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class="c-header__logo2" href="/"><picture><source srcSet="/images/logo_eschol-small.svg" media="(min-width: 870px)"/><img src="/images/logo_eschol-mobile.svg" alt="eScholarship"/></picture><div class="c-header__logo2-tagline">Open Access Publications from the University of California</div></a><div class="c-header__search"><form class="c-search2"><div class="c-search2__inputs"><div class="c-search2__form"><label class="c-search2__label" for="global-search">Search eScholarship</label><input type="search" name="q" id="global-search" class="c-search2__field" placeholder="Search" autoComplete="off" autoCapitalize="off"/></div><fieldset><legend>Refine Search</legend><div class="c-search2__refine"><input type="radio" id="c-search2__refine-eschol" name="searchType" value="eScholarship" checked=""/><label for="c-search2__refine-eschol">All of eScholarship</label><input type="radio" id="c-search2__refine-campus" name="searchType" value="bcoe"/><label for="c-search2__refine-campus">This 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class="o-button__3">Manage<span class="c-subheader__button-fragment">Submissions</span></button><div class="c-modal"></div></div></div><div class="c-navbar"><nav class="c-nav"><details open="" class="c-nav__main"><summary class="c-nav__main-button">Menu</summary><ul class="c-nav__main-items"><li><a href="/uc/bcoe">Unit Home</a></li><li><a href="/uc/bcoe/policyStatement">Policies</a></li><li><a href="/uc/bcoe/submissionGuidelines">Submission Guidelines</a></li><li><a href="/uc/bcoe/contactUs">Contact Us</a></li></ul></details></nav><div class="c-socialicons"><a href="/rss/unit/bcoe"><img src="/images/logo_rss-circle-black.svg" alt="RSS"/></a></div></div><nav class="c-breadcrumb"><ul><li><a href="/">eScholarship</a></li><li><a href="/uc/ucr">UC Riverside</a></li><li><a class="c-breadcrumb-link--active" href="/uc/bcoe">Bourns College of Engineering</a></li></ul></nav><div><section class="o-columnbox2"><header><h2>About</h2></header><div class="o-columnbox__truncate1"><div class="c-clientmarkup"><div><p>This series is home to publications and data sets from the Bourns College of Engineering at the University of California, Riverside.</p> <h3>Related Units</h3> <h4><a href="/uc/search?entity=bcoe_cert">Center for Environmental Research and Technology</a></h4></div><button class="c-marquee__sidebar-more">More</button></div></div></section><div class="c-columns"><main id="maincontent"><section class="o-columnbox1"><header><h2>Bourns College of Engineering</h2></header><div class="c-itemactions"><details class="c-share"><summary><span>Share</span></summary><div><div class="c-share__list"><a class="c-share__email" href="">Email</a><a class="c-share__facebook" href="">Facebook</a></div></div></details></div><div class="c-unitseries__publications1">There are 1874 publications in this collection, published between 1988 and 2025.</div><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_research">BCOE Research (29)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/05p9p3c9"><div class="c-clientmarkup">ECEF Position Accuracy and Reliability:Continent Scale Differential GNSS Approaches (Phase C Report)</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ARahman%2C%20Farzana">Rahman, Farzana</a>; </li><li><a href="/search/?q=author%3ASilva%2C%20Felipe">Silva, Felipe</a>; </li><li><a href="/search/?q=author%3AJiang%2C%20Zeyi">Jiang, Zeyi</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFARRELL%2C%20JAY%20A">FARRELL, JAY A</a> </li></ul></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/08m989gc"><div class="c-clientmarkup">Cooperative, Opportunistic Imaging within a Bayesian Distributed Constrained Optimization Framework</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AMorye%2C%20Akshay%20A.">Morye, Akshay A.</a>; </li><li><a href="/search/?q=author%3ADing%2C%20Chong">Ding, Chong</a>; </li><li><a href="/search/?q=author%3ARoy-Chowdhury%2C%20Amit%20K.">Roy-Chowdhury, Amit K.</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AFarrell%2C%20Jay%20A.">Farrell, Jay A.</a> </li></ul></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/08q8b2ng"><div class="c-clientmarkup">A Conditional Random Field Model For Tracking In Densely Packed Cell Structures - A Technical Report</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AChakraborty%2C%20Anirban">Chakraborty, Anirban</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ARoy-Chowdhury%2C%20Amit">Roy-Chowdhury, Amit</a> </li></ul></div></div><div class="c-unitseries__publications2">26 more works — <a href="/uc/bcoe_research">show all</a></div></details><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_rw">Other Recent Work (1398)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0036f4tg"><div class="c-clientmarkup">Gaussian accelerated molecular dynamics (GaMD): principles and applications.</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AWang%2C%20Jinan">Wang, Jinan</a>; </li><li><a href="/search/?q=author%3AArantes%2C%20Pablo%20R">Arantes, Pablo R</a>; </li><li><a href="/search/?q=author%3ABhattarai%2C%20Apurba">Bhattarai, Apurba</a>; </li><li><a href="/search/?q=author%3AHsu%2C%20Rohaine%20V">Hsu, Rohaine V</a>; </li><li><a href="/search/?q=author%3APawnikar%2C%20Shristi">Pawnikar, Shristi</a>; </li><li><a href="/search/?q=author%3AHuang%2C%20Yu-Ming%20M">Huang, Yu-Ming M</a>; </li><li><a href="/search/?q=author%3APalermo%2C%20Giulia">Palermo, Giulia</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AMiao%2C%20Yinglong">Miao, Yinglong</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined reaction coordinates or collective variables, GaMD provides unconstrained enhanced sampling and is advantageous for simulating complex biological processes. The GaMD boost potential exhibits a Gaussian distribution, thereby allowing for energetic reweighting via cumulant expansion to the second order (i.e., "Gaussian approximation"). This leads to accurate reconstruction of free energy landscapes of biomolecules. Hybrid schemes with other enhanced sampling methods, such as the replica exchange GaMD (rex-GaMD) and replica exchange umbrella sampling GaMD (GaREUS), have also been introduced, further improving sampling and free energy calculations. Recently, new "selective GaMD" algorithms including the ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD) enabled microsecond simulations to capture repetitive dissociation and binding of small-molecule ligands and highly flexible peptides. The simulations then allowed highly efficient quantitative characterization of the ligand/peptide binding thermodynamics and kinetics. Taken together, GaMD and its innovative variants are applicable to simulate a wide variety of biomolecular dynamics, including protein folding, conformational changes and allostery, ligand binding, peptide binding, protein-protein/nucleic acid/carbohydrate interactions, and carbohydrate/nucleic acid interactions. In this review, we present principles of the GaMD algorithms and recent applications in biomolecular simulations and drug design.