Made available in DSpace on 2014-08-20T13:32:55Z (GMT). No. of bitstreams: 1 dissertacao_fabiana_fonseca_santos.PDF: 358501 bytes, checksum: 566ce94854cb74cc7a2d26d876462a45 (MD5) Previous issue date: 2010-08-17 / The understanding of the genetic structure of the oat species can be obtained with the use of microsatellite molecular markers which represent powerful tools in the investigation of genetic parameters. This study aimed to search the identification and characterization of microsatellite markers occurrence in oat through bioinformatics, describing the possible role of individual genes based on the genome of rice and Arabidopsis thaliana. For the development and validation of EST (Expressed Sequence Tags) primers, sequences were obtained from a public database. A total of 7632 oat contigs were obtained after eliminating the redundancy. To characterize SSR (simple sequence repeats) loci, the SSRLocator program was used. For the design of primers, the module containing the program Primer3 was used. A total of 58 primers were found, from which ten were selected for validation by polymerase chain reaction. Ten genotypes were used to assess polymorphism detection ability of primers. Polymorphism was observed in 80% of primers, whereas the rest showed monomorphic bands. The high genetic diversity revealed by microsatellite markers in this study may reflect a high genetic diversity within the germplasm of Avena sativa. / O conhecimento da estrutura genética de diversas espécies de aveia pode ser obtido com o uso de marcadores moleculares microssatélites, os quais representam poderosa ferramenta na averiguação de parâmetros genéticos. Este trabalho teve como objetivo buscar a identificação e a caracterização da ocorrência de marcadores microssatélites em aveia através da bioinformática, descrevendo a possível função de cada um dos genes, com base no genoma do arroz e da Arabidopsis thaliana. Visando o desenvolvimento e a validação de primers, foram obtidos a partir de um banco de dados público de EST (Expressed Sequence Tag) de aveia um total de 7.632 contigs que tiveram eliminada sua redundância, e para caracterização de locos SSR (Simple Sequence Repeat) foi utilizado o programa SSRLocator. Para o desenho de iniciadores foi utilizado no SSRLocator o módulo contendo o programa Primer3 sendo encontrados 58 primers, dos quais dez foram selecionados para a validação através da reação em cadeia da polimerase. Dez genótipos de aveia foram avaliados quanto ao nível de polimorfismo. Foi verificado polimorfismo em 80% dos primers, sendo que, o restante apresentou bandas monomórficas. A alta diversidade gênica revelada pelos marcadores microssatélites neste estudo possivelmente reflete uma alta diversidade genética dentro do germoplasma de Avena sativa.

Modeling habitat suitability is beneficial for management and conservation of a species. Although data-rich models are commonly used, opinion-based models may be a beneficial alternative to estimate suitable habitat locations. Despite the increasing use of habitat models, few studies have linked habitat model covariates (i.e., land cover, weather, and normalized difference vegetation indexes (NDVI)) to demographic parameters. This study evaluates model performance and transferability of maximum entropy (MaxEnt) and expert opinion models for predicting American beaver (Castor canadensis) distribution in the southeastern US. I also investigated the relationship of environmental and habitat model covariates to beaver survival. The model’s predictive performance and transferability were evaluated using the area under the curve (AUC) index. Both model approaches performed well at predicting beaver presence. While MaxEnt had better performance, the expert models predicted greater areas as suitable for beaver. Beaver survival was estimated for northern Alabama and was found to be influenced by NDVI and weather covariates in this study.

The purpose was to evaluate the psychometric properties of an 8-item questionnaire instrument to support member checks in positivistic qualitative research. A sample of 1603 junior-level university nursing students (98.2% participation rate) a completed the questionnaire instrument which assessed how closely a written description of the lived experience of in-hospital training applied to their personal experience. The instrument had excellent psychometric properties, including high measurement reliability (α=0.94), strong concurrent validity (72.2%-77.4%), discriminant validity (p < 0.000001), a parametric score distribution with little kurtosis and no skew, and an average score (G score) was centered at midpoint of the scale (midpoint of 4 on a scale from 1 to 7). The experience match was at the level of “matches experience to high degree,” showing the transferability (generalizability) of the findings to the present sample. The instrument can be used to assess the credibility and transferability of findings from qualitative research, assist in finding negative cases, determine the degree of saturation and success of bracketing, and complement the constant comparative method. The instrument is recommended for general use in positivistic qualitative or naturalistic inquiry studies for any type of sample and any type of lived experience. This approach would magnify and empower the reach of the products of qualitative research.

