Physical Sciences and Mathematics Commons^™

Discerning Novel Splice Junctions Derived From Rna-Seq Alignment: A Deep Learning Approach, Yi Zhang, Xinan Liu, James N. Macleod, Jinze Liu

Computer Science Faculty Publications

Background: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both possible and widely available. RNA-seq provides unprecedented resolution to identify gene structures and resolve the diversity of splicing variants. However, currently available ab initio aligners are vulnerable to spurious alignments due to random sequence matches and sample-reference genome discordance. As a consequence, a significant set of false positive exon junction predictions would be introduced, which will further confuse downstream analyses of splice variant discovery and abundance estimation.

Results: …

Groundwater Level Response To The Wenchuan Earthquake Of May 2008, Anhua He, Ramesh Singh

Mathematics, Physics, and Computer Science Faculty Articles and Research

We have comprehensively analysed the co-seismic response of the groundwater levels of 280 wells in mainland China that were associated with the Wenchuan earthquake (Mw 7.9) that occurred on 12 May 2008. The observed co-seismic responses can be classified as step-like changes in 138 wells, variations in 69 wells and non-responses in 73 wells. After a quantitative analysis of spatial distribution, there was no spatially coherent signal found in the step-like changes (positive values indicate a step-like rise, and negative values indicate a step-like fall), even within 300 km of the epicenter. The amplitude and the phase shift of the …

About Wavefunctions In Low-Dimensional Semiconductors, B Akhmedov, J Rozikov, I Muminov, V Ruziboev

Central Asian Problems of Modern Science and Education

The impressive progress in the fabrication of low-dimensional semiconductor structures during the past two decades has made it possible to reduce the effective device dimension from three-dimensional bulk materials, to quasi-two dimensional quantum well systems, to quasi-one dimensional quantum wires, and even to quasi-zero dimensional quantum dots. In this article we discussed about wave function in these structures.

The Disk Substructures At High Angular Resolution Project (Dsharp). X. Multiple Rings, A Misaligned Inner Disk, And A Bright Arc In The Disk Around The T Tauri Star Hd 143006, Laura M. Pérez, Myriam Benisty, Sean M. Andrews, Andrea Isella, Cornelis P. Dellemond, Jane Huang, Nicolás T. Kurtovic, Viviana V. Guzmán, Zhaohuan Zhu, Tilman Birnstiel, Shangjia Zhang, John M. Carpenter, David J. Wilner, Luca Ricci, Xue-Ning Bai, Erik Weaver, Karin I. Öberg

Physics & Astronomy Faculty Research

We present a detailed analysis of new Atacama Large Millimeter/submillimeter Array (ALMA) observations of the disk around the T-Tauri star HD 143006, which at 46 mas (7.6 au) resolution reveals new substructures in the 1.25 mm continuum emission. The disk resolves into a series of concentric rings and gaps, together with a bright arc exterior to the rings that resembles hydrodynamical simulations of a vortex and a bridge-like feature connecting the two innermost rings. Although our 12CO observations at similar spatial resolution do not show obvious substructure, they reveal an inner disk depleted of CO emission. From the continuum emission …

Electron Transfer Plus Double Ionization In Slow He2+ + Ar Collisions, Y. Gao, Michael Schulz, D. L. Guo, S. F. Zhang, X. L. Zhu, R. T. Zhang, W. T. Feng, D. M. Zhao, X. Ma

Physics Faculty Research & Creative Works

We performed a kinematically complete experiment on double ionization accompanied by single capture in 30 keV/amu He2⁺ + Ar collisions. The data were systematically analyzed using three different techniques, namely, fully differential cross sections as a function of the electron emission angle of each electron, the correlation function, and four-particle Dalitz plots. The data can to a large extent be explained within the independent electron model. However, the correlation function reveals small but significant effects from correlations in the initial target state. These correlations strongly depend on the interaction between the nuclei of the collision partners. Furthermore, a surprisingly …

The Disk Substructures At High Angular Resolution Project (Dsharp). Ix. A High-Definition Study Of The Hd 163296 Planet-Forming Disk, Andrea Isella, Jane Huang, Sean M. Andrews, Cornelis P. Dellemond, Tilman Birnstiel, Shangjia Zhang, Zhaohuan Zhu, Viviana V. Guzmán, Laura M. Pérez, Xue-Ning Bai, Myriam Benisty, John M. Carpenter, Luca Ricci, David J. Wilner

