16 results
An Eye-Tracking Study to Identify the Most Observed Features in a Physical Prototype of a Tiny House
- A. Berni, S. Altavilla, L. Ruiz-Pastor, C. Nezzi, Y. Borgianni
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- Journal:
- Proceedings of the Design Society / Volume 2 / May 2022
- Published online by Cambridge University Press:
- 26 May 2022, pp. 841-850
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This exploratory work aims to understand which elements of a building mostly attract visitors’ attention. An experiment was conducted to allow participants to visit a prototype tiny house while wearing eye-tracking glasses. Identified gazed elements of the prototype were selected and the corresponding dwell times used as variables. The limited dwell times on structural elements show that they can be easily overshadowed by other features present in the building. This leads to a design problem when the novelty and the quality of a new product, markedly a building, reside in the materials used.
4549 Reproducible Informatics for Reproducible Translational Research
- Ram Gouripeddi, Katherine Sward, Mollie Cummins, Karen Eilbeck, Bernie LaSalle, Julio C. Facelli
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- Journal:
- Journal of Clinical and Translational Science / Volume 4 / Issue s1 / June 2020
- Published online by Cambridge University Press:
- 29 July 2020, pp. 66-67
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OBJECTIVES/GOALS: Characterize formal informatics methods and approaches for enabling reproducible translational research. Education of reproducible methods to translational researchers and informaticians. METHODS/STUDY POPULATION: We performed a scoping review [1] of selected informatics literature (e.g. [2,3]) from PubMed and Scopus. In addition we reviewed literature and documentation of translational research informatics projects [4–21] at the University of Utah. RESULTS/ANTICIPATED RESULTS: The example informatics projects we identified in our literature covered a broad spectrum of translational research. These include research recruitment, research data requisition, study design and statistical analysis, biomedical vocabularies and metadata for data integration, data provenance and quality, and uncertainty. Elements impacting reproducibility of research include (1) Research Data: its semantics, quality, metadata and provenance; and (2) Research Processes: study conduct including activities and interventions undertaken, collections of biospecimens and data, and data integration. The informatics methods and approaches we identified as enablers of reproducibility include the use of templates, management of workflows and processes, scalable methods for managing data, metadata and semantics, appropriate software architectures and containerization, convergence methods and uncertainty quantification. In addition these methods need to be open and shareable and should be quantifiable to measure their ability to achieve reproducibility. DISCUSSION/SIGNIFICANCE OF IMPACT: The ability to collect large volumes of data collection has ballooned in nearly every area of science, while the ability to capturing research processes hasn’t kept with this pace. Potential for problematic research practices and irreproducible results are concerns.
Reproducibility is a core essentially of translational research. Translational research informatics provides methods and means for enabling reproducibility and FAIRness [22] in translational research. In addition there is a need for translational informatics itself to be reproducible to make research reproducible so that methods developed for one study or biomedical domain can be applied elsewhere. Such informatics research and development requires a mindset for meta-research [23].
The informatics methods we identified covers the spectrum of reproducibility (computational, empirical and statistical) and across different levels of reproducibility (reviewable, replicable, confirmable, auditable, and open or complete) [24–29]. While there are existing and ongoing efforts in developing informatics methods for translational research reproducibility in Utah and elsewhere, there is a need to further develop formal informatics methods and approaches: the Informatics of Research Reproducibility.
In this presentation, we summarize the studies and literature we identified and discuss our key findings and gaps in informatics methods for research reproducibility. We conclude by discussing how we are covering these topics in a translational research informatics course.
1. Pham MT, Rajić A, Greig JD, Sargeant JM, Papadopoulos A, McEwen SA. A scoping review of scoping reviews: advancing the approach and enhancing the consistency. Res Synth Methods. 2014 Dec;5(4):371–85.
2. McIntosh LD, Juehne A, Vitale CRH, Liu X, Alcoser R, Lukas JC, Evanoff B. Repeat: a framework to assess empirical reproducibility in biomedical research. BMC Med Res Methodol [Internet]. 2017 Sep 18 [cited 2018 Nov 30];17. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604503/
3. Denaxas S, Direk K, Gonzalez-Izquierdo A, Pikoula M, Cakiroglu A, Moore J, Hemingway H, Smeeth L. Methods for enhancing the reproducibility of biomedical research findings using electronic health records. BioData Min. 2017;10:31.
4. Burnett N, Gouripeddi R, Wen J, Mo P, Madsen R, Butcher R, Sward K, Facelli JC. Harmonization of Sensor Metadata and Measurements to Support Exposomic Research. In: 2016 International Society of Exposure Science [Internet]. Research Triangle Park, NC, USA; 2017 [cited 2017 Jun 17]. Available from: http://www.intlexposurescience.org/ISES2017
5. Butcher R, Gouripeddi RK, Madsen R, Mo P, LaSalle B. CCTS Biomedical Informatics Core Research Data Service. In Salt Lake City; 2016.
