Validation of a Low-Cost Human Papillomavirus Genotyping Assay Based on PGMY PCR and Reverse Blotting Hybridization with Reusable Membranes.

The genotyping of human papillomaviruses (HPV) is essential for the surveillance of HPV vaccines. We describe and validate a low-cost PGMY-based PCR assay (PGMY-CHUV) for the genotyping of 31 HPV by reverse blotting hybridization (RBH). Genotype-specific detection limits were 50 to 500 genome equivalents per reaction. RBH was 100% specific and 98.61% sensitive using DNA sequencing as the gold standard (n = 1,024 samples). PGMY-CHUV was compared to the validated and commercially available linear array (Roche) on 200 samples. Both assays identified the same positive (n = 182) and negative samples (n = 18). Seventy-six percent of the positives were fully concordant after restricting the comparison to the 28 genotypes shared by both assays. At the genotypic level, agreement was 83% (285/344 genotype-sample combinations; κ of 0.987 for single infections and 0.853 for multiple infections). Fifty-seven of the 59 discordant cases were associated with multiple infections and with the weakest genotypes within each sample (P < 0.0001). PGMY-CHUV was significantly more sensitive for HPV56 (P = 0.0026) and could unambiguously identify HPV52 in mixed infections. PGMY-CHUV was reproducible on repeat testing (n = 275 samples; 392 genotype-sample combinations; κ of 0.933) involving different reagents lots and different technicians. Discordant results (n = 47) were significantly associated with the weakest genotypes in samples with multiple infections (P < 0.0001). Successful participation in proficiency testing also supported the robustness of this assay. The PGMY-CHUV reagent costs were estimated at $2.40 per sample using the least expensive yet proficient genotyping algorithm that also included quality control. This assay may be used in low-resource laboratories that have sufficient manpower and PCR expertise.

Drug Court Process Evaluation Report, February 2008

The Iowa Consortium for Substance Abuse Research and Evaluation conducted a process evaluation in 2007 on the seven adult and juvenile drug courts existing in Iowa in 2003. (A list of adult and juvenile drug courts established in Iowa from 2004 through 2007 appears in the appendix.) The drug courts evaluated in this study differ on several important factors, including the judicial supervision model used, resources available, and the severity level of clients served. The divergent resources and clients should be considered when comparing outcomes across courts. Section 1 provides an overview of each drug court included in this study.

Statewide Process and Comparative Outcomes Study of 2003 Iowa Adult and Juvenile Drug Courts, August 2009

A statewide evaluation of the six adult and three juvenile drug courts in operation during calendar year 2003 was conducted. Completion rates, recidivism, substance abuse treatment, and supervision and placement (juveniles only) costs were examined by model (Judge and Community Panel) and by Judicial District. In addition, adult drug court participants were compared with a group of offenders who were screened and declined or were rejected by drug court in 2003 (referred) and a sample of offenders starting probation in 2003 (probationer). The adult participant and comparison groups were tracked from their entry into drug court, or the study, through December 31, 2007. This yielded an average post-program follow-up time of almost 3 years (2.9) for drug court participants. For the juvenile portion, drug court participants were compared with a group matched on several demographic and offense variables (Matched Comparison group) and juveniles referred to drug court who did not enter the program (Referred Comparison group). The juvenile participant and comparison groups were tracked from their entry into drug court, or the study, through approximately 16 quarters after program discharge with an end date of December 31, 2007.

Process and Outcome Evaluation of the STAR (Sisters Together Achieving Recovery) Program, September, 2010

In July of 2009, the Division of Criminal and Juvenile Justice Planning (CJJP) received Byrne Justice Assistance Grant/American Recovery and Reinvestment Act funding from the Governor’s Office of Drug Control Policy to conduct a process and outcome evaluation of the STAR (Sisters Together Achieving Recovery) program housed at the Iowa Correctional Institution for Women (ICIW) in Mitchellville, Iowa. The STAR Program is a licensed inpatient substance abuse treatment program that utilizes a Therapeutic Community model (TC). All offenders exiting the STAR program between October 1, 2004 and June 30, 2008 were included in the study (n=173). A comparison sample was drawn of offenders exiting the ICIW during the same release time frame with identified but untreated substance abuse needs (n= 173). March 31, 2010 was designated as the cut-off date for the study. This yielded an average post-program follow-up time of 3.1 years. The STAR group was further divided into two groups by time of program exit. Participants exiting the program between October 1, 2004 and June 30, 2006 were designated as STAR 1 (n=78) and those exiting the program between July 1, 2006 and June 30, 2008 were designated as STAR 2 (n=95). In order to have comparable tracking time between STAR groups, tracking time for STAR 1 concluded July 31, 2008. This yielded an average post release follow-up time of 2.4 years for both groups. Demographic, Program, Intervention, and Outcome data were examined. Comparisons were made between groups as well as categories of participation.

