Slow Dynamics in Glasses

Minimalist theories of complex systems are broadly of two kinds: mean-field and axiomatic. So far all theories of complex properties absent from simple systems and intrinsic to glasses are axiomatic. Stretched Exponential Relaxation (SER) is the prototypical complex temporal property of glasses, discovered by Kohlrausch 150 years ago, and now observed almost universally in microscopically homogeneous, complex non-equilibrium materials, including luminescent electronic (Coulomb) glasses. Critical comparison of alternative axiomatic theories with both numerical simulations and experiments strongly favors dynamical trap models over static percolative or energy landscape models. PACS: 61.20.Lc; 67.40.F

Explaining Education to Engineers: Feedback Control Theory as a Metaphor

One of the barriers for engaging engineering faculty in the scholarship of learning and teaching is thechallenge of learning a new vocabulary. Becoming fluent in engineering education requires the acquisitionof new concepts and ideas that are often expressed in unfamiliar terms. Feedback control is a technical fieldcommon to a range of engineering disciplines that can be used as a model to help bridge the conceptual gapbetween traditional engineering and engineering education. Many of the key elements of engineering education can be represented by the elements of a feedback control system, with their behaviour in a learning environment paralleling their behaviour in a process control context. The feedback control model can be used to explain: the importance of timely feedback to students, the significance of assessment and evaluation in the learning process, the impact of learning styles upon learning outcomes, and the need for student-centered teaching approaches. While both fields have complexities that cannot be captured by simple models, the basic ideas can be explained simply. Feedback control metaphors make the basics accessible to a wider audience of engineering faculty

Special session: utopia university - building a roadmap for educating the next millennium's engineers

Ailing multibillionaire P. Oscar Utopia wishes to endow a university in honor of Rose B. Utopia, his beloved wife and long-practicing engineer. He will be at FIE to draw upon the expertise of our community to design the master plan for a university of the next millennium, unburdened by the assumptions of the present and the past. Conference attendees who subscribe to Utopia's vision are encouraged to participate in this workshop, challenge the assumptions inherent to the current practice, and brainstorm a plan for educating the engineer of 3030. During this session, we will identify and challenge assumptions that are inherent to the current practice of how we educate engineers. Participants will engage in a series of rapid planning sessions based on the “what if” scenario of being able to establish a new engineering schoolunfettered by standard constraints of money, facilities,or current educational practice

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Part-per-million gas detection from long-baseline THz spectroscopy

We report a long-baseline THz time domain spectrometer based on a White cell design capable of detecting gas species in the low part-per-million range in near real time. Coherent transients from methyl chloride vapor are observed directly in the time domain using a 5.0 m path length at pressures down to 1 Pa. Both phase sensitive (lock-in) detection and direct signal averaging using a rapid-scanning delay line are used for data acquisition.Peer reviewedElectrical and Computer Engineerin

Measurement and noise characterization of optically induced index changes using THz interferometry

A Michelson interferometer designed for broadband single-cycle THz pulses is used to characterize optically induced index changes in semiconductors which result in submicron changes in optical path length. The interferometric measurements are compared both to standard THz time-domain spectroscopy (THz-TDS) and differential THz-TDS based on modulation of the sample. By analyzing noise contributions in THz spectroscopy systems, it is shown that the destructive interference achieved in THz interferometry reduces both some sources of random errors as well as errors due to system drift.Peer reviewedElectrical and Computer Engineerin