gebhart/patrepeval huggingface dataset:
Ultra-high carbon fullerene-based spin-on-carbon hardmasks (2023)

Fullerene-based spin-on-carbon enables very high carbon content, and shows very high thermal stability, and etch resistance approaching amorphous carbon. Here we describe the performance of the HM1300 fullerene SOC, including results using high temperature inert atmosphere curing. Ohnishi numbers below 1.44 are achieved (measured by elemental analysis) and etch performance improved over the standard bake. A new high carbon crosslinker, designed to link directly to the fullerene cage, and with a carbon content comparable to the fullerene (significantly higher than the previous crosslinker) is also introduced. The new crosslinker is designed to enhance both etch and thermal stability performance.
Severe acute respiratory syndrome coronavirus 2 and influenza A virus co‐infection alters viral tropism and haematological composition in Syrian hamsters (2022)

The ongoing coronavirus disease 2019 pandemic and its overlap with the influenza season lead to concerns over severe disease caused by the influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infections. Using a Syrian hamster co-infection model with SARS-CoV-2 and the pandemic influenza virus A/California/04/2009 (H1N1), we found (a) more severe disease in co-infected animals, compared to those infected with influenza virus alone but not SARS-CoV-2 infection alone; (b) altered haematological changes in only co-infected animals and (c) altered influenza virus tropism in the respiratory tracts of co-infected animals. Overall, our study revealed that co-infection with SARS-CoV-2 and influenza virus is associated with altered disease severity and tissue tropism, as well as haematological changes, compared to infection with either virus alone.
hUNG2 Is the Major Repair Enzyme for Removal of Uracil from U:A Matches, U:G Mismatches, and U in Single-stranded DNA, with hSMUG1 as a Broad Specificity Backup (2002)

hUNG2 and hSMUG1 are the only known glycosylases that may remove uracil from both double- and single-stranded DNA in nuclear chromatin, but their relative contribution to base excision repair remains elusive. The present study demonstrates that both enzymes are strongly stimulated by physiological concentrations of Mg2+, at which the activity of hUNG2 is 2-3 orders of magnitude higher than of hSMUG1. Moreover, Mg2+ increases the preference of hUNG2 toward uracil in ssDNA nearly 40-fold. APE1 has a strong stimulatory effect on hSMUG1 against dsU, apparently because of enhanced dissociation of hSMUG1 from AP sites in dsDNA. hSMUG1 also has a broader substrate specificity than hUNG2, including 5-hydroxymethyluracil and 3,N(4)-ethenocytosine. hUNG2 is excluded from, whereas hSMUG1 accumulates in, nucleoli in living cells. In contrast, only hUNG2 accumulates in replication foci in the S-phase. hUNG2 in nuclear extracts initiates base excision repair of plasmids containing either U:A and U:G in vitro. Moreover, an additional but delayed repair of the U:G plasmid is observed that is not inhibited by neutralizing antibodies against hUNG2 or hSMUG1. We propose a model in which hUNG2 is responsible for both prereplicative removal of deaminated cytosine and postreplicative removal of misincorporated uracil at the replication fork. We also provide evidence that hUNG2 is the major enzyme for removal of deaminated cytosine outside of replication foci, with hSMUG1 acting as a broad specificity backup.
Identification of Homeodomain Proteins, PBX1 and PREP1, Involved in the Transcription of Murine Leukemia Virus (2003)

Cyclin-dependent kinase inhibitors (CDKIs) have been shown to block human immunodeficiency virus and herpes simplex virus. It is hypothesized that CDKIs block viral replication by inhibiting transcription of specific cellular genes. Here we find that three CDKIs, flavopiridol, purvalanol A, and methoxy-roscovitine, block Moloney murine leukemia virus (MLV) transcription events. Using gene expression microarray technology to examine the inhibitory effects of CDKIs, we observed a cellular gene, the pre-B-cell leukemia transcription factor 1 (Pbx1) gene, down-regulated by CDKI treatment. The PBX consensus element (PCE), TGATTGAC, is conserved in the long terminal repeats of several murine retroviruses, including Moloney MLV. Mutations in the PCE completely inhibited viral transcription whereas overexpression of PBX1 and a PBX1-associated protein, PREP1, enhanced viral transcription. The interaction between the PCE and PBX1-PREP1 proteins was confirmed by gel shift experiments. Blocking PBX1 protein synthesis resulted in a significant decrease in viral transcription. Collectively, our results represent the first work demonstrating that the homeodomain proteins PBX1 and PREP1 are cellular factors involved in Moloney MLV transcription regulation.
Trocylation of 3‐quinuclidinol, a key marker for the chemical warfare agent 3‐quinuclidinyl benzilate, for its enhanced detection at low levels in complex soil matrices by electron ionization gas chromatography–mass spectrometry (2021)

