Physical Sciences and Mathematics Commons^™

Identification Of Arabidopsis Gpat9 (At5g60620) As An Essential Gene Involved In Triacylglycerol Biosynthesis, Jay Shockey, Anushobha Regmi, Kimberly Cotton, Neil Adhikari, John Bowse, Philip D. Bates

Faculty Publications

The first step in the biosynthesis of nearly all plant membrane phospholipids and storage triacylglycerols is catalyzed by a glycerol-3-phosphate acyltransferase (GPAT). The requirement for an endoplasmic reticulum (ER)-localized GPAT for both of these critical metabolic pathways was recognized more than 60 years ago. However, identification of the gene(s) encoding this GPAT activity has remained elusive. Here, we present the results of a series of in vivo, in vitro, and in silico experiments in Arabidopsis (Arabidopsis thaliana) designed to assign this essential function to AtGPAT9. This gene has been highly conserved throughout evolution and is …

A Life Cycle Analysis Of Land Use In Us Pork Production, Greg Thoma, Marty Matlock, Ben Putman, Jasmina Burek

Food Systems

The goal of this study was to analyze land use in the production of US pork using Life Cycle Assessment (LCA). LCA is a comprehensive methodology for quantitatively analyzing potential environmental impacts associated with complex systems. Identification of processes contributing to high environmental impacts often highlights opportunities for gains in efficiency, which can increase the profitability and sustainability of US pork. The environmental impact category analyzed in this assessment was land use. After reviewing existing information regarding land use in agriculture and livestock production, analysis for US pork production was performed at two scales: cradle-to-grave and cradle-to-farm gate. The cradle-to-grave …

Entropyexplorer: An R Package For Computing And Comparing Differential Shannon Entropy, Kai Wang, Charles A. Philips, Arnold M. Saxton, Michael A. Langston

Department of Computer Science Faculty Publications

Background: Differential Shannon entropy (DSE) and differential coefficient of variation (DCV) are effective metrics for the study of gene expression data. They can serve to augment differential expression (DE), and be applied in numerous settings whenever one seeks to measure differences in variability rather than mere differences in magnitude. A general purpose, easily accessible tool for DSE and DCV would help make these two metrics available to data scientists. Automated p value computations would additionally be useful, and are often easier to interpret than raw test statistic values alone.

Results: EntropyExplorer is an R package for calculating DSE, DCV and …

Quantifying The Adaptive Cycle, David G. Angeler, Craig R. Allen, Ahjond S. Garmestani, Lance H. Gunderson, Olle Hjerne, Monika Winder

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term …

The Choice Of Prior Distribution For A Covariance Matrix In Multivariate Meta-Analysis: A Simulation Study, Sandra M. Hurtado Rua, Madhu Mazumdar, Robert L. Strawderman

Mathematics and Statistics Faculty Publications

Bayesian meta-analysis is an increasingly important component of clinical research, with multivariate meta-analysis a promising tool for studies with multiple endpoints. Model assumptions, including the choice of priors, are crucial aspects of multivariate Bayesian meta-analysis (MBMA) models. In a given model, two different prior distributions can lead to different inferences about a particular parameter. A simulation study was performed in which the impact of families of prior distributions for the covariance matrix of a multivariate normal random effects MBMA model was analyzed. Inferences about effect sizes were not particularly sensitive to prior choice, but the related covariance estimates were. A …

The Stationary Phase Method For Real Analytic Geometry, Domenico Napoletani, Daniele C. Struppa

Mathematics, Physics, and Computer Science Faculty Articles and Research

We prove that the existence of isolated solutions of systems of equations of analytical functions on compact real domains in R^p, is equivalent to the convergence of the phase of a suitable complex valued integral I(h) for h→∞. As an application, we then use this result to prove that the problem of establishing the irrationality of the value of an analytic function F(x) at a point x₀ can be rephrased in terms of a similar phase convergence.

