Digital Commons Network^™

Refinement Of Alphafold2 Models Against Experimental And Hybrid Cryo-Em Density Maps, Maytha Alshammari, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Recent breakthroughs in deep learning-based protein structure prediction show that it is possible to obtain highly accurate models for a wide range of difficult protein targets for which only the amino acid sequence is known. The availability of accurately predicted models from sequences can potentially revolutionise many modelling approaches in structural biology, including the interpretation of cryo-EM density maps. Although atomic structures can be readily solved from cryo-EM maps of better than 4 Å resolution, it is still challenging to determine accurate models from lower-resolution density maps. Here, we report on the benefits of models predicted by AlphaFold2 (the best-performing …

Loss Of Acta2 In Cardiac Fibroblasts Does Not Prevent The Myofibroblast Differentiation Or Affect The Cardiac Repair After Myocardial Infarction, Yuxia Li, Chaoyang Li, Qianglin Liu, Leshan Wang, Adam X. Bao, Jangwook P. Jung, Sanjeev Dodlapati, Jingwen Sun, Peidong Gao, Xujia Zhang, Joseph Francis, Jeffery D. Molkentin, Xing Fu

Computer Science Faculty Publications

In response to myocardial infarction (MI), quiescent cardiac fibroblasts differentiate into myofibroblasts mediating tissue repair. One of the most widely accepted markers of myofibroblast differentiation is the expression of Acta2 which encodes smooth muscle alpha-actin (SMαA) that is assembled into stress fibers. However, the requirement of Acta2/SMαA in the myofibroblast differentiation of cardiac fibroblasts and its role in post-MI cardiac repair remained unknown. To answer these questions, we generated a tamoxifen-inducible cardiac fibroblast-specific Acta2 knockout mouse line. Surprisingly, mice that lacked Acta2 in cardiac fibroblasts had a normal post-MI survival rate. Moreover, Acta2 deletion did …

Machine Learning-Based Event Generator For Electron-Proton Scattering, Y. Alanazi, P. Ambrozewicz, M. Battaglieri, A.N. Hiller Blin, M. P. Kuchera, Y. Li, T. Liu, R. E. Mcclellan, W. Melnitchouk, E. Pritchard, M. Robertson, N. Sato, R. Strauss, L. Velasco

Computer Science Faculty Publications

We present a new machine learning-based Monte Carlo event generator using generative adversarial networks (GANs) that can be trained with calibrated detector simulations to construct a vertex-level event generator free of theoretical assumptions about femtometer scale physics. Our framework includes a GAN-based detector folding as a fast-surrogate model that mimics detector simulators. The framework is tested and validated on simulated inclusive deep-inelastic scattering data along with existing parametrizations for detector simulation, with uncertainty quantification based on a statistical bootstrapping technique. Our results provide for the first time a realistic proof of concept to mitigate theory bias in inferring vertex-level event …

Toward A Real-Time Index Of Pupillary Activity As An Indicator Of Cognitive Load, Gavindya Jayawardena, Yasith Jayawardana, Sampath Jayarathna, Jonas Högström, Thomas Papa, Deepak Akkil, Andrew T. Duchowski, Vsevolod Peysakhovich, Izabela Krejtz, Nina Gehrer, Krzysztof Krejtz

Computer Science Faculty Publications

The Low/High Index of Pupillary Activity (LHIPA), an eye-tracked measure of pupil diameter oscillation, is redesigned and implemented to function in real-time. The novel Real-time IPA (RIPA) is shown to discriminate cognitive load in re-streamed data from earlier experiments. Rationale for the RIPA is tied to the functioning of the human autonomic nervous system yielding a hybrid measure based on the ratio of Low/High frequencies of pupil oscillation. The paper's contribution is drawn from provision of documentation of the calculation of the RIPA. As with the LHIPA, it is possible for researchers to apply this metric to their own experiments …

Ready Raider One: Exploring The Misuse Of Cloud Gaming Services, Guannan Liu, Daiping Liu, Shuai Hao, Xing Gao, Kun Sun, Haining Wang

