gebhart/patrepeval huggingface dataset:
Biomarkers of HPV in Head and Neck Squamous Cell Carcinoma (2012)

Human papillomavirus (HPV) is an accepted cause of head and neck squamous cell carcinoma (HNSCC), and patients with HPV-associated HNSCC have a favorable prognosis. Currently, there is no general guidance on the most appropriate biomarkers for clinical assessment of HPV in these malignancies. We compared PCR-based and serologic HPV assays, as well as p16 immunohistochemistry, individually and in combination in a single population-based study to assess their associations with overall survival among patients with HNSCC, and thus their potential value as biomarkers. HPV16 serology was determined for 488 patients; immunohistochemical detection of p16 expression in tumors was conducted in a subset of 233 cases, and PCR-based methods to assess the presence of HPV16 DNA in a subset of 179 cases of tumors. Considering each biomarker individually in the subset of patients studied for all endpoints, seropositivity for the E6 and E7 proteins was significantly associated with enhanced all-cause survival in oropharyngeal disease [HR(E6/E7+) = 0.1, 95% confidence interval (CI) = 0.02-0.3]. Neither the presence of HPV16 DNA nor p16 immunostaining was associated with significant enhanced overall survival in oropharyngeal disease (HR(DNA) = 0.9, 95% CI = 0.3-2.9; HR(p16) = 0.3, 95% CI = 0.1-1.1). However, the combination of HPV-positive DNA and E6 or E7 serology was associated with enhanced overall survival in oropharyngeal disease (HR(DNA+/E6/E7+) = 0.1, 95% CI = 0.02-1.0), whereas E6/E7 seronegative patients with evidence of HPV in tumor DNA did not show any evidence of favorable survival (HR(DNA+/E6-/E7-) = 3.4, 95% CI = 0.6-18.1). Furthermore, patients with p16 staining and E6 or E7 seropositivity had favorable survival from oropharyngeal disease (HR(p16+/E6/E7+) = 0.1, 95% CI = 0.02-0.4), whereas patients who were p16 positive and E6/E7 seronegative had significantly increased hazard of all causes of death (HR(p16+/E6-/E7-) = 3.1, 95% CI = 1.2-7.7). A stronger association of HPV presence with prognosis (assessed by all-cause survival) is observed when "HPV-associated" HNSCC is defined using tumor status (HPV DNA status or P16) and HPV E6/E7 serology in combination rather using tumor HPV status alone.
Structure-Based Design of Conformationally Constrained, Cell-Permeable STAT3 Inhibitors (2010)

We report herein the structure-based design of a class of conformationally constrained, potent, cell-permeable small-molecule inhibitors to target the SH2 domain in STAT3. Compound 11 (CJ-1383) binds to STAT3 with a K(i) value of 0.95 µM, dose-dependently inhibits cellular STAT3 signaling and cancer cell growth, and induces apoptosis in the MDA-MB-468 cancer cell line with constitutively activated STAT3.
The LRP toolbox for artificial neural networks (2016)

The Layer-wise Relevance Propagation (LRP) algorithm explains a classifier's prediction specific to a given data point by attributing relevance scores to important components of the input by using the topology of the learned model itself. With the LRP Toolbox we provide platform-agnostic implementations for explaining the predictions of pre-trained state of the art Caffe networks and stand-alone implementations for fully connected Neural Network models. The implementations for Matlab and python shall serve as a playing field to familiarize oneself with the LRP algorithm and are implemented with readability and transparency in mind. Models and data can be imported and exported using raw text formats, Matlab's .mat files and the .npy format for numpy or plain text.
Early signal transduction by the receptor to the chemokine monocyte chemotactic protein-1 in a murine T cell hybrid (1996)