6. Cummins M, Gouripeddi R, Facelli J. A low-cost, low-barrier clinical trials registry to support effective recruitment. In Salt Lake City, Utah, USA; 2016 [cited 2018 Nov 30]. Available from: //campusguides.lib.utah.edu/UtahRR16/abstracts
7. Gouripeddi R, Warner P, Madsen R, Mo P, Burnett N, Wen J, Lund A, Butcher R, Cummins MR, Facelli J, Sward K. An Infrastructure for Reproducibile Exposomic Research. In: Research Reproducibility 2016 [Internet]. Salt Lake City, Utah, USA; 2016 [cited 2018 Nov 30]. Available from: //campusguides.lib.utah.edu/UtahRR16/abstracts
8. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005;6:R44.
9. Gouripeddi R, Cummins M, Madsen R, LaSalle B, Redd AM, Presson AP, Ye X, Facelli JC, Green T, Harper S. Streamlining study design and statistical analysis for quality improvement and research reproducibility. J Clin Transl Sci. 2017 Sep;1(S1):18–9.
10. Gouripeddi R, Eilbeck K, Cummins M, Sward K, LaSalle B, Peterson K, Madsen R, Warner P, Dere W, Facelli JC. A Conceptual Architecture for Reproducible On-demand Data Integration for Complex Diseases. In: Research Reproducibility 2016 (UtahRR16) [Internet]. Salt Lake City, Utah, USA; 2016 [cited 2017 Apr 25]. Available from: https://zenodo.org/record/168067
11. Gouripeddi R, Lane E, Madsen R, Butcher R, LaSalle B, Sward K, Fritz J, Facelli JC, Cummins M, Shao J, Singleton R. Towards a scalable informatics platform for enhancing accrual into clinical research studies. J Clin Transl Sci. 2017 Sep;1(S1):20–20.
12. Gouripeddi R, Deka R, Reese T, Butcher R, Martin B, Talbert J, LaSalle B, Facelli J, Brixner D. Reproducibility of Electronic Health Record Research Data Requests. In Washington, DC, USA; 2018 [cited 2018 Apr 21]. Available from: https://zenodo.org/record/1226602#.WtvvyZch270
13. Gouripeddi R, Mo P, Madsen R, Warner P, Butcher R, Wen J, Shao J, Burnett N, Rajan NS, LaSalle B, Facelli JC. A Framework for Metadata Management and Automated Discovery for Heterogeneous Data Integration. In: 2016 BD2K All Hands Meeting [Internet]. Bethesda, MD; November 29-30 [cited 2017 Apr 25]. Available from: https://zenodo.org/record/167885
14. Groat D, Gouripeddi R, Lin YK, Dere W, Murray M, Madsen R, Gestaland P, Facelli J. Identification of High-Level Formalisms that Support Translational Research Reproducibility. In: Research Reproducibility 2018 [Internet]. Salt Lake City, Utah, USA; 2018 [cited 2018 Oct 30]. Available from: //campusguides.lib.utah.edu/UtahRR18/abstracts
15. Huser V, Kahn MG, Brown JS, Gouripeddi R. Methods for examining data quality in healthcare integrated data repositories. Pac Symp Biocomput Pac Symp Biocomput. 2018;23:628–33.
16. Lund A, Gouripeddi R, Burnett N, Tran L-T, Mo P, Madsen R, Cummins M, Sward K, Facelli J. Enabling Reproducible Computational Modeling: The Utah PRISMS Ecosystem. In Salt Lake City, Utah, USA; 2018 [cited 2018 Oct 30]. Available from: //campusguides.lib.utah.edu/UtahRR18/abstracts
17. Pflieger LT, Mason CC, Facelli JC. Uncertainty quantification in breast cancer risk prediction models using self-reported family health history. J Clin Transl Sci. 2017 Feb;1(1):53–9.
18. Shao J, Gouripeddi R, Facelli J. Improving Clinical Trial Research Reproducibility using Reproducible Informatics Methods. In Salt Lake City, Utah, USA; 2018 [cited 2018 Oct 30]. Available from: //campusguides.lib.utah.edu/UtahRR18/abstracts
19. Shao J, Gouripeddi R, Facelli JC. Semantic characterization of clinical trial descriptions from ClincalTrials.gov and patient notes from MIMIC-III. J Clin Transl Sci. 2017 Sep;1(S1):12–12.
20. Tiase V, Gouripeddi R, Burnett N, Butcher R, Mo P, Cummins M, Sward K. Advancing Study Metadata Models to Support an Exposomic Informatics Infrastructure. In Ottawa, Canada; 2018 [cited 2018 Oct 30]. Available from: = http://www.eiseverywhere.com/ehome/294696/638649/?&t=8c531cecd4bb0a5efc6a0045f5bec0c3
21. Wen J, Gouripeddi R, Facelli JC. Metadata Discovery of Heterogeneous Biomedical Datasets Using Token-Based Features. In: IT Convergence and Security 2017 [Internet]. Springer, Singapore; 2017 [cited 2017 Sep 6]. p. 60–7. (Lecture Notes in Electrical Engineering). Available from: https://link.springer.com/chapter/10.1007/978-981-10-6451-7_8
22. Wilkinson MD, Dumontier M, Aalbersberg IjJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S-A, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016 Mar 15;3:160018.
