cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Environment, culture, parenting, and children's development in an impoverished Latin American society
Creators: name: Foucault, Darlene C
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2005
Subjects: subject: Psychology, Social.
subject: Psychology, Developmental.
subject: Sociology, Individual and Family Studies.

description: This study investigated the effects of the Socioeconomic status (SES) community on the physical and social environment, maternal psychology, parenting values, parenting practices, and child development. It examined whether the effects of poverty as is noted in mostly North American research would be replicated in a collectivistic Latin society such as the Dominican Republic. The participants were 80 three year-olds, 154 six year-olds, 141 eight year-olds and their primary caregivers, with participants equally divided between the Campos (small agricultural villages) and higher SES San Cristobal. Maternal figures completed the Brief Symptom Inventory (BSI), Parenting Stress Index- Short Form (PSI-SF), Interpersonal Support Evaluation List (ISEL), Rank Order of Parental Values (ROPV), Child Development Inventory (CDI), and Strengths and Difficulties Questionnaire (SDQ). During a home visit, the researcher completed the Home Observation and Measurement of the Environment (HOME) Inventory and obtained information to fill out the physical and social environment measures. The Self-Perception for Children and the Peer Nomination and Assessment measures were administered to the children in the school setting. Teachers also completed the SDQ and provided information on children's academic performance. MANOVAs confirmed our first hypothesis that the Campos and San Cristobal environments are significantly different (p < .001) on all measures of the physical and social environment, with San Cristobal children benefiting overall from a better developmental context. Secondly, Campos mothers reported significantly (p < .001) more interpersonal support and less parental distress relative to their more affluent counterparts. These findings are contrary to those of present North-American research. We propose that belonging to a collectivistic culture may shield mothers from some of the pernicious effects of poverty. An examination of the SES/community effect demonstrated that San Cristobal parents provide a more stimulating (p < .001) and emotionally supportive (p < .001) HOME environment for their children than do Campos parents. MANOVAs conducted on child outcome measures revealed that Campos children were weaker then their San Cristobal counterparts on most developmental scales and all academic subjects (p < .001). Also, San Cristobal parents reported more prosocial behaviours for their children relative to Campos parents (p < .001), and San Cristobal children reported a more positive view of their social interactions and abilities as well as more satisfaction with their lives (p < .001) than the less affluent Campos children. (Abstract shortened by UMI.)
Staudämme und der Mythos der Entwicklungszusammenarbeit in Südostasien
Creators: name: Klöpper, Yvonne
Publisher: name: ASIEN: The German Journal on Contemporary Asia
Year: 2021

description: There is hardly a day passing by, where the media does not remind us of the critical stage of the global climate and the rising energy demands. Thus experts are calling for securing nations' power supplies and the therefore needed natural resources - mainly oil, gas and water. All these sources are becoming scarce and are often found in ‘developing countries’. Hence most of the ‘developed nations’ put the topic on their political agenda, closely linking it to geopolitical security issues and ‘development assistance’, which therefore more and more adopts a ‘neo-colonial’ style. New - and for Western Countries probably even more challenging - is the fact that nations such as China, India or Thailand are entering the competitive arena as well. Thus a ‘global footrace for energy resources’ takes shape - representing a sensitive and manifold issue that touches economical, socio-political and ecological spheres. Through increasing resource conflicts on diverse spatial levels - and formed by multiple features - the scenario becomes more and more visible. These controversies apparently represent a global phenomenon and symbolize a crucial issue in current debates. Particularly water is an essential and irreplaceable source for life that is getting rare. So it has become a disputed resource. And in (Southeast) Asia water conflicts are found especially around dam- and hydropower schemes. The article focuses this topic through examining three dam projects in Thailand, Laos and Burma. These dams are currently in different stages and are all interweaved by development assistance. Consequently this approach offers to analyze the complexity of the issue and to unveil the multiple actors involved, their networks, strategies and power relations.
description: ASIEN: The German Journal on Contemporary Asia, Nr. 106 (2008): ASIEN (Januar)
Taxonomy in Biology and Visualization
Creators: name: Maguire, Eamonn
Publisher: name: figshare
Year: 2012
Subjects: subject: Theoretical Computer Science
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences

description: Taxonomies are core to our everyday working. We constantly categorize entities to aid our understanding and navigation of the world around us. In the most basic of cases, we may categorize animals into dangerous or non-dangerous, pets or pests and people into friends and strangers. Since time began, our ancestors have used taxonomy to stay away from things carrying the potential to cause harm, and it is shown that we have the ability to classify complex entities even as children through evolved parts of the human brain. This paper explores the origin of taxonomy and how it carries immense importance in our world, its importance in biology and how it is used in visualization also.
 This is a short paper reviewing taxonomy in biology and visualization. It is not perfect, but it is a comprehensive review.
Evaluating methamphetamine use and risks of injection initiation among street youth: the ARYS study
Creators: name: Wood, Evan
name: Stoltz, Jo-Anne
name: Montaner, Julio
name: Kerr, Thomas
Publisher: name: BioMed Central
Year: 2015