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0052409q"><div class="c-clientmarkup">Hybrid millimeter-wave systems: a novel paradigm for hetnets</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AMehrpouyan%2C%20Hani">Mehrpouyan, Hani</a>; </li><li><a href="/search/?q=author%3AMatthaiou%2C%20Michail">Matthaiou, Michail</a>; </li><li><a href="/search/?q=author%3AWang%2C%20Rui">Wang, Rui</a>; </li><li><a href="/search/?q=author%3AKaragiannidis%2C%20George%20K">Karagiannidis, George K</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AHua%2C%20Yingbo">Hua, Yingbo</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Heterogeneous networks, HetNets, are known to enhance the bandwidth efficiency and throughput of wireless networks by more effectively utilizing the network resources. However, the higher density of users and access points in HetNets introduces significant inter-user interference that needs to be mitigated through complex and sophisticated interference cancellation schemes. Moreover, due to significant channel attenuation and the presence of hardware impairments, e.g. phase noise and amplifier nonlinearities, the vast bandwidth in the millimeterwave band has not been fully utilized to date. In order to enable the development of multi-Gigabit per second wireless networks, we introduce a novel millimeter-wave HetNet paradigm, termed hybrid HetNet, which exploits the vast bandwidth and propagation characteristics in the 60 GHz and 70-80 GHz bands to reduce the impact of interference in HetNets. Simulation results are presented to illustrate the performance advantage of hybrid HetNets with respect to traditional networks. Next, two specific transceiver structures that enable hand-offs from the 60 GHz band, i.e. the V-band to the 70-80 GHz band, i.e. the E-band, and vice versa are proposed. Finally, the practical and regulatory challenges for establishing a hybrid HetNet are outlined.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0080h493"><div class="c-clientmarkup">Leveraging off higher plant phylogenetic insights for antiplasmodial drug discovery.</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AMoyo%2C%20Phanankosi">Moyo, Phanankosi</a>; </li><li><a href="/search/?q=author%3AInvernizzi%2C%20Luke">Invernizzi, Luke</a>; </li><li><a href="/search/?q=author%3AMianda%2C%20Sephora">Mianda, Sephora</a>; </li><li><a href="/search/?q=author%3ARudolph%2C%20Wiehan">Rudolph, Wiehan</a>; </li><li><a href="/search/?q=author%3AAndayi%2C%20Warren">Andayi, Warren</a>; </li><li><a href="/search/?q=author%3ACrouch%2C%20Neil">Crouch, Neil</a>; </li><li><a href="/search/?q=author%3AMaharaj%2C%20Vinesh">Maharaj, Vinesh</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AWang%2C%20Mingxun">Wang, Mingxun</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>The antimalarial drug-resistance conundrum which threatens to reverse the great strides taken to curb the malaria scourge warrants an urgent need to find novel chemical scaffolds to serve as templates for the development of new antimalarial drugs. Plants represent a viable alternative source for the discovery of unique potential antiplasmodial chemical scaffolds. To expedite the discovery of new antiplasmodial compounds from plants, the aim of this study was to use phylogenetic analysis to identify higher plant orders and families that can be rationally prioritised for antimalarial drug discovery. We queried the PubMed database for publications documenting antiplasmodial properties of natural compounds isolated from higher plants. Thereafter, we manually collated compounds reported along with plant species of origin and relevant pharmacological data. We systematically assigned antiplasmodial-associated plant species into recognised families and orders, and then computed the resistance index, selectivity index and physicochemical properties of the compounds from each taxonomic group. Correlating the generated phylogenetic trees and the biological data of each clade allowed for the identification of 3 hot plant orders and families. The top 3 ranked plant orders were the (i) Caryophyllales, (ii) Buxales, and (iii) Chloranthales. The top 3 ranked plant families were the (i) Ancistrocladaceae, (ii) Simaroubaceae, and (iii) Buxaceae. The highly active natural compounds (IC50 ≤ 1 µM) isolated from these plant orders and families are structurally unique to the legacy antimalarial drugs. Our study was able to identify the most prolific taxa at order and family rank that we propose be prioritised in the search for potent, safe and drug-like antimalarial molecules.