gebhart/patrepeval huggingface dataset:
Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein–Protein Interactions (2015)

Many biologically active α-helical peptides adopt amphiphilic helical structures that contain hydrophobic residues on one side and hydrophilic residues on the other side. Therefore, α-helix mimetics capable of mimicking such amphiphilic helical peptides should possess higher binding affinity and specificity to target proteins. Here we describe an efficient method for generating amphiphilic α-helix mimetics. One-face α-helix mimetics having hydrophobic side chains on one side was readily converted into amphiphilic α-helix mimetics by introducing appropriate charged residues on the opposite side. We also demonstrate that such two-face amphiphilic α-helix mimetics indeed show remarkably improved binding affinity to a target protein, compared to one-face hydrophobic α-helix mimetics. We believe that generating a large combinatorial library of these amphiphilic α-helix mimetics can be valuable for rapid discovery of highly potent and specific modulators of protein-protein interactions.
Nucleotide sequence of the apocytochrome B gene in white sturgeon mitochondrial DNA (1989)

Journal Article Nucleotide sequence of the apocytochrome B gene in white sturgeon mitochondrial DNA Get access James R. Brown, James R. Brown Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser UniversityBurnaby, British Columbia V5A IS6, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Teresa L. Gilbert, Teresa L. Gilbert 1ZymoGenetics Inc.4225 Roosevelt Way NE, Seattle, WA 98105 Search for other works by this author on: Oxford Academic PubMed Google Scholar David J. Kowbel, David J. Kowbel Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser UniversityBurnaby, British Columbia V5A IS6, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Patrick J. O'Hara, Patrick J. O'Hara Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser UniversityBurnaby, British Columbia V5A IS6, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Norman E. Buroker, Norman E. Buroker 2School of Medicine, Department of Pediatrics, RD-20, University of WashingtonSeattle, WA 98195. USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Andrew T. Beckenbach, Andrew T. Beckenbach Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser UniversityBurnaby, British Columbia V5A IS6, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael J. Smith Michael J. Smith Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser UniversityBurnaby, British Columbia V5A IS6, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 11, 12 June 1989, Page 4389, https://doi.org/10.1093/nar/17.11.4389 Published: 12 June 1989 Article history Received: 18 April 1989 Published: 12 June 1989
Molten Salt Catalysis of Gas Reactions (1975)

Abstract Molten salts have been used for many centuries in metal extraction, glass manufacture, and, more recently, in applications such as fused salt electrolysis. Usually dissociated into ions, they are often good solvents for oxides, carbides, nitrides, and metals. Their high thermal stability, low vapor pressure, good thermal and electrical conductivity, and low viscosity may be expected to confer on them an increasing technological importance in the future, and as a result research on their physical and chemical properties has grown markedly in recent years. Thermodynamic and transport properties [l-41 have been surveyed within the last decade, and Sundermeyer [5] has also reviewed their use as reaction media. A selection of catalytic reactions has been discussed by Kenney [6].
Comparison of T-cell immune responses to SARS-CoV-2 spike (S) and nucleocapsid (N) protein using an in-house flow-cytometric assay in laboratory employees with and without previously confirmed COVID-19 in South Africa: nationwide cross-sectional study (2022)

A significant proportion of South African laboratory employees who were not previously diagnosed with COVID-19 demonstrated T-cell reactivity to SARS-CoV-2 N-proteins and S-proteins. The pre-existing T-cell proliferation responses may be attributable to cross-reactive immune responses to other human coronaviruses, or possibly asymptomatic infection.
In Vitro and In Vivo Characterization of Neurally Modified Mesenchymal Stem Cells Induced by Epigenetic Modifiers and Neural Stem Cell Environment (2008)

Mesenchymal stem cell (MSC)-mediated tissue regeneration is a promising strategy to treat several neurodegenerative diseases and traumatic injuries of the central nervous system. Bone marrow MSCs have great potential as therapeutic agents, since they are easy to isolate and expand and are capable of producing various cell types, including neural cells. Recently we developed a highly efficient methodology to produce neural stem-like and neural precursor-like cells from mice bone marrow-derived MSCs that eventually differentiate into neuronal- and glial-like cells in vitro. The aim of this study is to further elucidate neural expression profile of neurally induced mesenchymal stem cells (NI-MSCs) and their ability to retain neural differentiation potential when grafted into the intact spinal cord of rats. To this end, we further characterized in vitro and in vivo properties of NI-MSCs by immunocytochemistry, Western blot, ELISA, and immunohistochemistry. Immunocytochemical data demonstrated that NI-MSCs express several mature neural markers such as B3T, GFAP MAP-2, NF-200, and NeuN, which were confirmed through Western blot. ELISA data showed that NI-MSCs release nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF). In vivo studies demonstrated that grafted NI-MSCs survived after transplantation into intact spinal cord and produced cells that expressed neural markers. All these data suggest that neurally modified MSCs, induced by recently developed methodology, could be a potential source of cells to replace damaged neurons and glia in injured spinal cord, and/or to promote cell survival and axonal growth of host tissue.
OCF: A New Open IoT Consortium (2017)