description: Many Canadian cities are experiencing ongoing infectious disease and overdose epidemics among injection drug users (IDU). These health concerns have recently been exacerbated by the increasing availability and use of methamphetamine. The challenges of reducing health-related harms among IDU have led to an increased recognition that strategies to prevent initiation into injection drug use must receive renewed focus. In an effort to better explore the factors that may protect against or facilitate entry into injection drug use, the At Risk Youth Study (ARYS) has recently been initiated in Vancouver, Canada. The local setting is unique due to the significant infrastructure that has been put in place to reduce HIV transmission among active IDU. The ARYS study will seek to examine the impact of these programs, if any, on non-injection drug users. In addition, Vancouver has been the site of widespread use of methamphetamine in general and has seen a substantial increase in the use of crystal methamphetamine among street youth. Hence, the ARYS cohort is well positioned to examine the harms associated with methamphetamine use, including its potential role in facilitating initiation into injection drug use. This paper provides some background on the epidemiology of illicit drug use among street youth in North America and outlines the methodology of ARYS, a prospective cohort study of street youth in Vancouver, Canada.
Die Bedeutung des Islams zur Legitimation des Staates in Afghanistan
Creators: name: Von Schwerin, Ulrich
Publisher: name: ASIEN: The German Journal on Contemporary Asia
Year: 2021

description: The new Afghan constitution of January 2004 founds the legitimacy of the state on the respect of democratic principles and Islamic values. The success of this ‘Islamic Democracy’ depends on the ability of the government to implement a liberal interpretation of Islam that is in compliance with the principles of democracy. However as the Islamic forces continue to exercise significant influence on politics and as President Karzai has been weakened by his inability to fulfil his promise of security and development, he has increasingly tried to strengthen his legitimacy by the islamisation of the state.
description: ASIEN: The German Journal on Contemporary Asia, Nr. 106 (2008): ASIEN (Januar)
Innovative tool to reduce the arduousness of technical planting operations: the redesigned planting pickaxe
Creators: name: Snoussi, Bilal
Publisher: name: Zenodo
Year: 2025
Subjects: Sustainable forest management
Plantation
Working conditions
Societal expectations

description: Develop plantation management methods that meet the social and environmental expectations : characteristics of the planting tool to improve ergonomics and optimise the efficiency of the actions carried out by the operator.
Leptanilloides Mann 1923
Creators: name: The, In
name: Esteves, Flávia A.
name: Brandão, Carlos Roberto F.
name: Prado, Lívia P.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Leptanilloides

description: Genus Leptanilloides Mann
 Leptanilloides biconstricta Mann, 1923: 14. Paralectotypes: 3 w. Bolivia, La Paz, Tumupasa, [no date], W.M. Mann col. Two workers fragmented.
 Leptanilloides legionaria Brandão, Diniz, Agosti & Delabie, 1999: 29. Paratypes: 2 w. Colombia, Santa Marta M [oun]t[ain]s, Walker Expedition, 7.vii.1913, F.M. Gaige col., # 55.
 Leptanilloides mckennae Longino, 2003: 2. Paratypes: 2 w. CR [Costa Rica], Puntarenas Prov [ince], Monteverde, 1300 m, 10°18’N, 84°48’W, vii.1995, D. Mckenna col. Moist forest litter.
 Leptanilloides nomada Donoso, Vieira & Wild, 2006: 50. Paratypes: 3 w. Ecuador, Cotopaxi, Otonga Reserve, 1960 m, 00°25’S, 79°00’W, # AW2146, 2.xii.2003, A.L. Wild & J.M. Vieira cols, Cloud forest, column of ants on forest floor & in soil.
 Leptanilloides sculpturata Brandão, Diniz, Agosti & Delabie, 1999: 30. Paratype: 1 w. Colombia, Venice (near Medelin), v.1956, E. Flanders col., # 56-6029. Associated with Acropyga fuhrmanni on healthy coffe trees.
description: Published as part of The, In, Esteves, Flávia A., Brandão, Carlos Roberto F. & Prado, Lívia P., 2011, The Type Specimens Of " Dorylomorph " Ants (Hymenoptera, Formicidae: Aenictinae, Ecitoninae, Cerapachyinae, Leptanilloidinae) Deposited In The Museu De Zoologia Da Universidade De São Paulo, Brazil, pp. 341-357 in Papéis Avulsos de Zoologia 51 (22) on pages 341-357, DOI: 10.1590/S0031-10492011002200001, http://zenodo.org/record/13222746
Becoming an engineer: Doctoral women's perspectives on identity and learning in the culture of engineering
Creators: name: Wood, Shaunda L
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2004
Subjects: subject: Women's Studies.
subject: Education, Sciences.
subject: Education, Higher.

