gebhart/patrepeval huggingface dataset:
Full-length Vpu and human CD4(372–433) in phospholipid bilayers as seen by magic angle spinning NMR (2013)

HIV-1 Vpu and CD4(372-433), a peptide comprising the transmembrane and cytoplasmic domain of human CD4, were recombinantly expressed in Escherichia coli, uniformly labeled with 13C and 15N isotopes, and separately reconstituted into phospholipid bilayers. Highly resolved dipolar cross-polarization (CP)-based solid-state NMR spectra of the two transmembrane proteins were recorded under magic angle sample spinning. Partial assignment of 13C resonances was achieved. Site-specific assignments were obtained for 13 amino acid residues of CD4(372-433) and two Vpu residues. Additional amino acid type-specific assignments were achieved for 10 amino acid spin systems for both CD4(372-433) and Vpu. Further, structural flexibility was probed with different dipolar recoupling techniques, and the correct insertion of the transmembrane domains into the lipid bilayers was confirmed by proton spin diffusion experiments.
Improving single-ended channel performance with a dynamic reference voltage scheme (2009)

For high-speed signaling, differential channels are now commonly used because of the improved noise immunity and receiver sensitivity that can be achieved compared to the single-ended channels that had been widely used in electronic systems until recently. However, single-ended channels have the distinct advantage of only needing one signal trace per signal, which in a well-controlled impedance, low-noise environment can provide equivalent bandwidth per pin at a lower silicon area and lower power demand than differential signals. To provide an effective low-noise environment for the receiver threshold tolerance, a power noise compensation scheme consisting of a dynamic forwarded reference voltage, is proposed. This improves the overall performance of the Elastic Interface (El) bus (Berger et al., 2007), a single-ended high speed signaling technology used in IBM systems. We explore the range of voltage differences that could be observed at the transmit and receive circuits and how those differences can be mitigated to enhance the performance of the system. Simulations for channels with varying voltage characteristics confirm the anticipated performance improvement.
Asynchronous near-far resistant DS-CDMA receivers without a priori synchronization (1999)

Several receivers for data demodulation in an asynchronous direct-sequence code-division multiple access (DS-CDMA) system operating without prior knowledge of the propagation delays are proposed and compared. Special attention is paid to the near-far problem, and the proposed schemes are numerically shown to be near-far resistant. The near-far resistance is obtained by estimating the a priori unknown propagation delay using a subspace-based technique. Quantities obtained in the estimation procedure are used to design a filter used for suppression of interference, according to the minimum mean square error criterion. Either a decision feedback technique or a simple two-state Viterbi algorithm is subsequently used for the data demodulation in the uncoded case. By extending the trellis used in the Viterbi algorithm, error correcting coding is easily implemented.
Abstract IA18: Molecular signatures of circulating tumor cells (2020)

Abstract Circulating tumor cells (CTCs) are shed from primary cancers, as well as from metastatic deposits, into the blood circulation, where they may travel either as single cells or as CTC clusters, facing both mechanical and oxidative stress. Only a small subset of CTCs remain sufficiently viable to initiate metastatic growth upon dissemination to distant organs; their detection in patients with localized invasive cancer may present an opportunity for early detection, while their analysis in advanced cases provides a “whole cell biomarker,” enabling single-cell DNA, RNA, and protein studies, as well as functional drug-sensitivity testing using cultured CTCs. We have applied microfluidic technologies to deplete normal hematopoietic cells from blood specimens of patients with cancer, enhancing the ability of unmanipulated CTCs to proliferate ex vivo and recapitulating features of metastatic-competent cancer cells. Cultured CTCs from patients with either breast cancer or melanoma are highly tumorigenic when injected orthotopically at low inoculum into immunosuppressed mice. However, they display sensitivity to ROS and appear to upregulate compensatory mechanisms that are not commonly observed in primary tumors. In addition, they may undergo prolonged dormancy when lodged within distant organs. By combining single-cell RNA seq of patient-derived CTCs together with CRISPR and other genome-wide screens for modulators of metastasis phenotypes, we have sought to identify novel vulnerabilities in these cellular initiators of metastasis. While CTCs transit only very briefly through the blood circulation, these exceptional conditions may present new therapeutic opportunities to suppress the metastatic recurrence of cancer. Citation Format: Daniel Haber, Xin Hong, Richard Ebright, Doug Micalizi, Aditya Bardia, Ryan Sullivan, Mehmet Toner, Shyamala Maheswaran. Molecular signatures of circulating tumor cells [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr IA18.
The Renewable Energy (RE) Industry Workforce Needs: RE Simulation and Analysis Tools Teaching as an Effective Way to Enhance Undergraduate Engineering Students’ Learning (2021)

