Disentangling the impact of seroconversion age and set-point viral load on ART-free HIV survival

Thesis (Master's)--University of Washington, 2016-06

Development and Application of Improvements to the Tile-based Fisher Ratio Method and Fundamental Instrument Considerations for Non-targeted Analysis using Two-dimensional Gas Chromatography

Thesis (Ph.D.)--University of Washington, 2016-06

Discovering user access pattern based on probabilistic latent factor model

There has been an increased demand for characterizing user access patterns using web mining techniques since the informative knowledge extracted from web server log files can not only offer benefits for web site structure improvement but also for better understanding of user navigational behavior. In this paper, we present a web usage mining method, which utilize web user usage and page linkage information to capture user access pattern based on Probabilistic Latent Semantic Analysis (PLSA) model. A specific probabilistic model analysis algorithm, EM algorithm, is applied to the integrated usage data to infer the latent semantic factors as well as generate user session clusters for revealing user access patterns. Experiments have been conducted on real world data set to validate the effectiveness of the proposed approach. The results have shown that the presented method is capable of characterizing the latent semantic factors and generating user profile in terms of weighted page vectors, which may reflect the common access interest exhibited by users among same session cluster.

A semantic web environment for component model

Component-based development (CBD) has become an important emerging topic in the software engineering field. It promises long-sought-after benefits such as increased software reuse, reduced development time to market and, hence, reduced software production cost. Despite the huge potential, the lack of reasoning support and development environment of component modeling and verification may hinder its development. Methods and tools that can support component model analysis are highly appreciated by industry. Such a tool support should be fully automated as well as efficient. At the same time, the reasoning tool should scale up well as it may need to handle hundreds or even thousands of components that a modern software system may have. Furthermore, a distributed environment that can effectively manage and compose components is also desirable. In this paper, we present an approach to the modeling and verification of a newly proposed component model using Semantic Web languages and their reasoning tools. We use the Web Ontology Language and the Semantic Web Rule Language to precisely capture the inter-relationships and constraints among the entities in a component model. Semantic Web reasoning tools are deployed to perform automated analysis support of the component models. Moreover, we also proposed a service-oriented architecture (SOA)-based semantic web environment for CBD. The adoption of Semantic Web services and SOA make our component environment more reusable, scalable, dynamic and adaptive.

What makes online grocers work? A case study analysis of factors contributing to online grocery store profitability

This research examined the factors contributing to the performance of online grocers prior to, and following, the 2000 dot.com collapse. The primary goals were to assess the relationship between a company’s business model(s) and its performance in the online grocery channel and to determine if there were other company and/or market related factors that could account for company performance. ^ To assess the primary goals, a case based theory building process was utilized. A three-way cross-case analysis comprising Peapod, GroceryWorks, and Tesco examined the common profit components, the structural category (e.g., pure-play, partnership, and hybrid) profit components, and the idiosyncratic profit components related to each specific company. ^ Based on the analysis, it was determined that online grocery store business models could be represented at three distinct, but hierarchically, related levels. The first level was termed the core model and represented the basic profit structure that all online grocers needed in order to conduct operations. The next model level was termed the structural model and represented the profit structure associated with the specific business model configuration (i.e., pure-play, partnership, hybrid). The last model level was termed the augmented model and represented the company’s business model when idiosyncratic profit components were included. In relation to the five company related factors, scalability, rate of expansion, and the automation level were potential candidates for helping to explain online grocer performance. In addition, all the market structure related factors were deemed possible candidates for helping to explain online grocer performance. ^ The study concluded by positing an alternative hypothesis concerning the performance of online grocers. Prior to this study, the prevailing wisdom was that the business models were the primary cause of online grocer performance. However, based on the core model analysis, it was hypothesized that the customer relationship activities (i.e., advertising, promotions, and loyalty program tie-ins) were the real drivers of online grocer performance. ^

What Makes Online Grocers Work? A Case Study Analysis of Factors Contributing to Online Grocery Store Profitability

This research examined the factors contributing to the performance of online grocers prior to, and following, the 2000 dot.com collapse. The primary goals were to assess the relationship between a company’s business model(s) and its performance in the online grocery channel and to determine if there were other company and/or market related factors that could account for company performance. To assess the primary goals, a case based theory building process was utilized. A three-way cross-case analysis comprising Peapod, GroceryWorks, and Tesco examined the common profit components, the structural category (e.g., pure-play, partnership, and hybrid) profit components, and the idiosyncratic profit components related to each specific company. Based on the analysis, it was determined that online grocery store business models could be represented at three distinct, but hierarchically, related levels. The first level was termed the core model and represented the basic profit structure that all online grocers needed in order to conduct operations. The next model level was termed the structural model and represented the profit structure associated with the specific business model configuration (i.e., pure-play, partnership, hybrid). The last model level was termed the augmented model and represented the company’s business model when idiosyncratic profit components were included. In relation to the five company related factors, scalability, rate of expansion, and the automation level were potential candidates for helping to explain online grocer performance. In addition, all the market structure related factors were deemed possible candidates for helping to explain online grocer performance. The study concluded by positing an alternative hypothesis concerning the performance of online grocers. Prior to this study, the prevailing wisdom was that the business models were the primary cause of online grocer performance. However, based on the core model analysis, it was hypothesized that the customer relationship activities (i.e., advertising, promotions, and loyalty program tie-ins) were the real drivers of online grocer performance.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

Cd8+ Tumour-infiltrating Lymphocytes And Cox2 Expression May Predict Relapse In Differentiated Thyroid Cancer.

