gebhart/patrepeval huggingface dataset:
Energy-efficient biomass processing with pulsed electric fields for bioeconomy and sustainable development (2016)

Fossil resources-free sustainable development can be achieved through a transition to bioeconomy, an economy based on sustainable biomass-derived food, feed, chemicals, materials, and fuels. However, the transition to bioeconomy requires development of new energy-efficient technologies and processes to manipulate biomass feed stocks and their conversion into useful products, a collective term for which is biorefinery. One of the technological platforms that will enable various pathways of biomass conversion is based on pulsed electric fields applications (PEF). Energy efficiency of PEF treatment is achieved by specific increase of cell membrane permeability, a phenomenon known as membrane electroporation. Here, we review the opportunities that PEF and electroporation provide for the development of sustainable biorefineries. We describe the use of PEF treatment in biomass engineering, drying, deconstruction, extraction of phytochemicals, improvement of fermentations, and biogas production. These applications show the potential of PEF and consequent membrane electroporation to enable the bioeconomy and sustainable development.
Local Ionic Environment around Polyvalent Nucleic Acid-Functionalized Nanoparticles (2011)

Polyvalent oligonucleotide-functionalized gold nanoparticles are remarkably stable in a cellular environment against degradation by nucleases, a property that was recently attributed to the local high concentration of mono- and divalent ions. To evaluate this hypothesis in more detail, we investigate the composition of the ion cloud around spherical nanoparticles that are functionalized by stiff, highly charged polyelectrolyte chains by means of classical density functional theory and molecular dynamics simulations. We present a cell model that includes ligands explicitly and both applies over the entire relevant parameter space and is in excellent quantitative agreement with simulations. We study the ion cloud for varying oligonucleotide grafting densities and bulk ionic concentrations, as well as different sizes of nanoparticles and chains, and distinguish a parameter regime where many-body interactions between the ligands have a dominant effect on the local environment. For small particles with high oligonucleotide surface densities, we find strongly enhanced local salt concentrations, a large radial component of the electric field between the ligands, and a pronounced localization of divalent ions near the surface of the nanoparticle, thus providing multiple supporting arguments for the hypothesis.
Dielectric nanoantenna lasers: design concepts and experimental demonstrations (Conference Presentation) (2022)

In this talk, I will present several design concepts for nanolasers based on collective resonances of dielectric nanoantennas. The interference of collective resonances associated with the bound state in the continuum (BIC) or Van Hove singularity will be discussed in detail based on Mie theory analysis. I will show experimentally and theoretically various directional nanolasers made out of GaAs at cryogenic temperature. By using a more efficient gain material such as CdSe/CdxZn1-xS nanoplatelets or InGaP multi-quantum well, room temperature lasing operation is also illustrated. This work presents design guidelines for high-performance in-plane and out-of-plane lasers, which may find broad applications in nanophotonics.
Abstract 1577: GRK3 is a direct target of ADT-induced CREB1 activation and it promotes neuroendocrine differentiation of prostate cancer cells (2017)

Abstract Treatment-related neuroendocrine prostate cancer (t-NEPC) is an aggressive subtype of prostate cancer that is believed to arise through neuroendocrine differentiation (NED) from prostate adenocarcinoma (PAC) upon castration resistance to androgen deprivation treatment (ADT). t-NEPC is highly metastatic with poor prognosis. With the recent introduction of potent ADT drugs in clinic, the incidence of t-NEPC is expected to increase dramatically. No effective therapeutic is available for t-NEPC and its molecular mechanisms remain poorly understood. We reported that GRK3 (G protein-coupled receptor kinase 3) promotes prostate cancer progression. We further demonstrated that the ADT activates CREB1 (cAMP response element binding protein 1), which directly targets and induces GRK3. GRK3 expression is higher in t-NEPC than in PAC cells and mouse models, and it positively correlates with the expression and activity of CREB1 in human prostate cancers. Notably, overexpression of GRK3 in PAC cells increased the expression of NE markers. Conversely, silencing GRK3 blocked CREB1-induced NED in PAC cells, reversed NE phenotypes and inhibited proliferation of t-NEPC cells in culture and in xenograft. Currently, we are investigating the mechanisms underlying NEPC progression promoted by the CREB1/GRK3 axis. Taken together, these results indicate that GRK3 is a new critical activator of NE phenotypes and mediator of CREB1 activation in promoting NED of prostate cancer cells. Citation Format: Dayong Zheng, Mohit Hulsurkar, Meixiang Sang, Songlin Zhang, Jianming Xu, Martin Gleave, Michael Ittmann, Wenliang Li. GRK3 is a direct target of ADT-induced CREB1 activation and it promotes neuroendocrine differentiation of prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1577. doi:10.1158/1538-7445.AM2017-1577
Extracellular Electron Transfer Enables Cellular Control of Cu(I)-Catalyzed Alkyne–Azide Cycloaddition (2022)

Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the electroactive bacterium <i>Shewanella oneidensis</i> for metabolic and genetic control over Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring <i>S. oneidensis</i> cells. The reaction progress and kinetics were manipulated by tailoring the central carbon metabolism. Similarly, EET-CuAAC activity was dependent on specific EET pathways that could be regulated via inducible expression of EET-relevant proteins: MtrC, MtrA, and CymA. EET-driven CuAAC exhibited modularity and robustness in the ligand and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without regeneration, something inaccessible to traditional chemical reductants. Finally, <i>S. oneidensis</i> enabled bioorthogonal CuAAC membrane labeling on live mammalian cells without affecting cell viability, suggesting that <i>S. oneidensis</i> can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.
Max-Margin Deep Generative Models (2015)

Deep generative models (DGMs) are effective on learning multilayered representations of complex data and performing inference of input data by exploring the generative ability. However, little work has been done on examining or empowering the discriminative ability of DGMs on making accurate predictions. This paper presents max-margin deep generative models (mmDGMs), which explore the strongly discriminative principle of max-margin learning to improve the discriminative power of DGMs, while retaining the generative capability. We develop an efficient doubly stochastic subgradient algorithm for the piecewise linear objective. Empirical results on MNIST and SVHN datasets demonstrate that (1) max-margin learning can significantly improve the prediction performance of DGMs and meanwhile retain the generative ability; and (2) mmDGMs are competitive to the state-of-the-art fully discriminative networks by employing deep convolutional neural networks (CNNs) as both recognition and generative models.
Slow down, you move too fast (2011)

We examine how people perceive visual properties of new concepts for the design of animated vehicle instrument clusters, with emphasis on aesthetic aspects. The project is placed in the context of animations for eco-conscious driving. It consists of two stages: Creating animations and studying drivers' reactions to them. Two studies were conducted which provide various insights regarding tradeoff in the design process and drivers' preferences. The second study also serves as a first step towards the study of people's aesthetic perceptions of in-vehicle animations.
Defense Mechanisms Against BovineHerpesvirus: Relationship ofVirus-Host CellEventstoSusceptibility to Antibody-Complement CellLysis (1975)

lysis until 10h postinfection. Intracellular infectious viruswas alsodetectable at10h postinfection, andtransmission toadjacent cells bytheintracellular routebegan atthistime.Extracellular virus was notdetectable until 12to13hpostinfection. Bythecontinual addition ofantibody andcomplement, virusdissemination couldbereduced more than50-fold. Theseresults support thehypothesis that thehumoral immunemechanism may beinvolved intherecoveryfromherpesvirus infections.
A rationally designed dual role anode material for lithium-ion and sodium-ion batteries: case study of eco-friendly Fe3O4 (2013)

Identifying dual role electrode materials capable of storing both lithium and sodium are thought to be highly relevant, as these materials could find potential applications simultaneously in lithium and sodium ion batteries. In this regard, the concept of dual alkali storage is demonstrated in Fe(3)O(4) anode material undergoing conversion reaction. To enable improved storage, a rational active material and electrode design is proposed. Accordingly, the following features were simultaneously incorporated into the design: (i) an optimal particle size, (ii) a conducting matrix, (iii) adequately large active material surface area and (iv) strong electrode material-current collector integrity. Electrodes incorporating this rational design exhibit excellent high rate performance and impressive cyclability during lithium storage. For instance, Fe(3)O(4) electrodes deliver a charge capacity of 950 mAh g(-1) at 1.2 C (~2.6 times higher than graphite and 5.4 times higher than Li(4)Ti(5)O(12)). Further, these electrodes show no signs of capacity fade even up to 1100 cycles. Impressively, the cells could also be charged-discharged to 65% of their theoretical capacity in just 5 min or 12 C (11.11 A g(-1)). The rate performance and cyclability of lithium storage achieved here are amongst the highest reported values in the literature for the conversion reaction in Fe(3)O(4). Besides lithium storage, the dual role of this anode is shown by demonstrating its sodium storage ability by conversion reaction for the first time.
Effect of Permeate Flux and Backwashing on Quorum Sensing and Quenching within Biocake Layer in Membrane Bioreactor (2020)

