gebhart/patrepeval huggingface dataset:
HLA-A2.1-Associated Peptides from a Mutant Cell Line: A Second Pathway of Antigen Presentation (1992)

Peptides extracted from HLA-A2.1 class I major histocompatibility complex (MHC) molecules expressed on the antigen processing mutant CEMx721.174.T2 were characterized by electrospray ionization-tandem mass spectrometry. Only seven dominant peptides were found, in contrast to over 200 associated with HLA-A2.1 on normal cells. These peptides were derived from the signal peptide domains of normal cellular proteins, were usually larger than nine residues, and were also associated with HLA-A2.1 in normal cells. These results suggest that proteolysis of signal peptide domains in the endoplasmic reticulum is a second mechanism for processing and presentation of peptides for association with class I molecules.
PRAS40 and PRR5-Like Protein Are New mTOR Interactors that Regulate Apoptosis (2007)

TOR (Target of Rapamycin) is a highly conserved protein kinase and a central controller of cell growth. TOR is found in two functionally and structurally distinct multiprotein complexes termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2). In the present study, we developed a two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) based proteomic strategy to identify new mammalian TOR (mTOR) binding proteins. We report the identification of Proline-rich Akt substrate (PRAS40) and the hypothetical protein Q6MZQ0/FLJ14213/CAE45978 as new mTOR binding proteins. PRAS40 binds mTORC1 via Raptor, and is an mTOR phosphorylation substrate. PRAS40 inhibits mTORC1 autophosphorylation and mTORC1 kinase activity toward eIF-4E binding protein (4E-BP) and PRAS40 itself. HeLa cells in which PRAS40 was knocked down were protected against induction of apoptosis by TNFalpha and cycloheximide. Rapamycin failed to mimic the pro-apoptotic effect of PRAS40, suggesting that PRAS40 mediates apoptosis independently of its inhibitory effect on mTORC1. Q6MZQ0 is structurally similar to proline rich protein 5 (PRR5) and was therefore named PRR5-Like (PRR5L). PRR5L binds specifically to mTORC2, via Rictor and/or SIN1. Unlike other mTORC2 members, PRR5L is not required for mTORC2 integrity or kinase activity, but dissociates from mTORC2 upon knock down of tuberous sclerosis complex 1 (TSC1) and TSC2. Hyperactivation of mTOR by TSC1/2 knock down enhanced apoptosis whereas PRR5L knock down reduced apoptosis. PRR5L knock down reduced apoptosis also in mTORC2 deficient cells. The above suggests that mTORC2-dissociated PRR5L may promote apoptosis when mTOR is hyperactive. Thus, PRAS40 and PRR5L are novel mTOR-associated proteins that control the balance between cell growth and cell death.
Transformation of Primate and Rodent Cells by Temperature-sensitive Mutants of SV40 (1974)

Cells of mouse, hamster, human and monkey origin were transformed by wild-type SV40 and by temperature-sensitive mutants defective in gene A. The mutant-transformed cells appear to be temperature sensitive for maintenance of transformation. Evidence of reversion of the transformed phenotype of nonpermissive temperatures was obtained in experiments which assayed saturation density, colony formation, and uptake of 2-deoxy-D-glucose. In addition, S antigen modulated in shift experiments while T antigen did not. Based on these results, a model is presented for the mechanism of transformation by SV40.
Rapid Prototyping of Microfluidic Systems in Poly(dimethylsiloxane) (1998)