There is an increasing rate of papillary thyroid carcinomas that may never progress to cause symptoms or death. Predicting outcome and determining tumour aggressiveness could help diminish the number of patients submitted to aggressive treatments. We aimed to evaluate whether markers of the immune system response and of tumour-associated inflammation could predict outcome of differentiated thyroid cancer (DTC) patients. Retrospective cohort study. We studied 399 consecutive patients, including 325 papillary and 74 follicular thyroid carcinomas. Immune cell markers were evaluated using immunohistochemistry, including tumour-associated macrophages (CD68) and subsets of tumour-infiltrating lymphocytes (TIL), such as CD3, CD4, CD8, CD16, CD20, CD45RO, GRANZYME B, CD69 and CD25. We also investigated the expression of cyclooxygenase 2 (COX2) in tumour cells and the presence of concurrent lymphocytic infiltration characterizing chronic thyroiditis. Concurrent lymphocytic infiltration characterizing chronic thyroiditis was observed in 29% of the cases. Among all the immunological parameters evaluated, only the enrichment of CD8+ lymphocytes (P = 0·001) and expression of COX2 (P =0·01) were associated with recurrence. A multivariate model analysis identified CD8+ TIL/COX2 as independent risk factor for recurrence. A multivariate analysis using Cox's proportional-hazards model adjusted for the presence of concurrent chronic thyroiditis demonstrated that the presence of concurrent chronic thyroiditis had no effect on prognostic prediction mediated by CD8+ TIL and COX2. In conclusion, we suggest the use of a relatively simple pathology tool to help select cases that may benefit of a more aggressive approach sparing the majority of patients from unnecessary procedures.

Comparação entre o dano muscular de flexores do cotovelo e extensores do joelho em idosos= : Muscle damage comparison between elbow flexors and knee extensors in older adults

Universidade Estadual de Campinas . Faculdade de Educação Física

Determination of Threshold Dose of Photodynamic Therapy to Measure Superficial Necrosis

Background Data: Photodynamic therapy (PDT) involves the photoinduction of cytotoxicity using a photosensitizer agent, a light source of the proper wavelength, and the presence of molecular oxygen. A model for tissue response to PDT based on the photodynamic threshold dose (Dth) has been widely used. In this model cells exposed to doses below Dth survive while at doses above the Dth necrosis takes place. Objective: This study evaluated the light Dth values by using two different methods of determination. One model concerns the depth of necrosis and the other the width of superficial necrosis. Materials and Methods: Using normal rat liver we investigated the depth and width of necrosis induced by PDT when a laser with a gaussian intensity profile is used. Different light doses, photosensitizers (Photogem, Photofrin, Photosan, Foscan, Photodithazine, and Radachlorin), and concentrations were employed. Each experiment was performed on five animals and the average and standard deviations were calculated. Results: A simple depth and width of necrosis model analysis allows us to determine the threshold dose by measuring both depth and surface data. Comparison shows that both measurements provide the same value within the degree of experimental error. Conclusion: This work demonstrates that by knowing the extent of the superficial necrotic area of a target tissue irradiated by a gaussian light beam, it is possible to estimate the threshold dose. This technique may find application where the determination of Dth must be done without cutting the tissue.

Individual-level diet variation in four species of Brazilian frogs

Many natural populations exploiting a wide range of resources are actually composed of relatively specialized individuals. This interindividual variation is thought to be a consequence of the invasion of `empty` niches in depauperate communities, generally in temperate regions. If individual niches are constrained by functional trade-offs, the expansion of the population niche is only achieved by an increase in interindividual variation, consistent with the `niche variation hypothesis`. According to this hypothesis, we should not expect interindividual variation in species belonging to highly diverse, packed communities. In the present study, we measured the degree of interindividual diet variation in four species of frogs of the highly diverse Brazilian Cerrado, using both gut contents and delta(13)C stable isotopes. We found evidence of significant diet variation in the four species, indicating that this phenomenon is not restricted to depauperate communities in temperate regions. The lack of correlations between the frogs` morphology and diet indicate that trade-offs do not depend on the morphological characters measured here and are probably not biomechanical. The nature of the trade-offs remains unknown, but are likely to be cognitive or physiological. Finally, we found a positive correlation between the population niche width and the degree of diet variation, but a null model showed that this correlation can be generated by individuals sampling randomly from a common set of resources. Therefore, albeit consistent with, our results cannot be taken as evidence in favour of the niche variation hypothesis.