Concurrent Kleene Algebra With Tests And Branching Automata, Peter Jipsen, M. Andrew Moshier

Mathematics, Physics, and Computer Science Faculty Articles and Research

We introduce concurrent Kleene algebra with tests (CKAT) as a combination of Kleene algebra with tests (KAT) of Kozen and Smith with concurrent Kleene algebras (CKA), introduced by Hoare, Möller, Struth and Wehrman. CKAT provides a relatively simple algebraic model for reasoning about semantics of concurrent programs. We generalize guarded strings to guarded series-parallel strings , or gsp-strings, to give a concrete language model for CKAT. Combining nondeterministic guarded automata of Kozen with branching automata of Lodaya and Weil one obtains a model for processing gsp-strings in parallel. To ensure that the model satisfies the weak exchange law (x‖y)(z‖w)≤(xz)‖(yw) of …

A Data Science Course For Undergraduates: Thinking With Data, Benjamin Baumer

Mathematics Sciences: Faculty Publications

Data science is an emerging interdisciplinary field that combines elements of mathematics, statistics, computer science, and knowledge in a particular application domain for the purpose of extracting meaningful information from the increasingly sophisticated array of data available in many settings. These data tend to be nontraditional, in the sense that they are often live, large, complex, and/or messy. A first course in statistics at the undergraduate level typically introduces students to a variety of techniques to analyze small, neat, and clean datasets. However, whether they pursue more formal training in statistics or not, many of these students will end up …

Kohn–Sham Exchange-Correlation Potentials From Second-Order Reduced Density Matrices, Rogelio Cuevas-Saavedra, Paul W. Ayers, Viktor N. Staroverov

Chemistry Publications

We describe a practical algorithm for constructing the Kohn–Sham exchange-correlation potential corresponding to a given second-order reduced density matrix. Unlike conventional Kohn–Sham inversion methods in which such potentials are extracted from ground-state electron densities, the proposed technique delivers unambiguous results in finite basis sets. The approach can also be used to separate approximately the exchange and correlation potentials for a many-electron system for which the reduced density matrix is known. The algorithm is implemented for configuration-interaction wave functions and its performance is illustrated with numerical examples.

Unblocking Temperatures Of Viscous Remanent Magnetism In Displaced Granitic Boulders, Icicle Creek Glacial Moraines (Washington, Usa), Juliet G. Crider, Danika M. Globokar, Russ F. Burmester, Bernard A. Housen

Geology Faculty Publications

Viscous remanent magnetization (VRM) may partially overprint original magnetization in rocks displaced by geomorphic events. An established theoretical relationship between the time and temperature of acquisition of VRM and the time and temperature of demagnetization suggests that laboratory demagnetization (unblocking) of VRM can be used to estimate the displacement age of rocks. We test this hypothesis at four nested glacial moraines in the Icicle Creek drainage of central Washington, the ages of which were previously determined by cosmogenic surface exposure dating. The moraines are composed primarily of granodiorite boulders, and magnetic remanence is carried dominantly by magnetite. Both the maximum …

Advanced Techniques For Computational And Information Sciences, William Guo, Chih-Cheng Hung, Paul Scheunders, Bor-Chen Kuo

Faculty and Research Publications

New techniques in computational and information sciences have played an important role in keeping advancing the so called knowledge economy. Advanced techniques have been introduced to or emerging in almost every field of the scientific world for hundreds of years, which has been accelerated since the late 1970s when the advancement in computers and digital technologies brought the world into the Information Era. In addition to the rapid development of computational intelligence and new data fusion techniques in the past thirty years [1–4], mobile and cloud computing, grid computing driven numeric computation models, big data intelligence, and other emerging technologies …

System-Wide Prediction Of General, All-Cause, Preventable Hospital Readmissions, Ken Musselman, Brandon Pope, Steve Witz, Zhiyi Tian, Lingsong Zhang, Linda Leon, Ann Davis

RCHE Publications

Existing studies of hospital readmissions typically focus on specific diagnoses, age groups, discharge dispositions, payer classes, or hospitals, and often use small samples. It is not clear how predictive models generated from such studies generalize across diseases, hospitals, or time periods. In this study, a logistic regression model of readmission risk within 30 days based on hospital administrative data was constructed and validated across hospitals and time periods. The hospitals included both general and specialty hospitals such as long-term care, women’s, and children’s hospitals. The administrative data included information on patient’s demographics, diagnoses, procedures, and discharge disposition. Derivation and validation …

Statistical Handling Of Medical Data - An Ethical Perspective, Ajay Kumar Bansal Dr

COBRA Preprint Series

Medical Science is a delicate subject and the clinical data generated from the medical trials must be reliable and of good quality. Not only the quality of generated data is important, but the management is also crucial and is to be handled very carefully. In this paper, the ethical aspect of statistical handling of such data is discussed.