Computer Science Faculty Publications

Cloud gaming has become an emerging computing paradigm in recent years, allowing computer games to offload complex graphics and logic computation to the cloud. To deliver a smooth and high-quality gaming experience, cloud gaming services have invested abundant computing resources in the cloud, including adequate CPUs, top-tier GPUs, and high-bandwidth Internet connections. Unfortunately, the abundant computing resources offered by cloud gaming are vulnerable to misuse and exploitation for malicious purposes. In this paper, we present an in-depth study on security vulnerabilities in cloud gaming services. Specifically, we reveal that adversaries can purposely inject malicious programs/URLs into the cloud gaming services …

Scholarly Big Data Quality Assessment: A Case Study Of Document Linking And Conflation With S2orc, Jian Wu, Ryan Hiltabrand, Dominik Soós, C. Lee Giles

Computer Science Faculty Publications

Recently, the Allen Institute for Artificial Intelligence released the Semantic Scholar Open Research Corpus (S2ORC), one of the largest open-access scholarly big datasets with more than 130 million scholarly paper records. S2ORC contains a significant portion of automatically generated metadata. The metadata quality could impact downstream tasks such as citation analysis, citation prediction, and link analysis. In this project, we assess the document linking quality and estimate the document conflation rate for the S2ORC dataset. Using semi-automatically curated ground truth corpora, we estimated that the overall document linking quality is high, with 92.6% of documents correctly linking to six major …

Online Deep Learning From Doubly-Streaming Data, Heng Lian, John S. Atwood, Bo-Jian Hou, Jian Wu, Yi He

Computer Science Faculty Publications

This paper investigates a new online learning problem with doubly-streaming data, where the data streams are described by feature spaces that constantly evolve, with new features emerging and old features fading away. A plausible idea to deal with such data streams is to establish a relationship between the old and new feature spaces, so that an online learner can leverage the knowledge learned from the old features to better the learning performance on the new features. Unfortunately, this idea does not scale up to high-dimensional multimedia data with complex feature interplay, which suffers a tradeoff between onlineness, which biases shallow …

The Landscape Of Accessible Chromatin In Quiescent Cardiac Fibroblasts And Cardiac Fibroblasts Activated After Myocardial Infarction, Chaoyang Yi, Jiangwen Sun, Qianglin Liu, Sanjeeva Dodlapati, Hao Ming, Leshan Wang, Yuxia Li, Rui Li, Zongliang Jiang, Joseph Francis, Xing Fu

Computer Science Faculty Publications

After myocardial infarction, the massive death of cardiomyocytes leads to cardiac fibroblast proliferation and myofibroblast differentiation, which contributes to the extracellular matrix remodelling of the infarcted myocardium. We recently found that myofibroblasts further differentiate into matrifibrocytes, a newly identified cardiac fibroblast differentiation state. Cardiac fibroblasts of different states have distinct gene expression profiles closely related to their functions. However, the mechanism responsible for the gene expression changes during these activation and differentiation events is still not clear. In this study, the gene expression profiling and genome-wide accessible chromatin mapping of mouse cardiac fibroblasts isolated from the uninjured myocardium and the …

A Qualitative Comparison Of Parent And Childcare Provider Perceptions Of Communication And Family Engagement In Children's Healthy Eating And Physical Activity, Danae Dinkel, Maggie Rasmussen, John P. Rech, Kailey Snyder, Dipti Dev

Department of Child, Youth, and Family Studies: Faculty Publications

Background: Parents and childcare providers play a substantial role in the development of health behaviors among the children they care for. In order to ensure the optimal growth and development of children, communication and family engagement in childcare is critical. Previous studies examining parent or provider perceptions about healthy eating or physical activity have explored these concepts individually and/or have only included only parents or providers. Therefore, the purpose of this study was to compare childcare provider and parent perceptions of communication regarding healthy eating and physical activity as well as use of best practice strategies on family engagement for …