This paper describes a procedure that makes it possible to design and fabricate (including sealing) microfluidic systems in an elastomeric material [Formula: see text] poly(dimethylsiloxane) (PDMS) [Formula: see text] in less than 24 h. A network of microfluidic channels (with width >20 μm) is designed in a CAD program. This design is converted into a transparency by a high-resolution printer; this transparency is used as a mask in photolithography to create a master in positive relief photoresist. PDMS cast against the master yields a polymeric replica containing a network of channels. The surface of this replica, and that of a flat slab of PDMS, are oxidized in an oxygen plasma. These oxidized surfaces seal tightly and irreversibly when brought into conformal contact. Oxidized PDMS also seals irreversibly to other materials used in microfluidic systems, such as glass, silicon, silicon oxide, and oxidized polystyrene; a number of substrates for devices are, therefore, practical options. Oxidation of the PDMS has the additional advantage that it yields channels whose walls are negatively charged when in contact with neutral and basic aqueous solutions; these channels support electroosmotic pumping and can be filled easily with liquids with high surface energies (especially water). The performance of microfluidic systems prepared using this rapid prototyping technique has been evaluated by fabricating a miniaturized capillary electrophoresis system. Amino acids, charge ladders of positively and negatively charged proteins, and DNA fragments were separated in aqueous solutions with this system with resolution comparable to that obtained using fused silica capillaries.
Retinoic acid alters the intracellular trafficking of the mannose-6-phosphate/insulin-like growth factor II receptor and lysosomal enzymes (1998)

Previously, we showed that retinoic acid (RA) binds to the mannose-6-phosphate/insulin-like growth factor II receptor (M6P/IGF2R) with high affinity, suggesting that M6P/IGF2R may be a receptor for RA. Here, we show that RA, after 2-3 h of incubation with cultured neonatal-rat cardiac fibroblasts, dramatically alters the intracellular distribution of M6P/IGF2R as well as that of cathepsin B (a lysosomal protease bearing M6P). Immunofluorescence techniques indicate that this change in intracellular distribution is characterized by a shift of the proteins from the perinuclear area to cytoplasmic vesicles. The effect of RA was neither blocked by an RA nuclear receptor antagonist (AGN193109) nor mimicked by a selective RA nuclear-receptor agonist (TTNPB). Furthermore, the RA-induced translocation of cathepsin B was not observed in M6P/IGF2R-deficient P388D1 cells but occurred in stably transfected P388D1 cells expressing the receptor, suggesting that the effect of RA might be the result of direct interaction with M6P/IGF2R, rather than the result of binding to the nuclear receptors. These observations not only support the idea that M6P/IGF2R mediates an RA-response pathway but also indicate a role for RA in control of intracellular trafficking of lysosomal enzymes. Therefore, our observations may have important implications for the understanding of the diverse biological effects of retinoids.
Understanding the New Liquidity Coverage Ratio Requirements (2016)

In 2014, U.S. financial regulators introduced new liquidity coverage ratio requirements for qualified banking institutions. This regulation, based on guidelines from the Basel III accord, requires that banks hold minimum levels of liquid assets to withstand a period of financial stress. It is a response to the financial crisis of 2007?08, during which many banks found themselves suddenly cut off from short-term funding. But the impact of liquidity requirements remains an area of ongoing debate and economic research.
Prevalence of Cognitive Impairment without Dementia in the United States (2008)

Cognitive impairment without dementia is more prevalent in the United States than dementia, and its subtypes vary in prevalence and outcomes.
Potential Role of Fibroblast Growth Factor in Enhancement of Fracture Healing (1998)

Fibroblast growth factors are present in significant amounts in bone and several studies have suggested that they may be involved in normal fracture healing. It is well established that fibroblast growth factors have mitogenic and angiogenic activity on mesoderm and neuroectoderm derived cells. Of particular interest as a member of the fibroblast growth factor family, basic fibroblast growth factor stimulates mitogenesis, chemotaxis, differentiation, and angiogenesis. It also plays an important role in the development of vascular, nervous, and skeletal systems, promotes the maintenance and survival of certain tissues, and stimulates wound healing and tissue repair. Animal studies have shown that the direct injection of fibroblast growth factor into fresh fractures stimulates callus formation, which provides mechanical stability to the fracture, accelerates healing, and restores competence. The matrix used to present the fibroblast growth factor at the fracture site plays a critical role in the effectiveness of the treatment. The evaluation of injectable basic fibroblast growth factor in a sodium hyaluronate gel for its effectiveness in stimulating fracture healing is described. When applied directly into a freshly created fracture in the rabbit fibula, a single injection of the basic fibroblast growth factor and hyaluronan results in the stimulation of callus formation, increased bone formation, and earlier restoration of mechanical strength at the fracture site. The hyaluronan gel serves as a reservoir that sequesters the basic fibroblast growth factor at the injection site for the length of time necessary to create an environment conducive to fracture healing. It is concluded that basic fibroblast growth factor and sodium hyaluronate act synergistically to accelerate fracture healing and that the combination is suitable for clinical evaluation as a therapy in fracture treatment.
PP.31.12 (2015)