description: Women face many obstacles in their academic careers but there is a gap in the research with regards to their perceptions of science and engineering education and how non/participation in the culture of engineering affects their identities. Moreover, little research has been conducted with female Ph.D. students especially with regard to the reasons they have continued their studies, and their level of satisfaction with their career and lives. This study was guided by the sociocultural approach and theories of learning and identity. Methodologically, the design adopted is a naturalistic qualitative inquiry using two open-ended interviews with participant verification after the first interview. The life history narratives (Mishler, 1999) obtained from the seven doctoral electrical and mechanical women engineers, at various stages in their programs, were the primary source of data. By examining the path of becoming a doctoral woman engineer, this study makes the educational experiences of women intelligible to the general public as well as policy makers. It gives voice to the women engineers whose perspectives are rarely heard in academic settings or mainstream society. The findings of the study lend insight to the importance and necessity of more inclusive engineering education, incorporating not only women's studies courses into the curriculum but anti-racism education as well as including the perspective of 'Other' people of difference. Moreover, multi-perspective approaches to increasing enrolment and retention of women in engineering were more effective and in keeping with addressing notions of 'difference' in engineering populations.
Structure and Kinematics of the Nankai Trough Accretionary Prism, Japan
Creators: name: Kington, Joe
Publisher: name: figshare
Year: 2012
Subjects: subject: Geophysics
subject: FOS: Earth and related environmental sciences
subject: Geology

description: Subduction zone frontal prisms are among the most tectonically dynamic environments on Earth. 3D seismic data acquired as a part of the Nankai Trough Seismogenic Zone Experiment provides a unique opportunity to study accretionary prism processes. My research focuses on three aspects of the structure of the outer wedge fold and thrust belt.

Based on the geometry of thrust sheets in the outer wedge, the décollement has ramped up and then back down within the incoming sedimentary section. This has resulted in an unusually thick underthrust sediment volume, which has caused uplift and mass wasting ∼30 km landward of the deformation front. I hypothesize that changes in the depth of the décollement are due to the subduction of a basement high beneath the outer wedge ∼25 km to the east of the study area. This suggests that basement features may be associated with anomalously thick underthrust sediments for a significant distance along-strike.

Bed-length balancing suggests that it has accommodated 99±10 km of shortening in the last ∼2.3 myr, 34±17 km of which has been accommodated by a zone of out-of-sequence thrusting. Kinematic modeling of syn-kinematic sediments in the forearc basin indicates that the landward-most structure in the out-of- sequence thrust zone has accommodated 14.6±1.8 km of shortening. Additionally, our results demonstrate that uplift of the forearc and activity on the landward out-of-sequence thrust must have began at ∼0.9 Ma and continued until sometime younger than 0.5 Ma.

Finally, I use arrays of small (
Aboriginal status is a prognostic factor for mortality among antiretroviral naïve HIV-positive individuals first initiating HAART
Creators: name: Lima, Viviane D.
name: Kretz, Patricia
name: Palepu, Anita
name: Bonner, Simon
name: Kerr, Thomas
name: Moore, David M.
name: Daniel, Mark
name: Montaner, Julio
name: Hogg, Robert S.
Publisher: name: BioMed Central
Year: 2016

description: Background: Although the impact of Aboriginal status on HIV incidence, HIV disease progression, and access to treatment has been investigated previously, little is known about the relationship between Aboriginal ethnicity and outcomes associated with highly active antiretroviral therapy (HAART). We undertook the present analysis to determine if Aboriginal and non-Aboriginal persons respond differently to HAART by measuring HIV plasma viral load response, CD4 cell response and time to all-cause mortality. Methods: A population-based analysis of a cohort of antiretroviral therapy naïve HIV-positive Aboriginal men and women 18 years or older in British Columbia, Canada. Participants were antiretroviral therapy naïve, initiated triple combination therapy between August 1, 1996 and September 30, 1999. Participants had to complete a baseline questionnaire as well as have at least two follow-up CD4 and HIV plasma viral load measures. The primary endpoints were CD4 and HIV plasma viral load response and all cause mortality. Cox proportional hazards models were used to determine the association between Aboriginal status and CD4 cell response, HIV plasma viral load response and all-cause mortality while controlling for several confounder variables. Results: A total of 622 participants met the study criteria. Aboriginal status was significantly associated with no AIDS diagnosis at baseline (p = 0.0296), having protease inhibitor in the first therapy (p = 0.0209), lower baseline HIV plasma viral load (p < 0.001), less experienced HIV physicians (P = 0.0133), history of IDU (p < 0.001), not completing high school (p = 0.0046), and an income of less than $10,000 per year (p = 0.0115). Cox proportional hazards models controlling for clinical characteristics found that Aboriginal status had an increased hazard of mortality (HR = 3.12, 95% CI: 1.77–5.48) but did not with HIV plasma viral load response (HR = 1.15, 95% CI: 0.89–1.48) or CD4 cell response (HR = 0.95, 95% CI: 0.73–1.23). Conclusion: Our study demonstrates that HIV-infected Aboriginal persons accessing HAART had similar HIV treatment response as non-Aboriginal persons but have a shorter survival. This study highlights the need for continued research on medical interventions and behavioural changes among HIV-infected Aboriginal and other marginalized populations.
Factors Enabling the Decoupling of China’s Energy-related Emissions from Its Economic Growth
Creators: name: Yong, Li
name: Oberheitmann, Andreas
Publisher: name: Asien
Year: 2021

