gebhart/patrepeval huggingface dataset:
The Shelterin Component TPP1 Is a Binding Partner and Substrate for the Deubiquitinating Enzyme USP7 (2014)

The telomeric shelterin component TPP1 has critical functions in telomeric protein complex assembly and telomerase recruitment and regulation. Here we identify USP7 as a novel interacting protein of the oligonucleotide/oligosaccharide-binding fold of TPP1, which was previously known to recruit telomerase to telomeres. We identify amino acids in TPP1 and USP7 that are critical for their interaction and multiple lysines within TPP1 that are oligo-ubiquitinated and deubiquitinated by USP7. Mutational analysis indicated that human TPP1 does not require ubiquitination for telomere association in contrast to previous observations reported for mouse Tpp1. Ubiquitination of human TPP1 also had no detectable effects on known protein interactions of TPP1 with TIN2, POT1, the CTC1-STN1-TEN1 complex, and telomerase. However, the close proximity of USP7 and telomerase binding sites on TPP1 suggest possible cross-talks. In addition, we found that TPP1 is degraded in a proteasome-dependent manner. Prevention of TPP1 ubiquitination prolonged TPP1 half-life ∼ 2-fold from 45 to 90 min, and remarkably, proteasome inhibition prompted complete stability of TPP1. This indicates that the proteasome destabilizes TPP1 through both direct and indirect pathways possibly involving TPP1-interacting proteins. Altogether, our work identifies novel regulatory circuits that contribute to TPP1 stability and function.
A preliminary 3D mm wave indoor office channel model (2015)

With the ever increasing demands in higher data rate, there is a growing interest in exploiting the millimeter wave (mmWave) spectrum for future access communications. Aiming at characterizing the mmWave indoor propagation channel, a wideband measurement campaign using directional antennas has been conducted at 73 GHz in New York City in an office-type environment. In addition, ray-tracing using a database with the same environment has been performed to predict channel parameter statistics in conjunction with the measured data. A preliminary 3GPP-like 3D mmWave indoor channel model is proposed including the distance-dependent elevation model. The estimated channel characteristics such as delay spread and angular spread are validated with the measurements. The proposed channel model can be used in simulating mmWave indoor communications in office-type environments using multi-input multi-output (MIMO) antenna arrays.
Cell Surface-Binding Motifs of L2 That Facilitate Papillomavirus Infection (2003)

Human papillomavirus type 16 (HPV16) is the primary etiologic agent of cervical carcinoma, whereas bovine papillomavirus type 1 (BPV1) causes benign fibropapillomas. However, the capsid proteins, L1 and L2, of these divergent papillomaviruses exhibit functional conservation. A peptide comprising residues 1 to 88 of BPV1 L2 binds to a variety of cell lines, but not to the monocyte-derived cell line D32, and blocks BPV1 infection of mouse C127 cells. Residues 13 to 31 of HPV16 L2 and BPV1 L2 residues 1 to 88 compete for binding to the cell surface, and their binding, unlike that of HPV16 L1/L2 virus-like particles, is unaffected by heparinase or trypsin pretreatment of HeLa cells. A fusion of HPV16 L2 peptide 13-31 and GFP binds (K(d), approximately 1 nM) to approximately 45,000 receptors per HeLa cell. Furthermore, mutation of L2 residues 18 and 19 or 21 and 22 significantly reduces both the ability of the HPV16 L2 13-31-GFP fusion protein to bind to SiHa cells and the infectivity of HPV16 pseudovirions. Antibody to BPV1 L2 peptides comprising residues 115 to 135 binds to intact BPV1 virions, but fails to neutralize at a 1:10 dilution. However, deletion of residues 91 to 129 from L2 abolishes the infectivity of BPV1, but not their binding to the cell surface. In summary, L2 residues 91 to 129 contain epitopes displayed on the virion surface and are required for infection, but not virion binding to the cell surface. Upon the binding of papillomavirus to the cell surface, residues 13 to 31 of L2 interact with a widely expressed, trypsin- and heparinase-resistant cell surface molecule and facilitate infection.
Guard Ring Design and Synthesis (2011)