</p></div></div></div><div class="c-unitseries__publications2">1395 more works — <a href="/uc/bcoe_rw">show all</a></div></details><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_hk_nsf_workshop">Humboldt Kolleg/NSF Workshop: New Vistas in Molecular Thermodynamics (34)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/08b6g778"><div class="c-clientmarkup">Benefits of Ab-initio, Semi-theoretical, Semi-empirical and Empirical VLE&VLLE Prediction Methods as seen by an Industrial User1</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AKistenmacher%2C%20Hans">Kistenmacher, Hans</a> </li></ul></div><ul class="c-medialist"><li class="c-medialist__video">1 supplemental video</li></ul></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0d73b60f"><div class="c-clientmarkup">Control of Phase Separation by Electro-autocatalysis</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ABazant%2C%20Martin%20Z">Bazant, Martin Z</a> </li></ul></div><ul class="c-medialist"><li class="c-medialist__video">1 supplemental video</li></ul></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0nf9699n"><div class="c-clientmarkup">Molecular Modeling at the Interface of Biological and Polymer Physics</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ASpakowitz%2C%20Andrew">Spakowitz, Andrew</a> </li></ul></div><ul class="c-medialist"><li class="c-medialist__video">1 supplemental video</li></ul></div><div class="c-unitseries__publications2">31 more works — <a href="/uc/bcoe_hk_nsf_workshop">show all</a></div></details><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_be_oapolicydeposits">Bioengineering Department Open Access Policy Deposits (50)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/03n8t47m"><div class="c-clientmarkup">CIMNE-CRISPR: A novel amplification-free diagnostic for rapid early detection of African Swine Fever Virus.</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3APal%2C%20Tathagata">Pal, Tathagata</a>; </li><li><a href="/search/?q=author%3ALiu%2C%20Zilong">Liu, Zilong</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AChen%2C%20Juhong">Chen, Juhong</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>African Swine Fever Virus (ASFV) is a highly contagious pathogen with nearly 100% mortality in swine, causing severe global economic loss. Current detection methods rely on nucleic acid amplification, which requires specialized equipment and skilled operators, limiting accessibility in resource-constrained settings. To address these challenges, we developed the Covalently Immobilized Magnetic Nanoparticles Enhanced CRISPR (CIMNE-CRISPR) system. This amplification-free diagnostic system seamlessly combines target recognition, sequence-specific enrichment, and signal generation. This approach uses covalent immobilization of CRISPR-LbCas12a-crRNA complexes on Fe<sub>3</sub>O<sub>4</sub>@SiO<sub>2</sub> core-shell magnetic nanoparticles, which improves enzyme specificity and robustness over traditional adsorption. The CIMNE-CRISPR assay reached a limit of detection (LOD) of 8.1 × 10<sup>4</sup> copies/μL and a limit of quantification (LOQ) of 4.2 × 10<sup>5</sup> copies/μL, with a dynamic range spanning 10<sup>5</sup> to 10<sup>10</sup> copies/μL and a matrix factor of 100.29% in porcine plasma. It maintained great specificity and accurately detecting 10<sup>5</sup> copies/μL of ASFV DNA even with high mutant concentrations (10<sup>13</sup> copies/μL). The method demonstrated decent reproducibility across different nanoparticle synthesis batches, with an RSD of 9.63% and recovery rates between 97% and 103%, and features rapid processing well-suited for field diagnostics. Overall, this system's cost-effectiveness, simplicity, and reliability highlight its potential to pave the way for advanced CRISPR-based diagnostics, particularly for diverse viral and bacterial targets in agricultural, environmental, and zoonotic disease contexts.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/07j4r1gb"><div class="c-clientmarkup">Stereological Study of Amygdala Glial Populations in Adolescents and Adults with Autism Spectrum Disorder</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AMorgan%2C%20John%20T">Morgan, John T</a>; </li><li><a href="/search/?q=author%3ABarger%2C%20Nicole">Barger, Nicole</a>; </li><li><a href="/search/?q=author%3AAmaral%2C%20David%20G">Amaral, David G</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ASchumann%2C%20Cynthia%20M">Schumann, Cynthia M</a> </li><li class="c-authorlist__begin"><span class="c-authorlist__heading">Editor(s):</span> <a href="/search/?q=author%3AHadjikhani%2C%20Nouchine">Hadjikhani, Nouchine</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>The amygdala undergoes aberrant development in autism spectrum disorder (ASD). We previously found that there are reduced neuron numbers in the adult postmortem amygdala from individuals with ASD compared to typically developing controls. The current study is a comprehensive stereological examination of four non-neuronal cell populations: microglia, oligodendrocytes, astrocytes, and endothelial cells, in the same brains studied previously. We provide a detailed neuroanatomical protocol for defining each cell type that may be applied to other studies of the amygdala in neurodevelopmental and psychiatric disorders. We then assess whether cell numbers and average volumes differ between ASD and typically developing brains. We hypothesized that a reduction in neuron numbers in ASD might relate to altered immune function and/or aberrant microglial activation, as indicated by increased microglial number and cell body volume. Overall, average non-neuronal cell numbers and volumes did not differ between ASD and typically developing brains. However, there was evident heterogeneity within the ASD cohort. Two of the eight ASD brains displayed strong microglial activation. Contrary to our original hypothesis, there was a trend toward a positive correlation between neuronal and microglial numbers in both ASD and control cases. There were fewer oligodendrocytes in the amygdala of adult individuals with ASD ages 20 and older compared to typically developing controls. This finding may provide a possible sign of altered connectivity or impaired neuronal communication that may change across the lifespan in ASD.