gebhart/patrepeval huggingface dataset:
Ultra-Low Density Aerogel Mirror Substrates (1993)

Abstract : Despite the extremely low density and the hence low weight of aerogel materials, the applicability of these materials to reflective applications has had little attention due to the high porosities exhibited by the materials. This high porosity yields an intrinsically rough but uniform surface topology for aerogel of density in the low hundreds of milligrams per cubic centimeter and a fractal surface geometry for lower density aerogel (densities of the order of tens of milligrams per cubic centimeter). This paper presents new results of aerogel materials used as ultra-light substrates for reflective coatings by way of surface machining, polishing and planarization prior to metalization, and the optical characterization thereof. This paper presents a significant advance in the ability to polish and subsequently apply a thin film coating to low density aerogel materials, thus yielding ultra lightweight mirrors. The effects of ionizing radiation upon the aerogel heterostructures are found to be remarkably minimal up to a threshold of 35 Mrad y-ray irradiation. An exponential correlation was found to predict radiation effects at high y-doses.
Precision of Multiple Reaction Monitoring Mass Spectrometry Analysis of Formalin-Fixed, Paraffin-Embedded Tissue (2012)

We compared the reproducibility of multiple reaction monitoring (MRM) mass spectrometry-based peptide quantitation in tryptic digests from formalin-fixed, paraffin-embedded (FFPE) and frozen clear cell renal cell carcinoma tissues. The analyses targeted a candidate set of 114 peptides previously identified in shotgun proteomic analyses, of which 104 were detectable in FFPE and frozen tissue. Although signal intensities for MRM of peptides from FFPE tissue were on average 66% of those in frozen tissue, median coefficients of variation (CV) for measurements in FFPE and frozen tissues were nearly identical (18-20%). Measurements of lysine C-terminal peptides and arginine C-terminal peptides from FFPE tissue were similarly reproducible (19.5% and 18.3% median CV, respectively). We further evaluated the precision of MRM-based quantitation by analysis of peptides from the Her2 receptor in FFPE and frozen tissues from a Her2 overexpressing mouse xenograft model of breast cancer and in human FFPE breast cancer specimens. We obtained equivalent MRM measurements of HER2 receptor levels in FFPE and frozen mouse xenografts derived from HER2-overexpressing BT474 cells and HER2-negative Sum159 cells. MRM analyses of 5 HER2-positive and 5 HER-negative human FFPE breast tumors confirmed the results of immunohistochemical analyses, thus demonstrating the feasibility of HER2 protein quantification in FFPE tissue specimens. The data demonstrate that MRM analyses can be performed with equal precision on FFPE and frozen tissues and that lysine-containing peptides can be selected for quantitative comparisons, despite the greater impact of formalin fixation on lysine residues. The data further illustrate the feasibility of applying MRM to quantify clinically important tissue biomarkers in FFPE specimens.
Improved self‐healing properties of collagen using polyurethane microcapsules containing reactive diisocyanate (2016)

Abstract Collagen is a natural polymer much available as a waste material. However, a more extensive use of collagen as an engineering material is restricted due to its low mechanical strength. This work presents a collagen–microcapsules system and evaluates the hypothesis that a self‐healing ability can be imposed on a collagen matrix to improve its tensile strength. Collagen films containing various types of microcapsules were studied using tensile tests ( TTs ). To evaluate the self‐repairing capacity of the developed system, samples were submitted to a 20% strain (to develop micro‐cracks in the material that could lead to the rupture of microcapsules and release of diisocyanate) and then left to stand for 20 min. A new TT was performed, named paused tensile test ( PTT ). The samples of pure collagen underwent no alteration with respect to their mechanical properties comparing TT and PTT results. In contrast, some samples containing microcapsules presented an increase of around 70% in mechanical strength when compared with the pure collagen results, proving that the released diisocyanates were effective in reacting with collagen and improving its mechanical strength. This type of behavior and the observed enhanced property can extend the usage of collagen to a variety of engineering applications. © 2016 Society of Chemical Industry
Regulation of Epidermal Growth Factor Receptor Signaling by Endocytosis and Intracellular Trafficking (2001)