This thesis describes the development and evaluation of real-time crash risk assessment models for four freeway corridors, US-101 NB (northbound) and SB (southbound) as well as I-880 NB and SB. Crash data for these freeway segments for the 16-month period from January 2010 through April 2011 are used to link historical crash occurrences with real-time traffic patterns observed through loop detector data. The analysis techniques adopted for this study are logistic regression and classification trees, which are one of the most common data mining tools. The crash risk assessment models are developed based on a binary classification approach (crash and non-crash outcomes), with traffic parameters measured at surrounding vehicle detection station (VDS) locations as the independent variables. The classification performance assessment methodology accounts for rarity of crashes compared to non-crash cases in the sample instead of the more common pre-specified threshold-based classification. Prior to development of the models, some of the data-related issues such as data cleaning and aggregation were addressed. Based on the modeling efforts, it was found that the turbulence in terms of speed variation is significantly associated with crash risk on the US-101 NB corridor. The models estimated with data from US-101 NB were evaluated based on their classification performance, not only on US-101 NB, but also on the other three freeways for transferability assessment. It was found that the predictive model derived from one freeway can be readily applied to other freeways, although the classification performance decreases. The models which transfer best to other roadways were found to be those that use the least number of VDSs–that is, using one upstream and downstream station rather than two or three. The classification accuracy of the models is discussed in terms of how the models can be used for real-time crash risk assessment, which may be helpful to authorities for freeway segments with newly installed traffic surveillance apparatuses, since the real-time crash risk assessment models from nearby freeways with existing infrastructure would be able to provide a reasonable estimate of crash risk. These models can also be applied for developing and testing variable speed limits (VSLs) and ramp metering strategies that proactively attempt to reduce crash risk. The robustness of the model output is assessed by location, time of day and day of week. The analysis shows that on some locations the models may require further learning due to higher than expected false positive (e.g., the I-680/I-280 interchange on US-101 NB) or false negative rates. The approach for post-processing the results from the model provides ideas to refine the model prior to or during the implementation.

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The Roanoke logperch (Percina rex) is a federally endangered large darter that occurs only within the Roanoke and Chowan drainages of Virginia. This dissertation examines multi-scale habitat use patterns by logperch in three river systems in Virginia, including comparisons among rivers and life stages. The first study in this dissertation compares microhabitat use patterns of logperch among the Roanoke, Pigg, and Nottoway rivers. My objectives are to: 1) compare available microhabitat and microhabitat use by logperch among these rivers; and 2) examine the transfer of habitat models among rivers. Habitat availability in the three rivers indicates that the Nottoway River is least impacted by human activity, while the Pigg River is most impacted. The Roanoke and Pigg rivers are found within the same region of Virginia and share many habitat characteristics. Logperch consistently use silt free, loosely embedded gravel in all rivers and can occupy a variety of depths and velocities to accommodate substrate requirements. Microhabitat models transfer better between the similar Pigg and Roanoke rivers. The second study in this dissertation compares micro- and meso-habitat use patterns by Roanoke logperch in the Roanoke and Nottoway rivers. My objectives are to: 1) compare micro- and meso-habitat use patterns of logperch in the Roanoke and Nottoway rivers; and 2) examine transfer of habitat models at both scales. An increase in scale from micro- to meso- habitat did not improve model transfer. Habitat selectivity and transfer was strongest at the microhabitat scale. Logperch appear to be microhabitat substrate specialists and mesohabitat generalists. The final study in this dissertation examines ontogenetic patterns of habitat use by Roanoke logperch in the Roanoke and Nottoway rivers. My goals are to: 1) examine habitat use by three age classes of logperch and 2) compare ontogenetic patterns of habitat use between the Roanoke and Nottoway rivers. In the Roanoke River, adult and subadult logperch primarily used run and riffle habitat, often over gravel substrate. Subadults were found in lower water velocities and more embedded microhabitats than adults. Young-of-year logperch were found in shallow, stagnant backwaters and secondary channels. In the Nottoway River, both adult and subadult logperch were found over sand and gravel in deep, low velocity pools and runs. Subadults were observed in slightly more silted, lower velocity habitat. Younger age classes of logperch appear to be more vulnerable to sedimentation caused by human activity. Evidence in this dissertation strongly indicates that logperch have strict substrate requirements and the distribution of habitat types and pathways of dispersal will be critical for completion of the logperch life cycle. A watershed-level conservation approach that addresses sediment loading and preserves ecological processes that provide ephemeral, seasonal, and persistent types of habitat required over logperch ontogeny will be most effective for management geared towards the recovery of this endangered species. / Ph. D.