Members of the C-C family of chemotactic cytokines promote chemotaxis and adhesion of leukocytes. In this study, we have identified a murine T cell hybrid that expresses receptors to the chemotactic cytokine monocyte chemotactic protein-1 (MCP-1). This cell line was used to examine MCP-1 receptor-mediated signal transduction events in a homologous system in the absence of interference with other receptors. Our results show that in the 3B4 M1.9 T cell hybrid, MCP-1 receptors mediate intracellular calcium mobilization and extracellular calcium import without detectable increases in total water-soluble inositol phosphates. In addition, MCP-1 regulates the tyrosine phosphorylation of specific substrates at 42 and 44 kDa and induces mobility shift of p42/44 mitogen-activated protein kinases. MCP-1-mediated calcium responses, tyrosine phosphorylation, and the electrophoretic mobility shift of p42/44 mitogen-activated protein kinases can be inhibited by pretreatment of cells with pertussis toxin, indicating a role for Gi-like G proteins in coupling the MCP-1R to signal transduction.
Identification of Multiple Nuclear Factors That Interact with Cyclic Adenosine 3′,5′-Monophosphate Response Element-Binding Protein and Activating Transcription Factor-2 by Protein-Protein Interactions (1991)

Understanding the nature and importance of protein-protein interactions in the mechanisms of eukaryotic gene expression is essential to understanding the normal and aberrant regulation of gene transcription. Using 125I-labeled cAMP response element-binding protein (CREB) and activating transcription factor-2 (ATF-2) recombinant peptides to probe Western blots of HeLa nuclear extracts, we have identified multiple separate nuclear factors that form specific protein-protein interactions with these leucine zipper-containing transcriptional regulatory proteins. The interaction is specific because preincubation of blots with cold homologous protein blocks the binding of labeled protein, whereas preincubation of blots with cold heterologous protein has no effect on labeled protein interactions. Although these studies focus on two specific transactivators, CREB and ATF-2, the approach is of general use for the study of other leucine zipper-containing mammalian transcription factors. Furthermore, in addition to allowing the detection of protein-protein interactions of CREB and ATF-2 with nuclear factors, we have used this strategy to isolate cDNA clones expressing these nuclear proteins. We demonstrate that CREB will form heterodimers with ATF-1, but not ATF-2, Jun, Fos, or C/EBP whereas, ATF-2 will form heterodimers with Jun and Fos, but not with C/EBP or ATF-1. This strategy, therefore, allows a systematic approach to identifying, characterizing, and cloning proteins involved in the control of eukaryotic transcriptional regulation. The identification and characterization of the components of eukaryotic transcription complexes will allow studies that address the molecular mechanisms of normal and abnormal control of cellular gene expression.
In Situ Measurement of Cl- Concentrations and pH at the Reinforcing Steel/Concrete Interface by Combination Sensors (2006)

This paper presents an in situ, nondestructive method of monitoring Cl- concentrations and pH values at the steel/concrete interface. The Ag/AgCl electrodes prepared by the electrochemical anodization and the Ir/IrO2 electrodes prepared by thermal oxidation in carbonate served as Cl- concentration and pH sensors, respectively. The potentiometric response of the Ag/AgCl electrode to the logarithm of Cl- concentrations ranging from 1 x 10(-4) to 2 M in saturated Ca(OH)2 solution simulating the inner electrolytic medium of concrete shows good linearity. The Ir/IrO2 electrode also exhibits an ideal Nernstian response in the range of pH 1-14. The Ag/AgCl and Ir/IrO2 electrodes were combined into a multiplex Cl-/pH sensor, and the sensor was embedded in concrete close to the steel/concrete interface to realize an in situ and long-term measurement of Cl- concentrations and pH values. The results indicate that the combined sensor is robust and sensitive enough to in situ measure Cl- concentrations and pH quantitatively at the steel/concrete interface, which is of indispensable importance to the study of corrosion and protection of the steel in concrete.
Alpha Emitter Radium-223 and Survival in Metastatic Prostate Cancer (2013)