Physics & Astronomy Faculty Research

The Atacama Large Millimeter/submillimeter Array observations of protoplanetary disks acquired by the Disk Substructure at High Angular Resolution Project resolve the dust and gas emission on angular scales as small as 3 astronomical units, offering an unprecedented detailed view of the environment where planets form. In this Letter, we present and discuss observations of the HD 163296 protoplanetary disk that imaged the 1.25 mm dust continuum and 12CO J = 2–1 rotational line emission at a spatial resolution of 4 and 10 au, respectively. The continuum observations resolve and allow us to characterize the previously discovered dust rings at radii …

Quantifying Bee Assemblages And Attractiveness Of Flowering Woody Landscape Plants For Urban Pollinator Conservation, Bernadette M. Mach, Daniel A. Potter

Entomology Faculty Publications

Urban and suburban landscapes can be refuges for biodiversity of bees and other pollinators. Public awareness of declining pollinator populations has increased interest in growing plants that provide floral resources for bees. Various publications and websites list “bee-friendly” plants, but such lists are rarely based on empirical data, nor do they emphasize flowering trees and shrubs, which are a major component of urban landscapes. We quantified bee visitation to 72 species of flowering woody landscape plants across 373 urban and suburban sites in Kentucky and southern Ohio, USA, sampling and identifying the bee assemblages associated with 45 of the most …

Vibrational Analysis Of A Rate-Slowing Conformational Kinetic Isotope Effect, O. Maduka Ogba, Zichen Liu, Daniel J. O'Leary

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

An enthalpy-entropy approach to analyzing a rate-slowing conformational kinetic isotope effect (CKIE) in a deuterated doubly-bridged biaryl system is described. The computed isotope effect (kH/kD = 1.075, 368 K) agrees well with the measured value (kH/kD = 1.06, 368 K). The rateslowing (normal isotope effect) nature of the computed CKIE is shown to originate from a vibrational entropy contribution defined by the twenty lowest frequency normal modes in the ground state and transition state structures. This normal entropy contribution is offset by an inverse vibrational enthalpy contribution, which also arises from the twenty lowest frequency normal modes. Zero point vibrational …

The Disk Substructures At High Angular Resolution Project (Dsharp). I. Motivation, Sample, Calibration, And Overview, Sean M. Andrews, Jane Huang, Laura M. Pérez, Andrea Isella, Cornelis P. Dullemond, Nicolás T. Kurtovic, Viviana V. Guzmán, John M. Carpenter, David J. Wilner, Shangjia Zhang, Zhaohuan Zhu, Tilman Birstiel, Xue-Ning Bai, Myriam Benisty, A. Meredith Hughes, Karin I. Öberg, Luca Ricci

Physics & Astronomy Faculty Research

We introduce the Disk Substructures at High Angular Resolution Project (DSHARP), one of the initial Large Programs conducted with the Atacama Large Millimeter/submillimeter Array (ALMA). The primary goal of DSHARP is to find and characterize substructures in the spatial distributions of solid particles for a sample of 20 nearby protoplanetary disks, using very high resolution (~0 035, or 5 au, FWHM) observations of their 240 GHz (1.25 mm) continuum emission. These data provide a first homogeneous look at the small-scale features in disks that are directly relevant to the planet formation process, quantifying their prevalence, morphologies, spatial scales, spacings, symmetry, …

The Disk Substructures At High Angular Resolution Project (Dsharp). Iii. Spiral Structures In The Millimeter Continuum Of The Elias 27, Im Lup, And Waoph 6 Disks, Jane Huang, Sean M. Andrews, Laura M. Pérez, Zhaohuan Zhu, Cornelis P. Dullemond, Andrea Isella, Myriam Benisty, Xue-Ning Bai, Tilman Birnstiel, John M. Carpenter, Viviana V. Guzmán, A. Meredith Hughes, Karin I. Öberg, Luca Ricci, David J. Wilner, Shangjia Zhang

Physics & Astronomy Faculty Research

We present an analysis of Atacama Large Millimeter/submillimeter Array 1.25 mm continuum observations of spiral structures in three protoplanetary disks from the Disk Substructures at High Angular Resolution Project. See full text for full abstract.

