gebhart/patrepeval huggingface dataset:
Determination of Thrombopoietin‐Derived Peptides Recognized by Both Cellular and Humoral Immunities in Healthy Donors and Patients with Thrombocytopenia (2005)

Thrombopoietin (TPO) is a cytokine that promotes megakaryocytopoiesis and thrombopoiesis and is considered a drug suitable for patients with thrombocytopenia. However, unexpected severe thrombocytopenia has developed in some healthy individuals participating in phase I clinical trials with a pegylated recombinant human megakaryocyte growth factor (PEG-rHuMGDF) that contained the first 163 amino acids of endogenous TPO, which resulted in hampering the further development of clinical trials. Autoimmune responses to PEG-rHuMGDF, which cross-reacted with endogenous TPO, were suggested to be involved in this rare but severe adverse event, although the immunogenic epitopes have not yet been determined. To better understand the molecular basis of such autoimmune reactions, we investigated the reactivity of 18 TPO-derived peptides with HLA-A2-binding motifs to plasma and T cells, both from patients with thrombocytopenia (n=24) and from healthy donors (HDs) (n=24). Four peptides, including those possessing amino acids in receptor-binding sites, were preferentially reactive to plasma from at least 20% of the patients, whereas one peptide at position 101-109 was equally reactive to those of the patients and the HDs. Each of the five peptides had the ability to induce peptide-specific cytotoxic T lymphocytes (CTLs) in both groups, albeit with less frequency among the patients. More important, each of these five peptides had the ability to induce HLA-A2-restricted and peptide-specific CTL activity reactive to cells that produce TPO. These results may provide new insights to gain a better understanding of autoimmune reactions to TPO.
PAPR and other measures for OFDM systems with nonlinearity (2003)

In this paper, we discuss the effects of nonlinearity on the performance in transmission of OFDM signals. Furthermore, we study measures related to nonlinearities, such as PAPR (peak-to-average-power-ratio), with respect to their ability to correctly predict the effect of a nonlinearity in an OFDM system. We also propose new measures for signal distortion in nonlinear systems. The performance of the measures are studied using several examples.
The Oligosaccharide Side Chain on Asn-135 of α-Antithrombin, Absent in β-Antithrombin, Decreases the Heparin Affinity of the Inhibitor by Affecting the Heparin-Induced Conformational Change (1997)

The beta-form of antithrombin, lacking a carbohydrate side chain on Asn-135, is known to bind heparin more tightly than the fully glycosylated alpha-form. The molecular basis for this difference in affinity was elucidated by rapid-kinetic studies of the binding of heparin and the antithrombin-binding heparin pentasaccharide to plasma and recombinant forms of alpha- and beta-antithrombin. The dissociation equilibrium constant for the first step of the two-step mechanism of binding of both heparin and pentasaccharide to alpha-antithrombin was only slightly higher than that for the binding to the beta-form. The oligosaccharide at Asn-135 thus at most moderately interferes with the initial, weak binding of heparin to alpha-antithrombin. In contrast, the rate constant for the conformational change induced by heparin and pentasaccharide in the second binding step was substantially lower for alpha-antithrombin than for beta-antithrombin. Moreover, the rate constant for the reversal of this conformational change was appreciably higher for the alpha-form than for the beta-form. The carbohydrate side chain at Asn-135 thus reduces the heparin affinity of alpha-antithrombin primarily by interfering with the heparin-induced conformational change. These and previous results suggest a model in which the Asn-135 oligosaccharide of alpha-antithrombin is oriented away from the heparin binding site and does not interfere with the first step of heparin binding. This initial binding induces conformational changes involving extension of helix D into the adjacent region containing Asn-135, which are transmitted to the reactive-bond loop. The resulting decreased conformational flexibility of the Asn-135 oligosaccharide and its close vicinity to the heparin binding site destabilize the activated relative to the native conformation. This effect results in a higher energy for inducing the activated conformation in alpha-antithrombin, leading to a decrease in heparin binding affinity.
Modulo scheduling for the TMS320C6x VLIW DSP architecture (1999)

