A selection of published journal articles from faculty members of the School of Engineering and Computer Science at University of the Pacific.

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Submissions from 2024

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ChatReview: A ChatGPT-enabled natural language processing framework to study domain-specific user reviews, Brittany Ho, Ta'Rhonda Mayberry, Khanh Linh Nguyen, Manohar Dhulipala, and Vivek Krishnamani Pallipuram

Submissions from 2023

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Embodied Energy and Carbon Footprint of Concrete Compared to Other Construction Materials, Hector Estrada and Luke Lee

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Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation, Julia Olivieri and Joshua Salzman

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Improved Version of Double-Layer Enclosure Demo, Said Shakerin

Submissions from 2022

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Increasing SARS-Cov2 Cases, Hospitalizations, and Deaths among the Vaccinated Populations during the Omicron (B.1.1.529) Variant Surge in UK, Venkata R. Emani, Vivek Pallipuram Krishnamani, Kartik K. Goswami, Kailash R. Maddula, Raghunath Reddy, Abirath S. Nakka, Sravya Panga, Nikhila K. Reddy, Nidhi K. Reddy, Dheeraj Nandanoor, and Sanjeev Goswami

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Building a Sense of Community Online: Rapport Building Activities for a Remote Learning Environment, Shelly Gulati

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Publisher Correction: The SpliZ generalizes ‘percent spliced in’ to reveal regulated splicing at single-cell resolution (Nature Methods, (2022), 19, 3, (307-310), 10.1038/s41592-022-01400-x), Julia E. Olivieri, Roozbeh Dehghannasiri, and Julia Salzman

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The SpliZ generalizes ‘percent spliced in’ to reveal regulated splicing at single-cell resolution, Julia E. Olivieri, Roozbeh Dehghannasiri, and Julia Salzman

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Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes, Joshua P. Steimel, Kaeli Welsh, Derek Bolhuis, Anneroos Nederstigit, Joshua Boyer, Brenda Temple, Thomas Bonacci, Li Gu, Alban Ordureau, Qi Zhang, Michael Emanuele, Joseph Harrison, and Nicholas Brown

Submissions from 2021

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Specific splice junction detection in single cells with SICILIAN, Roozbeh Dehghannasiri, Julia E. Olivieri, Ana Damljanovic, and Julia Salzman

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A Simulation-Assisted Teaching Practice: Teaching AC Variable Speed Systems Using Simulation Models Library, Jinzhu Gao and Qian Yang

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A study of carbon emissions and energy consumption of wind power generation in the Panhandle of Texas, Rahim Khoie, Andrew Bose, and Joshua Saltsman

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Plan B-Design Methodology for Cyber-Physical Systems Robust to Timing Failures, Mohammadreza Mehrabian, Mohammad Khayatian, Edward Andert, Reese Grimsley, Kyle Liang, Yi Hu, Ian McCormack, Carlee Joe-Wong, Jonathan Aldrich, Bob Iannucci, and Aviral Shrivastava

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Plan B-Design Methodology for Cyber-Physical Systems Robust to Timing Failures, Mohammadreza Mehrabian, Khayatian Mohammad, Andret Edward, Grimsley Reese, Liang Kyle, Hu Yi, Ian McCormack, Joe-Wong Carlee, Aldrich Jonathan, and Bob Iannucci

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RNA splicing programs define tissue compartments and cell types at single-cell resolution, Julia E. Olivieri, Roozbeh Dehghannasiri, Peter Wang, Sori Jang, Antoine De Morree, Serena Y. Tan, Jingsi Ming, Angela R. Wu, Stephen R. Quake, Mark A. Krasnow, and Julia Salzman

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Mathematical Analysis of Line Intersection and Shortest Distance Algorithms, Sajina Pradhan, Suk-seung Hwang, and Dongbin Lee

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Fluids Demonstrations III: Viscous Flow in Modified Thin Enclosures, Centrifugal Effect, Vortical Flow, and Turbulence, Said Shakerin