A process for mining science & technology documents databases, illustrated for the case of "knowledge discovery and data mining"

This paper presents a process of mining research & development abstract databases to profile current status and to project potential developments for target technologies, The process is called "technology opportunities analysis." This article steps through the process using a sample data set of abstracts from the INSPEC database on the topic o "knowledge discovery and data mining." The paper offers a set of specific indicators suitable for mining such databases to understand innovation prospects. In illustrating the uses of such indicators, it offers some insights into the status of knowledge discovery research*.

State of Iowa Appropriations Process, 2013

State of Iowa Appropriations Process. Flow chart of the process.

Budget Process in Iowa, September 18, 2008

Budget Process: The Governor and the State Legislature appropriate the state resources after the revenue receipts are estimated by the Revenue Estimating Conference.

The construction process of pedagogical knowledge among nursing professors

Didactic knowledge about contents is constructed through an idiosyncratic synthesis between knowledge about the subject area, students' general pedagogical knowledge and the teacher's biography. This study aimed to understand the construction process and the sources of Pedagogical Content Knowledge, as well as to analyze its manifestations and variations in interactive teaching by teachers whom the students considered competent. Data collection involved teachers from an undergraduate nursing program in the South of Brazil, through non-participant observation and semistructured interviews. Data analysis was submitted to the constant comparison method. The results disclose the need for initial education to cover pedagogical aspects for nurses; to assume permanent education as fundamental in view of the complexity of contents and teaching; to use mentoring/monitoring and the value learning with experienced teachers with a view to the development of quality teaching.

Review of Iowa Department of Human Services Drug Testing Process, December 2008

This report outlines the current drugs testing practices and using these practices for testing requirements.

Looking for factors involved in the light-dependent degradation of phytochrome A

SUMMARY : Phytochromes constitute a family of red/far-red photoreceptors regulating all the major transitions during the life cycle of plants. In Arabidopsis, five members: phyA,_ B, C, D and E, were identified. Phytochromes are synthesized in their inactive red-light absorbing form called Pr. Upon light absorbance they convert to the far-red light absorbing Pfr form. The Pfr form is the active conformer which converts back to the Pr form either rapidly upon far-red perception or in a slower process called dark reversion. ph~A represents an exception, in that it does not significantly dark-revert and two specific processes have been developed by the plants to decrease the amount of biologically active phyA. The first one is alight-dependent repression of the PHYA gene expression and the second one is alight-dependent degradation of the phyA protein. The latter is the most efficient process to rapidly decrease the level of active phyA. The ability of plants to regulate the amount of active phyA is critical in a far-red rich environment, a situation observed under a canopy. In these conditions, phyA is essential to induce the germination and the deetiolation of the young seedling. Later in the development the ability of phyA to repress growth counteracts the shade avoidance response. Therefore decreasing the amount of phyA allows stem growth and to compete with neighbours for the light. In this thesis, I investigate the light-dependent degradation of phyA. I developed a reverse genetic approach based on the systematic analysis of the light-dependent accumulation of phyA in the different cullin mutant cull, cul3a; cul3b and cul4. This analysis allowed me to show that CUL1 and CUL3A-based E3 ligase complexes are involved in the regulation of phyA degradation. Surprisingly, our results also demonstrate that cu14 is not affected in the degradation of phyA whereas constitutive Photomorphogenic 1 (COP1) a subunit of one CUL4based E3 complex was reported to be involved. Further investigations showed that the phenotype of cop1 is conditional, the mutant being defective in phyA degradation only in the presence of metabolisable sugars. I also showed that phyA is degraded by a proteasome-dependent mechanism both in the cytoplasm and in the nucleus using mutants and transgenic lines affected in the localization of phyA. Interestingly, I observed that phyA degradation was faster in the nucleus than in the cytosol and that rapid degradation of Pr also occurred in the nucleus suggesting that cytosolic accumulation of phyA in the dark is a way to regulate its proteolysis. Finally, we identify a short region similar to a PEST sequence required for phyA stability and we developed a unbiased genetic screen to identify new components involved in the regulation of the light-dependent degradation of phyA. The significance of these results are discussed. RESUME : Les phytochromes (phy) constituent une famille de photorécepteurs absorbant la lumière rouge et rouge lointaine et régulant toutes les étapes de transitions majeures dans la vie des plantes. Chez Arabidopsis, cinq membres : phyA, B, C, D et E ont été identifiés. Les phytochromes sont synthétisés sous une forme inactive appelée Pr absorbant la lumière rouge. Après perception de lumière ils passent sous une forme active Pfr absorbant dans le rouge lointain. La forme Pfr peut retourner sous la forme Pr après absorption de lumiëre rouge lointaine ou dans un processus lent appelé «réversion à l'obscurité ». phyA représente une exception à cette règle car il ne retoune pas significativement sous sa forme inactive dans le noir. Deux processus spécifiques ont donc été développés pour diminuer le taux de phyA actif. Le premier consiste en la répression du gène PHYA en condition de lumière et le second en une dégradation induite par la lumière de la protéine phyA. Ce dernier processus est le plus efficace pour diminuer rapidement le niveau de phyA. La capacité des plantes à réguler le taux de phyA actifs est critique dans un environnement riche en lumière rouge lointaine, une situation observée sous une canopée. Sous une canopée, phyA est essentiel pour induire la germination et la dé-étiolation de la jeune pousse. Plus tard dans le développement la capacité de phyA de réprimer la croissance freine la «réponse à l'évitement de l'ombre ». Par conséquent diminuer le taux de phyA permet la croissance de la tige et donc de rentrer en compétition pour la lumière avec les plantes avoisinantes. Dans cette thèse, j'ai étudié la dégradation de phyA. J'ai développé une approche génétique inverse basée sur l'analyse systématique de l'accumulation de phyA en condition de lumière dans les différents mutants cullin, cul1, cul3a, cul3b et cul4. Ces analyses nous ont permis d'identifier qu'un complexe E3 ligase CUL1 et un complexe E3 ligase CUL3A sont impliqués dans la régulation de la dégradation de phyA. Mes résultats démontrent aussi que le mutant cul4 n'est pas affecté dans la dégradation de phyA alors que Çonstitutive Photomorphogenic 1 (COPI) une sous unité d'un complexe CUL4 à été identifier dans la régulation de cette dégradation. Des analyses supplémentaires suggèrent que l'effet de la mutation cop1 est dépendante dë la présence de sucres métabolisables. J'ai aussi montré que phyA est dégradé dans le noyau et dans le cytoplasme par un mécanisme dépendant du protéasome et que la dégradation dans le.noyau est non seulement aspécifique de la forme Pr ou Pfr mais aussi est plus rapide que dans le cytoplasme. Ceci suggère que l'accumulation de phyA dans le cytoplasme permet son accumulation à des niveaux élevés à l'obscurité. Enfin j'ai identifié une région similaire à un motif PEST requise pour la stabilité de phyA et j'ai aussi développé un criblage génétique non biaisé pour identifier de nouveaux composants impliqués dans la régulation de la dégradation de phyA. L'importance de ces résultats est discutée dans le dernier chapitre de cette thèse.