23. Ioannidis JPA. Meta-research: Why research on research matters. PLOS Biol. 2018 Mar 13;16(3):e2005468.
24. Stodden V, Borwein J, Bailey DH. Setting the default to reproducible. Comput Sci Res SIAM News. 2013;46(5):4–6.
25. Stodden V, McNutt M, Bailey DH, Deelman E, Gil Y, Hanson B, Heroux MA, Ioannidis JPA, Taufer M. Enhancing reproducibility for computational methods. Science. 2016 Dec 9;354(6317):1240–1.
26. Stodden V, McNutt M, Bailey DH, Deelman E, Gil Y, Hanson B, Heroux MA, Ioannidis JPA, Taufer M. Enhancing reproducibility for computational methods. Science. 2016 Dec 9;354(6317):1240–1.
27. Stodden V. Reproducible Research for Scientific Computing: Tools and Strategies for Changing the Culture. Comput Sci Eng. 2012 Jul 1;14(4):13–7.
28. Baker M. Muddled meanings hamper efforts to fix reproducibility crisis. Nat News Available from: http://www.nature.com/news/muddled-meanings-hamper-efforts-to-fix-reproducibility-crisis-1.20076
29. Barba LA. Terminologies for Reproducible Research. ArXiv180203311 Cs 2018 Feb 9; Available from: http://arxiv.org/abs/1802.03311
3339 Development of a Competency-based Informatics Course for Translational Researchers
- Ram Gouripeddi, Danielle Groat, Samir E. Abdelrahman, Tom Cheatham, Mollie Cummins, Karen Eilbeck, Bernie LaSalle, Katherine Sward, Julio C. Facelli
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- Journal:
- Journal of Clinical and Translational Science / Volume 3 / Issue s1 / March 2019
- Published online by Cambridge University Press:
- 26 March 2019, pp. 66-67
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OBJECTIVES/SPECIFIC AIMS: Translational researchers often require the use of informatics methods in their work. Lack of an understanding of key informatics principles and methods limits the abilities of translational researchers to successfully implement Findable, Accessible, Interoperable, Reusable (FAIR) principles in grant proposal submissions and performed studies. In this study we describe our work in addressing this limitation in the workforce by developing a competency-based, modular course in informatics to meet the needs of diverse translational researchers. METHODS/STUDY POPULATION: We established a Translational Research Informatics Education Collaborative (TRIEC) consisting of faculty at the University of Utah (UU) with different primary expertise in informatics methods, and working in different tiers of the translational spectrum. The TRIEC, in collaboration with the Foundation of Workforce Development of the Utah Center for Clinical and Translational Science (CCTS), gathered informatics needs of early investigators by consolidating requests for informatics services, assistance provided in grant writing, and consultations. We then reviewed existing courses and literature for informatics courses that focused on clinical and translational researchers [3–9]. Using the structure and content of the identified courses, we developed an initial draft of a syllabus for a Translational Research Informatics (TRI) course which included key informatics topics to be covered and learning activities, and iteratively refined it through discussions. The course was approved by the UU Department of Biomedical Informatics, UU Graduate School and the CCTS. RESULTS/ANTICIPATED RESULTS: The TRI course introduces informatics PhD students, clinicians, and public health practitioners who have a demonstrated interest in research, to fundamental principles and tools of informatics. At the completion of the course, students will be able to describe and identify informatics tools and methods relevant to translational research and demonstrate inter-professional collaboration in the development of a research proposal addressing a relevant translational science question that utilizes the state-of-the-art in informatics. TRI covers a diverse set of informatics content presented as modules: genomics and bioinformatics, electronic health records, exposomics, microbiomics, molecular methods, data integration and fusion, metadata management, semantics, software architectures, mobile computing, sensors, recruitment, community engagement, secure computing environments, data mining, machine learning, deep learning, artificial intelligence and data science, open source informatics tools and platforms, research reproducibility, and uncertainty quantification. The teaching methods for TRI include (1) modular didactic learning consisting of presentations and readings and face-to-face discussions of the content, (2) student presentations of informatics literature relevant to their final project, and (3) a final project consisting of the development, critique and chalk talk and formal presentations of informatics methods and/or aims of an National Institutes of Health style K or R grant proposal. For (3), the student presents their translational research proposal concept at the beginning of the course, and works with members of the TRIEC with corresponding expertise. The final course grade is a combination of the final project, paper presentations and class participation. We offered TRI to a first cohort of students in the Fall semester of 2018. DISCUSSION/SIGNIFICANCE OF IMPACT: Translational research informatics is a sub-domain of biomedical informatics that applies and develops informatics theory and methods for translational research. TRI covers a diverse set of informatics topics that are applicable across the translational spectrum. It covers both didactic material and hands-on experience in using the material in grant proposals and research studies. TRI’s course content, teaching methodology and learning activities enable students to initially learn factual informatics knowledge and skills for translational research correspond to the ‘Remember, Understand, and Apply’ levels of the Bloom’s taxonomy [10]. The final project provides opportunity for applying these informatics concepts corresponding to the ‘Analyze, Evaluate, and Create’ levels of the Bloom’s taxonomy [10]. This inter-professional, competency-based, modular course will develop an informatics-enabled workforce trained in using state-of-the-art informatics solutions, increasing the effectiveness of translational science and precision medicine, and promoting FAIR principles in research data management and processes. Future work includes opening the course to all Clinical and Translational Science Award hubs and publishing the course material as a reference book. While student evaluations for the first cohort will be available end of the semester, true evaluation of TRI will be the number of trainees taking the course and successful grant proposal submissions. References: 1. Wilkinson MD, Dumontier M, et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016 Mar 15. 