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Mechanically transduced immunosorbent assay to measure protein-protein interactions, Joshua P. Steimel, Joseph Harrison, Brian Strahl, Diego Sandoval, Michael Pappas, Kathyrn Randene, and Christopher Petell

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Identification of disease-linked hyperactivating mutations in UBE3A through large-scale functional variant analysis, Joshua P. Steimel, Kellan Weston, Xiaoyi Gao, Jinghan Zhao, Susan Maloney, Jill Gotoff, Sumit Parikh, Marwan Shinawi, and Joseph Harrison

Submissions from 2020

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Maybe-tainted data: Theory and a case study, Sepehr Amir-Mohammadian, Christian Skalka, and Samuel Clark

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Teaching Students about Usability Testing in Distance Learning Environments, Daniel Cliburn and Osvaldo Jimenez

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Correct Audit Logging in Concurrent Systems, Chadi El Kari and Sepehr Amir-Mohammadian

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A Study on the Relationship between the Rank of Input Data and the Performance of Random Weight Neural Network, Jinzhu Gao, Weipeng Cao, Lei Hu, Xizhao Wang, and Zhong Ming

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Spiking network optimized for word recognition in noise predicts auditory system hierarchy, Seyedeh F. Khatami Firoozabadi and Escabi A. Monty

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Performance Analysis of AOA Estimation for Concentric Ring Array Antenna in Beamforming Satellite System, Dongbin Lee

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An Experimental Investigation of Forces on Cortical Bone in Deep-Hole Bone Drilling, JuEun Lee and Serena Chu

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Injection water jet peening of carburised 18CrNiMo7-6 steel surfaces, Jiancheng Liu, Yongtao Ma, Lundun Zhang, and Lanrong Liu

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Hard milling of carburized and waterjet peened 18CrNiMo7-6 steel, Yongtao Ma, Yongbin Zhang, Jiancheng Liu, Lanrong Liu, and Junzhen Gong

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A2Cloud-RF: A random forest based statistical framework to guide resource selection for high-performance scientific computing on the cloud, David Mueller

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A2Cloud-RF: A Random Forest Based Statistical Framework to Guide Resource Selection for High-performance Scientific Computing on the Cloud, Venkittaraman Pallipuram Krishnamani, Chadi ElKari, David Mueller, David Samuel, Cody J. Balos, and Syeduzzaman Khan

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Improved demo of granular flow, Said Shakerin

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Distinct neural ensemble response statistics are associated with recognition and discrimination of natural sound textures, Xiu Zhai, Fatemeh Khatami, Mina Sadeghi, Fengrong He, Heather L. Read, Ian H. Stevenson, and Monty A. Escabí

Submissions from 2019

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Flowback verses first-flush: New information on the geochemistry of produced water from mandatory reporting, Mary Kay Camarillo and William T. Stringfellow

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Promoting an Accessible Learning Environment for Students with Disabilities via Faculty Development (Practice Brief), Michael E. Doherty, Daniel Nuss, Terri Johnson, Sheryl Burgstahler, and Feilin Hsiao

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Uncertain Knowledge Reasoning Based on the Fuzzy Multi-Entity Bayesian Network, Jinzhu Gao, Dun Li, Hong Wu, Zhuoyun Liu, Lun Li, and Zhiyun Zheng

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Applicability of Drug Response Metrics for Cancer Studies Using Biomaterials, Maria Gencoglu

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An Omentum-Inspired 3D PEG Hydrogel for Identifying ECM-drivers of Drug Resistant Ovarian Cancer, Maria Gencoglu, Elizabeth Brooks, Daniel Corbett, Kelly Stevens, and Shelly Peyton

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An Omentum-Inspired 3D PEG Hydrogel for Identifying ECM-drivers of Drug Resistant Ovarian Cancer, Maria Gencoglu, Elizabeth Brooks, Daniel Corbett, Kelly Stevens, and Shelly Peyton

