gebhart/patrepeval huggingface dataset:
Lingvo: a Modular and Scalable Framework for Sequence-to-Sequence Modeling (2019)

Lingvo is a Tensorflow framework offering a complete solution for collaborative deep learning research, with a particular focus towards sequence-to-sequence models. Lingvo models are composed of modular building blocks that are flexible and easily extensible, and experiment configurations are centralized and highly customizable. Distributed training and quantized inference are supported directly within the framework, and it contains existing implementations of a large number of utilities, helper functions, and the newest research ideas. Lingvo has been used in collaboration by dozens of researchers in more than 20 papers over the last two years. This document outlines the underlying design of Lingvo and serves as an introduction to the various pieces of the framework, while also offering examples of advanced features that showcase the capabilities of the framework.
Description and Evaluation of the Variability of Human Color Vision in an Anti-piracy Context (2009)

In the context of anti-piracy / anti-camcorder in digital cinemas a major requirement is invisibility of inserted pattern for the legal viewer watching the main cinema screen. On the basis of a multispectral projection system developed to create color metamers, we faced the need to explore and understand better color vision variability.This paper first presents the application context and the problem to solve. Then the CIE-2006 model is introduced, complemented with a brief overview of genetic aspects of color vision, as these were the basis for the study. Variability of color vision is then evaluated, first on a set of Stiles and Burch observers and then on observers in our digital cinema context.Two experiments are then presented, incremental steps towards the system improvement. The two experiments reveal coherent disparities for the different observers, modeling these disparities as L- and M- cone fundamentals shifts. The improvement between the first and the second experiment is shown in terms of closeness to a standard observer.This gain is a clear result of integrating color perception knowledge in the system design. It is as well a definite step towards acceptance of the metamer images by a wide and varied population of cinema observers.
Abstract 3448: Dasatinib attenuates Src pathway signaling and combined with veliparib and carboplatin potently inhibits tumor growth in a preclinical model of TNBC (2019)

Background: The combination of a poly ADP ribose polymerase (PARP) inhibitor with a DNA-damaging agent has shown promise in treating triple-negative breast cancer (TNBC); however, not all patients respond to this combination (Rugo HS et al. The New England Journal of Medicine. 2016). The Src protein kinase modulates multiple cancer cell properties and plays a key role in tumorigenic processes. However, Src inhibitors as single agents have shown limited effects in solid tumors (Finn RS et al. Clinical Cancer Research. 2011). In this study, we examined the antitumor effects of the Src inhibitor dasatinib, the PARP inhibitor veliparib, and the DNA-damaging agent carboplatin in TNBC cells in vitro and tumors in vivo to try to identify the combination with the most clinical potential.Methods: The KRAS/BRAF-mutated TNBC cell line, MDA-MB-231, was used in this study. For in vitro studies, proliferation, cellular apoptosis, and 3D on-top clonogenic growth were measured, tube formation assays and western blot analysis were performed. For in vivo studies, a xenograft model was used to examine treatment responses, and immunohistochemical analysis was performed.Results: Surprisingly, treatment with the combination of veliparib plus carboplatin led to an increase in Src phosphorylation. Importantly, addition of dasatinib attenuated Src overexpression induced by veliparib plus carboplatin and further inhibited the downstream signaling of Src, thereby enhancing the antitumor efficacy of veliparib plus carboplatin. In an MDA-MB-231 xenograft model, the triple combination of dasatinib with veliparib plus carboplatin showed greater tumor growth inhibitory effects compared with single agents or double combinations. No systemic toxicity was observed in mice treated with the triple combination.Conclusions: Here, we provide novel evidence that veliparib combined with carboplatin drives Src activation in the preclinical model tested. Moreover, we provide provocative in vitro and in vivo data highlighting the potential for increasing therapeutic efficacy by combining dasatinib with veliparib and carboplatin in patients with KRAS/BRAF-mutated TNBC.Citation Format: Yuliang Sun, Xiaoqian Lin, Jennifer C. Aske, Casey Williams, Mark Abramovitz, Brian Leyland-Jones. Dasatinib attenuates Src pathway signaling and combined with veliparib and carboplatin potently inhibits tumor growth in a preclinical model of TNBC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3448.
Individual Supramolecular Host-Guest Interactions Probed by Dynamic Single Molecule Force Spectroscopy (2000)