description: Economic growth has been one of the most important political goals in China since the reforms introduced by Deng Xiaoping in the late 1970s. The successful increase in economic welfare in China was accompanied by a decoupling of economic growth and energy-related emissions of carbon dioxide (CO2) and sulphur dioxide (SO2). The absolute values of these emissions has increased considerably. Two questions arise against this backdrop: what are the main factors behind the decoupling of economic growth and these energy-related emissions, and what is the impact of each of these factors on the rise in emissions? This paper aims to determine and analyse these factors, which are population, per-capita income, total CO2 or SO2 intensity of the primary energy supply, and the energy intensity of GDP. Factor decomposition reveals that the growth in per-capita income and the reduction in energy intensity have the largest balancing impact on energy consumption and emissions in China. The relationship between economic development and emission levels, however, is not linear over time, but follows a path commonly described by the Environmental Kuznets Curve: emissions decrease while per-capita income grows. In China, this phenomenon occurred between 1998 and 2000 and led to a curve much like the typical inverted U-shaped Environmental Kuznets Curve until 2001. Seen from a 2005 perspective, however, this merely turned out to be a structural break.
description: Asien, Nr. 106 (2008): ASIEN (Januar)
Lab scale plastic extruder
Creators: name: Kassel, Brendan
name: Thurman, Jonathon
name: Weinzapfel, Jack
Publisher: name: Unknown
Year: 2017

description: The goal for the senior design project is to make a Lab Scale Plastic Extruder. The purpose
for the small size is so that teachers/professors can demonstrate the process of plastic extrusion
rather than simply use diagrams or videos in a lecture setting. A secondary goal for the project is
to create the system at a price, which would be more economical than buying an assembly kit
already made. There is potential for future senior design projects that would use the project as a
foundation to build off.
New [5]helicene derivatives with large Stokes shifts for Hg2+ determination and their application in drinking water, river water and tuna fillet
Creators: name: Anuwut Petdum
name: Jitnapa Sirirak
name: Vannajan Sanghiran Lee
name: Nienaber, Hubert A.
name: Waraporn Panchan
name: Thanasat Sooksimuang
name: Nantanit Wanichacheva
Publisher: name: Silpakorn University Research, Innovation and Creativity Administration Office
Year: 2020
Subjects: mercury ion
fluorescence sensor
selectivity
[5]helicene

description: Science, Engineering and Health Studies, 14, 1, 32-46
Archean tectonics: Analog and gravity models
Creators: name: Peschler, Anne P
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2004
Subjects: subject: Geology.

description: This work investigates Archean continental geodynamics. Three cratonic areas were studied: the Pilbara Craton, Australia (3.5--3.2 Ga), the Yilgarn Craton, Australia (2.7 Ga) and the Abitibi Subprovince, Canada (2.7 Ga). Each region is modeled using several 2-D gravity profiles. In the 3.5 Ga Pilbara craton, some modeled batholiths have well defined roots that extend to depths greater than 10 km whereas others have roots extending to less than 6 km depth. The model results from the 2.7 Ga Yilgarn craton and the Abitibi Subprovince show no major differences between the two terranes. The rarity of deep roots and a thickness of 5 to 6 km are characteristics of the ca. 2.7 Ga batholiths. The surrounding greenstones form keels of up to 10 km depth, in the three modeled regions. Compassion of the results from the older and younger cratons suggests: (1) the presence (Middle Archean) or quasi-absence (Late Archean) of deep batholith roots may indicate changes in continental geodynamics from 3.5 Ga to 2.8 Ga. (2) greenstones in the Middle and Late Archean terranes form deep keels, which are consistent with the gravity driven, diapiric model in the case of the older greenstones, and may be explained by crustal folding in the younger cases. A more detailed gravity study was done on the Abitibi Subprovince using modeled gravity profiles and a wavelet based inversion method, leading to a new proposed model to explain the structures of the Abitibi Subprovince. In this model the Abitibi upper-middle crust is folded, the deformations zones interpreted as detachment folds. We used analog experiments to investigate folding of continental crust subjected to different geothermal gradients. In our experiments, folding is the main response to shortening of the analog crust. The middle and lower crust analogs respond to the shortening by buckling. In the upper crust analog, detachment folds, thrust faults and grabens above anticlines are developed. For the lowest thermal gradient, one anticline-syncline pair is formed. For warmer gradients, multiple folds develop that have smaller amplitudes. Based on our models, we interpret that the increase of crustal temperatures may result in a decrease of the amplitude of the crustal folds. Our results suggest that the deformation style preserved within Archean greenstone belts is strongly influenced by the syndeformational thermal regime of the crust.* *This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Microsoft Office.
The Western Palaeartic evolution of the water vole, Arvicola
Creators: name: Ruddy, Mark
Publisher: name: figshare
Year: 2012
Subjects: subject: Physical Geography
subject: Paleontology
subject: Geology
subject: FOS: Earth and related environmental sciences
subject: Evolutionary Biology
subject: FOS: Biological sciences

