gebhart/patrepeval huggingface dataset:
The kringle domain of urokinase-type plasminogen activator potentiates LPS-induced neutrophil activation through interaction with αVβ3 integrins (2005)

Urokinase plasminogen activator (uPA) is a serine protease that catalyzes the conversion of plasminogen to plasmin. In addition, uPA has been shown to have proinflammatory properties, particularly in potentiating lipopolysaccharide (LPS)-induced neutrophil responses. To explore the mechanisms by which uPA exerts these effects, we examined the ability of specific uPA domains to increase cytokine expression in murine and human neutrophils stimulated with LPS. Whereas the addition of intact uPA to neutrophils cultured with LPS increased mRNA and protein levels of interleukin-1beta, macrophage-inflammatory protein-2, and tumor necrosis factor alpha, deletion of the kringle domain (KD) from uPA resulted in loss of these potentiating effects. Addition of purified uPA KD to LPS-stimulated neutrophils increased cytokine expression to a degree comparable with that produced by single-chain uPA. Inclusion of the arginine-glycine-aspartic but not the arginine-glycine-glutamic peptide to neutrophil cultures blocked uPA kringle-induced potentiation of proinflammatory responses, demonstrating that interactions between the KD and integrins were involved. Antibodies to alpha(V) or beta(3) integrins or to the combination of alpha(V)beta(3) prevented uPA kringle-induced enhancement of expression of proinflammatory cytokines and also of adhesion of neutrophils to the uPA KD. These results demonstrate that the KD of uPA, through interaction with alpha(V)beta(3) integrins, potentiates neutrophil activation.
All-optical oscillator based on a single bistable vertical-cavity semiconductor optical amplifier (VCSOA) (2008)

A novel all-optical oscillator is demonstrated for the first time by employing a cascadable VCSOA inverter in a closed optical loop, which generates a self-sustained square-like waveform with ∼80ps switching time and 5:1 extinction ratio.
II. Effects on Hemostasis, Thrombosis, and Thrombolysis (1993)

The effects of plasminogen activator inhibitor-l (PAI-1) gene inactivation on hemostasis, thrombosis and thrombolysis were studied in homozygous PAI-i-deficient (PAT-I- ) mice, generated by homologous recombination in D3 embryonic stem cells. Diluted (10-fold) whole blood clots from PAI-1i-- and from PAI-1 wild type (PAI-i 1+) mice underwent limited but significantly different (P< 0.001 ) spontaneous lysis within 3 h (6±1 vs 3±1%, respectively). A 25-A1I '25-fibrin-labeled normal murine plasma clot, injected into a jugular vein, was lysed for 47±5, 66±3, and 87±7% within 8 h in PAI-1 +/+, heterozygous PAT-i-deficient (PA-i +1-), and PAT-i - mice, respectively (P = 0.002 for PAI-i 1+ vs PAI-1-i- mice). Corresponding values after pretreatment with 0.5 mg/kg endotoxin in PA-i +'+ and PAT-I- mice, were 35±5 and 91±3% within 4 h, respectively (P< 0.001).11 out of26 PA-i +'+ but only 1 out of 25 PAI-1-i- mice developed venous thrombosis (P = 0.004) within 6 d after injection of 10 or 50 ,ug endotoxin in the footpad. Spontaneous bleeding or delayed rebleeding could not be documented in PA -I - mice after partial amputation of the tail or of the caecum. Thus, disruption of the PAI-i gene in mice appears to in
Supplementary Figures 1-8 from Mesenchymal and MAPK Expression Signatures Associate with Telomerase Promoter Mutations in Multiple Cancers (2023)

&lt;p&gt;Fig. S1. Projecting the individual TERTp mutations transcriptional signatures on top of the Onco-GPS map of cellular states (Kim et al. 2017). Fig.S2. Association between the different mRNA signatures analyzed in this study. Fig S3. Expression of epithelial and mesenchymal markers in TERTp mutants (TPM) and wild-type (wt) cancer cell lines. Fig S4. CDH1 expression levels in CCLE lines. Fig S5. GABPa and GABPb1 expression by tissue type. Fig S6. Stratification of TERTp mutant cell lines in The Cancer Therapeutics Response Portal (CTRP) by BRAF status reveals inhibition of growth in the absence of BRAF mutation. Fig. S7. Representative immunoblots of TERT promoter cell lines treated with trametinib for 24 hours.&lt;/p&gt;
Design and Synthesis of a New Series of 4-Heteroarylamino-1′-azaspiro[oxazole-5,3′-bicyclo[2.2.2]octanes as α7 Nicotinic Receptor Agonists. 1. Development of Pharmacophore and Early Structure–Activity Relationship (2016)