Digital Signal Processing (DSP) architectures are specialized for high performance numerical algorithms such as those found in communication and multimedia applications. The development of efficient compilers for DSP processors is a growing research area. The Texas Instruments TMS320C6x (C6x) is a Very Long Instruction Word (VLIW) DSP architecture capable of issuing eight operations in parallel. In this paper, we present the results of implementing a software pipelining algorithm for the C6x. We provide a description of the C6x and detail the architectural features that impact software pipelining such as a moderately sized register file, constraints on code size, homogeneous resources, and multiple assignment code. We discuss how we adapted modulo scheduling to implement software pipelining for the C6x. Finally, we present the results of modulo scheduling a set of 40 loop kernel benchmarks and measure the algorithm in terms of schedule quality and algorithm complexity.
Modeling key pathological features of frontotemporal dementia with C9ORF72 repeat expansion in iPSC-derived human neurons (2013)

The recently identified GGGGCC repeat expansion in the noncoding region of C9ORF72 is the most common pathogenic mutation in patients with frontotemporal dementia (FTD) or amyotrophic lateral sclerosis (ALS). We generated a human neuronal model and investigated the pathological phenotypes of human neurons containing GGGGCC repeat expansions. Skin biopsies were obtained from two subjects who had >1,000 GGGGCC repeats in C9ORF72 and their respective fibroblasts were used to generate multiple induced pluripotent stem cell (iPSC) lines. After extensive characterization, two iPSC lines from each subject were selected, differentiated into postmitotic neurons, and compared with control neurons to identify disease-relevant phenotypes. Expanded GGGGCC repeats exhibit instability during reprogramming and neuronal differentiation of iPSCs. RNA foci containing GGGGCC repeats were present in some iPSCs, iPSC-derived human neurons and primary fibroblasts. The percentage of cells with foci and the number of foci per cell appeared to be determined not simply by repeat length but also by other factors. These RNA foci do not seem to sequester several major RNA-binding proteins. Moreover, repeat-associated non-ATG (RAN) translation products were detected in human neurons with GGGGCC repeat expansions and these neurons showed significantly elevated p62 levels and increased sensitivity to cellular stress induced by autophagy inhibitors. Our findings demonstrate that key neuropathological features of FTD/ALS with GGGGCC repeat expansions can be recapitulated in iPSC-derived human neurons and also suggest that compromised autophagy function may represent a novel underlying pathogenic mechanism.
Isothermal titration calorimetry (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsothermal titration calorimetryErnesto Freire, Obdulio L. Mayorga, and Martin StraumeCite this: Anal. Chem. 1990, 62, 18, 950A–959APublication Date (Print):September 1, 1990Publication History Published online22 September 2008Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ac00217a002https://doi.org/10.1021/ac00217a002research-articleACS PublicationsRequest reuse permissionsArticle Views11429Altmetric-Citations461LEARN 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
Development and Validation of Endogenous Reference Genes for Expression Profiling of Medaka (Oryzias latipes) Exposed to Endocrine Disrupting Chemicals by Quantitative Real-Time RT-PCR (2006)

The quantitative real-time reverse transcription polymerase chain reaction (Q-RT-PCR) technique has been increasingly used in endocrine disrupting chemicals (EDCs) research. Usually, an appropriate endogenous control gene is critical for Q-RT-PCR to normalize the errors and sample-to-sample variations that occur in the course of tissue collection, RNA isolation, and RT-PCR. In this study, we cloned ribosomal protein L7 (RPL-7) from medaka (Oryzias latipes), and then used Q-RT-PCR to study its transcription characteristics and those of glyceraldehyde-3-phosphate dehydrogenase, β-actin, mitochondrial 16S ribosomal RNA (16S rRNA), and 18S rRNA. Of the five genes, RPL-7 and 18S rRNA were expressed with the less variance among the same tissue samples, in different tissues, and stages of development and were unaffected by EDCs exposure. The expression levels of RPL-7 among different tissues were between 9.76 × 106 ± 9.49 × 105 and 1.39 × 107 ± 1.69 × 106 copies/μg RNA but those of 18S rRNA were as high as 4.48 × 1011 ± 5.95 × 1010 to 5.90 × 1011 ± 1.21 × 1010 copies/μg RNA, which is above the usual detection scope of Q-RT-PCR if no complementary DNA reaction dilution is performed. As a result, RPL-7 is the single suitable endogenous control gene for expression profiling in future studies, especially in studies on the EDCs issue using medaka.
Antiviral CD4+ memory T cells are IL-15 dependent (2007)

