gebhart/patrepeval huggingface dataset:
Pathogenesis of mucosal biofilm infections: challenges and progress (2008)

Living-tissue biofilms remained unrecognized until very recently, mainly as a result of traditional microbial sampling techniques or histologic processing, which disrupt the spatial organization of the tissue microorganisms. Thus, the biofilm nature of certain mucosal infections was frequently unintentionally missed or disregarded. To a large extent, the study of human tissue biofilms is still in its infancy. However, with the advent of newer methodologies, such as fluorescent in situ hybridization and endoscopic confocal laser scanning microscopy, which combine the identification of microbes with in situ, direct visualization of their relationships with each other and with their substratum, mucosal tissue biofilms are becoming easier to study and, thus, their role in human infections is becoming more apparent. This review summarizes the challenges in the study of tissue biofilms, proposes two inflammation-centered - albeit opposite - pathogenetic models of mucosal tissue biofilm infections and suggests directions for future research and novel therapeutic approaches.
Enhancement of Iodine Adsorption on Ruthenium Glue Layer for Seedless CECVD of Cu (2005)

Catalyst-enhanced chemical vapor deposition (CECVD) of copper (Cu) on ruthenium (Ru) layer using iodine as a catalytic-surfactant has been studied for the seedless Cu superfilling of submicron features of trenches and via holes. Hydrogen improved adsorption of iodine by assisting hydrogenation reaction when diiodomethane (CH2I2) vapor was provided onto Ru surface in hydrogen ambient. The iodine adatoms on Ru layer also showed catalytic-surfactant effect on the subsequent CVD of Cu as well as on Cu seed layer. As a result, the superfilling of Cu on submicrometer features was achieved on Ru glue layer without Cu seed layer. (C) 2005 The Electrochemical Society.
Global Assessment of the New ASTER Global Digital Elevation Model (2011)

In 2009, the US National Aeronautics and Space Administration and Japan’s Ministry of Economy, Trade and Industry released a new global digital elevation model (GDEM) derived from reprocessed Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data from the Terra satellite. An initial, empirical assessment of the accuracy and characteristics of the GDEM was carried out using a globally-distributed sample dataset. Statistical and visual analyses of the GDEM, using known reference DEMs and ground control points (GCPs) for comparison, revealed a systematic bias in the ASTER GDEM elevations, higher average noise levels, and a lower effective ground resolution compared to the reference data, as well as numerous topo-graphic artifacts and anomalies. The GDEM appears to meet its accuracy specifications when compared to the reference DEMs, but compared to the GCPs, some of the areas are questionable. In areas that lack good quality terrain data, the GDEM may prove useful, but must be used with care.
Tandem Cope-Claisen rearrangements for the construction of (E,E)-1,6-cyclodecadienes. Effect of ketene acetal substituents on .DELTA.G.dbldag.Claisen (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTandem Cope-Claisen rearrangements for the construction of (E,E)-1,6-cyclodecadienes. Effect of ketene acetal substituents on .DELTA.G.dbldag.ClaisenStanley Raucher, John E. Burks Jr., Ki-Jun Hwang, and Dana P. SvedbergCite this: J. Am. Chem. Soc. 1981, 103, 7, 1853–1855Publication Date (Print):April 1, 1981Publication History Published online1 May 2002Published inissue 1 April 1981https://pubs.acs.org/doi/10.1021/ja00397a053https://doi.org/10.1021/ja00397a053research-articleACS PublicationsRequest reuse permissionsArticle Views378Altmetric-Citations27LEARN 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-Alertsclose Get e-Alerts
Evidence implicating L3T4 in class II MHC antigen reactivity; monoclonal antibody GK1.5 (anti-L3T4a) blocks class II MHC antigen-specific proliferation, release of lymphokines, and binding by cloned murine helper T lymphocyte lines. (1983)