Ligand activation of the epidermal growth factor receptor (EGFR) leads to its rapid internalization and eventual delivery to lysosomes. This process is thought to be a mechanism to attenuate signaling, but signals could potentially be generated after endocytosis. To directly evaluate EGFR signaling during receptor trafficking, we developed a technique to rapidly and selectively isolate internalized EGFR and associated molecules with the use of reversibly biotinylated anti-EGFR antibodies. In addition, we developed antibodies specific to tyrosine-phosphorylated EGFR. With the use of a combination of fluorescence imaging and affinity precipitation approaches, we evaluated the state of EGFR activation and substrate association during trafficking in epithelial cells. We found that after internalization, EGFR remained active in the early endosomes. However, receptors were inactivated before degradation, apparently due to ligand removal from endosomes. Adapter molecules, such as Shc, were associated with EGFR both at the cell surface and within endosomes. Some molecules, such as Grb2, were primarily found associated with surface EGFR, whereas others, such as Eps8, were found only with intracellular receptors. During the inactivation phase, c-Cbl became EGFR associated, consistent with its postulated role in receptor attenuation. We conclude that the association of the EGFR with different proteins is compartment specific. In addition, ligand loss is the proximal cause of EGFR inactivation. Thus, regulated trafficking could potentially influence the pattern as well as the duration of signal transduction.
Cell Surface-Associated Lipoteichoic Acid Acts as an Adhesion Factor for Attachment of Lactobacillus johnsonii La1 to Human Enterocyte-Like Caco-2 Cells (1999)

The influence of pH on the adhesion of two Lactobacillus strains to Caco-2 human intestinal cells was investigated. One strain, Lactobacillus johnsonii La1, was adherent at any pH between 4 and 7. The other one, L. acidophilus La10, did not attach to this cell line under the same experimental conditions. On the basis of these results, we used the monoclonal antibody technique as a tool to determine differences on the surface of these bacteria and to identify a factor for adhesion. Mice were immunized with live La1, and the hybridomas produced by fusion of spleen cells with ONS1 cells were screened for the production of antibodies specific for L. johnsonii La1. A set of these monoclonal antibodies was directed against a nonproteinaceous component of the L. johnsonii La1 surface. It was identified as lipoteichoic acid (LTA). This molecule was isolated, chemically characterized, and tested in adhesion experiments in the same system. The adhesion of L. johnsonii La1 to Caco-2 cells was inhibited in a concentration-dependent way by purified LTA as well as by L. johnsonii La1 culture supernatant that contained LTA. These results showed that the mechanism of adhesion of L. johnsonii La1 to human Caco-2 cells involves LTA.
<title>Bend-enhanced fiber optic sensors in a teleoperation application</title> (1994)

Bend enhanced fiber (BEF) sensors are curvature-measuring optical analogs of elongation- measuring resistance strain gauges. They are made by treating optical fibers to have an optically absorptive zone along a thin axial stripe a few millimeters long. Light transmission through the fiber past this zone then becomes a robust function of curvature, three orders of magnitude more sensitive to bending than in the untreated fiber. Directionality and polarity of curvature are preserved in the light transmission function, over a linear range covering five orders of magnitude, centered about zero curvature. This paper describes a project in which BEF sensors were used to improve teleoperation of a small mobile robot, by instrumenting joint angles, an extension, and four forces. The operator, who formerly had only a televised view from a camera on the robot, now has additional information on a computer screen showing these parameters in graphical form. This information, provided entirely from fiber optic sensors, makes it considerably easier to manipulate the robot. The project also included demonstrations of a multiplexing system for larger BEF arrays, use of BEF sensors in prosthetics, and plasma enhanced chemical vapor deposition of a light absorptive coating on BEF sensors.
Serum‐free suspension cultivation of PER.C6® cells and recombinant adenovirus production under different pH conditions (2002)

