cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A comprehensive costing analysis of intensive case management for individuals with severe mental illness and a history of homelessness, including cost-effectiveness as compared to standard care
Creators: name: Birnie, Sarah
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2009
Subjects: subject: Health Sciences, Mental Health.
subject: Psychology, Clinical.
subject: Health Sciences, Health Care Management.

description: The current study used the comprehensive costing methodology of Knapp and Beecham (1990) to examine the comprehensive costs of community support services over the last six months (18--24 months) of a two-year study. The sample consisted of 77 clients with severe and persistent mental illness and a history of homelessness receiving either intensive case management (ICM) or standard care. Costs from the overall societal perspective were calculated by summing the direct and 'hidden' (e.g., travel time) costs associated with: (1) Agency costs (case management services), (2) governmental costs (e.g., non-agency health care costs, non-health care costs), and (3) family/friend costs. Subtracted from this initial total to reach a final societal cost were employment and/or volunteer 'benefits'. Of interest in the study was: (1) Examining the relationship between clients needs at 18 months of a two year trial, global societal costs per client for the six-month period from 18 to 24 months, and 24-month outcomes, and (2) cost-effectiveness of intensive case management over standard care from three costing perspectives (e.g., agency, government, society). Results yielded an overall average comprehensive cost of treatment (both ICM and standard care combined) per client of $57.08/day which is comparable to previous research investigating the costs of community support services. Needs did not predict six month total societal costs; however, receiving ICM and reporting more severe symptomatology predicted higher six-month agency costs. Higher total costs of services and supports predicted poorer housing stability at 24 months for our participants. Higher expenditures related to non-health care costs predicted poorer community ability at 24 months. In general, it seems that higher costs are related to poorer client functioning. Cost-effectiveness analyses revealed that ICM is more cost-effective than standard care from the perspective of the government (i.e., health-related expenses) and society overall, despite agency costs being significantly greater in ICM. Nonparametric bootstrapping methods using net monetary benefit revealed a 0.77 to 0.80 chance of ICM being a cost-effective alternative to standard care. It is clear from this study that increased costs are associated with clients who are doing the poorest in terms of symptoms, housing stability, and community ability. Despite the finding that more intensive treatment does not guarantee better clinical outcomes within our six month window, ICM is shown to be a more cost-effective treatment in the community when compared with standard care. Implications of this research are discussed.
The relationship between subjective and objective measures of health: A series of systematic reviews and analyses of data from national surveys
Creators: name: Connor Gorber, Sarah
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2009
Subjects: subject: Health Sciences, Public Health.

description: The goal of this research was to consolidate and expand on current knowledge about the use of objective and subjective measures to assess the health of Canadians. Specifically, this dissertation examined the relationship between self-report and direct measures of health to determine the extent of discrepancies between the two methods. This was accomplished through a series of five research papers, including three systematic reviews that examined the relationship between self-reported and directly measured estimates of height, weight and Body Mass Index (BMI), hypertension and smoking. An in-depth examination of the discrepancies in reported obesity followed. It included two additional papers, one examining the feasibility of establishing correction factors to increase the accuracy of reported estimates of obesity and a second examining the trends in the reporting bias over time and between two different population groups (Canada and the U.S.). Results clearly documented a bias in self-reported estimates of height, weight, BMI, hypertension and smoking; reported estimates of height were consistently overestimated while reported weight, BMI, hypertension and smoking were consistently underestimated in both men and women. Statistical adjustment of reported values generated estimates of height, weight and obesity that were more accurate than those generated by self-report alone. Historical analysis with Canadian and American datasets indicated that the bias in reported obesity is increasing, implying that the generalizability of the correction equations may be limited and that in Canada, monitoring trends in obesity based solely on self-reported height and weight may produce inaccurate estimates because of the diverging discrepancy between self-reported and measured data. This work has made an important contribution to understanding the bias in current surveillance practices that are grounded in the collection of self-reported data and presents a series of recommendations to improve population health surveillance in Canada.
OOVs in the Spotlight: How to Inflect them?
Creators: name: Sourada, Tomáš
name: Straková, Jana
name: Rosa, Rudolf
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: We focus on morphological inflection in out-of-vocabulary (OOV) conditions, an under-researched subtask in which state-of-the-art systems usually are less effective. We developed three systems: a retrograde model and two sequence-to-sequence (seq2seq) models based on LSTM and Transformer. For testing in OOV conditions, we automatically extracted a large dataset of nouns in the morphologically rich Czech language, with lemma-disjoint data splits, and we further manually annotated a real-world OOV dataset of neologisms. In the standard OOV conditions, Transformer achieves the best results, with increasing performance in ensemble with LSTM, the retrograde model and SIGMORPHON baselines. On the real-world OOV dataset of neologisms, the retrograde model outperforms all neural models. Finally, our seq2seq models achieve state-of-the-art results in 9 out of 16 languages from SIGMORPHON 2022 shared task data in the OOV evaluation (feature overlap) in the large data condition. We release the Czech OOV Inflection Dataset for rigorous evaluation in OOV conditions. Further, we release the inflection system with the seq2seq models as a ready-to-use Python library.
description: Published in the proceedings of LREC-COLING 2024. 12 pages, 3 figures
The regulation of phospholipid signaling and actin cytoskeletal remodeling by the eukaryotic translation elongation factor eEF1A2
Creators: name: Jeganathan, Sujeeve
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2009
Subjects: subject: Biology, Molecular.

