Case Study in Modeling Accessibility for Online Instruction.

Ph.D. Thesis. University of Hawaiʻi at Mānoa 2017

The Ubiquitous Inflaton in String-Inspired Models

A string theory based inflationary model is developed where the inflaton interacts with a multitude of massive string level states causing dissipation of vacuum energy. Inflation terminates in a warm Universe without the need for reheating.Comment: In Press Physical Review Letters 1999, modified titl

Utility of TERT Promoter Mutations for Cutaneous Primary Melanoma Diagnosis

Telomerase reverse transcriptase (TERT) promoter mutations are commonly found in malignant melanomas but rare in melanocytic nevi. To assess its potential diagnostic utility for the distinction of melanoma from nevus, we determined the TERT promoter mutation status of 86 primary melanomas, 72 melanocytic nevi, and 40 diagnostically problematic melanocytic proliferations. Of the 86 melanomas, 67 (77.9%) were TERT-positive, defined as harboring a hotspot TERT promoter mutation at positions -124C>T, -124_125CC>TT, -138_139CC>TT, or -146C>T. Of the 72 nevi, only 1 (1.4%) was TERT-positive. Of the 40 diagnostically uncertain melanocytic proliferations, 2 (5.0%) were TERT-positive. TERT positivity as a test for melanoma versus nevus had an accuracy of 87.3% [95% confidence interval (CI), 81.1-92.1], a sensitivity of 77.9% (95% CI, 68.9-85.4), a specificity of 98.6% (95% CI, 95.8-100), a positive predictive value of 98.5% (95% CI, 95.6-100), and a negative predictive value of 78.9% (95% CI, 72.6-85.4). Our results indicate that hotspot TERT promoter mutation status may be a useful ancillary parameter for the diagnosis of melanoma. In particular, the high specificity of these mutations for melanoma indicates the presence of a TERT promoter mutation in a melanocytic neoplasm associated with diagnostic controversy, or uncertainty should increase concern for a melanoma

Identification of a Robust Methylation Classifier for Cutaneous Melanoma Diagnosis

Early diagnosis improves melanoma survival, yet the histopathological diagnosis of cutaneous primary melanoma can be challenging, even for expert dermatopathologists. Analysis of epigenetic alterations, such as DNA methylation, that occur in melanoma can aid in its early diagnosis. Using a genome-wide methylation screening, we assessed CpG methylation in a diverse set of 89 primary invasive melanomas, 73 nevi, and 41 melanocytic proliferations of uncertain malignant potential, classified based on interobserver review by dermatopathologists. Melanomas and nevi were split into training and validation sets. Predictive modeling in the training set using ElasticNet identified a 40-CpG classifier distinguishing 60 melanomas from 48 nevi. High diagnostic accuracy (area under the receiver operator characteristic curve = 0.996, sensitivity = 96.6%, and specificity = 100.0%)was independently confirmed in the validation set (29 melanomas, 25 nevi)and other published sample sets. The 40-CpG melanoma classifier included homeobox transcription factors and genes with roles in stem cell pluripotency or the nervous system. Application of the 40-CpG melanoma classifier to the diagnostically uncertain samples assigned melanoma or nevus status, potentially offering a diagnostic tool to assist dermatopathologists. In summary, the robust, accurate 40-CpG melanoma classifier offers a promising assay for improving primary melanoma diagnosis

Dynamics of Light Antiquarks in the Proton

We present a comprehensive analysis of the recent data from the E866 experiment at Fermilab on Drell-Yan production in pD and pp collisions, which indicates a non-trivial x-dependence for the asymmetry between u-bar and d-bar quark distributions in the proton. The relatively fast decrease of the asymmetry at large x suggests the important role played by the chiral structure of the nucleon, in particular the pi-N and pi-Delta components of the nucleon wave function. At small x the data require an additional non-chiral component, which may be attributed to the Pauli exclusion principle as first suggested by Field and Feynman.Comment: version to appear in Phys. Rev.

Decreased expression of the mitochondrial bcat protein correlates with improved patient survival in idh-wt gliomas

Background and research question: Gliomas represent 43% of all solid intracranial tumours, of which glioblastomas have the poorest prognosis. Recently, the human cytosolic branched-chain aminotransferase protein (hBCATc), which metabolises the branched-chain amino acids (BCAA), was identified as a biomarker and therapeutic target for glioblastomas carrying wild-type isocitrate dehydrogenase (IDH-WT) genes. However, the clinical utility of the mitochondrial isoform, hBCATm, which also metabolises BCAAs, was not determined nor its potential role in predicting patient survival.Methods: Glioblastomas, of grades II-IV, from 53 patients were graded by a neuropathologist, where the IDH and MGMT status were assessed. Tumours positive for hBCATm, hBCATc and BCKDC were characterised using immunohistochemistry and Western blot analysis using antibodies specific to these proteins.Results: Here, we report that in IDH-WT tumours, the expression of hBCATm is significantly increased (p=0.034) relative to IDH mutation gliomas, and significantly correlates with patient survival, on Kaplan-Meier analysis, where low hBCATm expression is a positive prognostic factor (p=0.003). Moreover, increased hBCATm expression in these glioblastomas correlated with tumour grade indicating their role as a predictive biomarker of glioma progression. Multiple banding was observed for the branched-chain α-keto acid dehydrogenase complex, which catalyses the committed step in BCAA metabolism, but a significant change in expression was absent (p=0.690). Conclusion: Until now, IDH-WT glioblastomas have a uniformly poor prognosis, however we demonstrate for the first time that relatively low hBCATm may select for a better performing subset within this group and may represent a therapeutic target in these hard to treat patients