With a new focus on flow regulation by the Tennessee Valley Authority (TVA) in reservoir tailwaters, it is now possible to recover many mussel species that once occurred in these reaches. Before flows can be modified to create habitat for freshwater mussels, suitable microhabitat conditions must be defined. In this study, I used multiple approaches to define suitable microhabitats for species in the free-flowing upper Clinch River, Virginia and Tennessee, where reproducing mussel populations persist. During summer low flows in 2003 and 2004, I measured flow and substrate conditions in over 1000 microhabitat patches (0.25 m² quadrat samples) across five river reaches. Flow characteristics and embeddedness were significantly different between microhabitats occupied and unoccupied by the most abundant species (MRPP, p < 0.05). Comparison of simple and multiple logistic regression models with Akaike's Information Criteria (AIC) demonstrated that increasing Fleisswasserstammtisch (FST) hemisphere number (a measure of shear stress), decreasing degree of embeddedness, and increasing mean column velocity best explained species occurrences in a microhabitat patch. Subtle differentiation in habitat use among species was observed; however, most species appeared to be microhabitat generalists. Species were grouped into three habitat guilds using corresponding canonical analysis and cluster analysis: fast-flow specialists (FFS), fast-flow generalists (FFG), and slow-flow tolerant (SFT). I used the same data set to develop and test transferability of Habitat Suitability Criteria (HSC) for three habitat guilds and seven species of adult freshwater mussels. Nonparametric tolerance limits were used to define the range of suitable and optimal habitat during summer low flows. Optimal habitat was defined as those ranges of FST hemisphere number, mean column velocity, and embeddedness occupied by the central 50% of independent observations for a species or guild, whereas suitable habitat was defined by those ranges occupied by the central 90% of observations. The transferability of criteria to other reaches of the Clinch River was assessed using one-sided Chi-square tests. Criteria developed for the fast-flow specialist (FFS) and fast-flow generalist (FFG) guilds, as well as most criteria for species in those guilds, transferred to destination reaches. In contrast, criteria developed for the slow-flow tolerant (SFT) guild and individual constituent species consistently failed to transfer. Criteria for FFS and FFG guilds and their constituent species should be incorporated into flow simulation models such as PHABSIM to gauge the effect of minimum flows on mussel habitat quality and quantity. These criteria could also be used to determine suitable sites for mussel translocations. However, my criteria require further testing in other rivers before they can be transferred beyond the Clinch River. Behavior and physiological responses to laboratory manipulations of flow velocity and substrate particle size were used to elucidate microhabitat preferences of Actinonaias pectorosa, Potamilus alatus, and Ptychobranchus subtentum. These species appeared less stressed in the fastest flow treatment, demonstrating significantly higher oxygen consumption and oxygen-to-nitrogen (O:N) ratios than in slower flow treatments. Only P. alatus demonstrated a preference for substrate particle size, and consistently selected finer particle sizes. Actinonaias pectorosa and P. subtentum demonstrated preference for fast-flow microhabitats by readily burrowing in those conditions, while abandoning slow-flow conditions. The lack of preference for substrate particle size demonstrated by A. pectorosa and P. subtentum supports conclusions of previous studies that substrate particle size is of little or secondary importance for explaining mussel microhabitat use. These results, along with previous studies in the Clinch River, demonstrate that the stable habitats of riffles and runs; characterized by fast flows during summer low flows, low percent bedrock, and low embeddedness, are the most suitable habitats for mussel assemblages. To create and maintain suitable habitat conditions in tailwaters, releases should maintain flow over riffles at a minimum depth of no less than 30 cm in riffles that provide higher shear stress conditions (FST number > 7) and velocities (> 0.70 m/s). Periodic releases that are sufficient to transport silt and sand, but not high enough to transport larger substrate should be adequate to maintain substrates with a low degree of embeddedness. Doing so would create suitable habitat for all mussels, from the most to least specialized. Additionally, HSC developed for FFS and FFG guilds can be used to determine suitable destination sites for translocations of species belonging to these guilds. / Master of Science