In this study, which was terminated for efficacy at the prespecified interim analysis, radium-223 improved overall survival. (Funded by Algeta and Bayer HealthCare Pharmaceuticals; ALSYMPCA ClinicalTrials.gov number, NCT00699751.).
IFN‐γ synergistically enhances LPS signalling in alveolar macrophages from COPD patients and controls by corticosteroid‐resistant STAT1 activation (2012)

Our results demonstrate that IFN-γ-induced STAT-1 signalling is corticosteroid resistant in AMs, and that targeting IFN-γ signalling by JAK inhibitors is a potentially novel anti-inflammatory strategy in COPD.
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment (2004)

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
Liquid and supercritical carbon dioxide as organic solvents (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLiquid and supercritical carbon dioxide as organic solventsJohn A. HyattCite this: J. Org. Chem. 1984, 49, 26, 5097–5101Publication Date (Print):December 1, 1984Publication History Published online1 May 2002Published inissue 1 December 1984https://pubs.acs.org/doi/10.1021/jo00200a016https://doi.org/10.1021/jo00200a016research-articleACS PublicationsRequest reuse permissionsArticle Views2683Altmetric-Citations306LEARN 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
Antimicrobial Activity of Lidocaine Against Bacteria Associated With Nosocomial Wound Infection (1999)

The authors characterized the in vitro antibacterial properties of clinical doses of lidocaine on isolates of a variety of bacterial pathogens commonly encountered in the setting of nosocomial wound infection (Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) as well as a number of resistant strains of methicillin-resistant S. aureus and vancomycin-resistant enterococci. Time-kill studies were carried out on bacteria exposed to various clinical concentrations of lidocaine (0%, 1%, 2%, and 4%) with and without epinephrine (1:100,000). Minimum inhibitory concentrations and minimum bactericidal concentrations were determined for some strains using a broth macrodilution method recommended by the National Committee of Clinical Laboratory Standards. Lidocaine demonstrated a dose-dependent inhibition of growth for all strains of bacteria tested. The greatest sensitivity to lidocaine was shown by gram-negative organisms; the least sensitive was S. aureus. The addition of epinephrine to the local anesthetic had no effect on the susceptibility of the bacteria to lidocaine. These observations suggest that the surgical benefit of local anesthesia may extend beyond its analgesic properties and may have a role in the prophylaxis and, in the case of methicillin- and vancomycin-resistant bacteria, the treatment of surgical wound infection, mandating a wider application of this modality.
Induction of soybean vegetative storage proteins and anthocyanins by low-level atmospheric methyl jasmonate. (1991)

Soybean seedlings were exposed to atmospheric methyl jasmonate (MJ) to determine if low levels of this compound could regulate the expression and accumulation of the vegetative storage proteins (VSPs) in soybeans. Low levels of atmospheric MJ induced the accumulation of three VSPs with molecular masses of 27 kDa, 29 kDa, and 94 kDa (vsp27, vsp29, and vsp94, respectively). Atmospheric MJ caused vsp94 to be accumulated in all above-ground organs of the seedling uniformly after just 3 days of exposure. vsp27 preferentially accumulated in shoot tips and primary leaves, whereas vsp29 preferentially accumulated in the cotyledons. In addition to these effects, MJ also induced the biosynthesis of anthocyanins in light-grown seedlings but inhibited anthocyanin biosynthesis in etiolated seedlings. It is concluded that low levels of atmospheric MJ regulate anthocyanin biosynthesis and the organspecific accumulation of VSPs in developing soybean seedlings. The organ-specific differential accumulation may reflect changes in the pattern of nitrogen partitioning between various compounds and/or organs. These results lend substance to the hypothesis that volatile MJ may act as a gaseous messenger or growth regulator in plants.
Surface modification of bisphenol A polycarbonate material by ultraviolet Nd:YVO4laser high-speed microprocessing technology (2014)

