Physical Sciences and Mathematics Commons^™

A Copula Based Approach For Design Of Multivariate Random Forests For Drug Sensitivity Prediction, Saad Haider, Raziur Rahman, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Modeling sensitivity to drugs based on genetic characterizations is a significant challenge in the area of systems medicine. Ensemble based approaches such as Random Forests have been shown to perform well in both individual sensitivity prediction studies and team science based prediction challenges. However, Random Forests generate a deterministic predictive model for each drug based on the genetic characterization of the cell lines and ignores the relationship between different drug sensitivities during model generation. This application motivates the need for generation of multivariate ensemble learning techniques that can increase prediction accuracy and improve variable importance ranking by incorporating the relationships …

Design Of Probabilistic Random Forests With Applications To Anticancer Drug Sensitivity Prediction, Raziur Rahman, Saad Haider, Souparno Gosh, Ranadip Pal

Department of Statistics: Faculty Publications

Random forests consisting of an ensemble of regression trees with equal weights are frequently used for design of predictive models. In this article, we consider an extension of the methodology by representing the regression trees in the form of probabilistic trees and analyzing the nature of heteroscedasticity. The probabilistic tree representation allows for analytical computation of confidence intervals (CIs), and the tree weight optimization is expected to provide stricter CIs with comparable performance in mean error. We approached the ensemble of probabilistic trees’ prediction from the perspectives of a mixture distribution and as a weighted sum of correlated random variables. …

S1: Supplementary Information For Article: A Copula Based Approach For Design Of Multivariate Random Forests For Drug Sensitivity Prediction, Saad Haider, Raziur Rahman, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Changes in performance with prior feature selection

Random forest (RF) is designed to create uncorrelated trees using random subsets of features in each node of each tree. RF by itself is a great tool for feature selection from a high dimensional set of features. But we observed that the prediction accuracy is improved when a prior feature selection (RELIEFF) [1] approach is implemented. Table A shows the performance of RF, VMRF and CMRF with and without RELIEFF feature selection in 2 drug sets of GDSC.

Performance Analysis for drugsets consisting of more 8 than two drugs

We have generated empirical …

Basis Criteria For N-Cycle Integer Splines, Ester Gjoni

Senior Projects Spring 2015

In this project we work with integer splines on graphs with positive integer edge labels. We focus on graphs that are n-cycles for some natural number n. We find an explicit condition for when a set of splines can form a module basis for n-cycle splines. In general, a set of splines forms a Z-module basis if and only if their determinant is equal to the product of the edge labels divided by the greatest common divisor of those edge labels.

An Approach To Extract The Parameters Of Solar Cells From Their Illuminated I-V Curves Using The Lambert W Function, Ahmed A. El Tayyan

Turkish Journal of Physics

In this article an approach based on the Lambert W function is applied to analysis of various types solar cells and solar modules at a given insolation level and temperature; it can be used to extract accurate values of the parameters of a solar cell/module using experimental data or information available from the datasheet. These parameters are the photocurrent I_{ph}, the reverse saturation current I_o, the diode ideality factor a, the series resistance R_s, and the shunt resistance R_{sh}. The parameters I_o, a, R_s, and R_{sh} are calculated with the aid of 4 equations that can be solved simultaneously while …

The Effects Of Plaster On Radiation Doses Given To Patients, Onur Karaman, Ayşe Güneş Tanir, Mustafa Hi̇cabi̇ Bölükdemi̇r

Turkish Journal of Physics

The purpose of this investigation is to measure the total attenuation coefficients (TACs) of plaster materials using different geometries of the plaster, field sizes, and photon beam energies. The percent depth dose measurements were made using X-rays at 6 MV and 18 MV from the linear accelerator in order to plan the probable radiation dose to be given to the patient wearing a plaster cast. The TAC was experimentally determined in solid phantoms of various thicknesses both with and without plaster over areas of 5 x 5 cm^2, 10 x 10 cm^2, and 15 x 15 cm^2. The experimentally measured …

Cosmological Models Filled With A Perfect Fluid Source In The F(R,T) Theory Of Gravity, Dnyaneshwar Dadaji Pawar, Yadao Solanke

Turkish Journal of Physics

We investigated the physical behavior of an LRS Bianchi type I cosmological model in the framework of the f(R,T) theory of gravity in the presence of a perfect fluid, where R is the Ricci scalar and T is the trace of the stress energy tensor of the matter. In order to obtain a deterministic solution of the field equations we assumed the special law of variation of the Hubble parameter proposed by Berman that yields the constant deceleration parameter. Some physical properties of the models are discussed.