The share of renewables in the U.S. electricity generation mix is increasing and one of the major obstacles to enhancing employment in the renewable energy (RE) sector is finding skilled/qualified labor to fill positions. RE systems engineer jobs mostly need bachelor’s degrees but there are few RE engineering-focused degree programs. Therefore, there are needs to accurately train undergraduate engineering students at universities and match the education system offerings to meet RE industry demands. This study reviews RE employment by technology, RE industry workforce needs, and engineering programs accreditation, and then suggests possible means, along with theoretical RE concepts, to enhance undergraduate engineering students’ RE learning at universities. In particular, RE industries require technology skills, including analytical, scientific, and simulation software programs or tools. These RE simulation and analysis tools can be used for teaching, training, techno-economic analysis, planning, designing, optimization, etc., and are the focus of this review.
Collisional quenching and depolarization of NO2 A 2B2 state fluorescence as studied by Zeeman quantum beat spectroscopy (1984)

We have studied the effect of collisions on the time-resolved fluorescence arising from a single optically selected fine structure level (F1303) of the Ã 2B2 state of NO2 prepared via absorption near 5933 Å in the presence of a weak magnetic field. The fluorescence modulation induced by the magnetic field (Zeeman quantum beats) is used to monitor the time dependence of the alignment. The alignment decays exponentially and follows simple Stern–Volmer kinetics. The incoherent fluorescence intensity, used to determine population information, fits well a bi-exponential form at nonzero pressure. This is interpreted by a simple kinetic scheme involving cascade to additional fluorescing states. We find that only about 15% of the population removed from the initial level by collision produces subsequent emission that is detected (630–830 nm). We are unable to identify the exact nature of these emitting states. However, it is clear that pure rotationally inelastic collisions do not dominate the energy transfer process. Collisional population and alignment relaxation rate constants for the optically prepared level have been measured for excited state collisions with He, Ne, Ar, Kr, Xe, N2, CO, and NO2 at 295 K and low density (&amp;lt;1×1015 particle/cm3). In particular, we find that the rate for population removal of the initially excited level by collision is faster than the rate for elastic disalignment (depolarization within the same rotational level).
Stimulation of cardiac cardiolipin biosynthesis by PPARα activation (2004)

The role of peroxisome proliferator-activated receptor alpha (PPARalpha)-stimulated phospholipase A2 (PLA2) in cardiac mitochondrial cardiolipin (CL) biosynthesis was examined in both in vivo and in vitro models. Treatment of rat heart H9c2 cells with clofibrate increased the expression and activity of 14 kDa PLA2 but did not affect the pool size of CL. Clofibrate treatment stimulated de novo CL biosynthesis via an increase in phosphatidylglycerolphosphate (PGP) synthase activity, accounting for the unaltered CL content. Cardiac PLA2, PGP synthase, and CDP-1,2-diacyl-sn-glycerol synthase (CDS-2) activities and CDS-2 mRNA levels were elevated in mice fed clofibrate for 14 days compared with controls. In PPARalpha-null mice, clofibrate feeding did not alter cardiac PLA2, PGP synthase activities, or CDS-2 activity and mRNA level, confirming that these enzymes are regulated by PPARalpha activation. In contrast to mouse heart, clofibrate treatment did not affect the activity or mRNA levels of CDS-2 in H9c2 cells, indicating that CDS-2 is regulated differently in rat heart H9c2 cells in vitro and in mouse heart in vivo. These results clearly indicate that cardiac CL de novo biosynthesis is stimulated by PPARalpha activation in responsive rodent models and that CDS-2 is an example of an enzyme that exhibits alternative regulation in vivo and in cultured cell lines. This study is the first to demonstrate that CL de novo biosynthesis is regulated by PPARalpha activation.
Rapid Three‐Dimensional MAS NMR Spectroscopy at Critical Sensitivity (2010)