Objective: There has been no agreement among guidelines on the number of measurements of home blood pressure (BP) that should be taken on each occasion. The prognostic value of the first, second, and the difference between first and second measurements in on-treatment home BP was studied. Design and method: In the HONEST (Home blood pressure measurement with Olmesartan Naive patients to Establish Standard Target blood pressure) Study, a prospective 2-year observational study of an angiotensin receptor blocker, olmesartan-based treatment in outpatients with essential hypertension in Japan, the association between averaged home BP during follow-up period and development of cardiovascular (CV) events (stroke, myocardial infarction, coronary revascularization procedures for angina pectoris, or sudden death) was investigated in a total of 21,591 patients (mean age, 64.9 years; women, 50.6%). The patients measured home BP twice in the morning and twice at bed time. The association of the risk of major CV events with the first and second measurements, and with the difference between the first and second measurements was assessed using the Cox proportional hazard model adjusted for age, sex, and other CV risk factors. Results: A total of 280 CV events occurred (incidence, 6.46/1000 patient-years). After mean follow-up of 2.02 years, on-treatment first and second morning home BP (mean ± SD) measurements were 135.8 ± 10.9/79.1 ± 8.5 mmHg and 133.8 ± 11.1/78.4 ± 8.6 mmHg, respectively, and hazard ratios per 1-mmHg increase in systolic BP were 1.039(95% CI: 1.028 to 1.049) and 1.038 (95%CI: 1.027 to 1.049), respectively. The risk for CV events was higher in patients with a greater BP difference (> = 5 mmHg, n = 3624 or > -5 mmHg, n = 356) than those with a smaller difference (< = -5 to < 5 mmHg, n = 14,269). Conclusions: Both first and second on-treatment home BP measurements were predictive of CV events and a difference of 5 mmHg or more between first and second home BP measurements was associated with CV events.
NPPB is a novel candidate biomarker expressed by cancer‐associated fibroblasts in epithelial ovarian cancer (2014)

Most solid tumors contain cancer-associated fibroblasts (CAFs) that support tumorigenesis and malignant progression. However, the cellular origins of CAFs in epithelial ovarian cancers (EOCs) remain poorly understood, and their utility as a source of clinical biomarkers for cancer diagnosis has not been explored in great depth. Here, we report establishing in vitro and in vivo models of CAFs in ovarian cancer development. Normal ovarian fibroblasts and mesenchymal stem cells cultured in the presence of EOC cells acquired a CAF-like phenotype, and promoted EOC cell migration in vitro. CAFs also promoted ovarian cancer growth in vivo in both subcutaneous and intraperitoneal murine xenograft assays. Molecular profiling of CAFs identified gene expression signatures that were highly enriched for extracellular and secreted proteins. We identified novel candidate CAF-specific biomarkers for ovarian cancer including NPPB, which was expressed in the stroma of 60% primary ovarian cancer tissues (n = 145) but not in the stroma of normal ovaries (n = 4). NPPB is a secreted protein that was also elevated in the blood of 50% of women with ovarian cancer (n = 8). Taken together, these data suggest that the tumor stroma is a novel source of biomarkers, including NPPB, that may be of clinical utility for detection of EOC.
Combining Superdirective Beamforming and Frequency-Domain Blind Source Separation for Highly Reverberant Signals (2010)

