Physical Sciences and Mathematics Commons^™

Information Content, Charge Transport Properties, And Computational Capacities Of Proteins, Joseph Murphy Brisendine Jr.

Dissertations, Theses, and Capstone Projects

This thesis is the beginning of an attempt to build a coherent theory of the properties of proteins based in information theory and the duality of information theory and nonequilibrium thermodynamics. Throughout, we will adopt the viewpoint that information can act as a thermodynamic potential, which is necessary to understand how biological processes are both enabled and constrained by the laws of thermodynamics. Understanding information as a form of thermodynamic potential also clarifies the description of proteins and other biological macromolecules as “molecular machines”: meso-scale structures with emergent causal powers which perform work on their environments by irreversibly dissipating energy …

Predicting The Next Us President By Simulating The Electoral College, Boyan Kostadinov

Publications and Research

We develop a simulation model for predicting the outcome of the US Presidential election based on simulating the distribution of the Electoral College. The simulation model has two parts: (a) estimating the probabilities for a given candidate to win each state and DC, based on state polls, and (b) estimating the probability that a given candidate will win at least 270 electoral votes, and thus win the White House. All simulations are coded using the high-level, open-source programming language R. One of the goals of this paper is to promote computational thinking in any STEM field by illustrating how probabilistic …

College Algebra Through Problem Solving (2018 Edition), Danielle Cifone, Karan Puri, Debra Maslanko, Ewa Dabkowska

Open Educational Resources

This is a self-contained, open educational resource (OER) textbook for college algebra. Students can use the book to learn concepts and work in the book themselves. Instructors can adapt the book for use in any college algebra course to facilitate active learning through problem solving. Additional resources such as classroom assessments and online/printable homework is available from the authors.

Burden Of Rheumatoid Arthritis Among Us Medicare Population: Co-Morbidities, Health-Care Resource Utilization And Costs, Chieh-I Chen, Li Wang, Wenhui Wei, Huseyin Yuce, Kristine Phillips

Publications and Research

Objectives. The study aimed to assess the burden of RA among the US Medicare population (aged 65 years) by comparing co-morbidities, health-care resource utilization (HCRU) and costs against matched non-RA Medicare patients.

Methods. Data were obtained from the Medicare fee-for-service claims database from 2010 to 2013. RA Medicare patients were identically matched with Medicare patients without RA (controls) based on demographics. Bivariate analyses were conducted to examine differences between cohorts for comorbidities, HCRU and costs. A generalized linear model was used to test relationships between patient-level characteristics, HCRU and costs.

Results. The study population included 115 867 RA patients and …

An Information Theory Approach To Hypothesis Testing In Criminological Research, Gohar A. Petrossian, Mike Maxfield

Publications and Research

Background: This research demonstrates how the Akaike information criterion (AIC) can be an alternative to null hypothesis significance testing in selecting best fitting models. It presents an example to illustrate how AIC can be used in this way.

Methods: Using data from Milwaukee, Wisconsin, we test models of place-based predictor variables on street robbery and commercial robbery. We build models to balance explanatory power and parsimony. Measures include the presence of different kinds of businesses, together with selected age groups and social disadvantage.

Results: Models including place-based measures of land use emerged as the best models among the set of …

Cooperative Standing-Horizontalstanding Reentrant Transition For Numerous Solid Particles Under External Vibration, Satoshi Takatori, Hikari Baba, Takatoshi Ichino, Chwen-Yang Shew, Kenichi Yoshikawa

Publications and Research

We report the collective behavior of numerous plastic bolt-like particles exhibiting one of two distinct states, either standing stationary or horizontal accompanied by tumbling motion, when placed on a horizontal plate undergoing sinusoidal vertical vibration. Experimentally, we prepared an initial state in which all of the particles were standing except for a single particle that was placed at the center of the plate. Under continuous vertical vibration, the initially horizontal particle triggers neighboring particles to fall over into a horizontal state through tumbling-induced collision, and this effect gradually spreads to all of the particles, i.e., the number of horizontal particles …

Communication Based Control For Dc Microgrids, Mahmoud S. Saleh, Yusef Esa, Ahmed Mohamed

Publications and Research

Centralized communication-based control is one of the main methods that can be implemented to achieve autonomous advanced energy management capabilities in DC microgrids. However, its major limitation is the fact that communication bandwidth and computation resources are limited in practical applications. This can be often improved by avoiding redundant communications and complex computations. In this paper, an autonomous communication-based hybrid state/event driven control scheme is proposed. This control scheme is hierarchical and heuristic, such that on the primary control level, it encompasses state-driven local controllers, and on the secondary control level, an event-driven MG centralized controller (MGCC) is used. This …