description: The regulation of the actin cytoskeleton is vital in several cellular and physiological processes from cell movement and phagocytosis to embryonic development and immune response. Thus, it is imperative to not only understand the mechanisms that regulate actin cytoskeletal dynamics but to also identify novel signaling networks and proteins that impinge upon these pathways. Here, we identify the eukaryotic elongation factor, eEF1A2, as a mediator of actin cytoskeleton remodeling through the phosphatidylinositol signaling pathway. EEF1A2, the gene encoding eukaryotic elongation factor 1 alpha 2 (eEF1A2), is one of two functional transcripts of EEF1A . During protein translation, eEF1A2 binds to amino-acylated tRNAs and recruits them to the ribosome. Aside from protein synthesis, eEF1A proteins from several genera and species associate with the actin cytoskeleton by binding and bundling actin. This suggests that eEF1A proteins may regulate actin cytoskeleton dynamics in addition to, or independent of, protein translation. Furthermore, recent work has identified EEF1A2 as an oncogene of the ovary, lung and breast, however the mechanism by which eEF1A2 contributes to oncogenesis has yet to be elucidated. The work presented in this thesis provides a mechanism by which eEF1A2 promotes oncogenesis. We first demonstrate that eEF1A2 can regulate phospholipid signaling by interacting with, and activating, phosphatidylinositol-4 kinase III beta (PI4KIIIbeta), a lipid kinase that is important in the phosphatidylinositol signaling pathway. Through a series of biochemical, molecular, and imaging assays, we describe and detail this interaction and provide evidence that eEF1A2-mediated PI4KIIIbeta activation results in an increased pool of phosphatidylinositol-4 phosphate (PI4P), the product of PI4KIIIbeta lipid kinase activity. We then go on show that the interaction between eEF1A2 and PI4KIIIbeta leads to the production of finger-like, actin-based membrane protrusions termed filopodia. Specifically, eEF1A2-mediated filopodia formation occurs in a phosphatidylinositol-4,5 bisphosphate (PI(4,5)P2)- and Cdc42-dependent manner. Furthermore, we show that PI4KIIIbeta activation is necessary for eEF1A2-mediated filopodia development. Lastly, we describe some of the ways eEF1A2 regulates breast oncogenesis. We show that ectopic eEF1A2 expression in breast cancer cells increases in vitro growth rates, inhibits anoikis, and activates the Akt serine-threonine kinase. Importantly, eEFIA2 is shown to be a valid therapeutic target as ablation of eEF1A2 decreases tumour formation in mice. Taken together, the work presented in this thesis provides new insights into ways eEF1A2 contributes to oncogenesis and provides a mechanism as to how eEF1A2 regulates the actin cytoskeleton.
Characterization and microbial reduction of bacteriogenic iron oxides
Creators: name: Langley, Roger Sean
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2009
Subjects: subject: Geochemistry.

description: The main objectives of the present study were to first determine the chemical and mineralogical composition of bacteriogenic iron oxides (BIOS) collected from various locations (i.e., wetlands near Deep River, Ontario, hydrothermal sea vents along the Kermadec Arc between New-Zealand and Fiji, and from the Aspo tunnel in Sweden), to assess their sorptive capacity for Sr and to measure their rates of reduction in the presence of a well known iron-reducing bacterium. X-ray diffraction (XRD) and selected area electron diffraction indicated that both marine and freshwater BIOS were composed of the iron mineral, 2-line ferrihydrite, in combination with cellular structures of known iron-oxidizing microbes such as Gallionella spp., Leptothrix spp., and Mariprofundus spp. Mossbauer spectroscopy of marine BIOS confirmed 2-line ferrihydrite as the dominant mineral phase, but a small fraction of more crystalline oxides may also have been present (as detected by XRD). Using electron microscopy, the mineral phases were typically observed as 100-200 nm thick crusts of poorly structured material, attached to the surfaces of the associated microbial debris. Some well-defined crystal habits were observed in one marine sample. Sorption experiments showed that BIOS were effective adsorbents of dissolved strontium. Sorption isotherms indicated that Sr was bound to the BIOS via reversible outer-sphere complexation. Extended X-ray absorption fine structure (EXAFS) confirmed binding of hydrated Sr2+ but failed to elucidate whether sorption occurred to sites specific to the iron or organic component of the BIOS. All BIOS samples were more susceptible to microbial Fe(III) reduction than was synthetic 2-line ferrihydrite. This suggests that BIOS are not stabilized by precipitation along microbial surfaces, and that the use of synthetic analogs to model BIOS reactivity is insufficient. Reduction of BIOS resulted in the complete dissolution of the iron mineral phase, and a nearly complete solubilization of the sorbed Sr. This suggests that sorption occurs primarily to sites within the iron oxide component. In a natural BIOS deposit, levels of dissolved Sr in BIOS porewaters were elevated at depths where Fe(II) was also elevated, and levels of dissolved Sr were 2 to 3 times higher in aquifer waters that did not contain BIOS. These data suggest that BIOS may represent a natural means of Sr attenuation, provided oxidizing conditions are maintained.
Determining the response of tumour cells to UV light and cisplatin
Creators: name: Stubbert, Lawton James
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2009
Subjects: subject: Biology, Molecular.