description: The water vole is common in Middle and Late Pleistocene temperate Palaearctic faunas. It is widely used in biostratigraphy because of temporal trends in the size, shape and structure of the first lower molar (m1). However, geographic variation in the evolutionary development of the m1 has restricted the precision and accuracy of age-estimations. This thesis explores morphological variation in the m1 of fossil and extant populations of the lineage Mimomys savini–Arvicola, and uses the phenotype and the genotype to develop evolutionary hypotheses. Geometric and traditional morphometric methods are used to quantify tooth shape and enamel thickness from over 4000 digital photographs of m1s taken from specimens originating from 146 modern and fossil groups across the western Palaearctic. m1s are photographed to obtain a true cross-section, giving a more accurate description of molar shape. Morphological variation is explored in terms of sample-size, taphonomy, and ontogeny. Sample sizes of less than 10 are likely to provide inaccurate summary statistics of morphometric variables but depositional type appears to have no systematic effect on within-group variation. Change in the morphology of m1s through ontogeny is an important source of morphological variation, explaining up to 29% of molar shape within-specimens and up to 95% of enamel thickness within enamel layers of specimens. Removal of ontogenetic variation from mo- lar shape improves congruence between morphological and molecular data, indicating age-corrected variables should be used when assessing evolutionary patterns. Temporal and spatial patterns in the enamel thickness quotient (SDQ), based on age-corrected enamel thicknesses, mirror those from published data but differ in some details. Methodological differences mean absolute SDQ values cannot be compared. Qualitative patterns include a large decrease in SDQ across MIS 12 and a steep east–west morphocline during the late Middle Pleistocene.
Aerodynamics of a circular cylinder inclined to airflow and wind-induced vibrations of dry, inclined cables at high wind speeds
Creators: name: Zurell, Cory
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2004
Subjects: subject: Engineering, Civil.

description: Cable-stayed bridges are an efficient and elegant solution to bridging long spans. Though a widely used structural system, several significant issues are still unresolved regarding a cable-stayed bridge's performance, particularly with respect to the response of the cables to wind. As tension members, stay cables have a very low diameter-to-span ratio such that the effect of bending stiffness on a cable's vibration characteristics is inconsequential. Coupled with this, stay cables have very little internal mechanical damping, thus they are quite susceptible to dynamic excitation. Several vibration mechanisms have been identified, however for some, including the potentially more damaging mechanisms, the required conditions and generating mechanisms are not completely understood. Aerodynamically, a stay cable is simply a circular cylinder exposed to wind. A circular cylinder positioned normal to airflow is a touchstone topic in the fields of aerodynamics and fluid mechanics. A circular cylinder inclined to airflow, from a fundamental viewpoint, has been given very little attention considering the body of work concerning the former case. The objective of this study was to determine the characteristics of the airflow about an inclined circular cylinder, and to determine and clarify necessary conditions for the generation of galloping vibrations and high-speed vortex vibrations in dry, inclined stay cables. A wind tunnel study was conducted in which a static circular cylinder was exposed, at varying relative wind-cylinder angles, to wind speeds corresponding to a Reynolds number range of 1 x 105 to 6 x 105 Surface pressure data was recorded to determine both the instantaneous and time-averaged pressures and forces on the section. Using the matrix computation software Matlab, programs were written to evaluate and analyse lift and drag forces, and pressure, lift, and drag coefficients. From the extensive data compiled, several significant conclusions concerning flow about an inclined or yawed cylinder and about the galloping and high-speed vortex vibration phenomena result. Concerning flow about an inclined circular cylinder, the drag force coefficient is generally lower for lower relative inclination angles. This trend reverses over a small range of speeds within the critical Reynolds number range. Note that this and the following findings are based on the minimum inclination angle tested of 54.7°. (Abstract shortened by UMI.)
Improving the specificity of high-throughput ortholog prediction
Creators: name: Fulton, Debra L
name: Li, Yvonne Y
name: Laird, Matthew R
name: Horsman, Benjamin G
name: Roche, Fiona M
name: Brinkman, Fiona S
Publisher: name: BioMed Central
Year: 2015

description: Background: Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function. Results To address these issues, we present here a high-throughput computational method named Ortholuge that further evaluates previously predicted orthologs (including those predicted using an RBH-based approach) – identifying which orthologs most closely reflect species divergence and may more likely have similar function. Ortholuge analyzes phylogenetic distance ratios involving two comparison species and an outgroup species, noting cases where relative gene divergence is atypical. It also identifies some cases of gene duplication after species divergence. Through simulations of incomplete genome data/gene loss, we show that the vast majority of genes falsely predicted as orthologs by an RBH-based method can be identified. Ortholuge was then used to estimate the number of false-positives (predominantly paralogs) in selected RBH-predicted ortholog datasets, identifying approximately 10% paralogs in a eukaryotic data set (mouse-rat comparison) and 5% in a bacterial data set (Pseudomonas putida – Pseudomonas syringae species comparison). Higher quality (more precise) datasets of orthologs, which we term "ssd-orthologs" (supporting-species-divergence-orthologs), were also constructed. These datasets, as well as Ortholuge software that may be used to characterize other species' datasets, are available at http://www.pathogenomics.ca/ortholuge/ (software under GNU General Public License). Conclusion The Ortholuge method reported here appears to significantly improve the specificity (precision) of high-throughput ortholog prediction for both bacterial and eukaryotic species. This method, and its associated software, will aid those performing various comparative genomics-based analyses, such as the prediction of conserved regulatory elements upstream of orthologous genes.
Molecular regulation of the Ste20-like kinase (SLK) by SRC-dependent pathways
Creators: name: Chaar, Ziad Y
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2005
Subjects: subject: Health Sciences, Medicine and Surgery.