Component Tree Analysis Of Cystovirus Φ6 Nucleocapsid Cryo-Em Single Particle Reconstructions, Lucas Oliveira, Ze Ye, Al Katz, Alexandra Alimova, Hui Wei, Gabor T. Herman, Paul Gottlieb

Publications and Research

The 3-dimensional structure of the nucleocapsid (NC) of bacteriophage φ6 is described utilizing component tree analysis, a topological and geometric image descriptor. The component trees are derived from density maps of cryo-electron microscopy single particle reconstructions. Analysis determines position and occupancy of structure elements responsible for RNA packaging and transcription. Occupancy of the hexameric nucleotide triphosphorylase (P4) and RNA polymerase (P2) are found to be essentially complete in the NC. The P8 protein lattice likely fixes P4 and P2 in place during maturation. We propose that the viral procapsid (PC) is a dynamic structural intermediate where the P4 and P2 …

Regulation Of Radioactive Fracking Waste, Elizabeth Ann Glass Geltman, Nichole Leclair

Publications and Research

Natural gas extracted form shale reached record production totals in 2015 in the United States and the US Energy Information Administration (EIA) forecasts natural gas production will continue to increase. Wastes from shale gas extraction can contain the radioactive isotopes radium-226 (Ra-226) and radium-228 (Ra-228), which decay further into radon (Rn). Exposure to radon, a form of naturally occurring radioactive materials (NORM), is the leading cause of lung cancer in the United States, after smoking. This article explores how states handle the disposal of technologically enhanced naturally occurring radioactive materials (TENORM) and/or NORM waste from oil and gas operations to …

Models For Decision-Making, Steven Cosares

Open Educational Resources

No abstract provided.

Cis 4400 Data Warehousing For Analytics, Royce Kok, Nyc Tech-In-Residence Corps

Open Educational Resources

No abstract provided.

College Algebra Through Problem Solving (2018 Edition), Danielle Cifone, Karan Puri, Debra Masklanko, Ewa Dabkowska

Open Educational Resources

This is a self-contained, open educational resource (OER) textbook for college algebra. Students can use the book to learn concepts and work in the book themselves. Instructors can adapt the book for use in any college algebra course to facilitate active learning through problem solving. Additional resources such as classroom assessments and online/printable homework is available from the authors.

Trigonometry: A Brief Conversation, Carolyn D. King, Evelyn Tam, Fei Ye, Beata Ewa Carvajal

Open Educational Resources

These five units were specifically tailored to foster the mastery of a few selected trigonometry topics that comprise the one credit MA-121 Elementary Trigonometry course. Each unit introduces the topic, provides space for practice, but more importantly, provides opportunities for students to reflect on the work in order to deepen their conceptual understanding.

These units have also been assigned to students of other courses such as pre-calculus and calculus as a review of trigonometric basics essential to those courses.

We are grateful for the support we received from the Open Educational Research (OER) initiative of the City University of New …

Experiential Learning Activity: Biodiesel Inquiry Project, Ji Kim

Open Educational Resources

The activity described herein can be implemented in introductory chemistry and high school chemistry courses. The main goal of the project is to integrate a ubiquitous biodiesel production with experiential learning by providing a community-based project. The students work in groups, research the benefits of using biodiesel over petroleum-based diesel, collect waste cooking oil from home or restaurants, develop simple and cost-effective methods to produce biodiesel.

The Legacy Of Multics And Secure Operating Systems Today, John Schriner

Publications and Research

This paper looks to the legacy of Multics from 1963 and its influence on computer security. It discusses kernel-based and virtualization-based containment in projects like SELinux and Qubes, respectively. The paper notes the importance of collaborative and research-driven projects like Qubes and Tor Project.

Two-Dimensional Maximal Repetitions, Amihood Amir, Gad M. Landau, Shoshana Marcus, Dina Sokol

Publications and Research

Maximal repetitions or runs in strings have a wide array of applications and thus have been extensively studied. In this paper, we extend this notion to 2-dimensions, precisely defining a maximal 2D repetition. We provide initial bounds on the number of maximal 2D repetitions that can occur in a matrix. The main contribution of this paper is the presentation of the first algorithm for locating all maximal 2D repetitions in a matrix. The algorithm is efficient and straightforward, with runtime O(n^2 log n log log n+ rho log n), where n^2 is the size of the input, and rho is …

Mat 2675 Calculus Iii, Spring 2019, Oer Syllabus, Caner Koca

Open Educational Resources

No abstract provided.