description: Nucleotide excision repair (NER) recognizes and repairs sunlight-induced DNA damage as well as cisplatin induced intrastrand DNA cross-links. When treated with cisplatin, NER capacity of a tumour has been shown to be predictive of outcome in some human cancers. Similarly, in vitro, the response of tumours cells to cisplatin is dependent on NER, where polymorphisms in some NER components alter the outcome. NER consists of two sub-pathways, transcription-coupled (TC-) NER and global-genomic (GG-) NER, differing only in their recognition of DNA lesions. While GG-NER deficiency, resulting in xeroderma pigmentosum (XP), increases rates of cancer in man, TC-NER deficiency, resulting in Cockayne syndrome (CS) does not. Both these syndromes have multiple genetic causes whose study has allowed a more complete understanding of NER. In primary human fibroblasts, keratinocytes and mouse embryonic fibroblasts TC-NER and not GG-NER is important in the avoidance of apoptosis after UV and cisplatin. However, mouse embryonic stem cells do not require TC-NER to recover from this type of DNA damage and so it may be difficult to predict the role of this repair pathway in all cellular contexts. We assessed the importance of TC-NER in the cisplatin response of tumour cells by manipulating TC-NER and measuring DNA repair and sensitivity to DNA damaging agents UV-C and cisplatin. Targeting TC-NER by transient transfection of siRNA against Cockayne syndrome B (CSB), xeroderma pigmentosum A (XPA) and XPA-binding protein 2 (XAB2) sensitized tumour cells to cisplatin. This sensitization was largely independent of p53 tumour suppressor and mismatch repair status of these cells. As a preliminary in vivo test, we generated a colon cancer cell line in which CSB expression was stably reduced and used this cell line in a tumour xenograft model. Treating the animais with a singleweek regimen of cisplatin resulted in a decrease in tumour volume initially and delayed tumour re-growth compared to control tumours. Taken together, these results indicate that TC-NER is a potential target in combined cisplatin tumour therapy. This work also suggests that TC-NER capacity may be clinically predictive.
title: F2C2
title: a fast tool for the computation of flux coupling in genome-scale metabolic networks
titleType: Subtitle
Creators: name: Larhlimi, Abdelhalim
name: David, Laszlo
name: Selbig, Joachim
name: Bockmayr, Alexander
Publisher: name: Universität Potsdam
Year: 2020

description: Background: Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions. Results: We present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. Conclusions: We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/.
description: Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe, 921
Assessment of systematic effects of methodological characteristics on genetic associations
Creators: name: Aljasir, Badr Abdulrahman
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2009
Subjects: subject: Health Sciences, Medicine and Surgery.

description: Background. The effective use of knowledge related to gene-disease associations relies on the optimal conduct and reporting of research studies. Transparent reporting enables readers to identify the strengths and weaknesses of research studies and subsequently to determine the quality of evidence that they offer. Objective. To investigate the relation between methodological characteristics and the direction and magnitude of effects observed in case-control studies of gene-disease associations. Methods. Articles were randomly selected from a database of published studies on genetic associations and other epidemiologic research pertaining to the human genome (the HuGE Literature Finder). The analysis evaluated 511 articles indexed in HuGENet in 2007. Gene-gene interaction studies and gene-environment interaction studies were excluded. Univariate and multivariate meta-regression analyses using a random effects model were used to assess the relationship between methodological characteristics and the direction and magnitude of genetic associations. Results. The studies included in the analysis had been conducted in a total of 52 countries and were published in 220 journals (median impact factor 5.1). The multivariate meta-regression model of methodological characteristics was able to account for 17.2% of the between-study variance in the magnitude of gene-disease associations. Of the factors included in the multivariate regression model, the following tended to be associated with a smaller magnitude of effect: replication of a previously conducted study; nested case-control study design; individual matching of study participants; and reporting of sample size or of statistical power calculation. Moreover, the magnitude of effect tended to decrease as the number of controls increased. By contrast, studies that did not report the process of selecting control participants or that reported that the genotype distribution departed from Hardy-Weinberg equilibrium tended to be associated with larger magnitudes of effect. Studies conducted in North America, Europe, and China had similar magnitudes of effect. Conclusion. Within the constraints of limitations in reporting, a number of methodological features of gene-disease association studies are associated systematically with the magnitude of effect observed. This provides evidence to direct efforts to improve the reporting of research on genetic associations.
Inability to Access Addiction Treatment Among Street-Involved Youth in a Canadian Setting
Creators: name: Phillips, Mark
name: DeBeck, Kora
name: Desjarlais, Timothy
name: Morrison, Tracy
name: Feng, Cindy X.
name: Kerr, Thomas
name: Wood, Evan
Publisher: name: The University of British Columbia
Year: 2017

