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    <title>Recent ucsb_cmpsc items</title>
    <link>https://escholarship.org/uc/ucsb_cmpsc/rss</link>
    <description>Recent eScholarship items from Department of Computer Science</description>
    <pubDate>Fri, 19 Jun 2026 10:32:41 +0000</pubDate>
    <item>
      <title>Perceptual learning of prosthetic vision using video game training</title>
      <link>https://escholarship.org/uc/item/8sf6c0qq</link>
      <description>A key limitation shared by both electronic and optogenetic sight recovery technologies is that they cause simultaneous rather than complementary firing within on- and off-center cells. Here, using "virtual patients"-sighted individuals viewing distorted input-we examine whether gamified training improves the ability to compensate for distortions in neuronal population coding. We measured perceptual learning using dichoptic input, filtered so that regions of the image that produced on-center responses in one eye produced off-center responses in the other eye. The Non-Gaming control group carried out an object discrimination task over five sessions using this filtered input. The Gaming group carried out an additional 25 hours of gamified training using a similarly filtered variant of the video game Fruit Ninja. Both groups showed improvements over time in the object discrimination task. However, there was no significant transfer of learning from the "Fruit Ninja" task to the object...</description>
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      <pubDate>Thu, 23 Oct 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Esquenazi, Rebecca B</name>
      </author>
      <author>
        <name>Meier, Kimberly</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Wright, Drake</name>
      </author>
      <author>
        <name>Boynton, Geoffrey M</name>
      </author>
      <author>
        <name>Fine, Ione</name>
      </author>
    </item>
    <item>
      <title>Effects of noisy galvanic vestibular stimulation on spatial memory in virtual reality</title>
      <link>https://escholarship.org/uc/item/9hd7x6v2</link>
      <description>Spatial memory and navigation are foundational cognitive functions intricately tied to the hippocampal and striatal neural circuits. These regions integrate multisensory inputs from the environment, with the vestibular system exerting a particularly strong influence on visuospatial processing. While prior work has explored how Galvanic Vestibular Stimulation (GVS) can enhance spatial cognition in individuals with vestibular disorders, limited research has focused on its potentially beneficial effects in those without vestibular disorders. To address this gap, we present a study using a novel experimental paradigm that combines noisy GVS (nGVS) with virtual reality (VR) to systematically examine the impact of vestibular stimulation on spatial learning and memory in healthy adults. Our findings (n=32) suggest that nGVS can significantly improve spatial memory performance, facilitating learning and recollection compared to the without-nGVS condition. Unlike previous screen-based...</description>
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      <pubDate>Thu, 31 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Bhardwaj, Purav</name>
      </author>
      <author>
        <name>Sra, Misha</name>
        <uri>https://orcid.org/0000-0001-8154-8518</uri>
      </author>
    </item>
    <item>
      <title>Simulated prosthetic vision confirms checkerboard as an effective raster pattern for epiretinal implants.</title>
      <link>https://escholarship.org/uc/item/87b4t1hn</link>
      <description>&lt;i&gt;Objective:&lt;/i&gt;Spatial scheduling of electrode activation ("rastering") is essential for safely operating high-density retinal implants, yet its perceptual consequences remain poorly understood. This study systematically evaluates the impact of raster patterns, or spatial arrangements of sequential electrode activation, on performance and perceived difficulty in simulated prosthetic vision (SPV). By addressing this gap, we aimed to identify patterns that optimize functional vision in retinal implants.

&lt;i&gt;Approach:&lt;/i&gt;Sighted participants completed letter recognition and motion discrimination tasks under four raster patterns (horizontal, vertical, checkerboard, and random) using an immersive SPV system. The simulations emulated epiretinal implant perception and employed psychophysically validated models of electrode activation, phosphene appearance, nonlinear spatial summation, and temporal dynamics, ensuring realistic representation of prosthetic vision. Performance accuracy...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/87b4t1hn</guid>
      <pubDate>Fri, 18 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Kasowski, Justin M</name>
      </author>
      <author>
        <name>Varshney, Apurv</name>
      </author>
      <author>
        <name>Sadeghi, Roksana</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Network measurements for telehealth optimizations understanding internet paths in remote regions</title>
      <link>https://escholarship.org/uc/item/0h43030m</link>
      <description>Network measurements for telehealth optimizations understanding internet paths in remote regions</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0h43030m</guid>
      <pubDate>Fri, 4 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Caballero, Eleonora Stadtmüller</name>
      </author>
      <author>
        <name>Ramirez, Jaren</name>
      </author>
      <author>
        <name>Alisetti, Sai Vamsi</name>
      </author>
      <author>
        <name>Almario, Shanelle</name>
      </author>
      <author>
        <name>Kathiravelu, Pradeeban</name>
      </author>
    </item>
    <item>
      <title>Stramash: A Fused-Kernel Operating System For Cache-Coherent, Heterogeneous-ISA Platforms</title>
      <link>https://escholarship.org/uc/item/5fb6m0m4</link>
      <description>Stramash: A Fused-Kernel Operating System For Cache-Coherent, Heterogeneous-ISA Platforms</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5fb6m0m4</guid>
      <pubDate>Wed, 9 Apr 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Xing, Tong</name>
      </author>
      <author>
        <name>Xiong, Cong</name>
      </author>
      <author>
        <name>Wei, Tianrui</name>
      </author>
      <author>
        <name>Sanchez, April</name>
      </author>
      <author>
        <name>Ravindran, Binoy</name>
      </author>
      <author>
        <name>Balkind, Jonathan</name>
        <uri>https://orcid.org/0000-0003-1443-1373</uri>
      </author>
      <author>
        <name>Barbalace, Antonio</name>
      </author>
    </item>
    <item>
      <title>Assistive technology use in domestic activities by people who are blind</title>
      <link>https://escholarship.org/uc/item/0w33p0zm</link>
      <description>People who are blind employ unique strategies when performing instrumental activities of daily living (iADLs), often relying on multiple sensory modalities and assistive technologies. While prior research has extensively explored adaptive strategies for outdoor activities like wayfinding and navigation, less emphasis has been placed on the information needs and problem-solving strategies for managing domestic activities. To address this gap, our study presents insights from 16 semi-structured interviews with individuals who are either legally or completely blind, highlighting both the current use and potential future applications of technologies for home-based iADLs. Our findings reveal several underexplored challenges, including the difficulty of locating misplaced objects, a structured problem-solving approach where digital tools are a last resort, and limited awareness of assistive training programs. Participants also faced persistent usability barriers as software updates...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0w33p0zm</guid>
      <pubDate>Fri, 28 Mar 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Turkstra, Lily M</name>
        <uri>https://orcid.org/0009-0009-9669-9189</uri>
      </author>
      <author>
        <name>Bhatia, Tanya</name>
      </author>
      <author>
        <name>Van Os, Alexa</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Aligning Visual Prosthetic Development With Implantee Needs</title>
      <link>https://escholarship.org/uc/item/72n731tp</link>
      <description>Purpose: Visual prosthetics are a promising assistive technology for vision loss, yet research often overlooks the human aspects of this technology. While previous studies focus on the perceptual experiences or attitudes of implant recipients (implantees), a systematic account of how current implants are being used in everyday life is still lacking.
Methods: We interviewed six recipients of the most widely used visual implants (Argus II and Orion) and six leading researchers in the field. Through thematic analyses, we explored the daily usage of these implants by implantees and compared their responses to the expectations of researchers. We also sought implantees' input on desired features for future versions, aiming to inform the development of the next generation of implants.
Results: Although implants are designed to facilitate various daily activities, we found that implantees use them less frequently than researchers expect. This discrepancy primarily stems from issues with...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/72n731tp</guid>
      <pubDate>Thu, 16 Jan 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Nadolskis, Lucas</name>
      </author>
      <author>
        <name>Turkstra, Lily M</name>
        <uri>https://orcid.org/0009-0009-9669-9189</uri>
      </author>
      <author>
        <name>Larnyo, Ebenezer</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Home-Use and Portable Biofeedback Lowers Anxiety and Pain in Chronic Pain Subjects.</title>
      <link>https://escholarship.org/uc/item/4kj7h8wq</link>
      <description>In this study, we investigated the use of novel, home-use and portable biofeedback devices in a remote program for managing chronic pain. In three separate 4-week pilot studies, participants engaged in twice-daily, 10-minute biofeedback sessions, with self-assessed reductions in anxiety and pain levels using the 6-item State-Trait Anxiety Inventory (STAI-6) and Visual Analogue Scale (VAS), respectively, in Studies 2 and 3. Among these 113 (Study 2) and 237 (Study 3) biofeedback sessions, 81 (∼72%) and 130 (∼55%) showed reductions in pain, while 93 (∼82%) and 184 (∼78%) experienced reductions in anxiety. A positive relationship was found between anxiety and pain reduction, indicating that larger reductions in anxiety correspond to larger reductions in pain. In Study 1, only anxiety reductions were measured: across 143 biofeedback sessions, 127 experienced reductions in anxiety (∼89%). Participants in all studies demonstrated reductions in baseline to final results in pain, anxiety,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4kj7h8wq</guid>
      <pubDate>Fri, 22 Nov 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Ly, Franklin S</name>
      </author>
      <author>
        <name>Santander, Tyler</name>
      </author>
      <author>
        <name>Pavlov, Stephany</name>
      </author>
      <author>
        <name>Zhao, Jiayang</name>
      </author>
      <author>
        <name>Zhang, Minghao</name>
      </author>
      <author>
        <name>Arroyo, Dahyana</name>
      </author>
      <author>
        <name>Sokolovskiy, Sergey</name>
      </author>
      <author>
        <name>Iyer, Anirudh</name>
      </author>
      <author>
        <name>Yankauskas, Yanis</name>
      </author>
      <author>
        <name>Chen, John</name>
      </author>
      <author>
        <name>Miller, Michael B</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Yang, Henry T</name>
      </author>
      <author>
        <name>Hansma, Paul K</name>
      </author>
    </item>
    <item>
      <title>Bayesian polynomial neural networks and polynomial neural ordinary differential equations</title>
      <link>https://escholarship.org/uc/item/89b5699n</link>
      <description>Symbolic regression with polynomial neural networks and polynomial neural ordinary differential equations (ODEs) are two recent and powerful approaches for equation recovery of many science and engineering problems. However, these methods provide point estimates for the model parameters and are currently unable to accommodate noisy data. We address this challenge by developing and validating the following Bayesian inference methods: the Laplace approximation, Markov Chain Monte Carlo (MCMC) sampling methods, and variational inference. We have found the Laplace approximation to be the best method for this class of problems. Our work can be easily extended to the broader class of symbolic neural networks to which the polynomial neural network belongs.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/89b5699n</guid>
      <pubDate>Sat, 9 Nov 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Fronk, Colby</name>
      </author>
      <author>
        <name>Yun, Jaewoong</name>
      </author>
      <author>
        <name>Singh, Prashant</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Airflow Modeling for Citrus under Protective Screens</title>
      <link>https://escholarship.org/uc/item/46j613hb</link>
      <description>This study explores the development and validation of an airflow model to support climate prediction for Citrus Under Protective Screens (CUPS) in California. CUPS is a permeable screen structure designed to protect a field of citrus trees from large insects including the vector that causes the devastating citrus greening disease. Because screen structures modify the environmental conditions (e.g., temperature, relative humidity, airflow), farm management and treatment strategies (e.g., pesticide spraying events) must be modified to account for these differences. Toward this end, we develop a model for predicting wind speed and direction in a commercial-scale research CUPS, using a computational fluid dynamics (CFD) model. We describe the model and validate it in two ways. In the first, we model a small-scale replica CUPS under controlled conditions and compare modeled and measured airflow in and around the replica structure. In the second, we model the full-scale CUPS and use...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/46j613hb</guid>
      <pubDate>Fri, 8 Nov 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Kurafeeva, Liubov</name>
      </author>
      <author>
        <name>Wolski, Rich</name>
      </author>
      <author>
        <name>Krintz, Chandra</name>
        <uri>https://orcid.org/0000-0003-4972-0669</uri>
      </author>
      <author>
        <name>Smyth, Thomas</name>
      </author>
    </item>
    <item>
      <title>OpenPiton4HPC: Optimizing OpenPiton Toward High-Performance Manycores</title>
      <link>https://escholarship.org/uc/item/9xh0g7mz</link>
      <description>OpenPiton4HPC: Optimizing OpenPiton Toward High-Performance Manycores</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9xh0g7mz</guid>
      <pubDate>Thu, 10 Oct 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Leyva, Neiel</name>
      </author>
      <author>
        <name>Monemi, Alireza</name>
      </author>
      <author>
        <name>Oliete-Escuín, Noelia</name>
      </author>
      <author>
        <name>López-Paradís, Guillem</name>
      </author>
      <author>
        <name>Abancens, Xabier</name>
      </author>
      <author>
        <name>Balkind, Jonathan</name>
        <uri>https://orcid.org/0000-0003-1443-1373</uri>
      </author>
      <author>
        <name>Vallejo, Enrique</name>
      </author>
      <author>
        <name>Moretó, Miquel</name>
      </author>
      <author>
        <name>Alvarez, Lluc</name>
      </author>
    </item>
    <item>
      <title>The Efficacy of the Connect America Fund in Addressing US Internet Access Inequities</title>
      <link>https://escholarship.org/uc/item/4db0w1wf</link>
      <description>The Efficacy of the Connect America Fund in Addressing US Internet Access Inequities</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4db0w1wf</guid>
      <pubDate>Wed, 28 Aug 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Manda, Haarika</name>
      </author>
      <author>
        <name>Srinivasavaradhan, Varshika</name>
      </author>
      <author>
        <name>Koduru, Laasya</name>
      </author>
      <author>
        <name>Zhang, Kevin</name>
      </author>
      <author>
        <name>Zhou, Xuanhe</name>
      </author>
      <author>
        <name>Paul, Udit</name>
      </author>
      <author>
        <name>Belding, Elizabeth</name>
      </author>
      <author>
        <name>Gupta, Arpit</name>
        <uri>https://orcid.org/0000-0002-6378-7440</uri>
      </author>
      <author>
        <name>Narechania, Tejas N</name>
        <uri>https://orcid.org/0000-0001-6495-6413</uri>
      </author>
    </item>
    <item>
      <title>Regulation of CSF and Brain Tissue Sodium Levels by the Blood-CSF and Blood-Brain Barriers During Migraine</title>
      <link>https://escholarship.org/uc/item/6jw6f5n4</link>
      <description>Cerebrospinal fluid (CSF) and brain tissue sodium levels increase during migraine. However, little is known regarding the underlying mechanisms of sodium homeostasis disturbance in the brain during the onset and propagation of migraine. Exploring the cause of sodium dysregulation in the brain is important, since correction of the altered sodium homeostasis could potentially treat migraine. Under the hypothesis that disturbances in sodium transport mechanisms at the blood-CSF barrier (BCSFB) and/or the blood-brain barrier (BBB) are the underlying cause of the elevated CSF and brain tissue sodium levels during migraines, we developed a mechanistic, differential equation model of a rat's brain to compare the significance of the BCSFB and the BBB in controlling CSF and brain tissue sodium levels. The model includes the ventricular system, subarachnoid space, brain tissue and blood. Sodium transport from blood to CSF across the BCSFB, and from blood to brain tissue across the BBB were...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6jw6f5n4</guid>
      <pubDate>Sun, 18 Aug 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Ghaffari, Hamed</name>
      </author>
      <author>
        <name>Grant, Samuel C</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Harrington, Michael G</name>
      </author>
    </item>
    <item>
      <title>Stress affects navigation strategies in immersive virtual reality</title>
      <link>https://escholarship.org/uc/item/6008n591</link>
      <description>There are known individual differences in both the ability to learn the layout of novel environments and the flexibility of strategies for navigating known environments. However, it is unclear how navigational abilities are impacted by high-stress scenarios. Here we used immersive virtual reality (VR) to develop a novel behavioral paradigm to examine navigation under dynamically changing situations. We recruited 48 participants (24 female; ages 17–32) to navigate a virtual maze (7.5&amp;nbsp;m × 7.5&amp;nbsp;m). Participants learned the maze by moving along a fixed path past the maze’s landmarks (paintings). Subsequently, participants experienced either a non-stress condition, or a high-stress condition tasking them with navigating the maze. In the high-stress condition, their initial path was blocked, the environment was darkened, threatening music was played, fog obstructed more distal views of the environment, and participants were given a time limit of 20&amp;nbsp;s with a countdown timer...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6008n591</guid>