Until now single molecule force spectroscopy experiments have been performed almost exclusively on biologically relevant systems consisting of receptors with high molar masses and very slow unbinding kinetics. In this paper we report on force spectroscopy results of the complexation behavior of ferrocene moieties, self-assembled on an AFM tip, in β-cyclodextrin (β-CD) receptors, immobilized in highly ordered self-assembled monolayers on Au(111). For this system the unbinding kinetics are on a shorter time scale than the AFM time scale. Multiple pull-off events could be observed, while the addition of an external guest was shown to reversibly block the β-CD cavities. The adhesion between β-CD and ferrocene was found to be quantized. The force of 56 ± 10 pN could be identified as single host-guest complex rupture force. This rupture force was found to be independent of the (un-)loading rate which is indicative for a thermodynamically controlled experiment. Our report is the first example where single supramolecular host-guest interactions could be monitored for complexation reactions with fast unbinding kinetics.
Development of Continuous and Ultrathin Pt Electrocatalysts Using Plasma-Assisted ALD (2014)

High cost of Pt prevents wide-spread application of fuel cell vehicles. Fine nanoparticles (3-5nm in diameter) are traditionally used in order to increase electrochemically active surface area. A continuous Pt film is more stable and has a 5-10 fold higher area-specific activity than Pt nanoparticles. 1 This is only economically viable when the Pt film is less than ~3 nm thick. Pt ALD usually yields Pt nanoparticles during initial film growth. We have shown earlier in work on flat substrates that tungsten, with a higher surface energy than platinum (3.5 J/m 2 vs 2.5 J/m 2 ), can serve as an adhesion layer to achieve Pt ALD films that are dense and continuous at thicknesses of ~1.5 nm. 2,3 To fabricate a practical electrocatalyst we developed a plasma-assisted, open-ended rotary reactor to deposit W and Pt ALD films on the high surface area metal oxide particles. We also deposited the layers on 3M NSTF substrate, an oriented organic crystalline substrate. Transmission electron microscopy (TEM) showed uniform and continuous ~3-5 nm Pt films on the TiO 2 particles. The W ALD and Pt ALD films deposited on the 3M NSTF substrate were characterized using TEM with electron energy loss spectroscopy (EELS). The TEM-EELS analysis revealed W ALD and Pt ALD films with thicknesses of ~3 nm that were continuous and conformal on the high aspect ratio NSTF substrates. The production of these thin film on high surface area substrates demonstrates that it is possible to further reduce cost of fuel cell catalyst. Acknowledgements The authors thank Mark K. Debe, Edward M. Fischer, and Andrew Steinbach of 3M for providing non-platinized NSTF substrate. Thanks are also extended to Cristin Keary, Tom Moylan, and Peter Harvey for engineering support. References H. A. Gasteiger et al., Appl. Cat. B: Env. 56, 9 (2005). L. Baker et al., Appl. Phys. Lett. 101, 111601 (2012). US Patent 8,647,723.
Generative Classifiers as a Basis for Trustworthy Image Classification (2021)

With the maturing of deep learning systems, trustworthiness is becoming increasingly important for model assessment. We understand trustworthiness as the combination of explainability and robustness. Generative classifiers (GCs) are a promising class of models that are said to naturally accomplish these qualities. However, this has mostly been demonstrated on simple datasets such as MNIST and CIFAR in the past. In this work, we firstly develop an architecture and training scheme that allows GCs to operate on a more relevant level of complexity for practical computer vision, namely the ImageNet challenge. Secondly, we demonstrate the immense potential of GCs for trustworthy image classification. Explainability and some aspects of robustness are vastly improved compared to feed-forward models, even when the GCs are just applied naively. While not all trustworthiness problems are solved completely, we observe that GCs are a highly promising basis for further algorithms and modifications. We release our trained model for download in the hope that it serves as a starting point for other generative classification tasks, in much the same way as pretrained ResNet architectures do for discriminative classification.Code: github.com/VLL-HD/trustworthy_GCs
Improving the usability of remote eye gaze tracking for human-device interaction (2014)

