gebhart/patrepeval huggingface dataset:
Versatile Fluorescence Probes of Protein Kinase Activity (2003)

We introduce a versatile fluorescent peptide reporter of protein kinase activity. The probe can be modified to target a desired kinase by changing the kinase recognition motif in the peptide sequence. The reporter motif contains the Sox amino acid, which generates a fluorescence signal when bound to Mg2+ present in the reaction mixture. The phosphorylated peptide exhibits a much greater affinity for Mg2+ than its unphosphorylated analogue and, thus, a greater fluorescence intensity. Product formation during phosphorylation by the kinase is easily followed by the increase in fluorescence intensity over time. These probes exhibit a 3-5-fold increase in fluorescence intensity upon phosphorylation, the magnitude of which depends on the substrate. Peptides containing the reporter functionality are phosphorylated on serine by Protein Kinase C and cAMP-dependent protein kinase and are shown to be good substrates for these enzymes. The principle of this design extends to peptides phosphorylated on threonine and tyrosine.
A Sensitivity Analysis of Power Signal Methods for Detecting Hardware Trojans Under Real Process and Environmental Conditions (2009)

Trust in reference to integrated circuits addresses the concern that the design and/or fabrication of the integrated circuit (IC) may be purposely altered by an adversary. The insertion of a hardware Trojan involves a deliberate and malicious change to an IC that adds or removes functionality or reduces its reliability. Trojans are designed to disable and/or destroy the IC at some future time or they may serve to leak confidential information covertly to the adversary. Trojans can be cleverly hidden by the adversary to make it extremely difficult for chip validation processes, such as manufacturing test, to accidentally discover them. This paper investigates the sensitivity of a power supply transient signal analysis method for detecting Trojans. In particular, we focus on determining the smallest detectable Trojan, i.e., the least number of gates a Trojan may have and still be detected, using a set of process simulation models that characterize a TSMC 0.18 μm process. We also evaluate the sensitivity of our Trojan detection method in the presence of measurement noise and background switching activity.
Densely Connected Convolutional Networks (2017)

Recent work has shown that convolutional networks can be substantially deeper, more accurate, and efficient to train if they contain shorter connections between layers close to the input and those close to the output. In this paper, we embrace this observation and introduce the Dense Convolutional Network (DenseNet), which connects each layer to every other layer in a feed-forward fashion. Whereas traditional convolutional networks with L layers have L connections-one between each layer and its subsequent layer-our network has L(L+1)/2 direct connections. For each layer, the feature-maps of all preceding layers are used as inputs, and its own feature-maps are used as inputs into all subsequent layers. DenseNets have several compelling advantages: they alleviate the vanishing-gradient problem, strengthen feature propagation, encourage feature reuse, and substantially reduce the number of parameters. We evaluate our proposed architecture on four highly competitive object recognition benchmark tasks (CIFAR-10, CIFAR-100, SVHN, and ImageNet). DenseNets obtain significant improvements over the state-of-the-art on most of them, whilst requiring less memory and computation to achieve high performance. Code and pre-trained models are available at https://github.com/liuzhuang13/DenseNet.
Disulfide Mapping of the Cyclotide Kalata B1 (2003)

The cyclotides are a recently discovered family of plant proteins that have the fascinating structural feature of a continuous cyclic backbone and, putatively, a knotted arrangement of their three conserved disulfide bonds. We here show definite chemical proof of the I-IV, II-V, III-VI knotted disulfide connectivity of the prototypic cyclotide kalata B1. This has been achieved by a new approach for disulfide analysis, involving partial reduction and stepwise alkylation including introduction of charges and enzymatic cleavage sites by aminoethylation of cysteines. The approach overcomes the intrinsic difficulties for disulfide mapping of cyclotides, i.e. the cyclic amide backbone, lack of cleavage sites between cysteines, and a low or clustered content of basic amino acids, and allowed a direct determination of the disulfide bonds in kalata B1 using analysis by mass spectrometry. The established disulfide connectivity is unequivocally shown to be cystine knotted by a topological analysis. This is the first direct chemical determination of disulfides in native cyclotides and unambiguously confirms the unique cyclic cystine knot motif.
Experimental Infection of Guinea Pigs with Venezuelan Hemorrhagic Fever Virus (Guanarito): A Model of Human Disease (1996)