The design and synthesis of a series of quinuclidine-containing spirooxazolidines ("spiroimidates") and their utility as α7 nicotinic acetylcholine receptor partial agonists are described. Selected members of the series demonstrated excellent selectivity for α7 over the highly homologous 5-HT<sub>3A</sub> receptor. Modification of the N-spiroimidate heterocycle substituent led to (1S,2R,4S)-N-isoquinolin-3-yl)-4'H-4-azaspiro[bicyclo[2.2.2]octane-2,5'oxazol]-2'-amine (BMS-902483), a potent α7 partial agonist, which improved cognition in preclinical rodent models.
Abetimus sodium for renal flare in systemic lupus erythematosus: Results of a randomized, controlled phase III trial (2008)

Abetimus at 100 mg/week significantly reduced anti-dsDNA antibody levels but did not significantly prolong time to renal flare when compared with placebo. Multiple positive trends in renal end points were observed in the abetimus treatment group.
High-molecular-mass lipopolysaccharides are involved in Actinobacillus pleuropneumoniae adherence to porcine respiratory tract cells (1994)

Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia. The major adhesin of A. pleuropneumoniae has been identified as the lipopolysaccharides (LPSs) (M. Bélanger, D. Dubreuil, J. Harel, C. Girard, and M. Jacques, Infect. Immun. 58:3523-3530, 1990). Using immunoelectron microscopy and flow cytometry, we showed in the present study that LPSs were well exposed at the surface of this encapsulated microorganism. Immunolocalization with porcine lung and tracheal frozen sections showed that extracted LPS bound to the lung mesenchyme and vascular endothelium and to the tracheal epithelium, respectively. Inhibition of adherence of A. pleuropneumoniae with extracted LPS was also performed with lung and tracheal frozen sections. Acid hydrolysis of LPS revealed that the active component of LPS was not lipid A but the polysaccharides. LPSs from A. pleuropneumoniae serotypes 1 and 2 were separated by chromatography on Sephacryl S-300 SF, in the presence of sodium deoxycholate, according to their molecular masses. The adherence-inhibitory activity was found in the high-molecular-mass fractions. These high-molecular-mass fractions contained 2-keto-3-deoxyoctulosonic acid and neutral sugars, and they were recognized by a monoclonal antibody directed against A. pleuropneumoniae O antigen but not recognized by a monoclonal antibody against capsular antigen.
Ceramide Is Increased in the Lower Airway Epithelium of People with Advanced Cystic Fibrosis Lung Disease (2010)

Immunoreactive ceramide is increased in the lower airway epithelium of people with advanced cystic fibrosis. Detected by mass-spectrometry ceramide species C16:0, C18:0, and C20:0 but not C22:0 are increased.
Fourier components of Type I-IR ultrafast induced fiber Bragg gratings (2007)

‘ac’ and ‘dc’ coupling coefficients are related to the Fourier spectrum of a grating’s index profile. In this study the Fourier components of ultrafast induced fiber Bragg gratings are characterized and their intensity dependence is investigated.
CHARACTERIZATION AND MODELING OF RELAXOR SINGLE CRYSTALS (2005)

ABSTRACT The engineered multi-domain features and phase transition behavior of ⟨110⟩ and ⟨001⟩ oriented relaxor PZN-4.5%PT and PMN-32%PT single crystals have been characterized and modeled. A crystal variant approach to modeling the electromechanical properties has led to the identification of engineered domain states with properties optimized for specific applications, including the large transverse piezoelectric coefficients of the ⟨110⟩ orientation and large 33-mode piezoelectric coefficients of the ⟨001⟩ orientation. Polarization switching and phase transitions under combinations of stress, electric field, and temperature loading are reported. Features of field induced phase transitions in these crystals are discussed.
Correction to: EGFR/Ras-induced CCL20 production modulates the tumour microenvironment (2021)