This paper presents a novel single-point calibration-based remote eye gaze tracking (REGT) method. The proposed method consists primarily of two steps. First, a user calibration database (UCDB) that contains user-specific data associated with multiple calibration points (CPs) is constructed for a certain number of users. Second, for new users, the candidate calibrated data are retrieved from the UCDB by simply requesting the users to look at a single CP on the screen center (SC). Experimental results show that the proposed REGT method with single-point calibration demonstrates a highly competitive accuracy compared with conventional methods employing multipoint calibration.
Interventional cardiology : new techniques and strategies for diagnosis and treatment (1995)

Advanced Diagnostic Methods Intravascular Ultrasound Imaging, Peter J. Fitzgerald, Guy J. Friedrich, Dirk Hausmann, and Paul G. Yock Percutaneous Coronary Angioscopy, Christopher J. White Clinical Applications of Intracoronary Coronary Doppler Flow Velocity in Interventional Cardiology, Morton J. Kern and Michael S. Flynn The Practical Application of Quantitative Angiographic Methods for Investigating Newer Coronary Interventions and Balloon Angioplasty, Jeffrey J. Popma and Richard E. Kuntz Assessment of Myocardial Viability, Jorge Cheirif New Therapeutic Technologies Coronary Laser Angioplasty, Lawrence Deckelbaum Coronary and Saphenous Vein Graft Stents, Christopher J. White and Stephen R. Ramee Coronary Atherectomy: Directional, Rotational, and Extraction Catheters, Alaa E. Abdelmeguid and Patrick L. Whitlow Advanced Therapeutic Strategies Thrombolysis of Occluded Vein Grafts, Joseph R. Hartmann Adjunctive Thrombolysis in Angioplasty, Tyrone J. Collins Supported Coronary Angioplasty, John S. Wilson and E. Magnus Ohman Reducing Coronary Restenosis After Angioplasty, Robert S. Schwartz and David R. Holmes, Jr. Saphenous Vein Bypass Graft Angioplasty, Stephen R. Ramee and Christopher J. White Salvaging Failed Coronary Angioplasty, John R. Laird and Dale C. Wortham
The impact of nanoscale compositional variation on the properties of amorphous alloys (2020)

The atomic distribution in amorphous FeZr alloys is found to be close to random, nevertheless, the composition can not be viewed as being homogenous at the nm-scale. The spatial variation of the local composition is identified as the root of the unusual magnetic properties in amorphous Fe$_{Zahl}$1-xZr$_{x}$ alloys. The findings are discussed and generalised with respect to the physical properties of amorphous and crystalline materials.
Protéomique ciblée pour la quantification multiplexée de biomarqueurs protéiques chez le crustacé Gammarus fossarum : perspectives pour la surveillance environnementale (2017)

/ Le développement de biomarqueurs moléculaires chez les invertébrés aquatiques d'intérêt en écotoxicologie n'a connu que peu d'avancées ces dernières années. Parmi les principaux verrous, on peut citer l'absence de méthodes spécifiques et directes pour la quantification des biomarqueurs, notamment protéiques. Le fort développement et la démocratisation des techniques « omics », notamment la protégénoomique, permet l'acquisition rapide de connaissances au niveau moléculaire sur les espèces non-modèles. A l'aide du protéome récemment décrit chez G. fossarum (Trapp et al. 2014), l'objectif de cette étude a été de développer une approche pour quantifier simultanément plusieurs protéines d'intérêt, valider leurs rôles physiologiques et enfin de les appliquer en surveillance recourant à une approche active par encagement in situ. En transposant les méthodologies récentes développées en santé humaine, nous avons mis en place un dosage par spectrométrie de masse en mode « Selected Reaction Monitoring » pour quantifier simultanément 25 protéines candidates (protéines spécifiques du sexe et/ou de fonctions physiologiques comme la mue, l'immunité, l'osmoregulation). L'identification de peptides protéotypiques spécifiques pour chaque protéine, et donc leur pertinence en tant que biomarqueurs chez G. fossarum, a été réalisée en quantifiant leur teneur au cours du cycle de mue/reproduction mâle et femelle, lors d'un stress de privation alimentaire, ou encore suite à une exposition à des contaminations, au laboratoire et in situ. Une contamination en cadmium à 2µg/L et en plomb à 10µg/L a modulé les niveaux d'expression de certaines protéines annotées comme la prophenoloxidase (mue et système immunitaire), la catalase (défense oxydative) et la GST (détoxification). Lors des expositions sur 17 stations du réseau de surveillance de l'agence de l'eau RMC, des protéines liées à la mue, telles que la chitinase et l'enzyme JHE-carboxylestérase, ont été significativement inhibées sur certains sites identifiés comme sous pression chimique. Cette méthodologie innovante en écotoxicologie offre une alternative valable aux protocoles actuellement utilisés pour le dosage de biomarqueurs, indirectes et couteux en temps et échantillons, ouvrant la voie à une application pratique des biomarqueurs protéiques dans pour la surveillance des milieux.
Mechanism of caesium ion exchange on potassium cobalt hexacyanoferrates(II) (1990)