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0th8v0p9"><div class="c-clientmarkup">Transparent nanocrystalline yttria-stabilized-zirconia calvarium prosthesis</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ADamestani%2C%20Yasaman">Damestani, Yasaman</a>; </li><li><a href="/search/?q=author%3AReynolds%2C%20Carissa%20L">Reynolds, Carissa L</a>; </li><li><a href="/search/?q=author%3ASzu%2C%20Jenny">Szu, Jenny</a>; </li><li><a href="/search/?q=author%3AHsu%2C%20Mike%20S">Hsu, Mike S</a>; </li><li><a href="/search/?q=author%3AKodera%2C%20Yasuhiro">Kodera, Yasuhiro</a>; </li><li><a href="/search/?q=author%3ABinder%2C%20Devin%20K">Binder, Devin K</a>; </li><li><a href="/search/?q=author%3APark%2C%20B%20Hyle">Park, B Hyle</a>; </li><li><a href="/search/?q=author%3AGaray%2C%20Javier%20E">Garay, Javier E</a>; </li><li><a href="/search/?q=author%3ARao%2C%20Masaru%20P">Rao, Masaru P</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AAguilar%2C%20Guillermo">Aguilar, Guillermo</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Laser-based diagnostics and therapeutics show promise for many neurological disorders. However, the poor transparency of cranial bone (calvaria) limits the spatial resolution and interaction depth that can be achieved, thus constraining opportunity in this regard. Herein, we report preliminary results from efforts seeking to address this limitation through use of novel transparent cranial implants made from nanocrystalline yttria-stabilized zirconia (nc-YSZ). Using optical coherence tomography (OCT) imaging of underlying brain in an acute murine model, we show that signal strength is improved when imaging through nc-YSZ implants relative to native cranium. As such, this provides initial evidence supporting the feasibility of nc-YSZ as a transparent cranial implant material. Furthermore, it represents a crucial first step towards realization of an innovative new concept we are developing, which seeks to eventually provide a clinically-viable means for optically accessing the brain, on-demand, over large areas, and on a chronically-recurring basis, without need for repeated craniectomies.<h3>From the clinical editor</h3>In this study, transparent nanocrystalline yttria-stabilized-zirconia is used as an experimental "cranium prosthesis" material, enabling the replacement of segments of cranial bone with a material that allows for optical access to the brain on a recurrent basis using optical imaging methods such as OCT.</p></div></div></div><div class="c-unitseries__publications2">47 more works — <a href="/uc/bcoe_be_oapolicydeposits">show all</a></div></details><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_cee_oapolicydeposits">Chemical and Environmental Engineering Department Open Access Policy Deposits (54)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/02v9v0kf"><div class="c-clientmarkup">Epitope‐specific affinity maturation improved stability of potent protease inhibitory antibodies</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ALopez%2C%20Tyler">Lopez, Tyler</a>; </li><li><a href="/search/?q=author%3AChuan%2C%20Chen">Chuan, Chen</a>; </li><li><a href="/search/?q=author%3ARamirez%2C%20Aaron">Ramirez, Aaron</a>; </li><li><a href="/search/?q=author%3AChen%2C%20Kuan%E2%80%90Hui%20E">Chen, Kuan‐Hui E</a>; </li><li><a href="/search/?q=author%3ALorenson%2C%20Mary%20Y">Lorenson, Mary Y</a>; </li><li><a href="/search/?q=author%3ABenitez%2C%20Chris">Benitez, Chris</a>; </li><li><a href="/search/?q=author%3AMustafa%2C%20Zahid">Mustafa, Zahid</a>; </li><li><a href="/search/?q=author%3APham%2C%20Henry">Pham, Henry</a>; </li><li><a href="/search/?q=author%3ASanchez%2C%20Ramon">Sanchez, Ramon</a>; </li><li><a href="/search/?q=author%3AWalker%2C%20Ameae%20M">Walker, Ameae M</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AGe%2C%20Xin">Ge, Xin</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Targeting effectual epitopes is essential for therapeutic antibodies to accomplish their desired biological functions. This study developed a competitive dual color fluorescence-activated cell sorting (FACS) to maturate a matrix metalloprotease 14 (MMP-14) inhibitory antibody. Epitope-specific screening was achieved by selection on MMP-14 during competition with N-terminal domain of tissue inhibitor of metalloproteinase-2 (TIMP-2) (nTIMP-2), a native inhibitor of MMP-14 binding strongly to its catalytic cleft. 3A2 variants with high potency, selectivity, and improved affinity and proteolytic stability were isolated from a random mutagenesis library. Binding kinetics indicated that the affinity improvements were mainly from slower dissociation rates. In vitro degradation tests suggested the isolated variants had half lives 6-11-fold longer than the wt. Inhibition kinetics suggested they were competitive inhibitors which showed excellent selectivity toward MMP-14 over highly homologous MMP-9. Alanine scanning revealed that they bound to the vicinity of MMP-14 catalytic cleft especially residues F204 and F260, suggesting that the desired epitope was maintained during maturation. When converted to immunoglobulin G, B3 showed 5.0 nM binding affinity and 6.5 nM inhibition potency with in vivo half-life of 4.6 days in mice. In addition to protease inhibitory antibodies, the competitive FACS described here can be applied for discovery and engineering biosimilars, and in general for other circumstances where epitope-specific modulation is needed.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0d94g6rs"><div class="c-clientmarkup">Spectroscopic and Computational Investigation of Room-Temperature Decomposition of a Chemical Warfare Agent Simulant on Polycrystalline Cupric Oxide</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ATrotochaud%2C%20Lena">Trotochaud, Lena</a>; </li><li><a href="/search/?q=author%3ATsyshevsky%2C%20Roman">Tsyshevsky, Roman</a>; </li><li><a href="/search/?q=author%3AHoldren%2C%20Scott">Holdren, Scott</a>; </li><li><a href="/search/?q=author%3AFears%2C%20Kenan">Fears, Kenan</a>; </li><li><a href="/search/?q=author%3AHead%2C%20Ashley%20R">Head, Ashley R</a>; </li><li><a href="/search/?q=author%3AYu%2C%20Yi">Yu, Yi</a>; </li><li><a href="/search/?q=author%3AKarsl%C4%B1og%CC%86lu%2C%20Osman">Karslıoğlu, Osman</a>; </li><li><a href="/search/?q=author%3APletincx%2C%20Sven">Pletincx, Sven</a>; </li><li><a href="/search/?q=author%3AEichhorn%2C%20Bryan">Eichhorn, Bryan</a>; </li><li><a href="/search/?q=author%3AOwrutsky%2C%20Jeffrey">Owrutsky, Jeffrey</a>; </li><li><a href="/search/?q=author%3ALong%2C%20Jeffrey">Long, Jeffrey</a>; </li><li><a href="/search/?q=author%3AZachariah%2C%20Michael">Zachariah, Michael</a>; </li><li><a href="/search/?q=author%3AKuklja%2C%20Maija%20M">Kuklja, Maija M</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ABluhm%2C%20Hendrik">Bluhm, Hendrik</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Certain organophosphorus molecules are infamous