for VMS structures are contained in the American Association of State Highway Transportation Officials Standard Specification for Structural Support for Highway Signs, Luminaires, and Traffic Signals (AASHTO Specification). However the Specification does not take into account the prismatic geometry of VMS and the complex interaction of the applied aerodynamic forces to the support structure. In view of the lack of code guidance and the limited number research performed so far, targeted experimentation and large scale testing was conducted at the Florida International University (FIU) Wall of Wind (WOW) to provide reliable drag coefficients and investigate the aerodynamic instability of VMS. A comprehensive range of VMS geometries was tested in turbulence representative of the high frequency end of the spectrum in a simulated suburban atmospheric boundary layer. The mean normal, lateral and vertical lift force coefficients, in addition to the twisting moment coefficient and eccentricity ratio, were determined using the measured data for each model. Wind tunnel testing confirmed that drag on a prismatic VMS is smaller than the 1.7 suggested value in the current AASHTO Specification (2013). An alternative to the AASHTO Specification code value is presented in the form of a design matrix. Testing and analysis also indicated that vortex shedding oscillations and galloping instability could be significant for VMS signs with a large depth ratio attached to a structure with a low natural frequency. The effect of corner modification was investigated by testing models with chamfered and rounded corners. Results demonstrated an additional decrease in the drag coefficient but a possible Reynolds number dependency for the rounded corner configuration.

The Effects on Students' Self-Efficacy Beliefs Regarding Their Comprehension of American Literature When Aesthetic Reading and Reader Response Strategy are Implemented

High-stakes testing and accountability have infiltrated the education system in the United States; the top priority for all teachers must be student progress on standardized tests. This has resulted in the predominance of reading for test-taking, (efferent reading), in the English, language arts, and reading classrooms. Authentic uses of print activities, like aesthetic reading, that encourage students to engage individually with a text, have been pushed aside. During a 3-week time period, regular level, English 3/American literature students in a Title I magnet high school, participated in this quasi-experimental study (N = 62). It measured the effects of an intervention of reading American literature texts aesthetically and writing aesthetically-evoked reader responses on students’ self-efficacy beliefs regarding their comprehension of American literature. One trained teacher and the researcher participated in the study: student participants were pre- and post- tested using the Confidence in Reading American Literature Survey which examined their self-efficacy beliefs regarding their comprehension of American literature. Several statistical analyses were performed. The results of the linear regression analyses partially supported a positive relationship between aesthetically-evoked reader responses and students’ self-efficacy beliefs regarding their comprehension of American literature. Additionally, the results of the 2 (sex) x 2 (treatment) ANCOVAs conducted to test group differences in self-efficacy beliefs regarding the comprehension of American literature between treatment and control groups indicated a main effect for treatment (but not sex; nor was there a significant sex x treatment interaction), suggesting the treatment was partially effective in increasing students’ self-efficacy beliefs. Seven of the twelve ANCOVAs indicated a statistically significant increase in the treatment group’s adjusted group mean self-efficacy belief scores as a result of being exposed to the intervention. In six of these seven analyses, increases in self-efficacy beliefs occurred in tasks that required three or more higher-order levels of thinking/learning. The results are discussed in terms of theoretical, empirical and practical significance. Future research is recommended to extend the intervention beyond the narrow confines of a Title I magnet school to settings where the intervention could be tested longitudinally, e. g., honors and gifted students, elementary and middle schools.

The relationship of E. coli and total coliform culture to the quantitative molecular detection of various fecal indicators, sources, and pathogens in private drinking water wells

Water remains a predominant vector for human enteric pathogens not just for developing countries but also developed nations, where numerous infectious disease outbreaks, linked to the contamination of drinking water have been documented. Private drinking water wells are a source of drinking water that is largely unstudied even though a significant percentage of the population in Ontario relies on wells as their primary water source. As there exists little to no systematic surveillance for enteric infections or outbreaks related to well water sources, these individuals may be at higher risk of waterborne infectious diseases. The relationships between various fecal indicators in the water of private drinking water wells, including E. coli, Total Coliforms (TC) and Bacteroides, and enteric pathogens, including Campylobacter jejuni, Salmonella spp., and Shiga toxin producing E. coli, were studied. Convenience private well water samples collected from various regions of interest during the summer of 2014 underwent membrane filtration and culture to determine quantities of E. coli and TC colony forming units. 289 E. coli positive and 230 TC-only waters were successfully analyzed by individual qPCR assays for the aforementioned enteric pathogens. Microbial source tracking methods targeted to specific Bacteroides were used to determine the source of fecal contamination as either human or bovine. The source of fecal contamination varied by geographic region and is thought to be due to such things as differences in septic tank density and underlying geology, among others. Fecal indicators, E. coli and Bacteroides, were significantly correlated. E. coli as measured by qPCR was more strongly correlated to both total and human-specific Bacteroides genetic markers than culturable E. coli. Lastly, 1.9% of samples showed molecular evidence of contamination with enteric pathogens. Although low, this finding is significant given the limited volume of water available for testing, and suggests a potential health risk to consumers. Knowing the extent of contamination, as well as the biologic source, can better inform risk assessment and the development of potential intervention strategies for private well water in specific regions of Ontario.