Survival and intermittent proliferation of memory CD4(+) and CD8(+) T cells appear to be controlled by different homeostatic mechanisms. In particular, contact with interleukin (IL)-15 has a decisive influence on memory CD8(+) cells, but not memory CD4(+) cells. Past studies of memory CD4(+) cells have relied heavily on the use of naturally occurring memory phenotype (MP) cells as a surrogate for antigen (Ag)-specific memory cells. However, we show here that MP CD4(+) cells contain a prominent subset of rapidly proliferating major histocompatibility complex (MHC) II-dependent cells. In contrast, Ag-specific memory CD4 cells have a slow turnover rate and are MHC II independent. In irradiated hosts, these latter cells ignore IL-15 and expand in response to the elevated levels of IL-7 in the lymphopenic hosts. In contrast, in normal nonlymphopenic hosts where IL-7 levels are low, memory CD4 cells are heavily dependent on IL-15. Significantly, memory CD4(+) responsiveness to endogenous IL-15 reflects marked competition from other cells, especially CD8(+) and natural killer cells, and increases considerably after removal of these cells. Therefore, under normal physiological conditions, homeostasis of CD8(+) and CD4(+) memory cells is quite similar and involves IL-15 and IL-7.
Motility, Proliferation and Egress of Human AML Cells in Transplanted NOD/SCID Mice Are Regulated by Membrane Bound and Secreted Elastase. (2004)

Abstract Neutrophil -or leukocyte- elastase is a serine protease stored in azurophilic granules of myeloid cells and is released upon activation and degranulation. Elastase degrades a number of extracellular matrix proteins as well as various cytokines and their receptors and may facilitate neutrophil motility. Lately, others and we have shown that elastase is also involved in G-CSF induced mobilization of stem cells. In the present study we examined the role of elastase in motility and proliferation of leukemic AML cells. We demonstrate a correlation between abnormal high levels of secreted elastase in the peripheral blood plasma of AML patients and the number of leukemic blast cells in the circulation. Interestingly, we found that AML cells not only secrete elastase, but also express constitutively membrane-bound elastase on their cell surface. Confocal microscopy revealed uniform localization of elastase on the cell surface. Of note, incubation of some AML cells with the chemokine SDF-1 increased elastase cell surface expression whereas treatment with neutralizing anti CXCR4 Abs decreased it. Pretreatment of primary human AML cells and cell lines with various elastase inhibitors and neutralizing anti elastase Abs led to reduced spontaneous and SDF-1-induced transwell migration of the leukemic cells. In vivo homing of AML mononuclear cells and CD34-enriched progenitors cells to the BM and spleen of transplanted NOD/SCID/B2mnull mice was significantly impaired by elastase inhibition. Moreover, when leukemic AML cells were pretreated with elastase inhibitors, the formation of spontaneous and SDF-1 induced protrusions was prevented suggesting that elastase participates in leukemic cell motility through direct regulation of cytoskeletal rearrangements and cell polarization. In addition, we found that the proliferation rate of AML cells was likewise elastase-dependent. In contrast, treatment of enriched human cord blood CD34+ progeniotrs with elastase inhibitors enhanced their proliferation rate, the percentage of undifferentiated CD34+/38− cells and their in vivo homing to the BM and spleen of immune deficient mice. Finally, we examined whether elastase may play a role in the abnormal AML cell egress from the BM to the circulation. Primary AML cells from different patients with different FAB subtypes were injected into sublethally irradiated NOD/SCID mice to establish human AML chimeras and 3–4 weeks later elastase inhibitor (1mg) was administrated daily for 4 consecutive days. Egress of AML cells to the blood circulation including blast cells was significantly decreased as compared to untreated chimeric mice. Taken together, these results demonstrate that elastase participates in the regulation of human AML progenitor cell proliferation and cell emigration from the BM to the circulation and that elastase inhibition can efficiently prevent AML cell egress in NOD/SCID chimeric mice.
Estimating friction using incipient slip sensing during a manipulation task (2002)