The Disk Substructures At High Angular Resolution Project (Dsharp). Ii. Characteristics Of Annular Substructures, Jane Huang, Sean M. Andrews, Cornelis P. Dellemond, Andrea Isella, Laura M. Pérez, Viviana V. Guzmán, Karin I. Öberg, Zhaohuan Zhu, Shangjia Zhang, Xue-Ning Bai, Myriam Benisty, Tilman Birstiel, John M. Carpenter, A. Meredith Hughes, Luca Ricci, Erik Weaver, David J. Wilner

Physics & Astronomy Faculty Research

The Disk Substructures at High Angular Resolution Project (DSHARP) used ALMA to map the 1.25 mm continuum of protoplanetary disks at a spatial resolution of ~5 au. We present a systematic analysis of annular substructures in the 18 single-disk systems targeted in this survey. No dominant architecture emerges from this sample; instead, remarkably diverse morphologies are observed. Annular substructures can occur at virtually any radius where millimeter continuum emission is detected and range in widths from a few astronomical units to tens of astronomical units. Intensity ratios between gaps and adjacent rings range from near-unity to just a few percent. …

The Disk Substructures At High Angular Resolution Project (Dsharp). Vi. Dust Trapping In Thin-Ringed Protoplanetary Disks, Cornelis P. Dullemond, Tilman Birnstiel, Jane Huang, Nicolás T. Kurtovic, Sean M. Andrews, Viviana V. Guzmán, Laura M. Pérez, Andrea Isella, Zhaohuan Zhu, Myriam Benisty, David J. Wilner, Xue-Ning Bai, John M. Carpenter, Shangjia Zhang, Luca Ricci

Physics & Astronomy Faculty Research

A large fraction of the protoplanetary disks observed with ALMA display multiple well-defined and nearly perfectly circular rings in the continuum, in many cases with substantial peak-to-valley contrast. The DSHARP campaign shows that several of these rings are very narrow in radial extent. In this Letter we test the hypothesis that these dust rings are caused by dust trapping in radial pressure bumps, and if confirmed, put constraints on the physics of the dust trapping mechanism. We model this process analytically in 1D, assuming axisymmetry. By comparing this model to the data, we find that all rings are consistent with …

The Disk Substructures At High Angular Resolution Project (Dsharp). Vii. The Planet–Disk Interactions Interpretation, Shangjia Zhang, Zhaohuan Zhu, Jane Huang, Viviana V. Guzmán, Sean M. Andrews, Tilman Birnstiel, Cornelis P. Dullemond, John M. Carpenter, Andrea Isella, Laura M. Pérez, Myriam Benisty, David J. Wilner, Clément Baruteau, Xue-Ning Bai, Luca Ricci

Physics & Astronomy Faculty Research

The Disk Substructures at High Angular Resolution Project (DSHARP) provides a large sample of protoplanetary disks with substructures that could be induced by young forming planets. To explore the properties of planets that may be responsible for these substructures, we systematically carry out a grid of 2D hydrodynamical simulations, including both gas and dust components. We present the resulting gas structures, including the relationship between the planet mass, as well as (1) the gaseous gap depth/width and (2) the sub/super-Keplerian motion across the gap. We then compute dust continuum intensity maps at the frequency of the DSHARP observations. We provide …

The Disk Substructures At High Angular Resolution Program (Dsharp). Viii. The Rich Ringed Substructures In The As 209 Disk, Viviana V. Guzmán, Jane Huang, Sean M. Andrews, Andrea Isella, Laura M. Pérez, John M. Carpenter, Cornelis P. Dullemond, Luca Ricci, Tilman Birnstiel, Shangjia Zhang, Zhaohuan Zhu, Xue-Ning Bai, Myriam Benisty, Karin I. Öberg, David J. Wilner

Physics & Astronomy Faculty Research

The Disk Substructures at High Angular Resolution Program (DSHARP). VIII. The Rich Ringed Substructures in the AS 209 Disk

The Disk Substructures At High Angular Resolution Project (Dsharp). Iv. Characterizing Substructures And Interactions In Disks Around Multiple Star Systems, Nicolás T. Kurtovic, Laura M. Pérez, Myriam Benisty, Zhaohuan Zhu, Shangjia Zhang, Jane Huang, Sean M. Andrews, Cornelis P. Dullemond, Andrea Isella, Xue-Ning Bai, John M. Carpenter, Viviana V. Guzmán, Luca Ricci, David J. Wilner

Physics & Astronomy Faculty Research

To characterize the substructures induced in protoplanetary disks by the interaction between stars in multiple systems, we study the 1.25 mm continuum and the 12CO(J = 2–1) spectral line emission of the triple systems HT Lup and AS 205, at scales of ≈5 au, as part of the "Disk Substructures at High Angular Resolution Project" (DSHARP). In the continuum emission, we find two symmetric spiral arms in the disk around AS 205 N, with a pitch angle of 14°, while the southern component AS 205 S, itself a spectroscopic binary, is surrounded by a compact inner disk and a bright …

Predicting Post-Procedural Complications Using Neural Networks On Mimic-Iii Data, Namratha Mohan

