Graphics and Human Computer Interfaces Commons^™

Model File Name: Dna-420bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-420bp-handle-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (420 bp). The DNA model has small handles on the ends to aid in holding and manipulating the model. The model is designed to go with a teaching module on DNA supercoiling. The model can be accompanied by Nucleosome and H1 histone models to demonstrate DNA packaging in the cell. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “420bp DNA (handles)”. …

Model File Name: Dnalong-3pc-Lego.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNAlong-3pc-Lego.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a stick representation of the DNA to which the transcription factor lambda repressor binds (PDB: 1lmb). This model can be adapted to accompany a teaching module illustrating transcription factor-DNA binding. The model has been designed in 3 parts that can be joined together by Lego®-style junctions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lego DNA with GCbp”. This model has been printed successfully using these parameters on Shapeways’ laser …

Model File Name: Dna-420bp-Magnet-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-420bp-magnet-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (420 bp). The DNA model has small sites on the ends where the user can glue magnets to mimic circular DNA, and to aid in manipulating the model. Disc magnets with a diameter of 1/8” or 1/10” and thickness of 1/16” can be purchased online from K&J Magnetics and glued into the magnet sites. The model is designed to go with a teaching module on DNA supercoiling. The model can …

Model File Name: H1-Protein.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: H1-protein.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a crude representation of an H1-protein intended to accompany the nucleosome and a long, thin double stranded DNA helix model in order to illustrate DNA packaging and supercoiling. This model is designed to go with a teaching module on DNA supercoiling. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Histone H1 protein”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following materials: Strong …

Model File Name: Dna-Short-Helix.X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-short-helix.x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a DNA helix in which the atoms are colored by heteroatom (PDB: 1lmb). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions, and with one that studies transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “DNA helix - polynucleotide molecule”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full …

Model File Name: Ssdna.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: ssDNA.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a single stranded piece of DNA in stick representation (PDB: 1ehz). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “ssDNA”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Elasto Plastic material.

Model File Name: Nucleosome.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Nucleosome.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a crude representation of a nucleosome intended to accompany the H1 histone protein and a long, thin double stranded DNA helix model in order to illustrate DNA packaging and supercoiling. This model is designed to go with a teaching module on DNA supercoiling. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Nucleosome”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Strong & Flexible …

Model File Name: Tf-Monomer-Stick.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: TF-monomer-stick.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a ribbon and stick representation of a Lambda repressor transcription factor monomer that accompanies the full color DNA helix (PDB: 1lmb). This model is designed to go with a teaching module illustrating transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lambda TF monomer”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Strong & Flexible Plastic material.

Model File Name: Rna-Short-Helix.X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: RNA-short-helix.x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a DNA helix in which the atoms are colored by heteroatom (PDB: 1lmb). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “RNA helix - polynucleotide molecule”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full Color Sandstone material.

Video Guide To Design Flexible Dna.Mp4, Michelle Howell, Karin V. Van Dijk, Christine S. Booth, Tomáš Helikar, Brian Couch, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Video guide to design flexible DNA.mp4

Authors: Michelle E Howell, Karin van Dijk, Christine S Booth, Tomas Helikar, Brian A Couch, Rebecca L Roston

This 30-minute video includes step-by-step instructions to design and 3-D print a long flexible DNA model that mimics the structure and function of DNA. The instructions are applicable for designing the model using open-source 3-D computer graphics software Blender 2.79 which is available for download at https://www.blender.org/download/.

.mp4 file download (70 MB) below.

Model File Name: Ssrna.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: ssRNA.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a single stranded piece of RNA in stick representation (PDB: 1ehz). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “ssRNA”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Elasto Plastic material.

Model File Name: Helix_H2o_Sphere2.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Helix_H2O_sphere2.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a space fill representation of a protein α-helix (PDB: 3vjo). A space fill water molecule is also represented to illustrate the lack of space down the axis of an α-helix. This model can accompany a corresponding stick representation, a kinked α-helix, and a β-sheet. This model is designed to accompany a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Helix and Water (Space-fill) …

Model File Name: Beta-Sheet_Rod 0.7.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: beta-sheet_rod 0.7.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a stick representation of a protein β-sheet (PDB: 3vjo). This model is designed to accompany three other α-helix models: a space-fill representation of a straight α-helix, a stick representation of a straight α-helix, and a stick representation of a kinked α-helix. These models accompany a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Beta-sheet_Thick”. This model has been printed successfully using …