Frequency-domain blind source separation (BSS) performs poorly in high reverberation because the independence assumption collapses at each frequency bins when the number of bins increases. To improve the separation result, this paper proposes a method which combines two techniques by using beamforming as a preprocessor of blind source separation. With the sound source locations supposed to be known, the mixed signals are dereverberated and enhanced by beamforming; then the beamformed signals are further separated by blind source separation. To implement the proposed method, a superdirective fixed beamformer is designed for beamforming, and an interfrequency dependence-based permutation alignment scheme is presented for frequency-domain blind source separation. With beamforming shortening mixing filters and reducing noise before blind source separation, the combined method works better in reverberation. The performance of the proposed method is investigated by separating up to 4 sources in different environments with reverberation time from 100&#x2009;ms to 700&#x2009;ms. Simulation results verify the outperformance of the proposed method over using beamforming or blind source separation alone. Analysis demonstrates that the proposed method is computationally efficient and appropriate for real-time processing.
Broadband Modulation of Light by Using an Electro-Optic Polymer (2002)

A major challenge to increasing bandwidth in optical telecommunications is to encode electronic signals onto a lightwave carrier by modulating the light up to very fast rates. Polymer electro-optic materials have the necessary properties to function in photonic devices beyond the 40-GHz bandwidth currently available. An appropriate choice of polymers is shown to effectively eliminate the factors contributing to an optical modulator's decay in the high-frequency response. The resulting device modulates light with a bandwidth of 150 to 200 GHz and produces detectable modulation signal at 1.6 THz. These rates are faster than anticipated bandwidth requirements for the foreseeable future.
Re-evaluation of the Involvement of the Adhesion Molecules ICAM-1/LFA-1 in Syncytia Formation of HIV-1-Infected Subclones of a CEM T-Cell Leukemic Line (1991)

The role of the adhesion molecules intercellular adhesion molecule-1 (ICAM-1) and LFA-1 in human immunodeficiency virus type 1 (HIV-1)-induced cell fusion was investigated in subclones of a T-cell leukemic cell line (CEM) with differing abilities to form syncytia. Addition of monoclonal antibodies 84H10 directed against ICAM-1 and MHM23 directed against the common beta subunit of LFA-1 (CD18) resulted in greater than 50% suppression of syncytia formation in cultures of these clones infected with cell-free virus. Two subclones, 2G5-144-84 and 2G5-1, were deficient in their ability to form syncytia and expressed reduced amounts of LFA-1 compared with the parental line. The expression of ICAM-1 but not LFA-1 was upregulated on the clones following treatment with interferon-gamma (IFN gamma); however, this did not overcome the delay in syncytia formation observed in these cells. The syncytia-positive subclones 1B11-39 and 17D-9 expressed high levels of LFA-1. Basal expression of ICAM-1 was upregulated on these cells by treatment with tumor necrosis factor-alpha (TNF alpha), which also accelerated and enhanced syncytia formation. However, anti-ICAM-1 and anti-LFA-1 (CD18) antibodies did not reverse the TNF alpha-induced enhancement of syncytia formation of HIV-1-infected clones 1B11-39 and 17D-9. Under conditions of low viral expression, adhesion molecules may contribute to syncytia formation if adequate levels of both receptor and ligand in the ICAM-1/LFA-1 complex are expressed.(ABSTRACT TRUNCATED AT 250 WORDS)
Stereoselective Syntheses of Epothilones A and B via Directed Nitrile Oxide Cycloaddition1 (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTStereoselective Syntheses of Epothilones A and B via Directed Nitrile Oxide Cycloaddition1Jeffrey W. Bode and Erick M. CarreiraView Author Information Laboratorium für Organische Chemie, ETH-Zürich Universitätstrasse 16, CH-8092 Zürich, Switzerland Cite this: J. Am. Chem. Soc. 2001, 123, 15, 3611–3612Publication Date (Web):March 23, 2001Publication History Received19 January 2001Published online23 March 2001Published inissue 1 April 2001https://pubs.acs.org/doi/10.1021/ja0155635https://doi.org/10.1021/ja0155635rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views4501Altmetric-Citations134LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Coupling reactions,Cyclization,Nitrogen compounds,Oxides,Stereoselectivity Get e-Alerts
New Architectures for Dye‐Sensitized Solar Cells (2008)