A scheme is presented by which a manipulator can use dynamic tactile sensing to detect when it is about to lose hold of a grasped object. By detecting localized slips on the gripping surface which precede gross slip, the controller can modify the grasp force to prevent the object from slipping. Also, by monitoring normal and tangential forces at the contact when these incipient slip signals occur, the controller obtains an accurate estimate of the friction coefficient which can then be used during the manipulation task. Accurate knowledge of the friction coefficient is essential when grasping fragile objects or manipulating with sliding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression and Imaging of Connexin-GFP Chimeras in Live Mammalian Cells (2003)

Gap junction (GJ) proteins, connexins (Cx), possess many properties that are atypical of other well-characterized integral membrane proteins (). Oligomerization of Cxs into hemichannels (connexons) has been shown to occur after the protein exits the endoplasmic reticulum (). Once delivered to the cell surface, connexons from one cell dock with connexons from a neighboring cell and cluster into GJ plaques, a process that is facilitated by cadherins (). Connexins have short half-lives and GJs are turned over rapidly (). To study GJ formation, removal, and connexin intracellular trafficking in real time, we recently used the green fluorescent protein (GFP) as a fusion partner to construct Cx-GFP chimeras (see Fig. 1). Open image in new window Fig 1. Schematic diagram of the pEGFP vector containing the Cx43 insert. The Cx43 is fused in-frame to the N-terminal domain of GFP.
A Highly Enantioselective Hetero-Diels−Alder Reaction of Aldehydes with Danishefsky's Diene Catalyzed by Chiral Titanium(IV) 5,5‘,6,6‘,7,7‘,8,8‘-Octahydro-1,1‘-bi-2-naphthol Complexes (2002)

The catalytic effect of chiral Lewis acids on the hetero-Diels-Alder reaction between aldehydes and Danishefsky's diene (1) has been investigated. A variety of combinations of different ligands and Lewis acids have been examined as catalysts for the hetero-Diels-Alder reaction between benzaldehyde and 1, and it has been found that the readily accessible Ti(IV)-H(8)-BINOL (TiHBOL) complex is a very effective catalyst for the reaction, leading to products with very high enantioselectivity (up to 99% ee) and yield (92%). The hetero-Diels-Alder reaction of other aldehydes with 1 under the catalysis of TiHBOL is a general reaction which proceeds well with very high enantioselectivity and isolated yield for various aldehydes at 0 degrees C to room temperature. Based on the experimental results, the proposed mechanism of the hetero-Diels-Alder reaction and the dihedral angle effects of ligands are discussed.
Enantioselective Brønsted Base Catalysis with Chiral Cyclopropenimines (2012)

Cyclopropenimines are shown to be a highly effective new class of enantioselective Brønsted base catalysts. A chiral 2,3-bis(dialkylamino)cyclopropenimine catalyzes the rapid Michael reaction of a glycine imine substrate with high levels of enantioselectivity. A preparative scale reaction to deliver 25 g of product is demonstrated, and a trivial large scale synthesis of the optimal catalyst is shown. In addition, the basicity of a 2,3-bis(dialkylamino)cyclopropenimine is measured for the first time and shown to be approximately equivalent to the P(1)-tBu phosphazene base. An X-ray crystal structure of the protonated catalyst is shown along with a proposed mechanistic and stereochemical rationale.
The Alveolar Macrophage (2004)

Keywords: 15-hydroxyeicosatetraenoic acid, 15-HETE; airway hyperresponsiveness, AHR; alveolar macrophage, AM; interferon-γ, IFN-γ; interleukin, IL; macrophage, mφ; nitric oxide, NO; prostaglandin E2, PGE2; peroxisome proliferator activated receptor, PPAR; helper T lymphocyte, Th
Noiseless coding of correlated information sources (1973)