2. National Center for Advancing Translational Sciences. Translational Science Spectrum. National Center for Advancing Translational Sciences. 2015 [cited 2018 Nov 15]. Available from: https://ncats.nih.gov/translation/spectrum 3. Hu H, Mural RJ, Liebman MN. Biomedical Informatics in Translational Research. 1 edition. Boston: Artech House; 2008. 264 p. 4. Payne PRO, Embi PJ, Niland J. Foundational biomedical informatics research in the clinical and translational science era: a call to action. J Am Med Inform Assoc JAMIA. 2010;17(6):615–6. 5. Payne PRO, Embi PJ, editors. Translational Informatics: Realizing the Promise of Knowledge-Driven Healthcare. Softcover reprint of the original 1st ed. 2015 edition. Springer; 2016. 196 p. 6. Richesson R, Andrews J, editors. Clinical Research Informatics. 2nd ed. Springer International Publishing; 2019. (Health Informatics). 7. Robertson D, MD GHW, editors. Clinical and Translational Science: Principles of Human Research. 2 edition. Amsterdam: Academic Press; 2017. 808 p. 8. Shen B, Tang H, Jiang X, editors. Translational Biomedical Informatics: A Precision Medicine Perspective. Softcover reprint of the original 1st ed. 2016 edition. S.l.: Springer; 2018. 340 p. 9. Valenta AL, Meagher EA, Tachinardi U, Starren J. Core informatics competencies for clinical and translational scientists: what do our customers and collaborators need to know? J Am Med Inform Assoc. 2016 Jul 1;23(4):835–9. 10. Anderson LW, Krathwohl DR, Airasian PW, Cruikshank KA, Mayer RE, Pintrich PR, Raths J, Wittrock MC. A Taxonomy for Learning, Teaching, and Assessing: A Revision of Bloom’s Taxonomy of Educational Objectives, Abridged Edition. 1 edition. New York: Pearson; 2000.
2507: Towards a scalable informatics platform for enhancing accrual into clinical research studies
- Ram Gouripeddi, Elizabeth Lane, Randy Madsen, Ryan Butcher, Bernie LaSalle, Katherine Sward, Julie Fritz, Julio C. Facelli, Mollie Cummins, Jianyin Shao, Rob Singleton
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- Journal:
- Journal of Clinical and Translational Science / Volume 1 / Issue S1 / September 2017
- Published online by Cambridge University Press:
- 10 May 2018, p. 20
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OBJECTIVES/SPECIFIC AIMS: Issues with recruiting the targeted number of participants in a timely manner often results in underpowered studies, with more than 60% of clinical studies failing to complete or requiring extensions due to enrollment issues. The objective of this study is to develop and implement a scalable, organization wide platform to enhance accrual into clinical research studies. METHODS/STUDY POPULATION: We are developing and evaluating an informatics platform called Utah Utility for Research Recruitment (U2R2). U2R2 consists of 2 components: (i) Semantic Matcher: an automated trial criterion to patient matching component that also reports uncertainty associated with the match, and (ii) Match Delivery: mechanisms to deliver the list of matched patients for different research and clinical settings. As a first step, we limited the Semantic Matcher to utilize only structured data elements from the patient record and trial criteria. We are now including distributional semantic methods to match complete patient records and trial criteria as documents. We evaluated the first phase of U2R2 based on a randomized trial with a target enrollment of 220 participants that compares 2 treatment strategies for managing back pain (physical therapy and usual care) for individuals consulting a nonsurgical provider and symptomatic <90 days. RESULTS/ANTICIPATED RESULTS: U2R2 identified 9370 patients from the University of Utah Hospitals and Clinics as potential matches. Of these 9370, 1145 responded to the Back Pain study research team’s email or phone communications, and were further screened by phone. In total, 250 participants completed a screening visit, resulting in the current study enrollment of 130 participants. Forty-three of 1145 patients refused to participate, and 50 participants no-showed their screening visit. DISCUSSION/SIGNIFICANCE OF IMPACT: A recruitment platform can enhance potential participant identification, but requires attention to multiple issues involved with clinical research studies. Clinical eligibility criteria are usually unstructured and require human mediation and abstraction into discrete data elements for matching against patient records. In addition, key eligibility data are often embedded within text in the patient record. Distributional semantic approaches, by leveraging this content, can identify potential participants for screening with more specificity. The delivery of the list of matched patient results should consider characteristics of the research study, population, and targeted enrollment (eg, back pain being a common disorder and the possibility of the patient visiting different types of clinics), as well as organizational and socio-technical issues surrounding clinical practice and research. Embedding the delivery of match results into the clinical workflow by utilizing user-centered design approaches and involving the clinician, the clinic, and the patient in the recruitment process, could yield higher accrual indices.