Model File Name: Alpha Helix Pro-Gly 0.7.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: alpha helix pro-gly 0.7.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a stick representation of a protein α-helix with proline and glycine residues highlighted (PDB: 3vjo). This model is designed to accompany a straight α-helix in space fill representation, a straight α-helix in stick representation, and a stick β-sheet model as well as a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Alpha Helix_Pro-Gly”. This model has been printed successfully using these parameters …

Model File Name: Alpha Helix 0.7.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: alpha helix 0.7.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a stick representation of a protein α-helix (PDB: 3vjo). This model can accompany a corresponding space fill representation, a kinked α-helix, and a β-sheet. These models were designed to accompany a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Alpha Helix_Thick”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full Color …

Space Operations In The Suborbital Space Flight Simulator And Mission Control Center: Lessons Learned With Xcor Lynx, Pedro Llanos, Christopher Nguyen, David Williams, Kim O. Chambers, Erik Seedhouse, Robert Davidson

Journal of Aviation/Aerospace Education & Research

This study was conducted to better understand the performance of the XCOR Lynx vehicle. Because the Lynx development was halted, the best knowledge of vehicle dynamics can only be found through simulator flights. X-Plane 10 was chosen for its robust applications and accurate portrayal of dynamics on a vehicle in flight. The Suborbital Space Flight Simulator (SSFS) and Mission Control Center (MCC) were brought to the Applied Aviation Sciences department in fall 2015 at Embry-Riddle Aeronautical University, Daytona Beach campus. This academic and research tool is a department asset capable of providing multiple fields of data about suborbital simulated flights. …

Simulating Foodborne Pathogens In Poultry Production And Processing To Defend Against Intentional Contamination, Silas B. Lankford

Computer Science and Computer Engineering Undergraduate Honors Theses

There is a lack of data in recent history of food terrorism attacks, and as such, it is difficult to predict its impact. The food supply industry is one of the most vulnerable industries for terrorist threats while the poultry industry is one of the largest food industries in the United States. A small food terrorism attack against just a single poultry processing center has the potential to affect a much larger population than its immediate consumers. In this work, the spread of foodborne pathogens is simulated in a poultry production and processing system to defend against intentional contamination. An …

Unboxing Cluster Heatmaps, Sophie J. Engle, S. Whalen, Alark Joshi, K. Pollard

Computer Science

Background: Cluster heatmaps are commonly used in biology and related fields to reveal hierarchical clusters in data matrices. This visualization technique has high data density and reveal clusters better than unordered heatmaps alone. However, cluster heatmaps have known issues making them both time consuming to use and prone to error. We hypothesize that visualization techniques without the rigid grid constraint of cluster heatmaps will perform better at clustering-related tasks.

Results: We developed an approach to “unbox” the heatmap values and embed them directly in the hierarchical clustering results, allowing us to use standard hierarchical visualization techniques as alternatives …

A Pilot Study Of Comparison Gesture Analysis In Motion Driven Video Games, Fabrizio Valerio Covone, Brian Vaughan, Charlie Cullen

Conference Papers

This study investigates whether there are significant differences in the gestures made by gamers and non-gamers whilst playing commercial games that employ gesture inputs. Specifically, the study focuses on testing a prototype of multimodal capture tool that we used to obtain real-time audio, video and skeletal gesture data. Additionally, we developed an experimental design framework for the acquisition of spatio-temporal gesture data and analysed the vector magnitude of a gesture to compare the relative displacement of each participant whilst playing a game.

User-Centered Design Of Multi-Gene Sequencing Panel Reports For Clinicians., Elizabeth Cutting, Meghan Banchero, Amber L Beitelshees, James J Cimino, Guilherme Del Fiol, Ayse P Gurses, Mark A Hoffman, Linda Jo Bone Jeng, Kensaku Kawamoto, Mark Kelemen, Harold Alan Pincus, Alan R Shuldiner, Marc S Williams, Toni I Pollin, Casey Lynnette Overby

Manuscripts, Articles, Book Chapters and Other Papers

The objective of this study was to develop a high-fidelity prototype for delivering multi-gene sequencing panel (GS) reports to clinicians that simulates the user experience of a final application. The delivery and use of GS reports can occur within complex and high-paced healthcare environments. We employ a user-centered software design approach in a focus group setting in order to facilitate gathering rich contextual information from a diverse group of stakeholders potentially impacted by the delivery of GS reports relevant to two precision medicine programs at the University of Maryland Medical Center. Responses from focus group sessions were transcribed, coded and …

2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin

Bioinformatics Software Design Projects

Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.

Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …

A Flexible Pet-Based Wearable Sensor For Arterial Pulse Waveform Measurement, Dan Wang, Dean Krusienski, Zhili Hao

Mechanical & Aerospace Engineering Faculty Publications

In light of the need of health monitoring, the paper presents a flexible polyethylene terephthalate (PET)-based wearable sensor for arterial pulse waveform measurement. The sensor encompasses a polydimethylsiloxane (PDMS) microstructure embedded with an electrolyte-enabled 5×1 transducer array, which spans 6mm and has a spatial resolution of 1.5mm. A pulse signal exerts a deflection on the microstructure and is recorded as a resistance change by a transducer at the site of the pulse. An untrained individual can easily align the sensor on a targeted artery with a negligible margin and then acquire the arterial pulse waveform continuously and non-invasively. This sensor …

Design, Programming, And User-Experience, Kaila G. Manca

Honors Scholar Theses

This thesis is a culmination of my individualized major in Human-Computer Interaction. As such, it showcases my knowledge of design, computer engineering, user-experience research, and puts into practice my background in psychology, com- munications, and neuroscience.

I provided full-service design and development for a web application to be used by the Digital Media and Design Department and their students.This process involved several iterations of user-experience research, testing, concepting, branding and strategy, ideation, and design. It lead to two products.

The first product is full-scale development and optimization of the web appli- cation.The web application adheres to best practices. It was …

Taming The Software Chaos: True To Its Promise, Iftdss Eases The Burden Of Fuels Treatment Planning—And Does A Lot More Besides, Gail Wells

Joint Fire Science Program Digests

A key problem reported by the fuels treatment planning community is the difficulty and inefficiency of evaluating and then applying many planning tools and applications. Fuels specialists have struggled to find, load, and learn all the different fuels and fire planning models, not to mention the interface of running, adjusting, and inputting data specific to each model without the ability to easily share inputs/outputs between models.

The Interagency Fuels Treatment Decision Support System (IFTDSS) was conceived as a way for users to learn one interface, access a variety of data and models all in one place, and pass data (inputs …

Utilizing A Modular Approach To Gamification To Improve Nutrition And Fitness In Children, Chad Richards

Graduate Theses and Dissertations

Obesity is a worldwide epidemic that affects adults and children, impacts over 30% of the population in several states of the U.S., damages national economies, and is a factor in four out of the six of the leading causes of death, including diabetes and heart disease. Obesity is preventable: solution approaches include better education, more exercise, better nutrition, and changing eating habits. Still, it is difficult for many people to remain interested enough to educate themselves and to learn new behaviors to change their eating and exercise habits.

Gamification is a relatively new research area that involves using video game …

Three-Dimensional Reconstructions Of Tadpole Chondrocrania From Histological Sections, Gary P. Radice, Mary Kate Boggiano, Mark Desantis, Peter M. Larson, Joseph Oppong, Matthew T. Smetanick, Todd M. Stevens, James Tripp, Rebecca A. Weber, Michael Kerckhove, Rafael O. De Sá

Biology Faculty Publications

Reconstructing three dimensional structures (3DR) from histological sections has always been difficult but is becoming more accessible with the assistance of digital imaging. We sought to assemble a low cost system using readily available hardware and software to generate 3DR for a study of tadpole chondrocrania. We found that a combination of RGB camera, stereomicroscope, and Apple Macintosh PowerPC computers running NIH Image, Object Image, Rotater. and SURFdriver software provided acceptable reconstructions. These are limited in quality primarily by the distortions arising from histological protocols rather than hardware or software.

The Computer As A Collection Management Tool, Suzanne B. Mclaren, Hugh H. Genoways, Duane A. Schlitter

University of Nebraska State Museum: Mammalogy Papers

Since the mid-1960s, discussion of computer use for information retrieval in museum collections has usually focused on research potential. Much attention has been given to the idea of networking and the ability to access data across great distances. However, the potential for collection management usage has also proven to be a legitimate rationale for computerization. Numerous aspects of collection management are discussed for which the computer may be employed. Topics include creating cross-reference files, updating taxonomic and geographic information, pinpointing mismatched specimens, locating lost and uncataloged material, controlling loan procedures, producing accession files for insurance purposes, curating all or part …

Research Note: Getting Graphic: Computer Graphics In Biochemistry, Wilmon B. Chipman

Bridgewater Review

No abstract provided.