Venezuelan hemorrhagic fever (VHF), a newly described disease caused by an arenavirus (Guanarito), has resulted in multiple human deaths in Venezuela. To develop an animal model of this disease, strain 13 and Hartley strain guinea pigs were inoculated subcutaneously with Guananto strain 95551 of arenavirus in a pilot study to determine susceptibility of the species to the virus. All animals were killed when moribund 12-14 days following inoculation. Animals were necropsied and tissues were fixed and examined by both light and electron microscopy. Viral antigen was demonstrated in the tissues by immunohistochemistry at both the light and electron microscopic levels. Lesions were characterized by single cell necrosis of epithelium of the gastrointestinal tract, interstitial pneumonia, lymphoid and hematopoietic cell necrosis, and the presence of platelet thrombi in occasional blood vessels associated with hemorrhage. Viral antigen was demonstrated in lymphoid tissues and macrophages, endothelial cells of multiple organs, pulmonary epithelium, epithelium of the gastrointestinal tract, and in miscellaneous other tissues and cells. Intact virions and typical arenavirus inclusions were demonstrated by immunoelectron microscopy in these tissues. Based on these findings, the guinea pig appears to be a valid animal model of the human disease.
Measurement of outward translocation of phospholipids across human erythrocyte membrane. (1988)

Spin-labeled phospholipids have been used to study the outside----inside and inside----outside transport of phospholipids across the human erythrocyte membrane at 37 degrees C. As already shown, inward transport is much faster for aminophospholipids than for phosphatidylcholine. In addition, we show here that outward transport of the phosphatidylserine and phosphatidylethanolamine analogues is three to four times faster than that of phosphatidylcholine. Magnesium depletion of the erythrocytes considerably decreases the outward rate of both aminophospholipids to values close to that of phosphatidylcholine. These results suggest that the outward aminophospholipid translocation is, at least partly, protein mediated. The protein involved could be identical to the inward Mg-ATP-dependent aminophospholipid carrier.
Transient exposure to calcium ionophore enables in vitro fertilization in sterile mouse models (2016)

Mammalian sperm acquire fertilizing capacity in the female tract in a process called capacitation. At the molecular level, capacitation requires protein kinase A activation, changes in membrane potential and an increase in intracellular calcium. Inhibition of these pathways results in loss of fertilizing ability in vivo and in vitro. We demonstrated that transient incubation of mouse sperm with Ca(2+) ionophore accelerated capacitation and rescued fertilizing capacity in sperm with inactivated PKA function. We now show that a pulse of Ca(2+) ionophore induces fertilizing capacity in sperm from infertile CatSper1 (Ca(2+) channel), Adcy10 (soluble adenylyl cyclase) and Slo3 (K(+) channel) KO mice. In contrast, sperm from infertile mice lacking the Ca(2+) efflux pump PMACA4 were not rescued. These results indicate that a transient increase in intracellular Ca(2+) can overcome genetic infertility in mice and suggest this approach may prove adaptable to rescue sperm function in certain cases of human male infertility.
A foundation for universal T-cell based immunotherapy: T cells engineered to express a CD19-specific chimeric-antigen-receptor and eliminate expression of endogenous TCR (2012)

Clinical-grade T cells are genetically modified ex vivo to express a chimeric antigen receptor (CAR) to redirect specificity to a tumor associated antigen (TAA) thereby conferring antitumor activity in vivo. T cells expressing a CD19-specific CAR recognize B-cell malignancies in multiple recipients independent of major histocompatibility complex (MHC) because the specificity domains are cloned from the variable chains of a CD19 monoclonal antibody. We now report a major step toward eliminating the need to generate patient-specific T cells by generating universal allogeneic TAA-specific T cells from one donor that might be administered to multiple recipients. This was achieved by genetically editing CD19-specific CAR(+) T cells to eliminate expression of the endogenous αβ T-cell receptor (TCR) to prevent a graft-versus-host response without compromising CAR-dependent effector functions. Genetically modified T cells were generated using the Sleeping Beauty system to stably introduce the CD19-specific CAR with subsequent permanent deletion of α or β TCR chains with designer zinc finger nucleases. We show that these engineered T cells display the expected property of having redirected specificity for CD19 without responding to TCR stimulation. CAR(+)TCR(neg) T cells of this type may potentially have efficacy as an off-the-shelf therapy for investigational treatment of B-lineage malignancies.
The lysP gene encodes the lysine-specific permease (1992)

Escherichia coli transports lysine by two distinct systems, one of which is specific for lysine (LysP) and the other of which is inhibited by arginine ornithine. The activity of the lysine-specific system increases with growth in acidic medium, anaerobiosis, and high concentrations of lysine. It is inhibited by the lysine analog S-(beta-aminoethyl)-L-cysteine (thiosine). Thiosine-resistant (Tsr) mutants were isolated by using transpositional mutagenesis with TnphoA. A Tsr mutant expressing alkaline phosphatase activity in intact cells was found to lack lysine-specific transport. This lysP mutation was mapped to about 46.5 min on the E. coli chromosome. The lysP-phoA fusion was cloned and used as a probe to clone the wild-type lysP gene. The nucleotide sequence of the 2.7-kb BamHI fragment was determined. An open reading frame from nucleotides 522 to 1989 was observed. The translation product of this open reading frame is predicted to be a hydrophobic protein of 489 residues. The lysP gene product exhibits sequence similarity to a family of amino acid transport proteins found in both prokaryotes and eukaryotes, including the aromatic amino acid permease of E. coli (aroP) and the arginine permease of Saccharomyces cerevisiae (CAN1). Cells carrying a plasmid with the lysP gene exhibited a 10- to 20-fold increase in the rate of lysine uptake above wild-type levels. These results demonstrate that the lysP gene encodes the lysine-specific permease.
A Capacitorless 1T-DRAM on SOI Based on Dynamic Coupling and Double-Gate Operation (2008)