A number of significant challenges confront effective communication in partially distributed conceptual design teams (PDCDTs), mainly due to the ill-defined and open nature of conceptual design tasks and their associated solution spaces. In contrast to co-located team members who interact face-to-face, communication difficulties among PDCDTs can intensify as a result of the physical separation of team members and their heavy reliance on communication technologies to achieve desired outcomes. Despite advances in these technologies, the ability to convey contextual and paralinguistic cues is still more limited between distant partners in comparison to face-to-face interactions. Thus, team members often experience challenges in establishing and maintaining shared understanding. In addition, partially distributed teams are more vulnerable to in-group dynamics than fully distributed or fully co-located teams. There have been substantial theoretical advances in the field of computer-mediated communication (CMC) that seek to address these challenges. Although CMC theories are hypothetically convincing and generally accepted, actual empirical findings are to some extent either unconvincing or contradictory. Moreover, questions remain about whether CMC theories can hold up in the context of non-equivalent communication technologies. The proliferation of various communication devices (e.g., smart phones, tablets, laptops, and desktops)–not to mention the growing corporate use of fully immersive telepresence technologies–means that a variety of combinations of communication devices can be used. To date, however, the majority of CMC studies have focused on the use of equivalent communication technologies (e.g., laptop to laptop). Given these practical challenges and research gaps, the overall objective of this study was to investigate how to improve shared understanding in PDCDTs. The study encompassed four distinct research threads. Study 1 conceptualized shared understanding in PDCDTs. From Study 1, factors associated with shared understanding were identified, and an input-process-output (IPO) model of shared understanding was developed. Study 2 examined the intra- and inter-sub-group communication patterns among PDCDTs. From Study 2, three different analytical approaches for exploring communication patterns were used to elucidate valuable insights into how interactions within and across sub-groups change with design tasks, as well as how individual roles and interpersonal dynamics affect those interactions. Study 3 utilized the outcomes from Study 1 (IPO model of shared understanding) to develop and validate an instrument to measure shared understanding. Lastly, Study 4 examined how different combinations of non-equivalent communication technologies impacted shared understanding in PDCDTs by using the shared understanding instrument developed from Study 3. Specifically, four types of communication technology conditions were utilized: (1) telepresence to telepresence (two different sizes), (2) telepresence to laptops, (3) telepresence to mobile devices, and (4) laptops to mobile devices. The findings revealed significant impacts of communication technologies on co-located and distant shared understanding, as well as differences between co-located and distant shared understanding for each communication technology condition. In addition, the impacts of shared understanding on different communication technology user groups were identified. Based on these findings, a number of communication technology recommendations, as well as managerial intervention strategies to operate successful PDCDTs, were developed. / Ph. D.