This chapter presents the physics of a guard ring structure, and measurement of its effectiveness. It is followed by a “top-down” design approach instead of a “bottom-up” design method. The chapter starts with full-chip domain isolation, I/O to I/O, within I/O, within ESD, and eventually within circuit elements. It then describes special guard ring structures, such as high-voltage technology, deep trench, and through silicon via (TSV) structures. The chapter ends with a guard ring design methodologies and design rule checking (DRC). Controlled Vocabulary Terms electrostatic discharge; isolation technology; silicon devices
Measurement of pseudorapidity distributions of charged particles in proton–proton collisions at $$\sqrt{s} = 8$$ s = 8 TeV by the CMS and TOTEM experiments (2014)

Pseudorapidity () distributions of charged particles produced in proton-proton collisions at a centre-of-mass energy of 8 TeV are measured in the ranges || < 2.2 and 5.3 < || < 6.4 covered by the CMS and TOTEM detectors, respectively. The data correspond to an integrated luminosity of L = 45 b -1 . Measurements are presented for three event categories. The most inclusive category is sensitive to 91-96 % of the total inelastic proton-proton cross section. The other two categories are disjoint subsets of the inclusive sample that are either enhanced or depleted in single diffractive dissociation events. The data are compared to models used to describe high-energy hadronic interactions. None of the models considered provide a consistent description of the measured distributions.
Long-mean-free-path ballistic hot electrons in high-purity GaAs (1996)

The mean free path (mfp) of hot ballistic electrons, injected into high-purity GaAs, was measured and found to be several micrometers long. The hot electrons were injected at energies just below the LO-phonon emission threshold and their mfp was measured by two techniques: first, by comparing different devices with different layer thickness; and second, in a single device, utilizing the cyclotron motion of ballistic electrons in tilted magnetic fields. We find the mfp scales roughly inversely with impurity concentration. We suggest that the dominant scattering is due to impact ionization of neutral impurities.
Comparison of two methods for ginsenosides quantitation (2023)

The present study provides a comparison of two liquid chromatography-tandem mass spectrometry methods for ginsenosides analysis. The two methods have the same liquid chromatography separation procedure, and both use tandem mass spectrometry detection. However, one method uses multiple reaction monitoring transitions commonly recommended in the literature starting with [M + Na]<sup>+</sup> as the molecular ions and with detection of specific fragment ions from the molecules M, while the other is an original method using [M + Cs]<sup>+</sup> as molecular ions and Cs<sup>+</sup> as fragment ion. The method using [M + Cs]<sup>+</sup> as molecular ion has a very high sensitivity allowing the measurement of concentrations in the injecting solutions as low as 4 ng/ml with peaks at this concentration showing signal to noise ratio of 20 or higher. The procedures were utilized for the measurement of eight ginsenosides (Rb1, Rb2, Rc, Rd, Re, Rf (S), Rg1, and Rg2), although the method using [M + Cs]<sup>+</sup> has the potential for measuring other ginsenosides. As an application, the ginsenosides were measured in several types of ginseng root, several dietary supplements containing ginseng extracts, four energy drinks, and a sample of ashwagandha.
Antibiotic Resistance Due to Reduced Uptake (2009)

The introduction of antibiotic therapy for the treatment of bacterial infections has led to a greatly increased human lifespan compared to that in the pre-antibiotic era. However, a disturbing trend has also been noted in that, within a very short period of time following the introduction of a new antibiotic, resistance to that antibiotic begins to emerge, a factor that is becoming increasingly meaningful as the discovery of new antibiotics wanes (1-3). There are a number of mechanisms by which a bacterium may become resistant to a particular antibiotic. Generally these include, but are not limited to, modifi cation of the drug to render it inactive, modifi cation of the drug target, such that it is incapable of interacting with the drug and decreased uptake of the antibiotic into the cell, due to reduced transport and/or increased effl ux. Recent functional genomic studies have also implied that antibiotics may have more complex mechanisms of action than fi rst thought and we are beginning to appreciate that in addition to the mutation of primary targets, subtle mutations in secondary targets are likely to be infl uential (4, 5). This chapter will focus on the contribution of a decreased antibiotic uptake to an increase in antibacterial resistance.
Dual-Band RF Circuits and Components for Multi-Standard Software Defined Radios (2012)