description: From Sept 2005 to May 2012, 1015 street-involved youth were enrolled into the At-Risk Youth Study (ARYS), a prospective cohort of youth aged 14- 26 who use illicit drugs in Vancouver Canada. Data was collected through semiannual interviewer administered questionnaires. Generalized estimating equation (GEE) logistic regression was used to identify factors independently associated with being unable to access addiction treatment. The enclosed manuscript notes the implications and limitations of this study, as well as possible directions for future research. This study was funded by the US National Institutes of Health (NIH) and Canadian Institutes of Health (CIHR).
title: Comparison of hydraulic and tracer tomography for discrete fracture network inversion
Creators: name: Ringel, Lisa Maria
name: Somogyvári, Márk
name: Jalali, Mohammadreza
name: Bayer, Peter
Publisher: name: Universität Potsdam
Year: 2020

description: Fractures serve as highly conductive preferential flow paths for fluids in rocks, which are difficult to exactly reconstruct in numerical models. Especially, in low-conductive rocks, fractures are often the only pathways for advection of solutes and heat. The presented study compares the results from hydraulic and tracer tomography applied to invert a theoretical discrete fracture network (DFN) that is based on data from synthetic cross-well testing. For hydraulic tomography, pressure pulses in various injection intervals are induced and the pressure responses in the monitoring intervals of a nearby observation well are recorded. For tracer tomography, a conservative tracer is injected in different well levels and the depth-dependent breakthrough of the tracer is monitored. A recently introduced transdimensional Bayesian inversion procedure is applied for both tomographical methods, which adjusts the fracture positions, orientations, and numbers based on given geometrical fracture statistics. The used Metropolis-Hastings-Green algorithm is refined by the simultaneous estimation of the measurement error’s variance, that is, the measurement noise. Based on the presented application to invert the two-dimensional cross-section between source and the receiver well, the hydraulic tomography reveals itself to be more suitable for reconstructing the original DFN. This is based on a probabilistic representation of the inverted results by means of fracture probabilities.
description: Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe, 922
BioExcel Webinar #35 - GROMACS 2019 – overview of the new features and capabilities
Creators: name: Abraham, Mark
Publisher: name: Zenodo
Year: 2019
Subjects: webinar

description: Each new major release of GROMACS brings with it the latest in feature development, hardware support, performance enhancements, and usability improvements. In this webinar we will review and describe the major new changes, and guide you to make best use of the new opportunities.
Bewaren voor iedereen: de opbouw van de webcollectie XS4ALL-homepages
Creators: name: Teszelszky, Kees
Publisher: name: Zenodo
Year: 2020
Subjects: web archiving
XS4ALL
internet history

description: Het is vrijwel niet meer voor te stellen in deze online coronatijden, maar er is een periode geweest in de geschiedenis dat gewone mensen niet zomaar gebruik konden maken van het internet. Daar kwam verandering in toen in mei 1993 de nieuwe provider XS4ALL als één van de eerste van Nederland een internetverbinding beschikbaar stelde voor 500 particulieren.
description: Blogpost op KB-site. https://www.kb.nl/blogs/duurzame-toegang/bewaren-voor-iedereen-de-opbouw-van-de-webcollectie-xs4all-homepages
Development of Source and Treated Water Quality Indicators for drinking water in Canada from conceptual design to methodological development
Creators: name: D'Costa, Laura
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2008
Subjects: subject: Geology.
subject: Engineering, Sanitary and Municipal.
subject: Engineering, Environmental.

description: In September 2005, Health Canada took on the development of a Source Water Quality Indicator for Canada. The main objective was to develop a methodology by which source water quality could be linked to public health, the environment, society, and economy; and measured, tracked, and reported in the form of an indicator for decision making. A Treated Water Quality Indicator was also introduced to bridge the gap between source water quality and human health. With Federal/Provincial/Territorial and academic support, research into the approach and development of a conceptual design, parameter selection rationale, and two tools for the indicator calculations, along with recommendations for future work were completed. The tools developed included a modified Canadian Council of Ministers of the Environment water quality index calculator, and a Treatability Ranking tool (that determined the complexity of treatment required to achieve safe drinking water). The results of this project are described herein.
Prediction of stock market prices using neural network techniques
Creators: name: Wang, Zhuowen
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2004
Subjects: subject: Economics, Finance.
subject: Computer Science.