2469: Streamlining study design and statistical analysis for quality improvement and research reproducibility
- Ram Gouripeddi, Mollie Cummins, Randy Madsen, Bernie LaSalle, Andrew Middleton Redd, Angela Paige Presson, Xiangyang Ye, Julio C. Facelli, Tom Green, Steve Harper
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- Journal:
- Journal of Clinical and Translational Science / Volume 1 / Issue S1 / September 2017
- Published online by Cambridge University Press:
- 10 May 2018, pp. 18-19
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OBJECTIVES/SPECIFIC AIMS: Key factors causing irreproducibility of research include those related to inappropriate study design methodologies and statistical analysis. In modern statistical practice irreproducibility could arise due to statistical (false discoveries, p-hacking, overuse/misuse of p-values, low power, poor experimental design) and computational (data, code and software management) issues. These require understanding the processes and workflows practiced by an organization, and the development and use of metrics to quantify reproducibility. METHODS/STUDY POPULATION: Within the Foundation of Discovery – Population Health Research, Center for Clinical and Translational Science, University of Utah, we are undertaking a project to streamline the study design and statistical analysis workflows and processes. As a first step we met with key stakeholders to understand the current practices by eliciting example statistical projects, and then developed process information models for different types of statistical needs using Lucidchart. We then reviewed these with the Foundation’s leadership and the Standards Committee to come up with ideal workflows and model, and defined key measurement points (such as those around study design, analysis plan, final report, requirements for quality checks, and double coding) for assessing reproducibility. As next steps we are using our finding to embed analytical and infrastructural approaches within the statisticians’ workflows. This will include data and code dissemination platforms such as Box, Bitbucket, and GitHub, documentation platforms such as Confluence, and workflow tracking platforms such as Jira. These tools will simplify and automate the capture of communications as a statistician work through a project. Data-intensive process will use process-workflow management platforms such as Activiti, Pegasus, and Taverna. RESULTS/ANTICIPATED RESULTS: These strategies for sharing and publishing study protocols, data, code, and results across the spectrum, active collaboration with the research team, automation of key steps, along with decision support. DISCUSSION/SIGNIFICANCE OF IMPACT: This analysis of statistical methods and process and computational methods to automate them ensure quality of statistical methods and reproducibility of research.
Effects of horizontal pressure gradients on bed destabilization under waves
- C. Berni, H. Michallet, E. Barthélemy
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- Journal of Fluid Mechanics / Volume 812 / 10 February 2017
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- 05 January 2017, pp. 721-751
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We report on new experiments designed to investigate bed destabilization processes in a two-dimensional wave flume physical model of a beach. The mobile bed consists of non-cohesive granular material of low density. The wave conditions are provided by repeating a cycle of waves made of two bichromatic groups of different period. The horizontal and vertical velocities are acoustically profiled vertically from free-stream elevation down to the still bed level in the surf zone. Additional measurements of the fluid pressure at positions closely aligned horizontally and vertically in and slightly above the sediment bed are undertaken. Mobile bed interfaces, still bed and top interface, are detected via acoustic and optical methods. Both methods are cross-compared and give similar results. Flow turbulence over the bed is analysed, the Reynolds turbulent shear stress is found negligible compared to the orbital flow induced momentum diffusion. The shear stress and the horizontal pressure gradient are computed at near-bed elevation and used in the bed incipient plug flow model of Sleath (Cont. Shelf Res., vol. 19 (13), 1999, pp. 1643–1664). Both the model and the measurements confirm that destabilization occurs when the non-dimensional pressure gradient (or Sleath number) exceeds the threshold value of 0.3 which is simultaneous with strong flow acceleration. The near-bottom fluid shear stress detected during these flow accelerations at steep wave fronts is found experimentally to be negative, which is retrieved with an unsteady plug flow model. This is suggesting that the fluid above the bed resists the sediment layer motion at these particular phases.