Promising Findings That The Cultivating Healthy Intentional Mindful Educators’ Program (Chime) Strengthens Early Childhood Teachers’ Emotional Resources: An Iterative Study, Holly Hatton-Bowers, Caron Clark, Gilbert R. Parra, Jessica L. Calvi, Michael Yellow Bird, Pearl Avari, Jaclynn Foged, John Smith

Department of Child, Youth, and Family Studies: Faculty Publications

Findings suggest that an eight-week mindfulness compassion-based program, Cultivating Healthy Intentional Mindful Educators (CHIME), is a feasible professional development intervention for early childhood (EC) teachers to support their emotion regulation and psychological and workplace well-being. We offer preliminary evidence that learning about mindfulness, self-compassion, and social-emotional learning supports EC teachers in strengthening their knowledge and application of practices to be more mindful and less emotionally reactive and emotionally exhausted at work. In analyzing both EC teacher feedback and survey data from two pilot studies, there was promising evidence that participating in CHIME enhanced awareness of emotions and the development of …

Investigating Moderators Of Daily Marital To Parent–Child Spillover: Individual And Family Systems Approaches, Patty X. Kuo, Kejin Lee, Victoria J. Johnson, Emily J. Starr

Department of Child, Youth, and Family Studies: Faculty Publications

Objective: We tested whether cognitive reappraisal and coparenting quality moderate marital to parent–child spillover in mothers and fathers.

Background: The influence of marital relationship quality on parent–child relationships, referred to as the spillover effect, is well documented. Factors that may attenuate the occurrence of spillover, however, remain unclear. Cognitive reappraisal, an emotion regulation strategy that promotes the reframing of emotional situations as neutral or positive, and coparenting—the intermediate subsystem between the marital and parent–child relationships—may buffer the effects of marital to parent–child spillover.

Method: Using daily diary data from mother–father couples (N = 96) of young children (M_age = …

The Development Of Social Competence In Children With Disabilities, Soo-Young Hong, Elizabeth A. Steed, Lori E. Meyer, İbrahim H. Acar

Department of Child, Youth, and Family Studies: Faculty Publications

Children with disabilities experience unique challenges in developing social skills critical to achieve their social goals. Although there are individual differences, children with delays and disabilities may struggle to communicate with others, understand gestures, and take other people’s viewpoints. These differences may prevent children with disabilities from initiating and sustaining social interactions and, in turn, from developing high levels of social competence (Hebbeler & Spiker, 2016).

To support social development of children with disabilities, it is important to promote positive relationships within the family system as well as the teaching of social skills in inclusive early learning environments (Mahoney et …

The Dsa Toolkit Shines Light Into Dark And Stormy Archives, Shawn Morgan Jones, Himarsha R. Jayanetti, Alex Osborne, Paul Koerbin, Klein Martin, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

Web archive collections are created with a particular purpose in mind. A curator selects seeds, or original resources, which are then captured by an archiving system and stored as archived web pages, or mementos. The systems that build web archive collections are often configured to revisit the same original resource multiple times. This is incredibly useful for understanding an unfolding news story or the evolution of an organization. Unfortunately, over time, some of these original resources can go off-topic and no longer suit the purpose for which the collection was originally created. They can go off-topic due to web site …

Is Ethereum's Progpow Asic Resistant?, Jason Orender, Ravi Mukkamala, Mohammad Zubair, Steven Furnell (Ed.), Paolo Mori (Ed.), Edgar Weippl (Ed.), Oliver Camp (Ed.)