description: The Ste20-like kinase (SLK) is a conserved serine/threonine kinase that induces the dissociation of actin stress fibers in a Rac1-dependent manner. Recently, our laboratory has shown that SLK is a microtubule-associated protein regulating migratory components at the cell periphery in membrane ruffles and lamellipodia (Storbeck et al.; Wagner et al. unpublished data). To investigate the role of SLK during cell adhesion and migration, we used the Polyomavirus Enhancer Activator 3-null (PEA3(-/-/)) cell line, known to exhibit migration deficiencies. We observed that SLK redistribution to the cell periphery is altered in the PEA3(-/-) cells and that this phenotype could be rescued by the re-expression of PEA3 cDNA into PEA3(-/-) cells. Further analysis revealed that the PEA3(-/-) cells exhibit impaired c-src activation highlighted by decreased focal adhesion kinase (FAK) cleavage and reduced p130Cas tyrosine phosphorylation following fibronectin stimulation, suggesting that c-src activity and proper adhesion signaling may be required for SLK recruitment to the cell periphery. To further investigate FAK and c-src involvement in SLK redistribution to the cell periphery, we used FAK- or src, yes and fyn (SYF)-deficient cells. We have shown that SLK redistribution to the cell periphery is also altered in SYF deficient cells but not in FAK-deficient cells, suggesting that c-src mediates SLK redistribution to the cell periphery independently of FAK. SLK in vitro kinase assays performed on PEA3(-/-), FAK- and SYF-deficient cells revealed that SLK kinase activity is unaffected. However, v-src and c-srcY527F transformed cells displayed a 2- to 3-fold decrease in SLK kinase activity. Biochemical analysis revealed that SLK is hyperphosphorylated on serine residues in these cells with the kinase domain being the main target. Further analysis revealed that casein kinase II (CK2) phosphorylates the SLK kinase domain on serine 347/348 to downregulate SLK kinase activity. In addition, we also showed that CK2 kinase activity is dramatically increased in v-src-transformed cells and that the inhibition of CK2 restores SLK kinase activity. Overall, we showed that SLK redistribution to the cell periphery requires c-src, which can also regulate SLK kinase activity via CK2 to allow the turnover of adhesion sites and cytoskeletal rearrangements.
Boreal ecosystems sequestered more carbon in warmer years
Creators: name: Higuchi, Kaz
name: Chen, Baozhang
name: Chen, Jing M.
name: Black, T. Andrew
name: Chan, Douglas
name: Liu, Jane
name: Tans, Pieter
name: Worthy, Douglas E. J.
Publisher: name: American Geophysical Union
Year: 2011

description: A 13-year (1990–1996, 1999–2004), hourly air CO2 record measured on a 40 m tower in northern Canada is analyzed against interpolated marine boundary layer CO2 data representing the free troposphere above the tower. In warmer years, the planetary boundary layer was more depleted with CO2, suggesting that the land area (103–104 km2) upwind of the tower sequestered more carbon. After using a novel approach to derive the photosynthetic flux from the air CO2 diurnal variation pattern, it is confirmed that boreal ecosystem photosynthesis increased more than ecosystem respiration in warmer years. An edited version of this paper was published by AGU. Copyright 2006 American Geophysical Union.
The Western Palaeartic evolution of the water vole, Arvicola
Creators: name: Ruddy, Mark
Publisher: name: figshare
Year: 2013
Subjects: subject: Physical Geography
subject: Paleontology
subject: Geology
subject: FOS: Earth and related environmental sciences
subject: Evolutionary Biology
subject: FOS: Biological sciences

description: The water vole is common in Middle and Late Pleistocene temperate Palaearctic faunas. It is widely used in biostratigraphy because of temporal trends in the size, shape and structure of the first lower molar (m1). However, geographic variation in the evolutionary development of the m1 has restricted the precision and accuracy of age-estimations. This thesis explores morphological variation in the m1 of fossil and extant populations of the lineage Mimomys savini–Arvicola, and uses the phenotype and the genotype to develop evolutionary hypotheses. Geometric and traditional morphometric methods are used to quantify tooth shape and enamel thickness from over 4000 digital photographs of m1s taken from specimens originating from 146 modern and fossil groups across the western Palaearctic. m1s are photographed to obtain a true cross-section, giving a more accurate description of molar shape. Morphological variation is explored in terms of sample-size, taphonomy, and ontogeny. Sample sizes of less than 10 are likely to provide inaccurate summary statistics of morphometric variables but depositional type appears to have no systematic effect on within-group variation. Change in the morphology of m1s through ontogeny is an important source of morphological variation, explaining up to 29% of molar shape within-specimens and up to 95% of enamel thickness within enamel layers of specimens. Removal of ontogenetic variation from mo- lar shape improves congruence between morphological and molecular data, indicating age-corrected variables should be used when assessing evolutionary patterns. Temporal and spatial patterns in the enamel thickness quotient (SDQ), based on age-corrected enamel thicknesses, mirror those from published data but differ in some details. Methodological differences mean absolute SDQ values cannot be compared. Qualitative patterns include a large decrease in SDQ across MIS 12 and a steep east–west morphocline during the late Middle Pleistocene.
Development and reproductive cycle of the sea biscuit Clypeaster subdepressus (Echinodermata: Echinoidea) from São Sebastião, SP
Creators: name: Vellutini, Bruno C.
Publisher: name: figshare
Year: 2013
Subjects: Developmental Biology