The article ‘EGFR/Ras-induced CCL20 production modulates the tumour microenvironment’, written by Andreas Hippe, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, Katharina Jannasch, Andor Pivarcsi, Bettina Buhren, Holger Schrumpf, Andreas Kislat, Erich Bünemann, Martin Steinhoff, Jens Fischer, Sérgio A. Lira, Petra Boukamp, Peter Hevezi, Nikolas Hendrik Stoecklein, Thomas Hoffmann, Frauke Alves, Jonathan Sleeman, Thomas Bauer, Jörg Klufa, Nicole Amberg, Maria Sibilia, Albert Zlotnik, Anja Müller- Homey and Bernhard Homey, was originally published electronically on the publisher’s internet portal on 30 June 2020 without open access. With the author(s)’ decision to opt for Open Choice the copyright of the article changed on 16 September 2021 to © The Author(s) 2021 and the article is forthwith distributed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/ licenses/by/4.0/. Open Access funding enabled and organized by Projekt DEAL.
Modeling the autocorrelation of wavelet coefficients for image denoising (2002)

The undecimated discrete wavelet transform (UDWT) is a powerful image denoising tool, well-known to perform better than orthogonal wavelets. Unlike the case of orthogonal wavelets, noise as well as signal in the UDWT domain are non-white. Because of this inter-pixel correlation, scalar operations such as thresholding do not take full advantage of the power of UDWT. In this paper, we present a model for autocorrelations in the UDWT domain, and use it in a Wiener-type denoising algorithm. This algorithm accounts for colored signal and noise, and also aims to implicitly match the directional information due to the local edges in the image.
Next-Gen<sup>3</sup>: Sequencing, Modeling, and Advanced Biofuels - Final Technical Report (2017)

Successful, scalable implementation of biofuels is dependent on the efficient and near complete utilization of diverse biomass sources. One approach is to utilize the large recalcitrant biomass fraction (or any organic waste stream) through the thermochemical conversion of organic compounds to syngas, a mixture of carbon monoxide (CO), carbon dioxide (CO2), and hydrogen (H2), which can subsequently be metabolized by acetogenic microorganisms to produce next-gen biofuels. The goal of this proposal was to advance the development of the acetogen Clostridium ljungdahlii as a chassis organism for next-gen biofuel production from cheap, renewable sources and to detail the interconnectivity of metabolism, energy conservation, and regulation of acetogens using next-gen sequencing and next-gen modeling. To achieve this goal we determined optimization of carbon and energy utilization through differential translational efficiency in C. ljungdahlii. Furthermore, we reconstructed a next-generation model of all major cellular processes, such as macromolecular synthesis and transcriptional regulation and deployed this model to predicting proteome allocation, overflow metabolism, and metal requirements in this model acetogen. In addition we explored the evolutionary significance of tRNA operon structure using the next-gen model and determined the optimal operon structure for bioproduction. Our study substantially enhanced the knowledgebaase for chemolithoautotrophs and their potential for advanced biofuel production. It provides next-generation modeling capability, offer innovative tools for genome-scale engineering, and provide novel methods to utilize next-generation models for the design of tunable systems that produce commodity chemicals from inexpensive sources.
Advanced Solar Cell with Back Side Engineering and Implanted Phosphorus Emitter (2012)

In this paper the high potential of solar cells with homogeneous implanted emitters and screen printed metallization is assessed on p-type wafers 239 cm2. A 0.8% absolute gain efficiency is achieved compared to a standard solar cell including a phosphorus diffused emitter, leading the efficiency up to 19.2%. In order to improve the solar cell efficiency, focus is placed on well known advanced PERC solar cell architecture with optimized back side passivation. The approach is to combine the surface passivation provided by a thin oxide layer grown during the post-implantation annealing process with a deposited capping silicon nitridre layer. This paper presents the influence of the silicon nitride layer content on passivation and optical properties of solar cells. Laser ablation is also studied and conditions are found to properly remove the dielectric layers without inducing silicon surface damages. Based on this development, implanted emitter and local Al-BSF with SiO2/SiNx back passivation are integrated in solar cells reaching 19.4% efficiency. The presence of a detrimental parasitic shunting effect finally highlights the importance of developing dielectric layers less positively charged to lead the way on achieving 20% efficiency.
VLSI performance metric based on minimum TCAD simulations (1996)