Mehrdimensionale NMR-Spektroskopie mit stichprobenhafter Datenaufnahme (non-uniform sampling, NUS) eignet sich auch für die wenig empfindliche MAS-NMR-Spektroskopie von Biomakromolekülen. Durch Spektroskopie unter Integration der Information aus Frequenz- und Zeitdomäne (SIFT) können 3D-MAS-NMR-Experimente ohne Verlust an Empfindlichkeit und Auflösung deutlich schneller ausgeführt werden (3.4-fach im Beispiel).
Pattern formation in an incoherent cavity (2003)

We report the first experimental observation of pattern-formation in a nonlinear cavity for which the circulating light is both spatially and temporally incoherent. The pattern-formation process is associated with two consecutive thresholds: one when self-focusing overcomes diffraction and the other when feedback overcomes losses.
Hydrodynamics of a self-propelled flexible fin near the ground (2017)

Many animals in nature experience hydrodynamic benefits by swimming near the ground. Inspired by near-ground swimmers, a flexible fin flapping near the ground was modeled in a two-dimensional Cartesian coordinate system. The transverse heaving motion was prescribed at the leading edge and the posterior part of the fin fluttered passively under the fin–fluid interaction. The fin freely moved horizontally in a quiescent flow, which dynamically determined the swimming speed. The fluid–flexible fin interaction was considered by using an immersed boundary method. The fin could swim up to 14% faster near the ground than in the bulk fluid, and the vortices in the wake moved away from the ground. The body kinematics was passively altered by flapping near the ground, and the trailing edge amplitude decreased as the ground proximity increased. The benefits or penalties in the thrust and the power input by swimming near the ground were not only the direct results of the hydrodynamic changes, but also the indirect results of the altered body kinematics. The thrust was enhanced by approximately 37% and the power input increased by about 17% at the ground proximity of 1.5, which were the pure results of the hydrodynamic changes near the ground. The flexible fin could generate more thrust near the ground with a smaller penalty in the power input, leading to the enhancement of the Froude propulsive efficiency by about 17%.
Successful Treatment of Metastatic Renal Cell Carcinoma With a Nonmyeloablative Allogeneic Peripheral-Blood Progenitor-Cell Transplant: Evidence for a Graft-Versus-Tumor Effect (1999)

The complete regression of metastatic disease, which has now been maintained for more than 1 year, is compatible with a graft-versus-tumor effect.
The Expression of Functional Vpx during Pathogenic SIVmac Infections of Rhesus Macaques Suppresses SAMHD1 in CD4+ Memory T Cells (2015)

For nearly 20 years, the principal biological function of the HIV-2/SIV Vpx gene has been thought to be required for optimal virus replication in myeloid cells. Mechanistically, this Vpx activity was recently reported to involve the degradation of Sterile Alpha Motif and HD domain-containing protein 1 (SAMHD1) in this cell lineage. Here we show that when macaques were inoculated with either the T cell tropic SIVmac239 or the macrophage tropic SIVmac316 carrying a Vpx point mutation that abrogates the recruitment of DCAF1 and the ensuing degradation of endogenous SAMHD1 in cultured CD4+ T cells, virus acquisition, progeny virion production in memory CD4+ T cells during acute infection, and the maintenance of set-point viremia were greatly attenuated. Revertant viruses emerging in two animals exhibited an augmented replication phenotype in memory CD4+ T lymphocytes both in vitro and in vivo, which was associated with reduced levels of endogenous SAMHD1. These results indicate that a critical role of Vpx in vivo is to promote the degradation of SAMHD1 in memory CD4+ T lymphocytes, thereby generating high levels of plasma viremia and the induction of immunodeficiency.
Antisense Inhibition of Gene Expression: A Tool for Studying the Role of NMYC in the Growth and Differentiation of Neuroectoderm-Derived Cells (1992)