Every profession has some set of norms to follow to achieve its objectives. These norms are called professional ethics which shows the essence of human behaviour. Same way, the field of medical research is expected to follow ethical norms, to obtain reliable …

Mapping Gravitational-Wave Backgrounds Of Arbitrary Polarisation Using Pulsar Timing Arrays, Jonathan Gair, Joseph D. Romano, Stephen R. Taylor

Physics and Astronomy Faculty Publications and Presentations

We extend our previous work on mapping gravitational-wave backgrounds using techniques borrowed from the analysis of cosmic microwave background data to backgrounds which have non-general-relativity (non-GR) polarisations. Our analysis and results are presented in the context of pulsar timing array observations, but the overarching methods are general, and can be easily applied to LIGO or eLISA observations using appropriately modified response functions. Analytic expressions for the pulsar timing response to gravitational waves with non-GR polarisation are given for each mode of a spin-weighted spherical-harmonic decomposition of the background, which permit the signal to be mapped across the sky to any …

Consequences Of Shifts In Abundance And Distribution Of American Chestnut For Restoration Of A Foundation Forest Tree, Harmony J. Dalgleish, Charles Dana Nelson, John A. Scrivani, Douglass F. Jacobs

Forestry and Natural Resources Faculty Publications

Restoration of foundation species, such as the American chestnut (Castanea dentata) that was devastated by an introduced fungus, can restore ecosystem function. Understanding both the current distribution as well as biogeographic patterns is important for restoration planning. We used United States Department of Agriculture Forest Service Forest Inventory and Analysis data to quantify the current density and distribution of C. dentata. We then review the literature concerning biogeographic patterns in C. dentata. Currently, 431 ± 30.2 million stems remain. The vast majority (360 ± 22 million) are sprouts < 2.5 cm dbh. Although this number is approximately 10% of the estimated pre-blight population, blight has caused a major shift in the size structure. The current-day population has a larger range, particularly west and north, likely due to human translocation. While climate change could facilitate northward expansion, limited seed reproduction makes this unlikely without assisted migration. Previous research demonstrates that the current, smaller population contains slightly higher genetic diversity than expected, although little information exists on biogeographic patterns in the genetics of adaptive traits. Our research provides a baseline characterization of the contemporary population of C. dentata, to enable monitoring stem densities …

Semi-Parametric Estimation And Inference For The Mean Outcome Of The Single Time-Point Intervention In A Causally Connected Population, Oleg Sofrygin, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

We study the framework for semi-parametric estimation and statistical inference for the sample average treatment-specific mean effects in observational settings where data are collected on a single network of connected units (e.g., in the presence of interference or spillover). Despite recent advances, many of the current statistical methods rely on estimation techniques that assume a particular parametric model for the outcome, even though some of the most important statistical assumptions required by these models are most likely violated in the observational network settings, often resulting in invalid and anti-conservative statistical inference. In this manuscript, we rely on the recent methodological …

Long-Term Landscape Changes In A Subalpine Spruce-Fir Forest In Central Utah, Usa, Jesse L. Morris, R. Justin Derose, Andrea R. Brunelle

Wildland Resources Faculty Publications

Background: In Western North America, increasing wildfire and outbreaks of native bark beetles have been mediated by warming climate conditions. Bioclimatic models forecast the loss of key high elevation species throughout the region. This study uses retrospective vegetation and fire history data to reconstruct the drivers of past disturbance and environmental change. Understanding the relationship among climate, antecedent disturbances, and the legacy effects of settlement-era logging can help identify the patterns and processes that create landscapes susceptible to bark beetle epidemics. Methods: Our analysis uses data from lake sediment cores, stand inventories, and historical records. Sediment cores were dated with …

Geometric Auxetics, Ciprian Borcea, Ileana Streinu

Computer Science: Faculty Publications

We formulate a mathematical theory of auxetic behavior based on one-parameter deformations of periodic frameworks. Our approach is purely geometric, relies on the evolution of the periodicity lattice and works in any dimension. We demonstrate its usefulness by predicting or recognizing, without experiment, computer simulations or numerical approximations, the auxetic capabilities of several well-known structures available in the literature. We propose new principles of auxetic design and rely on the stronger notion of expansive behavior to provide an infinite supply of planar auxetic mechanisms and several new three-dimensional structures.