Group problem-solving skills training for self-harm: randomised controlled trial
- Carmel McAuliffe, Breda C. McLeavey, Tony Fitzgerald, Paul Corcoran, Bernie Carroll, Louise Ryan, Brian O'Keeffe, Eva Fitzgerald, Portia Hickey, Mary O'Regan, Jillian Mulqueen, Ella Arensman
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- The British Journal of Psychiatry / Volume 204 / Issue 5 / May 2014
- Published online by Cambridge University Press:
- 02 January 2018, pp. 383-390
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- May 2014
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Background
Rates of self-harm are high and have recently increased. This trend and the repetitive nature of self-harm pose a significant challenge to mental health services.
AimsTo determine the efficacy of a structured group problem-solving skills training (PST) programme as an intervention approach for self-harm in addition to treatment as usual (TAU) as offered by mental health services.
MethodA total of 433 participants (aged 18–64 years) were randomly assigned to TAU plus PST or TAU alone. Assessments were carried out at baseline and at 6-week and 6-month follow-up and repeated hospital-treated self-harm was ascertained at 12-month follow-up.
ResultsThe treatment groups did not differ in rates of repeated self-harm at 6-week, 6-month and 12-month follow-up. Both treatment groups showed significant improvements in psychological and social functioning at follow-up. Only one measure (needing and receiving practical help from those closest to them) showed a positive treatment effect at 6-week (P = 0.004) and 6-month (P = 0.01) follow-up. Repetition was not associated with waiting time in the PST group.
ConclusionsThis brief intervention for self-harm is no more effective than treatment as usual. Further work is required to establish whether a modified, more intensive programme delivered sooner after the index episode would be effective.
Eradication of black rats Rattus rattus from Anacapa Island
- Gregg Howald, C. Josh Donlan, Kate R. Faulkner, Steve Ortega, Holly Gellerman, Donald A. Croll, Bernie R. Tershy
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Removing invasive rats from islands is a powerful conservation tool, and practitioners are now targeting larger islands for rat eradication. As they do so, they face the challenge of mitigating for potential non-target impacts on native biodiversity that may be susceptible to rodenticides. We report on the eradication of black rats Rattus rattus from Anacapa Island, California, in 2001–2002, which was the first-ever invasive rodent eradication from an entire island where an endemic rodent was present and the first aerial application of a rodenticide in North America. As a mitigation strategy we staggered the rodenticide application over 2 years and held a representative sample of the Anacapa deer mouse Peromyscus maniculatus anacapae in captivity. We also mitigated for bird species potentially susceptible to brodifacoum poisoning and monitored aspects of the terrestrial and marine environments. The free-ranging native rodent population severely declined following rodenticide applications but reintroduction and translocation efforts were successful, and the population quickly recovered to pre-eradication levels. Non-target impacts also included mortality of raptors, gulls and passerines, including high mortality of rufous-crowned sparrows Aimophila ruficeps obscura despite planned mitigation. All observed non-target impacts are expected to be ephemeral; however, further monitoring should reveal details on the dynamics of those impacts. Brodifacoum was not detected in the marine environment or in significant amounts in terrestrial soil, plants and arthropods. Seabird benefits from the rat eradication were quickly realized.
Influence of body mass index and slimming habits on menstrual pain and cycle irregularity
- P. Montero, C. Bernis, V. Fernandez, S. Castro
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- Journal of Biosocial Science / Volume 28 / Issue 3 / July 1996
- Published online by Cambridge University Press:
- 31 July 2008, pp. 315-323
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Using a cross-sectional sample of 1147 urban adolescents, aged between 14 and 20 years, the variability of some menstrual cycle indicators was related to weight loss. Nearly 40% of the adolescents tried to lose weight and the results showed that attempting to lose weight is significantly associated with increased prevalence of menstrual irregularity and menstrual pain. This finding is independent of body mass index.
Organic amendment effects on tuber yield, plant N uptake and soil mineral N under organic potato production
- Derek H. Lynch, Zhiming Zheng, Bernie J. Zebarth, Ralph C. Martin
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- Journal:
- Renewable Agriculture and Food Systems / Volume 23 / Issue 3 / September 2008
- Published online by Cambridge University Press:
- 22 July 2008, pp. 250-259
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The market for certified organic potatoes in Canada is growing rapidly, but the productivity and dynamics of soil N under commercial organic potato systems remain largely unknown. This study examined, at two sites in Atlantic Canada (Winslow, PEI, and Brookside, NS), the impacts of organic amendments on Shepody potato yield, quality and soil mineral nitrogen dynamics under organic management. Treatments included a commercial hog manure–sawdust compost (CP) and pelletized poultry manure (NW) applied at 300 and 600 kg total N ha−1, plus an un-amended control (CT). Wireworm damage reduced plant stands at Brookside in 2003 and those results are not presented. Relatively high tuber yields (~30 Mg ha−1) and crop N uptake (112 kg N ha−1) were achieved for un-amended soil in those site-years (Winslow 2003 and 2004) when soil moisture was non-limiting. Compost resulted in higher total yields than CT in one of three site-years. Apparent recovery of N from CP was negligible; therefore CP yield benefits were attributed to factors other than N availability. At Winslow, NW300, but not NW600, significantly increased total and marketable yields by an average of 5.8 and 7.0 Mg ha−1. Plant available N averaged 39 and 33% for NW300 and NW600, respectively. Soil (0–30 cm) NO3−-N at harvest was low (<25 kg N ha−1) for CT and CP, but increased substantially both in season and at harvest (61–141 kg N ha−1) when NW was applied. Most leaching losses of NO3−-N occur between seasons and excessive levels of residual soil NO3-N at harvest, as obtained for NW600, must be avoided. Given current premiums for certified organic potatoes, improving yields through application of amendments supplying moderate rates of N or organic matter appears warranted.