Rigorous modeling of the spatial species distributions is critical in biogeography, conservation, resource management, and assessment of climate change. The goal of chapter 2 of this dissertation was to evaluate the potential of using historical samples to develop high-resolution species distribution models (SDMs) of stream fishes of the United States. I explored the spatial transferability and temporal transferability of stream–fish distribution models in chapter 3 and chapter 4 respectively. Chapter 2 showed that the discrimination power of SDMs for 76 non-game fish species depended on data quality, species' rarity, statistical modeling technique, and incorporation of spatial autocorrelation. The area under the Receiver-Operating-Characteristic curve (AUC) in the cross validation tended to be higher in the logistic regression and boosted regression trees (BRT) than the presence-only MaxEnt models. AUC in the cross validation was also higher for species with large geographic ranges and small local populations. Species prevalence affected discrimination power in the model training but not in the validation. In chapter 3, spatial transferability of SDMs was low for over 70% of the 21 species examined. Only 24% of logistic regression, 12% of BRT, and 16% of MaxEnt had AUC > 0.6 in the spatial transfers. Friedman's rank sum test showed that there was no significant difference in the performance of the three modeling techniques. Spatial transferability could be improved by using spatial logistic regression under Lasso regularization in the training of SDMs and by matching the range and location of predictor variables between training and transfer regions. In chapter 4, testing of temporal SDM transfer on independent samples resulted in discrimination power of the moderate to good range, with AUC > 0.6 for 80% of species in all three types of models. Most cool water species had good temporal transferability. However, biases and misspecified spread occurred frequently in the temporal model transfers. To reduce under- or over-estimation bias, I suggest rescaling the predicted probability of species presence to ordinal ranks. To mitigate inappropriate spread of predictions in the climate change scenarios, I recommended to use large training datasets with good coverage of environmental gradients, and fine-tune predictor variables with regularization and cross validation. / Ph. D.

Dans la pratique de la planification urbaine, la prévision de la demande de transport fait en général appel au modèle à quatre étapes (génération, distribution, répartition modale et affectation), malgré des avancées théoriques considérables dans le domaine. Cette persistance s’explique par une facilité relative de mise en oeuvre, liée notamment à la forme des données disponibles et susceptibles d’alimenter les modèles. Cependant, la nature statique de l’approche pose des interrogations quant à sa pertinence pour faire des prévisions de moyen-long terme. Cette thèse étudie, la validité de l’hypothèse de stabilité temporelle des trois premières étapes du modèle de prévision. Pour ce faire, en prenant l’agglomération lyonnaise comme terrain d’étude, nous avons codifié des réseaux routiers et de transports en commun à différentes dates (1985, 1995 et 2006). Cette donne, généralement indisponible, combinée aux enquêtes ménages déplacements correspondantes, nous permet de calibrer les trois premières étapes du modèle traditionnel et de tester leur capacité prédictive. Pour les modèles de génération, on note des prévisions acceptables à un horizon de 10 ans. À 20 ans, certaines évolutions dans les styles de vie se sont traduites par une baisse du nombre moyen de sorties pour le motif travail, que les modèles traditionnels ne permettent pas de prévoir complètement. Au niveau de la distribution, l’allongement des distances entre lieux de réalisation de certaines activités et le lieu de domicile peut être relativement bien reproduit par des modèles gravitaires avec des paramètres stables dans le temps. Au niveau de la répartition modale, les paramètres ne sont pas stables et les modèles estimés n’auraient pas permis de prévoir le regain de parts de marché des transports en commun observé ces dernières années. / In the practice of urban planning, travel demand forecasts are generally obtained by using the four-step model (generation, distribution, modal split and assignment), despite considerable theoretical advances in the field. This persistence can be explained by the relative ease of implementation of the four-step modelling sequence, which is related, in particular, to the kind of data available that could be used as an input in a model. However, the static nature of the approach raises questions as it pertains to its relevance in producing medium and long range forecasts. This thesis investigates the validity of the hypothesis of temporal stability of the parameters of the first three stages of the traditional forecasting sequence. To do this, taking the Lyon conurbation as our case study, we coded the road and transit networks at different points in time (1985, 1995 and 2006). We then combine this temporal data, which is generally unavailable, with the corresponding household travel surveys in order to calibrate the first three steps of the traditional model and test their predictive ability. For the generation models tested, we note acceptable performance for a 10-year forecast. For a 20-year forecast, some changes in lifestyles have resulted in a decrease in the average number of work trips that traditional models do not predict accurately. Regarding trip distribution, the increase in travel distances observed for certain purposes is reproduced fairly well by the gravity model. At the modal split level, the parameters are not stable and the estimated models would be unable to predict accurately the recent increase in the market share of public transport.