Constructability in the Bridge Design Process, HR-320, 1991

In the United States many bridge structures have been designed without consideration for their unique construction problems. Many problems could have been avoided if construction knowledge and experience was utilized in the design process. A systematic process is needed to create and capture construction knowledge for use in the design process. This study was conducted to develop a system to capture construction considerations from field people and incorporate it into a knowledge-base for use by the bridge designers. This report presents the results of this study. As a part of this study a microcomputer-based constructability system has been developed. The system is a user-friendly microcomputer database which codifies construction knowledge, provides easy access to specifications, and provides simple design computation checks for the designer. A structure for the final database was developed and used in the prototype system. A process for collecting, developing and maintaining the database is presented and explained. The study involved a constructability survey, interviews with designers and constructors, and visits to construction sites to collect constuctability concepts. The report describes the development of the constructability system and addresses the future needs for the Iowa Department of Transportation to make the system operational. A user's manual for the system is included along with the report.

Development of a New Process for Determining Design Year Traffic Demands, TR-528, 2007

Researchers should continuously ask how to improve the models we rely on to make financial decisions in terms of the planning, design, construction, and maintenance of roadways. This project presents an alternative tool that will supplement local decision making but maintain a full appreciation of the complexity and sophistication of today’s regional model and local traffic impact study methodologies. This alternative method is tailored to the desires of local agencies, which requested a better, faster, and easier way to evaluate land uses and their impact on future traffic demands at the sub-area or project corridor levels. A particular emphasis was placed on scenario planning for currently undeveloped areas. The scenario planning tool was developed using actual land use and roadway information for the communities of Johnston and West Des Moines, Iowa. Both communities used the output from this process to make regular decisions regarding infrastructure investment, design, and land use planning. The City of Johnston case study included forecasting future traffic for the western portion of the city within a 2,600-acre area, which included 42 intersections. The City of West Des Moines case study included forecasting future traffic for the city’s western growth area covering over 30,000 acres and 331 intersections. Both studies included forecasting a.m. and p.m. peak-hour traffic volumes based upon a variety of different land use scenarios. The tool developed took goegraphic information system (GIS)-based parcel and roadway information, converted the data into a graphical spreadsheet tool, allowed the user to conduct trip generation, distribution, and assignment, and then to automatically convert the data into a Synchro roadway network which allows for capacity analysis and visualization. The operational delay outputs were converted back into a GIS thematic format for contrast and further scenario planning. This project has laid the groundwork for improving both planning and civil transportation decision making at the sub-regional, super-project level.