BRAF mutation testing algorithm for vemurafenib treatment in melanoma: recommendations from an expert panel.

The incidence of melanoma has increased rapidly over the past 30 years, and the disease is now the sixth most common cancer among men and women in the U.K. Many patients are diagnosed with or develop metastatic disease, and survival is substantially reduced in these patients. Mutations in the BRAF gene have been identified as key drivers of melanoma cells and are found in around 50% of cutaneous melanomas. Vemurafenib (Zelboraf(®) ; Roche Molecular Systems Inc., Pleasanton, CA, U.S.A.) is the first licensed inhibitor of mutated BRAF, and offers a new first-line option for patients with unresectable or metastatic melanoma who harbour BRAF mutations. Vemurafenib was developed in conjunction with a companion diagnostic, the cobas(®) 4800 BRAF V600 Mutation Test. The purpose of this paper is to make evidence-based recommendations to facilitate the implementation of BRAF mutation testing and targeted therapy in patients with metastatic melanoma in the U.K. The recommendations are the result of a meeting of an expert panel and have been reviewed by melanoma specialists and representatives of the National Cancer Research Network Clinical Study Group on behalf of the wider melanoma community. This article is intended to be a starting point for practical advice and recommendations, which will no doubt be updated as we gain further experience in personalizing therapy for patients with melanoma.

An investigation of routes to cancer diagnosis in 10 international jurisdictions, as part of the International Cancer Benchmarking Partnership: survey development and implementation

Objectives This paper describes the methods used in the International Cancer Benchmarking Partnership Module 4 Survey (ICBPM4) which examines time intervals and routes to cancer diagnosis in 10 jurisdictions. We present the study design with defining and measuring time intervals, identifying patients with cancer, questionnaire development, data management and analyses.
Design and setting Recruitment of participants to the ICBPM4 survey is based on cancer registries in each jurisdiction. Questionnaires draw on previous instruments and have been through a process of cognitive testing and piloting in three jurisdictions followed by standardised translation and adaptation. Data analysis focuses on comparing differences in time intervals and routes to diagnosis in the jurisdictions.
Participants Our target is 200 patients with symptomatic breast, lung, colorectal and ovarian cancer in each jurisdiction. Patients are approached directly or via their primary care physician (PCP). Patients’ PCPs and cancer treatment specialists (CTSs) are surveyed, and ‘data rules’ are applied to combine and reconcile conflicting information. Where CTS information is unavailable, audit information is sought from treatment records and databases.
Main outcomes Reliability testing of the patient questionnaire showed that agreement was complete (κ=1) in four items and substantial (κ=0.8, 95% CI 0.333 to 1) in one item. The identification of eligible patients is sufficient to meet the targets for breast, lung and colorectal cancer. Initial patient and PCP survey response rates from the UK and Sweden are comparable with similar published surveys. Data collection was completed in early 2016 for all cancer types.
Conclusion An international questionnaire-based survey of patients with cancer, PCPs and CTSs has been developed and launched in 10 jurisdictions. ICBPM4 will help to further understand international differences in cancer survival by comparing time intervals and routes to cancer diagnosis.

Software and Space: Investigating How a Cosmology Research Group Enacts Infrastructure by Producing Software

Thesis (Ph.D.)--University of Washington, 2016-08

Evaluating statistical and machine learning methods to predict risk of in-hospital child mortality in Uganda

Thesis (Master's)--University of Washington, 2016-08

Workforce Patterns and the Prevention of Mother-to-Child Transmission of HIV Option B Cascade in Côte d'Ivoire