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Applicability of Drug Response Metrics for Cancer Studies Using Biomaterials, Maria Gencoglu, Elizabeth Brooks, Sualyneth Galarza, Shelly Peyton, Jennifer Munson, and Chase Cornelison

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Fantasy Football as Sport and Game, Osvaldo Jimenez

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Spiking network optimized for word recognition in noise predicts auditory system hierarchy, Seyedeh Fatemeh Khatami and Monty Escabí

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Drilling performance monitoring and optimization: a data-driven approach, Mehdi Khazaeli, S. Lashari, A. Takbiri-Borujeni, E. Fathi, and T. Sun

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Renewable resources of the northern half of the United States: potential for 100% renewable electricity, Rahim Khoie, Kyle Ugale, and James Benefield

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Analysis of blade fragment risk at a wind energy facility, Scott Larwood and David Simms

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Volumetric Tooth Wear Measurement of Scraper Conveyor Sprocket Using Shape from Focus-Based Method, Jiancheng Liu, Yinchuan Liu, and Hua Ding

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Global Biobank Engine: Enabling genotype-phenotype browsing for biobank summary statistics, Gregory McInnes, Yosuke Tanigawa, Chris Deboever, Adam Lavertu, Julia E. Olivieri, Matthew Aguirre, and Manuel A. Rivas

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The ASCE ExCEEd Teaching Workshop: Assessing 20 Years of Instructional Development, Camilla M. Saviz, Allen Estes, Stephen Ressler, Brock Barry, Carol Considine, Norman Dennis, Scott Hamilton, David Hurwitz, Tanya Kunberger, Thomas Lenox, Tonya Nilsson, James O'brien, Robert Oneill, David Saftner, Kelly Salyards, Ronald Welch, and Dion Coward

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Fluids Demonstrations II: Bubbles in Mondrian Painting, Eruption-Like Flow, Rotational Instability, and Wake Vortices, Said Shakerin

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Aggregation Dynamics of Active Rotating Particles in Dense Passive Media, Joshua P. Steimel, Alfredo Alexander-Katz, and Juan Aragones

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Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments, Ning Wang, Ya Yang, Michael J. Moore, Samuel F. Brockington, Joseph F. Walker, Joseph W. Brown, Bin Liang, Tao Feng, Caroline Edwards, Jessica Mikenas, Julia E. Olivieri, Vera Hutchison, Alfonso Timoneda, Tommy Stoughton, Raúl Puente, Lucas C. Majure, Urs Eggli, and Stephen A. Smith

Submissions from 2018

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Biological treatment of oil and gas produced water: a review and meta-analysis, Mary Kay Camarillo and William T. Stringfellow

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Fuzziness based Online Sequential Extreme Learning Machine for Classification Problems, Weipeng Cao, Jinzhu Gao, Zhong Ming, Shubin Cai, and Zhiguang Shan

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A review on neural networks with random weights, Weipeng Cao, Xizhao Wang, Zhong Ming, and Jinzhu Gao

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Study of microcutting fundamentals for peripheral and end cutting edges in micro-end-milling, Xiang Cheng, Jiancheng Liu, Guangming Zheng, Xianhai Yang, and Yebing Tian

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Viscosity of CNT Loaded Epoxy Resin, Hector Estrada, Luke Lee, Jonathan Trovillion, Maciej Tusz, Ashok Kumar, and Larry Stephenson

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Experimental Results of Accelerated Long-term Durability Performance of E-glass Fiber Reinforced Polymer Composite Materials, Hector Estrada, Jonathan Trovillion, Hugh McManus, Ashok Kumar, Larry Stephenson, and William Lewis

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Fuzziness-based online sequential extreme learning machine for classification problems, Jinzhu Gao, Zhong Ming, Weipeng Cao, Zhiguang Shan, and Shubin Cai

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Comparative Study of Multicellular Tumor Spheroid Formation Methods and Implications for Drug Screening, Maria Gencoglu, Lauren Barney, Christopher Hall, Elizabeth Brooks, Alyssa Schwartz, Daniel Corbett, Kelly Stevens, and Shelly Peyton