Supercycle In Great Earthquake Recurrence Along The Japan Trench Over The Last 4000 Years, Kazuko Usami, Ken Ikehara, Toshiya Kanamatsu, Cecilia M. Mchugh

Publications and Research

On the landward slope of the Japan Trench, the mid-slope terrace (MST) is located at a depth of 4000–6000 m. Two piston cores from the MST were analyzed to assess the applicability of the MST for turbidite paleoseismology and to find out reliable recurrence record of the great earthquakes along the Japan Trench. The cores have preserved records of ~ 12 seismo-turbidites (event deposits) during the last 4000 years. In the upper parts of the two cores, only the following earthquakes (magnitude M ~ 8 and larger) were clearly recorded: the 2011 Tohoku, the 1896 Sanriku, the 1454 Kyotoku, and …

Convective Transport Of Tropical Marine Boundary Layer Species Into The Upper Troposphere And Relation To Species Lifetime: In Situ Measurements And Global Model Simulation, Sofia M. Chelpon

Dissertations and Theses

This study investigates the influence of tropical deep convection on distribution of trace gasses in the tropical upper troposphere (UT) using data from the Convective Transport of Active Species in the Tropics (CONTRAST) Experiment conducted over the tropical western Pacific during January and February of 2014. Fifty-five chemical species measured during the CONTRAST campaign are analyzed with lifetimes ranging from less than a day to several years. The vertical profiles of these species suggest that they fall into three main groups delineated by their lifetime: 1) very long-lived trace gases demonstrating a nearly constant vertical structure, 2) intermediate lifetime species …

Evolution Of The Modern Baboon (Papio Hamadryas): A Reassessment Of The African Plio-Pleistocene Record, Christopher C. Gilbert, Stephen R. Frost, Kelsey D. Pugh, Monya Anderson, Eric Delson

Publications and Research

Baboons ( Papio hamadryas) are among the most successful extant primates, with a minimum of six distinctive forms throughout Sub-Saharan Africa. However, their presence in the fossil record is unclear. Three early fossil taxa are generally recognized, all from South Africa: Papio izodi , Papio robinsoni and Papio angusticeps. Because of their derived appearance, P. angusticeps and P. robinsoni have sometimes been considered subspecies of P. hamadryas and have been used as biochronological markers for the Plio- Pleistocene hominin sites where they are found.

We reexamined fossil Papio forms from across Africa with an emphasis on their distinguishing features and …

Social Science Perspectives On Drivers Of And Responses To Global, Andrew K. Jorgenson, Shirley Fiske, Klaus Hubacek, Jia Li, Tom Mcgovern, Torben Rick, Juliet B. Schor, William Solecki, Richard York, Ariela Zycherman

Publications and Research

This article provides a review of recent anthropological, archeological, geographical, and sociological research on anthropogenic drivers of climate change, with a particular focus on drivers of carbon emissions, mitigation and adaptation. The four disciplines emphasize cultural, economic, geographic, historical, political, and social‐structural factors to be important drivers of and responses to climate change. Each of these disciplines has unique perspectives and makes noteworthy contributions to our shared understanding of anthropogenic drivers, but they also complement one another and contribute to integrated, multidisciplinary frameworks. The article begins with discussions of research on temporal dimensions of human drivers of carbon emissions, highlighting …

Developing A 3d In Vitro Model By Microfluidics, Hung-Ta Chien

Dissertations and Theses

In vitro tissue models play an important role in providing a platform that mimics the realistic tissue microenvironment for stimulating and characterizing the cellular behavior. In particular, the hydrogel-based 3D in vitro models allow the cells to grow and interact with their surroundings in all directions, thus better mimicking in vivo than their 2D counterparts. The objective of this thesis is to establish a 3D in vitro model that mimics the anatomical and functional complexity of the realistic cancer microenvironment for conveniently studying the transport coupling in porous tissue structures. We pack uniform-sized PEGDA-GelMA microgels in a microfluidic chip to …

Deep Convolutional Neural Networks Enable Discrimination Of Heterogeneous Digital Pathology Images, Pegah Khosravi, Ehsan Kazemi, Marcin Imielinski, Olivier Elemento, Iman Hajirasouliha

Publications and Research

Pathological evaluation of tumor tissue is pivotal for diagnosis in cancer patients and automated image analysis approaches have great potential to increase precision of diagnosis and help reduce human error.

In this study, we utilize several computational methods based on convolutional neural networks (CNN) and build a stand-alone pipeline to effectively classify different histopathology images across different types of cancer.