An expedient and practical derivatization method for 3Q, a chemical warfare degradation product difficult to detect by GC/MS, has been realized using trichloroethyl chloroformate. The reaction provides 3Q-Troc, a derivative with better detectability than 3Q by electron ionization GC/MS such as peak sharpness and a unique mass spectrum for its unambiguous identification.
Deflecting light into resonant cavities for spectroscopy (2023)

Light is coupled into a cavity ring down spectroscopy (CRDS) resonant cavity using an acousto-optic modulator. The AOM allows in-coupling efficiencies in excess of 40%, which is two to three orders of magnitude higher than in conventional systems using a cavity mirror for in-coupling. The AOM shutoff time is shorter than the roundtrip time of the cavity. The higher light intensities lead to a reduction in shot noise, and allow the use of relatively insensitive but fast-responding detectors such as photovoltaic detectors. Other deflection devices such as electro-optic modulators or elements used in conventional Q-switching may be used instead of the AOM. The method is particularly useful in the mid-infrared, far-infrared, and ultraviolet wavelength ranges, for which moderately reflecting input mirrors are not widely available.
Role of RANTES in the pathogenesis of experimental colitis (2007)

Platelets and platelet‐derived chemokines eg RANTES have been implicated in the pathogenesis of chronic inflammatory bowel disease (IBD). However, it remains unclear if and how platelet‐derived RANTES contributes to the blood cell recruitment and tissue injury associated with intestinal inflammation. We addressed these issues in dextran sodium sulfate (DSS)‐induced colitis in wildtype (WT) mice, WT receiving blocking antibody (mAb) to RANTES, RANTES‐deficient (RANTES −/− ) mice, and RANTES −/− →WT bone marrow chimeras. Disease activity index (DAI), histopathologic injury, vascular permeability to albumin, and the adhesive interactions between leukocytes, platelets, and endothelial cells were monitored. All parameters were increased by DSS and were attenuated in RANTES −/− mice and by RANTES mAb in WT mice. A similar protection was noted in RANTES −/− →WT chimeras, suggesting that blood cells (eg, platelets) are a major source of the chemokine. Our findings implicate RANTES, likely derived from platelets, in the vascular dysfunction, inflammation, and tissue injury associated with experimental colitis, and suggest that this chemokine may be an important therapeutic target in IBD. (Supported by R01 DK65649).
Continuous production of hyperbranched polyhydrocarbons by electrochemical polymerization of chlorinated methanes (2022)

Continuous production of polyhydrocarbon (PHC) by electrochemical polymerization of chlorinated methanes: Monomer loading/product transfer in a home-built flow system operating in inert environment, for scaled up synthesis of sufficient PHC product.
ChemInform Abstract: Synthetic Approaches to Homocamptothecin Antitumor Agents (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Protected QUIC Initial Packets (2021)

QUIC encrypts its Initial Packets using keys derived from well-known
constants, meaning that observers can inspect the contents of these
packets and successfully spoof them. This document proposes a new
version of QUIC that encrypts Initial Packets more securely by
leveraging a Public Key distributed via the Domain Name System (DNS)
or other out-of-band system. Discussion of this work is encouraged to
happen on the QUIC IETF mailing list quic@ietf.org or on the GitHub
repository which contains the draft: https://github.com/martinduke
/quic-version-aliasing.
Three-dimensionally ordered macroporous carbons having walls composed of hollow mesosized spheres (2006)

Three-dimensionally ordered macroporous carbons were prepared from bimodal polymer-silica colloidal crystals; the resulting carbons had interconnected macropores, and the walls of the macropores were composed of hollow mesosized spheres.
Self-assembled nucleolipids: from supramolecular structure to soft nucleic acid and drug delivery devices (2011)