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Comparative Study of Multicellular Tumor Spheroid Formation Methods and Implications for Drug Screening, Maria Gencoglu, Lauren Barney, Christopher L. Hall, Elizabeth A. Brooks, Alyssa D. Schwartz, Daniel C. Corbett, Kelly R. Stevens, and Shelly R. Peyton

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Complementary, Semi-automated Methods for Creating Multi-dimensional, PEG-based Biomaterials, Maria Gencoglu, Elizabeth Brooks, Lauren Jansen, Annali Yurkevicz, and Shelly Peyton

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Complementary, Semi-automated Methods for Creating Multi-dimensional, PEG-based Biomaterials, Maria Gencoglu, Lauren Jansen, Annali Yurkevicz, Elizabeth A. Brooks, and Shelly Peyton

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Origins of scale invariance in vocalization sequences and speech, Fatemeh Khatami, Markus Wöhr, Heather L. Read, and Monty A. Escabí

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Reconsidering downwind operation by analysis of the NREL Phase VI data, Scott Larwood and Raymond Chow

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Molecular mechanism of GPCR-mediated arrestin activation, Naomi R. Latorraca, Jason K. Wang, Brian Bauer, Raphael J.L. Townshend, Scott A. Hollingsworth, Julia E. Olivieri, H. Eric Xu, Martha A. Sommer, and Ron O. Dror

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Parameters affecting mechanical and thermal responses in bone drilling: A review, JuEun Lee, Craig Chavez, and Joorok Park

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Experimental Determination of Thermal Conductivity of Cortical Bone by Compensating Heat Loss in Parallel Plate Method, JuEun Lee, SeonJeong Huh, and HeeJoon Lee

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Effective Engineering Video Tutorials, Luke Lee, Hector Estrada, and Mehdi Khazaeli

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Effect of SiCp/Al micromilling feed on cutting force and surface topography, Jiancheng Liu, Kai Cheng, Hui Ding, and Shijin Chen

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Micro Finite Element Simulation of Cutting Process of SiCp/Al Particle Reinforced Composites, Jiancheng Liu and Xialoe Qi

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Fluids Demonstrations: Trailing Vortices, Plateau Border, Angle of Repose, and Flow Instability, Said Shakerin

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Mysterious soda can, Said Shakerin and Edwin Pejack

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From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales, Joseph F. Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia E. Olivieri, Nathanael Walker-Hale, Lucas A. Majure, Raúl Puente, Gudrun Kadereit, Maximilian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore, and Stephen A. Smith

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Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events, Ya Yang, Michael J. Moore, Samuel F. Brockington, Jessica Mikenas, Julia E. Olivieri, Josepf F. Walker, and Stephen A. Smith

Submissions from 2017

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Identifying chemicals of concern in hydraulic fracturing fluids used for oil production, Mary Kay Camarillo, William T. Stringfellow, J. K. Domen, W. L. Sandelin, and C. Varadharajan

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Comparison of chemical-use between hydraulic fracturing, acidizing, and routine oil and gas development, Mary Kay Camarillo, William T. Stringfellow, J. K. Domen, and S. B. Shonkoff

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Dynamic localization of HmpF regulates type IV pilus activity and directional motility in the filamentous cyanobacterium Nostoc punctiforme, Ye Won Cho, Alfonso Gonzales, Thomas V. Harwood, Jessica Huynh, Yeji Hwang, Jun Sang Park, Anthony Q. Trieu, Parth Italia, Vivek K. Pallipuram, and Douglas D. Risser

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An Interdisciplinary Course on Human-Computer Interaction, Daniel Cliburn

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Assessment of Levee Erosion using Image Processing and Contextual Cueing, Mehdi A. Khazaeli, Leili Javadpour, Hector Estrada, and Alo Takbiri-Borujeni

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Gesture based Human Computer Interaction for Athletic Training, Mehdi Khazaeli, Chadi ElKari, J. Baizer, and L. Javadpour