Effect of eccentric contraction velocity on muscle damage in repeated bouts of elbow flexor exercise

Eccentric exercise induces muscle damage, but controversy exists concerning the effect of contraction velocity on the magnitude of muscle damage, and little is known about the effect of contraction velocity on the repeated-bout effect. This study examined slow (60 degrees.s(-1)) and fast (180 degrees.s(-1)) velocity eccentric exercises for changes in indirect markers of muscle damage following 3 exercise bouts that were performed every 2 weeks. Fifteen young men were divided into 2 groups based on the velocity of eccentric exercise: 7 in the Ecc60 (60 degrees.s(-1)) group, and 8 in the Ecc180 (180 degrees.s(-1)) group. The exercise consisted of 30 maximal eccentric contractions of the elbow flexors at each velocity, in which the elbow joint was forcibly extended from 60 degrees to 180 degrees (full extension) on an isokinetic dynamometer. Changes in maximal voluntary isometric contraction strength, range of motion, muscle soreness, and plasma creatine kinase activity before and for 4 days after the exercise were compared in the 2 groups using a mixed-model analysis (group x bout x time). No significant differences between groups were evident for changes in any variables following exercise bouts; however, the changes were significantly smaller (p < 0.05) after the second and third bouts than after the first bout. These results indicate that the contraction velocity does not influence muscle damage or the repeated-bout effect.

Mechanical properties of Y-TPZ ceramics obtained by liquid phase sintering using bioglass as additive

Yttria stabilized tetragonal zirconia (Y-TZP) ceramics were sintered by liquid phase sintering at low temperatures using bioglass as sintering additive. ZrO2-bioglass ceramics were prepared by mixing a ZrO2 stabilized with 3 Mol%Y2O3 and different amounts of bioglass based on 3CaO center dot P2O5-MgO-SiO2 system. Mixtures were compacted by uniaxial cold pressing and sintered in air, at 1200 and 1300 degrees C for 120 min. The influence of the bioglass content on the densification, tetragonal phase stability, bending strength, hardness and fracture toughness was investigated. The ceramics sintered at 1300 degrees C and prepared by addition of 3% of bioglass, exhibited the highest strength of 435 MPa, hardness of 1170 HV and fracture toughness of 6.3 MPa m(1/2). These results are related to the low monoclinic phase content, high relative density and the presence of the thermal residual stress generated between the ZrO2-matrix and bioglass grain boundary, contributing to the activation of the toughening mechanisms. (c) 2007 Elsevier B.V. All rights reserved.

Effect of bioglass additions on the sintering of Y-TZP bioceramics

The objective of this work was to evaluate the influence of bioglass additions on the sintering and mechanical properties of yttria-stabilized zirconia ceramics, Y-TZP Samples containing different bioglass additions, varying between 0 and 30 wt.%, were cold uniaxial pressed at 80 MPa and sintered in air at 1200 degrees C or 1300 degrees C for 120 min. Sintered samples were characterized by X-ray Diffractometry and Scanning Electron Microscopy. Hardness and fracture toughness were determined using Vickers indentation method. As a preliminary biological evaluation, in vitro cytotoxicity tests by Neutral Red Uptake method (using mouse connective tissue cells, NCTC clone L929 from ATCC bank) were realized to determine the cytotoxicity level of ZrO(2)-bioglass ceramics. The increasing of bioglass amount leads to the decreasing of relative density due to martensitic (tetragonal-monoclinic) transformation during cooling of the sintered samples. Y-TZP samples sintered at 1300 degrees C containing 5 wt.% of bioglass presented the best results. with high relative density, hardness and fracture toughness of 11.3 GPa and 6.1 MPa m(1/2), respectively. Furthermore, the un-cytotoxic behavior was observed in all sintering conditions and bioglass amounts used in this study. (C) 2009 Elsevier B.V. All rights reserved.

Toughened ZrO2 ceramics sintered with a La2O3-rich glass as additive

In this study, the influence of the glass addition and sintering parameters on the densification and mechanical properties of tetragonal zirconia polycrystals (3Y-TZP) ceramics were evaluated. High-purity tetragonal ZrO2 powder and La2O3-rich glass were used as starting powders. Two compositions based on ZrO2 and containing 5wt.% and 10wt.% of La2O3-rich glass were studied in this work. The starting powders were mixed/milled by planetary milling, dried at 90 degrees C for 24 h, sieved through a 60 mesh screen and uniaxially cold pressed under 80 MPa. The samples were sintered in air at 1200 degrees C, 1300 degrees C, 1400 degrees C for 60 min and at 1450 degrees C for 120 min, with heating and cooling rates of 10 degrees C/min. Sintered samples were characterized by relative density, X-ray diffraction (XRD) and scanningelectron microscopy (SEM). Hardness and fracture toughness were obtained by Vickers indentation method. Dense sintered samples were obtained for all conditions. Furthermore, only tetragonal-ZrO2 was identified as crystalline phase in sintered samples, independently of the conditions studied. Samples sintered at 1300 degrees C for 60 min presented the optimal mechanical properties with hardness and fracture toughness values near to 12 GPa and 8.5 MPa m(1/2) respectively. (c) 2007 Elsevier B.V, All rights reserved.