      <pubDate>Mon, 1 Jul 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Varshney, Apurv</name>
      </author>
      <author>
        <name>Munns, Mitchell E</name>
      </author>
      <author>
        <name>Kasowski, Justin</name>
      </author>
      <author>
        <name>Zhou, Mantong</name>
      </author>
      <author>
        <name>He, Chuanxiuyue</name>
      </author>
      <author>
        <name>Grafton, Scott T</name>
      </author>
      <author>
        <name>Giesbrecht, Barry</name>
      </author>
      <author>
        <name>Hegarty, Mary</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Comparison of Rapid-, Kaolin-, and Native-TEG Parameters in Burn Patient Cohorts With Acute Burn-induced Coagulopathy and Abnormal Fibrinolytic Function</title>
      <link>https://escholarship.org/uc/item/2zz8m965</link>
      <description>Although use of thromboelastography (TEG) to diagnose coagulopathy and guide clinical decision-making is increasing, relative performance of different TEG methods has not been well-defined. Rapid-TEG (rTEG), kaolin-TEG (kTEG), and native-TEG (nTEG) were performed on blood samples from burn patients presenting to a regional center from admission to 21 days. Patients were categorized by burn severity, mortality, and fibrinolytic phenotypes (Shutdown [SD], Physiologic [PHYS], and Hyperfibrinolytic [HF]). Manufacturer ranges and published TEG cutoffs were examined. Concordance correlations (Rc) of TEG parameters (R, α-angle, maximum amplitude [MA], LY30) measured agreement and Cohen's Kappa (κ) determined interclass reliability. Patients (n = 121) were mostly male (n = 84; 69.4%), with median age 40 years, median TBSA burn 13%, and mortality 17% (n = 21). Severe burns (≥40% TBSA) were associated with lower admission α-angle for rTEG (P = .03) and lower MA for rTEG (P = .02) and kTEG...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2zz8m965</guid>
      <pubDate>Wed, 26 Jun 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Keyloun, John W</name>
      </author>
      <author>
        <name>Le, Tuan D</name>
      </author>
      <author>
        <name>Moffatt, Lauren T</name>
      </author>
      <author>
        <name>Orfeo, Thomas</name>
      </author>
      <author>
        <name>McLawhorn, Melissa M</name>
      </author>
      <author>
        <name>Bravo, Maria-Cristina</name>
      </author>
      <author>
        <name>Tejiram, Shawn</name>
      </author>
      <author>
        <name>Bravo, Maria-Cristina</name>
      </author>
      <author>
        <name>Brummel-Ziedins, Kathleen E</name>
      </author>
      <author>
        <name>Callcut, Rachael A</name>
        <uri>https://orcid.org/0000-0002-1582-6716</uri>
      </author>
      <author>
        <name>Cohen, Mitchell J</name>
      </author>
      <author>
        <name>Freeman, Kalev</name>
      </author>
      <author>
        <name>Gautam, Aarti</name>
      </author>
      <author>
        <name>Hammamieh, Rasha</name>
      </author>
      <author>
        <name>Jett, Marti</name>
      </author>
      <author>
        <name>McLawhorn, Melissa M</name>
      </author>
      <author>
        <name>Moffatt, Lauren T</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Pusateri, Anthony E</name>
      </author>
      <author>
        <name>Shupp, Jeffrey W</name>
      </author>
      <author>
        <name>Varner, Jeffrey D</name>
      </author>
      <author>
        <name>Shupp, Jeffrey W</name>
      </author>
      <author>
        <name>Pusateri, Anthony E</name>
      </author>
    </item>
    <item>
      <title>Challenges and Opportunities for Beyond-5G Wireless Security</title>
      <link>https://escholarship.org/uc/item/2v16x5pm</link>
      <description>Challenges and Opportunities for Beyond-5G Wireless Security</description>
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      <pubDate>Tue, 4 Jun 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Ruzomberka, Eric</name>
      </author>
      <author>
        <name>Love, David J</name>
      </author>
      <author>
        <name>Brinton, Christopher G</name>
      </author>
      <author>
        <name>Gupta, Arpit</name>
      </author>
      <author>
        <name>Wang, Chih-Chun</name>
      </author>
      <author>
        <name>Poor, H Vincent</name>
      </author>
    </item>
    <item>
      <title>Cohort: Software-Oriented Acceleration for Heterogeneous SoCs</title>
      <link>https://escholarship.org/uc/item/3j15k564</link>
      <description>Philosophically, our approaches to acceleration focus on the extreme. We must optimise accelerators to the maximum, leaving software to fix any hardware-software mismatches. Today's software abstractions for programming accelerators leak hardware details, requiring changes to data formats and manual memory and coherence management, among other issues. This harms generality and requires deep hardware knowledge to efficiently program accelerators, a state which we consider hardware-oriented. This paper proposes Software-Oriented Acceleration (SOA), where software uses existing abstractions, like software shared-memory queues, to interact with accelerators. We introduce the Cohort engine which exploits these queues' standard semantics to efficiently connect producers and consumers in software with accelerators with minimal application changes. Accelerators are even usable in chains which can be runtime reconfigured by software. Cohort significantly reduces the burden to add new accelerators...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3j15k564</guid>
      <pubDate>Wed, 8 May 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Wei, Tianrui</name>
      </author>
      <author>
        <name>Turtayeva, Nazerke</name>
      </author>
      <author>
        <name>Orenes-Vera, Marcelo</name>
      </author>
      <author>
        <name>Lonkar, Omkar</name>
      </author>
      <author>
        <name>Balkind, Jonathan</name>
        <uri>https://orcid.org/0000-0003-1443-1373</uri>
      </author>
    </item>
    <item>
      <title>Zoomie: A Software-like Debugging Tool for FPGAs</title>
      <link>https://escholarship.org/uc/item/177918cz</link>
      <description>Zoomie: A Software-like Debugging Tool for FPGAs</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/177918cz</guid>
      <pubDate>Wed, 8 May 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Wei, Tianrui</name>
      </author>
      <author>
        <name>Laeufer, Kevin</name>
      </author>
      <author>
        <name>Lim, Katie</name>
      </author>
      <author>
        <name>Zhao, Jerry</name>
      </author>
      <author>
        <name>Sen, Koushik</name>
      </author>
      <author>
        <name>Balkind, Jonathan</name>
        <uri>https://orcid.org/0000-0003-1443-1373</uri>
      </author>
      <author>
        <name>Asanovic, Krste</name>
      </author>
    </item>
    <item>
      <title>Non-Abelian braiding of graph vertices in a superconducting processor</title>
      <link>https://escholarship.org/uc/item/1k9033cx</link>
      <description>Indistinguishability of particles is a fundamental principle of quantum mechanics1. For all elementary and quasiparticles observed to date—including fermions, bosons and Abelian anyons—this principle guarantees that the braiding of identical particles leaves the system unchanged2,3. However, in two spatial dimensions, an intriguing possibility exists: braiding of non-Abelian anyons causes rotations in a space of topologically degenerate wavefunctions4–8. Hence, it can change the observables of the system without violating the principle of indistinguishability. Despite the well-developed mathematical description of non-Abelian anyons and numerous theoretical proposals9–22, the experimental observation of their exchange statistics has remained elusive for decades. Controllable many-body quantum states generated on quantum processors offer another path for exploring these fundamental phenomena. Whereas efforts on conventional solid-state platforms typically involve Hamiltonian dynamics...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1k9033cx</guid>
      <pubDate>Mon, 1 Apr 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Andersen, TI</name>
      </author>
      <author>
        <name>Lensky, YD</name>
      </author>
      <author>
        <name>Kechedzhi, K</name>
      </author>
      <author>
        <name>Drozdov, IK</name>
      </author>
      <author>
        <name>Bengtsson, A</name>
      </author>
      <author>
        <name>Hong, S</name>
      </author>
      <author>
        <name>Morvan, A</name>
      </author>
      <author>
        <name>Mi, X</name>
      </author>
      <author>
        <name>Opremcak, A</name>
      </author>
      <author>
        <name>Acharya, R</name>
      </author>
      <author>
        <name>Allen, R</name>
      </author>
      <author>
        <name>Ansmann, M</name>
      </author>
      <author>
        <name>Arute, F</name>
      </author>
      <author>
        <name>Arya, K</name>
      </author>
      <author>
        <name>Asfaw, A</name>
      </author>
      <author>
        <name>Atalaya, J</name>
      </author>
      <author>
        <name>Babbush, R</name>
      </author>
      <author>
        <name>Bacon, D</name>
      </author>
      <author>
        <name>Bardin, JC</name>
      </author>
      <author>
        <name>Bortoli, G</name>
      </author>
      <author>
        <name>Bourassa, A</name>
      </author>
      <author>
        <name>Bovaird, J</name>
      </author>
      <author>
        <name>Brill, L</name>
      </author>
      <author>
        <name>Broughton, M</name>
      </author>
      <author>
        <name>Buckley, BB</name>
      </author>
      <author>
        <name>Buell, DA</name>
      </author>
      <author>
        <name>Burger, T</name>
      </author>
      <author>
        <name>Burkett, B</name>
      </author>
      <author>
        <name>Bushnell, N</name>
      </author>
      <author>
        <name>Chen, Z</name>
      </author>
      <author>
        <name>Chiaro, B</name>
      </author>
      <author>
        <name>Chik, D</name>
      </author>
      <author>
        <name>Chou, C</name>
      </author>
      <author>
        <name>Cogan, J</name>
      </author>
      <author>
        <name>Collins, R</name>
      </author>
      <author>
        <name>Conner, P</name>
      </author>
      <author>
        <name>Courtney, W</name>
      </author>
      <author>
        <name>Crook, AL</name>
      </author>
      <author>
        <name>Curtin, B</name>
      </author>
      <author>
        <name>Debroy, DM</name>
      </author>
      <author>
        <name>Del Toro Barba, A</name>
      </author>
      <author>
        <name>Demura, S</name>
      </author>
      <author>
        <name>Dunsworth, A</name>
      </author>
      <author>
        <name>Eppens, D</name>
      </author>
      <author>
        <name>Erickson, C</name>
      </author>
      <author>
        <name>Faoro, L</name>
      </author>
      <author>
        <name>Farhi, E</name>
      </author>
      <author>
        <name>Fatemi, R</name>
      </author>
      <author>
        <name>Ferreira, VS</name>
      </author>
      <author>
        <name>Burgos, LF</name>
      </author>
      <author>
        <name>Forati, E</name>
      </author>
      <author>
        <name>Fowler, AG</name>
      </author>
      <author>
        <name>Foxen, B</name>
      </author>
      <author>
        <name>Giang, W</name>
      </author>
      <author>
        <name>Gidney, C</name>
      </author>
      <author>
        <name>Gilboa, D</name>
      </author>
      <author>
        <name>Giustina, M</name>
      </author>
      <author>
        <name>Gosula, R</name>
      </author>
      <author>
        <name>Dau, AG</name>
      </author>
      <author>
        <name>Gross, JA</name>
      </author>
      <author>
        <name>Habegger, S</name>
      </author>
      <author>
        <name>Hamilton, MC</name>
      </author>
      <author>
        <name>Hansen, M</name>
      </author>
      <author>
        <name>Harrigan, MP</name>
      </author>
      <author>
        <name>Harrington, SD</name>
      </author>
      <author>
        <name>Heu, P</name>
      </author>
      <author>
        <name>Hilton, J</name>
      </author>
      <author>
        <name>Hoffmann, MR</name>
      </author>
      <author>
        <name>Huang, T</name>
      </author>
      <author>
        <name>Huff, A</name>
      </author>
      <author>
        <name>Huggins, WJ</name>
      </author>
      <author>
        <name>Ioffe, LB</name>
      </author>
      <author>
        <name>Isakov, SV</name>
      </author>
      <author>
        <name>Iveland, J</name>
      </author>
      <author>
        <name>Jeffrey, E</name>
      </author>
      <author>
        <name>Jiang, Z</name>
      </author>
      <author>
        <name>Jones, C</name>
      </author>
      <author>
        <name>Juhas, P</name>
      </author>
      <author>
        <name>Kafri, D</name>
      </author>
      <author>
        <name>Khattar, T</name>
      </author>
      <author>
        <name>Khezri, M</name>
      </author>
      <author>
        <name>Kieferová, M</name>
      </author>
      <author>
        <name>Kim, S</name>
      </author>
      <author>
        <name>Kitaev, A</name>
      </author>
      <author>
        <name>Klimov, PV</name>
      </author>
      <author>
        <name>Klots, AR</name>
      </author>
      <author>
        <name>Korotkov, AN</name>
      </author>
      <author>
        <name>Kostritsa, F</name>
      </author>
      <author>
        <name>Kreikebaum, JM</name>
      </author>
      <author>
        <name>Landhuis, D</name>
      </author>
      <author>
        <name>Laptev, P</name>
      </author>
      <author>
        <name>Lau, K-M</name>
      </author>
      <author>
        <name>Laws, L</name>
      </author>
      <author>
        <name>Lee, J</name>
      </author>
      <author>
        <name>Lee, KW</name>
      </author>
      <author>
        <name>Lester, BJ</name>
      </author>
      <author>
        <name>Lill, AT</name>
      </author>
      <author>
        <name>Liu, W</name>
      </author>
      <author>
        <name>Locharla, A</name>
      </author>
      <author>
        <name>Lucero, E</name>
      </author>
    </item>
    <item>
      <title>A Computational Model of Phosphene Appearance for Epiretinal Prostheses</title>
      <link>https://escholarship.org/uc/item/9x8888nh</link>
      <description>Retinal neuroprostheses are the only FDA-approved treatment option for blinding degenerative diseases. A major outstanding challenge is to develop a computational model that can accurately predict the elicited visual percepts (phosphenes) across a wide range of electrical stimuli. Here we present a phenomenological model that predicts phosphene appearance as a function of stimulus amplitude, frequency, and pulse duration. The model uses a simulated map of nerve fiber bundles in the retina to produce phosphenes with accurate brightness, size, orientation, and elongation. We validate the model on psychophysical data from two independent studies, showing that it generalizes well to new data, even with different stimuli and on different electrodes. Whereas previous models focused on either spatial or temporal aspects of the elicited phosphenes in isolation, we describe a more comprehensive approach that is able to account for many reported visual effects. The model is designed to...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9x8888nh</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Granley, Jacob</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Biophysical model of axonal stimulation in epiretinal visual prostheses</title>
      <link>https://escholarship.org/uc/item/9rc735dq</link>
      <description>Abstract: 
Visual prostheses aim to restore vision to people blinded from degenerative photoreceptor diseases by electrically stimulating surviving neurons in the retina. However, a major challenge with epiretinal prostheses is that they may accidentally activate passing axon fibers, causing severe perceptual distortions. To investigate the effect of axonal stimulation on the retinal response, we developed a computational model of a small population of morphologically and biophysically detailed retinal ganglion cells, and simulated their response to epiretinal electrical stimulation. We found that activation thresholds of ganglion cell somas and axons varied systematically with both stimulus pulse duration and electrode-retina distance. These findings have important implications for the improvement of stimulus encoding methods for epiretinal prostheses.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9rc735dq</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Explainable AI for Retinal Prostheses: Predicting Electrode Deactivation from Routine Clinical Measures</title>
      <link>https://escholarship.org/uc/item/8ws6w3vm</link>
      <description>To provide appropriate levels of stimulation, retinal prostheses must be calibrated to an individual’s perceptual thresholds (‘system fitting’). Nonfunctional electrodes may then be deactivated to reduce power consumption and improve visual outcomes. However, thresholds vary drastically not just across electrodes but also over time, thus calling for a more flexible electrode deactivation strategy. Here we present an explainable artificial intelligence (XAI) model fit on a large longitudinal dataset that can 1) predict at which point in time the manufacturer chose to deactivate an electrode as a function of routine clinical measures (‘predictors’) and 2) reveal which of these predictors were most important. The model predicted electrode deactivation from clinical data with 60.8% accuracy. Performance increased to 75.3% with system fitting data, and to 84% when thresholds from follow-up examinations were available. The model further identified subject age and time since blindness...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8ws6w3vm</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Hu, Zuying</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Model-Based Recommendations for Optimal Surgical Placement of Epiretinal Implants</title>
      <link>https://escholarship.org/uc/item/8m23f2md</link>
      <description>A major limitation of current electronic retinal implants is that in addition to stimulating the intended retinal ganglion cells, they also stimulate passing axon fibers, producing perceptual ‘streaks’ that limit the quality of the generated visual experience. Recent evidence suggests a dependence between the shape of the elicited visual percept and the retinal location of the stimulating electrode. However, this knowledge has yet to be incorporated into the surgical placement of retinal implants. Here we systematically explored the space of possible implant configurations to make recommendations for optimal intraocular positioning of the electrode array. Using a psychophysically validated computational model, we demonstrate that better implant placement has the potential to reduce the spatial extent of axonal activation in existing implant users by up to ∼55 %. Importantly, the best implant location, as inferred from a population of simulated virtual patients, is both surgically...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8m23f2md</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Boynton, Geoffrey M</name>