Monoclonal antibody GK1.5 recognizes a determinant, designated L3T4a, on the murine T cell surface molecule L3T4. The expression of L3T4a by functional murine T cell clones appears to correlate primarily with class II MHC antigen reactivity rather than with functional phenotype. In previous studies, antigen-specific cytolysis by a cloned class II MHC antigen(I-Ak)-reactive CTL line was found to be blocked entirely by monoclonal antibody (mAb) GK1.5, at a step before the lethal hit. In the present studies, we demonstrate that mAb GK1.5 profoundly blocks antigen-specific proliferation and release of lymphokines by cloned murine class II MHC antigen-reactive helper T lymphocyte (HTL) lines. Analysis of cloned T cell hybridomas, however, suggests that there exists clonal heterogeneity in the degree of inhibition of class II MHC antigen-specific function by mAb GK 1.5. Finally, we present evidence that mAb GK1.5 blocks class II MHC antigen-specific function by blocking class II MHC antigen-specific binding. The data presented here lend considerable support to the concept both that L3T4 and the human Leu-3/T4 molecules are similar and that L3T4 plays a role in class II MHC antigen-reactivity by murine T cells.
Inhibition of Uptake of Thyroid Hormone into Rat Hepatocytes by Preincubation withN-Bromoacetyl 3,3′,5-Triiodothy r onine (1988)

To investigate whether affinity coupling of N-bromoacetyl-T3 (BrAcT3) to the T3 membrane carrier results in an inhibition of transport of T3 into the cell, rat hepatocytes in monolayer were incubated for 2 h at 21 C with 1.3 mumol/liter BrAcT3 in medium without protein. After extensive washing, cells were incubated during 20 h at 37 C with [125I]T3 in medium with 0.5% BSA, and products in supernatants were analyzed by LH-20 column chromatography. In addition the apparent affinity constant (Km) and maximal uptake velocity (Vmax) of the high affinity uptake process were estimated using 1 min incubations of hepatocytes with various concentrations of T3. In control experiments (i.e. without BrAcT3 affinity coupling) about 57% of the added T3 was cleared from the medium and further metabolized, 85% of the cleared T3 reappeared in the medium as I-, 15% as conjugates. Addition of propylthiouracil during the 20 h incubation with T3 strongly inhibited deiodination, without a change in T3 clearance. Because T3 is sulfated before deiodination, a concomitant rise in conjugates was observed. Addition of ouabain to control cells during the 20 h incubation with T3 strongly inhibited uptake, with a parallel decrease in I- and conjugate formation. After affinity coupling of BrAcT3, T3 clearance was inhibited (by 30% P less than 0.001). Since I- production was more depressed (by 73%) than T3 clearance, with some rise in conjugate formation (P less than 0.001), inhibition of deiodinase by BrAcT3 also took place. The effects of BrAcT3 and ouabain on uptake of T3 appeared to be additive as were the effects of propylthiouracil and BrAcT3 on deiodination. After affinity coupling of BrAcT3, the Km of T3 uptake did not change significantly; however Vmax was 54% lower (P less than 0.025) indicating a noncompetitive inhibition of the transport system. Preincubation of the cells with N-acetyl-T3 does not alter the characteristics of uptake of T3 by rat hepatocytes as compared to controls, indicating that no binding of this compound occurs. It is concluded that preincubation of hepatocytes with BrAcT3 diminished I- formation from T3; 50% of this inhibition is due to decreased membrane transport and 50% by reduction of deiodination. Inhibition of membrane transport by BrAcT3 is substantiated by a 54% lower Vmax without a significant change in Km as compared to control. The effect of transport of thyroid hormone on metabolism stresses the importance of the membrane carrier in the translocation process.
Reversible gel formation induced by ion complexation. 1. Borax-galactomannan interactions (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReversible gel formation induced by ion complexation. 1. Borax-galactomannan interactionsE. Pezron, A. Ricard, F. Lafuma, and R. AudebertCite this: Macromolecules 1988, 21, 4, 1121–1125Publication Date (Print):April 1, 1988Publication History Published online1 May 2002Published inissue 1 April 1988https://pubs.acs.org/doi/10.1021/ma00182a045https://doi.org/10.1021/ma00182a045research-articleACS PublicationsRequest reuse permissionsArticle Views1268Altmetric-Citations125LEARN 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-Alertsclose Get e-Alerts
Loss of Cardiac microRNA-Mediated Regulation Leads to Dilated Cardiomyopathy and Heart Failure (2009)