The advent of multi-standard and multi-band software defined radio (SDR) applications has necessitated the design and deployment of dual-band RF components and circuits considering the numerous advantages of such designs over the traditional narrow band circuits and components. For example, a dual-band power amplifier (PA) not only simplifies the hardware complexity but also provides higher reconfigurability [1] and hence makes it a front runner for deployment in SDR architectures [2][3]. Furthermore, the evolution of communication technologies demands the use of dualband/ multi-band RF circuits so as to acc ommodate many standards simultaneously for facilitating and guaranteeing the backward compatibility of future standards (such as 4 G) based system for smooth network migration and upgrades. These technological requirements have also led to commercial introduction of dual-band base stations and repeaters [4][6]. Furthermore, the advancement in CMOS and other MMIC technologies, although, is challenging the transmission line based passive circuit techniques but the high power handling ability of transmission line based circuits are potentially very useful in applications such as the design of high power/high efficiency PAs and transmitters. This article elaborates on the techniques employed in the design of transmission line based dual-band RF components in the context of multi-band/multi-mode SDR architecture, highlighting the problems which need to be addressed during the design process.
Balloon Angioplasty and Endoluminal Stenting of Clinically Significant Human Carotid Artery Occlusive Lesions: A New Model for Ex Vivo Morphological Analysis (1996)

The successful use of balloon angioplasty and intravascular stenting for the treatment of atherosclerotic lesions in the coronary and peripheral arteries has recently led to the application of these techniques to the management of carotid artery stenosis. We have, therefore, attempted to determine the local consequences of these interventions in the carotid circulation by developing an ex vivo model of simultaneous balloon angioplasty and endoluminal stenting of clinically significant human internal carotid artery occlusive lesions. The following report describes this model and discusses the related clinical issues.
Controlling light with light at the nanoscale: Backward-wave optical parametric amplification and generation in negative-index metamaterials (2009)

Negative-index (negative phase) metamaterials (NIMs) form a novel class of electromagnetic media that promises revolutionary breakthroughs in photonics [1]. A significant progress has been achieved recently in the design of bulk multilayer negative-index plasmonic structures [2–3]. The majority of NIMs realized to date consist of metal dielectric nanostructures that have highly controllable magnetic and dielectric responses. The problem, however, is that these structures have losses that are difficult to avoid, especially in the visible range of frequencies. The losses originate from a number of sources. Irrespective of their origin, losses constitute a major hurdle to the practical realization of the unique optical applications of these structures. Therefore, developing efficient loss-compensating techniques is of paramount importance. Herein, we explore the feasibility of the developing of such techniques making use the nonlinear-optical (NLO) response of the NIMs. Nonlinear optics in the NIMs remains so far a less-developed branch of optics. On a fundamental level, the NLO response of nanostructured metamaterials is not completely understood or characterized, and cannot be predicted effectively to date. Nevertheless, the fact of the local-field enhanced nonlinearities attributed to the plasmonic nanostructures is well established and some rough estimates of their magnitude can be done. The feasibility of crafting NIMs with strong NLO responses have been demonstrated in [4]. Unlike natural positive-index materials, the energy flow and the phase velocity are counter-directed in NIMs, which determines their extraordinary linear and NLO propagation properties. Counterintuitive properties of nonlinear propagation processes in NIMs, such as three-wave mixing (TWM) optical parametric amplification (OPA), second harmonic generation and changes in the optical bistability, which are in a stark contrast with their counterparts in natural materials, were shown in [5].
Primary cervical carcinoma cell lines overexpress epithelial cell adhesion molecule (EpCAM) and are highly sensitive to immunotherapy with MT201, a fully human monoclonal anti-EpCAM antibody. (2010)