Usage Of Attenuation Coefficients Of Some Tissue-Equivalent Materials, Ayşe Güneş Tanir, Fatma Serap Ketenci̇, Mustafa Hi̇cabi̇ Bölükdemi̇r

Turkish Journal of Physics

The total attenuation coefficients of 11 biological targets against photon energies were plotted within the energy range 1-10 MeV. From these plots a possible equation describing the relationship between photon energy and the total attenuation coefficient was derived. The suggested equation is mu/ rho = 0.0696/ surd E. To test the validity of the equation and to compare the results of the total attenuation coefficients of 3 tissue-equivalent materials (bolus, rice grains, and boiled rice) that could not be determined before, they were determined experimentally by using X-rays produced at 6 MV and 18 MV. The results of the experiment …

Analysis And Simulation Of Semiconductor Laser Dynamics With Optoelectronic Delay Feedback, Varghese Bejoy, Sivasankaran Rajesh, Vadakkedath Madhom Nandakumaran

Turkish Journal of Physics

In this work we investigate semiconductor laser dynamics with optoelectronic delay feedback, both analytically and numerically. Stability criteria are derived from the delay differential equations of the system. Stability curves are obtained in the feedback strength-delay parameter space. We show that delay has a role in determining the stability only for a range of feedback strength and this range can vary depending on other parameters. Effects of bias current and nonlinear gain reduction on the stability curves are shown in the analysis and numerically verified.

Adiabatic Loading Of Rotating Bosons Into 1d Optical Lattice, Shemi S. M. Soliman, Yehya Elsharkawy

Turkish Journal of Physics

In this paper, the entropy-temperature curves are investigated for rotating boson gases in a 1D optical lattice with transverse harmonic confinement. Regimes at which the atomic sample can be significantly heated or cooled by adiabatically changing the lattice depth and the rotation rate are demonstrated. The suggested approach, which is the semiclassical approximation, includes the correction due to the finite size effect. The obtained results show that the entropy--temperature curves have a monotonically increasing nature for this system, in agreement with the standard thermodynamic arguments. For fixed temperature, entropy always increases with the increasing of the rotation rate or optical …

Survey Of Muon Stripping In The Muon-Catalyzed $D-D$ Fusion Cycle In Pure Deuterium, Seyed Mohammad Motevalli, Maedeh Mohammdapourfard

Turkish Journal of Physics

Muon-catalyzed fusion is a very efficient nuclear fusion method to which a wide variety of experimental and theoretical studies have been devoted in recent years. The mixtures of hydrogen isotopes are the most appropriate particles to do this kind of fusion. The efficiency of muon-catalyzed fusion in mixtures of pure deuterium is due to the abundance of this isotope as compared to other hydrogen isotopes. The most important issue of reducing the efficiency of the muon-catalyzed fusion chain in pure deuterium mixtures is the probability of muons sticking to the helium-3 particle produced after the $d-d$ nuclear fusion reaction. In …

Synthesis And Properties Of A Spinel Cathode Material For Lithium Ion Battery With Flat Potential Plateau, Ahmed Abdulrahman Ahmed Al-Tabbakh, Norlida Kamarulzaman, Aseel Al-Zubaidi

Turkish Journal of Physics

A potential cathode material for lithium ion battery was synthesised by combustion reaction. The thermal behaviour of the as-synthesised precursor was measured using a thermogravimetric analyser and the range of calcination temperature from 500 $^{\circ}$C to 800 $^{\circ}$C was determined. X-ray diffraction analysis showed that all calcined powders crystallised in the cubic spinel structure of the $Fd\bar{3}m$ space group. The particle size distributions and morphologies of the powders were obtained using a particle size analyser and scanning electron microscope. The effect of calcination temperature on the electrochemical performance was investigated using galvanostatic charge/discharge measurements. The potential profiles of charge and …

Symmetry And The Order Of Events In Time: The Thermodynamics Of Blackbodies Composed Of Positive Or Negative Masssymmetry And The Order Of Events In Time: The Thermodynamics Of Blackbodies Composed Of Positive Or Negative Mass, Randy Wayne