This short review aims at presenting some recent illustrative examples of spontaneous nucleolipids self-assembly. High-resolution structural investigations reveal the diversity and complexity of assemblies formed by these bioinspired amphiphiles, resulting from the interplay between aggregation of the lipid chains and base-base interactions. Nucleolipids supramolecular assemblies are promising soft drug delivery systems, particularly for nucleic acids. Regarding prodrugs, squalenoylation is an innovative concept for improving efficacy and delivery of nucleosidic drugs.
Asthma Management in the Emergency Department (2000)

Adherence with published Canadian guidelines for the emergency department management of acute asthma exacerbations was suboptimal. Corticosteroid use in the emergency department was significantly less than recommended. Increased emphasis on education and implementation of accepted asthma management guidelines is necessary.
High temperature nucleation and growth of glutathione protected ∼Ag75 clusters (2012)

We report the first high temperature solution state synthesis of glutathione (-SG) protected atomically precise silver clusters. Noble metal cluster synthesis from metal ions generally requires ice cold temperatures as they are extremely sensitive and high temperature routes are used only for core reduction methods, starting from nanoparticles. The clusters formed by the new route have distinct features in their absorption profile and they exhibit red luminescence. They are characterised by other spectroscopic and microscopic techniques and a tentative formula of Ag(75)(SG)(40) has been assigned.
Alteration of mRNA and microRNA expression profiles in rat muscular type vasculature in early postnatal development (2015)

The vascular system is characterized by a high degree of plasticity. In particular, functional and structural remodeling of the arterial system takes place during early postnatal development. However, the mechanisms providing such alterations in the rapidly growing organisms are poorly understood, especially for the peripheral vasculature. To explore this, we performed mRNA- and miRNA microarray analysis on muscular type saphenous arteries of young (10-12 days) and adult (2-3 months) rats. Thirty-eight significant pathways (such as oxidative phosphorylation, MAPK signaling, metabolism, cell cycle, DNA replication and focal adhesion) were obtained on differentially regulated genes during postnatal development. Many differentially regulated genes were determined as target- and miRNA-hubs. We also found 92 miRNAs differentially expressed in arteries of young and adult rats. Several significantly regulated pathways were found on these regulated miRNAs. Interestingly, these biological cascades also contain those significantly enriched pathways that were previously identified based on the differently expressed genes. Our data indicate that the expression of many genes involved in the regulation of pathways that are relevant for different functions in arteries may be under the control of miRNAs and these miRNAs regulate the functional, and structural remodeling occurring in the vascular system during early postnatal development.
Flame retardancy and heat resistance of phenol‐biphenylene‐type epoxy resin compound modified with benzoguanamine (2003)

Abstract The flame retardancy and heat resistance of a phenol‐biphenylene‐type epoxy resin compound, which forms a self‐extinguishing network structure, were increased by the inclusion of a benzoguanamine‐modified phenol biphenylene resin. The benzoguanamine‐modified phenol biphenylene resin contains a benzoguanamine unit to release non‐flammable nitrogen substances during ignition and to increase the resin's reactivity toward epoxy resins, and biphenylene units to keep the resin's thermal degradation and water resistance. The addition of the benzoguanamine‐modified phenol biphenylene resin in the epoxy resin compound improved the epoxy resin compound's flame retardancy and heat resistance, and also increased its glass transition temperature while maintaining its water resistance and mechanical properties. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Dynamic Response of Shallow Water Monopod Platforms (2002)

This paper describes a systematic desktop study of the non-linear dynamic behavior of monopod platforms. The aim of this work is to highlight some important factors in the dynamics of minimum structures in shallow water. The analysis is performed in the time domain with regular wave loading. The non-linearities are due to the wave theory (Stream function of 8th order), to the shallow water environment and to the drag-dominated situation. Idealizations of two braced monopod configurations are compared with the simpler and more commonly studied unbraced monopod. Aspects highlighted for each configuration include the effect of wave period and top mass on the dynamic amplification factor. In particular, the analysis focuses on the highly non-linear behavior in the wave zone. The results show that braced monopods are dynamically more sensitive than unbraced monopods. In particular, braced monopods exhibit more energy at higher harmonics in the quasi-static response. This yields a consistently stronger dynamic response even if the wave period and the natural period of the structure are very different. The importance of the mass at the top of the structure in the dynamic response and in particular its role in increasing the dynamic amplification factor up the water column are highlighted.
Oscillatory three-phase flow reactor for studies of bi-phasic catalytic reactions (2015)