In particular, we demonstrate the utility of our pipeline to discriminate between two subtypes of lung cancer, four biomarkers of bladder cancer, and five biomarkers of breast cancer. In addition, we apply our pipeline to discriminate among four immunohistochemistry …

Design Of Cloud Based Robots Using Big Data Analytics And Neuromorphic Computing, Ashwin Satyanarayana, Janusz Kusyk, Yu-Wen Chen

Publications and Research

Understanding the brain is perhaps one of the greatest challenges facing twenty-first century science. While a traditional computer excels in precision and unbiased logic, its abilities to interact socially lags behind those of biological neural systems. Recent technologies, such as neuromorphic engineering, cloud infrastructure, and big data analytics, have emerged that can narrow the gap between traditional robots and human intelligence. Neuromorphic robotics mimicking brain functions can contribute in developing intelligent machines capable of learning and making autonomous decisions. Cloud-based robotics take advantage of remote resources for parallel computation and sharing large amounts of information while benefiting from analysis of …

Computational Methods In Civil Engineering, Nir Krakauer

Open Educational Resources

No abstract provided.

Differentiation In Impact Melt Sheets As A Mechanism To Produce Evolved Magmas On Mars, Ari Koeppel

Dissertations and Theses

Asteroid bombardment contributed to extensive melting and resurfacing of ancient (> 3 Ga) Mars, thereby influencing the early evolution of the Martian crust. However, information about how impact melting has altered Mars’ crustal petrology is limited. Evidence from some of the largest impact structures on Earth, such as Sudbury and Manicouagan, suggests that some impact melt sheets experience chemical differentiation. If these processes occur on Mars, we expect to observe differentiated igneous materials in some exhumed rock samples. Some rocks observed in Gale crater are enriched in alkalis (up to 14 wt% Na₂O + K₂O) and …

Mlb Rule Iv Draft: Valuing Draft Pick Slots, Anthony Cacchione

Dissertations and Theses

This study explored the Net Present Value (NPV) in dollar terms of draft pick slots in the Major League Rule IV Draft. In order to accomplish this, the cumulative performance of players selected in each slot within the draft was evaluated and brought to the Present Value of the time they were selected using a discount rate. The performance of the players was determined using the baseball-reference Wins Above Replacement (WAR) metric. It is intuitive that earlier draft picks are the most valuable; however, it is unclear how quickly the value of draft picks decline. This research demonstrates that the …

Synthesis Of 1,4-Triazolyl Combretacoumarins As Potential Anticancer Agents, Tashrique A. Khandaker

Dissertations and Theses

Coumarins are natural compounds that have various physiological and therapeutic properties, making them pharmacologically important. Combretastatin A-4 (CA-4) is a microtubule-binding agent that has potent cytotoxic effects against human cell lines. In CA-4 the trimethoxyarene moiety plays a crucial role in its carcinopreventive effect. Thus, we decided to synthesize novel, potential anti-cancer agents called 1,4-triazolyl combretacoumarins, by coupling different coumarins and the functionally relevant group of CA-4 i.e, the trimethoxyarene moiety, via a 1,2,3-triazolyl ring using a copper-catalyzed [3 + 2] azide-alkyne cycloaddition (CuAAC) reaction, which is a very atom-economical reaction. The coupling partners, 4-azidocoumarins, required for making these …

The Study Of The Degradation Of Hexabromocyclododecane In A Heterogeneous System Containing Fe(Ii) Adsorbed To The Iron Oxide Hematite., Kristian K. Roopnarine

Dissertations and Theses

The reaction of hexabromocyclododecane (HBCDD), a widely used brominated flame retardant, was studied in a heterogenous mixture containing reactive Fe(II) adsorbed to the iron oxide hematite. The adsorbed Fe(II)/iron oxide system has shown to be a potent reductant in the transformation of organic contaminants with relatively water soluble organic contaminants. There currently aren’t many studies involving hydrophobic organic contaminants, such as HBCDD, in this reducing Fe(II)/iron oxide system. The results indicate that across the pHs 6.86, 6.95, 7.15 and 7.35 γ and β-HBCDD are degraded within a couple days. The pseudo-first order rate constants at pH 6.95 are 0.049 hr …

The Weizsäcker-Williams Distribution Of Linearly Polarized Gluons (And Its Fluctuations) At Small X, Adrian Dumitru, Vladimir Skokov

Publications and Research

The conventional and linearly polarized Weizsäcker-Williams gluon distributions at small x are defined from the two-point function of the gluon field in light-cone gauge. They appear in the cross section for dijet production in deep inelastic scattering at high energy. We determine these functions in the small-x limit from solutions of the JIMWLK evolution equations and show that they exhibit approximate geometric scaling. Also, we discuss the functional distributions of these WW gluon distributions over the JIMWLK ensemble at rapidity Y ∼ 1/α_s. These are determined by a 2d Liouville action for the logarithm of the …