Computer Science Faculty Publications

Cryptocurrencies are more than a decade old and several issues have been discovered since their then. One of these issues is a partial negation of the intent to “democratize” money by decentralizing control of the infrastructure that creates, transmits, and stores monetary data. The Programmatic Proof of Work (ProgPoW) algorithm is intended as a possible solution to this problem for the Ethereum cryptocurrency. This paper examines ProgPow’s claim to be Application Specific Integrated Circuit (ASIC) resistant. This is achieved by isolating the proof-of-work code from the Ethereum blockchain, inserting the ProgPoW algorithm, and measuring the performance of the new implementation …

Theory Entity Extraction For Social And Behavioral Sciences Papers Using Distant Supervision, Xin Wei, Lamia Salsabil, Jian Wu

Computer Science Faculty Publications

Theories and models, which are common in scientific papers in almost all domains, usually provide the foundations of theoretical analysis and experiments. Understanding the use of theories and models can shed light on the credibility and reproducibility of research works. Compared with metadata, such as title, author, keywords, etc., theory extraction in scientific literature is rarely explored, especially for social and behavioral science (SBS) domains. One challenge of applying supervised learning methods is the lack of a large number of labeled samples for training. In this paper, we propose an automated framework based on distant supervision that leverages entity mentions …

A Synthetic Prediction Market For Estimating Confidence In Published Work, Sarah Rajtmajer, Christopher Griffin, Jian Wu, Robert Fraleigh, Laxmann Balaji, Anna Squicciarini, Anthony Kwasnica, David Pennock, Michael Mclaughlin, Timothy Fritton, Nishanth Nakshatri, Arjun Menon, Sai Ajay Modukuri, Rajal Nivargi, Xin Wei, Lee Giles

Computer Science Faculty Publications

[First paragraph] Concerns about the replicability, robustness and reproducibility of findings in scientific literature have gained widespread attention over the last decade in the social sciences and beyond. This attention has been catalyzed by and has likewise motivated a number of large-scale replication projects which have reported successful replication rates between 36% and 78%. Given the challenges and resources required to run high-powered replication studies, researchers have sought other approaches to assess confidence in published claims. Initial evidence has supported the promise of prediction markets in this context. However, they require the coordinated, sustained effort of collections of human experts …

Reciprocal Regulation Of Mitofusin 2-Mediated Mitophagy And Mitochondrial Fusion By Different Pink1 Phosphorylation Events, Jiajia Li, Xiawei Dang, Antonietta Franco, Gerald W Dorn

2020-Current year OA Pubs

Mitochondrial repair is essential to metabolic homeostasis. Outer mitochondrial membrane mitofusin (MFN) proteins orchestrate mitochondrial fusion that opposes mitochondrial degeneration caused by senescence. Depending upon physiological context, MFN2 can either mediate mitochondrial fusion or recruit cytosolic Parkin to initiate mitophagic elimination. Because it is not clear how these events are counter-regulated we engineered and expressed MFN2 mutants that mimic phosphorylated or non-phosphorylatable MFN2 at its PINK1 phosphorylation sites: T111, S378, and S442. By interrogating mitochondrial fusion, polarization status, and Parkin binding/mitophagy as a function of inferred MFN2 phosphorylation, we discovered that individual MFN2 phosphorylation events act as a biological "bar-code", …

Association Of Pretreatment Hippocampal Volume With Neurocognitive Function In Patients Treated With Hippocampal Avoidance Whole Brain Radiation Therapy For Brain Metastases: Secondary Analysis Of Nrg Oncology/Rtog 0933, Christopher D. Abraham, Stephanie L. Pugh, Joseph A. Bovi, Vinai Gondi, Minesh P. Mehta, Tammie Benzinger, Christopher J. Owen, Simon S. Lo, Vijayananda Kundapur, Paul D. Brown, Alexander Y. Sun, Steven P. Howard, Albert S Denittis, Clifford G. Robinson, Lisa A. Kachnic

2020-Current year OA Pubs

PURPOSE: Hippocampal volume (HV) is an established predicting factor for neurocognitive function (NCF) in neurodegenerative disease. Whether the same phenomenon exists with hippocampal-avoidant whole brain radiation therapy is not known; therefore, we assessed the association of baseline HV with NCF among patients enrolled on RTOG 0933.