This paper illustrates on the new Internet of Things Consortium as OCF stands for Open Connectivity Foundation that is creating a specification and open source simultaneously tobe broadly adopted in various industries. OCF is a unique specification and open source project that delivers just-works interconnectivity for developers, manufacturers and end users.
Assessment of a new device (aerochamber) for use with aerosol drugs in asthmatic children. (1983)

We compared the pulmonary response to fenoterol delivered by a conventional MDI with the response after MDI plus the aerochamber (AC). Twelve children with moderate to severe asthma (mean age 10.8 years) participated in this double-blind crossover study. On two consecutive days, in random order, subjects received one puff of fenoterol hydrobromide (200 mcg) either by MDI or MDI plus AC. Pulmonary function, cardiovascular response and tremor were assessed over a period of four hours. In a similar fashion, the children received one puff of fenoterol three times a day for six weeks by either method in a randomized open study. Daily symptoms and peak flows before and after drug were recorded in daily diaries. The patients returned to the pulmonary function laboratory at 6 and 12 weeks for four hour pulmonary function tests. In the short-term study, the magnitude and time course of pulmonary response was similar for both treatment regimens (p greater than 0.4). No significant effects on blood pressure or pulse or differences in tremor assessment were seen. Similarly, in the long term study the baseline pulmonary function and pulmonary response were markedly consistent between the two treatment regimens (p greater than 0.05). Peak flows were significantly higher in the evening than in the morning (p less than 0.001) and the magnitude of the response to drug was higher in the morning than the evening (p less than 0.001). There were no differences between MDI and MDI plus AC in daily symptom scores or use of concomitant medication. We conclude that acute or chronic administration of fenoterol aerosol to asthmatic children by MDI with or without the AC produces similar benefits in pulmonary function, symptomatology and concomitant medication. The AC device would be a useful adjunct for a child who has difficulty in coordinating the metered dose inhaler.
Efficient self-adjusting, similarity-based location fingerprinting with passive UHF RFID (2011)

In this paper we present extensive experimental results of location fingerprinting with passive UHF radio-frequency identification (RFID). As recent passive RFID hardware provides information about received signal strength (RSS), we evaluate its usefulness in the context of fingerprinting based on classical vector similarity measures. We analyze the impact of decisive parameters of the applied approach and also select them automatically via cross-validation, including the most appropriate similarity measure. A further novelty is an RSS thresholding mechanism which reduces the computational demands of comparing fingerprints. This technique is especially useful in surroundings which are densely equipped with RFID tags, such as future supermarkets or logistic centers. We conducted real-world experiments with a mobile robot and two different RFID readers. Results are reported both for global localization in each time frame and for time-filtered position tracking. We provide the experimental data of this work for download.
Enhanced Hexagonal Search for Fast Block Motion Estimation (2004)

Fast block motion estimation normally consists of low-resolution coarse search and the following fine-resolution inner search. Most motion estimation algorithms developed attempt to speed up the coarse search without considering accelerating the focused inner search. On top of the hexagonal search method recently developed, an enhanced hexagonal search algorithm is proposed to further improve the performance in terms of reducing number of search points and distortion, where a novel fast inner search is employed by exploiting the distortion information of the evaluated points. Our experimental results substantially justify the merits of the proposed algorithm.
Voltage-Gated Calcium Channels (2019)

Abstract Voltage-gated calcium channels are important contributors to the transmission and processing of nociceptive information in the primary afferent pain pathway. Several types of calcium channels and their ancillary subunits are dysregulated in response to nerve injury or inflammation. Notably, calcium channels have emerged as prominent targets for analgesics. This article discusses the roles of specific types of voltage-gated calcium channels in the afferent pain pathway and their utility as pharmacological targets for therapeutic intervention in chronic pain. Several calcium channel subtypes are dysregulated during chronic pain conditions, giving rise to increased neuronal excitability and synaptic transmission. N-type calcium channels, Cav3.2 T-type calcium channels, and the Cavα2δ subunit are validated targets for the development and clinical use of small organic analgesics, with R-type channels showing potential as possible targets based on preclinical studies.
A Radiometric Aerial Triangulation for the Equalization of Digital Aerial Images and Orthoimages (2009)