description: Issuing stocks is the key method to raise money for corporations. Today, stocks have become the most important financial instruments. Currently, there are several methods by which one can predict financial markets, but none of them is quite accurate. After introducing same basic concepts and the history of stocks, this work continues to introduce some typical fundamental and technical analysis methods already developed by economists, and then presents a relatively new system to forecast the stack market using revised Back Propagation (BP) algorithms. The system exploits BP neural networks to help find the correlation between stock price and the affecting factors hidden behind the financial market. The topology is a typical three-layer neural network with one input layer, one hidden layer and one output layer. The supervised algorithms are the Feed-forward, Cascade-forward, and Elman BP. They are trained respectively by seven BP techniques: the Gradient Descent BP, the Gradient Descent With Momentum BP, the Gradient Descent With Adaptive Learning Rate BP, the Gradient Descent With Momentum & Adaptive Learning Rate BP, the Levenberg-Marquardt BP, the Broyden-Fletcher-Goldfarb-Shanno (BFGS) Quasi-Newton, and the Resilient Propagation (RPROP) BP. Data used to train and test the neural networks involve the Shanghai Stock Exchange Composite Index, and the Shenzhen Stock Exchange Component Index.
Development of a Survey to Assess the Acceptability of an Innovative Contraception Practice among Rural Pharmacists
Creators: name: Wong, Michael
name: Soon, Judith A.
name: Zed, Peter J.
name: Norman, Wendy V.
Publisher: name: Multidisciplinary Digital Publishing Institute
Year: 2019

description: Improved access to effective contraceptive methods is needed in Canada, particularly in rural areas, where unintended pregnancy rates are high and specific sexual health services may be further away. A rural pharmacist may be the most accessible health care professional. Pharmacy practice increasingly incorporates cognitive services. In Canada many provinces allow pharmacists to independently prescribe for some indications, but not for hormonal contraception. To assess the acceptability for the implementation of this innovative practice in Canada, we developed and piloted a survey instrument. We chose questions to address the components for adoption and change described in Rogers’ “diffusion of innovations” theory. The proposed instrument was iteratively reviewed by 12 experts, then focus group tested among eight pharmacists or students to improve the instrument for face validity, readability, consistency and relevancy to community pharmacists in the Canadian context. We then pilot tested the survey among urban and rural pharmacies. 4% of urban and 35% of rural pharmacies returned pilot surveys. Internal consistency on repeated re-phrased questions was high (Cronbach’s Alpha = 0.901). We present our process for the development of a survey instrument to assess the acceptability and feasibility among Canadian community pharmacists for the innovative practice of the independent prescribing of hormonal contraception.
Application modeling description language for reconfigurable co-processor computing
Creators: name: Fu, Peng
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2005
Subjects: subject: Computer Science.

description: Growing demands on functionality in today's electronic products are leading to an increasing shift towards developing in-system programmable hardware, to increase design flexibility. As a result, the development of embedded applications is becoming more and more important. As part of the "Embedded Research Architectures for Co-Design Environments" (ERACE) project, we developed the Application Description Language (ADL) which is a new kind of powerful language that enables embedded system users to model applications that can utilize the advantages provided by embedded systems, and its translator which translates ADL provided by the user into application source code. Note that in the traditional model, this is the source code that would be compiled and executed on a host processor. We then present it to the Just-In-Time compiler, which prepares the source code for the reconfiguration flow and application flow of the system. The ADL project that included the Application Description Language, Translator, and a Destination Language are named "PACO v0.1". The Destination Language was chosen to be ANSI C language, although it can be any other high level programming language. The PACO v0.1 system was developed using LEX & YACC. Any application that looks for patterns in its input, or has an input or command language is suitable for development using LEX & YACC. When the user inputs instructions based on the PACO ADL grammar (syntax), the PACO translator will translate it into C source code, which will be sent to a profiler for further processing. In PACO v0.1, we provide some features such as scientific calculations, logic algebra, matrix computations, and programming logic-control flow performance.
Hapto-visual representation of three dimensional incompressible flows
Creators: name: Mora, Javier
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2008
Subjects: subject: Computer Science.

description: Imagine a videogame in which you impersonate a wizard who needs to create a potion by stirring substances in a cauldron. Through a desktop haptic probe, you are able to stir and feel how the fluid changes its viscosity, velocity and other properties. So far solid or deformable objects have been experimented for haptic-tactile feedback. In this thesis we innovate by devising techniques that enable the haptical rendering of shape-less objects, such as fluids. We achieved the real-time 3D fluid simulation of multiple substances based on the Navier-Stokes equation and coupled it with a discreet mass-spring particle system representing its deformable surface. We overcame the challenges that arise during the integration of both haptics and graphics workspaces, the free-view visualization of 3D fluid volume, and the rendering of haptic forces. Our system is flexible to accommodate different kinds of fluids, such as liquid and smoke, to be co-simulated.
Temporal Changes in the Microbial Community of a PAH-Contaminated Soil during Bench-Top Bioremediation
Creators: name: Rose, Caroline Gayle
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2010
Subjects: subject: Biology, Microbiology.