METHODS AND MATERIALS: Hippocampal volume and total brain volume were calculated from the radiation therapy plan. Hippocampal volume was correlated with baseline and 4-month NCF scores (Hopkins Verbal Learning Test-Revised [HVLT-R] Total Recall [TR], Immediate Recognition, and Delayed Recall [DR]) using Pearson correlation. Deterioration in NCF was defined per the primary endpoint of RTOG …

Predicting Coronary Stenosis Progression Using Plaque Fatigue From Ivus-Based Thin-Slice Models: A Machine Learning Random Forest Approach, Xiaoya Guo, Akiko Maehara, Mingming Yang, Liang Wang, Jie Zheng, Habib Samady, Gary S Mintz, Don P Giddens, Dalin Tang

2020-Current year OA Pubs

No abstract provided.

Creation Of Philadelphia Chromosome By Crispr/Cas9-Mediated Double Cleavages On Bcr And Abl1 Genes As A Model For Initial Event In Leukemogenesis, Minori Tamai, Kenji Kamimoto, Kohei Omachi, Et Al.

2020-Current year OA Pubs

The Philadelphia (Ph) chromosome was the first translocation identified in leukemia. It is supposed to be generated by aberrant ligation between two DNA double-strand breaks (DSBs) at the BCR gene located on chromosome 9q34 and the ABL1 gene located on chromosome 22q11. Thus, mimicking the initiation process of translocation, we induced CRISPR/Cas9-mediated DSBs simultaneously at the breakpoints of the BCR and ABL1 genes in a granulocyte-macrophage colony-stimulating factor (GM-CSF) dependent human leukemia cell line. After transfection of two single guide RNAs (sgRNAs) targeting intron 13 of the BCR gene and intron 1 of the ABL1 gene, a factor-independent subline was …

Edge-Centric Analysis Of Stroke Patients: An Alternative Approach For Biomarkers Of Lesion Recovery, Sebastian Idesis, Joshua Faskowitz, Richard F Betzel, Maurizio Corbetta, Olaf Sporns, Gustavo Deco

2020-Current year OA Pubs

Most neuroimaging studies of post-stroke recovery rely on analyses derived from standard node-centric functional connectivity to map the distributed effects in stroke patients. Here, given the importance of nonlocal and diffuse damage, we use an edge-centric approach to functional connectivity in order to provide an alternative description of the effects of this disorder. These techniques allow for the rendering of metrics such as normalized entropy, which describes the diversity of edge communities at each node. Moreover, the approach enables the identification of high amplitude co-fluctuations in fMRI time series. We found that normalized entropy is associated with stroke lesion severity …

All The Princesses' Men: Working For The British Columbia Coast Steamship Service 1901-1928, Neil H. Christenson

EWU Masters Thesis Collection

No abstract provided.

The Value Hierarchies Of J.R.R. Tolkien And His Legacy: A Reimagining Of Fantasy Fiction And The Propagation Of Colonial Racism, Alexander Richburg

EWU Masters Thesis Collection

J.R.R. Tolkien’s impact on modern fantasy fiction is remarkable. However, while some of the changes to the genre ushered in by Tolkien’s work are positive, other aspects of his legacy are more problematic. Tolkien’s The Hobbit, The Lord of the Rings, and The Silmarillion are based on his colonial worldview. They are biographical in that Tolkien draws heavily from his life experience to tell his stories. The biographical influence manifests in a hierarchical representation of everything from trees and their ancestry to the elves, humans, dwarves, hobbits, and orcs that populate his fiction. The hierarchies are value structures and the …

Empirical Comparison Of Machine Learning Methods For Wind Power Predictions, Sidny M. Stewart

EWU Masters Thesis Collection

No abstract provided.