A new approach to performance metrology and qualification of digital VLSI processes with TCAD simulations is proposed. The method yields performance data on the system level directly from raw electrical device data obtained with a minimum set of device simulations. The key performance and qualification parameters are identified, pointing out the differences between these and traditional device performance metrics, and the methods to determine these parameters from the device data are described.
<title>Design and application of binary differencing filters</title> (1995)

For given binary image and degradation processes, an optimal mean-absolute-error translation- invariant filter can be designed via the representation of such filters as a union of morphological hit-or-miss transforms. The present paper investigates a different optimization methodology by representing translation-invariant filters as differencing filters. Rather than employing structuring templates to build the entire output image, as is done with direct hit-or- miss representation, differencing filters only employ templates that locate value flips (black-to- white or white-to-black). Differencing filters play a central role in several digital document processing tasks. It is shown how differencing filters are statistically designed and applied for image restoration and resolution conversion.
Membrane phospholipids in temperature adaptation of Candida utilis: alterations in fatty acid chain length and unsaturation (1997)

The effect of decreasing environmental temperature on membrane phospholipids (PL), the neutral lipid (NL) composition, and their fatty acid profiles was studied in exponentially growing Candida utilis from 40 to 10 degrees C, at intervals of 5-9 centigrade degrees. According to the results, fatty acid unsaturation increased with decreasing growth temperature from 40 to 26-20 degrees C, due to the increase in PL containing the most unsaturated fatty acid, linolenic acid (mp. -11.3 to -12.8 degrees C). Concomitantly, an equal (phosphatidylcholine, PC; phosphatidylethanolamine, PE) or more pronounced (phosphatidylinositol and phosphatidylserine, PI + PS) decrease occurred in fatty acids with lower unsaturation and, consequently, the cellular fatty acid content decreased as the temperature was reduced from 40 to 26-20 degrees C. In addition, when the temperature decreased within the lower growth temperature range from 26-20 to 10 degrees C, the fatty acid chain length also shortened in PL, due to the increase in palmitoleic acid (mp. 0 degrees C), and equal (PC and PE) or more pronounced (PI + PS) decrease in other acids. Concomitantly, triacylglycerols accumulated as the temperature decreased from 26-20 to 10 degrees C. Thus, the results showed that C. utilis can adapt cellular membranes to decreases in the environmental temperature so that fatty acid unsaturation increases down to 26-20 degrees C, and t temperatures below that the fatty acid chain length also shortens.
Bevacizumab (Avastin), a humanized anti-VEGF monoclonal antibody, alone reduces the growth rate of gastric cancer cell line, MKN45, in nude mice (2006)

242 Gastric cancer is the second commonest cancer worldwide. Angiogenesis, the process of new blood vessel development, is a key-step in tumor metastasis. We aim to investigate the growth inhibitory effect of bevacizumab, a humanized anti-VEGF monoclonal antibody, on gastric cancer cell line, MKN45. This anti-angiogenic drug targets and binds to VEGF, a mediator in vessel development, and has been used in combination with chemotherapy as a first-line treatment in colon cancer. In this study, fifteen 4 to 6 weeks old female nude mice were randomized into 3 groups. MKN45 cells were injected subcutaneously. Until tumor developed, the control group was injected with 0.9 % normal saline. The low dose arm was administered at a dose of 5 mg/kg and the high dose arm was 10 mg/kg of bevacizumab once weekly. The change in tumor volume and body weight of the nude mice were inspected and recorded daily. We showed that bevacizumab significantly reduced the growth rate of MKN45 on nude mice. The average tumor net weight of the control, low dose and high dose group were 1.56 g, 0.54 g and 1.02 g respectively. The tumor weight of the low dose and high dose group were only 34.6 % and 65 % respectively of the control. The increase in tumor volume of the control, low dose and high dose group was 649 %, 179 % and 49.7 % respectively. Therefore, the use of anti-vascular drug, bevacizumab, has demonstrated the growth inhibitory effect on MKN45 growth in nude mice. Therefore, the use of bevacizumab alone in blocking VEGF ligand may become a potential therapeutic against gastric cancer.
Forward Λ production and nuclear stopping power ind+Aucollisions atsNN=200GeV (2007)

