The Characterization Of The Infrasonic Noise Field And Its Effects On Least Squares Estimation

Thesis (Ph.D.) University of Alaska Fairbanks, 2007Localization of the source of an acoustic wave propagating through the atmosphere is not a new problem. Location methods date back to World War I, when sound location was used to determine enemy artillery positions. Since the drafting of the Comprehensive Nuclear-Test-Ban Treaty in 1996 there has been increased interest in the accurate location of distant sources using infrasound. A standard method of acoustic source location is triangulation of the source from multi-array back azimuth estimates. For waves traveling long distances through the atmosphere, the most appropriate method of estimating the back azimuth is the least squares estimate (LSE). Under the assumption of an acoustic signal corrupted with additive Gaussian, white, uncorrelated noise the LSE is theoretically the minimum variance, unbiased estimate of the slowness vector. The infrasonic noise field present at most arrays is known to violate the assumption of white, uncorrelated noise. The following work characterizes the noise field at two infrasound arrays operated by the University of Alaska Fairbanks, The power distribution and coherence of the noise fields was determined from atmospheric pressure measurements collected from 2003-2006. The estimated power distribution and coherence of the noise field were not the white, uncorrelated noise field assumed in the analytic derivation of the LSE of the slowness vector. The performance of the LSE of azimuth and trace velocity with the empirically derived noise field was numerically compared to its performance under the standard noise assumptions. The effect of violating the correlation assumption was also investigated. The inclusion of clutter in the noise field introduced a dependence to the performance of the LSE on the relative signal amplitude. If the signal-to-clutter ratio was above 10 dB, the parameter estimates made with the correlated noise field were comparable to the estimates made with uncorrelated noise. From the results of these numerical studies, it was determined that the assumption of Gaussian, white, uncorrelated noise had little effect on the performance of the LSE at signal-to-noise ratios greater than 10 dB, but tended to over estimate the performance of the LSE at lower signal-to-noise ratios

A hall plate based instrument to measure the snapback in the Large Hadron Collider superconducting dipole magnets

The decay and snapback of the magnetic field multipoles in superconducting particle accelerators like the Large Hadron Collider (LHC) could result in a significant particle beam loss unless adequately compensated. Whilst standard instrumentation used to measure the field quality of the superconducting magnets is good enough to measure the harmonic decay, it is not fast enough to measure the snapback. Therefore, a state of the art instrument was recently developed at CERN to measure the most important harmonics with a high measurement frequency and hence improve the understanding of the snapback phenomenon. In this paper we describe the instrument's principle of operation, its mechanical arrangement, its compensation system and its digital acquisition system. We also compare the performance of two different techniques implemented to achieve the necessary measurement resolution of 6 orders of magnitude lower than the main superimposed dipole field.peer-reviewe

A pedagogical model for team-based, problem-focused interdisciplinary doctoral education

Interdisciplinarity is crucial for addressing the complex problems society faces. We present a model for educating doctoral students for careers involving interdisciplinary, team-based research to address problem-focused questions. The educational model is theoretically based and evaluated in light of the literature, faculty perspectives, and an assessment by students of educational successes and challenges they experienced. The educational model involves (a) the identification of integrated research questions combining team members' disciplines, (b) course work to review theoretical underpinnings of interdisciplinarity and to develop integrated research proposals to address the questions, (c) meetings and workshops to enhance team cohesiveness, (d) engagement with stakeholders, and (e) interdisciplinary team research that yields joint dissertation chapters and publications. The model achieved a high level of integration among students. This model addresses the widely acknowledged need to impart interdisciplinary research and team membership skills as part of graduate education. (Résumé d'auteur