      </author>
      <author>
        <name>Fine, Ione</name>
      </author>
      <author>
        <name>Rokem, Ariel</name>
      </author>
    </item>
    <item>
      <title>Data-driven models in human neuroscience and neuroengineering</title>
      <link>https://escholarship.org/uc/item/6139q377</link>
      <description>Discoveries in modern human neuroscience are increasingly driven by quantitative understanding of complex data. Data-intensive approaches to modeling have promise to dramatically advance our understanding of the brain and critically enable neuroengineering capabilities. In this review, we provide an accessible primer to modern modeling approaches and highlight recent data-driven discoveries in the domains of neuroimaging, single-neuron and neuronal population responses, and device neuroengineering. Further, we suggest that meaningful progress requires the community to tackle open challenges in the realms of model interpretability and generalizability, training pipelines of data-fluent human neuroscientists, and integrated consideration of data ethics.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6139q377</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Brunton, Bingni W</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Explainable machine learning predictions of perceptual sensitivity for retinal prostheses</title>
      <link>https://escholarship.org/uc/item/5sk1g670</link>
      <description>&lt;i&gt;Objective.&lt;/i&gt;Retinal prostheses evoke visual precepts by electrically stimulating functioning cells in the retina. Despite high variance in perceptual thresholds across subjects, among electrodes within a subject, and over time, retinal prosthesis users must undergo 'system fitting', a process performed to calibrate stimulation parameters according to the subject's perceptual thresholds. Although previous work has identified electrode-retina distance and impedance as key factors affecting thresholds, an accurate predictive model is still lacking.&lt;i&gt;Approach.&lt;/i&gt;To address these challenges, we (1) fitted machine learning models to a large longitudinal dataset with the goal of predicting individual electrode thresholds and deactivation as a function of stimulus, electrode, and clinical parameters ('predictors') and (2) leveraged explainable artificial intelligence (XAI) to reveal which of these predictors were most important.&lt;i&gt;Main results.&lt;/i&gt;Our models accounted for up to...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5sk1g670</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Pogoncheff, Galen</name>
      </author>
      <author>
        <name>Hu, Zuying</name>
      </author>
      <author>
        <name>Rokem, Ariel</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>U-Net with Hierarchical Bottleneck Attention for Landmark Detection in Fundus Images of the Degenerated Retina</title>
      <link>https://escholarship.org/uc/item/5g01j68p</link>
      <description>U-Net with Hierarchical Bottleneck Attention for Landmark Detection in Fundus Images of the Degenerated Retina</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5g01j68p</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Tang, Shuyun</name>
      </author>
      <author>
        <name>Qi, Ziming</name>
      </author>
      <author>
        <name>Granley, Jacob</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>A model of ganglion axon pathways accounts for percepts elicited by retinal implants</title>
      <link>https://escholarship.org/uc/item/4jr4z3xv</link>
      <description>Abstract: 
Retinal prostheses, now implanted in over 250 patients worldwide, electrically stimulate surviving cells in order to evoke neuronal responses that are interpreted by the brain as visual percepts (‘phosphenes’). However, instead of seeing focal spots of light, current implant users perceive highly distorted phosphenes that vary in shape both across subjects and electrodes. We characterized these distortions by asking users of the Argus retinal prosthesis system (Second Sight Medical Products) to draw elicited percepts on a touchscreen. We found that phosphene shape could be accurately predicted by simulating the topographic organization of nerve fiber bundles in each subject’s retina. Our model shows that activation of ganglion axons contributes to a rich repertoire of phosphene shapes, successfully replicating percepts ranging from ‘blobs’ to oriented ‘streaks’ and ‘wedges’ depending on electrode location. This work provides a first step towards future devices that...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4jr4z3xv</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Nanduri, Devyani</name>
      </author>
      <author>
        <name>Weiland, James D</name>
      </author>
      <author>
        <name>Rokem, Ariel</name>
      </author>
      <author>
        <name>Boynton, Geoffrey M</name>
      </author>
      <author>
        <name>Fine, Ione</name>
      </author>
    </item>
    <item>
      <title>Axonal stimulation affects the linear summation of single-point perception in three Argus II users</title>
      <link>https://escholarship.org/uc/item/0zd074xs</link>
      <description>&lt;i&gt;Objective.&lt;/i&gt;Retinal implants use electrical stimulation to elicit perceived flashes of light ('phosphenes'). Single-electrode phosphene shape has been shown to vary systematically with stimulus parameters and the retinal location of the stimulating electrode, due to incidental activation of passing nerve fiber bundles. However, this knowledge has yet to be extended to paired-electrode stimulation.&lt;i&gt;Approach.&lt;/i&gt;We retrospectively analyzed 3548 phosphene drawings made by three blind participants implanted with an Argus II Retinal Prosthesis. Phosphene shape (characterized by area, perimeter, major and minor axis length) and number of perceived phosphenes were averaged across trials and correlated with the corresponding single-electrode parameters. In addition, the number of phosphenes was correlated with stimulus amplitude and neuroanatomical parameters: electrode-retina and electrode-fovea distance as well as the electrode-electrode distance to ('between-axon') and along...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0zd074xs</guid>
      <pubDate>Thu, 28 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Hou, Yuchen</name>
      </author>
      <author>
        <name>Nanduri, Devyani</name>
      </author>
      <author>
        <name>Granley, Jacob</name>
      </author>
      <author>
        <name>Weiland, James D</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Retinal ganglion cells undergo cell type—specific functional changes in a computational model of cone-mediated retinal degeneration</title>
      <link>https://escholarship.org/uc/item/9qp2k3s9</link>
      <description>Introduction: Understanding the retina in health and disease is a key issue for neuroscience and neuroengineering applications such as retinal prostheses. During degeneration, the retinal network undergoes complex and multi-stage neuroanatomical alterations, which drastically impact the retinal ganglion cell (RGC) response and are of clinical importance. Here we present a biophysically detailed &lt;i&gt;in silico&lt;/i&gt; model of the cone pathway in the retina that simulates the network-level response to both light and electrical stimulation.
Methods: The model included 11, 138 cells belonging to nine different cell types (cone photoreceptors, horizontal cells, ON/OFF bipolar cells, ON/OFF amacrine cells, and ON/OFF ganglion cells) confined to a 300 × 300 × 210μm patch of the parafoveal retina. After verifying that the model reproduced seminal findings about the light response of retinal ganglion cells (RGCs), we systematically introduced anatomical and neurophysiological changes (e.g.,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9qp2k3s9</guid>
      <pubDate>Fri, 22 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Xu, Aiwen</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>A systematic review of extended reality (XR) for understanding and augmenting vision loss</title>
      <link>https://escholarship.org/uc/item/3kq8p52r</link>
      <description>Over the past decade, extended reality (XR) has emerged as an assistive technology not only to augment residual vision of people losing their sight but also to study the rudimentary vision restored to blind people by a visual neuroprosthesis. A defining quality of these XR technologies is their ability to update the stimulus based on the user's eye, head, or body movements. To make the best use of these emerging technologies, it is valuable and timely to understand the state of this research and identify any shortcomings that are present. Here we present a systematic literature review of 227 publications from 106 different venues assessing the potential of XR technology to further visual accessibility. In contrast to other reviews, we sample studies from multiple scientific disciplines, focus on technology that augments a person's residual vision, and require studies to feature a quantitative evaluation with appropriate end users. We summarize prominent findings from different...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3kq8p52r</guid>
      <pubDate>Fri, 22 Mar 2024 00:00:00 +0000</pubDate>
      <author>
        <name>Kasowski, Justin</name>
      </author>
      <author>
        <name>Johnson, Byron A</name>
      </author>
      <author>
        <name>Neydavood, Ryan</name>
      </author>
      <author>
        <name>Akkaraju, Anvitha</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Detecting Performance Anomalies in Cloud Platform Applications</title>
      <link>https://escholarship.org/uc/item/5cg1r13m</link>
      <description>We present Roots, a full-stack monitoring and analysis system for performance anomaly detection and bottleneck identification in cloud platform-as-a-service (PaaS) systems. Roots facilitates application performance monitoring as a core capability of PaaS clouds, and relieves the developers from having to instrument application code. Roots tracks HTTP/S requests to hosted cloud applications and their use of PaaS services. To do so it employs lightweight monitoring of PaaS service interfaces. Roots processes this data in the background using multiple statistical techniques that in combination detect performance anomalies (i.e. violations of service-level objectives). For each anomaly, Roots determines whether the event was caused by a change in the request workload or by a performance bottleneck in a PaaS service. By correlating data collected across different layers of the PaaS, Roots is able to trace high-level performance anomalies to bottlenecks in specific components in the...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5cg1r13m</guid>
      <pubDate>Mon, 4 Dec 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Jayathilaka, Hiranya</name>
      </author>
      <author>
        <name>Krintz, Chandra</name>
        <uri>https://orcid.org/0000-0003-4972-0669</uri>
      </author>
      <author>
        <name>Wolski, Rich</name>
      </author>
    </item>
    <item>
      <title>Integrating machine learning and multiscale modeling—perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences</title>
      <link>https://escholarship.org/uc/item/4w75b3gd</link>
      <description>Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret these data to advance human health. The recent rise of machine learning as a powerful technique to integrate multimodality, multifidelity data, and reveal correlations between intertwined phenomena presents a special opportunity in this regard. However, machine learning alone ignores the fundamental laws of physics and can result in ill-posed problems or non-physical solutions. Multiscale modeling is a successful strategy to integrate multiscale, multiphysics data and uncover mechanisms that explain the emergence of function. However, multiscale modeling alone often fails to efficiently combine large datasets from different sources and different levels of resolution. Here we demonstrate that machine learning and multiscale modeling can naturally...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4w75b3gd</guid>
      <pubDate>Sun, 22 Oct 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Alber, Mark</name>
        <uri>https://orcid.org/0000-0002-7153-1138</uri>
      </author>
      <author>
        <name>Buganza Tepole, Adrian</name>
      </author>
      <author>
        <name>Cannon, William R</name>
        <uri>https://orcid.org/0000-0003-3789-7889</uri>
      </author>
      <author>
        <name>De, Suvranu</name>
      </author>
      <author>
        <name>Dura-Bernal, Salvador</name>
      </author>
      <author>
        <name>Garikipati, Krishna</name>
      </author>
      <author>
        <name>Karniadakis, George</name>
      </author>
      <author>
        <name>Lytton, William W</name>
      </author>
      <author>
        <name>Perdikaris, Paris</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Kuhl, Ellen</name>
      </author>
    </item>
    <item>
      <title>Towards a Smart Bionic Eye: AI-powered artificial vision for the treatment of incurable blindness</title>
      <link>https://escholarship.org/uc/item/26s3b5jk</link>
      <description>&lt;i&gt;Objective.&lt;/i&gt;How can we return a functional form of sight to people who are living with incurable blindness? Despite recent advances in the development of visual neuroprostheses, the quality of current prosthetic vision is still rudimentary and does not differ much across different device technologies.&lt;i&gt;Approach.&lt;/i&gt;Rather than aiming to represent the visual scene as naturally as possible, a&lt;i&gt;Smart Bionic Eye&lt;/i&gt;could provide visual augmentations through the means of artificial intelligence-based scene understanding, tailored to specific real-world tasks that are known to affect the quality of life of people who are blind, such as face recognition, outdoor navigation, and self-care.&lt;i&gt;Main results.&lt;/i&gt;Complementary to existing research aiming to restore natural vision, we propose a patient-centered approach to incorporate deep learning-based visual augmentations into the next generation of devices.&lt;i&gt;Significance.&lt;/i&gt;The ability of a visual prosthesis to support everyday...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/26s3b5jk</guid>
      <pubDate>Wed, 4 Oct 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Sanchez-Garcia, Melani</name>
      </author>
    </item>
    <item>
      <title>Validation data for a hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) method</title>
      <link>https://escholarship.org/uc/item/4dc937zg</link>
      <description>We present the validation of the hybrid sSSA-SDPD method for advection-diffusion-reaction problems coupled to discrete biochemical systems, as presented in the publication "A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems" (Drawert et al., 2019). We validate 1D diffusion, and 2D diffusion cases against their analytical solutions. We present graphs and tables of data showing the error in the simulation method.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4dc937zg</guid>
      <pubDate>Wed, 20 Sep 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Jacob, Bruno</name>
      </author>
      <author>
        <name>Li, Zhen</name>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection–diffusion–reaction problems</title>
      <link>https://escholarship.org/uc/item/3b13b4db</link>
      <description>We have developed a new algorithm which merges discrete stochastic simulation, using the spatial stochastic simulation algorithm (sSSA), with the particle based fluid dynamics simulation framework of smoothed dissipative particle dynamics (SDPD). This hybrid algorithm enables discrete stochastic simulation of spatially resolved chemically reacting systems on a mesh-free dynamic domain with a Lagrangian frame of reference. SDPD combines two popular mesoscopic techniques: smoothed particle hydrodynamics and dissipative particle dynamics (DPD), linking the macroscopic and mesoscopic hydrodynamics effects of these two methods. We have implemented discrete stochastic simulation using the reaction-diffusion master equations (RDME) formalism, and deterministic reaction-diffusion equations based on the SDPD method. We validate the new method by comparing our results to four canonical models, and demonstrate the versatility of our method by simulating a flow containing a chemical gradient...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3b13b4db</guid>
      <pubDate>Wed, 20 Sep 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Jacob, Bruno</name>
      </author>
      <author>
        <name>Li, Zhen</name>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Combinatorial BLAS 2.0: Scaling Combinatorial Algorithms on Distributed-Memory Systems</title>
      <link>https://escholarship.org/uc/item/97f5g1vw</link>
      <description>Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial BLAS library implements key computational primitives for rapid development of combinatorial algorithms in distributed-memory systems. During the decade since its first introduction, the Combinatorial BLAS library has evolved and expanded significantly. This article details many of the key technical features of Combinatorial BLAS version 2.0, such as communication avoidance, hierarchical parallelism via in-node multithreading, accelerator support via GPU kernels, generalized semiring support, implementations of key data structures and functions, and scalable distributed I/O operations for human-readable files. Our article also presents several rules of thumb for choosing the right data structures and functions in Combinatorial BLAS 2.0, under various common application scenarios.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/97f5g1vw</guid>
      <pubDate>Tue, 12 Sep 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Azad, Ariful</name>
      </author>
      <author>
        <name>Selvitopi, Oguz</name>
      </author>
      <author>
        <name>Hussain, Taufique</name>
      </author>
      <author>
        <name>Gilbert, John R</name>
      </author>
      <author>
        <name>Buluç, Aydın</name>
      </author>
    </item>
    <item>
      <title>Functional network inference of the suprachiasmatic nucleus</title>
      <link>https://escholarship.org/uc/item/47g4k5q7</link>
      <description>In the mammalian suprachiasmatic nucleus (SCN), noisy cellular oscillators communicate within a neuronal network to generate precise system-wide circadian rhythms. Although the intracellular genetic oscillator and intercellular biochemical coupling mechanisms have been examined previously, the network topology driving synchronization of the SCN has not been elucidated. This network has been particularly challenging to probe, due to its oscillatory components and slow coupling timescale. In this work, we investigated the SCN network at a single-cell resolution through a chemically induced desynchronization. We then inferred functional connections in the SCN by applying the maximal information coefficient statistic to bioluminescence reporter data from individual neurons while they resynchronized their circadian cycling. Our results demonstrate that the functional network of circadian cells associated with resynchronization has small-world characteristics, with a node degree distribution...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/47g4k5q7</guid>