To understand the role of individual genes in regulating biological processes, one must be able to interfere specifically with either their expression or function. While monoclonal antibodies have proven very useful in studying cell surface proteins, the specific inhibition of intracellular proteins in viable cells is a much more difficult problem. The goal of antisense technology is to develop small oligonucleotides, plasmids, or retroviral vectors that can be introduced easily into viable cells in order to inhibit gene products specifically. In this report, we will describe our use of antisense DNA and RNA to study the role of the NMYC proto-oncogene in neuroectodermal cell growth and differentiation.
Antenne 3D multisecteurs à base d'antennes Vivaldi verticales (2007)

International audience
High-energy collision-induced dissociation with Fourier transform mass spectrometry (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh-energy collision-induced dissociation with Fourier transform mass spectrometryD. L. Bricker, T. A. Adams, and D. H. RussellCite this: Anal. Chem. 1983, 55, 14, 2417–2418Publication Date (Print):December 1, 1983Publication History Published online1 May 2002Published inissue 1 December 1983https://pubs.acs.org/doi/10.1021/ac00264a048https://doi.org/10.1021/ac00264a048research-articleACS PublicationsRequest reuse permissionsArticle Views112Altmetric-Citations22LEARN 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
One Step Lithography of Polypyrrole (2011)

Abstract Large areas of polypyrrole (PPy) thin films deposited onto inert polymeric substrates are structured by direct laser interference patterning (DLIP). Several square millimeter areas could be produced with one single (10 ns) pulse, at room temperature and atmospheric pressure. Nanometric arrays of lines (&gt;600 nm) or grids of PPy deposited on dielectric polymers polypropilene or polypirrol (PP or PE) are fabricated by DLIP at 355 nm. The period of the lines structures, measured by white light interferometry (WLI), is 3.5 µm. Regular structures are analyzed using scanning electron microscope (SEM) and a focus ion beam (FIB) tomography. It is shown that only the PPy film is structured while the PP or PE substrate remains unaltered. Fourier transform infrared spectroscopy (FTIR) and UV‐vis spectroscopy, permit to ensure that PPy chemical structure remains unaltered after the structuration process. The width of PPy lines can be tailored by controlling the fluence of the laser beam. Contact angle measurement shows that the wettability is affected by the structuring, making the surface more hydrophobic. The structuring technique seems to be suitable for the fabrication of PPy regular structures over various substrates.
Influence of adsorbates on the piezoresponse of KNbO3 (2006)

Abstract We report on the reduction of piezoresponse in KNbO 3 originating from a surface layer. An analysis with surface sensitive measurements shows that this layer consists of chemisorbates and physisorbates. Heating the sample under ultra high vacuum conditions removes the surface layer on the perovskite to a large extend. This treatment has a drastic effect on the piezoresponse as the potential difference applied to the sample is no longer reduced by a voltage drop across the adsorbate layer, leading to a higher electric field compared to the case with an adsorbate layer. Experiments and simulations are presented confirming this postulation on KNbO 3 . (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Silymarin (milk thistle extract) as a therapeutic agent in gastrointestinal cancer (2021)

Silymarin contains a group of closely-related flavonolignan compounds including silibinin, and is extracted from Silybum marianum species, also called milk thistle. Silymarin has been shown to protect the liver in both experimental models and clinical studies. The chemopreventive activity of silymarin has shown some efficacy against cancer both in vitro and in vivo. Silymarin can modulate apoptosis in vitro and survival in vivo, by interfering with the expression of cell cycle regulators and apoptosis-associated proteins. In addition to its anti-metastatic activity, silymarin has also been reported to exhibit anti-inflammatory activity. The chemoprotective effects of silymarin and silibinin (its major constituent) suggest they could be applied to reduce the side effects and increase the anti-cancer effects of chemotherapy and radiotherapy in various cancer types, especially in gastrointestinal cancers. This review examines the recent studies and summarizes the mechanistic pathways and down-stream targets of silymarin in the therapy of gastrointestinal cancer.
GdVO4as a new medium for solid-state lasers: some optical and thermal properties of crystals doped with Cd3+, Tm3+, and Er3+ions (1995)