Modern dye-sensitized solar cell (DSSC) technology was built upon nanoparticle wide bandgap semiconductor photoanodes. While versatile and robust, the sintered nanoparticle architecture exhibits exceedingly slow electron transport that ultimately restricts the diversity of feasible redox mediators. The small collection of suitable mediators limits both our understanding of an intriguing heterogeneous system and the performance of these promising devices. Recently, a number of pseudo-1D photoanodes that exhibit accelerated charge transport and greater materials flexibility were fabricated. The potential of these alternative photoanode architectures for advancing, both directly and indirectly, the performance of DSSCs is explored.
Wavelength and bandwidth-tunable silicon comb filter based on Sagnac loop mirrors with Mach-Zehnder interferometer couplers (2016)

We propose and experimentally demonstrate a wavelength and bandwidth-tunable comb filter based on silicon Sagnac loop mirrors (SLMs) with Mach-Zehnder interferometer (MZI) couplers. By thermally tuning the MZI couplers in common and differential modes, the phase shift and reflectivity of the SLMs can be changed, respectively, leading to tunable wavelength and bandwidth of the comb filter. The fabricated comb filter has 93 comb lines in the wavelength range from 1535 nm to 1565 nm spaced by ~0.322 nm. The central wavelength can be red-shifted by ~0.462 nm with a tuning efficiency of ~0.019 nm/mW. A continuously tunable bandwidth from 5.88 GHz to 24.89 GHz is also achieved with a differential heating power ranging from 0.00 mW to 0.53 mW.
NMR chemical shift imaging in three dimensions. (1982)

A method for obtaining the three-dimensional distribution of chemical shifts in a spatially inhomogeneous sample using Fourier transform NMR is presented. The method uses a sequence of pulsed field gradients to measure the Fourier transform of the desired distribution on a rectangular grid in (k,t) space. Simple Fourier inversion then recovers the original distribution. An estimated signal/noise ratio of 20 in 10 min is obtained for an "image" of the distribution of a 10 mM phosphorylated metabolite in the human head at a field of 20 kG with 2-cm resolution.
Neutrophil cathepsin G increases transendothelial albumin flux. (1989)

Neutrophils are involved in the development of inflammatory edema in some animal models, but their mechanisms of action are not completely understood. Among injurious agents available for neutrophil-mediated injury are cationic proteins such as cathepsin G. Previous articles have reported that cationic agents decrease the barrier properties of the endothelium both in vivo and in vitro. Using an ex vitro isolated, perfused rabbit lung and a cultured porcine pulmonary artery endothelial cell monolayer (ENDO) as models, we asked whether neutrophil cathepsin G could decrease the barrier properties of the intact vasculature and cultured endothelial monolayers. After the addition of cathepsin G (10 micrograms/ml) to the perfusate of the isolated, perfused lung, there was a fourfold increase in net weight gain after a venous pressure challenge (p less than 0.01). The addition of cathepsin G to a cultured ENDO directly increased the movement of albumin across the monolayers in a dose-dependent fashion (10 micrograms/ml led to a 59% +/- 5% increase, 15 micrograms/ml to a 135% +/- 55% increase, 20 micrograms/ml to a 247% +/- 78% increase, and 30 micrograms/ml to a 381% +/- 89% increase, p less than 0.05 at all concentrations). Heat-inactivation of the enzyme only partially protected the ENDO, but exposure in the presence of either the polyanion heparin or the polyanion dextran sulfate completely protected the ENDO. Normal human serum also protected the ENDO, but serum from two patients with alpha 1-proteinase inhibitor (alpha 1-PI) deficiency was only partially protective. The protection afforded by human serum was time dependent, because addition of the serum 5 or 15 minutes after the addition of cathepsin G offered no protection. Oxidation of alpha 1-PI, as may occur at sites of inflammation, also destroyed its protective effect. Cytotoxic injury of the porcine pulmonary artery endothelial cell monolayer by cathepsin G, which was also prevented by the polyanions, only partially explained these results, because cathepsin G increased albumin transfer across the ENDO at concentrations of 10 to 20 micrograms/ml, which were minimally cytolytic to the ENDO. Additionally, cathepsin G caused cell retraction, with the development of intercellular gaps visible on light microscopy of the ENDO. This effect was also prevented by the polyanions. These results demonstrate that cathepsin G has direct effects on a cultured ENDO that may be caused by the charge or charged site(s) on cathepsin G.