description: M.Sc. thesis on the development and reproduction of the sea biscuit Clypeaster subdepressus. Text is in portuguese. Original title: "Desenvolvimento e ciclo reprodutivo da bolacha-do-mar Clypeaster subdepressus (Echinodermata: Echinoidea) de São Sebastião, SP" Developmental chapter was published in PLOS ONE http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009654
Fragile fixings: An exploration of the self-representations of white women teachers in one isolated northern Indigenous community
Creators: name: Aitken, Avril
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2005
Subjects: subject: Women's Studies.
subject: Education, Administration.
subject: Native American Studies.

description: This thesis examines how white women teachers, who have worked or are working in one isolated, Indigenous community in Northern Canada, construct a sense of self and their work. It offers an analysis of the self-representations of seven white women teachers that draws on poststructural, psychoanalytic and postcolonial theory. The thesis demonstrates the ways in which the social and the psychic, the exterior and the interior, and discourse and the unconscious interconnect in the construction of gendered and racialized teacher identity. The thesis takes the position that identity formation is worked out in the intersubjective space between individuals as they position themselves through the continuous renegotiation of power relations and the differentiated discourses that are available to them. Further, the thesis explores the way in which conscious and unconscious processes influence how white women teachers position themselves. The research methodology highlights the use of film as a research tool. Judith P. Robertson's (2004) technique of Screenplay Pedagogy, which brings unconscious processes to the attention of the researcher and participants, was employed as one of the primary techniques. This approach involves: collective viewing of a film text; attention to deeply felt psychic and somatic moments; writing; and discussion. In subsequent phases of the data collection for the project, each participant wrote a monologue and was interviewed. The thesis is structured around three major themes that emerged through the research process: communities and relationships; teacher role, values, beliefs and actions; and student and teacher potential. The women's monologues are investigated as individual cases that contribute to the exploration of the importance of each theme in the process of identity formation. The thesis demonstrates the significance of the dreams, fantasies and hopes that the women associate with teaching. It highlights the impact of the phenomenon of 'othering' on the Indigenous students and community. It demonstrates the role of communities and of competing discourses in education in the formation of professional identity and in the women's sense of being able, or not, to continue to teach in the isolated Indigenous community.
Factors Affecting to Goods Purchasing Decision by using QR CodeTransactions of Nakhon Pathom Rajabhat University Students
Creators: name: Tanatip Puapornpong
Publisher: name: Faculty of Management Science Nakhon Pathom Rajabhat University
Year: 2019
Subjects: Marketing mix
Attitude
Trustworthiness
QR Code

description: Journal of Management Science Nakhon Pathom Rajabhat University, 6, 2, 324-338
Assessment of health-related quality of life in arthritis: conceptualization and development of five item banks using item response theory
Creators: name: Kopeć, Jacek A.
name: Sayre, E. C.
name: Davis, Aileen M.
name: Badley, Elizabeth M.
name: Abrahamowicz, Michal
name: Sherlock, Lesley
name: Williams, J. I.
name: Anis, Aslam H. (Aslam Hayat), 1959-
name: Esdaile, John
Publisher: name: BioMed Central
Year: 2016

description: Background: Modern psychometric methods based on item response theory (IRT) can be used to develop adaptive measures of health-related quality of life (HRQL). Adaptive assessment requires an item bank for each domain of HRQL. The purpose of this study was to develop item banks for five domains of HRQL relevant to arthritis. Methods: About 1,400 items were drawn from published questionnaires or developed from focus groups and individual interviews and classified into 19 domains of HRQL. We selected the following 5 domains relevant to arthritis and related conditions: Daily Activities, Walking, Handling Objects, Pain or Discomfort, and Feelings. Based on conceptual criteria and pilot testing, 219 items were selected for further testing. A questionnaire was mailed to patients from two hospital-based clinics and a stratified random community sample. Dimensionality of the domains was assessed through factor analysis. Items were analyzed with the Generalized Partial Credit Model as implemented in Parscale. We used graphical methods and a chi-square test to assess item fit. Differential item functioning was investigated using logistic regression. Results: Data were obtained from 888 individuals with arthritis. The five domains were sufficiently unidimensional for an IRT-based analysis. Thirty-one items were deleted due to lack of fit or differential item functioning. Daily Activities had the narrowest range for the item location parameter (-2.24 to 0.55) and Handling Objects had the widest range (-1.70 to 2.27). The mean (median) slope parameter for the items ranged from 1.15 (1.07) in Feelings to 1.73 (1.75) in Walking. The final item banks are comprised of 31–45 items each. Conclusion: We have developed IRT-based item banks to measure HRQL in 5 domains relevant to arthritis. The items in the final item banks provide adequate psychometric information for a wide range of functional levels in each domain.
BioExcel Webinar #22 - GROMACS 2018 – overview of the new features and capabilities
Creators: name: Abraham, Mark
Publisher: name: Zenodo
Year: 2018
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, including support for PME on GPUs, and guide you to make best use of the new opportunities.
BioExcel Webinar #23 - MC_DNA: A web server for the detailed study of the structure and dynamics of DNA and chromatin fibers
Creators: name: Walther, Jürgen
Publisher: name: Zenodo
Year: 2018
Subjects: webinar