We report the measurement of \ensuremath{\Lambda} and $\overline{\ensuremath{\Lambda}}$ yields and inverse slope parameters in $d+\mathrm{Au}$ collisions at $\sqrt{{s}_{\mathit{NN}}}=200$ GeV at forward and backward rapidities ($y=\ifmmode\pm\else\textpm\fi{}2.75$), using data from the STAR forward time projection chambers. The contributions of different processes to baryon transport and particle production are probed exploiting the inherent asymmetry of the $d+\mathrm{Au}$ system. Comparisons to model calculations show that baryon transport on the deuteron side is consistent with multiple collisions of the deuteron nucleons with gold participants. On the gold side, HIJING-based models without a hadronic rescattering phase do not describe the measured particle yields, while models that include target remnants or hadronic rescattering do. The multichain model can provide a good description of the net baryon density in $d+\mathrm{Au}$ collisions at energies currently available at the BNL Relativistic Heavy Ion Collider, and the derived parameters of the model agree with those from nuclear collisions at lower energies.
Additive anti-tumor effect of Avastin and Immunotoxin combination therapy on tumor-bearing mouse models (2005)

4989 Avastin (Bevacizumab; Genentech, South San Francisco, CA) is a human mAb against VEGF-A. Avastin slows or prevents blood vessel growth and thereby inhibits tumor growth. Avastin has been approved for the treatment of colon cancer and is being tested in other cancers. Additionally, the combination of the Avastin and chemotherapy in nude mice with human cancer xenografts shows an increased activity compared with chemotherapy alone or antibody alone. Because tumor penetration is an essential step in immunotoxin action and Avastin affects capillary density and function, we investigated the effect of combining Avastin with immunotoxins. Mice bearing human tumor xenografts (A431/K5 expressing mesothelin or CA46 Burkitt’s lymphoma expressing CD22) were treated with 1. Avastin (5 mg/ kg i.p. 2 times/week for 1 week), 2. immunotoxin (SS1P, 0.2 mg/ kg QOD x 3 for A431/K5 or HA22, 0.2 mg/ kg QOD x 3 for CA46, or 3. a combination of immunotoxin plus Avastin. Mice were implated with tumors subcutaneously and treated began on day 7. In the A431/K5 model, mice treated with the Avastin plus SS1P exhibited significantly reduced mean tumor volumes compared with mice treated with the control (88.8 mm3 vs. 1,715 mm3 at day 17, P
Cluster-like resistive switching of SrTiO3:Nb surface layers (2013)

The understanding of the resistive switching mechanisms in perovskites is of particular importance for the development of novel non-volatile memories. Nanoscale investigations recently revealed that in the model material SrTiO 3 a filamentary type of switching is present. In this paper, we show that upon donor doping with Nb the switching type changes fundamentally. We report on the observation of conducting clusters that can be switched independently between a high resistance and a low resistance state when applying a voltage. Furthermore, we show that the resistive switching takes place in a semiconducting surface layer on top of the metallic bulk of SrTiO3:Nb single crystals, which can change its properties easily under external gradients. Based on various measurements, we postulate that ionic movements leading to the creation of secondary phases as nano-filaments between the clusters have to be taken into account in modelling the resistive switching.
Silica-induced Chronic Inflammation Promotes Lung Carcinogenesis in the Context of an Immunosuppressive Microenvironment (2013)

The association between inflammation and lung tumor development has been clearly demonstrated. However, little is known concerning the molecular events preceding the development of lung cancer. In this study, we characterize a chemically induced lung cancer mouse model in which lung cancer developed in the presence of silicotic chronic inflammation. Silica-induced lung inflammation increased the incidence and multiplicity of lung cancer in mice treated with N-nitrosodimethylamine, a carcinogen found in tobacco smoke. Histologic and molecular analysis revealed that concomitant chronic inflammation contributed to lung tumorigenesis through induction of preneoplastic changes in lung epithelial cells. In addition, silica-mediated inflammation generated an immunosuppressive microenvironment in which we observed increased expression of programmed cell death protein 1 (PD-1), transforming growth factor-β1, monocyte chemotactic protein 1 (MCP-1), lymphocyte-activation gene 3 (LAG3), and forkhead box P3 (FOXP3), as well as the presence of regulatory T cells. Finally, the K-RAS mutational profile of the tumors changed from Q61R to G12D mutations in the inflammatory milieu. In summary, we describe some of the early molecular changes associated to lung carcinogenesis in a chronic inflammatory microenvironment and provide novel information concerning the mechanisms underlying the formation and the fate of preneoplastic lesions in the silicotic lung.