These observations reveal a critical role for microRNAs in maintaining cardiac function in mature cardiomyocytes and raise the possibility that only a handful of microRNAs may ultimately be responsible for the dramatic cardiac phenotype seen in the absence of dgcr8.
Infrared Colorization Using Deep Convolutional Neural Networks (2016)

This paper proposes a method for transferring the RGB color spectrum to near-infrared (NIR) images using deep multi-scale convolutional neural networks. A direct and integrated transfer between NIR and RGB pixels is trained. The trained model does not require any user guidance or a reference image database in the recall phase to produce images with a natural appearance. To preserve the rich details of the NIR image, its high frequency features are transferred to the estimated RGB image. The presented approach is trained and evaluated on a real-world dataset containing a large amount of road scene images in summer. The dataset was captured by a multi-CCD NIR/RGB camera, which ensures a perfect pixel to pixel registration.
Chameleon: A Color-Adaptive Web Browser for Mobile OLED Displays (2012)

Displays based on organic light-emitting diode (OLED) technology are appearing on many mobile devices. Unlike liquid crystal displays (LCD), OLED displays consume dramatically different power for showing different colors. In particular, OLED displays are inefficient for showing bright colors. This has made them undesirable for mobile devices because much of the web content is of bright colors. To tackle this problem, we present the motivational studies, design, and realization of Chameleon, a color adaptive web browser that renders webpages with power-optimized color schemes under user-supplied constraints. Driven by the findings from our motivational studies, Chameleon provides end users with important options, offloads tasks that are not absolutely needed in real time, and accomplishes real-time tasks by carefully enhancing the codebase of a browser engine. According to measurements with OLED smartphones, Chameleon is able to reduce average system power consumption for web browsing by 41 percent and is able to reduce display power consumption by 64 percent without introducing any noticeable delay.
Telesoftware: adding intelligence to teletext (1979)

The authors seek to show how, by using a microprocessor, teletext may be extended to provide many new and useful facilities, while remaining compatible with existing teletext transmissions. The design and implementation of an experimental telesoftware terminal are described, and a summary of current thinking is given, indicating the probable future software and hardware constraints of the system and its potential applications.
Adenovirus-mediated transfer of siRNA against PTTG1 inhibits liver cancer cell growth in vitro and in vivo (2006)

The pituitary tumor transforming (PTTG) gene family comprises PTTG1, 2, and 3. Forced expression of PTTG1 (securin) induces cellular transformation and promotes tumor development in animal models. PTTG1 is overexpressed in various human cancers. However, the expression and pathogenic implications of the PTTG gene family in hepatocellular carcinoma are largely unknown. Gene silencing using short interfering RNA (siRNA) has become an efficient means to study the functions of genes and has been increasingly used for cancer gene therapy approaches. We report that PTTG1, but not PTTG2 and 3, was highly and frequently expressed in liver cancer tissues from patients and highly in SH-J1, SK-Hep1, and Huh-7 hepatoma cell lines. Adenoviral vector encoding siRNA against PTTG1 (Ad.PTTG1-siRNA) depleted PTTG1 specifically and efficiently in SH-J1 hepatoma cells, which resulted in activation of p53 that led to increased p21 expression and induction of apoptosis. The depletion of PTTG1 in HCT116 colorectal cancer cells exhibited a cytotoxic effect in a p53-dependent manner. Ad.PTTG1-siRNA-mediated cytotoxic effect was dependent on expression levels of PTTG1 and p53 in hepatoma cell lines. Huh-7 hepatoma cells, once transduced with Ad.PTTG1-siRNA, displayed markedly attenuated growth potential in nude mice. Intra-tumor delivery of Ad.PTTG1-siRNA led to significant inhibition of tumor growth in SH-J1 tumor xenograft established in nude mice. In conclusion, PTTG1 overexpressed in hepatoma cell lines negatively regulates the ability of p53 to induce apoptosis. PTIG1 gene silencing using siRNA may be an effective modality to treat liver cancer, in which PTTG1 is abundantly expressed. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/ suppmat/index.html).
Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways (2004)

