Physical Sciences and Mathematics Commons^™

Structural Evidence Of A Major Conformational Change Triggered By Substrate Binding In Dape Enzymes: Impact On The Catalytic Mechanism, Boguslaw Nocek, Cory Reid, Anna Starus, Tahirah Heath, David Bienvenues, Jerzy Osipiuk, Robert Jedrzeczak, Andrzej Joachimiak, Daniel P. Becker Ph.D., Richard C. Holz

Chemistry: Faculty Publications and Other Works

The X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ∼50° and shifts ∼10.1 Å (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to …

Predicted Suitable Habitat Declines For Midwestern United States Amphibians Under Future Climate And Land-Use Change Scenarios, Brock Struecker, Joseph Milanovich

Biology: Faculty Publications and Other Works

With current declines of vertebrate taxa meeting or exceeding those of historic mass extinction events, there is a growing need to investigate the main drivers of losses. Two of the main drivers of declines are global climate and land-use changes, both affecting multiple groups of taxa. Amphibians are at great risk from these two drivers of change and investigations into the impact of future change could assist with the formation of conservation plans to mitigate losses. Forecasting changes in suitable habitat with ecological niche modeling serves as a useful tool to begin to understand how species may respond to anthropogenic …

Multivariate Statistical Analyses Of Air Pollutants And Meteorology In Chicago During Summers 2010–2012, Katrina Binaku, Martina Schmeling

Chemistry: Faculty Publications and Other Works

Aerosol, trace gas, and meteorological data were collected in Chicago, Illinois during 2010–2012 summer air studies. Ozone, nitrogen oxides, acetate, formate, chloride, nitrate, sulfate, and oxalate concentrations as well as temperature, wind speed, wind direction, and humidity data were explored by both principal component analysis (PCA) and canonical correlation analysis (CCA). Multivariate statistical techniques were applied to uncover existing relationships between meteorology and air pollutant concentrations and also reduce data dimensions.

In PCA, principal components (PC) revealed a relationship of ozone and nitrate concentrations with respect to temperature and humidity, coupled with transport of species from the south in relation …

The Graph Database: Jack Of All Trades Or Just Not Sql?, George F. Hurlburt, Maria R. Lee, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

This special issue of IT Professional focuses on the graph database. The graph database, a relatively new phenomenon, is well suited to the burgeoning information era in which we are increasingly becoming immersed. Here, the guest editors briefly explain how a graph database works, its relation to the relational database management system (RDBMS), and its quantitative and qualitative pros and cons, including how graph databases can be harnessed in a hybrid environment. They also survey the excellent articles submitted for this special issue.

Identifying Worldviews On Corporate Sustainability: A Content Analysis Of Corporate Sustainability Reports, Nancy E. Landrum, Brian M. Ohsowski

School of Environmental Sustainability: Faculty Publications and Other Works

Companies commonly issue sustainability or corporate social responsibility (CSR) reports. This study seeks to understand worldviews of corporate sustainability, or the corporate message conveyed regarding what sustainability or CSR is and how to enact it. Content analysis of corporate sustainability reports is used to position each company report within stages of corporate sustainability. Results reveal that there are multiple coexisting worldviews of corporate sustainability, but the most dominant worldview is focused on the business case for sustainability, a position anchored in the weak sustainability paradigm. We contend that the business case and weak sustainability advanced in corporate sustainability reports and …

Reproducible Research For Computing In Science & Engineering, Lorena A. Barba, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

The editors of the new track for reproducible research outline the parameters for future peer review, submission, and access, highlighting the magazine’s previous work in this field and some of the challenges still to come.

Separating Markup From Text, Ronald I. Greenberg, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

As more and more online versions of Humanities texts are created, it is becoming commonplace to embed elaborate formatting, for example, through the use of HTML. But this can interfere with computerized analyses of the original text. While it may seem, at first, straightforward to simply strip markup from text, this is not the reality. Many digital texts add things that appear to be legitimate content according to the markup syntax, for example, line numbers, and even apart from this issue, existing tools for stripping markup produce inconsistent results. Apart from adopting and enforcing strict conventions for adding markup to …

Menagerie Of Ads2 Boundary Conditions, Daniel Grumiller, Robert A. Mcnees Iv, Jakob Salzer, Carlos Valcárcel, Dmitri Vassilevich