PER.C6(R) cell growth, metabolism, and adenovirus production were studied in head-to-head comparisons in stirred bioreactors under different pH conditions. Cell growth rate was found to be similar in the pH range of 7.1-7.6, while a long lag phase and a slower growth rate were observed at pH 6.8. The specific consumption rates of glucose and glutamine decreased rapidly over time during batch cell growth, as did the specific lactate and ammonium production rates. Cell metabolism in both infected and uninfected cultures was very sensitive to culture pH, resulting in dramatic differences in glucose/glutamine consumption and lactate/ammonium production under different pH conditions. It appeared that glucose metabolism was suppressed at low pH but the efficiency of energy production from glucose was enhanced. Adenovirus infection resulted in profound changes in cell growth and metabolism. Cell growth was largely arrested under all pH conditions, while glucose consumption and lactate production were elevated post virus infection. Virus infection induced a reduction in glutamine consumption at low pH but an increase at high pH. The optimal pH for adenovirus production was found to be 7.3 under the experimental conditions used in the study. Deviations from this optimum resulted in significant reductions of virus productivity. The results indicate that culture pH is a very critical process parameter in PER.C6(R) cell culture and adenovirus production.
β‐Glucans and Dectin‐1 (2008)

beta-Glucans are naturally occurring carbohydrates that possess immune-modulating activities, but their mechanisms of action are largely unknown. Recent discoveries, however, including identification of beta-glucan receptors, such as dectin-1, have started to shed some light on the mechanisms underlying the properties of these carbohydrates. The characterization of dectin-1, in particular, has revealed some of the processes involved in beta-glucan sensing, intracellular signaling, and induction of cellular responses and has provided new insights into the role of beta-glucans in immunity and disease. Here we review both beta-glucans and their receptor, dectin-1.
Preclinical evaluation of the penciclovir analog 9-(4-[(18)F]fluoro-3-hydroxymethylbutyl)guanine for in vivo measurement of suicide gene expression with PET. (2001)

These results indicate that [(18)F]FHBG may yield high-contrast PET images of HSV-tk expression in tumors and, therefore, it is a very promising radiotracer for monitoring of gene therapy of cancer with PET.
Thebaine Synthase: A New Enzyme in the Morphine Pathway in Papaver Somniferum (2007)

Along the poppy morphine biosynthetic pathway, the transition from salutaridinol-7-O-acetate to thebaine had previously been claimed to proceed non-enzymatically between pH 8–9. At pH 6–7, the acetate was transformed to an azonine derivative. These transformation reactions were revisited using Papaver somniferum protein extracts in search for a possible protein catalyst. After removal of residues and inhibitory low molecular weight compounds from the latex of P. somniferum, this latex serum was shown to convert salutaridinol-7-O-acetate to thebaine in high yield at the physiological pH of 7.0. A new enzyme, which was partly purified, was shown to catalyze this reaction and was partly characterized. As a result, a further enzymatic step had to be added to the morphine pathway in the poppy plant, involved in the transformation of 2 moles L-tyrosine to one mole of morphine.
CD40 Agonists Alter Tumor Stroma and Show Efficacy Against Pancreatic Carcinoma in Mice and Humans (2011)

Immunosuppressive tumor microenvironments can restrain antitumor immunity, particularly in pancreatic ductal adenocarcinoma (PDA). Because CD40 activation can reverse immune suppression and drive antitumor T cell responses, we tested the combination of an agonist CD40 antibody with gemcitabine chemotherapy in a small cohort of patients with surgically incurable PDA and observed tumor regressions in some patients. We reproduced this treatment effect in a genetically engineered mouse model of PDA and found unexpectedly that tumor regression required macrophages but not T cells or gemcitabine. CD40-activated macrophages rapidly infiltrated tumors, became tumoricidal, and facilitated the depletion of tumor stroma. Thus, cancer immune surveillance does not necessarily depend on therapy-induced T cells; rather, our findings demonstrate a CD40-dependent mechanism for targeting tumor stroma in the treatment of cancer.
Vaccine adjuvant materials for cancer immunotherapy and control of infectious disease (2015)

Adjuvants can be defined as pharmacological and immunological components that are able to modify and/or enhance antigen-specific immune responses. Based on the interdisciplinary research between immunology and material science/engineering, various vaccine adjuvant materials have been developed. By rational design and engineering of antigen or adjuvant materials, immune-modulatory vaccine systems generated to activate immune system. Here, we review the current progress of bioengineered prophylactic and/or therapeutic vaccine adjuvant for cancer and/or infectious disease, and discuss the prospect of future vaccine adjuvant materials.
Laparoscopic Palomo Varicocele Ligation in Children and Adolescents (2002)