In mammalian cells, both microRNAs (miRNAs) and small interfering RNAs (siRNAs) are thought to be loaded into the same RNA-induced silencing complex (RISC), where they guide mRNA degradation or translation silencing depending on the complementarity of the target. In Drosophila, Argonaute2 (AGO2) was identified as part of the RISC complex. Here we show that AGO2 is an essential component for siRNA-directed RNA interference (RNAi) response and is required for the unwinding of siRNA duplex and in consequence assembly of siRNA into RISC in Drosophila embryos. However, Drosophila embryos lacking AGO2, which are siRNA-directed RNAi-defective, are still capable of miRNA-directed target RNA cleavage. In contrast, Argonaute1 (AGO1), another Argonaute protein in fly, which is dispensable for siRNA-directed target RNA cleavage, is required for mature miRNA production that impacts on miRNA-directed RNA cleavage. The association of AGO1 with Dicer-1 and pre-miRNA also suggests that AGO1 is involved in miRNA biogenesis. Our findings show that distinct Argonaute proteins act at different steps of the small RNA silencing mechanism and suggest that there are inherent differences between siRNA-initiated RISCs and miRNA-initiated RISCs in Drosophila.
In-line E-beam metrology and defect inspection: industry reflections, hybrid E-beam opportunities, recommendations and predictions (2017)

At SPIE 2013 in Metrology, Inspection, and Process Control for Microlithography an invited paper was published titled “In-line E-beam wafer metrology and defect inspection: the end of an era for image-based critical dimensional metrology? New life for defect inspection”. Three years have passed and numerous developments have occurred as predicted in this paper. The development of E-beam tools that can concurrently handle metrology and defect applications is one of the primary developments. In this paper, the capabilities of these new E-beam tools and their current use cases will be discussed in the areas of Critical Dimension Uniformity (CDU), In-die overlay, Hot spot and Physical defect inspection. Emphasis will be placed on use cases where “massive” CDU data is collected in order to increase yield learning for manufacturing (14nm) and decrease cycles of learning for development (7nm). Additionally, some of the other subject material from the previous publication will also be discussed such as the current state of E-beam critical dimension image fidelity and physical defect detection capabilities. Lastly, future directions and opportunities for In-line E-beam including Multi-beam and/or Multi-column E-beam will be discussed.
Hypoxia Drives Breast Tumor Malignancy through a TET–TNFα–p38–MAPK Signaling Axis (2015)

Hypoxia is a hallmark of solid tumors that drives malignant progression by altering epigenetic controls. In breast tumors, aberrant DNA methylation is a prevalent epigenetic feature associated with increased risk of metastasis and poor prognosis. However, the mechanism by which hypoxia alters DNA methylation or other epigenetic controls that promote breast malignancy remains poorly understood. We discovered that hypoxia deregulates TET1 and TET3, the enzymes that catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), thereby leading to breast tumor-initiating cell (BTIC) properties. TET1/3 and 5hmC levels were closely associated with tumor hypoxia, tumor malignancy, and poor prognosis in breast cancer patients. Mechanistic investigations showed that hypoxia leads to genome-wide changes in DNA hydroxymethylation associated with upregulation of TNFα expression and activation of its downstream p38-MAPK effector pathway. Coordinate functions of TET1 and TET3 were also required to activate TNFα-p38-MAPK signaling as a response to hypoxia. Our results reveal how signal transduction through the TET-TNFα-p38-MAPK signaling axis is required for the acquisition of BTIC characteristics and tumorigenicity in vitro and in vivo, with potential implications for how to eradicate BTIC as a therapeutic strategy.
The Information Warefare Advisor: An Architecture for Interacting with Intelligent Agents Across the Web (1998)