Physics: Faculty Publications and Other Works

We consider different sets of AdS2 boundary conditions for the Jackiw-Teitelboim model in the linear dilaton sector where the dilaton is allowed to fluctuate to leading order at the boundary of the Poincaré disk. The most general set of boundary conditions is easily motivated in the gauge theoretic formulation as a Poisson sigma model and has an sl(2)" role="presentation" style="box-sizing: inherit; display: inline; line-height: normal; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative;">𝔰𝔩(2)sl(2) current algebra as asymptotic symmetries. Consistency of the …

Computer Science And Cultural History: A Dialogue, David B. Dennis, George K. Thiruvathukal

History: Faculty Publications and Other Works

No abstract provided.

History Of Computing, George K. Thiruvathukal, David B. Dennis

Computer Science: Faculty Publications and Other Works

The social and organizational history of humanity is intricately entangled with the history of technology in general and the technology of information in particular. Advances in this area have often been closely involved in social and political transformations. While the contemporary period is often referred to by such names as the Computing and Information Age, this is the culmination of a series of historical transformations that have been centuries in the making. This course will provide a venue for students to learn about history through the evolution of number systems and arithmetic, calculating and computing machines, and advanced communication technology …

Comparison Of Visual Datasets For Machine Learning, Kent Gauen, Ryan Dailey, John Laiman, Yuxiang Zi, Nirmal Asokan, Yung-Hsiang Lu, George K. Thiruvathukal, Mei-Ling Shyu, Shu-Ching Chen

Computer Science: Faculty Publications and Other Works

One of the greatest technological improvements in recent years is the rapid progress using machine learning for processing visual data. Among all factors that contribute to this development, datasets with labels play crucial roles. Several datasets are widely reused for investigating and analyzing different solutions in machine learning. Many systems, such as autonomous vehicles, rely on components using machine learning for recognizing objects. This paper compares different visual datasets and frameworks for machine learning. The comparison is both qualitative and quantitative and investigates object detection labels with respect to size, location, and contextual information. This paper also presents a new …

Examining The Use Of Amazon’S Mechanical Turk For Edge Extraction Of The Occlusal Surface Of Fossilized Bovid Teeth, George K. Thiruvathukal, Gregory J. Matthews, Maxwell P. Luetkemeier, Juliet K. Brophy

Computer Science: Faculty Publications and Other Works

In order to reconstruct environments associated with Plio-Pleistocene hominins in southern Africa, researchers frequently rely upon the animals associated with the hominins, in particular, animals in the Family Bovidae. Bovids in southern Africa are typically identified by their teeth. However, identifying the taxon of a bovid tooth is challenging due to various biasing factors. Furthermore, inaccurate identification of fossil bovids can have significant consequences on the reconstructed paleoenvironment. Recent research on the classification of bovid fossil teeth has relied on using elliptical Fourier analysis to summarize the shape of the outline of the occlusal surface of the tooth and the …

Generating Enzyme And Radical‐Mediated Bisubstrates As Tools For Investigating Gcn5‐Related N‐Acetyltransferases, Cory T. Reidl, Karolina A. Majorek, Joseph Dang, David Tran, Kristen Jew, Melissa Law, Yasmine Payne, Wladek Minor, Daniel P. Becker, Misty L. Kuhn

Chemistry: Faculty Publications and Other Works

Gcn5‐related N‐acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor‐bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X‐ray induced radical‐mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely …

Analysis Of Beverages By Total Reflection X-Ray Fluorescence, Martina Schmeling

Chemistry: Faculty Publications and Other Works

In advance of the Denver X-Ray Conference, we asked leading scientists who will be speaking at the conference about current trends and advances in X-ray fluorescence and X-ray diffraction. Here, these investigators discuss their work to advance these techniques and the sample preparation for such analyses, in areas such as photonics for telecommunications, steel structures, metals in pharmaceuticals, and imaging.

Motion Planning For Simple Two-Wheeled Robots, Ronald I. Greenberg, Jeffery M. Karp

Computer Science: Faculty Publications and Other Works

This paper considers various simple ways of navigating in a 2-dimensianal territory with a two-wheeled robot of a type typical in educational robotics. We determine shortest paths under various modes of operation and compare.