description: Contamination of soils with PAHs, substances that can pose serious environmental and human health risks, is a serious problem. Removal of risk requires effective and sustainable methods to decrease or eliminate toxicological hazard. Bioremediation is a sustainable option that can be accomplished by a variety of means. However, due to the limitations of classical culturing methods, there is a paucity of information regarding the composition of soil microbial communities, and moreover, the identity of organisms involved in contaminant catabolism. Newer, molecular techniques directly examine metagenomic DNA or RNA, and provide opportunities to investigate the genetic constitution of soil samples without the need for culturing. 16S rRNA has proven to be a valuable tool in the identification of soil microbes due to its highly conserved nature throughout the bacterial kingdom, in addition to inclusion of variable regions that are unique to a particular organism, or closely related group of organisms. This study used analysis of 16S rRNA gene sequences to examine the temporal changes in the soil microbial community in a PAH-contaminated soil during bioremediation. These results were compared with previously observed temporal changes in the chemical composition of the same soil during bioremediation. Interplay between the temporal changes of soil microbial community and the temporal changes of the PAH concentration was observed. The PAH concentration decreased an average of 77% across all treatments and reactors. Soil micro-organisms whose growth during treatment corresponded with a decline in PAH concentration included several known PAH-degraders such as Achromobacter, Acidovorax, Pseudomonas, Rhodanobacter and Stenotrophomonas. The metagenomic approach employed in this study can be used to evaluate innovative bioremediation methods, and moreover, identify members of the microbial community that are critical for the catabolism of PAHs.
Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens
Creators: name: Nielsen, Torsten
name: Wallden, Brett
name: Schaper, Carl
name: Ferree, Sean
name: Liu, Shuzhen
name: Gao, Dongxia
name: Barry, Garrett
name: Dowidar, Naeem
name: Maysuria, Malini
name: Storhoff, James
Publisher: name: BioMed Central
Year: 2016

description: Background: NanoString’s Prosigna™ Breast Cancer Prognostic Gene Signature Assay is based on the PAM50 gene expression signature. The test outputs a risk of recurrence (ROR) score, risk category, and intrinsic subtype (Luminal A/B, HER2-enriched, Basal-like). The studies described here were designed to validate the analytical performance of the test on the nCounter Analysis System across multiple laboratories. Methods: Analytical precision was measured by testing five breast tumor RNA samples across 3 sites. Reproducibility was measured by testing replicate tissue sections from 43 FFPE breast tumor blocks across 3 sites following independent pathology review at each site. The RNA input range was validated by comparing assay results at the extremes of the specified range to the nominal RNA input level. Interference was evaluated by including non-tumor tissue into the test. Results: The measured standard deviation (SD) was less than 1 ROR unit within the analytical precision study and the measured total SD was 2.9 ROR units within the reproducibility study. The ROR scores for RNA inputs at the extremes of the range were the same as those at the nominal input level. Assay results were stable in the presence of moderate amounts of surrounding non-tumor tissue (<70% by area). Conclusions: The analytical performance of NanoString’s Prosigna assay has been validated using FFPE breast tumor specimens across multiple clinical testing laboratories.
Core religious experience and the process of self actualization within the context of a religious congregation.
Creators: name: Dickson, Elinor J.
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 1977
Subjects: subject: Religion, General.

description: This study was designed to examine intense religious experience within the constructs of self-actualization and core religious experience proposed by Maslow. Three groups of 26 religious women each were studied over a 28 day period in settings allowing for graded degrees of solitude, i.e. work, vacation and retreat. The results show that a high degree of solitude (retreat condition) is necessary but not sufficient for the occurance of core religious experiences. That is, those who had core religious experiences were also significantly more time-competent and had a constructive view of the Nature of Man as measured by the POI scale. A covariate analysis of the post-test scores showed no significant differences between those who had core religious experiences and those who did not. However, an interesting trend was revealed across 10 of the 12 POI scales which showed that those on retreat who had core religious experiences had increased self-actualization scores while those who did not have core religious experiences actually decreased in level of self-actualization.
Measurement of gas-liquid diffusion coefficients by steady-state capillary cell method.
Creators: name: Malik, Vinod Kumar.
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 1968
Subjects: subject: Engineering, Chemical.

description: A capillary cell apparatus was developed for the measurement of gas-liquid diffusivities. The diffusion coefficients of the systems carbon dioxide-water, methane-carbon tetrachloride, carbondioxide-ethanol, ethane-normal hexane, ethane-normal heptane and ethane-hexane, heptane mixtures were determined using this apparatus. Solubilities of ethane in n-hexane, ethane in n-heptane and ethane in mixtures of n-hexane and n-heptane were also determined.
Structure of a low-momentum elevated jet in a cross-flow
Creators: name: Cameron, Andrew William
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2008
Subjects: subject: Engineering, Mechanical.