Atmospheric haze variations, temporal differences, atmosphere’s or ground surfaces’ and Bidirectional Reflectance Distribution Function (BRDF), are well-known sources of radiometric heterogeneities in aerial images. It is necessary to correct them for many applications, such as the generation of large seamless mosaics of orthoimages, or land-cover classifications. This contribution describes a method for equalizing digital aerial images based on a parametric, semiempirical radiometric model. The model’s parameters are computed through a global least-squares minimization process, using radiometric tie-points in overlapping areas between images. The method may be called a “radiometric aerial triangulation” since its principle is quite similar to a standard aerial triangulation. It leads to a relative equalization between images, keeping their original contrast and color information. The method has been successfully applied operationally to more than forty projects comprising three to four thousands digital images each, for the creation of orthoimages over France. The results are good as long as atmospheric conditions are favorable and stable.
Post-Quantum Lattice-Based Cryptography Implementations (2019)

The advent of quantum computing threatens to break many classical cryptographic schemes, leading to innovations in public key cryptography that focus on post-quantum cryptography primitives and protocols resistant to quantum computing threats. Lattice-based cryptography is a promising post-quantum cryptography family, both in terms of foundational properties as well as in its application to both traditional and emerging security problems such as encryption, digital signature, key exchange, and homomorphic encryption. While such techniques provide guarantees, in theory, their realization on contemporary computing platforms requires careful design choices and tradeoffs to manage both the diversity of computing platforms (e.g., high-performance to resource constrained), as well as the agility for deployment in the face of emerging and changing standards. In this work, we survey trends in lattice-based cryptographic schemes, some recent fundamental proposals for the use of lattices in computer security, challenges for their implementation in software and hardware, and emerging needs for their adoption. The survey means to be informative about the math to allow the reader to focus on the mechanics of the computation ultimately needed for mapping schemes on existing hardware or synthesizing part or all of a scheme on special-purpose har dware.
A new palladium-catalyzed coupling reaction of vinylic and allylic triflates with pyrimidine nucleosides (1991)

Vinylic trifluoromethane sulfonates (triflates) form palladium intermediates that react with pyrimidine nucleosides to produce C-5 alkyl substituted nucleosides after hydrogenation of the vinylic coupling products with hydrogen and Pd/C in methanol. The reaction, which is run under mild conditions, appears to be a general one since both mono- and disubstituted vinylic triflates, as well as the cyclic ones, gave high yields of the corresponding C-5 alkyl-substituted nucleoside. The reaction with allyl triflate requires the use of the 5-chloromercurinucleoside. Key words: nucleosides, triflates, palladium catalysis
Ultrahigh-Speed Signal Transmission Over Nonlinear and Dispersive Fiber Optic Channel: The Multicarrier Advantage (2010)

There is a common belief that coherent optical orthogonal frequency-division multiplexing (CO-OFDM) has inferior nonlinear performance in the fiber optic channel due to its high peak-to-average power ratio (PAPR). In this paper, we show that due to the uniqueness of chromatic dispersion in the optical fiber, properly designed CO-OFDM can, in fact, possess a nonlinearity advantage over a coherent single carrier (SC) for ultrahigh-speed transport at 100 Gb/s and beyond. In particular, we propose a novel approach called multiband DFT-spread OFDM (MB-DFT-S-OFDM), by which the DFT-S-OFDM is applied to each subband of the multiband CO-OFDM to reduce the PAPR within each subband. It is found that eight-band DFT-S-OFDM surpasses the conventional OFDM and the coherent SC by 1.3 and 0.5 dB, respectively, for SSMF107-Gb/s transmission over a 1000-km standard-single-mode-fiber (SSMF).
Portable Fourier transform infrared spectrometer for use as a gas analyser in industrial hygiene (1996)

A portable, real-time, gas analyser (GASMET), based on the Fourier transform infrared (FTIR) principle, was compared with the adsorption tube method in four factories using organic solvent mixtures. The usefulness of the gas analyser data was also evaluated from the point of view of preventive measures. The gas analyser incorporates the use of a low-resolution FTIR spectrometer, a 486 computer and a temperature-controlled gas cell. The gas analyser was calibrated with the expected pure compounds and solvent mixtures in different concentrations. CALCMET software based on a modified classical least-squares lineshape fitting is used for the identification and quantification of compounds. The typical detection limit of the gas analyser is about 1 mg m–3. The correlation of the total hygienic effect between the gas analyser and the adsorption tubes was good (correlation coefficient = 0.978). With small concentrations of some single compounds, some discrepancy occurs between the results obtained with the two methods. Continuous monitoring with the gas analyser reveals the worktasks with exposure peaks and makes precise preventive measures possible.
Muscle-specific interaction of caveolin isoforms: differential complex formation between caveolins in fibroblastic vs. muscle cells (2004)