Turkish Journal of Physics

I have previously proposed a discrete symmetry called CPM (charge-parity-mass) symmetry that defines matter as having positive mass and antimatter as having negative mass-both being involved in processes that proceed forward in time. I have generalized the second law of thermodynamics to describe and predict the order of events in time that take place in reversible thermodynamic systems composed of positive or negative mass. Here I extend the CPM symmetry to irreversible thermo-optical radiation systems characterized by the Stefan-Boltzmann law, Planck's blackbody radiation law, and Einstein's law of specific heat. The laws of radiation analyzed in terms of CPM symmetry …

Crystal Dynamics Of Zinc Chalcogenides I: An Application To Znscrystal Dynamics Of Zinc Chalcogenides I: An Application To Zns, Jay Prakash Dubey, Raj Kishor Tiwari, Kripa Shankar Upadhyaya, Pramod Kumar Pandey

Turkish Journal of Physics

A van der Waals three body force rigid shell model (VTRSM) developed earlier for NaCl and CsCl structure was expanded by us for zinc blende structure (ZBS). This model includes the effect of three body interactions and van der Waals interactions in the rigid shell model where short-range interactions were considered up to the second neighbor. Our model thus developed was applied to study the phonon dispersion curves, Debye temperature variation, two phonon Raman/IR spectra, and anharmonic elastic properties of ZnS. Our results are in good agreement with the measured data wherever available.

Sfp Effect On Majorana Type Solar Neutrinos In The Presence Of Nonstandard Neutrino Interactionssfp Effect On Majorana Type Solar Neutrinos In The Presence Of Nonstandard Neutrino Interactions, Deni̇z Yilmaz

Turkish Journal of Physics

Assuming neutrinos are Majorana particles, neutrino oscillation is examined in the case of spin flavor precession (SFP) and nonstandard neutrino interaction (NSI). It is seen that the combined effect of them (SFP and NSI) is not ignorable for the neutrino oscillation.

Two Common Terminological Mistakes In Scientific Paperstwo Common Terminological Mistakes In Scientific Papers, Şaki̇r Erkoç

Turkish Journal of Physics

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Crystal Structure Of {2,20-[N,N0-Bis(Pyridin-2-Yl-Methyl)Cyclohexane-Trans-1,2-Diyldi(Nitrilo)]- Diacetato}Cobalt(Iii) Hexafluoridophosphate, Craig C. Mclauchlan, Daniel S. Kissel, Albert W. Herlinger

Faculty Publications – Chemistry

The title compound [Co(C22H26N4O4)]PF6, commonly known as [Co(bpcd)]PF6, where bpcd2- is derived from the historical ligand name N,N'-bis­(2-pyridyl­meth­yl)-trans-1,2-di­amino­cyclo­hexane-N,N'-di­acetate, crystallized by slow evaporation of a saturated aceto­nitrile solution in air. The cation of the hexa­fluorido­phosphate salt has the CoIII atom in a distorted octa­hedral coordination geometry provided by an N4O2 donor atom set. The acetate groups, which are oriented trans with respect to each other, exhibit monodentate coordination whereas the pyridyl N atoms are coordinating in a cis configuration. The geometry of the cation is compared to the geometries of other di­amino …

Spatial And Temporal Variation In Penetrative Strain During Compression: Insights From Analog Models, Caroline M. Burberry

Department of Earth and Atmospheric Sciences: Faculty Publications

Penetrative strain constitutes the proportion of the total shortening across an orogen that is not accommodated by the development of macroscale structures such as folds and thrusts. The accommodation of shortening by penetrative strain is widely considered to be an important process during compression, but variation in the distribution of penetrative strain during a deformation sequence is not well understood. This study provides some first-order constraints on magnitude, timing, and distribution of penetrative strain during deformation. Eight simple models, each with a geometrically and mechanically similar starting configuration, within the limits of sandbox models, were shortened to different amounts. Model …

Temporal Dynamics Of Groundwater-Dissolved Inorganic Carbon Beneath A Drought-Affected Braided Stream: Platte River Case Study, Audrey R. Boerner, John B. Gates

Department of Earth and Atmospheric Sciences: Faculty Publications

Impacts of environmental changes on groundwater carbon cycling are poorly understood despite their potentially high relevance to terrestrial carbon budgets. This study focuses on streambed groundwater chemistry during a period of drought-induced river drying and consequent disconnection between surface water and groundwater. Shallow groundwater underlying vegetated and bare portions of a braided streambed in the Platte River (Nebraska, USA) was monitored during drought conditions in summer 2012. Water temperature and dissolved inorganic carbon (dominated by HCO₃^-) in streambed groundwater were correlated over a 3 month period coinciding with a decline in river discharge from 35 to 0 …