The caesium uptakes by K2[CoFe(CN)6] and non-stoicheiometric compounds K2–xCox/2[CoFe(CN)6] were found to correlate directly with the specific surface areas of the products with x < 1. The exchange process is assumed to involve only the outermost surface layer of their crystals, which have a cubic lattice, i.e. only potassium (or cobalt) ions inside the elementary cubes closest to the surface of the crystals are exchanged for caesium ions. Compounds with x > 1 are mixtures of cubic potassium cobalt hexacyanoferrate(II) and tetragonal Co2Fe(CN)6. The thermodynamic equilibrium constant of the caesium exchange on K2[CoFe(CN)6] was found to have a high value of 125.
Correction to Dipicolinic Acid Derivatives as Inhibitors of New Delhi Metallo-β-lactamase-1 (2018)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Dipicolinic Acid Derivatives as Inhibitors of New Delhi Metallo-β-lactamase-1Allie Y. ChenAllie Y. ChenMore by Allie Y. Chen, Pei W. ThomasPei W. ThomasMore by Pei W. Thomas, Alesha C. StewartAlesha C. StewartMore by Alesha C. Stewart, Alexander BergstromAlexander BergstromMore by Alexander Bergstrom, Zishuo ChengZishuo ChengMore by Zishuo Cheng, Callie MillerCallie MillerMore by Callie Miller, Christopher R. BethelChristopher R. BethelMore by Christopher R. Bethel, Steven H. MarshallSteven H. MarshallMore by Steven H. Marshall, Cy V. CredilleCy V. CredilleMore by Cy V. Credille, Christopher L. RileyChristopher L. RileyMore by Christopher L. Riley, Richard C. PageRichard C. PageMore by Richard C. Pagehttp://orcid.org/0000-0002-3006-3171, Robert A. Bonomo*Robert A. BonomoMore by Robert A. Bonomohttp://orcid.org/0000-0002-3299-894X, Michael W. Crowder*Michael W. CrowderMore by Michael W. Crowder, David L. Tierney*David L. TierneyMore by David L. Tierney, Walter Fast*Walter FastMore by Walter Fasthttp://orcid.org/0000-0001-7567-2213, and Seth M. Cohen*Seth M. CohenMore by Seth M. Cohenhttp://orcid.org/0000-0002-5233-2280Cite this: J. Med. Chem. 2018, 61, 14, 6400Publication Date (Web):July 18, 2018Publication History Published online18 July 2018Published inissue 26 July 2018https://pubs.acs.org/doi/10.1021/acs.jmedchem.8b01057https://doi.org/10.1021/acs.jmedchem.8b01057correctionACS PublicationsCopyright © 2018 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1360Altmetric-Citations1LEARN 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 PDF (288 KB) Get e-Alertsclose Get e-Alerts
Supplemental Tables, Figures and Legends from Targeting Cancer Stem Cells in Castration-Resistant Prostate Cancer (2023)

&lt;p&gt;Table S1. Primers for quantitative RT-PCR. Table S2. The list of primers for ChIP detection; CD44 promoter region. Figure S1. Loss of DAB2IP increased clonogenicity and stemness in normal prostate epithelial cells. Figure S2. Loss of DAB2IP increased in vitro invasion and motility in normal prostate epithelial cells. Figure S3. DAB2IP inhibits CD44 expression in human prostate epithelial cell lines. Figure S4. Wnt pathway correlates with CRPC progression. Figure S5. AR inhibitor doesn't affect the expression of CD44. Figure S6. All CD44 variants respond to Wnt inhibitor. Figure S7. Wnt signal regulates CD44 expression and stem cell properties. Figure S8. Wnt signal pathway mediates the expression of CD44. Figure S9. Wnt inhibitors diminish the chemo-resistance of KD cells. Figure S10. Overexpression of CD44 rescues the growth inhibition by LGK974. Figure S11. Synergistic effect of Wnt inhibitors combined with docetaxel on Du145 cells.&lt;/p&gt;
Optical communication link with an adaptive transmitter based on interference metric optimization (1999)