Virtual SEM (VSEM) - Evaluation of a Teaching and Training Tool
- MGC Martin, DD M Holburn, DN H M Caldwell, MB C Bernie
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- Journal:
- Microscopy and Microanalysis / Volume 13 / Issue S02 / August 2007
- Published online by Cambridge University Press:
- 05 August 2007, pp. 1724-1725
- Print publication:
- August 2007
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Extended abstract of a paper presented at Microscopy and Microanalysis 2007 in Ft. Lauderdale, Florida, USA, August 5 – August 9, 2007
DAILY COST PREDICTION MODEL IN NEONATAL INTENSIVE CARE
- John A. F. Zupancic, Douglas K. Richardson, Bernie J. O'Brien, Barbara Schmidt, Milton C. Weinstein
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- Journal:
- International Journal of Technology Assessment in Health Care / Volume 19 / Issue 2 / April 2003
- Published online by Cambridge University Press:
- 18 June 2003, pp. 330-338
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Objectives: One barrier to economic evaluation alongside neonatal randomized controlled trials is the expense of collecting detailed patient resource information. To reduce this data collection burden, we identified the key resource items that predict daily ancillary costs for extremely low birth weight infants.
Methods: Participants were 385 infants enrolled in the Trial of Indomethacin Prophylaxis for Preterms in nine tertiary level neonatal intensive care units in Canada. Information on eighty-nine nonpersonnel resource items was abstracted from the hospital chart from admission to tertiary hospital discharge. Unit costs were derived from a provincially standardized cost accounting system. Using stepwise linear regression, models correlating total daily ancillary costs with key resource items were constructed for each of five periods of admission. Models were derived in a randomly split half of the total sample of patient days and validated against the remainder.
Results: The 385 infants contributed resource information from 23,354 admission days. The regression model for weeks one to twelve included the covariates surfactant, chest radiograph, red blood cell transfusion, cranial ultrasound, abdominal radiograph, parenteral amino acid infusion, surgery, platelet transfusion, and echocardiogram and explained 91% of the variability in daily nonpersonnel costs (P<.0001). Models for other admission periods similarly included between four and eight covariates, were highly significant (P<.0001) and explained between 76% and 94% of daily ancillary cost variability. The regression equations showed excellent predictive power when applied to the second half of the patient data set.
Conclusions: Daily nonpersonnel costs for extremely low birth weight infants are driven by a limited number of key resource variables. The ability to predict total ancillary costs with minimal data collection will facilitate inclusion of economic evaluations in neonatal trials.
The effect of feral cats on the population viability of black-vented shearwaters (Puffinus opisthomelas) on Natividad Island, Mexico
- Bradford S. Keitt, Chris Wilcox, Bernie R. Tershy, Donald A. Croll, C. Josh Donlan
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- Journal:
- Animal Conservation forum / Volume 5 / Issue 3 / August 2002
- Published online by Cambridge University Press:
- 25 September 2002, pp. 217-223
- Print publication:
- August 2002
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Insular breeding seabirds are likely to be particularly vulnerable to introduced mammalian predators because they often lack behavioural, morphological and life-history defenses against predation. We studied the life-history of the black-vented shearwater (Puffinus opisthomelas) on Natividad Island, Baja California Sur, Mexico, to examine its vulnerability to introduced feral cats. Using an allometric equation, we estimated that feral cats consumed 328 g of food day-1 to satisfy their nutritional requirements. We used stable isotope analysis of cat scat to estimate that 90% of the cats' diet was composed of shearwaters. Using data from our focal species and from the closely related manx shearwater (Puffinus puffinus), we created a demographic model to evaluate the effects of cat population size on the annual growth rate (λ) of the shearwater. The annual growth rate for black-vented shearwaters was estimated to be 1.006 in the absence of cat predation. With predation, we estimated that annual growth rate declined approximately 5% for every 20 cats in a population of 150,000 birds. Persistence times of bird colonies decreased both with an increase in the size of the feral cat population and with a decrease in the size of the initial bird population.