Thunderstorm Observation By Radar (Thor): An Algorithm To Develop A Climatology Of Thunderstorms, Adam L. Houston, Noah A. Lock, Jamie Lahowetz, Brian L. Barjenbruch, George L. Limpert, Cody Oppermann

Department of Earth and Atmospheric Sciences: Faculty Publications

The Thunderstorm Observation by Radar (ThOR) algorithm is an objective and tunable Lagrangian approach to cataloging thunderstorms. ThOR uses observations from multiple sensors (principally multisite surveillance radar data and cloud-to-ground lightning) along with established techniques for fusing multisite radar data and identifying spatially coherent regions of radar reflectivity (clusters) that are subsequently tracked using a new tracking scheme. The main innovation of the tracking algorithm is that, by operating offline, the full data record is available, not just previous cluster positions, so all possible combinations of object sequences can be developed using all observed object positions. In contrast to Eulerian …

Trans-Amazon Drilling Project (Tadp): Origins And Evolution Of The Forests, Climate, And Hydrology Of The South American Tropics, P. A. Baker, S. C. Fritz, C. G. Silva, C. A. Rigsby, M. L. Absy, R. P. Almeida, M. Caputo, C. M. Chiessi, F. W. Cruz, C. W. Dick, S. J. Feakins, J. Figueiredo, K. H. Freeman, C. Hoorn, C. Jaramillo, A. K. Kern, E. M. Latrubesse, M. P. Ledru, A. Marzoli, A. Myrbo, A. Noren, W. E. Piller, M. I. F. Ramos, C. C. Ribas, R. Trnadade, A. J. West, I. Wahnfried, D. A. Willard

Department of Earth and Atmospheric Sciences: Faculty Publications

This article presents the scientific rationale for an ambitious ICDP drilling project to continuously sample Late Cretaceous to modern sediment in four different sedimentary basins that transect the equatorial Amazon of Brazil, from the Andean foreland to the Atlantic Ocean. The goals of this project are to document the evolution of plant biodiversity in the Amazon forests and to relate biotic diversification to changes in the physical environment, including climate, tectonism, and the surface landscape. These goals require long sedimentary records from each of the major sedimentary basins across the heart of the Brazilian Amazon, which can only be obtained …

Polarimetric Tornadic Debris Signature Variability And Debris Fallout Signatures, Matthew S. Van Den Broeke

Department of Earth and Atmospheric Sciences: Faculty Publications

Values of polarimetric radar variables may vary substantially between and through tornadic debris signature (TDS) events. Tornadoes with higher intensity ratings are associated with higher average and extreme values of reflectivity factor at horizontal polarization ZHH and lower values of copolar cross-correlation coefficient rhv. Although values of these variables often fluctuate through reported tornado life cycles, ZHH repeatably decreases and rhv repeatably increases across the volume scan immediately following reported tornado demise. Land cover has a relatively small effect on values of the polarimetric variables within TDSs, although near-radar urban TDSs may exhibit relatively high ZHH values. TDS areal extent …

Synthesis And Molecular Modeling Studies Of Naproxen-Based Acyl Hydrazone Derivatives, Tuğba Taşkin Tok, Özgün Özaşik, Deni̇z Sarigöl, Ayşe Uzgören Baran

Turkish Journal of Chemistry

A series of N-acylhydrazone derivatives (2a--2p) containing 6-methoxy-naphthalene and acylhydrazone moieties were synthesized in good yield using microwave irradiation and developed as potential COX-2 inhibitors. Furthermore, the interactions between COX-2 and the compounds were examined in detail by molecular modeling studies such as structure--activity relationship and molecular docking performed using Gaussian 09 and Discovery Studio 3.5. As a result, it was found that N-acylhydrazone compounds displayed a different mechanism than SC-558 as COX-2 inhibitor by binding to different active sites of the protein, COX-2. Compound 2c would be a good COX-2 inhibitor candidate for preclinical studies.

