Research articles, presentations, and other scholarship

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  • Access to Autism Spectrum Disorder Services for Rural Appalachian Citizens 

    Scarpa, Angela; Jensen, Laura S.; Gracanin, Denis; Ramey, Sharon L.; Dahiya, Angela V.; Ingram, L. Maria; Albright, Jordan; Gatto, Alyssa J.; Scott, Jen Pollard; Ruble, Lisa (2020-01)
    Background: Low-resource rural communities face significant challenges regarding availability and adequacy of evidence-based services. Purposes: With respect to accessing evidence-based services for Autism Spectrum ...
  • Hypergraph-based connectivity measures for signaling pathway topologies 

    Franzese, Nicholas; Groce, Adam; Murali, T. M.; Ritz, Anna (2019-10)
    Signaling pathways describe how cells respond to external signals through molecular interactions. As we gain a deeper understanding of these signaling reactions, it is important to understand how molecules may influence ...
  • Unsupervised discovery of solid-state lithium ion conductors 

    Zhang, Ying; He, Xingfeng; Chen, Zhiqian; Bai, Qiang; Nolan, Adelaide M.; Roberts, Charles A.; Banerjee, Debasish; Matsunaga, Tomoya; Mo, Yifei; Ling, Chen (2019-11-20)
    Although machine learning has gained great interest in the discovery of functional materials, the advancement of reliable models is impeded by the scarcity of available materials property data. Here we propose and demonstrate ...
  • Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment 

    Drozdetski, Aleksander V.; Mukhopadhyay, Abhishek; Onufriev, Alexey V. (2019-11-29)
    The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general ...
  • Application and Evaluation of Surrogate Models for Radiation Source Search 

    Cook, Jared A.; Smith, Ralph C.; Hite, Jason M.; Stefanescu, Razvan; Mattingly, John (MDPI, 2019-12-12)
    Surrogate models are increasingly required for applications in which first-principles simulation models are prohibitively expensive to employ for uncertainty analysis, design, or control. They can also be used to approximate ...
  • A Bayesian approach to multivariate adaptive localization in ensemble-based data assimilation with time-dependent extensions 

    Popov, Andrey A.; Sandu, Adrian (Copernicus Publications, 2019-06-14)
    Ever since its inception, the ensemble Kalman filter (EnKF) has elicited many heuristic approaches that sought to improve it. One such method is covariance localization, which alleviates spurious correlations due to finite ...
  • Uncovering missed indels by leveraging unmapped reads 

    Hasan, Mohammad Shabbir; Wu, Xiaowei; Zhang, Liqing (Springer Nature, 2019-07-31)
    In current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic variants. Although existing alignment tools have shown ...
  • Stratified Feature Sampling for Semi-Supervised Ensemble Clustering 

    Tian, Jialin; Ren, Yazhou; Cheng, Xiang (IEEE, 2019)
    Ensemble Clustering (EC), which seeks to generate a consensus clustering by integrating multiple base clusterings, has attracted increasing attentions. However, traditional EC methods typically have three main limitations: ...
  • BRIoT: Behavior Rune Specification-Based Misbehavior Detection for IoT-Embedded Cyber-Physical Systems 

    Sharma, Vishal; You, Ilsun; Vim, Kangbin; Chen, Ing-Ray; Cho, Jin-Hee (IEEE, 2019)
    The identification of vulnerabilities in a mission-critical system is one of the challenges faced by a cyber-physical system (CPS). The incorporation of embedded Internet of Things (IoT) devices makes it tedious to identify ...
  • Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells 

    Banerjee, Sharmi; Zhu, Hongxiao; Tang, Man; Feng, Wu-chun; Wu, Xiaowei; Xie, Hehuang (Frontiers, 2019-01-15)
    Gene expression regulation is a complex process involving the interplay between transcription factors and chromatin states. Significant progress has been made toward understanding the impact of chromatin states on gene ...
  • Acoustic differences between healthy and depressed people: a cross-situation study 

    Wang, Jingying; Zhang, Lei; Liu, Tianli; Pan, Wei; Hu, Bin; Zhu, Tingshao (2019-10-15)
    Abstract Background Abnormalities in vocal expression during a depressed episode have frequently been reported in people with depression, but less is known about if these ...
  • Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping 

    Tabor, Kathryn M.; Marquart, Gregory D.; Hurt, Christopher; Smith, Trevor S.; Geoca, Alexandra K.; Bhandiwad, Ashwin A.; Subedi, Abhignya; Sinclair, Jennifer L.; Rose, Hannah M.; Polys, Nicholas F.; Burgess, Harold A. (2019-02-08)
    Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad ...
  • Hinge-Loss Markov Random Fields and Probabilistic Soft Logic 

    Bach, Stephen H.; Broecheler, Matthias; Huang, Bert; Getoor, Lise (MIT Press, 2017)
    A fundamental challenge in developing high-impact machine learning technologies is balancing the need to model rich, structured domains with the ability to scale to big data. Many important problem areas are both richly ...
  • Reorganize Your Blogs: Supporting Blog Re-visitation with Natural Language Processing and Visualization 

    Niu, Shuo; McCrickard, D. Scott; Stelter, Timothy L.; Dix, Alan; Taylor, G. Don (MDPI, 2019-10-07)
    Temporally-connected personal blogs contain voluminous textual content, presenting challenges in re-visiting and reflecting on experiences. Other data repositories have benefited from natural language processing (NLP) and ...
  • MetaCompare: a computational pipeline for prioritizing environmental resistome risk 

    Oh, Min; Pruden, Amy; Chen, Chaoqi; Heath, Lenwood S.; Xia, Kang; Zhang, Liqing (2018-07)
    The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means ...
  • Cyberbiosecurity Challenges of Pathogen Genome Databases 

    Vinatzer, Boris A.; Heath, Lenwood S.; Almohri, Hussain MJ J.; Stulberg, Michael J.; Lowe, Christopher; Li, Song (Frontiers, 2019-05-15)
    Pathogen detection, identification, and tracking is shifting from non-molecular methods, DNA fingerprinting methods, and single gene methods to methods relying on whole genomes. Viral Ebola and influenza genome data are ...
  • Polynomial-Sized Topological Approximations Using the Permutahedron 

    Choudhary, Aruni; Kerber, Michael; Raghvendra, Sharath (2019-01)
    Classical methods to model topological properties of point clouds, such as the Vietoris-Rips complex, suffer from the combinatorial explosion of complex sizes. We propose a novel technique to approximate a multi-scale ...
  • Reconstructing signaling pathways using regular language constrained paths 

    Wagner, Mitchell J.; Pratapa, Aditya; Murali, T. M. (2019-07-15)
    Motivation High-quality curation of the proteins and interactions in signaling pathways is slow and painstaking. As a result, many experimentally detected interactions are not annotated to any pathways. A natural question ...
  • Higher Education Student Body Diversification as Glocal Practice 

    Alvarado, Jose Gerardo (2012-07)
    Georg Simmel's assertion that strangeness organizes nearness and remoteness helps to understand how the social category of First Generation College Student (FGCS, first in the family to attend college) is used at a public ...
  • COSTA: Composite Trust-Based Asset-Task Assignment in Mobile Ad Hoc Networks 

    Cho, Jin-Hee; Al-Hamadi, Hamid; Chen, Ing-Ray (IEEE, 2019)
    In mobile ad hoc networks (MANETs), asset-task assignment problems have been explored with vastly different approaches. Considering the unique characteristics of MANET environments, such as no centralized trusted entity, ...

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