      <pubDate>Sat, 9 Sep 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Abel, John H</name>
      </author>
      <author>
        <name>Meeker, Kirsten</name>
      </author>
      <author>
        <name>Granados-Fuentes, Daniel</name>
      </author>
      <author>
        <name>St. John, Peter C</name>
      </author>
      <author>
        <name>Wang, Thomas J</name>
      </author>
      <author>
        <name>Bales, Benjamin B</name>
      </author>
      <author>
        <name>Doyle, Francis J</name>
      </author>
      <author>
        <name>Herzog, Erik D</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Decision heuristics in contexts integrating action selection and execution</title>
      <link>https://escholarship.org/uc/item/8rw6v5pm</link>
      <description>Heuristics can inform human decision making in complex environments through a reduction of computational requirements (accuracy-resource trade-off) and a robustness to overparameterisation (less-is-more). However, tasks capturing the efficiency of heuristics typically ignore action proficiency in determining rewards. The requisite movement parameterisation in sensorimotor control questions whether heuristics preserve efficiency when actions are nontrivial. We developed a novel action selection-execution task requiring joint optimisation of action selection and spatio-temporal skillful execution. State-appropriate choices could be determined by a simple spatial heuristic, or by more complex planning. Computational models of action selection parsimoniously distinguished human participants who adopted the heuristic from those using a more complex planning strategy. Broader comparative analyses then revealed that participants using the heuristic showed combined decisional (selection)...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8rw6v5pm</guid>
      <pubDate>Fri, 4 Aug 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Dundon, Neil M</name>
      </author>
      <author>
        <name>Colas, Jaron T</name>
      </author>
      <author>
        <name>Garrett, Neil</name>
      </author>
      <author>
        <name>Babenko, Viktoriya</name>
      </author>
      <author>
        <name>Rizor, Elizabeth</name>
      </author>
      <author>
        <name>Yang, Dengxian</name>
      </author>
      <author>
        <name>MacNamara, Máirtín</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Grafton, Scott T</name>
      </author>
    </item>
    <item>
      <title>An arbitrary Lagrangian Eulerian smoothed particle hydrodynamics (ALE-SPH) method with a boundary volume fraction formulation for fluid-structure interaction</title>
      <link>https://escholarship.org/uc/item/8vv0v48r</link>
      <description>We present a new weakly-compressible smoothed particle hydrodynamics (SPH) method capable of modeling non-slip fixed and moving wall boundary conditions. The formulation combines a boundary volume fraction (BVF) wall approach with the transport-velocity SPH method. The resulting method, named SPH-BVF, offers detection of arbitrarily shaped solid walls on-the-fly, with small computational overhead due to its local formulation. This simple framework is capable of solving problems that are difficult or infeasible for standard SPH, namely flows subject to large shear stresses or at moderate Reynolds numbers, and mass transfer in deformable boundaries. In addition, the method extends the transport-velocity formulation to reaction-diffusion transport of mass in Newtonian fluids and linear elastic solids, which is common in biological structures. Taken together, the SPH-BVF method provides a good balance of simplicity and versatility, while avoiding some of the standard obstacles associated...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8vv0v48r</guid>
      <pubDate>Tue, 4 Jul 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Jacob, Bruno</name>
      </author>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Reaction rates for reaction-diffusion kinetics on unstructured meshes</title>
      <link>https://escholarship.org/uc/item/6g4420j5</link>
      <description>The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system. A viable approach to resolve the complex geometry of cells accurately is to discretize space with an unstructured mesh. Diffusion is modeled as discrete jumps between nodes on the mesh, and the diffusion jump rates can be obtained through a discretization of the diffusion equation on the mesh. Reactions can occur when molecules occupy the same voxel. In this paper, we develop a method for computing accurate reaction rates between molecules occupying the same voxel in an unstructured mesh. For large voxels, these rates are known to be well approximated by the reaction rates derived by Collins and Kimball, but as the mesh is refined, no analytical expression for the rates exists. We reduce the problem of computing accurate reaction rates to a...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6g4420j5</guid>
      <pubDate>Tue, 4 Jul 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Hellander, Stefan</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Local error estimates for adaptive simulation of the reaction–diffusion master equation via operator splitting</title>
      <link>https://escholarship.org/uc/item/46f068kt</link>
      <description>The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/46f068kt</guid>
      <pubDate>Tue, 4 Jul 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Hellander, Andreas</name>
      </author>
      <author>
        <name>Lawson, Michael J</name>
      </author>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Cortical Motion Perception Emerges from Dimensionality Reduction with Evolved Spike-Timing-Dependent Plasticity Rules</title>
      <link>https://escholarship.org/uc/item/9n03981j</link>
      <description>The nervous system is under tight energy constraints and must represent information efficiently. This is particularly relevant in the dorsal part of the medial superior temporal area (MSTd) in primates where neurons encode complex motion patterns to support a variety of behaviors. A sparse decomposition model based on a dimensionality reduction principle known as non-negative matrix factorization (NMF) was previously shown to account for a wide range of monkey MSTd visual response properties. This model resulted in sparse, parts-based representations that could be regarded as basis flow fields, a linear superposition of which accurately reconstructed the input stimuli. This model provided evidence that the seemingly complex response properties of MSTd may be a by-product of MSTd neurons performing dimensionality reduction on their input. However, an open question is how a neural circuit could carry out this function. In the current study, we propose a spiking neural network (SNN)...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9n03981j</guid>
      <pubDate>Sat, 1 Jul 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Chen, Kexin</name>
        <uri>https://orcid.org/0000-0001-5360-8114</uri>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Krichmar, Jeffrey L</name>
        <uri>https://orcid.org/0000-0003-0739-2468</uri>
      </author>
    </item>
    <item>
      <title>Protecting Web-based Single Sign-on Protocols against Relying Party Impersonation Attacks through a Dedicated Bi-directional Authenticated Secure Channel</title>
      <link>https://escholarship.org/uc/item/4bg658n9</link>
      <description>&lt;p&gt;Web-based single sign-on describes a class of protocols where a user signs into a web site with the authentication provided as a service by a third party. In exchange for the increased complexity of the authentication procedure, SSO makes it convenient for users to authenticate themselves to many different web sites (relying parties), using just a single account at an identity provider such as Facebook or Google.&lt;/p&gt;&lt;p&gt;Single sign-on (SSO) protocols, however, are not immune to vulnerabilities. Recent research introduced several attacks against existing SSO protocols, and further work showed that these problems are prevalent: 6.5% of the investigated relying parties were vulnerable to impersonation attacks, which can lead to account compromises and privacy breaches. Prior work used formal verification methods to identify vulnerabilities in SSO protocols or leveraged invariances of SSO interaction traces to identify logic flaws. No prior work, however, systematically studied...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4bg658n9</guid>
      <pubDate>Tue, 27 Jun 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Cao, Yinzhi</name>
      </author>
      <author>
        <name>Shoshitaishvili, Yan</name>
      </author>
      <author>
        <name>Borgolte, Kevin</name>
      </author>
      <author>
        <name>Kruegel, Christopher</name>
      </author>
      <author>
        <name>Vigna, Giovanni</name>
      </author>
      <author>
        <name>Chen, Yan</name>
      </author>
    </item>
    <item>
      <title>Early abnormal fibrinolysis and mortality in patients with thermal injury: a prospective cohort study</title>
      <link>https://escholarship.org/uc/item/0nc5p2d7</link>
      <description>INTRODUCTION: Abnormal fibrinolysis early after injury has been associated with increased mortality in trauma patients, but no studies have addressed patients with burn injury. This prospective cohort study aimed to characterize fibrinolytic phenotypes in burn patients and to see if they were associated with mortality.
METHODS: Patients presenting to a regional burn centre within 4 h of thermal injury were included. Blood was collected for sequential viscoelastic measurements using thromboelastography (RapidTEG™) over 12 h. The percentage decrease in clot strength 30 min after the time of maximal clot strength (LY30) was used to categorize patients into hypofibrinolytic/fibrinolytic shutdown (SD), physiological (PHYS) and hyperfibrinolytic (HF) phenotypes. Injury characteristics, demographics and outcomes were compared.
RESULTS: Of 115 included patients, just over two thirds were male. Overall median age was 40 (i.q.r. 28-57) years and median total body surface area (TBSA) burn...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0nc5p2d7</guid>
      <pubDate>Tue, 20 Jun 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Pusateri, AE</name>
      </author>
      <author>
        <name>Le, TD</name>
      </author>
      <author>
        <name>Keyloun, JW</name>
      </author>
      <author>
        <name>Moffatt, LT</name>
      </author>
      <author>
        <name>Orfeo, T</name>
      </author>
      <author>
        <name>Brummel-Ziedins, KE</name>
      </author>
      <author>
        <name>McLawhorn, MM</name>
      </author>
      <author>
        <name>Callcut, RA</name>
        <uri>https://orcid.org/0000-0002-1582-6716</uri>
      </author>
      <author>
        <name>Shupp, JW</name>
      </author>
      <author>
        <name>Cohen, MJ</name>
      </author>
      <author>
        <name>Petzold, LR</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Varner, JD</name>
      </author>
      <author>
        <name>Bravo, MC</name>
      </author>
      <author>
        <name>Freeman, K</name>
      </author>
      <author>
        <name>Mann, KG</name>
      </author>
      <author>
        <name>Gautam, A</name>
      </author>
      <author>
        <name>Hammamieh, R</name>
      </author>
      <author>
        <name>Jett, M</name>
      </author>
    </item>
    <item>
      <title>Multiscale Modeling Meets Machine Learning: What Can We Learn?</title>
      <link>https://escholarship.org/uc/item/2v25637h</link>
      <description>Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. 
There can be no argument that this technique is incredibly successful in image recognition with immediate applications in diagnostics including electrophysiology, radiology, or pathology, where we have access to massive amounts of annotated data. However, machine learning often performs poorly in prognosis, especially when dealing with sparse data. 
This is a field where classical physics-based simulation seems to remain irreplaceable. In this review, we identify areas in the biomedical sciences where machine learning and multiscale modeling can mutually benefit from one another: Machine learning can integrate physics-based knowledge in the form of governing equations, boundary conditions, or constraints to manage ill-posted problems and robustly handle sparse and noisy data; multiscale modeling can integrate machine learning to create surrogate models,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2v25637h</guid>
      <pubDate>Wed, 7 Jun 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Peng, Grace CY</name>
      </author>
      <author>
        <name>Alber, Mark</name>
        <uri>https://orcid.org/0000-0002-7153-1138</uri>
      </author>
      <author>
        <name>Buganza Tepole, Adrian</name>
      </author>
      <author>
        <name>Cannon, William R</name>
        <uri>https://orcid.org/0000-0003-3789-7889</uri>
      </author>
      <author>
        <name>De, Suvranu</name>
      </author>
      <author>
        <name>Dura-Bernal, Savador</name>
      </author>
      <author>
        <name>Garikipati, Krishna</name>
      </author>
      <author>
        <name>Karniadakis, George</name>
      </author>
      <author>
        <name>Lytton, William W</name>
      </author>
      <author>
        <name>Perdikaris, Paris</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Kuhl, Ellen</name>
      </author>
    </item>
    <item>
      <title>A theory for the slip and drag of superhydrophobic surfaces with surfactant</title>
      <link>https://escholarship.org/uc/item/73p26393</link>
      <description>Superhydrophobic surfaces (SHSs) have the potential to reduce drag at solid boundaries. However, multiple independent studies have recently shown that small amounts of surfactant, naturally present in the environment, can induce Marangoni forces that increase drag, at least in the laminar regime. To obtain accurate drag predictions, one must solve the mass, momentum, bulk surfactant and interfacial surfactant conservation equations. This requires expensive simulations, thus preventing surfactant from being widely considered in SHS studies. To address this issue, we propose a theory for steady, pressure-driven, laminar, two-dimensional flow in a periodic SHS channel with soluble surfactant. We linearise the coupling between flow and surfactant, under the assumption of small concentration, finding a scaling prediction for the local slip length. To obtain the drag reduction and interfacial shear, we find a series solution for the velocity field by assuming Stokes flow in the bulk...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/73p26393</guid>
      <pubDate>Sat, 3 Jun 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Landel, Julien R</name>
      </author>
      <author>
        <name>Peaudecerf, François J</name>
      </author>
      <author>
        <name>Temprano-Coleto, Fernando</name>
      </author>
      <author>
        <name>Gibou, Frédéric</name>
      </author>
      <author>
        <name>Goldstein, Raymond E</name>
      </author>
      <author>
        <name>Luzzatto-Fegiz, Paolo</name>
      </author>
    </item>
    <item>
      <title>Learning to see again: biological constraints on cortical plasticity and the implications for sight restoration technologies</title>
      <link>https://escholarship.org/uc/item/5kp7822p</link>
      <description>The 'bionic eye'-so long a dream of the future-is finally becoming a reality with retinal prostheses available to patients in both the US and Europe. However, clinical experience with these implants has made it apparent that the visual information provided by these devices differs substantially from normal sight. Consequently, the ability of patients to learn to make use of this abnormal retinal input plays a critical role in whether or not some functional vision is successfully regained. The goal of the present review is to summarize the vast basic science literature on developmental and adult cortical plasticity with an emphasis on how this literature might relate to the field of prosthetic vision. We begin with describing the distortion and information loss likely to be experienced by visual prosthesis users. We then define cortical plasticity and perceptual learning, and describe what is known, and what is unknown, about visual plasticity across the hierarchy of brain regions...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5kp7822p</guid>
      <pubDate>Fri, 2 Jun 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Rokem, Ariel</name>
      </author>
      <author>
        <name>Boynton, Geoffrey M</name>
      </author>
      <author>
        <name>Fine, Ione</name>
      </author>
    </item>
    <item>
      <title>Interpretable polynomial neural ordinary differential equations</title>
      <link>https://escholarship.org/uc/item/063153hd</link>
      <description>Neural networks have the ability to serve as universal function approximators, but they are not interpretable and do not generalize well outside of their training region. Both of these issues are problematic when trying to apply standard neural ordinary differential equations (ODEs) to dynamical systems. We introduce the polynomial neural ODE, which is a deep polynomial neural network inside of the neural ODE framework. We demonstrate the capability of polynomial neural ODEs to predict outside of the training region, as well as to perform direct symbolic regression without using additional tools such as SINDy.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/063153hd</guid>
      <pubDate>Fri, 12 May 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Fronk, Colby</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Preliminary study: quantification of chronic pain from physiological data</title>
      <link>https://escholarship.org/uc/item/7xs730h9</link>
      <description>Introduction: It is unknown if physiological changes associated with chronic pain could be measured with inexpensive physiological sensors. Recently, acute pain and laboratory-induced pain have been quantified with physiological sensors.
Objectives: To investigate the extent to which chronic pain can be quantified with physiological sensors.
Methods: Data were collected from chronic pain sufferers who subjectively rated their pain on a 0 to 10 visual analogue scale, using our recently developed pain meter. Physiological variables, including pulse, temperature, and motion signals, were measured at head, neck, wrist, and finger with multiple sensors. To quantify pain, features were first extracted from 10-second windows. Linear models with recursive feature elimination were fit for each subject. A random forest regression model was used for pain score prediction for the population-level model.