LSU Master's Theses

The primary focus of this paper is the creation of a Machine Learning based algorithm for the analysis of large health based data sets. Our input was extracted from MIMIC-III, a large Health Record database of more than 40,000 patients. The main question was to predict if a patient will have complications during certain specified procedures performed in the hospital. These events are denoted by the icd9 code 996 in the individuals' health record. The output of our predictive model is a binary variable which outputs the value 1 if the patient is diagnosed with the specific complication or 0 …

The Disk Substructures At High Angular Resolution Project (Dsharp). V. Interpreting Alma Maps Of Protoplanetary Disks In Terms Of A Dust Model, Tilman Birnstiel, Cornelis P. Dullemond, Zhaohuan Zhu, Sean M. Andrews, Xue-Ning Bai, David J. Wilner, John M. Carpenter, Jane Huang, Andrea Isella, Myriam Benisty, Laura M. Pérez, Shangjia Zhang

Physics & Astronomy Faculty Research

The Disk Substructures at High Angular Resolution Project (DSHARP) is the largest homogeneous high-resolution (~0 035, or ~5 au) disk continuum imaging survey with the Atacama Large Millimeter/submillimeter Array (ALMA) so far. In the coming years, many more disks will be mapped with ALMA at similar resolution. Interpreting the results in terms of the properties and quantities of the emitting dusty material is, however, a very non-trivial task. This is in part due to the uncertainty in the dust opacities, an uncertainty that is not likely to be resolved any time soon. It is also partly due to the fact …

Shock-Absorbing Vibrations Of The Elastic Elastomeric End Of The Rotary Inertia, N.J Khujatov, N.I Abdikarimov

Central Asian Problems of Modern Science and Education

The problem of the longitudinal vibrations of the elastic strerin of the longitudinal impact of the second free end of the end of the tape is settled on the basis of the second order (classic) differential equation. Depending on the nature of stroke endings and the nature and conditions of the impact, the initial and boundary conditions of the problem were found. To solve the problem, a structured block scheme was created, using a duplicate scheme. Created a structured block-scheme based on "Pascal" and the results were obtained.

Simulating Detection-Censored Movement Records For Home Range Analysis Planning, Lyndsie S. Wszola, Victoria L. Simonsen, Lucía Corral, Christopher J. Chizinski, Joseph J. Fontaine

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Home range estimation is an important analytical method in applied spatial ecology, yet best practices for addressing the effects of spatial variation in detection probability on home range estimates remain elusive. We introduce the R package “DiagnoseHR,” simulation tools for assessing how variation in detection probability arising from landscape, animal behavior, and methodological processes affects home range inference. We demonstrate the utility of simulation methods for home range analysis planning by comparing bias arising from three home range estimation methods under multiple detection scenarios. We simulated correlated random walks in three landscapes that varied in detection probability and constructed home …

Intercapacitance Between Two Charges Located In The Different Environments, A.E Abdikarimov, A Yusupov, A.E Atamuratov

Central Asian Problems of Modern Science and Education

It is investigated the dependence of intercapacitance between two point charges located in different environments on the relative position of border. The image method is used. It is considered two cases: the charges is located at line which is perpendicular to the border and the charges is located at line which is not perpendicular to the border. The result show that in both cases the capacitance is increased with displacement the border.

Investigation Of The Pressed Grunt Cement Blocks, A,A Tulaganov, I.M Hadjiev, E.D Ismailov

Central Asian Problems of Modern Science and Education

In order to increase the strength and seismicity of the traditional grunt cement blocks, the grunt cement block is proposed to be pressed together with fiber waste and data on the study of grunt cement blocks made from local raw materials are provided.

Cyclic Surfaces In The Pseudoevklit Region, B.M Sultanov, Sh,Sh Ismailov

Central Asian Problems of Modern Science and Education

The article describes the hypothesis of the cyclic surface determined in the Galileo domain, the smallest dimensional pseudo-squid space, which is summarized in the five-dimensional two-indexed pseudo-squidoid space and then on the full cyclic surface. Full-scale surfaces have been proven to be in the four-dimensional pseudo-squidoid phase.

Improved Measurement Of The Longitudinal Spin Transfer To Λ And Bar(Λ) Hyperons In Polarized Proton-Proton Collisions At Sqrt(S) = 200 Gev, James Drachenberg

Engineering and Physics

No abstract provided.