Photonic Topological Chern Insulators Based On Tellegen Metacrystals, Daniel A. Jacobs, Andrey E. Miroshnichenko, Yuri S. Kivshar, Alexander B. Khanikaev

Publications and Research

We demonstrate that topologically nontrivial states of light can be engineered in periodic photonic structures containing media with a Tellegen-type bianisotropic response. Whilst in such bianisotropic materials the time-reversal symmetry is broken, they are characterized by an intrinsic magnetic order which does not require macroscopic magnetization. Our design can therefore be considered as a direct analog of the solid state Chern insulator which exhibits a topological order in the absence of an external bias. Numerical simulations of such Tellegen photonic crystals reveal the existence of one way edge transport at domain walls and perfectly conducting boundaries not sensitive to structural …

Statistical Estimation Of White Matter Microstructure From Conventional Mri, Leah Suttner, Amanda Mejia, Blake Dewey, Pascal Sati, Daniel S. Reich, Russell T. Shinohara

UPenn Biostatistics Working Papers

Diffusion tensor imaging (DTI) has become the predominant modality for studying white matter integrity in multiple sclerosis (MS) and other neurological disorders. Unfortunately, the use of DTI-based biomarkers in large multi-center studies is hindered by systematic biases that confound the study of disease-related changes. Furthermore, the site-to-site variability in multi-center studies is significantly higher for DTI than that for conventional MRI-based markers. In our study, we apply the Quantitative MR Estimation Employing Normalization (QuEEN) model to estimate the four DTI measures: MD, FA, RD, and AD. QuEEN uses a voxel-wise generalized additive regression model to relate the normalized intensities of …

Unique Pseudo-Expectations For C∗-Inclusions, David R. Pitts, Vrej Zarikian

Department of Mathematics: Faculty Publications

Given an inclusion D⊆C of unital C ∗ -algebras (with common unit), a unital completely positive linear map Φ of C into the injective envelope I(D) of D which extends the inclusion of D into I(D) is a pseudo-expectation. Pseudo-expectations are generalizations of conditional expectations, but with the advantage that they always exist. The set PsExp(C,D) of all pseudo-expectations is a convex set, and when D is Abelian, we prove a Krein–Milman type theorem showing that PsExp(C,D) can be recovered from its set of extreme points. In general, PsExp(C,D) is not a singleton. However, there are large and natural classes …

The Varieties Of Indispensability Arguments, Marco Panza, Andrea Sereni

MPP Published Research

The indispensability argument (IA) comes in many different versions that all reduce to a general valid schema. Providing a sound IA amounts to providing a full interpretation of the schema according to which all its premises are true. Hence, arguing whether IA is sound results in wondering whether the schema admits such an interpretation. We discuss in full details all the parameters on which the specification of the general schema may depend. In doing this, we consider how different versions of IA can be obtained, also through different specifications of the notion of indispensability. We then distinguish between schematic and …

2014 Chesapeake Bay Sav Coverage, Sav Data Administrator, Virginia Institute Of Marine Science

Data

Abstract: The 2014 Chesapeake Bay SAV Coverage was mapped from 1:24,000 black and white aerial photography and digital multispectral imagery with a 25cm GSD to assess water quality in the Bay. Each area of SAV was interpreted from the rectified photography and classified into one of four density classes by the percentage of cover. The SAV beds were entered into an SDE GIS fetaure class using the quality control procedures documented below. The dataset contains all SAV areas that were identified from the areas flown. Some areas that are presumed to contain no SAV were not flown. Some small beds, …

U.S. Drought Monitor, December 22, 2015, Richard R. Heim Jr.

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for December 22, 2015 (12/22/15) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

Reliability And Validity Of Neurobehavioral Function On The Psychology Experimental Building Language Test Battery In Young Adults, Brian J. Piper, Shane Mueller, Alexander R. Geerken, Kyle L. Dixon, Gregory Kroliczak, Reid H. Olsen, Jeremy K. Miller

Michigan Tech Publications

Background. The Psychology Experiment Building Language (PEBL) software consists of over one-hundred computerized tests based on classic and novel cognitive neuropsychology and behavioral neurology measures. Although the PEBL tests are becoming more widely utilized, there is currently very limited information about the psychometric properties of these measures.