Results: Predictive performance was assessed using leave-one-recording-out cross-validation...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7xs730h9</guid>
      <pubDate>Thu, 11 May 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Cheng, Zhuowei</name>
      </author>
      <author>
        <name>Ly, Franklin</name>
      </author>
      <author>
        <name>Santander, Tyler</name>
      </author>
      <author>
        <name>Turki, Elyes</name>
      </author>
      <author>
        <name>Zhao, Yun</name>
      </author>
      <author>
        <name>Yoo, Jamie</name>
      </author>
      <author>
        <name>Lonergan, Kian</name>
      </author>
      <author>
        <name>Gray, Jordan</name>
      </author>
      <author>
        <name>Li, Christopher H</name>
      </author>
      <author>
        <name>Yang, Henry</name>
      </author>
      <author>
        <name>Miller, Michael</name>
      </author>
      <author>
        <name>Hansma, Paul</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Efficient multi-scale representation of visual objects using a biologically plausible spike-latency code and winner-take-all inhibition</title>
      <link>https://escholarship.org/uc/item/28n197x7</link>
      <description>Deep neural networks have surpassed human performance in key visual challenges such as object recognition, but require a large amount of energy, computation, and memory. In contrast, spiking neural networks (SNNs) have the potential to improve both the efficiency and biological plausibility of object recognition systems. Here we present a SNN model that uses spike-latency coding and winner-take-all inhibition (WTA-I) to efficiently represent visual stimuli using multi-scale parallel processing. Mimicking neuronal response properties in early visual cortex, images were preprocessed with three different spatial frequency (SF) channels, before they were fed to a layer of spiking neurons whose synaptic weights were updated using spike-timing-dependent-plasticity. We investigate how the quality of the represented objects changes under different SF bands and WTA-I schemes. We demonstrate that a network of 200 spiking neurons tuned to three SFs can efficiently represent objects with...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/28n197x7</guid>
      <pubDate>Thu, 27 Apr 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Sanchez-Garcia, Melani</name>
      </author>
      <author>
        <name>Chauhan, Tushar</name>
      </author>
      <author>
        <name>Cottereau, Benoit R</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Optimal and human eye movements to clustered low value cues to increase decision rewards during search</title>
      <link>https://escholarship.org/uc/item/4kb5x7k1</link>
      <description>Rewards have important influences on the motor planning of primates and the firing of neurons coding visual information and action. When eye movements to a target are differentially rewarded across locations, primates execute saccades towards the possible target location with the highest expected value, a product of sensory evidence and potentially earned reward (saccade to maximum expected value model, sMEV). Yet, in the natural world eye movements are not directly rewarded. Their role is to gather information to support subsequent rewarded search decisions and actions. Less is known about the effects of decision rewards on saccades. We show that when varying the decision rewards across cued locations following visual search, humans can plan their eye movements to increase decision rewards. Critically, we report a scenario for which five of seven tested humans do not preferentially deploy saccades to the possible target location with the highest reward, a strategy which is optimal...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4kb5x7k1</guid>
      <pubDate>Mon, 17 Apr 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Eckstein, Miguel P</name>
      </author>
      <author>
        <name>Schoonveld, Wade</name>
      </author>
      <author>
        <name>Zhang, Sheng</name>
      </author>
      <author>
        <name>Mack, Stephen C</name>
      </author>
      <author>
        <name>Akbas, Emre</name>
      </author>
    </item>
    <item>
      <title>Opinion Dynamics and Social Power Evolution over Reducible Influence Networks</title>
      <link>https://escholarship.org/uc/item/31p930j5</link>
      <description>Opinion Dynamics and Social Power Evolution over Reducible Influence Networks</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/31p930j5</guid>
      <pubDate>Sat, 8 Apr 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Jia, Peng</name>
      </author>
      <author>
        <name>Friedkin, Noah E</name>
      </author>
      <author>
        <name>Bullo, Francesco</name>
        <uri>https://orcid.org/0000-0002-4785-2118</uri>
      </author>
    </item>
    <item>
      <title>The Coevolution of Appraisal and Influence Networks Leads to Structural Balance</title>
      <link>https://escholarship.org/uc/item/4h88j94z</link>
      <description>The Coevolution of Appraisal and Influence Networks Leads to Structural Balance</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4h88j94z</guid>
      <pubDate>Wed, 5 Apr 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Jia, Peng</name>
      </author>
      <author>
        <name>Friedkin, Noah E</name>
      </author>
      <author>
        <name>Bullo, Francesco</name>
      </author>
    </item>
    <item>
      <title>Dynamic Models of Appraisal Networks Explaining Collective Learning</title>
      <link>https://escholarship.org/uc/item/3m17d3qv</link>
      <description>Dynamic Models of Appraisal Networks Explaining Collective Learning</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3m17d3qv</guid>
      <pubDate>Wed, 5 Apr 2023 00:00:00 +0000</pubDate>
      <author>
        <name>Mei, Wenjun</name>
      </author>
      <author>
        <name>Friedkin, Noah E</name>
      </author>
      <author>
        <name>Lewis, Kyle</name>
      </author>
      <author>
        <name>Bullo, Francesco</name>
        <uri>https://orcid.org/0000-0002-4785-2118</uri>
      </author>
    </item>
    <item>
      <title>Contributed Session I: What limits the spatial resolution of artificial vision in epiretinal implant patients?</title>
      <link>https://escholarship.org/uc/item/8dc2z85m</link>
      <description>&lt;h4&gt;Introduction&lt;/h4&gt;Retinal implants provide artificial vision to blind individuals through electrically stimulating remaining non-photoreceptor retinal cells. For epiretinal implants, placed over the ganglion cell layer, individual electrodes produce elongated 'streaks' due to the unselective stimulation of underlying ganglion axons (Beyeler, 2019). Here, to examine whether these axonal streaks explain the poor spatial acuity of prosthetic patients, we measured two-point discrimination performance in three patients implanted with an Argus 2 epiretinal implant (Second Sight Medical Products Inc).&lt;h4&gt;Methods&lt;/h4&gt;On each trial two electrodes were simultaneously stimulated (0.45 um pulse width, 6-20 Hz pulse train, 250-500ms duration, current amplitude 2x threshold). Participants verbally reported the number of distinct percepts they saw.&lt;h4&gt;Results&lt;/h4&gt;A regression analysis found that current amplitude, physical distance, distance along the axon, and distance between axons all...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8dc2z85m</guid>
      <pubDate>Thu, 15 Dec 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Yucel, Ezgi Irmak</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Sadeghi, Roksana</name>
      </author>
      <author>
        <name>Rokem, Ariel</name>
      </author>
      <author>
        <name>Fine, Ione</name>
      </author>
      <author>
        <name>Kartha, Arathy</name>
      </author>
      <author>
        <name>Dagnelie, Gislin</name>
      </author>
    </item>
    <item>
      <title>Immersive Virtual Reality Simulations of Bionic Vision</title>
      <link>https://escholarship.org/uc/item/7327s0dm</link>
      <description>Bionic vision uses neuroprostheses to restore useful vision to people living with incurable blindness. However, a major outstanding challenge is predicting what people "see" when they use their devices. The limited field of view of current devices necessitates head movements to scan the scene, which is difficult to simulate on a computer screen. In addition, many computational models of bionic vision lack biological realism. To address these challenges, we present VR-SPV, an open-source virtual reality toolbox for simulated prosthetic vision that uses a psychophysically validated computational model to allow sighted participants to "see through the eyes" of a bionic eye user. To demonstrate its utility, we systematically evaluated how clinically reported visual distortions affect performance in a letter recognition and an immersive obstacle avoidance task. Our results highlight the importance of using an appropriate phosphene model when predicting visual outcomes for bionic vision.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7327s0dm</guid>
      <pubDate>Thu, 15 Dec 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Kasowski, Justin</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Learning to see again: Perceptual learning of simulated abnormal on- off-cell population responses in sighted individuals</title>
      <link>https://escholarship.org/uc/item/5xn5j3dr</link>
      <description>Many forms of artificial sight recovery, such as electronic implants and optogenetic proteins, generally cause simultaneous, rather than complementary firing of on- and off-center retinal cells. Here, using virtual patients-sighted individuals viewing distorted input-we examine whether plasticity might compensate for abnormal neuronal population responses. Five participants were dichoptically presented with a combination of original and contrast-reversed images. Each image (I) and its contrast-reverse (I') was filtered using a radial checkerboard (F) in Fourier space and its inverse (F'). [I * F'] + [I' * F] was presented to one eye, and [I * F] + [I' * F'] was presented to the other, such that regions of the image that produced on-center responses in one eye produced off-center responses in the other eye, and vice versa. Participants continuously improved in a naturalistic object discrimination task over 20 one-hour sessions. Pre-training and post-training tests suggest that...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5xn5j3dr</guid>
      <pubDate>Thu, 15 Dec 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Esquenazi, Rebecca B</name>
      </author>
      <author>
        <name>Meier, Kimberly</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
      <author>
        <name>Boynton, Geoffrey M</name>
      </author>
      <author>
        <name>Fine, Ione</name>
      </author>
    </item>
    <item>
      <title>Factors affecting two-point discrimination in Argus II patients</title>
      <link>https://escholarship.org/uc/item/3hc4k8zj</link>
      <description>Two of the main obstacles to the development of epiretinal prosthesis technology are electrodes that require current amplitudes above safety limits to reliably elicit percepts, and a failure to consistently elicit pattern vision. Here, we explored the causes of high current amplitude thresholds and poor spatial resolution within the Argus II epiretinal implant. We measured current amplitude thresholds and two-point discrimination (the ability to determine whether one or two electrodes had been stimulated) in 3 blind participants implanted with Argus II devices. Our data and simulations show that axonal stimulation, lift and retinal damage all play a role in reducing performance in the Argus 2, by either limiting sensitivity and/or reducing spatial resolution. Understanding the relative role of these various factors will be critical for developing and surgically implanting devices that can successfully subserve pattern vision.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3hc4k8zj</guid>
      <pubDate>Thu, 15 Dec 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Yücel, Ezgi I</name>
      </author>
      <author>
        <name>Sadeghi, Roksana</name>
      </author>
      <author>
        <name>Kartha, Arathy</name>
      </author>
      <author>
        <name>Montezuma, Sandra Rocio</name>
      </author>
      <author>
        <name>Dagnelie, Gislin</name>
      </author>
      <author>
        <name>Rokem, Ariel</name>
      </author>
      <author>
        <name>Boynton, Geoffrey M</name>
      </author>
      <author>
        <name>Fine, Ione</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>A Computational Model of Phosphene Appearance for Epiretinal Prostheses</title>
      <link>https://escholarship.org/uc/item/3931s2d5</link>
      <description>Retinal neuroprostheses are the only FDA-approved treatment option for blinding degenerative diseases. A major outstanding challenge is to develop a computational model that can accurately predict the elicited visual percepts (phosphenes) across a wide range of electrical stimuli. Here we present a phenomenological model that predicts phosphene appearance as a function of stimulus amplitude, frequency, and pulse duration. The model uses a simulated map of nerve fiber bundles in the retina to produce phosphenes with accurate brightness, size, orientation, and elongation. We validate the model on psychophysical data from two independent studies, showing that it generalizes well to new data, even with different stimuli and on different electrodes. Whereas previous models focused on either spatial or temporal aspects of the elicited phosphenes in isolation, we describe a more comprehensive approach that is able to account for many reported visual effects. The model is designed to...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3931s2d5</guid>
      <pubDate>Thu, 15 Dec 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Granley, Jacob</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Functional neuronal circuitry and oscillatory dynamics in human brain organoids</title>
      <link>https://escholarship.org/uc/item/2n55r713</link>
      <description>Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiology of neuronal circuits within organoids remains under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. We inferred functional connectivity from spike timing, revealing a large number of weak connections within a skeleton of significantly fewer strong connections. A benzodiazepine increased the uniformity of firing patterns and decreased the relative fraction of weakly connected edges. Our analysis of the local field potential demonstrate that brain organoids contain neuronal assemblies of sufficient size and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2n55r713</guid>
      <pubDate>Tue, 6 Sep 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Sharf, Tal</name>
      </author>
      <author>
        <name>van der Molen, Tjitse</name>
      </author>
      <author>
        <name>Glasauer, Stella MK</name>
      </author>
      <author>
        <name>Guzman, Elmer</name>
      </author>
      <author>
        <name>Buccino, Alessio P</name>
      </author>
      <author>
        <name>Luna, Gabriel</name>
      </author>
      <author>
        <name>Cheng, Zhuowei</name>
      </author>
      <author>
        <name>Audouard, Morgane</name>
      </author>
      <author>
        <name>Ranasinghe, Kamalini G</name>
      </author>
      <author>
        <name>Kudo, Kiwamu</name>
      </author>
      <author>
        <name>Nagarajan, Srikantan S</name>
      </author>
      <author>
        <name>Tovar, Kenneth R</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Hierlemann, Andreas</name>
      </author>
      <author>
        <name>Hansma, Paul K</name>
      </author>
      <author>
        <name>Kosik, Kenneth S</name>
        <uri>https://orcid.org/0000-0003-3224-5179</uri>
      </author>
    </item>
    <item>
      <title>BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum</title>
      <link>https://escholarship.org/uc/item/68q8n732</link>
      <description>The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/68q8n732</guid>
      <pubDate>Thu, 1 Sep 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Griesemer, Marc</name>
      </author>
      <author>
        <name>Young, Carissa</name>
      </author>
      <author>
        <name>Robinson, Anne S</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Noise resistant synchronization and collective rhythm switching in a model of animal group locomotion</title>
      <link>https://escholarship.org/uc/item/53j7j69m</link>
      <description>Biology is suffused with rhythmic behaviour, and interacting biological oscillators often synchronize their rhythms with one another. Colonies of some ant species are able to synchronize their activity to fall into coherent bursts, but models of this phenomenon have neglected the potential effects of intrinsic noise and interspecific differences in individual-level behaviour. We investigated the individual and collective activity patterns of two &lt;i&gt;Leptothorax&lt;/i&gt; ant species. We show that in one species (&lt;i&gt;Leptothorax&lt;/i&gt; sp. W), ants converge onto rhythmic cycles of synchronized collective activity with a period of about 20 min. A second species (&lt;i&gt;Leptothorax crassipilis&lt;/i&gt;) exhibits more complex collective dynamics, where dominant collective cycle periods range from 16 min to 2.8 h. Recordings that last 35 h reveal that, in both species, the same colony can exhibit multiple oscillation frequencies. We observe that workers of both species can be stimulated by nest-mates...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/53j7j69m</guid>
      <pubDate>Thu, 1 Sep 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Doering, Grant Navid</name>
      </author>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Lee, Carmen</name>
      </author>
      <author>
        <name>Pruitt, Jonathan N</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Dalnoki-Veress, Kari</name>
      </author>
    </item>
