Path finding on a spherical self-organizing map using distance transformations

Spatialization methods create visualizations that allow users to analyze high-dimensional data in an intuitive manner and facilitates the extraction of meaningful information. Just as geographic maps are simpli ed representations of geographic spaces, these visualizations are esssentially maps of abstract data spaces that are created through dimensionality reduction. While we are familiar with geographic maps for path planning/ nding applications, research into using maps of high-dimensional spaces for such purposes has been largely ignored. However, literature has shown that it is possible to use these maps to track temporal and state changes within a high-dimensional space. A popular dimensionality reduction method that produces a mapping for these purposes is the Self-Organizing Map. By using its topology preserving capabilities with a colour-based visualization method known as the U-Matrix, state transitions can be visualized as trajectories on the resulting mapping. Through these trajectories, one can gather information on the transition path between two points in the original high-dimensional state space. This raises the interesting question of whether or not the Self-Organizing Map can be used to discover the transition path between two points in an n-dimensional space. In this thesis, we use a spherically structured Self-Organizing Map called the Geodesic Self-Organizing Map for dimensionality reduction and the creation of a topological mapping that approximates the n-dimensional space. We rst present an intuitive method for a user to navigate the surface of the Geodesic SOM. A new application of the distance transformation algorithm is then proposed to compute the path between two points on the surface of the SOM, which corresponds to two points in the data space. Discussions will then follow on how this application could be improved using some form of surface shape analysis. The new approach presented in this thesis would then be evaluated by analyzing the results of using the Geodesic SOM for manifold embedding and by carrying out data analyses using carbon dioxide emissions data

Total Body Skin Exam and Number Needed to Screen

Introduction/Background: Skin cancer screening could impact mortality and morbidity in US adults; however, the effectiveness of widespread screening remains unclear. Further research is necessary to determine what age groups, with what risk factors, might benefit from routine total body skin exams (TBSE) in the US. Objective: This study sought to determine, on average, the number of patients, per decade, needed to screen via TBSE to identify one person with skin cancer. Methods: A retrospective review of Jefferson Dermatology outpatient data in Epic was conducted. All patient charts from 1/1/2017 - 1/1/2018 were reviewed if they received a TBSE. The type of skin cancer diagnosed after each visual skin exam was documented and data on the results of the patient interview and biopsy were collected in RedCap and analyzed in SPSS. Results: 3153 patients received a TBSE. Skin cancer was identified in 180 people; 8 people were found to have melanoma. By decade, the number needed to screen to identify 1 person with skin cancer was as follows: 20s: 331, 30s: 64, 40s: 60, 50s: 22, 60s: 12, 70s: 10, 80s: 6, 90s: 5. By decade, the number needed to screen to identify 1 person with melanoma was as follows: 20s: 331, 30s: Undefined, 40s: Undefined, 50s: 559, 60s: 153, 70s: 452, 80s: undefined, 90s: undefined. Conclusion: As patient age increases, less people need to be screened to detect skin cancer. It may be beneficial for Americans over 50 to obtain routine TBSEs. This data can contribute to the growing body of evidence needed for the USPSTF to provide skin cancer screening guidelines

Path finding on a spherical SOM using the distance transform and floodplain analysis

Data visualization has become an important tool for analyzing very complex data. In particular, spatial visualization enables users to view data in a intuitive manner. It has typically been used to externalize clusters and their relationships which exist in highly complex multidimensional data. We envisage that not only cluster formation and relationships but also other types of information, such as temporal changes of datum, can be extracted through the spatialization. In this paper, we investigate an application of trajectory/path analysis carried out using a Self-Organizing Map as a spatialization method. We propose an application of distance transformations to the Geodesic Self-Organizing Map. This new approach allows a user to visually inspect the trajectory of multidimensional knowledge pieces on a two-dimensional space. The trajectories discovered through this approach are essentially the shortest paths between two points on the Self-Organizing Map. However, those paths might go outside of the input dataspace due to the connectivity of neurons imposed by the grid structure. We also present a method to find the shortest path, which falls within the input dataspace using simple floodplain analysis

Impact of Human Immunodeficiency Virus in the Pathogenesis and Outcome of Patients with Glioblastoma Multiforme.

BackgroundImprovement in antiviral therapies have been accompanied by an increased frequency of non-Acquired Immune Deficiency Syndrome (AIDS) defining malignancies, such as glioblastoma multiforme. Here, we investigated all reported cases of human immunodeficiency virus (HIV)-positive patients with glioblastoma and evaluated their clinical outcomes. A comprehensive review of the molecular pathogenetic mechanisms underlying glioblastoma development in the setting of HIV/AIDS is provided.MethodsWe performed a PubMed search using keywords "HIV glioma" AND "glioblastoma," and "AIDS glioma" AND "glioblastoma." Case reports and series describing HIV-positive patients with glioblastoma (histologically-proven World Health Organization grade IV astrocytoma) and reporting on HAART treatment status, clinical follow-up, and overall survival (OS), were included for the purposes of quantitative synthesis. Patients without clinical follow-up data or OS were excluded. Remaining articles were assessed for data extraction eligibility.ResultsA total of 17 patients met our inclusion criteria. Of these patients, 14 (82.4%) were male and 3 (17.6%) were female, with a mean age of 39.5±9.2 years (range 19-60 years). Average CD4 count at diagnosis of glioblastoma was 358.9±193.4 cells/mm3. Tumor progression rather than AIDS-associated complications dictated patient survival. There was a trend towards increased median survival with HAART treatment (12.0 vs 7.5 months, p=0.10).ConclusionOur data suggests that HAART is associated with improved survival in patients with HIV-associated glioblastoma, although the precise mechanisms underlying this improvement remain unclear

A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia.

The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in regulating multiple biological processes in plants. However, there are few reports about the function of bHLHs in flower senescence. In this study, a bHLH TF, PhFBH4, was found to be dramatically upregulated during flower senescence. Transcription of PhFBH4 is induced by plant hormones and abiotic stress treatments. Silencing of PhFBH4 using virus-induced gene silencing or an antisense approach extended flower longevity, while transgenic petunia flowers with an overexpression construct showed a reduction in flower lifespan. Abundance of transcripts of senescence-related genes (SAG12, SAG29) was significantly changed in petunia PhFBH4 transgenic flowers. Furthermore, silencing or overexpression of PhFBH4 reduced or increased, respectively, transcript abundances of important ethylene biosynthesis-related genes, ACS1 and ACO1, thereby influencing ethylene production. An electrophoretic mobility shift assay showed that the PhFBH4 protein physically interacted with the G-box cis-element in the promoter of ACS1, suggesting that ACS1 was a direct target of the PhFBH4 protein. In addition, ectopic expression of this gene altered plant development including plant height, internode length, and size of leaves and flowers, accompanied by alteration of transcript abundance of the gibberellin biosynthesis-related gene GA2OX3. Our results indicate that PhFBH4 plays an important role in regulating plant growth and development through modulating the ethylene biosynthesis pathway