Purpose: To assess laparoscopic high spermatic cord interruption (Palomo ligation) in children and adolescents with varicoceles. Patients and Methods: Between 1994 and 2000, all patients with surgical indications for varicocele correction were offered the traditional choices of annual observation, radiologic occlusion, or surgical interruption using open (suprainguinal, inguinal, subinguinal/high scrotal) or laparoscopic venous interruption (LVI). Thirty eight patients chose LVI and are the subject of this analysis. Results: Patient ages ranged from 10 to 18 years (mean 14.6 years). The operating time was 18 to 52 minutes (mean 28 minutes). In three patients, adhesions were lysed laparoscopically, but otherwise, no ancillary procedures were performed. No intraoperative or early complications related to the surgical procedure were encountered. All operations were performed as day surgical cases, except one. The patients were off oral narcotics and back to full activity within 48 hours of the surgery. At 3- and 12-month follow-up, there were no recurrent/persistent varicoceles. All testes that were initially smaller than the contralateral gonad either demonstrated catch-up growth or remained stable in size. Two patients (5%) developed ipsilateral secondary hydroceles, one of which required surgical correction. Conclusions: Laparoscopic venous interruption is a rapid, effective, and safe method to treat varicoceles in young males. Given all therapeutic options, it appears that, given informed consent, LVI is an attractive alternative to traditional techniques in most males in the adolescent and peripubertal age groups. As with the open Palomo technique, hydrocele is a bothersome complication that may necessitate a second surgical procedure. This risk must be discussed preoperatively.
Induction of a Cross-Reactive CD8+T Cell Response following Foot-and-Mouth Disease Virus Vaccination (2010)

Foot-and-mouth disease virus (FMDV) causes a highly contagious infection in cloven-hoofed animals. Current inactivated FMDV vaccines generate short-term, serotype-specific protection, mainly through neutralizing antibody. An improved understanding of the mechanisms of protective immunity would aid design of more effective vaccines. We have previously reported the presence of virus-specific CD8(+) T cells in FMDV-vaccinated and -infected cattle. In the current study, we aimed to identify CD8(+) T cell epitopes in FMDV recognized by cattle vaccinated with inactivated FMDV serotype O. Analysis of gamma interferon (IFN-γ)-producing CD8(+) T cells responding to stimulation with FMDV-derived peptides revealed one putative CD8(+) T cell epitope present within the structural protein P1D, comprising residues 795 to 803 of FMDV serotype O UKG/2001. The restricting major histocompatibility complex (MHC) class I allele was N*02201, expressed by the A31 haplotype. This epitope induced IFN-γ release, proliferation, and target cell killing by αβ CD8(+) T cells, but not CD4(+) T cells. A protein alignment of representative samples from each of the 7 FMDV serotypes showed that the putative epitope is highly conserved. CD8(+) T cells from FMDV serotype O-vaccinated A31(+) cattle recognized antigen-presenting cells (APCs) loaded with peptides derived from all 7 FMDV serotypes, suggesting that CD8(+) T cells recognizing the defined epitope are cross-reactive to equivalent peptides derived from all of the other FMDV serotypes.
Human plasmacytoid predendritic cells activate NK cells through glucocorticoid-induced tumor necrosis factor receptor-ligand (GITRL) (2006)

Plasmacytoid dendritic cell precursors (pDCs) are professional type I interferon-producing cells, a critical cell type in regulating innate and adaptive immune responses. By microarray gene expression analysis, we found that pDCs activated by virus or CpG-ODN preferentially express the ligand for the glucocorticoid-induced tumor necrosis factor receptor (GITRL), which was confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR) and flow cytometry analysis. Using the same approaches, we found GITR is expressed by activated natural killer (NK) cells and T cells. We show that pDCs activated by CpG-ODN promote NK cell cytotoxicity and interferon (IFN)-gamma production through type I IFNs and GITRL. Using a GITRL-transfected cell line, we further demonstrate that GITRL promotes NK cell cytotoxicity and IFN-gamma production in synergy with interleukin-2 (IL-2), IFN-alpha, and NKG2D triggering. We also demonstrated that pDCs localized in close contact to NK cells in T-cell areas of the tonsils, and a subpopulation of the pDCs expressed GITRL. This study reveals a novel function of GITR/GITRL in pDC-mediated coactivation of NK cells.
Interferon γ, IL2, IL4, IL10 and TNFα Secretions in Multiple Sclerosis Patients Treated with an Anti-CD4 Monoclonal Antibody (1999)