Modeling Document Classification To Automate Mental Health Diagnosis, William M. Tadlock

EWU Masters Thesis Collection

The objective of this study is to determine if diagnosis documents can be used with document classification to automatically diagnose mental health conditions. Document classification allows text documents to be analyzed and organized into their appropriate classes based on the features and words presented in the text. One application of this is within the medical field to automatically classify different patient diagnosis based on medical or patient notes. This research applied mental health diagnosis documents to automatically diagnose a group of patients with a mental health condition based on text-based survey data. This classification was approached through several feature engineering …

Towards Cloud-Based Cost-Effective Serverless Information System, Isaac C. Angle

EWU Masters Thesis Collection

E-commerce information systems are becoming increasingly popular for businesses to adopt. In this work, we propose a serverless information system that will reduce costs for small businesses trying to create an e-commerce website. The proposed serverless system is built entirely in Amazon Web Services (AWS). The proposed serverless system allows businesses to pay for the use of cloud resources on a per-order granularity. This model reduces the cost of the information system when compared to a traditional cloud-based system. As e-commerce websites become more vital for small businesses, a cost effective serverless approach is promising.

Influenza: Toward Understanding The Immune Response In The Young, Sonia Sakleshpur, Ashley L Steed

2020-Current year OA Pubs

Annually influenza causes a global epidemic resulting in 290,000 to 650,000 deaths and extracts a massive toll on healthcare and the economy. Infants and children are more susceptible to infection and have more severe symptoms than adults likely mitigated by differences in their innate and adaptive immune responses. While it is unclear the exact mechanisms with which the young combat influenza, it is increasingly understood that their immune responses differ from adults. Specifically, underproduction of IFN-γ and IL-12 by the innate immune system likely hampers viral clearance while upregulation of IL-6 may create excessive damaging inflammation. The infant's adaptive immune …

Analysis Of Neuronal Injury Transcriptional Response Identifies Ctcf And Yy1 As Co-Operating Factors Regulating Axon Regeneration, Oshri Avraham, Jimmy Le, Kathleen Leahy, Tiandao Li, Guoyan Zhao, Valeria Cavalli

2020-Current year OA Pubs

Injured sensory neurons activate a transcriptional program necessary for robust axon regeneration and eventual target reinnervation. Understanding the transcriptional regulators that govern this axon regenerative response may guide therapeutic strategies to promote axon regeneration in the injured nervous system. Here, we used cultured dorsal root ganglia neurons to identify pro-regenerative transcription factors. Using RNA sequencing, we first characterized this neuronal culture and determined that embryonic day 13.5 DRG (eDRG) neurons cultured for 7 days are similar to e15.5 DRG neurons

Binary Acoustic Metasurfaces For Dynamic Focusing Of Transcranial Ultrasound, Zhongtao Hu, Yaoheng Yang, Lu Xu, Yao Hao, Hong Chen

2020-Current year OA Pubs

Transcranial focused ultrasound (tFUS) is a promising technique for non-invasive and spatially targeted neuromodulation and treatment of brain diseases. Acoustic lenses were designed to correct the skull-induced beam aberration, but these designs could only generate static focused ultrasound beams inside the brain. Here, we designed and 3D printed binary acoustic metasurfaces (BAMs) for skull aberration correction and dynamic ultrasound beam focusing. BAMs were designed by binarizing the phase distribution at the surface of the metasurfaces. The phase distribution was calculated based on time reversal to correct the skull-induced phase aberration. The binarization enabled the ultrasound beam to be dynamically steered …

In And Out: Leishmania Metastasis By Hijacking Lymphatic System And Migrating Immune Cells, Baijayanti Jha, Marta Reverte, Catherine Ronet, Florence Prevel, Florence D Morgenthaler, Chantal Desponds, Lon-Fye Lye, Katherine L Owens, Leonardo Scarpellino, Lalit Kumar Dubey, Amélie Sabine, Tatiana V Petrova, Sanjiv A Luther, Stephen M Beverley, Nicolas Fasel

2020-Current year OA Pubs

The lymphatic system plays a crucial role in mounting immune response against intracellular pathogens, and recent studies have documented its role in facilitating tumor dissemination linked largely with cancer cells. However, in mucocutaneous leishmaniasis (MCL) caused by