An Ornithological Investigation Of The Relationships Among Species Assemblages In Diverse Landscapes In Portland, Oregon, Trevor Attenberg

Environmental Science and Management Professional Master's Project Reports

This study involves geographic variables of the urban landscape and how they affect bird species assemblage. I utilized bird point count data from observation sites in the Portland, OR metropolitan region provided by Portland Environmental Services. Species data and its relationship with environmental variables were evaluated using Bray-Curtis Dissimilarity measurements together with Non-metric Multidimensional scaling (NMDS) to provide a clear image of the spatial relationships between sites. Land classification, water and canopy in 500 m buffers were quantified in order to describe important geographic variability among collection areas of bird data. Patterns indicating spatial trends in the urban landscape emerged. …

4-D Evolution Of Anticlines And Implications For Hydrocarbon Exploration Within The Zagros Fold-Thrust Belt, Kurdistan Region, Iraq, Mjahid M. Zebari, Caroline M. Burberry

Department of Earth and Atmospheric Sciences: Faculty Publications

The Zagros Fold-Thrust Belt, extending from southern Iran, through northern Iraq and into Turkey, is characterized by elongate NW-trending anticlines that house large hydrocarbon accumulations. In recent years, the Kurdistan region of northern Iraq has become an area of interest for both structural studies and petroleum exploration-related investigation. Key questions to be answered concern the nature of the anticlines and whether the geometry of any associated thrusts can be predicted from surface geomorphology, as well the 4-D evolution of the area and along-strike continuity of the anticlines. To address these questions, this study combines field data, remote-sensing data concerning the …

Global Analysis Of Saturation Artifacts In The Viirs Infrared Channels And The Effects Of Sample Aggregation, Thomas N. Polivka, Edward Hyer, Jun Wang, David A. Peterson

Department of Earth and Atmospheric Sciences: Faculty Publications

Unlike previous spaceborne Earth observing sensors, the Visible Infrared Imaging Radiometer Suite (VIIRS) employs onboard sample aggregation to reduce downlink bandwidth requirements and preserve spatial resolution across the scan. To examine the potentially deleterious impacts of onboard sample aggregation when encountering detector saturation, nearly four months of the National Oceanic and Atmospheric Administration’s Nightfire product are analyzed, which contains a subset of the hottest observed nighttime pixels. An empirical method for identifying saturation is devised. The M12 band (3.69 μm) is the most frequently saturating band with 0.15% of the Nightfire pixels at or near the ~359-K detector saturation limit; …

Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang

Theses and Dissertations--Computer Science

The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We …

Consistency Checking Of Natural Language Temporal Requirements Using Answer-Set Programming, Wenbin Li

Theses and Dissertations--Computer Science

Successful software engineering practice requires high quality requirements. Inconsistency is one of the main requirement issues that may prevent software projects from being success. This is particularly onerous when the requirements concern temporal constraints. Manual checking whether temporal requirements are consistent is tedious and error prone when the number of requirements is large. This dissertation addresses the problem of identifying inconsistencies in temporal requirements expressed as natural language text. The goal of this research is to create an efficient, partially automated, approach for checking temporal consistency of natural language requirements and to minimize analysts' workload.

The key contributions of this …

Graphs Obtained From Collections Of Blocks, Colton Magnant, Pouria Salehi Nowbandegani, Hua Wang

Department of Mathematical Sciences Faculty Publications

Given a collection of d-dimensional rectangular solids called blocks, no two of which sharing interior points, construct a block graph by adding a vertex for each block and an edge if the faces of the two corresponding blocks intersect nontrivially. It is known that if d ≥ 3, such block graphs can have arbitrarily large chromatic number. We prove that the chromatic number can be bounded with only a mild restriction on the sizes of the blocks. We also show that block graphs of block configurations arising from partitions of d-dimensional hypercubes into sub-hypercubes are at least d-connected. Bounds on …

Respiratory Particle Deposition Probability Due To Sedimentation With Variable Gravity And Electrostatic Forces, Ioannis Haranas, Ioannis Gkigkitzis, George D. Zouganelis, Maria K. Haranas, Samantha Kirk

Physics and Computer Science Faculty Publications

In this paper, we study the effects of the acceleration gravity on the sedimentation deposition probability, as well as the aerosol deposition rate on the surface of the Earth and Mars, but also aboard a spacecraft in orbit around Earth and Mars as well for particles with density ρ_p = 1300 kg/m³, diameters d_p = 1, 3, 5 µm and residence times t = 0.0272, 0.2 s respectively. For particles of diameter 1 µm we find that, on the surface of Earth and Mars the deposition probabilities are higher at the poles when compared to the …