Submissions from 2016

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Physical-chemical analysis of hydraulic fracturing chemicals in the context of produced water treatment, Mary Kay Camarillo, William T. Stringfellow, and J. K. Domen

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Physical, chemical, and biological characteristics of compounds used in hydraulic fracturing, Mary Kay Camarillo, William T. Stringfellow, J. K. Domen, W. L. Sandelin, and S. Borglin

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Treatment of oil-water emulsion from the machinery industry by Fenton’s reagent, Mary Kay Camarillo, William T. Stringfellow, C. Feng, H. Sun, and S. Li

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Performance of sanitary sewer collection system odour control devices operating in diverse conditions, Mary Kay Camarillo, William T. Stringfellow, J. S. Hanlon, and Elizabeth Basha

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Pairing high-frequency data with a link-node model to manage dissolved oxygen impairment in a dredged estuary., Mary K. Camarillo, Gregory Weissmann, Shelly Gulati, Joel Herr, Scott Sheeder, and William T. Stringfellow

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Research on the algorithm of shearer power prediction based on extreme learning machine, Hua Ding, Qi Chang, Zhao Jian Yang, and Jiancheng Liu

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A Study on the Cytotoxicity of Carbon-based Materials, Maria Gencoglu, Saha Dipendu, Caryn L. Heldt, Vijayaragavan K. Saagar, Jihua Chen, and Saksule Ashish

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A Study on the Cytotoxicity of Carbon-based Materials, Maria Gencoglu, Dipendu Saha, Caryn Heldt, Jihua Chen, and Ashish Saksule

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Pairing high-frequency data with a link-node model to manage dissolved oxygen impairment in a dredged estuary, Shelly Gulati, Joel Herr, Gregory A. Weissmann, and MaryKay Camarillo

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Evaluation of watershed-derived mass loads to prioritize TMDL decision-making, Shelly Gulati, Ashley Stubblefield, Jeremy Hanlon, C. L. Spier, Mary K. Camarillo, and William T. Stringfellow

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Microdroplet formation in rounded flow-focusing junctions, Shelly Gulati, Kalpana Vijayakumar, Wilson W. Good, Warren L. Tamayo, Akhil R. Patel, and Xize Niu

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Evaluation of the relationship of tibiofemoralkinematics before and after total knee replacement in an in vitro model of cranial cruciate deficiency in the dog, R. N. Howie, T. L. Foutz, C. C. Cathcart, Jeffrey S. Burmeister, and S. C. Budsberg

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Machine Learning Approach for Pronominal Anaphora Resolution Based on Linguistic and Computational Features, Leili Javadpour, Mehdi Khazaeli, and Gerald Knapp

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Scrum in the Undergraduate Computer Science Curriculum, Osvaldo Jimenez and Daniel Cliburn

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MR elastography for evaluating regeneration of tissue-engineered cartilage in an ectopic mouse model., Vahid Khalilzad-Sharghi, Zhongji Han, Huihui Xu, and Shadi F. Othman

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Image Segmentation from RGBD Images by 3D Point Cloud Attributes and High-Level Features, Mehdi A. Khazaeli, Leili Javadpour, and Gerald M. Knapp

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Image processing for erosion control of open-pit mines, Mehdi Khazaeli, Leili Javadpour, and Hector Estrada

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Flutter of Variations on a 5 MW Swept Wind Turbine Blade, Scott M. Larwood

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Pipelining Image Compositing in Heterogeneous Networking Environments, Ning Liu, Dengming Zhu, Zhaoqi Wang, Hong Qin, Jianfeng Zhan, and Jinzhu Gao

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Design and Performance Monitoring of Snow-Supporting Structures for the Milepost 151 Avalanche near Jackson, WY, Scott Merry, Rand Decker, Sean Strain, and Joshua Hewes

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Three-Dimensional Levee and Floodwall Underseepage, Scott Merry, Aaron Leopold, Timothy Stark, and Navid Jafari