Computer Sciences Commons^™

Surveying Digital Collections Stewardship In Nebraska [Original Survey Form], Jennifer L. Thoegersen, Blake Graham

University of Nebraska-Lincoln Data Repository

No abstract provided.

Modelling And Visualizing Selected Molecular Communication Processes In Biological Organisms: A Multi-Layer Perspective, Aditya Immaneni

School of Computing: Dissertations, Theses, and Student Research

The future pervasive communication and computing devices are envisioned to be tightly integrated with biological systems, i.e., the Internet of Bio-Nano Things. In particular, the study and exploitation of existing processes for the biochemical information exchange and elaboration in biological systems are currently at the forefront of this research direction. Molecular Communication (MC), which studies biochemical information systems with theory and tools from computer communication engineering, has been recently proposed to model and characterize the aforementioned processes. Combined with the rapidly growing field of bio-informatics, which creates a rich profusion of biological data and tools to mine the underlying information, …

Speech Emotion Recognition Using Convolutional Neural Networks, Somayeh Shahsavarani

School of Computing: Dissertations, Theses, and Student Research

Automatic speech recognition is an active field of study in artificial intelligence and machine learning whose aim is to generate machines that communicate with people via speech. Speech is an information-rich signal that contains paralinguistic information as well as linguistic information. Emotion is one key instance of paralinguistic information that is, in part, conveyed by speech. Developing machines that understand paralinguistic information, such as emotion, facilitates the human-machine communication as it makes the communication more clear and natural. In the current study, the efficacy of convolutional neural networks in recognition of speech emotions has been investigated. Wide-band spectrograms of the …

Internet Of Underground Things: Sensing And Communications On The Field For Precision Agriculture, Mehmet C. Vuran, Abdul Salam, Rigoberto Wong, Suat Irmak

School of Computing: Conference and Workshop Papers

The projected increases in World population and need for food have recently motivated adoption of information technology solutions in crop fields within precision agriculture approaches. Internet of underground things (IOUT), which consists of sensors and communication devices, partly or completely buried underground for real-time soil sensing and monitoring, emerge from this need. This new paradigm facilitates seamless integration of underground sensors, machinery, and irrigation systems with the complex social network of growers, agronomists, crop consultants, and advisors. In this paper, state-of-the-art communication architectures are reviewed, and underlying sensing technology and communication mechanisms for IOUT are presented. Recent advances in the …

Scheduling In Mapreduce Clusters, Chen He

School of Computing: Dissertations, Theses, and Student Research

MapReduce is a framework proposed by Google for processing huge amounts of data in a distributed environment. The simplicity of the programming model and the fault-tolerance feature of the framework make it very popular in Big Data processing.

As MapReduce clusters get popular, their scheduling becomes increasingly important. On one hand, many MapReduce applications have high performance requirements, for example, on response time and/or throughput. On the other hand, with the increasing size of MapReduce clusters, the energy-efficient scheduling of MapReduce clusters becomes inevitable. These scheduling challenges, however, have not been systematically studied.

The objective of this dissertation is to …

Increasing Our Vision For 21st-Century Digital Libraries, Elizabeth M. Lorang, Leen-Kiat Soh

University of Nebraska-Lincoln Libraries: Presentations

This presentation

1. Reads digital library interfaces—or their "main door" interfaces—as glimpses into what we have thus far valued in the development of digital libraries
2. Frames a visual way of thinking about textual materials
3. Introduces the work of our research team—where we are now, and where we're headed
4. Draws some connections between the parts

This presentation is very much a look into thinking in process and work in progress and proposes the following ideas:

1. As a community, we can do much more with the digital images we're creating of textual materials than we've heretofore done.
2. We aspire to have additional layers …

Model File Name: 1ehz-Trna(Thick).Stl, Michelle Howell, Karin Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thick).stl

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

This is a teaching model of Phe-tRNA in a thick stick-representation (PDB: 1ehz), designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com under the name “tRNA-Phe small”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following materials: Strong & Flexible Plastic and Elasto Plastic.

Model File Name: 1lmb-Dbd-Tfmono.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DBD-TFmono.stl

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

This is a teaching model of the DNA binding domain of a Lambda repressor transcription factor monomer that accompanies the full color DNA helix (PDB: 1lmb). It is in a cartoon ribbon representation with key amino acid residues in stick representation to highlight interactions with the DNA. This model is designed to accompany 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 DBD”. This model has been printed …

Model File Name: 1ehz-Trna(Thin-Big).X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thin-big).x3d

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

This is a teaching model of Phe-tRNA in a large, but thin stick-representation (PDB: 1ehz), 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 “Full color Phe-tRNA (1ehz)”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Strong & Flexible Plastic.

Model File Name: 1lmb-Dnalong_Fordimer-Test6b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DNAlong_fordimer-test6b.stl

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

This is a teaching model of the 19-bp segment of DNA to which Lambda repressor transcription factor interacts (PDB: 1lmb). It is in a stick representation and has been designed with sites to add magnets to illustrate binding interactions with the transcription factor. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. The model can interact with the dimer form of the transcription factor. This model is designed to accompany a teaching module illustrating transcription factor-DNA binding. The printable model …

Model File Name: 1lmb-Tfdimer-Mags-Joints-Jnd-Sc1-8-Parts-V4b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-TFdimer-mags-joints-jnd-sc1-8-parts-v4b.stl

Additional files: 1lmb-Lys-Ser-extras-v4b.stl and 1lmb-TFdimer-Leu-v4b.stl

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

This is a teaching model of a ribbon and stick representation of the transcription factor lambda repressor (PDB: 1lmb). Key amino acid residues are in stick representation to illustrate the interactions between the repressor and the DNA to which it binds. Some of these residues have been designed with sites to add magnets to illustrate these interactions. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. Some of the residues can be interchanged with other …

Model File Name: Dna-294bp-Magnet-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-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 (294 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: Dna-294bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-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 (294 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 “294bp DNA (handles)”. …

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 …

Expression Of The Microrna-143/145 Cluster Is Decreased In Hepatitis B Virus-Associated Hepatocellular Carcinoma And May Serve As A Biomarker For Tumorigenesis In Patients With Chronic Hepatitis B, Qi Zhao, Xiangfei Sun, Chao Liu, Tao Li, Juan Cui, Chengyong Qin

School of Computing: Faculty Publications

The aims of the present study were to identify the expression profile of microRNA (miR)‑143/145 in hepatitis B virus (HBV)‑associated hepatocellular carcinoma (HCC), explore its association with prognosis and investigate whether the serum miR‑143/145 expression levels may serve as a diagnostic indicator of HBV‑associated HCC. The microRNA (miRNA) chromatin immunoprecipitation dataset was obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus databases, and analyzed using the Wilcoxon signed‑rank test. It was observed that the expression of miR‑143 and miR‑145 was decreased 1.5‑fold in HBV‑associated HCC samples compared with non‑tumor tissue in the TCGA and the GSE22058 datasets …

Cyber Security And Risk Society: Estonian Discourse On Cyber Risk And Security Strategy, Lauren Kook

Copyright, Fair Use, Scholarly Communication, etc.

The main aim of this thesis is to call for a new analysis of cyber security which departs from the traditional security theory. I argue that the cyber domain is inherently different in nature, in that it is lacking in traditional boundaries and is reflexive in nature. Policy-makers are aware of these characteristics, and in turn this awareness changes the way that national cyber security strategy is handled and understood. These changes cannot be adequately understood through traditional understanding of security, as they often are, without missing significant details. Rather, examining these changes through the lens of Ulrich Beck’s risk …