Filtration and backwashing during the operation of a membrane bioreactor (MBR) physically induce the cyclic attachment and detachment of microbes on the membrane surface. Thus, permeate flux and backwashing affect the microbial quorum sensing (QS) and quorum quenching (QQ) processes taking place in a biocake layer on a membrane surface. From an analysis of the time to reach a transmembrane pressure (TMP) of 40 kPa (TTMP) under different water flux levels, 20 or 40 liter per square meter per hour (LMH), with QQ beads or vacant beads in MBRs, it was found that the accelerated deposition of microbial cells on membrane surfaces at 40 LMH significantly reduced the time for bacteria to initiate QS and, thus, allowed less room for QQ compared with the results at 20 LMH. On the application of backwashing, the TMP jump with QQ beads is more delayed than that with vacant beads in both the 20 and 40 LMH cases. However, the extracellular polymeric substance (EPS) level with backwashing decreased at 20 LMH but increased at 40 LMH regardless of bead type because the reduced fouling rate caused by backwashing provided the bacteria with more time to activate QS, facilitating active EPS production when backwashing is employed at 40 LMH. A biocake porosity analysis revealed that when backwashing was applied, the porosity increased significantly at 40 LMH but remained nearly unchanged at 20 LMH. It is suggested that, at the higher flux level, backwashing allowed enough time for bacteria to initiate QS and, thus, form biofilm with a porous mushroom-like structure. Similarly, the inhibition of QS through the addition of QQ beads indicated dependence on the permeate flux and backwashing. These results suggest that a hydrodynamic condition near the membrane surface could have a considerable influence on the activation of microbial QS, which in turn can affect membrane biofouling in an MBR.
Ring Closure of 1,4-Pentadiene to Cyclopentene by a Zwitterionic Nickel Catalyst (2004)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTRing Closure of 1,4-Pentadiene to Cyclopentene by a Zwitterionic Nickel CatalystJulia-Christina Wasilke, Zachary J. A. Komon, Xianhui Bu, and Guillermo C. BazanView Author Information Departments of Chemistry and Materials, Center for Polymers and Organic Solids, The University of California, Santa Barbara, California 93106 Cite this: Organometallics 2004, 23, 18, 4174–4177Publication Date (Web):August 7, 2004Publication History Received4 June 2004Published online7 August 2004Published inissue 1 August 2004https://pubs.acs.org/doi/10.1021/om049600nhttps://doi.org/10.1021/om049600nrapid-communicationACS PublicationsCopyright © 2004 American Chemical SocietyRequest reuse permissionsArticle Views412Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Adducts,Aromatic compounds,Cyclization,Hydrocarbons,Nickel Get e-Alerts
Copper/Carbon Nanocomposites for Electrocatalytic Reduction of Oxygen to Hydrogen Peroxide (2022)

Electrocatalytic synthesis of hydrogen peroxide (H2O2) via two-electron reduction of oxygen has emerged as an effective strategy to replace the traditional anthraquinone oxidation route. Herein, copper/carbon nanocomposites are prepared by pyrolytic treatment of a metal organic framework precursor, which consists of copper oxide (CuOx) nanoparticles dispersed within a carbon matrix, as evidenced by results from transmission electron microscopy and X-ray photoelectron spectroscopy measurements. Deliberate electrochemical activation enriches the Cu2O species on the nanocomposite surface and markedly enhances the performance of electrocatalytic oxygen reduction to H2O2 with the selectivity increased to 68% from ca. 45% (at +0.1 V) for the as-produced counterparts. This can be exploited for the effective electrochemical degradation of methylene blue. This is accounted for by the weakened interaction with peroxide intermediates on Cu2O, as confirmed by results from first-principles calculations. Results from this study underline the significance of structural engineering based on electrochemical activation for the enhanced selectivity of oxygen reduction reaction for H2O2 production.
SUV varies with time after injection in (18)F-FDG PET of breast cancer: characterization and method to adjust for time differences. (2003)

In untreated breast cancer, the SUV at any time point approximately predicts the rate of change of SUV over time. A comparison method based on this finding appears feasible and may improve the usefulness of the SUV by providing a means of comparing SUV acquired at different times after injection.
Spectral derivative based image reconstruction provides inherent insensitivity to coupling and geometric errors (2005)

A reconstruction algorithm for multiwavelength diffuse optical tomography is presented, where instead of using data at each wavelength separately or even simultaneously, the difference in data for multiple wavelength pairs is used to reconstruct absolute concentration maps of chromophores. The results indicate a dramatic improvement in image reconstruction and the elimination of image artifacts, which are often associated with unknown measurement errors such as coupling coefficients and external boundary variations, because these errors are often less dependent on wavelength, and are effectively removed from the data set of the first derivative of intensity with respect to wavelength.
Multi-tier $\mathrm{N}=4$ Binary Stacking, combining Face-to-Face and Back-to-Back Hybrid Wafer-to-Wafer Bonding Technology (2021)