Adaptive optical systems used to date for laser communication applications have been based on adaptive optics technology specifically developed for astronomical imaging, where intensity fluctuations are considerably smaller than those encountered by ground-to-ground (or ground-to-space) lasercom systems. These adaptive optical systems are based on direct wavefront measurements (Hartmann-Shack sensor, shearing interferometers, etc.) and the wavefront conjugation principle. In the presence of strong intensity fluctuations these types of systems perform poorly. Here we propose an optical communication link with an adaptive transmitter based on optimization of a beam quality metric that can be measured using a corner-cube interferometer. This beam quality metric is examined to determine its suitability for use in an adaptive laser communication system.
ZFYVE26/SPASTIZIN and SPG11/SPATACSIN mutations in hereditary spastic paraplegia types AR-SPG15 and AR-SPG11 have different effects on autophagy and endocytosis (2018)

ZFYVE26/Spastizin and SPG11/Spatacsin encode 2 large proteins that are mutated in hereditary autosomal-recessive spastic paraplegia/paraparesis (HSP) type 15 (AR-SPG15) and type 11 (AR-SPG11), respectively. We previously have reported that AR-SPG15-related ZFYVE26 mutations lead to autophagy defects with accumulation of immature autophagosomes. ZFYVE26 and SPG11 were found to be part of a complex including the AP5 (adaptor related protein complex 5) and to have a critical role in autophagic lysosomal reformation with identification of autophagic and lysosomal defects in cells with both AR-SPG15- and AR-SPG11-related mutations. In spite of these similarities between the 2 proteins, here we report that ZFYVE26 and SPG11 are differently involved in autophagy and endocytosis. We found that both ZFYVE26 and SPG11 interact with RAB5A and RAB11, 2 proteins regulating endosome trafficking and maturation, but only ZFYVE26 mutations affected RAB protein interactions and activation. ZFYVE26 mutations lead to defects in the fusion between autophagosomes and endosomes, while SPG11 mutations do not affect this step and lead to a milder autophagy defect. We thus demonstrate that ZFYVE26 and SPG11 affect the same cellular physiological processes, albeit at different levels: both proteins have a role in autophagic lysosome reformation, but only ZFYVE26 acts at the intersection between endocytosis and autophagy, thus representing a key player in these 2 processes. Indeed expression of the constitutively active form of RAB5A in cells with AR-SPG15-related mutations partially rescues the autophagy defect. Finally the model we propose demonstrates that autophagy and the endolysosomal pathway are central processes in the pathogenesis of these complicated forms of hereditary spastic paraparesis. Abbreviations: ALR, autophagic lysosome reformation; AP5, adaptor related protein complex 5; AR, autosomal-recessive; HSP, hereditary spastic paraplegia/paraparesis; ATG14, autophagy related 14; BafA, bafilomycin A<sub>1</sub>; BECN1, beclin 1; EBSS, Earle balanced salt solution; EEA1, early endosome antigen 1; EGF, epidermal growth factor; EGFR, epidermal growth factor receptor; GDP, guanosine diphosphate; GFP, green fluorescent protein; GTP, guanosine triphosphate; HSP, hereditary spastic paraplegias; LBPA, lysobisphosphatidic acid; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; MVBs, multivesicular bodies; PIK3C3, phosphatidylinositol 3-kinase, catalytic subunit type 3; PIK3R4, phosphoinositide-3-kinase regulatory subunit 4; PtdIns3P, phosphatidylinositol-3-phosphate; RFP, red fluorescent protein; RUBCN, RUN and cysteine rich domain containing beclin 1 interacting protein; shRNA, short hairpin RNA; SQSTM1/p62, sequestosome 1; TCC: thin corpus callosum; TF, transferrin; UVRAG, UV radiation resistance associated.