It is generally well accepted that caveolin-3 expression is muscle specific, whereas caveolin-1 and -2 are coexpressed in a variety of cell types, including adipocytes, endothelial cells, epithelial cells, and fibroblasts. Caveolin-1 and -2 are known to form functional hetero-oligomeric complexes in cells where they are coexpressed, whereas caveolin-3 forms homo-oligomeric high molecular mass complexes. Although caveolin-2 might be expected to interact in a similar manner with caveolin-3, most studies indicate that this is not the case. However, this view has recently been challenged as it has been demonstrated that caveolin-2 and -3 are coexpressed in primary cultures of cardiac myocytes, where these two proteins can be coimmunoprecipitated. Thus it remains controversial whether caveolin-2 interacts with caveolin-3. Here, we directly address the issue of caveolin isoform protein-protein interactions by means of three distinct molecular genetic approaches. First, using caveolin-1-deficient mouse embryonic fibroblasts, in which we have stably expressed caveolin-1, -2, or -3, we find that caveolin-1 interacts with caveolin-2 in this setting, whereas caveolin-3 does not, in agreement with most published observations. Next, we used a transfected L6 myoblast cell system expressing all three caveolin proteins. Surprisingly, we found that caveolin-1, -2, and -3 all coimmunoprecipitate in this cell type, suggesting that this interaction is muscle cell specific. Similar results were obtained when the skeletal muscle of caveolin-1 transgenic animals was analyzed for caveolin-1 and caveolin-3 coimmunoprecipitation. Thus we conclude that all three caveolins can interact to form a discrete hetero-oligomeric complex, but that such complex formation is clearly muscle specific.
PharmVar GeneFocus: <i>CYP2D6</i> (2019)

The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocus provides a comprehensive overview and summary of CYP2D6 genetic variation and describes how the information provided by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
Reconfigurable K-best MIMO detector architecture and FPGA implementation (2007)

In a MIMO communication system, K-best decoding algorithm achieves near optimal performance with reduced complexity. Simulation results show that a reconfigurable MIMO detector can improve system performance over a wide range of operating conditions. In this paper we present a low complexity reconfigurable architecture for implementation of K-best algorithm. Implementation results using FPGA technology demonstrate a throughput of 240Mbps.
HIF-2 -mediated activation of the epidermal growth factor receptor potentiates head and neck cancer cell migration in response to hypoxia (2010)

Despite their individual key roles in promoting head and neck squamous cell carcinoma (HNSCC) progression and treatment resistance, little is known about the impact of intratumoral hypoxia on the activity of the epidermal growth factor receptor (EGFR) signaling pathway in this cancer type. Here, we show that in highly EGFR-expressing HNSCC cells, hypoxic stress triggers the activation of the EGFR and downstream targets, including Akt and phospholipase C (PLC) gamma1. In support of these findings, we also demonstrate that EGFR activation takes place within hypoxic foci in a subset of human HNSCC tissues. Whereas hypoxia had no major effect on HNSCC cell proliferation, it markedly altered tumor cell shape by inducing morphological changes consistent with a more spindle-shaped, fibroblast-like morphology together with an enhanced migratory capacity. We found that hypoxia-induced EGFR activation and cell migration could be prevented by targeting EGFR signaling with the tyrosine kinase inhibitor tyrphostin, the phospholipase C inhibitor U73122, or by inhibiting the expression of the alpha subunit of hypoxia-inducible factor 2 via RNA interference or the topoisomerase II inhibitor etoposide. Our results position hypoxia-inducible factor-2alpha as a novel regulator of EGFR activation under low oxygen conditions, and suggest that hypoxia-induced EGFR signaling may promote a more aggressive phenotype in a fraction of HNSCC tumors. Because EGFR continues in the forefront as a highly attractive target in clinical oncology, further studies are warranted to define the mechanistic and therapeutic implications of the hypoxic response relative to the EGFR signaling pathway in head and neck cancer.
Mass resolution of 11,000 to 22,000 with a multiple pass quadrupole mass analyzer (2000)

CO+ and N+2 are separated with resolution of 11,000 [full width half maximum (FWHM)] using a conventional quadrupole mass spectrometer by applying square wave voltages to the entrance and exit lenses to trap or reflect the ions for multiple passes. A resolution of 22,000 (FWHM) with 63% of the total signal remaining is attained using multiple passes when ions are stored between injection pulses. Gated ion extraction also reduces the mass shift and number and intensity of artifact peaks and permits better resolution compared to the performance obtained when the ions are injected continuously.