Thesis (Master's)--University of Washington, 2016-08

The Design and Implementation of a SD Card File System

SD card (Secure Digital Memory Card) is widely used in portable storage medium. Currently, latest researches on SD card, are mainly SD card controller based on FPGA (Field Programmable Gate Array). Most of them are relying on API interface (Application Programming Interface), AHB bus (Advanced High performance Bus), etc. They are dedicated to the realization of ultra high speed communication between SD card and upper systems. Studies about SD card controller, really play a vital role in the field of high speed cameras and other sub-areas of expertise. This design of FPGA-based file systems and SD2.0 IP (Intellectual Property core) does not only exhibit a nice transmission rate, but also achieve the systematic management of files, while retaining a strong portability and practicality. The file system design and implementation on a SD card covers the main three IP innovation points. First, the combination and integration of file system and SD card controller, makes the overall system highly integrated and practical. The popular SD2.0 protocol is implemented for communication channels. Pure digital logic design based on VHDL (Very-High-Speed Integrated Circuit Hardware Description Language), integrates the SD card controller in hardware layer and the FAT32 file system for the entire system. Secondly, the document management system mechanism makes document processing more convenient and easy. Especially for small files in batch processing, it can ease the pressure of upper system to frequently access and process them, thereby enhancing the overall efficiency of systems. Finally, digital design ensures the superior performance. For transmission security, CRC (Cyclic Redundancy Check) algorithm is for data transmission protection. Design of each module is platform-independent of macro cells, and keeps a better portability. Custom integrated instructions and interfaces may facilitate easily to use. Finally, the actual test went through multi-platform method, Xilinx and Altera FPGA developing platforms. The timing simulation and debugging of each module was covered. Finally, Test results show that the designed FPGA-based file system IP on SD card can support SD card, TF card and Micro SD with 2.0 protocols, and the successful implementation of systematic management for stored files, and supports SD bus mode. Data read and write rates in Kingston class10 card is approximately 24.27MB/s and 16.94MB/s.

Large-Scale Controlled-Condition Experiment to Evaluate Light Weight Deflectometers for Modulus Determination and Compaction Quality Assurance of Unbound Pavement Materials

Compaction control using lightweight deflectometers (LWD) is currently being evaluated in several states and countries and fully implemented for pavement construction quality assurance (QA) by a few. Broader implementation has been hampered by the lack of a widely recognized standard for interpreting the load and deflection data obtained during construction QA testing. More specifically, reliable and practical procedures are required for relating these measurements to the fundamental material property—modulus—used in pavement design. This study presents a unique set of data and analyses for three different LWDs on a large-scale controlled-condition experiment. Three 4.5x4.5 m2 test pits were designed and constructed at target moisture and density conditions simulating acceptable and unacceptable construction quality. LWD testing was performed on the constructed layers along with static plate loading testing, conventional nuclear gauge moisture-density testing, and non-nuclear gravimetric and volumetric water content measurements. Additional material was collected for routine and exploratory tests in the laboratory. These included grain size distributions, soil classification, moisture-density relations, resilient modulus testing at optimum and field conditions, and an advanced experiment of LWD testing on top of the Proctor compaction mold. This unique large-scale controlled-condition experiment provides an excellent high quality resource of data that can be used by future researchers to find a rigorous, theoretically sound, and straightforward technique for standardizing LWD determination of modulus and construction QA for unbound pavement materials.

Biological Principles of Information Storage and Retrieval

Published in Electronic Handling of Information: Testing and Evaluation, Kent, Taubee, Beltzer, and Goldstein (ed.), Academic Press, London(1967), pp. 123–147.

Architecture for IoT Node and Platform

Only recently, during the past five years, consumer electronics has been evolving rapidly. Many products have started to include “smart home” capabilities, enabling communication and interoperability of various smart devices. Even more devices and sensors can be remote controlled and monitored through cloud services. While the smart home systems have become very affordable to average consumer compared to the early solutions decades ago, there are still many issues and things that need to be fixed or improved upon: energy efficiency, connectivity with other devices and applications, security and privacy concerns, reliability, and response time. This paper focuses on designing Internet of Things (IoT) node and platform architectures that take these issues into account, notes other currently used solutions, and selects technologies in order to provide better solution. The node architecture aims for energy efficiency and modularity, while the platform architecture goals are in scalability, portability, maintainability, performance, and modularity. Moreover, the platform architecture attempts to improve user experience by providing higher reliability and lower response time compared to the alternative platforms. The architectures were developed iteratively using a development process involving research, planning, design, implementation, testing, and analysis. Additionally, they were documented using Kruchten’s 4+1 view model, which is used to describe the use cases and different views of the architectures. The node architecture consisted of energy efficient hardware, FC3180 microprocessor and CC2520 RF transceiver, modular operating system, Contiki, and a communication protocol, AllJoyn, used for providing better interoperability with other IoT devices and applications. The platform architecture provided reliable low response time control, monitoring, and initial setup capabilities by utilizing web technologies on various devices such as smart phones, tablets, and computers. Furthermore, an optional cloud service was provided in order to control devices and monitor sensors remotely by utilizing scalable high performance technologies in the backend enabling low response time and high reliability.