description: An elevated jet in a cross-flow is a free jet issuing orthogonally into a dominant cross-wind from a pipe extending above a ground-induced boundary layer. The present thesis is concerned with jets having low momentum-flux relative to the cross-flow. It presents flow visualization and velocity measurements conducted in a variable-speed, closed-circuit water channel. Four major types of coherent structures were identified: von Karman vortices, a pipe-end vortex, shear-layer vortices, and tendrils. The von Karman vortices are similar to those shed by a finite cylinder with a free end. The pipe-end vortex is a stationary vortex forming immediately downstream of the pipe-end. The shear-layer vortices are formed by the Kelvin-Helmholtz instability in the mixing layer between the cross-flow and the jet. Finally, the tendrils are evolutions of sections of the shear-layer vortices, formed under certain conditions as the latter are stretched by the pipe-end vortex and move downstream. The size of the pipe-end vortex is insensitive to the momentum-flux ratio as long as the latter is less than a critical value. For higher momentum-flux ratios, the pipe-end vortex grows in size and shifts beyond the free-end of the pipe. The Strouhal numbers of the shear-layer vortices and the tendrils increase drastically as the momentum-flux ratio decreases. The shear-layer vortices, marking the jet fluid, move away from the pipe exit upon their generation, then reverse direction as they pass over the pipe-end vortex, while accelerating in the streamwise direction until their velocities approach the cross-flow speed. A vorticity balance for each type of the vortices has been attempted. The von Karman vortices obtain their vorticity from the pressure gradient along the outer surface of the pipe. The pipe-end vortex acquires its vorticity from the shear-layer vortices and generates some vorticity in a pressure gradient on the outer surface of the pipe as well. The shear-layer vortices acquire their vorticity from the cross-flow fluid flowing over the edge of the upstream pipe tip as well as from the vorticity inside the pipe from the jet flow. The vorticity in the tendrils originates in the shear-layer vortices.
L'alternance locative en arabe marocain et en arabe standard
Creators: name: Ennamsaoui, Mouna
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2008
Subjects: subject: Language, Linguistics.
subject: Language, Modern.

description: L'alternance locative implique la possibilité pour certains verbes locatifs de réaliser syntaxiquement leurs arguments différemment. Un verbe comme to load, en anglais, permet que le constituant Locatum et le constituant Lieu soient réalisés dans la position d'objet direct alternativement, nommément une construction standard, ou le Locatum occupe la position d'objet direct et le Lieu la position d'objet oblique et la construction croisée ou le Lieu occupe la position d'objet direct et le Locatum la position d'objet oblique. Cette thèse examine les verbes locatifs en arabe marocain et en arabe standard dans une perspective sémantique. Trois types de verbes ont été identifiés: des verbes standards, des verbes croisés et des verbes alternants. Les deux variantes de l'arabe partagent plusieurs traits communs avec l'anglais et le francais, ils ont par contre quelques particularités qui se conforment, par ailleurs, aux généralisations théoriques. Au terme de cette étude, nous avons conclu que la possibilité pour un verbe d'alterner est contrainte par le sens du verbe et la possibilité pour celui-ci de prédire un changement de Lieu ou un changement d'état. Il a été montré que seuls les verbes d'activité ont ce potentiel d'alterner sous réserve que la condition sus-mentionnée soit satisfaite. Le sens du verbe est de ce fait capital pour déterminer et comprendre le comportement syntaxique des verbes. Mots cles: Alternance locative, structure argumentale, arabe marocain, arabe standard.
Coping with constraints: Agentic strategies in the micro-practices of independent adult sex workers in their relations with clients
Creators: name: Sauve, Genevieve
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2004
Subjects: subject: Sociology, General.

description: Issues of structural constraint and personal agency permeate the discourses of sex workers concerning their everyday practices in sex work, specifically surrounding their interactions with clients. While it appears fruitful and meaningful to respect and value the agency, experiences, and skills of sex workers, their actions remain in part constrained and contextualized by (material and symbolic) structural forces. Nonetheless, sex workers deploy agentic strategies in order to maximize their well-being within sex work. This study is based on qualitative interviews with 12 independent adult female sex workers in Ottawa and Toronto, who work in two settings (street and in-call). Different strategies (individual and collective) are identified and discussed, surrounding the sex worker/client interaction. Eight dimensions are specifically examined: makeup of the clientele, solicitation, contractual terms, pricing, location, boundaries, payment and bad dates. Women's reflective capacities as agents are demonstrated through their articulations of the justifications for actions surrounding their working practices.
Lexicographic traditions and prefatory discourse of 17 th century dictionaries: Monolingual English, monolingual French, and bilingual French-English works
Creators: name: Burlingham, Bronwyn
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2005
Subjects: subject: Language, Modern.
subject: Language, General.