A binary wafer-to-wafer stacking scheme is advantageous over a sequential approach in terms of manufacturing cost and its impact on the stacked system yield. In this paper, such a binary wafer-to-wafer stacking flow is demonstrated. Two full thickness wafers are paired Face-to-Face using a 2μm pitch hybrid bonding technology, followed by top wafer thinning to 2μm. The Face-to-Face connections are fed through to the thinned top wafer surface by means of a 1μm diameter by 5μm deep via-last TSV. 2μm pitch hybrid backside pads are realized on top of these via-last TSVs, at the same time levelling out and planarizing the backside of the Face-to-Face bonded wafer pairs. Two N=2 Face-to-Face bonded wafer pairs are Back-to-Back hybrid bonded to each other, realizing an N=4 multi-tier wafer stack. The N4 top wafer is thinned to 5μm, revealing the nails of 5μm diameter by 8μm deep via-middle TSVs, implemented on this N4 wafer prior to the Face-to-Face bonding. An N4 backside passivation and an aluminum METPASS module finishes the multi-tier N=4 process flow. The paper describes the realization of the above explained integration flow. Several process challenges are extensively elaborated. Electrical results, featuring 100% yielding Back-to-Back kelvin and interwoven chains connections, demonstrate the maturity of this multi-tier N=4 binary stacking process.
Effect of ARS1 mutations on chromosome stability in Saccharomyces cerevisiae. (1985)

We have used a set of deletion mutations in the ARS1 element of Saccharomyces cerevisiae to measure their effect on chromosome stability. This work establishes the previously proposed existence of three domains in ARS1. Domain C, which we have previously inferred, but not proved, to be a part of ARS1, is now established. In addition, we show that increasingly large deletions of the domain have increasingly large effects, which was not realized before. Furthermore, we have provided the first positive evidence for the central importance of a 14-base-pair core sequence containing the ARS consensus element by showing that it has the ability to act as a replicator on a plasmid containing no other ARS1 flanking sequence. The method of analyzing plasmid stability used in our study employs a novel and sensitive flow cytometry assay for beta-galactosidase. We discuss ways in which flow cytometry, based on this assay, could be generalized beyond its particular application in this work to studying other aspects of the cell biology of yeast and higher cells. The actual flow cytometry method will be described in detail elsewhere.
Building Competitive Direct Acoustics-to-Word Models for English Conversational Speech Recognition (2018)

Direct acoustics-to-word (A2W) models in the end-to-end paradigm have received increasing attention compared to conventional subword based automatic speech recognition models using phones, characters, or context-dependent hidden Markov model states. This is because A2W models recognize words from speech without any decoder, pronunciation lexicon, or externally-trained language model, making training and decoding with such models simple. Prior work has shown that A2W models require orders of magnitude more training data in order to perform comparably to conventional models. Our work also showed this accuracy gap when using the English Switchboard-Fisher data set. This paper describes a recipe to train an A2W model that closes this gap and is at-par with state-of-the-art sub-word based models. We achieve a word error rate of 8.8.8%/13.9% on the Hub5-2000 Switchboard/CallHome test sets without any decoder or language model. We find that model initialization, training data order, and regularization have the most impact on the A2W model performance. Next, we present a joint word-character A2W model that learns to first spell the word and then recognize it. This model provides a rich output to the user instead of simple word hypotheses, making it especially useful in the case of words unseen or rarely-seen during training.
Laparoscopic Enterocystoplasty: The Clinical Technique (2000)

No AccessJournal of UrologyUrological Survey: Video Review: Ureteroscopy/Laparoscopy/Bladder Reconstruction1 Dec 2000Laparoscopic Enterocystoplasty: The Clinical Technique Julio M. Pow-Sang, andM.D. Ralph V. ClaymanM.D. Julio M. Pow-SangJulio M. Pow-Sang More articles by this author , and Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)67002-4AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Laparoscopic Enterocystoplasty: The Clinical Technique." The Journal of Urology, 164(6), p. 2201 References 1 : Laparoscopic radical cystoprostatectomy with ileal conduit performed completely intracorporeally: the initial 2 cases. Urology2000; 56: 26. Google Scholar © 2000FiguresReferencesRelatedDetails Volume 164Issue 6December 2000Page: 2201 Advertisement Copyright & Permissions© 2000MetricsAuthor Information Julio M. Pow-Sang More articles by this author Ralph V. Clayman More articles by this author Expand All Advertisement PDF DownloadLoading ...
Preparation of fused 1,3‐oxazine‐2,4‐diones as potential antitumor agents (1995)

Abstract A series of indole, thiophene and pyrrole‐fused 1,3‐oxazine‐2,4‐diones, 2‐methyl‐1,3‐oxazin‐4‐ones and 2‐dimethylamino‐1,3‐oxazin‐4‐ones were synthesized and evaluated as antitumor agents.