In this paper, a low-cost and high-efficiency microprocessing modification technology for the surface of bisphenol A polycarbonate (BAPC) material was achieved (in particular, from hydrophilicity to hydrophobicity) at high laser scanning speeds (600–1000 mm s − 1) and using an all-solid state, Q-switched, high-average power and nanosecond pulse Nd:YVO4 laser (355 nm wavelength). During the modification, it was found that the laser fluence and pulse width were the two main parameters affecting the modification effect. Moreover, the modification had a significant effect on the water contact angle, wetting behavior, microstructure, average roughness and chemical composition of the surface. When the laser fluences applied were low (i.e., less than the so-called critical fluence of the UV laser modification of the BAPC material), the water contact angle was found to be a little less than the original, the hydrophilicity was slightly improved, the relative content of the oxygen-containing groups (e.g. O–C and COO − ) increased, the microstructure and average roughness only had a very slight change, and the wetting behavior complied with the Wenzel regime. On the other hand, when the laser fluences applied were high, the water contact angle significantly increased, the hydrophilicity markedly decreased and the relative content of the oxygen-containing groups also increased. Here, a porous microstructure with periodical v-type grooves was generated and the average roughness had an obvious increase. In this case, the wetting behavior could be explained by the Cassie-Baxter regime, i.e., the microstructure and average roughness change played a deciding role. The reason for this might be that different laser parameters result in different material deformation and removal processes, thereby resulting in different surface chemical compositions, microstructures, roughnesses and wetting properties.
Treatment of chronic migraine with transcutaneous stimulation of the auricular branch of the vagal nerve (auricular t-VNS): a randomized, monocentric clinical trial (2015)

Treatment of chronic migraine by t-VNS at 1 Hz was safe and effective. The mean reduction of headache days after 12 weeks of treatment exceeded that reported for other nerve stimulating procedures.
Natural fiber polymer composites: A review (1999)

Natural fiber reinforced composites is an emerging area in polymer science. These natural fibers are low cost fibers with low density and high specific properties. These are biodegradable and non-abrasive. The natural fiber composites offer specific properties comparable to those of conventional fiber composites. However, in development of these composites, the incompatibility of the fibers and poor resistance to moisture often reduce the potential of natural fibers and these draw backs become critical issue. This review presents the reported work on natural fiber reinforced composites with special reference to the type of fibers, matrix polymers, treatment of fibers and fiber-matrix interface. © 1999 John Wiley & Sons, Inc. Adv in Polymer Techn 18: 351–363, 1999
The Wolff-Kishner Reaction with α-Oximinoketones1 (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Wolff-Kishner Reaction with α-Oximinoketones1Henry Rapoport and William NilssonCite this: J. Am. Chem. Soc. 1961, 83, 20, 4262–4267Publication Date (Print):October 1, 1961Publication History Published online1 May 2002Published inissue 1 October 1961https://pubs.acs.org/doi/10.1021/ja01481a039https://doi.org/10.1021/ja01481a039research-articleACS PublicationsRequest reuse permissionsArticle Views284Altmetric-Citations8LEARN 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
B-1 Cell Development: Evidence for an Uncommitted Immunoglobulin (Ig)M+ B Cell Precursor in B-1 Cell Differentiation (1998)

Murine phosphatidyl choline (PtC)-specific B cells in normal mice belong exclusively to the B-1 subset. Analysis of anti-PtC (VH12 and VH12/Vkappa4) transgenic (Tg) mice indicates that exclusion from B-0 (also known as B-2) occurs after immunoglobulin gene rearrangement. This predicts that PtC-specific B-0 cells are generated, but subsequently eliminated by either apoptosis or differentiation to B-1. To investigate the mechanism of exclusion, PtC-specific B cell differentiation was examined in mice expressing the X-linked immunodeficiency (xid) mutation. xid mice lack functional Bruton's tyrosine kinase (Btk), a component of the B cell receptor signal transduction pathway, and are deficient in B-1 cell development. We find in C57BL/ 6.xid mice that VH12 pre-BII cell selection is normal and that PtC-specific B cells undergo modest clonal expansion. However, the majority of splenic PtC-specific B cells in anti-PtC Tg/xid mice are B-0, rather than B-1 as in their non-xid counterparts. These data indicate that PtC-specific B-0 cell generation precedes segregation as predicted, and that Btk function is required for efficient segregation to B-1. Since xid mice exhibit defective B cell differentiation, not programmed cell death, these data are most consistent with an inability of PtC-specific B-0 cells to convert to B-1 and a single B cell lineage.
Angiogenic and cell survival functions of Vascular Endothelial Growth Factor (VEGF) (2005)