description: In this study, we have explored the prefaces of monolingual English, monolingual French, and bilingual French-English dictionaries of the 17 th century. The monolingual works studied constitute the first of this kind to have been published. Over the course of this research, we have demonstrated that despite different lexicographic traditions, dictionary prefaces convey basically the same type of information, and address the same general issues. This study is divided into two main sections. In the first, we have provided historical information on the dictionaries, so as to illustrate the historical context in which they were published. In the second section, we have examined the prefaces themselves, first giving an overview of each text studied, and then providing a thematic analysis of the prefaces within each group as a whole, observing topics that are commonly treated among them, within the broader categories of dictionary content, lexicographic context, and linguistic context. Over the course of the research, we have established that though each text is unique, certain features are shared not only among the prefaces within one same category, but in fact across all three types of dictionary.
Les réceptions franco-ontarienne et québécoise du "Chien", d'"Il n'y a que l'amour" et d'"Un vent se lève qui éparpille" de Jean Marc Dalpé
Creators: name: Desabrais, Tina
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2005
Subjects: subject: Literature, Canadian (French).

description: Même s'il vit au Québec depuis plusieurs années, Jean Marc Dalpé continue de jouir d'une grande réputation en tant qu'écrivain franco-ontarien. Trois livres se démarquent de l'ensemble de son oeuvre, parce qu'ils ont obtenu la plus haute distinction littéraire au Canada, soit le prix du Gouverneur général: la pièce Le Chien en 1988, le recueil de pièces Il n'y a que l'amour en 1999, ainsi que le roman Un vent se lève qui éparpille en 2000. Dans cette thèse, nous nous proposons d'étudier les réceptions critiques immédiates franco-ontarienne et québécoise de ces trois livres primes de Dalpé. Il importera avant tout d'examiner les articles parus avant l'obtention du Gouverneur général et ceux parus dans la foulée du prix. Ce faisant, notre ambition est double: d'une part, mettre en relief les points de convergence et de divergence des discours critiques des champs littéraires franco-ontarien et québécois, d'autre part, voir si le prestige institutionnel lié aux prix du Gouverneur général a modifié ces réceptions. Pour ce faire, nous opterons pour une formule chronologique afin de mieux procéder à l'analyse des discours, et surtout afin de mieux voir si l'accumulation du capital symbolique de Jean Marc Dalpé n'aurait pas par moments influence la réception. De manière concomitante, nous serons à même d'évaluer comment intervient---si tel est le cas---la double appartenance de Jean Marc Dalpé qui vit au Québec, mais qui est toujours demeuré fidèle aux Éditions Prise de parole de Sudbury. Ainsi, nous tenterons de cerner les enjeux à l'oevre dans les champs franco-ontariens et québécois---ces derniers étant déterminés en fonction du lieu de publication des articles---à l'aune de la double réception critique des trois oeuvres de Jean Marc Dalpé. (Abstract shortened by UMI.)
Improving access to care for survivors of sexual violence: knowledge, attitudes, practices and perceptions in Port au Prince, Haiti and New Delhi, India
Creators: name: Meggy Verputten
name: Siddiqui, Ruby
name: Himanshu Mohan
name: Borgundvaag, Emily
name: Dockerty, Colleen
name: Verdecchia, Maria
name: Ariti, Cono
name: Stoeckl, Heidi
name: Prachi Renjhen
name: T Grand Pierre
name: Gray, Nell
Publisher: name: F1000 Research Limited
Year: 2020

description: Improving access to care for survivors of sexual violence: key lessons from two mixed-methods studies, Haiti and India presented at MSF Scientific Days International (London) Medical Research Day, May 13, 2020 by Meggy Verputten
Efficient private information retrieval
Creators: name: Malek, Behzad
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2005
Subjects: subject: Engineering, Electronics and Electrical.

description: In this thesis, we study Private Information Retrieval and Oblivious Transfer, two strong cryptographic tools that are widely used in various security-related applications, such as private data-mining schemes and secure function evaluation protocols. The first non-interactive, secure dot-product protocol, widely used in private data-mining schemes, is proposed based on trace functions over finite fields. We further improve the communication overhead of the best, previously known Oblivious Transfer protocol from O ((log(n))2) to O (log(n)), where n is the size of the database. Our communication-efficient Oblivious Transfer protocol is a non-interactive, single-database scheme that is generally built on Homomorphic Encryption Functions. We also introduce a new protocol that reduces the computational overhead of Private Information Retrieval protocols. This protocol is shown to be computationally secure for users, depending on the security of McEliece public-key cryptosystem. The total online computational overhead is the same as the case where no privacy is required. The computation-saving protocol can be implemented entirely in software, without any need for installing a secure piece of hardware, or replicating the database among servers.