due to their use as highly toxic nerve agents. The filtration materials currently in common use for protection against chemical warfare agents were designed before organophosphorus compounds were used as chemical weapons. A better understanding of the surface chemistry between simulant molecules and the individual filtration-material components is a critical precursor to the development of more effective materials for filtration, destruction, decontamination, and/or sensing of nerve agents. Here, we report on the surface adsorption and reactions of a sarin simulant molecule, dimethyl methylphosphonate (DMMP), with cupric oxide surfaces. In situ ambient pressure X-ray photoelectron and infrared spectroscopies are coupled with density functional calculations to propose mechanisms for DMMP decomposition on CuO. We find extensive room temperature decomposition of DMMP on CuO, with the majority of decomposition fragments bound to the CuO surface. We observe breaking of PO-CH3, P-OCH3, and P-CH3 bonds at room temperature. On the basis of these results, we identify specific DMMP decomposition mechanisms not seen on other metal oxides. Participation of lattice oxygen in the decomposition mechanism leads to significant changes in chemical and electronic surface environment, which are manifest in the spectroscopic and computational data. This study establishes a computational baseline for the study of highly toxic organophosphorous compounds on metal oxide surfaces.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0hv063rr"><div class="c-clientmarkup">Aerobic Biotransformation and Defluorination of Fluoroalkylether Substances (ether PFAS): Substrate Specificity, Pathways, and Applications</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AJin%2C%20Bosen">Jin, Bosen</a>; </li><li><a href="/search/?q=author%3AZhu%2C%20Yiwen">Zhu, Yiwen</a>; </li><li><a href="/search/?q=author%3AZhao%2C%20Weiyang">Zhao, Weiyang</a>; </li><li><a href="/search/?q=author%3ALiu%2C%20Zekun">Liu, Zekun</a>; </li><li><a href="/search/?q=author%3AChe%2C%20Shun">Che, Shun</a>; </li><li><a href="/search/?q=author%3AChen%2C%20Kunpeng">Chen, Kunpeng</a>; </li><li><a href="/search/?q=author%3ALin%2C%20Ying-Hsuan">Lin, Ying-Hsuan</a>; </li><li><a href="/search/?q=author%3ALiu%2C%20Jinyong">Liu, Jinyong</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AMen%2C%20Yujie">Men, Yujie</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Fluoroalkylether substances (ether PFAS) constitute a large group of emerging PFAS with uncertain environmental fate. Among them, GenX is the well-known alternative to perfluorooctanoic acid and one of the six proposed PFAS to be regulated by the U.S. Environmental Protection Agency. This study investigated the structure-biodegradability relationship for 12 different ether PFAS with a carboxylic acid headgroup in activated sludge communities. Only polyfluorinated ethers with at least one -CH<sub>2</sub>- moiety adjacent to or a C=C bond in the proximity of the ether bond underwent active biotransformation via oxidative and hydrolytic O-dealkylation. The bioreactions at ether bonds led to the formation of unstable fluoroalcohol intermediates subject to spontaneous defluorination. We further demonstrated that this aerobic biotransformation/defluorination could complement the advanced reduction process in a treatment train system to achieve more cost-effective treatment for GenX and other recalcitrant perfluorinated ether PFAS. These findings provide essential insights into the environmental fate of ether PFAS, the design of biodegradable alternative PFAS, and the development of cost-effective ether PFAS treatment strategies.</p></div></div></div><div class="c-unitseries__publications2">51 more works — <a href="/uc/bcoe_cee_oapolicydeposits">show all</a></div></details><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_cse_oapolicydeposits">Computer Science and Engineering Department Open Access Policy Deposits (61)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0kj1821d"><div class="c-clientmarkup">A study on parallelizing XML path filtering using accelerators</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AMoussalli%2C%20Roger">Moussalli, Roger</a>; </li><li><a href="/search/?q=author%3ASalloum%2C%20Mariam">Salloum, Mariam</a>; </li><li><a href="/search/?q=author%3AHalstead%2C%20Robert">Halstead, Robert</a>; </li><li><a href="/search/?q=author%3ANajjar%2C%20Walid">Najjar, Walid</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ATsotras%2C%20Vassilis%20J">Tsotras, Vassilis J</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Publish-subscribe systems present the state of the art in information dissemination to multiple users. Such systems have evolved from simple topic-based to the current XML-based systems. XML-based pubsub systems provide users with more flexibility by allowing the formulation of complex queries on the content as well as the structure of the streaming messages. Messages that match a given user query are forwarded to the user. This article examines how to exploit the parallelism found in XPath filtering. Using an incoming XML stream, parsing and matching thousands of user profiles are performed simultaneously by matching engines. We show the benefits and trade-offs of mapping the proposed filtering approach onto FPGAs, processing streams of XML at wire speed, and GPUs, providing the flexibility of software. This is in contrast to conventional approaches bound by the sequential aspect of software computing, associated with a large memory footprint. By converting XPath expressions into custom stacks, our solution is the first to provide support for complex XPath structural constructs, such as parent-child and ancestor descendant relations, whilst allowing wildcarding and recursion. The measured speedups resulting from the GPU and FPGA accelerations versus single-core CPUs are up to 6.6X and 2.5 orders of magnitude, respectively. The FPGA approaches are up to 31X faster than software running on 12 CPU cores.