    <item>
      <title>BioSimulators: a central registry of simulation engines and services for recommending specific tools</title>
      <link>https://escholarship.org/uc/item/2d80h1vd</link>
      <description>Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line&amp;nbsp;and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML&amp;nbsp;and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services....</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2d80h1vd</guid>
      <pubDate>Mon, 25 Jul 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Shaikh, Bilal</name>
      </author>
      <author>
        <name>Smith, Lucian P</name>
      </author>
      <author>
        <name>Vasilescu, Dan</name>
      </author>
      <author>
        <name>Marupilla, Gnaneswara</name>
      </author>
      <author>
        <name>Wilson, Michael</name>
      </author>
      <author>
        <name>Agmon, Eran</name>
      </author>
      <author>
        <name>Agnew, Henry</name>
        <uri>https://orcid.org/0000-0003-1447-6045</uri>
      </author>
      <author>
        <name>Andrews, Steven S</name>
      </author>
      <author>
        <name>Anwar, Azraf</name>
      </author>
      <author>
        <name>Beber, Moritz E</name>
      </author>
      <author>
        <name>Bergmann, Frank T</name>
      </author>
      <author>
        <name>Brooks, David</name>
      </author>
      <author>
        <name>Brusch, Lutz</name>
      </author>
      <author>
        <name>Calzone, Laurence</name>
      </author>
      <author>
        <name>Choi, Kiri</name>
      </author>
      <author>
        <name>Cooper, Joshua</name>
      </author>
      <author>
        <name>Detloff, John</name>
      </author>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Dumontier, Michel</name>
      </author>
      <author>
        <name>Ermentrout, G Bard</name>
      </author>
      <author>
        <name>Faeder, James R</name>
      </author>
      <author>
        <name>Freiburger, Andrew P</name>
      </author>
      <author>
        <name>Fröhlich, Fabian</name>
      </author>
      <author>
        <name>Funahashi, Akira</name>
      </author>
      <author>
        <name>Garny, Alan</name>
      </author>
      <author>
        <name>Gennari, John H</name>
      </author>
      <author>
        <name>Gleeson, Padraig</name>
      </author>
      <author>
        <name>Goelzer, Anne</name>
      </author>
      <author>
        <name>Haiman, Zachary</name>
      </author>
      <author>
        <name>Hasenauer, Jan</name>
      </author>
      <author>
        <name>Hellerstein, Joseph L</name>
      </author>
      <author>
        <name>Hermjakob, Henning</name>
      </author>
      <author>
        <name>Hoops, Stefan</name>
      </author>
      <author>
        <name>Ison, Jon C</name>
      </author>
      <author>
        <name>Jahn, Diego</name>
      </author>
      <author>
        <name>Jakubowski, Henry V</name>
      </author>
      <author>
        <name>Jordan, Ryann</name>
      </author>
      <author>
        <name>Kalaš, Matúš</name>
      </author>
      <author>
        <name>König, Matthias</name>
      </author>
      <author>
        <name>Liebermeister, Wolfram</name>
      </author>
      <author>
        <name>Sheriff, Rahuman S Malik</name>
      </author>
      <author>
        <name>Mandal, Synchon</name>
      </author>
      <author>
        <name>McDougal, Robert</name>
      </author>
      <author>
        <name>Medley, J Kyle</name>
      </author>
      <author>
        <name>Mendes, Pedro</name>
      </author>
      <author>
        <name>Müller, Robert</name>
      </author>
      <author>
        <name>Myers, Chris J</name>
      </author>
      <author>
        <name>Naldi, Aurelien</name>
      </author>
      <author>
        <name>Nguyen, Tung VN</name>
      </author>
      <author>
        <name>Nickerson, David P</name>
      </author>
      <author>
        <name>Olivier, Brett G</name>
      </author>
      <author>
        <name>Patoliya, Drashti</name>
      </author>
      <author>
        <name>Paulevé, Loïc</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Priya, Ankita</name>
      </author>
      <author>
        <name>Rampadarath, Anand K</name>
      </author>
      <author>
        <name>Rohwer, Johann M</name>
      </author>
      <author>
        <name>Saglam, Ali S</name>
      </author>
      <author>
        <name>Singh, Dilawar</name>
      </author>
      <author>
        <name>Sinha, Ankur</name>
      </author>
      <author>
        <name>Snoep, Jacky</name>
      </author>
      <author>
        <name>Sorby, Hugh</name>
      </author>
      <author>
        <name>Spangler, Ryan</name>
      </author>
      <author>
        <name>Starruß, Jörn</name>
      </author>
      <author>
        <name>Thomas, Payton J</name>
      </author>
      <author>
        <name>van Niekerk, David</name>
      </author>
      <author>
        <name>Weindl, Daniel</name>
      </author>
      <author>
        <name>Zhang, Fengkai</name>
      </author>
      <author>
        <name>Zhukova, Anna</name>
      </author>
      <author>
        <name>Goldberg, Arthur P</name>
      </author>
      <author>
        <name>Schaff, James C</name>
      </author>
      <author>
        <name>Blinov, Michael L</name>
      </author>
      <author>
        <name>Sauro, Herbert M</name>
      </author>
      <author>
        <name>Moraru, Ion I</name>
      </author>
      <author>
        <name>Karr, Jonathan R</name>
      </author>
    </item>
    <item>
      <title>Inhalation Injury Is Associated With Endotheliopathy and Abnormal Fibrinolytic Phenotypes in Burn Patients: A Cohort Study</title>
      <link>https://escholarship.org/uc/item/2qn66960</link>
      <description>Burn injury is associated with endothelial dysfunction and coagulopathy and concomitant inhalation injury (IHI) increases morbidity and mortality. The aim of this work is to identify associations between IHI, coagulation homeostasis, vascular endothelium, and clinical outcomes in burn patients. One hundred and twelve patients presenting to a regional burn center were included in this retrospective cohort study. Whole blood was collected at set intervals from admission through 24 hours and underwent viscoelastic assay with rapid thromboelastography (rTEG). Syndecan-1 (SDC-1) on admission was quantified by ELISA. Patients were grouped by the presence (n = 28) or absence (n = 84) of concomitant IHI and rTEG parameters, fibrinolytic phenotypes, SDC-1, and clinical outcomes were compared. Of the 112 thermally injured patients, 28 (25%) had IHI. Most patients were male (68.8%) with a median age of 40 (interquartile range, 29-57) years. Patients with IHI had higher overall mortality...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2qn66960</guid>
      <pubDate>Fri, 22 Jul 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Keyloun, John W</name>
      </author>
      <author>
        <name>Le, Tuan D</name>
      </author>
      <author>
        <name>Brummel-Ziedins, Kathleen E</name>
      </author>
      <author>
        <name>Mclawhorn, Melissa M</name>
      </author>
      <author>
        <name>Bravo, Maria C</name>
      </author>
      <author>
        <name>Orfeo, Thomas</name>
      </author>
      <author>
        <name>Johnson, Laura S</name>
      </author>
      <author>
        <name>Moffatt, Lauren T</name>
      </author>
      <author>
        <name>Pusateri, Anthony E</name>
      </author>
      <author>
        <name>Shupp, Jeffrey W</name>
      </author>
      <author>
        <name>McLawhorn, Melissa M</name>
      </author>
      <author>
        <name>Moffatt, Lauren T</name>
      </author>
      <author>
        <name>Shupp, Jeffrey W</name>
      </author>
      <author>
        <name>Callcut, Rachael A</name>
        <uri>https://orcid.org/0000-0002-1582-6716</uri>
      </author>
      <author>
        <name>Cohen, Mitchell J</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Varner, Jeffrey D</name>
      </author>
      <author>
        <name>Bravo, Maria Cristina</name>
      </author>
      <author>
        <name>Brummel-Ziedins, Kathleen E</name>
      </author>
      <author>
        <name>Freeman, Kalev</name>
      </author>
      <author>
        <name>Mann, Kenneth G</name>
      </author>
      <author>
        <name>Orfeo, Thomas</name>
      </author>
      <author>
        <name>Gautam, Aarti</name>
      </author>
      <author>
        <name>Hammamieh, Rasha</name>
      </author>
      <author>
        <name>Jett, Marti</name>
      </author>
      <author>
        <name>Pusateri, Anthony E</name>
      </author>
    </item>
    <item>
      <title>Assessing Factor V Antigen and Degradation Products in Burn and Trauma Patients</title>
      <link>https://escholarship.org/uc/item/9xd62548</link>
      <description>INTRODUCTION: Proposed mechanisms of acute traumatic coagulopathy (ATC) include decreased clotting potential due to factor consumption and proteolytic inactivation of factor V (FV) and activated factor V (FVa) by activated protein C (aPC). The role of FV/FVa depletion or inactivation in burn-induced coagulopathy is not well characterized. This study evaluates FV dynamics following burn and nonburn trauma.
METHODS: Burn and trauma patients were prospectively enrolled. Western blotting was performed on admission plasma to quantitate levels of FV antigen and to assess for aPC or other proteolytically derived FV/FVa degradation products. Statistical analysis was performed with Spearman's, Chi-square, Mann-Whitney U test, and logistic regression.
RESULTS: Burn (n&amp;nbsp;=&amp;nbsp;60) and trauma (n&amp;nbsp;=&amp;nbsp;136) cohorts showed similar degrees of FV consumption with median FV levels of 76% versus 73% (P&amp;nbsp;=&amp;nbsp;0.65) of normal, respectively. Percent total body surface area (TBSA) was...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9xd62548</guid>
      <pubDate>Wed, 16 Mar 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Keyloun, John W</name>
      </author>
      <author>
        <name>Le, Tuan D</name>
      </author>
      <author>
        <name>Orfeo, Thomas</name>
      </author>
      <author>
        <name>Brummel-Ziedins, Kathleen E</name>
      </author>
      <author>
        <name>Bravo, Maria C</name>
      </author>
      <author>
        <name>Kaye, Matthew D</name>
      </author>
      <author>
        <name>Bourne, Dana E</name>
      </author>
      <author>
        <name>Carney, Bonnie C</name>
      </author>
      <author>
        <name>Freeman, Kalev</name>
      </author>
      <author>
        <name>Mann, Kenneth G</name>
      </author>
      <author>
        <name>Pusateri, Anthony E</name>
      </author>
      <author>
        <name>Shupp, Jeffrey W</name>
      </author>
      <author>
        <name>Group, the SYSCOT Study</name>
      </author>
      <author>
        <name>McLawhorn, Melissa M</name>
      </author>
      <author>
        <name>Moffatt, Lauren T</name>
      </author>
      <author>
        <name>Shupp, Jeffrey W</name>
      </author>
      <author>
        <name>Callcut, Rachael A</name>
        <uri>https://orcid.org/0000-0002-1582-6716</uri>
      </author>
      <author>
        <name>Cohen, Mitchell J</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Varner, Jeffrey D</name>
      </author>
      <author>
        <name>Bravo, Maria Cristina</name>
      </author>
      <author>
        <name>Brummel-Ziedins, Kathleen E</name>
      </author>
      <author>
        <name>Freeman, Kalev</name>
      </author>
      <author>
        <name>Mann, Kenneth G</name>
      </author>
      <author>
        <name>Orfeo, Thomas</name>
      </author>
      <author>
        <name>Gautam, Aarti</name>
      </author>
      <author>
        <name>Hammamieh, Rasha</name>
      </author>
      <author>
        <name>Jett, Marti</name>
      </author>
      <author>
        <name>Pusateri, Anthony E</name>
      </author>
    </item>
    <item>
      <title>Associations of longitudinal D-Dimer and Factor II on early trauma survival risk</title>
      <link>https://escholarship.org/uc/item/96j612g9</link>
      <description>BackgroundTrauma-induced coagulopathy (TIC) is a disorder that occurs in one-third of severely injured trauma patients, manifesting as increased bleeding and a 4X risk of mortality. Understanding the mechanisms driving TIC, clinical risk factors are essential to mitigating this coagulopathic bleeding and is therefore essential for saving lives. In this retrospective, single hospital study of 891 trauma patients, we investigate and quantify how two prominently described phenotypes of TIC, consumptive coagulopathy and hyperfibrinolysis, affect survival odds in the first 25 h, when deaths from TIC are most prevalent.MethodsWe employ a joint survival model to estimate the longitudinal trajectories of the protein Factor II (% activity) and the log of the protein fragment D-Dimer (μ$$\upmu$$g/ml), representative biomarkers of consumptive coagulopathy and hyperfibrinolysis respectively, and tie them together with patient outcomes. Joint models have recently gained popularity in medical...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/96j612g9</guid>
      <pubDate>Wed, 2 Mar 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Jiang, Richard M</name>
      </author>
      <author>
        <name>Pourzanjani, Arya A</name>
      </author>
      <author>
        <name>Cohen, Mitchell J</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>The extended parameter filter</title>
      <link>https://escholarship.org/uc/item/3vs313d2</link>
      <description>The parameters of temporal models, such as dynamic Bayesian networks, may be modelled in a Bayesian context as static or atemporal variables that influence transition probabilities at every time step. Particle filters fail for models that include such variables, while methods that use Gibbs sampling of parameter variables may incur a per-sample cost that grows linearly with the length of the observation sequence. Storvik (2002) devised a method for incremental computation of exact sufficient statistics that, for some cases, reduces the per-sample cost to a constant. In this paper, we demonstrate a connection between Storvik's filter and a Kalman filter in parameter space and establish more general conditions under which Storvik's filter works. Drawing on an analogy to the extended Kalman filter, we develop and analyze, both theoretically and experimentally, a Taylor approximation to the parameter posterior that allows Storvik's method to be applied to a broader class of models....</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3vs313d2</guid>
      <pubDate>Wed, 2 Mar 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Erol, YB</name>
      </author>
      <author>
        <name>Li, L</name>
        <uri>https://orcid.org/0000-0003-3095-9776</uri>
      </author>
      <author>
        <name>Ramsundar, B</name>
      </author>
      <author>
        <name>Russell, S</name>
      </author>
    </item>
    <item>
      <title>Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators</title>
      <link>https://escholarship.org/uc/item/1sz8k5kf</link>
      <description>BackgroundApproximate Bayesian Computation (ABC) has become a key tool for calibrating the parameters of discrete stochastic biochemical models. For higher dimensional models and data, its performance is strongly dependent on having a representative set of summary statistics. While regression-based methods have been demonstrated to allow for the automatic construction of effective summary statistics, their reliance on first simulating a large training set creates a significant overhead when applying these methods to discrete stochastic models for which simulation is relatively expensive. In this τ work, we present a method to reduce this computational burden by leveraging approximate simulators of these systems, such as ordinary differential equations and τ-Leaping approximations.ResultsWe have developed an algorithm to accelerate the construction of regression-based summary statistics for Approximate Bayesian Computation by selectively using the faster approximate algorithms...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1sz8k5kf</guid>
      <pubDate>Wed, 2 Mar 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Jiang, Richard M</name>
      </author>
      <author>
        <name>Wrede, Fredrik</name>
      </author>
      <author>
        <name>Singh, Prashant</name>
      </author>
      <author>
        <name>Hellander, Andreas</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Extracellular detection of neuronal coupling</title>
      <link>https://escholarship.org/uc/item/1rf4r3n0</link>
      <description>We developed a method to non-invasively detect synaptic relationships among neurons from in vitro networks. Our method uses microelectrode arrays on which neurons are cultured and from which propagation of extracellular action potentials (eAPs) in single axons are recorded at multiple electrodes. Detecting eAP propagation bypasses ambiguity introduced by spike sorting. Our methods identify short latency spiking relationships between neurons with properties expected of synaptically coupled neurons, namely they were recapitulated by direct stimulation and were sensitive to changing the number of active synaptic sites. Our methods enabled us to assemble a functional subset of neuronal connectivity in our cultures.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1rf4r3n0</guid>
      <pubDate>Wed, 2 Mar 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Guzman, Elmer</name>
      </author>
      <author>
        <name>Cheng, Zhuowei</name>
      </author>
      <author>
        <name>Hansma, Paul K</name>
      </author>
      <author>
        <name>Tovar, Kenneth R</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Kosik, Kenneth S</name>
        <uri>https://orcid.org/0000-0003-3224-5179</uri>
      </author>
    </item>
    <item>
      <title>Epidemiological modeling in StochSS Live!</title>
      <link>https://escholarship.org/uc/item/1m39n3b0</link>
      <description>SUMMARY: We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results.