Vascular endothelial growth factor (VEGF) was originally identified as an endothelial cell specific growth factor stimulating angiogenesis and vascular permeability. Some family members, VEGF C and D, are specifically involved in lymphangiogenesis. It now appears that VEGF also has autocrine functions acting as a survival factor for tumour cells protecting them from stresses such as hypoxia, chemotherapy and radiotherapy. The mechanisms of action of VEGF are still being investigated with emerging insights into overlapping pathways and cross-talk between other receptors such as the neuropilins which were not previously associated with angiogenesis. VEGF plays an important role in embryonic development and angiogenesis during wound healing and menstrual cycle in the healthy adult. VEGF is also important in a number of both malignant and non-malignant pathologies. As it plays a limited role in normal human physiology, VEGF is an attractive therapeutic target in diseases where VEGF plays a key role. It was originally thought that in pathological conditions such as cancer, VEGF functioned solely as an angiogenic factor, stimulating new vessel formation and increasing vascular permeability. It has since emerged it plays a multifunctional role where it can also have autocrine pro-survival effects and contribute to tumour cell chemoresistance. In this review we discuss the established role of VEGF in angiogenesis and the underlying mechanisms. We discuss its role as a survival factor and mechanisms whereby angiogenesis inhibition improves efficacy of chemotherapy regimes. Finally, we discuss the therapeutic implications of targeting angiogenesis and VEGF receptors, particularly in cancer therapy.
Protection of oligonucleotide primers against degradation by DNA polymerase I (1987)

By use of a mutational assay employing an octadecamer with a mismatch in the center, it is shown that the introduction of phosphorothioate groups near the 5'-end can protect the mismatch against degradation by the 5'-3'-exonuclease activity of Escherichia coli DNA polymerase I. An optimal level of protection is achieved when the phosphorothioate groups are incorporated in at least the second and third internucleotidic linkages from the 5'-end. However, gel electrophoretic analysis as well as the use of an octadecamer with a mismatch closer to the 5'-end in the mutational assay reveals that degradation of the oligonucleotide is not completely blocked but only slowed down.
A Comparison of Omeprazole with Ranitidine for Ulcers Associated with Nonsteroidal Anti-inflammatory Drugs (1999)

YEOMANS, NEVILLE D.; TULASSAY, ZSOLT; JUHÁSZ, LÁSZLÓ; RÁCZ, ISTVÁN; HOWARD, JOHN M.; VAN RENSBURG, CHRISTOFFEL J.; SWANNELL, ANTHONY J.; HAWKEY, CHRISTOPHER J. FOR THE ACID SUPPRESSION TRIAL: RANITIDINE VERSUS OMEPRAZOLE FOR NSAID-ASSOCIATED ULCER TREATMENT (ASTRONAUT) STUDY GROUP Author Information
Reactions of diazenediyl compounds with pyridones: A novel [4 + 2] cycloaddition (1976)

Abstract Low temperature cycloaddition of 1,4‐phthalazinedione (2) and 4‐phenyl‐1,2,4‐triazoline‐3,5‐dione (10) with a variety of N ‐substituted pyridones affording novel azabicyclic structures is described. The structures of these compounds were confirmed by spectral analyses and hydrogenation to their dihydro derivatives.