The refractive indices of new Nd3+ : GdVO4, Tm3+ : GdVO4, and Er3+ : GdVO4 laser crystals were determined with an error of ±5×10-5 in the range 400–1100 nm. The birefringence of these crystals was on the average 0.24, and the dispersion was described by the formula 1/Δn2 = a+ b/λ2. The thermal conductivity of the Nd : GdVO4 crystal (atomic neodymium concentration 1.3%) was determined in the temperature range 77-300 K. At 300 K the conductivity along the <110> direction was 11.7 W m-1 K-1, which was higher than the conductivity of Nd : YAG crystals.
Monolithically integrated InGaAsP/InP 1x2 SOA optical switch (2007)

This paper describes a monolithically integrated 1x2 SOA-based switch in InGaAsP/InP. It can be fabricated in one epitaxial growth step, has a footprint of only 4.2mm x 0.35mm, operates on sub-ns time scales and is meant to be integrated with other passive and active waveguide devices on the same InP substrate. The design process optimized the device dimensions using a modified finite-element modal-overlap method. This method provides significant computational savings compared to full beam-propagation method (BPM) simulations. The device uses a single-mode vertical integration technique for a monolithic integration of active and passive waveguide components. To compensate for the polarization sensitivity, tensile-strained quantum well active regions are used. To switch a signal to an output waveguide, the SOA in that waveguide is forward-biased while the SOA in the other output waveguide is reverse-biased to provide a large attenuation (>30dB), resulting in minimal crosstalk. This switch has an estimated insertion loss of 4dB, with a polarization dependent loss of < 1dB.
Immunochemical detection of cytochrome P450 enzymes in small intestine microsomes of male and female untreated juvenile cynomolgus monkeys (2014)

The expression of small intestinal cytochromes P450 (P450s) has not been systematically measured in cynomolgus monkeys, which are widely used in preclinical drug studies to predict pharmacokinetics and toxicity in humans: therefore, P450 content of small intestine was quantified in 35 cynomolgus monkeys by immunoblotting using 11 selective antibodies. CYP2D, CYP2J2, CYP3A4 and CYP3A5 were detected in all 35 animals, while CYP1A and CYP2C9/19 were detected in 31 and 17 animals, respectively. CYP2C9 and CYP2C19 were detected with the same antibody. CYP1D, CYP2A, CYP2B6, CYP2C76 and CYP2E1 were not detected in any of the 35 animals examined. On analysis of pooled microsomes (35 animals), CYP3A (3A4+3A5) was most abundant (79% of total immunoquantified CYP1-3 proteins), followed by CYP2J2 (13%), CYP2C9/19 (4%), CYP1A (3%) and CYP2D (0.4%). On the analysis of individual microsome samples, each P450 content varied 2-to-6-fold between animals, and no sex differences were observed in any P450 content. These findings should help to increase the understanding of drug metabolism, especially the first-pass effect, in cynomolgus monkey small intestines.
Questionnaire-Based Survey Conducted in 2011 concerning Endoscopic Management of Barrett’s Esophagus in East Asian Countries (2012)

Among East Asian countries, we found both similarities and differences regarding diagnosis and management of Barrett's esophagus. The findings in the present survey are helpful to understand the current situation of Barrett's esophagus in East Asian countries.
Direct Synthesis of Nano‐Ferrierite along the 10‐Ring‐Channel Direction Boosts Their Catalytic Behavior (2018)

Ferrierite zeolites with nanosized crystals and external surface areas higher than 250 m<sup>2</sup> g<sup>-1</sup> have been prepared at relatively low synthesis temperature (120 °C) by means of the collaborative effect of two organic structure directing agents (OSDA). In this way, hierarchical porosity is achieved without the use of post-synthesis treatments that usually involve leaching of T atoms and solid loss. Adjusting the synthesis conditions it is possible to decrease the crystallite size in the directions of the 8- and 10-ring channels, [010] and [001] respectively, reducing their average pore length to 10-30 nm and increasing the number of pores accessible. The small crystal size of the nano-ferrierites results in an improved accessibility of reactants to the catalytic active centers and enhanced product diffusion, leading to higher conversion and selectivity with lower deactivation rates for the oligomerization of 1-pentene into longer-chain olefins.