The global spread of digital communications and automated information systems, and the ever widening dependence on these systems for critical economic, political and military needs, has made the protection of these systems, as well as the ability to attack an enemyâs systems, an important part of military strategy and tactics. Information warfare (IW) has grown into a military specialty which seeks to use information and information systems to gain military advantages over an opponent. The US Army War College has several IW experts on its faculty, but during its annual Strategic Crisis Exercise (SCE) these experts are generally not available to assist students with questions on IW background or response planning since they have other duties during the exercise. In order to make the expertise of its faculty available to all students during each SCE, as well as preserve and expand this expertise as faculty come and go, a research project was established between the War Collegeâs Knowledge Engineering Branch and George Washington University to design and demonstrate an architecture for an on-line expert advisor in Information Warfare. The objective of the IW Advisor was to provide any SCE student or War College faculty member the ability to access the captured knowledge and expertise of IW experts through the collegeâs private intranet using standard off-the- shelf web browser technology.
Therapeutic potential of products derived from mesenchymal stem/stromal cells in pulmonary disease (2018)

Multipotent mesenchymal stem/stromal cells (MSCs) possess robust self-renewal characteristics and the ability to differentiate into tissue-specific cells. Their therapeutic potential appears promising as evident from their efficacy in several animal models of pulmonary disorders as well as early-phase clinical trials of acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary disease (COPD). Such therapeutic efficacy might be attributed to MSC-derived products (the "secretome"), namely conditioned media (CM) and extracellular vesicles (EVs), which have been shown to play pivotal roles in the regenerative function of MSCs. Importantly, the EVs secreted by MSCs can transfer a variety of bioactive factors to modulate the function of recipient cells via various mechanisms, including ligand-receptor interactions, direct membrane fusion, endocytosis, or phagocytosis.Herein, we review the current state-of-the-science of MSC-derived CM and EVs as potential therapeutic agents in lung diseases. We suggest that the MSC-derived secretome might be an appropriate therapeutic agent for treating aggressive pulmonary disorders because of biological and logistical advantages over live cell therapy. Nonetheless, further studies are warranted to elucidate the safety and efficacy of these components in combating pulmonary diseases.
Highly multiplexed single-cell in situ RNA and DNA analysis with bioorthogonal cleavable fluorescent oligonucleotides (2018)

The ability to profile transcripts and genomic loci comprehensively in single cells <i>in situ</i> is essential to advance our understanding of normal physiology and disease pathogenesis. Here we report a highly multiplexed single-cell <i>in situ</i> RNA and DNA analysis approach using bioorthogonal cleavable fluorescent oligonucleotides. In this approach, oligonucleotides tethered to fluorophores through an azide-based cleavable linker are used to detect their nucleic acids targets by <i>in situ</i> hybridization. After fluorescence imaging, the fluorophores in the whole specimen are efficiently cleaved in 30 minutes without loss of RNA or DNA integrity. Through reiterative cycles of hybridization, imaging, and cleavage, this method has the potential to quantify hundreds to thousands of different RNA species or genomic loci in single cells <i>in situ</i> at the single-molecule sensitivity. Applying this approach, we demonstrate that different nucleic acids can be detected in each hybridization cycle by multi-color staining, and at least ten continuous hybridization cycles can be carried out in the same specimen. We also show that the integrated single-cell <i>in situ</i> analysis of DNA, RNA and protein can be achieved using cleavable fluorescent oligonucleotides combined with cleavable fluorescent antibodies. This highly multiplexed imaging platform will have wide applications in systems biology and biomedical research.