Chems4EU: chemsex use and its impacts across four European countries in HIV-positive men who have sex with men attending HIV services

Introduction: Chemsex in a European context is the use of any of the following drugs to facilitate sex: crystal methamphetamine, mephedrone and gamma-hydroxybutyrate (GHB)/gamma-butyrolactone (GBL) and, to a lesser extent, cocaine and ketamine. This study describes the prevalence of self-reported recreational drug use and chemsex in HIV-positive men who have sex with men (MSM) accessing HIV services in four countries. It also examines the problematic impacts and harms of chemsex and access to chemsex-related services. Methods: This is a cross-sectional multi-centre questionnaire study of HIV-positive MSM accessing nine HIV services in the UK, Spain, Greece and Italy. Results: In all, 1589 HIV-positive MSM attending HIV services in four countries completed the questionnaire. The median age of participants was 38 years (interquartile range: 32–46 years) and 1525 (96.0%) were taking antiretroviral therapy (ART). In the previous 12 months, 709 (44.6%) had used recreational drugs, 382 (24.0%) reported chemsex and 104 (6.5%) reported injection of chemsex-associated drugs (‘slamsex’). Of the 382 engaging in chemsex, 155 (40.6%) reported unwanted side effects as a result of chemsex and 81 (21.2%) as a result of withdrawal from chemsex. The reported negative impacts from chemsex were on work (25.1%, 96), friends/family (24.3%, 93) and relationships (28.3%, 108). Fifty-seven (14.9%) accessed chemsex-related services in the past year, 38 of whom (67%) felt the service met their needs. Discussion: A quarter of participants self-reported chemsex in the past 12 months. There were high rates of harms from chemsex across all countries, including negative impacts on work, friends/family and relationships. Although a minority of those engaging in chemsex accessed support, most found this useful

Gellan Gum Fluid Gels for Topical Administration of Diclofenac

Diclofenac topical formulations are often preferred for drug administration to patients who experience serious GIT problems. Absorption of the drug through the skin, however, can be challenging due to the natural protective feature of the stratum corneum (SC). In this article, fluid gels prepared from gellan gum were explored as a topical drug delivery vehicle. Rheological analysis of the formulations showed that it was possible to produce a topical gel with a viscosity and the mechanical strength similar to that of the commercially available Voltaren® gel using 1 % w/w of a 50:50 low acyl/high acyl (LA/HA) gellan blend. Soft-tribology was used to assess the lubrication properties of gellan fluid gels. The lubrication of the gellan gum fluid gel formulations at high rubbing speeds was similar to the lubrication of the Voltaren® gel. The use of gellan gum dramatically increased skin permeation of diclofenac when compared with the commercially available formulation and could be controlled by changing the gellan gum concentration and/or sodium ion concentration in the formulation. This study highlights the potential use of fluid gels that can be easily tuned to have physical properties suitable for topical formulations with the added advantage of increasing drug permeation

Logical Characterization of Weighted Pebble Walking Automata

International audienceWeighted automata are a conservative quantitative extension of finite automata that enjoys applications, e.g., in language processing and speech recognition. Their expressive power, however, appears to be limited, especially when they are applied to more general structures than words, such as graphs. To address this drawback, weighted automata have recently been generalized to weighted pebble walking automata, which proved useful as a tool for the specification and evaluation of quantitative properties over words and nested words. In this paper, we establish the expressive power of weighted pebble walking automata in terms of transitive closure logic, lifting a similar result by Engelfriet and Hoogeboom from the Boolean case to a quantitative setting. This result applies to a general class of graphs that subsumes all the aforementioned classes

The Lost Library of Anne Conway

The philosopher Anne Conway (1631-1679) owned a large library, and her reading and book ownership shaped her intellectual life in distinctive ways. Until now, however, almost nothing has been known about the details of her reading or her book collection. Current scholarship assumes that her library, like that of her husband, the third Viscount Conway (c. 1623–1683), was lost or dispersed after her death. This article presents previously unrecognised evidence of Conway’s book ownership, and identifies, for the first time, the only books currently known to survive from her personal library. It traces their path to their current location in the Old Library of Jesus College, Cambridge, through the library of the soldier, book collector, and Cambridge Fellow Francis Sterling (c. 1652-1692). The article demonstrates that the newly identified books reveal previously unknown patterns of intellectual exchange amongst Conway’s family, and argues that they have significant implications for our understanding of her early intellectual development