description: MC_DNA is a new web tool for the three-dimensional simulation of free DNA and
 medium-sized chromatin fibers. The program implements a Monte Carlo algorithm based on a
 mesoscopic model, using a tetramer-dependent base-pair step model fitted to reproduce
 parmbsc1 atomistic molecular dynamics (MD) simulations. The Monte Carlo ensembles can be
 projected to the atomistic level of resolution and processed to obtain quasi-time-dependent
 trajectories. The method provides ensembles of quality comparable to those obtained from
 atomistic MD, but at a tiny fraction of the computational cost, allowing to study systems much
 larger than those explored by atomistic MD. The trajectories (at atomistic or bp resolution levels)
 can be downloaded and/or subjected to a large variety of analysis in the server. All the tools are
 implemented in a friendly web interface where the user needs to specify only the DNA
 sequence, its topology (linear or circular) and whether the DNA fiber is free or protein-bound.
 In the case of protein(s) bound to the DNA, the user needs to provide also the PDB code of the protein(s) and
 the position(s) of DNA where the protein(s) is(are) placed. Alternatively, the user can scan for
 the region(s) of DNA which are better shaped to adopt the bioactive conformation.
 The tool uses state-of-the-art technologies such as i) Open Nebula cloud infrastructure with
 virtual machines deployed on demand for computations, ii) WebGL-programmed NGL molecular
 viewer and the javascript plotly library for interactive plots, and iii) noSQL-MongoDB for
 storage. The server is accessible at http://mmb.irbbarcelona.org/MCDNA/. In the webinar the theory behind the simulation will be discussed and possible inputs for simulations will be pointed out. Afterwards, all the individual analysis tools will be explained and illustrated with examples.
Data Clone Detection and Visualization in Spreadsheets
Creators: name: Felienne Hermans
Publisher: name: figshare
Year: 2012
Subjects: subject: 80309 Software Engineering
subject: FOS: Computer and information sciences
subject: Applied Computer Science

description: Abstract Spreadsheets are widely used in industry: it is estimated that end-user programmers outnumber programmers by a factor 5. However, spreadsheets are error-prone, numerous companies have lost money because of spreadsheet errors. One of the causes for spreadsheet problems in the prevalence of copy-pasting. In this paper, we study this cloning in spreadsheets. Based on existing text-based clone detection algorithms, we have developed an algorithm to detect data clones in spreadsheets: formulas whose values are copied as plain text in a different location. To evaluate the usefulness of the proposed approach, we conducted two evaluations. A quantitative evaluation in which we analyzed the EUSES corpus and a qualitative evaluation consisting of two case studies. The results of the evaluation clearly indicate that 1) data clones are common, 2) data clones pose threats similar to those code clones pose and 3) our approach supports users in finding and resolving data clones.
Comparative rates of evolution in endosymbiotic nuclear genomes
Creators: name: Patron, Nicola J.
name: Rogers, Matthew B.
name: Keeling, Patrick J. (Patrick John), 1969-
Publisher: name: BioMed Central
Year: 2015

description: Background: The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded. Results Here, we test whether the phylogenetically distinct nucleomorph genomes of the cryptomonad, Guillardia theta, and the chlorarachniophyte, Bigelowiella natans, have experienced similar evolutionary pressures during their transformation to reduced organelles. We compared the evolutionary rates of genes from nuclear, nucleomorph, and plastid genomes, all of which encode proteins that function in the same cellular compartment, the plastid, and are thus subject to similar selection pressures. Furthermore, we investigated the divergence of nucleomorphs within cryptomonads by comparing G. theta and Rhodomonas salina. Conclusion Chlorarachniophyte nucleomorph genes have accumulated errors at a faster rate than other genomes within the same cell, regardless of the compartment where the gene product functions. In contrast, most nucleomorph genes in cryptomonads have evolved faster than genes in other genomes on average, but genes for plastid-targeted proteins are not overly divergent, and it appears that cryptomonad nucleomorphs are not presently evolving rapidly and have therefore stabilized. Overall, these analyses suggest that the forces at work in the two lineages are different, despite the similarities between the structures of their genomes.