Epithelial cell adhesion molecule is highly expressed in primary cervical carcinoma cell lines, and these biologically aggressive tumors are highly sensitive to MT201-mediated cytotoxicity in vitro. MT201 may represent a novel, potentially highly effective treatment option for patients with cervical carcinoma, especially for those with advanced, recurrent, or metastatic disease refractory to standard salvage therapy.
Stochastic resonance in a superconducting loop with a Josephson junction (1995)

A simple superconducting loop with a Josephson junction subject to a time-sinusoidal magnetic flux embedded in a noise background is considered. Cooperative effects, arising from the interplay between the noise and modulation are described; they manifest themselves in the response, measured as an output signal-to-noise ratio. In particular, it is shown that the response displays the stochastic resonance effect, wherein the output signal-to-noise ratio passes through a maximum at a critical value of the noise strength. A simple theory, based on the characterization of the superconducting quantum interference device as a bistable switching element, is seen to yield good qualitative agreement with the experimental results.
Multidrug Resistance-Associated Protein 2 (MRP2) Enhances 4-Hydroxynonenal-Induced Toxicity in Madin−Darby Canine Kidney II Cells (2004)

4-Hydroxy-trans-2,3-nonenal (HNE) is a toxic end product of lipid peroxidation. This multifunctional aldehyde reacts with proteins, phospholipids, and nucleic acids, consequently activating/inactivating enzymes, affecting signal transduction and gene expression. HNE is mainly detoxified by glutathione (GSH) conjugation. In our previous report, we showed that GSH conjugates of 4-hydroxynonenal (HNE-SG) are substrates of multidrug resistance-associated protein 2 (MRP2). MRP2 has been shown to export HNE-SG conjugates into the extracellular space. In the present study, the role of MRP2 in the detoxification of HNE was studied using Madin-Darby canine kidney II (MDCK II) cells expressing human MRP2. MRP2 reduced the intracellular accumulation of HNE-SG conjugate but unexpectedly increased the susceptibility of cells to HNE. The viability of cells was reduced to approximately 70% in the presence of 62.5 microM HNE in MDCK II cells expressing MRP2, whereas MDCK II cells remained unaffected. MRP2 accelerated the elimination of intracellular GSH via a conjugation reaction with HNE (half-life of GSH was 30.1 and 12.2 min for MDCK II cells and MDCK II cells expressing MRP2, respectively). Moreover, the consumption of GSH was unlimited in MDCK II cells expressing MRP2, finally resulting in necrosis. These results indicate that MRP2 has an adverse effect during the detoxification of HNE in MDCK II cells and suggest that expression of MRP2 may enhance the damage caused by oxidative stress.
Rational design of a phthalocyanine–perylenediimide dyad with a long-lived charge-separated state (2012)

A new ZnPc-PDI dyad presenting for the first time a charge-separated state lower in energy than the triplet excited state of the ZnPc and PDI has been synthesized. The rational design implies the substitution of the ZnPc with phenoxy groups and the bay substitution of the PDI with sulfonyl substituents. The lifetime of the charge-separated state was 72 μs.
Synthesis of 2,1‐Borazaroquinolines and 2,1‐Borazaroisoquinolines from Vinylaminopyridines and Potassium Organotrifluoroborates by Microwave‐Assisted Heating (2015)

Abstract Azaborines are an emerging class of compounds with applications in medicinal chemistry and materials science. The synthesis of a wide variety of borazaronaphthalenes has been reported in the last decade. However, access to other borazaro derivatives has been limited. A new approach to synthesize 2,1‐borazaroquinolines and 2,1‐borazaroisoquinolines from (vinylamino)pyridines and potassium organotrifluoroborates using microwave‐assisted heating is reported. A substituted diverse set of new azaborines has been synthesized by this method, providing the first access to a family of 2,1‐borazaroquinolines and 2,1‐borazaroisoquinolines.
Effects of focal plane array offset and beam steering on sensitivity (2008)