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0m48f2xh"><div class="c-clientmarkup">Proton Pump Inhibitor Usage and the Risk of Myocardial Infarction in the General Population</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AShah%2C%20Nigam%20H">Shah, Nigam H</a>; </li><li><a href="/search/?q=author%3ALePendu%2C%20Paea">LePendu, Paea</a>; </li><li><a href="/search/?q=author%3ABauer-Mehren%2C%20Anna">Bauer-Mehren, Anna</a>; </li><li><a href="/search/?q=author%3AGhebremariam%2C%20Yohannes%20T">Ghebremariam, Yohannes T</a>; </li><li><a href="/search/?q=author%3AIyer%2C%20Srinivasan%20V">Iyer, Srinivasan V</a>; </li><li><a href="/search/?q=author%3AMarcus%2C%20Jake">Marcus, Jake</a>; </li><li><a href="/search/?q=author%3ANead%2C%20Kevin%20T">Nead, Kevin T</a>; </li><li><a href="/search/?q=author%3ACooke%2C%20John%20P">Cooke, John P</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ALeeper%2C%20Nicholas%20J">Leeper, Nicholas J</a> </li><li class="c-authorlist__begin"><span class="c-authorlist__heading">Editor(s):</span> <a href="/search/?q=author%3AGuo%2C%20Yiru">Guo, Yiru</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p><h3>Background and aims</h3>Proton pump inhibitors (PPIs) have been associated with adverse clinical outcomes amongst clopidogrel users after an acute coronary syndrome. Recent pre-clinical results suggest that this risk might extend to subjects without any prior history of cardiovascular disease. We explore this potential risk in the general population via data-mining approaches.<h3>Methods</h3>Using a novel approach for mining clinical data for pharmacovigilance, we queried over 16 million clinical documents on 2.9 million individuals to examine whether PPI usage was associated with cardiovascular risk in the general population.<h3>Results</h3>In multiple data sources, we found gastroesophageal reflux disease (GERD) patients exposed to PPIs to have a 1.16 fold increased association (95% CI 1.09-1.24) with myocardial infarction (MI). Survival analysis in a prospective cohort found a two-fold (HR = 2.00; 95% CI 1.07-3.78; P = 0.031) increase in association with cardiovascular mortality. We found that this association exists regardless of clopidogrel use. We also found that H2 blockers, an alternate treatment for GERD, were not associated with increased cardiovascular risk; had they been in place, such pharmacovigilance algorithms could have flagged this risk as early as the year 2000.<h3>Conclusions</h3>Consistent with our pre-clinical findings that PPIs may adversely impact vascular function, our data-mining study supports the association of PPI exposure with risk for MI in the general population. These data provide an example of how a combination of experimental studies and data-mining approaches can be applied to prioritize drug safety signals for further investigation.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0tt974fv"><div class="c-clientmarkup">GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3APetras%2C%20Daniel">Petras, Daniel</a>; </li><li><a href="/search/?q=author%3APhelan%2C%20Vanessa%20V">Phelan, Vanessa V</a>; </li><li><a href="/search/?q=author%3AAcharya%2C%20Deepa">Acharya, Deepa</a>; </li><li><a href="/search/?q=author%3AAllen%2C%20Andrew%20E">Allen, Andrew E</a>; </li><li><a href="/search/?q=author%3AAron%2C%20Allegra%20T">Aron, Allegra T</a>; </li><li><a href="/search/?q=author%3ABandeira%2C%20Nuno">Bandeira, Nuno</a>; </li><li><a href="/search/?q=author%3ABowen%2C%20Benjamin%20P">Bowen, Benjamin P</a>; </li><li><a href="/search/?q=author%3ABelle-Oudry%2C%20Deirdre">Belle-Oudry, Deirdre</a>; </li><li><a href="/search/?q=author%3ABoecker%2C%20Simon">Boecker, Simon</a>; </li><li><a href="/search/?q=author%3ACummings%2C%20Dale%20A">Cummings, Dale A</a>; </li><li><a href="/search/?q=author%3ADeutsch%2C%20Jessica%20M">Deutsch, Jessica M</a>; </li><li><a href="/search/?q=author%3AFahy%2C%20Eoin">Fahy, Eoin</a>; </li><li><a href="/search/?q=author%3AGarg%2C%20Neha">Garg, Neha</a>; </li><li><a href="/search/?q=author%3AGregor%2C%20Rachel">Gregor, Rachel</a>; </li><li><a href="/search/?q=author%3AHandelsman%2C%20Jo">Handelsman, Jo</a>; </li><li><a href="/search/?q=author%3ANavarro-Hoyos%2C%20Mirtha">Navarro-Hoyos, Mirtha</a>; </li><li><a href="/search/?q=author%3AJarmusch%2C%20Alan%20K">Jarmusch, Alan K</a>; </li><li><a href="/search/?q=author%3AJarmusch%2C%20Scott%20A">Jarmusch, Scott A</a>; </li><li><a href="/search/?q=author%3ALouie%2C%20Katherine">Louie, Katherine</a>; </li><li><a href="/search/?q=author%3AMaloney%2C%20Katherine%20N">Maloney, Katherine N</a>; </li><li><a href="/search/?q=author%3AMarty%2C%20Michael%20T">Marty, Michael T</a>; </li><li><a href="/search/?q=author%3AMeijler%2C%20Michael%20M">Meijler, Michael M</a>; </li><li><a href="/search/?q=author%3AMizrahi%2C%20Itzhak">Mizrahi, Itzhak</a>; </li><li><a href="/search/?q=author%3ANeve%2C%20Rachel%20L">Neve, Rachel L</a>; </li><li><a href="/search/?q=author%3ANorthen%2C%20Trent%20R">Northen, Trent R</a>; </li><li><a href="/search/?q=author%3AMolina-Santiago%2C%20Carlos">Molina-Santiago, Carlos</a>; </li><li><a href="/search/?q=author%3APanitchpakdi%2C%20Morgan">Panitchpakdi, Morgan</a>; </li><li><a href="/search/?q=author%3APullman%2C%20Benjamin">Pullman, Benjamin</a>; </li><li><a href="/search/?q=author%3APuri%2C%20Aaron%20W">Puri, Aaron W</a>; </li><li><a href="/search/?q=author%3ASchmid%2C%20Robin">Schmid, Robin</a>; </li><li><a href="/search/?q=author%3ASubramaniam%2C%20Shankar">Subramaniam, Shankar</a>; </li><li><a href="/search/?q=author%3AThukral%2C%20Monica">Thukral, Monica</a>; </li><li><a href="/search/?q=author%3AVasquez-Castro%2C%20Felipe">Vasquez-Castro, Felipe</a>; </li><li><a href="/search/?q=author%3ADorrestein%2C%20Pieter%20C">Dorrestein, Pieter C</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AWang%2C%20Mingxun">Wang, Mingxun</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.