Correlated information sequences <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\cdots ,X_{-1},X_0,X_1, \cdots</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\cdots,Y_{-1},Y_0,Y_1, \cdots</tex> are generated by repeated independent drawings of a pair of discrete random variables <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X, Y</tex> from a given bivariate distribution <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P_{XY} (x,y)</tex> . We determine the minimum number of bits per character <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_X</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_Y</tex> needed to encode these sequences so that they can be faithfully reproduced under a variety of assumptions regarding the encoders and decoders. The results, some of which are not at all obvious, are presented as an admissible rate region <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\mathcal{R}</tex> in the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_X - R_Y</tex> plane. They generalize a similar and well-known result for a single information sequence, namely <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R_X \geq H (X)</tex> for faithful reproduction.
Y and blood group B type 2 glycolipid antigens accumulate in a human gastric carcinoma cell line as detected by monoclonal antibody. Isolation and characterization by mass spectrometry and NMR spectroscopy. (1987)

A monoclonal antibody (mAb), BR55-2, was generated from mice immunized with MCF-7 human breast carcinoma cells. This mAb specifically detected glycolipids with the Y determinant Fuc alpha 1----2Gal beta 1----4GlcNAc(3----1 alpha Fuc)-beta 1----3Gal beta 1----4Glc beta 1----1 Cer and the Y-related B-active difucosylated determinant Gal alpha 1----3Gal(2----1 alpha Fuc) beta 1----4GlcNAc(3----1 alpha Fuc) beta 1----3Gal beta 1----4Glc beta 1----1 Cer, but was not reactive with related monofucosylated glycolipids of type 2 chain (X-antigen, blood group H), type 1 chain (Lea antigen, blood group H and B) or with difucosylated type 2 and type 1 chain structures (A blood group antigen or blood group B and Leb, respectively). A series of glycolipids with Y and blood group B type 2 determinants were detected in human gastric adenocarcinoma cell line KATO III with mAb BR55-2 and with a previously characterized anti-blood group B mAb PA83-52 (Hansson, G. C., Karlsson, K.-A., Larson, G., McKibbin, J. M., Blaszczyk, M., Herlyn, M., Steplewski, Z., and Koprowski, H. (1983) J. Biol. Chem. 258, 4091-4097). The isolated antigens were structurally characterized by mass spectrometry of permethylated and permethylated-reduced derivatives and by proton NMR spectroscopy. In a chromatogram binding assay, mAb BR55-2 and mAb PA83-52 detected minor components with slower mobility than the Y-6 and blood group B-7-type 2 structures. The detection of a B type 2 determinant is the first chemical evidence for the presence of an autologous difucosyl blood group B type 2 antigen in human adenocarcinoma cells.
Recovering Dielectric Loss of Low Dielectric Constant Organic Siloxane during the Photoresist Removal Process (2002)

The interaction between low dielectric constant (low-k) hybrid organic siloxane polymer (HOSP) and plasma ashing has been investigated. plasma ashing is commonly performed to remove the photoresist (PR) during integrated circuit fabrication. However, dielectric loss usually occurs in the HOSP films during the PR removal process. In order to eliminate dielectric loss originating from an plasma attack, hexamethyldisilazane (HMDS) treatment is proposed to repair the damage in the HOSP film. HMDS can react with Si-OH bonds and reduce moisture uptake. Moreover, the leakage current and the dielectric constant is decreased significantly when damaged HOSP film undergoes HMDS treatment. For this reason, HMDS treatment is a promising method to apply to the photoresist removal. © 2002 The Electrochemical Society. All rights reserved.
BlySfulness Does Not Equal Blissfulness in Systemic Lupus Erythematosus: A Therapeutic Role for BLyS Antagonists (2004)

B lymphocyte stimulator (BLyS) is a vital B cell survival factor. Constitutive overexpression of BLyS in mice can lead to systemic lupus erythematosus (SLE)-like disease. Mice which naturally develop SLE harbor elevated circulating levels of BLyS, and treatment of these mice with BLyS antagonists ameliorates disease progression and enhances survival. In human SLE, BLyS overexpression is also common. Results from a phase-I clinical trial in human SLE with a neutralizing anti-BLyS monoclonal antibody have shown the antagonist to be biologically active and safe. These features collectively point to BLyS and/or its receptors as attractive therapeutic targets in human SLE.