Climate Evolution Across The Mid-Brunhes Transition, Aaron M. Barth, Peter U. Clark, Nicholas S. Bill, Feng He, Nicklas G. Pisias

School of Earth & Environment Departmental Research

The Mid-Brunhes Transition (MBT) began ∼ 430 ka with an increase in the amplitude of the 100 kyr climate cycles of the past 800 000 years. The MBT has been identified in ice-core records, which indicate interglaciations became warmer with higher atmospheric CO2 levels after the MBT, and benthic oxygen isotope (δ18O) records, which suggest that post-MBT interglaciations had higher sea levels and warmer temperatures than pre-MBT interglaciations. It remains unclear, however, whether the MBT was a globally synchronous phenomenon that included other components of the climate system. Here, we further characterize changes in the climate system across the MBT …

1996 - Monterey County Hydrogeologic Study, Volume Ii -- Critical Issues Report And Interim Management Plan, Final Report

Monterey County Water Resources Agency Engineering Reports

This document was a companion report to the North Monterey County Hydrogeologic Study, Volume I, dated October 1995. The document built from the technical understanding and problem identification developed in Volume I and focuses on key issues relative to developing a management plan for the water resources of the area. These included the interrelated policy, legal and financial issues that complicate the management of the resource. The purpose of the report was to provide an analysis of these issues towards the development of long-range management objectives.

A Tree-Based Multiscale Regression Method, Haiyan Cai, Qingtang Jiang

Educator Preparation & Leadership Faculty Works

A tree-based method for regression is proposed. In a high dimensional feature space, the method has the ability to adapt to the lower intrinsic dimension of data if the data possess such a property so that reliable statistical estimates can be performed without being hindered by the “curse of dimensionality.” The method is also capable of producing a smoother estimate for a regression function than those from standard tree methods in the region where the function is smooth and also being more sensitive to discontinuities of the function than smoothing splines or other kernel methods. The estimation process in this …

1998 - 2030 Land Use And Water Needs Conditions

Miscellaneous Monterey and San Luis Obispo County Documents and Reports

Documentation of the methodology and data used to estimate the land use, M&I water needs, and pumped agricultural water under the 2030 conditions. One of the primary goals of the Salinas River Basin Management Plan (BMP) is to meet the agricultural, and municipal and industrial water needs of the Valley under the existing conditions (1995 level of development) as well as, under the future conditions (2030 level of development), while stopping the seawater intrusion and balancing the hydrologic conditions in the basin. In order to meet the 2030 water needs, a reasonable estimate of land use and water use conditions …

Lozenge Tilings Of A Halved Hexagon With An Array Of Triangles Removed From The Boundary, Part Ii, Tri Lai

Department of Mathematics: Faculty Publications

Proctor's work on staircase plane partitions yields an exact enumeration of lozenge tilings of a halved hexagon on the triangular lattice. Rohatgi later ex- tended this tiling enumeration to a halved hexagon with a triangle cut o from the boundary. In his previous paper, the author proved a common generalization of Proctor's and Rohatgi's results by enumerating lozenge tilings of a halved hexagon in the case an array of an arbitrary number of triangles has been removed from a non-staircase side. In this paper we consider the other case when the array of tri- angles has been removed from the …

Atom-Specific Activation In Co Oxidation, Simon Schreck, Elias Diesen, Jerry Larue, Hirohito Ogasawara, Kess Marks, Dennis Nordlund, Matthew Weston, Martin Beye, Filippo Cavalca, Fivos Perakis, Jonas Sellberg, André Eilert, Kyung Hwan Kim, Giacomo Coslovich, Ryan Coffee, Jacek Krzywinski, Alex Reid, Stefan Moeller, Alberto Lutman, Henrik Öström, Lars G. M. Pettersson, Anders Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report on atom-specific activation of CO oxidation on Ru(0001) via resonant X-ray excitation. We show that resonant 1s core-level excitation of atomically adsorbed oxygen in the co-adsorbed phase of CO and oxygen directly drives CO oxidation. We separate this direct resonant channel from indirectly driven oxidation via X-ray induced substrate heating. Based on density functional theory calculations, we identify the valence-excited state created by the Auger decay as the driving electronic state for direct CO oxidation. We utilized the fresh-slice multi-pulse mode at the Linac Coherent Light Source that provided time-overlapped and 30 fs delayed pairs of soft …

Characterizing Ancient Chemoclines Through The Use Of Pigment Biomarkers And Sedimentary Stable Isotope Signatures, Benjamin T. Uveges

Dissertations - ALL

This dissertation focuses on identifying and qualifying chemocline dynamics, namely depth and stability, in stratified aquatic systems through the use of sedimentary pigments and the stable carbon and nitrogen isotopes of organic matter. The central aim of the research comprising this volume is to identify how chemocline fluctuations are expressed in the pigment and stable isotope signatures of aquatic sediments, and how those fluctuations may have impacted nutrient cycling in past intervals of marine anoxia and mass extinction.

In order to help gauge how the depth of the chemocline may affect specific pigment signatures and concentrations in sediments, I first …