Educational Magic Tricks Based On Error-Detection Schemes, Ronald I. Greenberg

Computer Science: Faculty Publications and Other Works

Magic tricks based on computer science concepts help grab student attention and can motivate them to delve more deeply. Error detection ideas long used by computer scientists provide a rich basis for working magic; probably the most well known trick of this type is one included in the CS Unplugged activities. This paper shows that much more powerful variations of the trick can be performed, some in an unplugged environment and some with computer assistance. Some of the tricks also show off additional concepts in computer science and discrete mathematics.

Allosteric Control Of Substrate Specificity Of The Escherichia Coli Adp-Glucose Pyrophosphorylase, Ana C. Ebrecht, Ligin Solamen, Benhamin L. Hill, Alberto A. Iglesias, Ken W. Olsen, Miguel A. Ballicora

Chemistry: Faculty Publications and Other Works

The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives. This selection will guide the flow of carbohydrate metabolism toward the synthesis of reserve polysaccharides. Here, we show that …

Postitive Youth Development, Tania Schusler, Jacqueline Davis-Manigaulte, Amy Cutter-Mackenzie

School of Environmental Sustainability: Faculty Publications and Other Works

• Positive youth development is an assets-based approach for cultivating competencies essential to personal well-being.

• When environmental education enables children and youths to contribute to improving urban environments, it can not only increase cities' sustainability and resilience but also foster young people's personal growth.

• Participatory action research, peer education, and youth civic engagement are three educational approaches that can lead to positive change for both urban environments and youths living within them.

Ecological Restoration, Elizabeth P. Mccann, Tania Schusler

School of Environmental Sustainability: Faculty Publications and Other Works

Ecological restoration involves revitalizing neglected, degraded, damaged, or destroyed habitats.

• Restoration-based education involves learners in ecological restoration with an intentional educational purpose.

• Urban restoration-based education can enhance personal and community well-being while improving ecosystem services in degraded environments.

• Restoration-based education can benefit from consciously forming partner ships, integrating local values alongside socioeconomic and ecological considerations, and being sensitive to issues of power and diverse cultures.

Constitutionalism And Democracy Dataset, Version 1.0, Todd A. Eisenstadt, Carl Levan, Tofigh Maboudi

Political Science: Faculty Publications and Other Works

The main objective of the CDD is to quantify the process of constitution-making since 1974. This is the first public release of any data on the process of constitution-making. This release includes data on 144 national constitutions promulgated in 119 countries from 1974 to 2014. The unit of analysis in the data is national constitutions. The data in this release includes only “new” constitutions and does not include suspended, re-installed, amended, or interim constitutions. In this release, only countries with a population larger than 500,000 are included. The authors intend to update the data by including all countries, expanding the …

A Distributed Graph Approach For Pre-Processing Linked Rdf Data Using Supercomputers, Michael J. Lewis, George K. Thiruvathukal, Venkatram Vishwanath, Michael J. Papka, Andrew Johnson

Computer Science: Faculty Publications and Other Works

Efficient RDF, graph based queries are becoming more pertinent based on the increased interest in data analytics and its intersection with large, unstructured but connected data. Many commercial systems have adopted distributed RDF graph systems in order to handle increasing dataset sizes and complex queries. This paper introduces a distribute graph approach to pre-processing linked data. Instead of traversing the memory graph, our system indexes pre-processed join elements that are organized in a graph structure. We analyze the Dbpedia data-set (derived from the Wikipedia corpus) and compare our access method to the graph traversal access approach which we also devise. …

Galileo's Contribution To Mechanics, Asim Gangopadhyaya

Physics: Faculty Publications and Other Works

Asim Gangopadhyaya writes about Galileo's contributions to mechanics and physics in this chapter in Where Have All the Heavens Gone? Galileo's Letter to the Grand Duchess Christina edited by John P. McCarthy and Edmondo F. Lupieri.

Experiences With Scala Across The College-Level Curriculum, Konstantin Läufer, George K. Thiruvathukal, Mark C. Lewis

Emerging Technologies Laboratory

Various hybrid-functional languages, designed to balance compile-time error detection, conciseness, and performance, have emerged. Scala, e.g., is interoperable with Java and has become an early leader in adoption, especially in the start-up and open-source spaces.