</p></div></div></div><div class="c-unitseries__publications2">58 more works — <a href="/uc/bcoe_cse_oapolicydeposits">show all</a></div></details><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_ece_oapolicydeposits">Electrical and Computer Engineering Department Open Access Policy Deposits (34)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/04c7r6qn"><div class="c-clientmarkup">Role of turgor-pressure induced boundary tension in the maintenance of the shoot apical meristem of Arabidopsis thaliana</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AMichael%2C%20Christian">Michael, Christian</a>; </li><li><a href="/search/?q=author%3ABanwarth-Kuhn%2C%20Mikahl">Banwarth-Kuhn, Mikahl</a>; </li><li><a href="/search/?q=author%3ARodriguez%2C%20Kevin">Rodriguez, Kevin</a>; </li><li><a href="/search/?q=author%3ATa%2C%20Calvin-Khang">Ta, Calvin-Khang</a>; </li><li><a href="/search/?q=author%3ARoy-Chowdhury%2C%20Amit">Roy-Chowdhury, Amit</a>; </li><li><a href="/search/?q=author%3AChen%2C%20Weitao">Chen, Weitao</a>; </li><li><a href="/search/?q=author%3AReddy%2C%20G%20Venugopala">Reddy, G Venugopala</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AAlber%2C%20Mark">Alber, Mark</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>In plants, the robust maintenance of tissue structure is crucial to supporting its functionality. The multi-layered shoot apical meristem (SAM) of <i>Arabidopsis,</i> containing stem cells<i>,</i> is an approximately radially symmetric tissue whose shape and structure is maintained throughout the life of the plant. In this paper, a new biologically calibrated pseudo-three-dimensional (P3D) computational model of a longitudinal section of the SAM is developed. It includes anisotropic expansion and division of cells out of the cross-section plane, as well as representation of tension experienced by the SAM epidermis. Results from the experimentally calibrated P3D model provide new insights into maintenance of the structure of the SAM epidermal cell monolayer under tension and quantify dependence of epidermal and subepidermal cell anisotropy on the amount of tension. Moreover, the model simulations revealed that out-of-plane cell growth is important in offsetting cell crowding and regulating mechanical stresses experienced by tunica cells. Predictive model simulations show that tension-determined cell division plane orientation in the apical corpus may be regulating cell and tissue shape distributions needed for maintaining structure of the wild-type SAM. This suggests that cells' responses to local mechanical cues may serve as a mechanism to regulate cell- and tissue-scale patterning.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/07g817kw"><div class="c-clientmarkup">Extraction of Blebs in Human Embryonic Stem Cell Videos</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AGuan%2C%20Benjamin%20X">Guan, Benjamin X</a>; </li><li><a href="/search/?q=author%3ABhanu%2C%20Bir">Bhanu, Bir</a>; </li><li><a href="/search/?q=author%3ATalbot%2C%20Prue">Talbot, Prue</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AWeng%2C%20Nikki%20Jo-Hao">Weng, Nikki Jo-Hao</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Blebbing is an important biological indicator in determining the health of human embryonic stem cells (hESC). Especially, areas of a bleb sequence in a video are often used to distinguish two cell blebbing behaviors in hESC: dynamic and apoptotic blebbings. This paper analyzes various segmentation methods for bleb extraction in hESC videos and introduces a bio-inspired score function to improve the performance in bleb extraction. Full bleb formation consists of bleb expansion and retraction. Blebs change their size and image properties dynamically in both processes and between frames. Therefore, adaptive parameters are needed for each segmentation method. A score function derived from the change of bleb area and orientation between consecutive frames is proposed which provides adaptive parameters for bleb extraction in videos. In comparison to manual analysis, the proposed method provides an automated fast and accurate approach for bleb sequence extraction.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/093690m2"><div class="c-clientmarkup">Correlators Exceeding One in Continuous Measurements of Superconducting Qubits</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AAtalaya%2C%20Juan">Atalaya, Juan</a>; </li><li><a href="/search/?q=author%3AHacohen-Gourgy%2C%20Shay">Hacohen-Gourgy, Shay</a>; </li><li><a href="/search/?q=author%3ASiddiqi%2C%20Irfan">Siddiqi, Irfan</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AKorotkov%2C%20Alexander%20N">Korotkov, Alexander N</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>We consider the effect of phase backaction on the correlator ⟨I(t)I(t+τ)⟩ for the output signal I(t) from continuous measurement of a qubit. We demonstrate that the interplay between informational and phase backactions in the presence of Rabi oscillations can lead to the correlator becoming larger than 1, even though |⟨I⟩|≤1. The correlators can be calculated using the generalized "collapse recipe," which we validate using the quantum Bayesian formalism. The recipe can be further generalized to the case of multitime correlators and arbitrary number of detectors, measuring non-commuting qubit observables. The theory agrees well with experimental results for continuous measurement of a transmon qubit. The experimental correlator exceeds the bound of 1 for a sufficiently large angle between the amplified and informational quadratures, causing the phase backaction. The demonstrated effect can be used to calibrate the quadrature misalignment.</p></div></div></div><div class="c-unitseries__publications2">31 more works — <a href="/uc/bcoe_ece_oapolicydeposits">show all</a></div></details><details class="c-togglecontent c-unitseries"><summary><a href="/uc/bcoe_me_oapolicydeposits">Mechanical Engineering Department Open Access Policy Deposits (23)</a></summary><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/00r7p436"><div class="c-clientmarkup">Micro- and Nanopatterned Topographical Cues for Regulating Macrophage Cell Shape and Phenotype</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3ALuu%2C%20Thuy%20U">Luu, Thuy U</a>; </li><li><a href="/search/?q=author%3AGott%2C%20Shannon%20C">Gott, Shannon C</a>; </li><li><a href="/search/?q=author%3AWoo%2C%20Bryan%20WK">Woo, Bryan WK</a>; </li><li><a href="/search/?q=author%3ARao%2C%20Masaru%20P">Rao, Masaru P</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3ALiu%2C%20Wendy%20F">Liu, Wendy F</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Controlling the interactions between macrophages and biomaterials is critical for