A multi-phase flow strategy, based on oscillatory motion of a bi-phasic slug within a fluorinated ethylene propylene (FEP) tubular reactor, under inert atmosphere, is designed and developed to address mixing and mass transfer limitations associated with continuous slug flow chemistry platforms for studies of bi-phasic catalytic reactions. The technique is exemplified with C–C and C–N Pd catalyzed coupling reactions.
Quorum sensing: an emerging link between temperature and membrane biofouling in membrane bioreactors (2019)

Lab-scale membrane bioreactors (MBRs) were investigated at 12, 18, and 25 °C to identify the correlation between quorum sensing (QS) and biofouling at different temperatures. The lower the reactor temperature, the more severe the membrane biofouling measured in terms of the transmembrane pressure (TMP) during filtration. More extracellular polymeric substances (EPSs) that cause biofouling were produced at 18 °C than at 25 °C, particularly polysaccharides, closely associated with QS <i>via</i> the production of <i>N</i>-acyl homoserine lactone (AHL). However, at 12 °C, AHL production decreased, but the release of EPSs due to deflocculation increased the soluble EPS concentration. To confirm the temperature effect related to QS, bacteria producing AHL were isolated from MBR sludge and identified as <i>Aeromonas</i> sp., <i>Leclercia</i> sp., and <i>Enterobacter</i> sp. through a 16S rDNA sequencing analysis. Batch assays at 18 and 25 °C showed that there was a positive correlation between QS through AHL and biofilm formation in that temperature range.
LeFlow: Enabling Flexible FPGA High-Level Synthesis of Tensorflow Deep Neural Networks (2018)

Recent work has shown that Field-Programmable Gate Arrays (FPGAs) play an important role in the acceleration of Machine Learning applications. Initial specification of machine learning applications are often done using a high-level Python-oriented framework such as Tensorflow, followed by a manual translation to either C or RTL for synthesis using vendor tools. This manual translation step is time-consuming and requires expertise that limit the applicability of FPGAs in this important domain. In this paper, we present an open-source tool-flow that maps numerical computation models written in Tensorflow to synthesizable hardware. Unlike other tools, which are often constrained by a small number of inflexible templates, our flow uses Google's XLA compiler which emits LLVM code directly from a Tensorflow specification. This LLVM code can then be used with a high-level synthesis tool to automatically generate hardware. We show that our flow allows users to generate Deep Neural Networks with very few lines of Python code.
Computational 3D photography: extracting shape, motion and appearance from images (2008)

One of the fundamental problems of computer vision is to extract 3D shape and motion from images. This can be achieved when a scene or object is observed from different viewpoints or over a period of time. There is a wide range of applications, ranging from digitizing cultural heritage to vision-based autonomous robot navigation. This talk will present several approaches to solve this problem. First, we’ll discuss techniques for 3D shape recovery for static objects and scenes. One particular case is the 3D mapping and localization in large environments from images, e.g. urban 3D reconstruction from vehicleborne cameras or localization from cell-phone images. Next, we’ll shift our focus to modeling dynamic scenes, e.g. people who are moving around. In addition to explicitly 3D modeling an event, we'll consider the possibility to perform video-based rendering from casually captured videos. Speaker Bio-Sketch: Marc Pollefeys is a full professor in the Dept. of Computer Science of ETH Zurich since 2007 where he is the head of the Institute for Visual Computing and leads the Computer Vision and Geometry lab. He currently also remains associated with the Dept. of Computer Science of the University of North Carolina at Chapel Hill where he started as an assistant professor in 2002 and became an associate professor in 2005. Before this he was a postdoctoral researcher at the Katholieke Universiteit Leuven in Belgium, where he also received his M.S. and Ph.D. degrees in 1994 and 1999, respectively. His main area of research is computer vision. One of his main research goals is to develop flexible approaches to capture visual representations of real world objects, scenes and events. Dr. Pollefeys has received several prizes for his research, including a Marr prize, an NSF CAREER award, a Packard Fellowship and a European Research Council Starting Grant. He is the author or co-author of more than 130 peer-reviewed publications. He is the General Chair for the European Conference on Computer Vision 2014 (ECCV), was a Program Co-Chair for the IEEE Conference on Computer Vision and Pattern Recognition 2009 (CVPR), was general/program co-chair of the Third Symposium on 3D Data Processing, Visualization and Transmission and has organized workshops and courses at major vision and graphics conferences and has served on the program committees of many conferences. Prof. Pollefeys is/was on the Editorial Board of the IEEE Transactions on Pattern Analysis and Machine Intelligence and the International Journal of Computer Vision as well as several other journals in computer vision, graphics and robotics.
Structural Disorder of AlMg‐Oxide Phase Supporting Cu/ZnO Catalyst Improves Efficiency and Selectivity for CO2 Hydrogenation to Methanol (2023)