AVAILABILITY AND IMPLEMENTATION: StochSS Live! is freely available at https://live.stochss.org/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1m39n3b0</guid>
      <pubDate>Wed, 2 Mar 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Jiang, Richard</name>
      </author>
      <author>
        <name>Jacob, Bruno</name>
      </author>
      <author>
        <name>Geiger, Matthew</name>
      </author>
      <author>
        <name>Matthew, Sean</name>
      </author>
      <author>
        <name>Rumsey, Bryan</name>
      </author>
      <author>
        <name>Singh, Prashant</name>
      </author>
      <author>
        <name>Wrede, Fredrik</name>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Hellander, Andreas</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods</title>
      <link>https://escholarship.org/uc/item/8j6391dm</link>
      <description>Identifying the reactions that govern a dynamical biological system is a crucial but challenging task in systems biology. In this work, we present a data-driven method to infer the underlying biochemical reaction system governing a set of observed species concentrations over time. We formulate the problem as a regression over a large, but limited, mass-action constrained reaction space and utilize sparse Bayesian inference via the regularized horseshoe prior to produce robust, interpretable biochemical reaction networks, along with uncertainty estimates of parameters. The resulting systems of chemical reactions and posteriors inform the biologist of potentially several reaction systems that can be further investigated. We demonstrate the method on two examples of recovering the dynamics of an unknown reaction system, to illustrate the benefits of improved accuracy and information obtained.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8j6391dm</guid>
      <pubDate>Mon, 28 Feb 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Jiang, Richard</name>
      </author>
      <author>
        <name>Singh, Prashant</name>
      </author>
      <author>
        <name>Wrede, Fredrik</name>
      </author>
      <author>
        <name>Hellander, Andreas</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>A positive feedback loop involving the Spa2 SHD domain contributes to focal polarization</title>
      <link>https://escholarship.org/uc/item/2t33m3sz</link>
      <description>Focal polarization is necessary for finely arranged cell-cell interactions. The yeast mating projection, with its punctate polarisome, is a good model system for this process. We explored the critical role of the polarisome scaffold protein Spa2 during yeast mating with a hypothesis motivated by mathematical modeling and tested by in vivo experiments. Our simulations predicted that two positive feedback loops generate focal polarization, including a novel feedback pathway involving the N-terminal domain of Spa2. We characterized the latter using loss-of-function and gain-of-function mutants. The N-terminal region contains a Spa2 Homology Domain (SHD) which is conserved from yeast to humans, and when mutated largely reproduced the spa2Δ phenotype. Our work together with published data show that the SHD domain recruits Msb3/4 that stimulates Sec4-mediated transport of Bud6 to the polarisome. There, Bud6 activates Bni1-catalyzed actin cable formation, recruiting more Spa2 and completing...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2t33m3sz</guid>
      <pubDate>Mon, 28 Feb 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Lawson, Michael J</name>
      </author>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
    </item>
    <item>
      <title>How truth wins in opinion dynamics along issue sequences</title>
      <link>https://escholarship.org/uc/item/9g897495</link>
      <description>How truth wins in social groups is an important open problem. Classic experiments on social groups dealing with truth statement issues present mixed findings on the conditions of truth abandonment and reaching a consensus on the truth. No theory has been developed and evaluated that might integrate these findings with a mathematical model of the interpersonal influence system that alters some or all of its members' positions on an issue. In this paper we provide evidence that a general model in the network science on opinion dynamics substantially clarifies how truth wins in groups.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9g897495</guid>
      <pubDate>Wed, 26 Jan 2022 00:00:00 +0000</pubDate>
      <author>
        <name>Friedkin, Noah E</name>
      </author>
      <author>
        <name>Bullo, Francesco</name>
        <uri>https://orcid.org/0000-0002-4785-2118</uri>
      </author>
    </item>
    <item>
      <title>Monitoring of Technical Variation in Quantitative High-Throughput Datasets</title>
      <link>https://escholarship.org/uc/item/1xw2r2qq</link>
      <description>High-dimensional datasets can be confounded by variation from technical sources, such as batches. Undetected batch effects can have severe consequences for the validity of a study's conclusion(s). We evaluate high-throughput RNAseq and miRNAseq as well as DNA methylation and gene expression microarray datasets, mainly from the Cancer Genome Atlas (TCGA) project, in respect to technical and biological annotations. We observe technical bias in these datasets and discuss corrective interventions. We then suggest a general procedure to control study design, detect technical bias using linear regression of principal components, correct for batch effects, and re-evaluate principal components. This procedure is implemented in the R package swamp, and as graphical user interface software. In conclusion, high-throughput platforms that generate continuous measurements are sensitive to various forms of technical bias. For such data, monitoring of technical variation is an important analysis step.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1xw2r2qq</guid>
      <pubDate>Mon, 15 Nov 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Lauss, Martin</name>
      </author>
      <author>
        <name>Visne, Ilhami</name>
      </author>
      <author>
        <name>Kriegner, Albert</name>
      </author>
      <author>
        <name>Ringnér, Markus</name>
      </author>
      <author>
        <name>Jönsson, Göran</name>
      </author>
      <author>
        <name>Höglund, Mattias</name>
      </author>
    </item>
    <item>
      <title>Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus</title>
      <link>https://escholarship.org/uc/item/0wv3578f</link>
      <description>Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus &lt;i&gt;Neocallimastix lanati&lt;/i&gt; from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0wv3578f</guid>
      <pubDate>Wed, 28 Jul 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Wilken, Elmo</name>
      </author>
      <author>
        <name>Monk, Jonathan M</name>
      </author>
      <author>
        <name>Leggieri, Patrick A</name>
      </author>
      <author>
        <name>Lawson, Christopher E</name>
      </author>
      <author>
        <name>Lankiewicz, Thomas S</name>
      </author>
      <author>
        <name>Seppälä, Susanna</name>
      </author>
      <author>
        <name>Daum, Chris G</name>
        <uri>https://orcid.org/0000-0003-3895-5892</uri>
      </author>
      <author>
        <name>Jenkins, Jerry</name>
      </author>
      <author>
        <name>Lipzen, Anna M</name>
        <uri>https://orcid.org/0000-0003-2293-9329</uri>
      </author>
      <author>
        <name>Mondo, Stephen J</name>
        <uri>https://orcid.org/0000-0001-5797-0647</uri>
      </author>
      <author>
        <name>Barry, Kerrie W</name>
        <uri>https://orcid.org/0000-0002-8999-6785</uri>
      </author>
      <author>
        <name>Grigoriev, Igor V</name>
        <uri>https://orcid.org/0000-0002-3136-8903</uri>
      </author>
      <author>
        <name>Henske, John K</name>
      </author>
      <author>
        <name>Theodorou, Michael K</name>
      </author>
      <author>
        <name>Palsson, Bernhard O</name>
        <uri>https://orcid.org/0000-0003-2357-6785</uri>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>O’Malley, Michelle A</name>
      </author>
    </item>
    <item>
      <title>Robust estimation of SARS-CoV-2 epidemic in US counties.</title>
      <link>https://escholarship.org/uc/item/3ks6j87g</link>
      <description>The COVID-19 outbreak is asynchronous in US counties. Mitigating the COVID-19 transmission requires not only the state and federal level order of protective measures such as social distancing and testing, but also public awareness of time-dependent risk and reactions at county and community levels. We propose a robust approach to estimate the heterogeneous progression of SARS-CoV-2 at all US counties having no less than 2 COVID-19 associated deaths, and we use the daily probability of contracting (PoC) SARS-CoV-2 for a susceptible individual to quantify the risk of SARS-CoV-2 transmission in a community. We found that shortening by $5\%$ of the infectious period of SARS-CoV-2 can reduce around $39\%$ (or $78$K, $95\%$ CI: $[66$K $, 89$K $]$) of the COVID-19 associated deaths in the US as of 20 September 2020. Our findings also indicate that reducing infection and deaths by a shortened infectious period is more pronounced for areas with the effective reproduction number close to...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3ks6j87g</guid>
      <pubDate>Mon, 14 Jun 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Li, Hanmo</name>
      </author>
      <author>
        <name>Gu, Mengyang</name>
      </author>
    </item>
    <item>
      <title>Advances in deep space exploration via simulators &amp;amp; deep learning</title>
      <link>https://escholarship.org/uc/item/07p9406r</link>
      <description>Advances in deep space exploration via simulators &amp;amp; deep learning</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/07p9406r</guid>
      <pubDate>Thu, 27 May 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Bird, James</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Lubin, Philip</name>
        <uri>https://orcid.org/0000-0003-1847-2201</uri>
      </author>
      <author>
        <name>Deacon, Julia</name>
      </author>
    </item>
    <item>
      <title>Towards Immersive Virtual Reality Simulations of Bionic Vision</title>
      <link>https://escholarship.org/uc/item/8t7121bg</link>
      <description>Bionic vision is a rapidly advancing field aimed at developing visual
neuroprostheses ('bionic eyes') to restore useful vision to people who are
blind. However, a major outstanding challenge is predicting what people 'see'
when they use their devices. The limited field of view of current devices
necessitates head movements to scan the scene, which is difficult to simulate
on a computer screen. In addition, many computational models of bionic vision
lack biological realism. To address these challenges, we propose to embed
biologically realistic models of simulated prosthetic vision (SPV) in immersive
virtual reality (VR) so that sighted subjects can act as 'virtual patients' in
real-world tasks.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8t7121bg</guid>
      <pubDate>Wed, 31 Mar 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Kasowski, Justin</name>
      </author>
      <author>
        <name>Wu, Nathan</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Deep Learning--Based Scene Simplification for Bionic Vision</title>
      <link>https://escholarship.org/uc/item/8c12d0wc</link>
      <description>Retinal degenerative diseases cause profound visual impairment in more than
10 million people worldwide, and retinal prostheses are being developed to
restore vision to these individuals. Analogous to cochlear implants, these
devices electrically stimulate surviving retinal cells to evoke visual percepts
(phosphenes). However, the quality of current prosthetic vision is still
rudimentary. Rather than aiming to restore "natural" vision, there is potential
merit in borrowing state-of-the-art computer vision algorithms as image
processing techniques to maximize the usefulness of prosthetic vision. Here we
combine deep learning--based scene simplification strategies with a
psychophysically validated computational model of the retina to generate
realistic predictions of simulated prosthetic vision, and measure their ability
to support scene understanding of sighted subjects (virtual patients) in a
variety of outdoor scenarios. We show that object segmentation may better
support scene...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8c12d0wc</guid>
      <pubDate>Wed, 31 Mar 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Han, Nicole</name>
      </author>
      <author>
        <name>Srivastava, Sudhanshu</name>
      </author>
      <author>
        <name>Xu, Aiwen</name>
      </author>
      <author>
        <name>Klein, Devi</name>
      </author>
      <author>
        <name>Beyeler, Michael</name>
      </author>
    </item>
    <item>
      <title>Scalable Bayesian Functional Connectivity Inference for Multi-Electrode Array Recordings</title>
      <link>https://escholarship.org/uc/item/6m2244p7</link>
      <description>Multi-electrode arrays (MEAs) can record extracellular action potentials
(also known as 'spikes') from hundreds or thousands of neurons simultaneously.
Inference of a functional network from a spike train is a fundamental and
formidable computational task in neuroscience. With the advancement of MEA
technology, it has become increasingly crucial to develop statistical tools for
analyzing multiple neuronal activity as a network. In this paper, we propose a
scalable Bayesian framework for inference of functional networks from MEA data.
Our framework makes use of the hierarchical structure of networks of neurons.
We split the large scale recordings into smaller local networks for network
inference, which not only eases the computational burden from Bayesian sampling
but also provides useful insights on regional connections in organoids and
brains. We speed up the expensive Bayesian sampling process by using parallel
computing. Experiments on both synthetic datasets and large-scale...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6m2244p7</guid>
      <pubDate>Wed, 3 Mar 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Zhao, Yun</name>
      </author>
      <author>
        <name>Jiang, Richard</name>
      </author>
      <author>
        <name>Xu, Zhenni</name>
      </author>
      <author>
        <name>Guzman, Elmer</name>
      </author>
      <author>
        <name>Hansma, Paul K</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Coordinating cell polarization and morphogenesis through mechanical feedback</title>
      <link>https://escholarship.org/uc/item/8z75h7cm</link>
      <description>Many cellular processes require cell polarization to be maintained as the cell changes shape, grows or moves. Without feedback mechanisms relaying information about cell shape to the polarity molecular machinery, the coordination between cell polarization and morphogenesis, movement or growth would not be possible. Here we theoretically and computationally study the role of a genetically-encoded mechanical feedback (in the Cell Wall Integrity pathway) as a potential coordination mechanism between cell morphogenesis and polarity during budding yeast mating projection growth. We developed a coarse-grained continuum description of the coupled dynamics of cell polarization and morphogenesis as well as 3D stochastic simulations of the molecular polarization machinery in the evolving cell shape. Both theoretical approaches show that in the absence of mechanical feedback (or in the presence of weak feedback), cell polarity cannot be maintained at the projection tip during growth, with...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8z75h7cm</guid>
      <pubDate>Mon, 1 Mar 2021 00:00:00 +0000</pubDate>
      <author>
        <name>Banavar, Samhita P</name>
      </author>
      <author>
        <name>Trogdon, Michael</name>
      </author>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Campàs, Otger</name>
      </author>
    </item>
    <item>
      <title>Graphs, Matrices, and the GraphBLAS: Seven Good Reasons</title>
      <link>https://escholarship.org/uc/item/8hn2t21h</link>
      <description>The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istcbigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8hn2t21h</guid>
      <pubDate>Wed, 30 Dec 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Kepner, Jeremy</name>
      </author>
      <author>
        <name>Bader, David</name>
      </author>
      <author>
        <name>Buluç, Aydın</name>
      </author>
      <author>
        <name>Gilbert, John</name>
      </author>
      <author>
        <name>Mattson, Timothy</name>
      </author>
      <author>
        <name>Meyerhenke, Henning</name>
      </author>
    </item>
    <item>
      <title>Realizing uncertainty-aware timing stack in embedded operating system</title>
      <link>https://escholarship.org/uc/item/7398g4zg</link>
      <description>Time synchronization has been studied extensively over the recent years with an advent of time critical applications for wireless sensor networks. The distribution of the global reference time over the radio links is the most popular synchronization mechanism. Often overlooked, the timing uncertainties spread across transmitter to the receiver, limit the accuracy of state-of-the-art synchronization protocols. These timing uncertainties are due to the instability of crystal oscillators and timestamping mechanisms. The effect of these uncertainties is cumulative in nature and build up the synchronization error. On the other hand, limited resources of energy, computational units, storage, and bandwidth are a driving force towards lightweight protocols. Hence, this paper presents a deep analysis of each source of timing uncertainty and motivates uncertainty-aware time synchronization. Extensive experiments are conducted to highlight the contribution of each source and provide recommendations...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7398g4zg</guid>
      <pubDate>Wed, 30 Dec 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Alanwar, A</name>
      </author>
      <author>
        <name>Anwar, FM</name>
      </author>
      <author>
        <name>Hespanha, JP</name>
        <uri>https://orcid.org/0000-0003-2809-4718</uri>
      </author>
      <author>
        <name>Srivastava, MB</name>
        <uri>https://orcid.org/0000-0002-3782-9192</uri>
      </author>
    </item>
    <item>
      <title>Supervisory Control of Discrete-Event Systems Under Attacks</title>
      <link>https://escholarship.org/uc/item/5gg2642f</link>
      <description>We consider a multi-adversary version of the supervisory control problem for discrete-event systems (DES), in which an adversary corrupts the observations available to the supervisor. The supervisor’s goal is to enforce a specific language in spite of the opponent’s actions and without knowing which adversary it is playing against. This problem is motivated by applications to computer security in which a cyber defense system must make decisions based on reports from sensors that may have been tampered with by an attacker. We start by showing that the problem has a solution if and only if the desired language is controllable (in the DES classical sense) and observable in a (novel) sense that takes the adversaries into account. For the particular case of attacks that insert symbols into or remove symbols from the sequence of sensor outputs, we show that testing the existence of a supervisor and building the supervisor can be done using tools developed for the classical DES supervisory...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5gg2642f</guid>
      <pubDate>Wed, 30 Dec 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Wakaiki, Masashi</name>
      </author>
      <author>
        <name>Tabuada, Paulo</name>
        <uri>https://orcid.org/0000-0002-3417-0951</uri>
      </author>
      <author>
        <name>Hespanha, João P</name>
        <uri>https://orcid.org/0000-0003-2809-4718</uri>
      </author>
    </item>
    <item>
      <title>Subsampled Rényi Differential Privacy and Analytical Moments Accountant</title>
      <link>https://escholarship.org/uc/item/4wp0c3th</link>
      <description>We study the problem of subsampling in differential privacy (DP), a question that is the centerpiece behind many successful differentially private machine learning algorithms. Specifically, we provide a tight upper bound on the Renyi Differential Privacy (RDP) [Mironov, 2017] parameters for algorithms that: (1) subsample the dataset, and then (2) apply a randomized mechanism M to the subsample, in terms of the RDP parameters of M and the subsampling probability parameter.Our results generalize the moments accounting technique, developed by [Abadi et al. 2016] for the Gaussian mechanism, to any subsampled RDP mechanism.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4wp0c3th</guid>
      <pubDate>Wed, 30 Dec 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Wang, Yu-Xiang</name>
        <uri>https://orcid.org/0000-0002-6403-212X</uri>
      </author>
      <author>
        <name>Balle, Borja</name>
      </author>
      <author>
        <name>Kasiviswanathan, Shiva</name>
      </author>
    </item>
    <item>
      <title>Opinion Dynamics and Social Power Evolution: A SingleTimescale Model</title>
      <link>https://escholarship.org/uc/item/2311g11p</link>
      <description>This paper studies the evolution of self-appraisal and social power, for a
group of individuals who discuss and form opinions. We consider a modification
of the recently proposed DeGroot-Friedkin (DF) model, in which the opinion
formation process takes place on the same timescale as the reflected appraisal
process; we call this new model the single-timescale DF model. We provide a
comprehensive analysis of the equilibria and convergence properties of the
model for the settings of irreducible and reducible influence networks. For the
setting of irreducible influence networks, the single-timescale DF model has
the same behavior as the original DF model, that is, it predicts among other
things that the social power ranking among individuals is asymptotically equal
to their centrality ranking, that social power tends to accumulate at the top
of the centrality ranking hierarchy, and that an autocratic (resp., democratic)
power structure arises when the centrality scores are maximally...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2311g11p</guid>
      <pubDate>Wed, 30 Dec 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Jia, Peng</name>
      </author>
      <author>
        <name>Friedkin, Noah E</name>
      </author>
      <author>
        <name>Bullo, Francesco</name>
        <uri>https://orcid.org/0000-0002-4785-2118</uri>
      </author>
    </item>
    <item>
      <title>Maat</title>
      <link>https://escholarship.org/uc/item/5f94t2t6</link>
      <description>Maat</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5f94t2t6</guid>
      <pubDate>Fri, 9 Oct 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Reyes Santiesteban, Luis</name>
      </author>
    </item>
    <item>
      <title>MetaSpace II: Object and full-body tracking for interaction and navigation in social VR</title>
      <link>https://escholarship.org/uc/item/9nt3r5xr</link>
      <description>MetaSpace II (MS2) is a social Virtual Reality (VR) system where multiple
users can not only see and hear but also interact with each other, grasp and
manipulate objects, walk around in space, and get tactile feedback. MS2 allows
walking in physical space by tracking each user's skeleton in real-time and
allows users to feel by employing passive haptics i.e., when users touch or
manipulate an object in the virtual world, they simultaneously also touch or
manipulate a corresponding object in the physical world. To enable these
elements in VR, MS2 creates a correspondence in spatial layout and object
placement by building the virtual world on top of a 3D scan of the real world.