SECULAR TREND AND INTRAPOPULATIONAL VARIATION IN AGE AT MENOPAUSE IN SPANISH WOMEN
- C. VAREA, C. BERNIS, P. MONTERO, S. ARIAS, A. BARROSO, B. GONZÁLEZ
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- Journal:
- Journal of Biosocial Science / Volume 32 / Issue 3 / July 2000
- Published online by Cambridge University Press:
- 01 July 2000, pp. 383-393
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Menopause is associated with the general ageing process and marks the end of follicular depletion, a process that begins in the intrauterine stage and lasts throughout the lifetime of women until their reproductive senescence. Controversy persists about whether the age at menopause is sensitive to the ecological determinants prevailing during the lifecycle or whether it has a predominantly genetic component that would allow groups of women to be characterized with respect to particular menstrual characteristics manifested throughout their fertile life. By contrast, there is a definite secular trend in age at menarche in populations that have registered improvements in their environment: sexual maturation is closely associated with the general processes of growth and development. These aspects were analysed in a sample of Spanish women, mothers and daughters, born between 1883 and 1941. The results show (a) indications – although not conclusive – of a secular trend in the age at menopause, (b) a possible association between the age at menopause of mothers and their daughters, and (c) an association at the individual level between age at menarche, particular characteristics of ovarian function (fetal loss) and age at menopause. The reproductive ageing process therefore seems to result from the expression of the influence of ecological conditions in which the lifecycle of the women develops and of a degree of heritability that affects not only the age at menopause but also a range of characteristics of ovarian function.
Undifferentiated dementia, Alzheimer's disease and vascular dementia: Age- and gender-related incidence in Liverpool: The MRC–ALPHA Study
- J. R. M. Copeland, Cherie McCracken, M. E. Dewey, K. C. M. Wilson, Mark Doran, Chris Gilmore, Anne Scott, Bernie Larkin
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- Journal:
- The British Journal of Psychiatry / Volume 175 / Issue 5 / November 1999
- Published online by Cambridge University Press:
- 03 January 2018, pp. 433-438
- Print publication:
- November 1999
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Background
Does incidence of dementia follow the age pattern of prevalence? Is gender a risk factor? Do patterns of incidence differ between dementias?
AimsTo assess age-specific incidence rates of undifferentiated dementias, Alzheimer's disease and vascular dementia.
Method5222 individuals aged $65 years, were interviewed using the Geriatric Mental State/History and Aetiology Schedule. The AGECAT package was used to identify cases at three interviewing waves at two-year intervals. Diagnoses were made using ICD −10 Research Criteria and validated against neurological and psychological examination, with imaging and neuropathology on unselected subsamples.
ResultsIncidence rates of the dementias increase with age. Age patterns are similar between Alzheimer's disease and vascular dementia. Gender appears influential in Alzheimer's disease. In England and Wales, 39 437 new cases of Alzheimer's disease (4.9/1000 person-years at risk); 20 513 of vascular dementia (2.6/1000 person-years) and 155 169 of undifferentiated dementia (19/1000 person-years) can be expected each year.
ConclusionsIncidence rates for Alzheimer's disease and vascular dementia appear to behave differently with an increased risk of Alzheimer's disease for women compared to vascular dementia.
Prise en compte des paramètres contextuels en radioécologie post-accidentelle
- Ph. Renaud, H. Maubert, J.-C. Bernié
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- Journal:
- Radioprotection / Volume 32 / Issue 2 / April 1997
- Published online by Cambridge University Press:
- 17 June 2005, pp. 181-195
- Print publication:
- April 1997
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Les conséquences d'un rejet radioactif accidentel sur les productions agricoles et d'élevage dépendent dans une large mesure du contexte dans lequel se sont effectués les dépôts de radioactivité : conditions et occurrence du dépôt dans les calendriers agricoles et d'affouragement des animaux. Ces paramètres contextuels sont une source de variation des résultats des modèles souvent plus grande que les incertitudes liées aux facteurs de transfert eux-mêmes. Ainsi, la contamination du lait de vache évolue sur plusieurs décades dans les mois qui suivent le dépôt en fonction des pratiques zootechniques d'alimentation des animaux. De même, un plant de blé qui recevrait un dépôt d'éléments radioactifs en phase de maturation aura, à la récolte, des grains 103 à 104 plus contaminés que si le dépôt était intervenu avant la montaison. Pour élaborer un outil d'aide à la décision comme le logiciel ASTRAL, il a été nécessaire de réaliser une modélisation de la prise en compte de ces paramètres contextuels. De plus, afin d'assister l'expert dans ses évaluations, des bases de données par défaut relatives aux pratiques agricoles et d'élevage sont proposées pour la France métropolitaine. Toutefois dans le cas d'un accident réel, pour affiner les résultats, il serait important de rapidement mettre à jour ces paramètres contextuels, qui peuvent varier d'une année à l'autre.