As educators, we have recognized Scala’s value as a teaching language across the CS curriculum. In CS1, the read-eval-print loop and simple, uniform syntax aid programming in the small. In CS2, higher-order methods allow concise, efficient manipulation of collections. In a programming languages course, advanced constructs facilitate the separation of concerns, program representation and interpretation, and concurrent programming. In advanced applied courses, language mechanisms and …

Chronic Toxicity Of Binary‐Metal Mixtures Of Cadmium And Zinc To Daphnia Magna, Edgar Pérez, Tham C. Hoang

School of Environmental Sustainability: Faculty Publications and Other Works

The present study characterized the chronic effect of binary‐metal mixtures of cadmium (Cd) and zinc (Zn) on Daphnia magna. The titration design was chosen to characterize the 21‐d chronic effects of the binary‐metal mixtures on survival, growth, reproduction, and metal accumulation in D. magna. Using this design, increasing concentrations of Zn (10, 20, 40, 80, 120, 160, and 200 μg/L) were titrated against a constant concentration of 1.5 μg/L Cd. The results demonstrated that Cd was highly toxic to D. magna. In a mixture with Cd and Zn, sublethal concentrations of 10 and 20 μg/L Zn were …

Emphasizing Experience And Refelction During Online Math Hw, Kieran Flahive

Ignatian Pedagogy Educational Resources

No abstract provided.

Can Newton’S Third Law Be “Derived” From The Second?, Asim Gangopadhyaya, James T. Harrington

Physics: Faculty Publications and Other Works

Newton’s laws1 have engendered much discussion over several centuries.2,3 Today, the internet is awash with a plethora of information on this topic. We find many references to Newton’s laws, often discussions of various types of misunderstandings and ways to explain them. Here we present an intriguing example that shows an assumption hidden in Newton’s third law that is often overlooked. As is well known, the first law defines an inertial frame of reference and the second law determines the acceleration of a particle in such a frame due to an external force. The third law describes forces exerted …

Does A Taste Of Computing Increase Computer Science Enrollment?, Steven Mcgee, Randi Mcgee-Tekula, Jennifer Duck, Ronald I. Greenberg, Lucia Dettori, Dale F. Reed, Brenda Wilkerson, Don Yanek, Andrew Rasmussen, Gail Chapman

Computer Science: Faculty Publications and Other Works

The Exploring Computer Science (ECS) high school curriculum is designed to foster deep engagement through equitable inquiry around computer science concepts. We have shown that students find ECS courses personally relevant, are increasing their expectancies of success and perceived value for the field of computer science, and are more likely to take another computing course.

Pythagorean Approximations For Lego: Merging Educational Robot Construction With Programming And Data Analysis, Ronald I. Greenberg

Computer Science: Faculty Publications and Other Works

Abstract. This paper can be used in two ways. It can provide reference information for incorporating diagonal elements (for bracing or gear meshing) in educational robots built from standard LEGO kits. Alternatively, it can be used as the basis for an assignment for high school or college students to recreate this information; in the process, students will exercise skills in both computer programming and data analysis. Using the paper in the second way can be an excellent integrative experience to add to an existing course; for example, the Exploring Computer Science high school curriculum concludes with the units “Introduction to …

Plp And Gaba Trigger Gabr-Mediated Transcription Regulation In Bacillus Subtilis Via External Aldimine Formation, Rui Wu, Ruslan Sanishvili, Boris R. Belitsky, Jose I. Juncosa, Hoang V. Le, Helaina J. S. Lehrer, Michael Farley, Richard B. Silverman, Gregory A. Petsko, Dagmar Ringe, Dali Liu

Chemistry: Faculty Publications and Other Works

The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of γ-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5′-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the “active site” in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic γ-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, ( …

Higher-Order Power Harmonics Of Pulsed Electrical Stimulation Modulates Corticospinal Contribution Of Peripheral Nerve Stimulation, Chiun-Fan Chen, Marom Bikson, Li-Wei Chou, Chunlei Shan, Niranjan Khadka, Wen-Shiang Chen, Felipe Fregni

Engineering Science Faculty Publications

It is well established that electrical-stimulation frequency is crucial to determining the scale of induced neuromodulation, particularly when attempting to modulate corticospinal excitability. However, the modulatory effects of stimulation frequency are not only determined by its absolute value but also by other parameters such as power at harmonics. The stimulus pulse shape further influences parameters such as excitation threshold and fiber selectivity. The explicit role of the power in these harmonics in determining the outcome of stimulation has not previously been analyzed. In this study, we adopted an animal model of peripheral electrical stimulation that includes an amplitude-adapted pulse train …