Simulating the global distribution of nitrogen isotopes in the ocean

We present a new nitrogen isotope model incorporated into the three-dimensional ocean component of a global Earth system climate model designed for millennial timescale simulations. The model includes prognostic tracers for the two stable nitrogen isotopes, 14N and 15N, in the nitrate (NO3−), phytoplankton, zooplankton, and detritus variables of the marine ecosystem model. The isotope effects of algal NO3− uptake, nitrogen fixation, water column denitrification, and zooplankton excretion are considered as well as the removal of NO3− by sedimentary denitrification. A global database of δ15NO3− observations is compiled from previous studies and compared to the model results on a regional basis where sufficient observations exist. The model is able to qualitatively and quantitatively reproduce many of the observed patterns such as high subsurface values in water column denitrification zones and the meridional and vertical gradients in the Southern Ocean. The observed pronounced subsurface minimum in the Atlantic is underestimated by the model presumably owing to too little simulated nitrogen fixation there. Sensitivity experiments reveal that algal NO3− uptake, nitrogen fixation, and water column denitrification have the strongest effects on the simulated distribution of nitrogen isotopes, whereas the effect from zooplankton excretion is weaker. Both water column and sedimentary denitrification also have important indirect effects on the nitrogen isotope distribution by reducing the fixed nitrogen inventory, which creates an ecological niche for nitrogen fixers and, thus, stimulates additional N2 fixation in the model. Important model deficiencies are identified, and strategies for future improvement and possibilities for model application are outlined

Pine sawdust biochar as a potential amendment for establishing trees in Appalachian mine spoils

Early growth and survival of tree seedlings is often poor on reclaimed coal surface mines in Appalachia. Biochar produced in bioenergy generation has potential for use as an amendment to improve seedling performance. Mine soil was collected from a recently reclaimed coal surface mine in Wise County, Virginia and mixed with loblolly pine (Pinus taeda L.) sawdust biochar, simulating application rates of 2.3, 11.2 and 22.5 Mg ha-1. Unplanted leaching columns and 4 L tree planting pots were filled with these biochar-soil mixtures, plus controls of pure mine soil and pure biochar. For the tree planting pots, additional pots were created where the biochar was applied as a topdressing at the same application rates as in the mixtures. One-year-old seedlings of both American sycamore (Platanus occidentalis L.) and black locust (Robinia pseudoacacia L.) were planted. Unplanted leaching columns were leached with collected rainwater for six months to simulate weathering. Trees were grown for one growing season. Black locust had higher average above-ground dry woody biomass (24.4 g) than American sycamore (17.0 g), and also higher below-ground biomass (61.0 g compared to 30.2 g). The pure biochar produced greater average below-ground biomass (99.9 g) than the pure mine soil (46.9 g). All of the biochar treatments produced greater average above-ground woody biomass (19.1 g – 33.4 g) than the pure mine soil (10.9 g). After weathering, biochar provided less available soil phosphorus, calcium and iron than the mine soil itself while increasing soil carbon and organic matter. High (22.5 Mg ha-1) biochar applications increased soil volumetric water holding capacity to 18.6% compared to 13.4% for pure mine soil. Naturally-occurring herbaceous biomass in the pots was negatively correlated with above-ground woody biomass at r = -0.483. Topdressing and full incorporation of biochar were not significantly different in their effects on biomass. Results suggest that pine biochar either broadcast at 2.3 - 22.5 Mg ha‑1, or mixed in planting holes with backfill soil, will promote faster above-ground growth and larger root systems in seedlings in mine soils. Further studies should test these methods in the field over multiple years and further refine recommendations of the rate of biochar to use and how best to apply it. New systems are being developed in Appalachia to produce biofuels and biochar from local biomass and to recycle biochar into the land base to enhance future biomass productivity. Applying 4 L of biochar mixed with the backfill of newly-planted trees is the top recommended practice for tree performance

THE ROLE OF INTERDEPENDENCE IN THE MICRO-FOUNDATIONS OF ORGANIZATION DESIGN: TASK, GOAL, AND KNOWLEDGE INTERDEPENDENCE

Interdependence is a core concept in organization design, yet one that has remained consistently understudied. Current notions of interdependence remain rooted in seminal works, produced at a time when managers’ near-perfect understanding of the task at hand drove the organization design process. In this context, task interdependence was rightly assumed to be exogenously determined by characteristics of the work and the technology. We no longer live in that world, yet our view of interdependence has remained exceedingly task-centric and our treatment of interdependence overly deterministic. As organizations face increasingly unpredictable workstreams and workers co-design the organization alongside managers, our field requires a more comprehensive toolbox that incorporates aspects of agent-based interdependence. In this paper, we synthesize research in organization design, organizational behavior, and other related literatures to examine three types of interdependence that characterize organizations’ workflows: task, goal, and knowledge interdependence. We offer clear definitions for each construct, analyze how each arises endogenously in the design process, explore their interrelations, and pose questions to guide future research

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

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

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