In order to better understand the mechanisms of action of a monoclonal anti-CD4/BF5 antibody(mAb), cytokine secretions were studied in 14 multiple sclerosis (MS) patients treated in a phase 1 trial. Secretion patterns of IFNgamma, IL2, IL4, IL10 and TNFalpha by peripheral blood mononuclear cells were studied before (DO) and after (D30) the treatment. We decided to undertake this study because in a previous one we observed no variations in serum levels of TNFalpha, IFNgamma, IL1, IL6. Results showed significant reductions in IFNgamma, IL2 and TNFalpha secretions after treatment. The anti-CD4 mAb seemed to act on both Th1- and Th2-cells but with preferential action on Th1-cells. Results on Th2-cells were less obvious even though a significant decrease in IL10 was observed. There was no correlation between any of the immunological markers studied and disease activity. This study demonstrates that pharmacological modifications of the CD4 receptor can induce variations in several cytokine secretion levels. It also stresses the role played by Th1- and Th2-cells in the etiopathogenesis of MS.
EXTRACTION OF DRUM TRACKS FROM POLYPHONIC MUSIC USING INDEPENDENT SUBSPACE ANALYSIS (2003)

The analysis and separation of audio signals into their original components is an important prerequisite to automatic transcription of music, extraction of metadata from audio data, and speaker separation in video conferencing. In this paper, a method for the separation of drum tracks from polyphonic music is proposed. It consists of an Independent Component Analysis and a subsequent partitioning of the derived components into subspaces containing the percussive and harmonic sustained instruments. With the proposed method, different samples of popular music have been analyzed. The results show sufficient separation of drum tracks and non-drum tracks for subsequent metadata extraction. Informal listening tests prove a moderate audio quality of the resulting audio signals. 1.1. Motivation 1.
Inhibition of heparanase activity and heparanase‐induced angiogenesis by suramin analogues (2003)

Heparanase, a heparan sulfate-specific endo-beta-D-glucuronidase, plays an important role in tumor cell metastasis through the degradation of extracellular matrix heparan sulfate proteoglycans (ECM HSPG). Heparanase activity correlates with the metastatic propensity of tumor cells. Suramin, a polysulfonated naphthylurea, is an inhibitor of heparanase with suramin analogues shown to possess antiangiogenic and antiproliferative properties. We investigated the effects of selected suramin analogues (NF 127, NF 145 and NF 171) on heparanase activity and heparanase-driven angiogenesis. Studies of the ability of cellular extracts and purified heparanase from human, highly invasive and brain-metastatic melanoma (70W) cells revealed that heparanase expressed by these cells was effectively inhibited by suramin analogues in a dose-dependent manner. These analogues possessed more potent heparanase inhibitory activities than suramin: The concentrations required for 50% heparanase inhibition (IC(50)) were 20-30 microM, or at least 2 times lower than that for suramin. One hundred percent inhibition was observed at concentrations of 100 microM and higher. Of relevance, these compounds significantly decreased (i) the invasive capacity of human 70W cells by chemoinvasion assays performed with filters coated with purified HSPG or Matrigel trade mark, and (ii) blood vessel formation by in vivo angiogenic assays, thus linking their antiangiogenic properties with impedance of heparanase-induced angiogenesis. Specifically, inhibition of invasion by NF 127, NF 145 and NF 171 was found at 10 microM concentrations of compounds with a significant decrease of invasive values at concentrations as low as 1.5 microM. In addition, NF 127, NF 145 and NF 171 promoted nearly complete inhibition of heparanase-induced angiogenesis at values ranging from 236 microM (for NF 145) to 362 microM (for NF 127). These results further emphasize the importance of heparanase in invasive and angiogenic mechanisms and the potential clinical application of heparanase inhibitors such as suramin analogues in cancers and angiogenesis-dependent diseases.