Focal plane antenna array (FPA) feeds for large reflector antennas can provide radio astronomers with the ability to electronically scan the sky without physically moving the position of the antennas. FPAs may also enable radio frequency interference mitigation using spatial filtering algorithms.
Alginate microbeads are coagulation compatible, while alginate microcapsules activate coagulation secondary to complement or directly through FXII (2017)

Alginate microcapsules are prospective candidate materials for cell encapsulation therapy. The material surface must be free of host cell adhesion to ensure free diffusion of nutrition and oxygen to the encapsulated cells. Coagulation activation is one gateway to cellular overgrowth through deposition of fibrin. Herein we used a physiologically relevant whole blood model to investigate the coagulation potential of alginate microcapsules and microbeads. The coagulation potentials and the pathways of activation were depending on the surface properties of the materials. Activation of the complement system could also be involved, thus emphasizing a complement-coagulation cross-talk. Our findings points to complement and coagulation inhibition as intervention point for preventing host reactions, and enhance functional cell-encapsulation devices.
Self-aligned quadruple patterning-aware routing (2014)

Self-Aligned Quadruple Patterning (SAQP) is one of the most leading techniques in 14 nm node and beyond. However, the construction of feasible layout configurations must follow stricter constraints than in LELELE triple patterning process. Some SAQP layout decomposition methods were recently proposed. However, due to strict constraints required for feasible SAQP layout, the decomposition strategy considering an arbitrary layout does not seem realistic. In this paper, we propose a new routing method for feasible SAQP layout requiring no decomposition. Our method performs detailed routing by correct-by-construction approach and offers compliant layout configuration without any pitch conflict.
Development of AAVLP(HPV16/31L2) Particles as Broadly Protective HPV Vaccine Candidate (2012)

The human papillomavirus (HPV) minor capsid protein L2 is a promising candidate for a broadly protective HPV vaccine yet the titers obtained in most experimental systems are rather low. Here we examine the potential of empty AAV2 particles (AAVLPs), assembled from VP3 alone, for display of L2 epitopes to enhance their immunogenicity. Insertion of a neutralizing epitope (amino acids 17-36) from L2 of HPV16 and HPV31 into VP3 at positions 587 and 453, respectively, permitted assembly into empty AAV particles (AAVLP(HPV16/31L2)). Intramuscularly vaccination of mice and rabbits with AAVLP(HPV16/31L2)s in montanide adjuvant, induced high titers of HPV16 L2 antibodies as measured by ELISA. Sera obtained from animals vaccinated with the AAVLP(HPV16/31L2)s neutralized infections with several HPV types in a pseudovirion infection assay. Lyophilized AAVLP(HPV16/31L2) particles retained their immunogenicity upon reconstitution. Interestingly, vaccination of animals that were pre-immunized with AAV2--simulating the high prevalence of AAV2 antibodies in the population--even increased cross neutralization against HPV31, 45 and 58 types. Finally, passive transfer of rabbit antisera directed against AAVLP(HPV16/31L2)s protected naïve mice from vaginal challenge with HPV16 pseudovirions. In conclusion, AAVLP(HPV16/31L2) particles have the potential as a broadly protective vaccine candidate regardless of prior exposure to AAV.
Packaging The DM-1062 gigabit Optical Module (2005)

Abstract The DM-1062 is IBM's offering to meet the ANSI X3T9.3 Fiber Channel Standard for a 1.0625 Gb/s optoelectronic transceiver with integrated serializer/deserializer functions. We describe packaging technology and performance data for this module.
Performance of quadrature phase shift frequency selective receiver in presence of blockers (2018)

This paper evaluates the performance of a linear, low-power and blocker tolerant quadrature phase shift frequency selective (QPS-FS) receiver in the presence of blockers. The QPS-FS receiver has been tested to tolerate more than 0 dBm of continuous wave (CW) blocker power at a frequency offset of 40 MHz away from the RF signal carrier frequency with 6 dB degradation in the voltage conversion gain and without any significant loss in the receiver performance in terms of error vector magnitude (EVM) between the transmitted and the received constellation points. The QPS-FS receiver separates the undesired blockers and interferers from the desired band RF signal, which are collected for energy harvesting purposes.
Probability-Based Matching (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.