modulating the response to implants. While it has long been thought that biomaterial surface chemistry regulates the immune response, recent studies have suggested that material geometry may in fact dominate. Our previous work demonstrated that elongation of macrophages regulates their polarization toward a pro-healing phenotype. In this work, we elucidate how surface topology might be leveraged to alter macrophage cell morphology and polarization state. Using a deep etch technique, we fabricated titanium surfaces containing micro- and nanopatterned grooves, which have been previously shown to promote cell elongation. Morphology, phenotypic markers, and cytokine secretion of murine bone marrow derived macrophages on different groove widths were analyzed. The results suggest that micro- and nanopatterned grooves influenced macrophage elongation, which peaked on substrates with 400-500 nm wide grooves. Surface grooves did not affect inflammatory activation but drove macrophages toward an anti-inflammatory, pro-healing phenotype. While secretion of TNF-alpha remained low in macrophages across all conditions, macrophages secreted significantly higher levels of anti-inflammatory cytokine, IL-10, on intermediate groove widths compared to cells on other Ti surfaces. Our findings highlight the potential of using surface topography to regulate macrophage function, and thus control the wound healing and tissue repair response to biomaterials.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0481538f"><div class="c-clientmarkup">Heterostructured materials: superior properties from hetero-zone interaction</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AZhu%2C%20Yuntian">Zhu, Yuntian</a>; </li><li><a href="/search/?q=author%3AAmeyama%2C%20Kei">Ameyama, Kei</a>; </li><li><a href="/search/?q=author%3AAnderson%2C%20Peter%20M">Anderson, Peter M</a>; </li><li><a href="/search/?q=author%3ABeyerlein%2C%20Irene%20J">Beyerlein, Irene J</a>; </li><li><a href="/search/?q=author%3AGao%2C%20Huajian">Gao, Huajian</a>; </li><li><a href="/search/?q=author%3AKim%2C%20Hyoung%20Seop">Kim, Hyoung Seop</a>; </li><li><a href="/search/?q=author%3ALavernia%2C%20Enrique">Lavernia, Enrique</a>; </li><li><a href="/search/?q=author%3AMathaudhu%2C%20Suveen">Mathaudhu, Suveen</a>; </li><li><a href="/search/?q=author%3AMughrabi%2C%20Hael">Mughrabi, Hael</a>; </li><li><a href="/search/?q=author%3ARitchie%2C%20Robert%20O">Ritchie, Robert O</a>; </li><li><a href="/search/?q=author%3ATsuji%2C%20Nobuhiro">Tsuji, Nobuhiro</a>; </li><li><a href="/search/?q=author%3AZhang%2C%20Xiangyi">Zhang, Xiangyi</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AWu%2C%20Xiaolei">Wu, Xiaolei</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Heterostructured materials are an emerging class of materials with superior performances that are unattainable by their conventional homogeneous counterparts. They consist of heterogeneous zones with dramatic (>100%) variations in mechanical and/or physical properties. The interaction in these hetero-zones produces a synergistic effect where the integrated property exceeds the prediction by the rule-of-mixtures. The heterostructured materials field explores heterostructures to control defect distributions, long-range internal stresses, and nonlinear inter-zone interactions for unprecedented performances. This paper is aimed to provide perspectives on this novel field, describe the state-of-the-art of heterostructured materials, and identify and discuss key issues that deserve additional studies.</p></div></div></div><div class="c-pub"><h3 class="c-pub__heading"><a href="/uc/item/0m90d01t"><div class="c-clientmarkup">Ultrafast laser welding of ceramics</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3APenilla%2C%20EH">Penilla, EH</a>; </li><li><a href="/search/?q=author%3ADevia-Cruz%2C%20LF">Devia-Cruz, LF</a>; </li><li><a href="/search/?q=author%3AWieg%2C%20AT">Wieg, AT</a>; </li><li><a href="/search/?q=author%3AMartinez-Torres%2C%20P">Martinez-Torres, P</a>; </li><li><a href="/search/?q=author%3ACuando-Espitia%2C%20N">Cuando-Espitia, N</a>; </li><li><a href="/search/?q=author%3ASellappan%2C%20P">Sellappan, P</a>; </li><li><a href="/search/?q=author%3AKodera%2C%20Y">Kodera, Y</a>; </li><li><a href="/search/?q=author%3AAguilar%2C%20G">Aguilar, G</a>; </li><li class="c-authorlist__end"><a href="/search/?q=author%3AGaray%2C%20JE">Garay, JE</a> </li></ul></div><div class="c-pub__abstract"><div class="c-clientmarkup"><p>Welding of ceramics is a key missing component in modern manufacturing. Current methods cannot join ceramics in proximity to temperature-sensitive materials like polymers and electronic components. We introduce an ultrafast pulsed laser welding approach that relies on focusing light on interfaces to ensure an optical interaction volume in ceramics to stimulate nonlinear absorption processes, causing localized melting rather than ablation. The key is the interplay between linear and nonlinear optical properties and laser energy-material coupling. The welded ceramic assemblies hold high vacuum and have shear strengths comparable to metal-to-ceramic diffusion bonds. Laser welding can make ceramics integral components in devices for harsh environments as well as in optoelectronic and/or electronic packages needing visible-radio frequency transparency.</p></div></div></div><div class="c-unitseries__publications2">20 more works — <a href="/uc/bcoe_me_oapolicydeposits">show all</a></div></details><div class="c-unitlist"><h3>Related Research Centers & Groups</h3><ul><li><a href="/uc/bcoe_cert">Center for Environmental Research and Technology</a></li></ul></div></section></main><aside><div><section class="o-columnbox1"><header><h2>Recent Articles</h2></header><ul class="c-relateditems"><li><h3><a class="o-textlink__secondary" href="/uc/item/2wr0z6pv"><div class="c-clientmarkup">Flexibility in PAM recognition expands DNA targeting in xCas9.</div></a></h3><div class="c-authorlist"><ul class="c-authorlist__list"><li class="c-authorlist__begin"><a href="/search/?q=author%3AHossain%2C%20Kazi">Hossain, Kazi</a>; </li><li><a href="/search/?q=author%3ANierzwicki%2C%20Lukasz">Nierzwicki, Lukasz</a>; 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