Computer Sciences Commons^™

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 …

Knowing And Designing: Understanding Information Use In Open Source Design Through The Lens Of Information Archetypes, Kevin Lumbard, Ammar Abid, Christine Toh, Matt Germonprez

Interdisciplinary Informatics Faculty Proceedings & Presentations

The early phases of the product design process are crucial to the success of design outcomes. While information utilized during idea development has tremendous potential to impact the final design, there is a lack of understanding about the types of information utilized in industry, making it challenging to develop and teach methodologies that support the design of competitive products. As a first step in understanding this process, this study focuses on developing a framework of Information Archetypes utilized by designers in industry. This was accomplished through in-depth analysis of qualitative interviews with large software engineering companies. The results reveal two …

A Study Into The Feasibility Of Using Natural Language Processing And Machine Learning For The Identification Of Alcohol Misuse In Trauma Patients, Andrew Phillips

Master's Theses

Alcohol misuse is a leading cause of premature death in the United States, with nearly a third of trauma patients found to have elevated blood alcohol levels upon admission. However, timely intervention has been shown to reduce this. It is thus important to be able to quickly screen patients to identify alcohol misuse. Many medical centers use standardized questionnaires to identify alcohol misuse, but since these instruments are not usually a part of routine care, there are many cases where it is not done.

In this study, large quantities of notes were processed with natural language processing and machine learning …

Toddler Activity Recognition Using Machine Learning, Pinky Sindhu

Master's Theses

Pinky Sindhu

Loyola University Chicago

TODDLER ACTIVITY RECOGNITION USING MACHINE LEARNING

Toddlers behave differently than adults, to say the least. It is valuable to accurately measure the specific types of physical activity (PA) in toddlers; such information can be analyzed to predict future health prospects in relation to conditions like obesity.

We attached ActiGraph accelerometers to the wrist and waist of toddlers and recorded PAs. Toddlers were videotaped, and their movements were annotated as 20 specific activities. These activities were classified into 3 summary activity intensities including sedentary, light intensity PA (LPA), and moderate to vigorous intensity PA (MVPA).

Automated …

Predicting Opioid Epidemic By Using Twitter Data, Yubao Wu, Pavel Skums, Alex Zelikovsky, David Campo Rendon, Xueting Liao

EBCS Proceedings

Opioid crisis was declared as a public health emergency in 2017 by the President of USA. According to the Centers for Disease Control and Prevention, more than 91 Americans die every day from an opioid overdose. Nearly $4B is provided to address the opioid epidemic in the 2018 spending bill and help fulfill the President’s Opioid Initiative.

How to monitor and predict the opioid epidemic accurately and in real time? The traditional methods mainly use the hospital data and usually have a lag of several years. Even though they are accurate, the long lag period prevents us from monitoring and …

High Performance Attack Estimation In Large-Scale Network Flows, Christopher B. Freas, Robert W. Harrison, Yuan Long

EBCS Proceedings

Network based attacks are the major threat to security on the Internet. The volume of traffic and the high variability of the attacks place threat detection squarely in the domain of big data. Conventional approaches are mostly based on signatures. While these are relatively inexpensive computationally, they are inflexible and insensitive to small variations in the attack vector. Therefore we explored the use of machine learning techniques on real flow data. We found that benign traffic could be identified with high accuracy.

Lightning Draft, Benjamin Sweedler

Computer Science and Software Engineering

Lightning Draft is a web application for drafting Magic: the Gathering cards. Users can visit www.lightningdraft.online to build a deck from randomly generated booster packs. This app was inspired by digital card games such as Hearthstone. Lightning Draft is a quick, fun, and simple alternative to drafting with physical cards.

Scalable Syriac Paleography Using Interactive Visualization, R. Jordan Crouser, Michael Penn, Nicholas Howe

Computer Science: Faculty Publications

Syriac (a dialect of Aramaic) was the primary language spoken in the late ancient Middle East between the second and eighth centuries AD, and continues to be a language of Christian scholarship and liturgy up to the present day. There are approximately 20,000 known surviving Syriac manuscripts. Among early manuscripts, only around 10% include a scribal note that provides information regarding when, where, and by whom a given manuscript was written. For the remaining 90%, close examination of subtle differences in the handwritten script remains the primary tool for determining provenance. Prior to this study, scholars classified early Syriac manuscripts …