Pathway-Based Multi-Omics Data Integration for Breast Cancer Diagnosis and Prognosis.

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

Development of a temperature control system for spectroscopic measurements with rare-earth doped crystals

This thesis describes the development of a temperature control system for optical spectroscopy experiments with rare-earth doped samples. Low temperature emission spectra were afterwards recorded for a series for Eu3+ singly doped and Ce3+, Eu3+ codoped Y2SiO5 samples. The analysis and assignment of the different energy transitions is presented. The experimental setups used in this thesis involve the optics part, the electronic part and the cooling down system. For the optical measurements, two kinds of pumping laser were used: Dye laser (580 nm) and UV laser (370 nm). A suitable optics system was designed for the collection of fluorescence signals. Electronic circuits were on the other hand built to connect two thermal sensors within the cryostat used for the optical measurements. Two reference temperature sensors were set up so that they could be readout simultaneously by using a switch connected with a temperature monitor. A good control of the cooling down process and the final temperature reached by the samples under investigation is fundamental for spectroscopic investigations performed at cryogenic temperatures as the ones described here

A Survey of Document-Level Information Extraction

Document-level information extraction (IE) is a crucial task in natural language processing (NLP). This paper conducts a systematic review of recent document-level IE literature. In addition, we conduct a thorough error analysis with current state-of-the-art algorithms and identify their limitations as well as the remaining challenges for the task of document-level IE. According to our findings, labeling noises, entity coreference resolution, and lack of reasoning, severely affect the performance of document-level IE. The objective of this survey paper is to provide more insights and help NLP researchers to further enhance document-level IE performance

Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis

Comparison of logistic regression, SVM and random forest performance in the plasma training data set. Table S2. Pathway significance and relative log fold changes in our metabolomics data and TCGA breast cancer RNA-Seq data. Table S3. Detected metabolites and their differential test results among the two models. a All-stage diagnosis model. b Early-stage diagnosis model. Table S4. Single-variate logistic analysis of metabolites or pathways selected as features in the metabolite-based or pathway-based early-stage diagnosis model. Table S5. Comparison of pathway features in the full-size (101 input pathways) and half-size (51 input pathways) pathway-based early-stage diagnosis models. (DOCX 34 kb

One-Pot 3D Printing of Robust Multimaterial Devices

Polymer 3D printing is a broad set of manufacturing methods that permit the fabrication of complex architectures, and, as a result, numerous efforts focus on formulating processible chemistries that produce desirable material behavior in printed parts. However, current resin chemistries typically result in a single fixed set of properties once fully polymerized, a fact that poses significant engineering challenges to obtaining multimaterial devices. As an alternative to single-property materials, we introduce a ternary sequential reaction scheme that exhibits diverse multimaterial properties by profoundly altering the polymer microstructure from within a single resin composition. In this system, the photodosage during 3D printing sets both the shape and extent of conversion for each subsequent reaction. This different polymerization mechanisms of the subsequent stages yield disparate crosslink densities and viscoelastic properties. As a result, our materials possess Young's Moduli spanning over three orders of magnitude (400 kPa < E < 1.6 GPa) with smooth transitions between soft and stiff regions. We successfully pattern a 500x change in modulus in under a millimeter while the sequential assembly of our polymer networks ensures robust interfaces and enhances toughness by 10x compared to the single property materials. Most importantly, the final objects remain stable to UV and thermal aging, a key limitation to applications of previous multimaterial chemistries. We demonstrate the ability to 3D print intricate multimaterial architectures by fabricating a soft, wearable braille display.Comment: 54 pages including supplemental information, 5 main text figure