Abstract The performance of the Cu/ZnO catalyst system with the AlMg‐oxide phase is studied for CO 2 hydrogenation to methanol. The catalyst is prepared by thermal treatment of the hydrotalcite phase containing intimately mixed metal cations in the hydroxide form. CuO in the presence of ZnO and disordered AlMg‐oxide phase gets easily reduced to Cu during the hydrogenation reaction. Its catalytic activity at relatively low Cu metal content (∼14 at.%) remains stable during 100 hours on stream at 260 °C with constant space‐time yield for methanol (∼1.8 g MeOH g cat −1 h −1 ) and high methanol selectivity (&gt;85 %) The improved performance is attributed to the neutralization of surface acidity, increased number of weak basic sites in the disordered phase, and lower tendency for coke formation.
769 USP18 STIMULATES HCV PRODUCTION: UPREGULATION OF THE SURFACE ENTRY RECEPTOR CD81 IN VITRO (2011)

767 C-SRC IS REQUIRED FOR VIRAL REPLICATION AS IT MEDIATES COMPLEX FORMATION BETWEEN THE HEPATITIS C VIRUS ENCODED PROTEINS NS5A AND NS5B A. Pfannkuche, B. Katrin, J. Karthe, M. Poenisch, R. Bartenschlager, D. Willbold, D. Haussinger, J.G. Bode. Department of Gastroenterology, Hepatology and Infectiology, Faculty of Medicine, Heinrich-Heine University, Dusseldorf, University of Munster, Munster, Department of Infectious Diseases, Molecular Virology, Ruprecht-Karls-University, Heidelberg, Institut fur Physikalische Biochemie, Heinrich-Heine University, Dusseldorf, Institute of Structural Biology and Biophysics, Research Centre Julich, Julich, Germany E-mail: johannes_bode@t-online.de
Newly Exerted T Cell Pressures on Mutated Epitopes following Transmission Help Maintain Consensus HIV-1 Sequences (2015)

CD8+ T cells are important for HIV-1 virus control, but are also a major contributing factor that drives HIV-1 virus sequence evolution. Although HIV-1 cytotoxic T cell (CTL) escape mutations are a common aspect during HIV-1 infection, less is known about the importance of T cell pressure in reversing HIV-1 virus back to a consensus sequences. In this study we aimed to assess the frequency with which reversion of transmitted mutations in T cell epitopes were associated with T cell responses to the mutation. This study included 14 HIV-1 transmission pairs consisting of a 'source' (virus-donor) and a 'recipient' (newly infected individual). Non-consensus B sequence amino acids (mutations) in T cell epitopes in HIV-1 gag regions p17, p24, p2 and p7 were identified in each pair and transmission of mutations to the recipient was verified with population viral sequencing. Longitudinal analyses of the recipient's viral sequence were used to identify whether reversion of mutations back to the consensus B sequence occurred. Autologous 12-mer peptides overlapping by 11 were synthesized, representing the sequence region surrounding each reversion and longitudinal analysis of T cell responses to source-derived mutated and reverted epitopes were assessed. We demonstrated that mutations in the source were frequently transmitted to the new host and on an average 17 percent of mutated epitopes reverted to consensus sequence in the recipient. T cell responses to these mutated epitopes were detected in 7 of the 14 recipients in whom reversion occurred. Overall, these findings indicate that transmitted non-consensus B epitopes are frequently immunogenic in HLA-mismatched recipients and new T cell pressures to T cell escape mutations following transmission play a significant role in maintaining consensus HIV-1 sequences.