Through the association between the real and virtual world, users are able to
walk freely while wearing a head-mounted device, avoid obstacles like walls and
furniture, and interact with people and objects. Most current virtual reality
(VR) environments are designed for a single user experience where interactions
with...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9nt3r5xr</guid>
      <pubDate>Tue, 1 Sep 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Sra, Misha</name>
        <uri>https://orcid.org/0000-0001-8154-8518</uri>
      </author>
      <author>
        <name>Schmandt, Chris</name>
      </author>
    </item>
    <item>
      <title>Design Strategies for Playful Technologies to Support Light-intensity Physical Activity in the Workplace</title>
      <link>https://escholarship.org/uc/item/3920b8t2</link>
      <description>Moderate to vigorous intensity physical activity has an established
preventative role in obesity, cardiovascular disease, and diabetes. However
recent evidence suggests that sitting time affects health negatively
independent of whether adults meet prescribed physical activity guidelines.
Since many of us spend long hours daily sitting in front of a host of
electronic screens, this is cause for concern. In this paper, we describe a set
of three prototype digital games created for encouraging light-intensity
physical activity during short breaks at work. The design of these kinds of
games is a complex process that must consider motivation strategies,
interaction methodology, usability and ludic aspects. We present design
guidelines for technologies that encourage physical activity in the workplace
that we derived from a user evaluation using the prototypes. Although the
design guidelines can be seen as general principles, we conclude that they have
to be considered differently for...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3920b8t2</guid>
      <pubDate>Tue, 1 Sep 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Sra, Misha</name>
        <uri>https://orcid.org/0000-0001-8154-8518</uri>
      </author>
      <author>
        <name>Schmandt, Chris</name>
      </author>
    </item>
    <item>
      <title>Improving Sleep-Wake Schedule Using Sleep Behavior Visualization and a Bedtime Alarm</title>
      <link>https://escholarship.org/uc/item/1h59k42s</link>
      <description>Improving Sleep-Wake Schedule Using Sleep Behavior Visualization and a Bedtime Alarm</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1h59k42s</guid>
      <pubDate>Tue, 1 Sep 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Chen, Weixuan</name>
      </author>
      <author>
        <name>Sra, Misha</name>
        <uri>https://orcid.org/0000-0001-8154-8518</uri>
      </author>
      <author>
        <name>Picard, Rosalind</name>
      </author>
    </item>
    <item>
      <title>Expanding social mobile games beyond the device screen</title>
      <link>https://escholarship.org/uc/item/051351rb</link>
      <description>Expanding social mobile games beyond the device screen</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/051351rb</guid>
      <pubDate>Tue, 1 Sep 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Sra, Misha</name>
        <uri>https://orcid.org/0000-0001-8154-8518</uri>
      </author>
      <author>
        <name>Schmandt, Chris</name>
      </author>
    </item>
    <item>
      <title>Computational model of tranexamic acid on urokinase mediated fibrinolysis</title>
      <link>https://escholarship.org/uc/item/61m1t8k0</link>
      <description>Understanding the coagulation process is critical to developing treatments for trauma and coagulopathies. Clinical studies on tranexamic acid (TXA) have resulted in mixed reports on its efficacy in improving outcomes in trauma patients. The largest study, CRASH-2, reported that TXA improved outcomes in patients who received treatment prior to 3 hours after the injury, but worsened outcomes in patients who received treatment after 3 hours. No consensus has been reached about the mechanism behind the duality of these results. In this paper we use a computational model for coagulation and fibrinolysis to propose that deficiencies or depletions of key anti-fibrinolytic proteins, specifically antiplasmin, a1-antitrypsin and a2-macroglobulin, can lead to worsened outcomes through urokinase-mediated hyperfibrinolysis.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/61m1t8k0</guid>
      <pubDate>Fri, 12 Jun 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Wu, Tie Bo</name>
      </author>
      <author>
        <name>Orfeo, Thomas</name>
      </author>
      <author>
        <name>Moore, Hunter B</name>
      </author>
      <author>
        <name>Sumislawski, Joshua J</name>
      </author>
      <author>
        <name>Cohen, Mitchell J</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Regulation of CSF and Brain Tissue Sodium Levels by the Blood-CSF and Blood-Brain Barriers During Migraine</title>
      <link>https://escholarship.org/uc/item/0b4131ct</link>
      <description>Cerebrospinal fluid (CSF) and brain tissue sodium levels increase during migraine. However, little is known regarding the underlying mechanisms of sodium homeostasis disturbance in the brain during the onset and propagation of migraine. Exploring the cause of sodium dysregulation in the brain is important, since correction of the altered sodium homeostasis could potentially treat migraine. Under the hypothesis that disturbances in sodium transport mechanisms at the blood-CSF barrier (BCSFB) and/or the blood-brain barrier (BBB) are the underlying cause of the elevated CSF and brain tissue sodium levels during migraines, we developed a mechanistic, differential equation model of a rat's brain to compare the significance of the BCSFB and the BBB in controlling CSF and brain tissue sodium levels. The model includes the ventricular system, subarachnoid space, brain tissue and blood. Sodium transport from blood to CSF across the BCSFB, and from blood to brain tissue across the BBB were...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0b4131ct</guid>
      <pubDate>Fri, 12 Jun 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Ghaffari, Hamed</name>
      </author>
      <author>
        <name>Grant, Samuel C</name>
      </author>
      <author>
        <name>Petzold, Linda R</name>
      </author>
      <author>
        <name>Harrington, Michael G</name>
      </author>
    </item>
    <item>
      <title>Structural balance emerges and explains performance in risky decision-making</title>
      <link>https://escholarship.org/uc/item/2cb3g9pq</link>
      <description>Polarization affects many forms of social organization. A key issue focuses on which affective relationships are prone to change and how their change relates to performance. In this study, we analyze a financial institutional over a two-year period that employed 66 day traders, focusing on links between changes in affective relations and trading performance. Traders’ affective relations were inferred from their IMs (&amp;gt;2 million messages) and trading performance was measured from profit and loss statements (&amp;gt;1 million trades). Here, we find that triads of relationships, the building blocks of larger social structures, have a propensity towards affective balance, but one unbalanced configuration resists change. Further, balance is positively related to performance. Traders with balanced networks have the “hot hand”, showing streaks of high performance. Research implications focus on how changes in polarization relate to performance and polarized states can depolarize.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2cb3g9pq</guid>
      <pubDate>Thu, 21 May 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Askarisichani, Omid</name>
      </author>
      <author>
        <name>Lane, Jacqueline Ng</name>
      </author>
      <author>
        <name>Bullo, Francesco</name>
        <uri>https://orcid.org/0000-0002-4785-2118</uri>
      </author>
      <author>
        <name>Friedkin, Noah E</name>
      </author>
      <author>
        <name>Singh, Ambuj K</name>
      </author>
      <author>
        <name>Uzzi, Brian</name>
      </author>
    </item>
    <item>
      <title>Detection of a MicroRNA Signal in an In Vivo Expression Set of mRNAs</title>
      <link>https://escholarship.org/uc/item/8ng4h95n</link>
      <description>BACKGROUND: microRNAs (miRNAs) are approximately 21 nucleotide non-coding transcripts capable of regulating gene expression. The most widely studied mechanism of regulation involves binding of a miRNA to the target mRNA. As a result, translation of the target mRNA is inhibited and the mRNA may be destabilized. The inhibitory effects of miRNAs have been linked to diverse cellular processes including malignant proliferation, apoptosis, development, differentiation, and metabolic processes. We asked whether endogenous fluctuations in a set of mRNA and miRNA profiles contain correlated changes that are statistically distinguishable from the many other fluctuations in the data set.
METHODOLOGY/PRINCIPAL FINDINGS: RNA was extracted from 12 human primary brain tumor biopsies. These samples were used to determine genome-wide mRNA expression levels by microarray analysis and a miRNA profile by real-time reverse transcription PCR. Correlation coefficients were determined for all possible...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8ng4h95n</guid>
      <pubDate>Sat, 16 May 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Liu, Tsunglin</name>
      </author>
      <author>
        <name>Papagiannakopoulos, Thales</name>
      </author>
      <author>
        <name>Puskar, Kathy</name>
      </author>
      <author>
        <name>Qi, Shuping</name>
      </author>
      <author>
        <name>Santiago, Fernando</name>
      </author>
      <author>
        <name>Clay, William</name>
      </author>
      <author>
        <name>Lao, Kaiqin</name>
      </author>
      <author>
        <name>Lee, Yohan</name>
      </author>
      <author>
        <name>Nelson, Stanley F</name>
        <uri>https://orcid.org/0000-0002-2082-3114</uri>
      </author>
      <author>
        <name>Kornblum, Harley I</name>
      </author>
      <author>
        <name>Doyle, Frank</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Shraiman, Boris</name>
      </author>
      <author>
        <name>Kosik, Kenneth S</name>
        <uri>https://orcid.org/0000-0003-3224-5179</uri>
      </author>
    </item>
    <item>
      <title>Validation data for a hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) method.</title>
      <link>https://escholarship.org/uc/item/9m68z6zh</link>
      <description>We present the validation of the hybrid sSSA-SDPD method for advection-diffusion-reaction problems coupled to discrete biochemical systems, as presented in the publication "A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems" (Drawert et al., 2019). We validate 1D diffusion, and 2D diffusion cases against their analytical solutions. We present graphs and tables of data showing the error in the simulation method.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9m68z6zh</guid>
      <pubDate>Mon, 2 Mar 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Jacob, Bruno</name>
      </author>
      <author>
        <name>Li, Zhen</name>
        <uri>https://orcid.org/0000-0002-0936-6928</uri>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Bayesian inference of elastic properties with resonant ultrasound spectroscopy</title>
      <link>https://escholarship.org/uc/item/62w9j37p</link>
      <description>Bayesian modeling and Hamiltonian Monte Carlo (HMC) are utilized to formulate a robust algorithm capable of simultaneously estimating anisotropic elastic properties and crystallographic orientation of a specimen from a list of measured resonance frequencies collected via Resonance Ultrasound Spectroscopy (RUS). Unlike typical optimization procedures which yield point estimates of the unknown parameters, computing a Bayesian posterior yields probability distributions for the unknown parameters, and HMC is an efficient way to compute this posterior. The algorithms described are demonstrated on RUS data collected from two parallelepiped specimens of structural metal alloys. First, the elastic constants for a specimen of fine-grain polycrystalline Ti-6Al-4 V with random crystallographic texture and isotropic elastic symmetry are estimated. Second, the elastic constants and crystallographic orientation for a single crystal Ni-based superalloy CMSX-4 specimen are accurately determined,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/62w9j37p</guid>
      <pubDate>Mon, 2 Mar 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Bales, Ben</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Goodlet, Brent R</name>
      </author>
      <author>
        <name>Lenthe, William C</name>
      </author>
      <author>
        <name>Pollock, Tresa M</name>
      </author>
    </item>
    <item>
      <title>Integrating machine learning and multiscale modeling-perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences.</title>
      <link>https://escholarship.org/uc/item/4577m58c</link>
      <description>Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret these data to advance human health. The recent rise of machine learning as a powerful technique to integrate multimodality, multifidelity data, and reveal correlations between intertwined phenomena presents a special opportunity in this regard. However, machine learning alone ignores the fundamental laws of physics and can result in ill-posed problems or non-physical solutions. Multiscale modeling is a successful strategy to integrate multiscale, multiphysics data and uncover mechanisms that explain the emergence of function. However, multiscale modeling alone often fails to efficiently combine large datasets from different sources and different levels of resolution. Here we demonstrate that machine learning and multiscale modeling can naturally...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4577m58c</guid>
      <pubDate>Mon, 2 Mar 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Alber, Mark</name>
        <uri>https://orcid.org/0000-0002-7153-1138</uri>
      </author>
      <author>
        <name>Buganza Tepole, Adrian</name>
        <uri>https://orcid.org/0000-0001-8531-0603</uri>
      </author>
      <author>
        <name>Cannon, William R</name>
        <uri>https://orcid.org/0000-0003-3789-7889</uri>
      </author>
      <author>
        <name>De, Suvranu</name>
      </author>
      <author>
        <name>Dura-Bernal, Salvador</name>
        <uri>https://orcid.org/0000-0002-8561-5324</uri>
      </author>
      <author>
        <name>Garikipati, Krishna</name>
      </author>
      <author>
        <name>Karniadakis, George</name>
      </author>
      <author>
        <name>Lytton, William W</name>
      </author>
      <author>
        <name>Perdikaris, Paris</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
      <author>
        <name>Kuhl, Ellen</name>
        <uri>https://orcid.org/0000-0002-6283-935X</uri>
      </author>
    </item>
    <item>
      <title>A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection–diffusion–reaction problems</title>
      <link>https://escholarship.org/uc/item/33045642</link>
      <description>We have developed a new algorithm which merges discrete stochastic simulation, using the spatial stochastic simulation algorithm (sSSA), with the particle based fluid dynamics simulation framework of smoothed dissipative particle dynamics (SDPD). This hybrid algorithm enables discrete stochastic simulation of spatially resolved chemically reacting systems on a mesh-free dynamic domain with a Lagrangian frame of reference. SDPD combines two popular mesoscopic techniques: smoothed particle hydrodynamics and dissipative particle dynamics (DPD), linking the macroscopic and mesoscopic hydrodynamics effects of these two methods. We have implemented discrete stochastic simulation using the reaction-diffusion master equations (RDME) formalism, and deterministic reaction-diffusion equations based on the SDPD method. We validate the new method by comparing our results to four canonical models, and demonstrate the versatility of our method by simulating a flow containing a chemical gradient...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/33045642</guid>
      <pubDate>Mon, 2 Mar 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Drawert, Brian</name>
      </author>
      <author>
        <name>Jacob, Bruno</name>
      </author>
      <author>
        <name>Li, Zhen</name>
      </author>
      <author>
        <name>Yi, Tau-Mu</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
    <item>
      <title>Computational Model for Hyperfibrinolytic Onset of Acute Traumatic Coagulopathy</title>
      <link>https://escholarship.org/uc/item/1zf8t9dd</link>
      <description>The onset of acute traumatic coagulopathy in trauma patients exacerbates hemorrhaging and dramatically increases mortality. The disease is characterized by increased localized bleeding, and the mechanism for its onset is not yet known. We propose that the fibrinolytic response, specifically the release of tissue-plasminogen activator (t-PA), within vessels of different sizes leads to a variable susceptibility to local coagulopathy through hyperfibrinolysis which can explain many of the clinical observations in the early stages from severely injured coagulopathic patients. We use a partial differential equation model to examine the consequences of vessel geometry and extent of injury on fibrinolysis profiles. In addition, we simulate the efficacy of tranexamic acid treatment on coagulopathy initiated through endothelial t-PA release, and are able to reproduce the time-sensitive nature of the efficacy of this treatment as observed in clinical studies.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1zf8t9dd</guid>
      <pubDate>Mon, 2 Mar 2020 00:00:00 +0000</pubDate>
      <author>
        <name>Wu, Tie Bo</name>
      </author>
      <author>
        <name>Wu, Sheng</name>
      </author>
      <author>
        <name>Buoni, Matthew</name>
      </author>
      <author>
        <name>Orfeo, Thomas</name>
      </author>
      <author>
        <name>Brummel-Ziedins, Kathleen</name>
      </author>
      <author>
        <name>Cohen, Mitchell</name>
      </author>
      <author>
        <name>Petzold, Linda</name>
        <uri>https://orcid.org/0000-0001-6251-6078</uri>
      </author>
    </item>
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