Methods. Study I examined inter-relationships among nine PEBL tests including indices of motor-function (Pursuit Rotor and Dexterity), attention (Test of Attentional Vigilance and Time-Wall), working memory (Digit Span Forward), and executive-function (PEBL Trail Making Test, Berg/Wisconsin Card Sorting Test, Iowa Gambling Test, and Mental Rotation) in a normative sample (N = 189, …

Evaluating Different Distributed-Cyber-Infrastructure For Data And Compute Intensive Scientific Application, Arghya Kusum Das, Seung Jong Park, Jaeki Hong, Wooseok Chang

Computer Science Faculty Research & Creative Works

Scientists are increasingly using the current state of the art big data analytic software (e.g., Hadoop, Giraph, etc.) for their data-intensive applications over HPC environment. However, understanding and designing the hardware environment that these data- and compute-intensive applications require for good performance is challenging. With this motivation, we evaluated the performance of big data software over three different distributed-cyber-infrastructures, including a traditional HPC-cluster called SuperMikeII, a regular datacenter called SwatIII, and a novel MicroBrick-based hyperscale system called CeresII, using our own benchmark Parallel Genome Assembler (PGA). PGA is developed atop Hadoop and Giraph and serves as a good real-world example …

Sensor Resource Management: Intelligent Multi-Objective Modularized Optimization Methodology And Models, Boris Kovalerchuk, Leonid Perlovsky

All Faculty Scholarship for the College of the Sciences

The importance of the optimal Sensor Resource Management (SRM) problem is growing. The number of Radar, EO/IR, Overhead Persistent InfraRed (OPIR), and other sensors with best capabilities, is limited in the stressing tasking environment relative to sensing needs. Sensor assets differ significantly in number, location, and capability over time. To determine on which object a sensor should collect measurements during the next observation period k, the known algorithms favor the object with the expected measurements that would result in the largest gain in relative information. We propose a new tasking paradigm OPTIMA for sensors that goes beyond information gain. It …

Enriched Continental Flood Basalts From Depleted Mantle Melts: Modeling The Lithospheric Contamination Of Karoo Lavas From Antarctica, Jussi S. Heinonen, Arto V. Luttinen, Wendy A. Bohrson

All Faculty Scholarship for the College of the Sciences

Continental flood basalts (CFBs) represent large-scale melting events in the Earth’s upper mantle and show considerable geochemical heterogeneity that is typically linked to substantial contribution from underlying continental lithosphere. Large-scale partial melting of the cold subcontinental lithospheric mantle and the large amounts of crustal contamination suggested by traditional binary mixing or assimilation-fractional crystallization models are difficult to reconcile with the thermal and compositional characteristics of continental lithosphere, however. The well-exposed CFBs of Vestfjella, western Dronning Maud Land, Antarctica, belong to the Jurassic Karoo large igneous province and provide a prime locality to quantify mass contributions of lithospheric and sublithospheric sources …

A Deep Look At The Nuclear Region Of Ugc 5101 Through High Angular Resolution Mid-Ir Data With Gtc/Canaricam, M. Martínez-Paredes, Almudena Alonso-Herrero, Itziar Aretxaga, C. Ramos Almeida, A. Hernán-Caballero, O. González-Martín, M. Pereira-Santaella, Christopher Packham, A. Asensio Ramos, T. Díaz-Santos, Moshe Elitzur, P. Esquej, I. García-Bernete, Masatoshi Imanishi, Nancy A. Levenson, José Miguel Rodríguez Espinosa

Physics and Astronomy Faculty Publications

We present an analysis of the nuclear infrared (IR, 1.6–18 μm) emission of the ultraluminous IR galaxy UGC 5101 to derive the properties of its active galactic nucleus (AGN) and its obscuring material. We use new mid-IR high angular resolution (0.3–0.5 arcsec) imaging using the Si-2 filter (λ_C = 8.7 μm) and 7.5–13 μm spectroscopy taken with CanariCam (CC) on the 10.4 m Gran Telescopio CANARIAS. We also use archival Hubble Space Telescope/NICMOS and Subaru/COMICS imaging and Spitzer/IRS spectroscopy. We estimate the near- and mid-IR unresolved nuclear emission by modelling the imaging data with GALFIT. We decompose …

Strong Variability Of The Coronal Line Region In Ngc 5548, Hermine Landt, Martin J. Ward, Katrien C. Steenbrugge, Gary J. Ferland

Physics and Astronomy Faculty Publications

We present the second extensive study of the coronal line variability in an active galaxy. Our data set for the well-studied Seyfert galaxy NGC 5548 consists of five epochs of quasi-simultaneous optical and near-infrared spectroscopy spanning a period of about five years and three epochs of X-ray spectroscopy overlapping in time with it. Whereas the broad emission lines and hot dust emission varied only moderately, the coronal lines varied strongly. However, the observed high variability is mainly due to a flux decrease. Using the optical [Fe vii] and X-ray O vii emission lines we estimate that the coronal line gas …