The scaling requirements of conventional DRAMs lead to the recent developments of capacitorless single-transistor (1T) DRAM in SOI technology. We propose a new concept of 1T-DRAM (named MSDRAM), which is simple to fabricate, program, and read. Its basic mechanism is the metastable dip hysteresis effect, which takes advantage of the dynamic coupling between front and back interfaces in SOI transistors. Systematic measurements and simulations show that MSDRAMs are suitable for low-power applications, as they exhibit negligible off-state current and long retention time even for 50-nm devices.
FLP-mediated DNA mobilization to specific target sites in Drosophila chromosomes (1997)

The ability to place a series of gene constructs at a specific site in the genome opens new possibilities for the experimental examination of gene expression and chromosomal position effects. We report that the FLP- FRT site-specific recombination system of the yeast 2mu plasmid can be used to integrate DNA at a chromosomal FRT target site in Drosophila. The technique we used was to first integrate an FRT- flanked gene by standard P element-mediated transformation. FLP was then used to excise the FRT- flanked donor DNA and screen for FLP-mediated re-integration at an FRT target at a different chromosome location. Such events were recovered from up to 5% of the crosses used to screen for mobilization and are easily detectable by altered linkage of a white reporter gene or by the generation of a white + gene upon integration.
The Competitive Environment (1989)

The decade of the 1980s has been one of profound change in the building society industry. In particular the competitive environment has intensified dramatically on both sides of the balance sheet. In the retail deposit market, the building societies traditional funding base, societies have faced strong competition from National Savings in the early 1980s from banks and from equity investments in the form of successive privatisation issues and competition from unit trusts. In the mortgage market, building societies have been subject to an unprecedented level of competition since 1981 when the banks, freed from lending constraints, began to enter the mortgage market in a significant way.
Assessment of access control systems (2006)

The Information Technology Laboratory (ITL) at the National Institute of Standards and Technology (NIST) promotes the U.S. economy and public welfare by providing technical leadership for the Nation's measurement and standards infrastructure. ITL develops tests, test methods, reference data, proof of concept implementations, and technical analyses to advance the development and productive use of information
The Siphon: managing distant replicated repositories (2002)

A joint project was undertaken by Digital's Paris Research Laboratory and the Systems Research Center in Palo Alto, USA, to seek novel techniques to support software development over a wide-area network. The specific goal was to present the image of a single shared software repository to researchers at both sites, with a minimum of interactive delay due to transatlantic communications. The system, called the Siphon, which emerged from this effort is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The tRNA Primer Activation Signal in the Human Immunodeficiency Virus Type 1 Genome Is Important for Initiation and Processive Elongation of Reverse Transcription (2002)

Human immunodeficiency virus type 1 (HIV-1) reverse transcription is primed by the cellular tRNA(3)(Lys) molecule, which binds, with its 3"-terminal 18 nucleotides (nt), to a complementary sequence in the viral genome, the primer-binding site (PBS). Besides PBS-anti-PBS pairing, additional interactions between viral RNA sequences and the tRNA primer are thought to regulate the process of reverse transcription. We previously identified a novel 8-nt sequence motif in the U5 region of the HIV-1 RNA genome that is critical for tRNA(3)(Lys)-mediated initiation of reverse transcription in vitro. This motif activates initiation from the natural tRNA(3)(Lys) primer but is not involved in tRNA placement and was therefore termed primer activation signal (PAS). It was proposed that the PAS interacts with the anti-PAS motif in the TphiC arm of tRNA(3)(Lys). In this study, we analyzed several PAS-mutated viruses and performed reverse transcription assays with virion-extracted RNA-tRNA complexes. Mutation of the PAS reduced the efficiency of tRNA-primed reverse transcription. In contrast, mutations in the opposing leader sequence that trigger release of the PAS from base pairing stimulated reverse transcription. These results are similar to the reverse transcription effects observed in vitro. We also selected revertant viruses that partially overcome the reverse transcription defect of the PAS deletion mutant. Remarkably, all revertants acquired a single nucleotide substitution that does not restore the PAS sequence but that stimulates elongation of reverse transcription. These combined results indicate that the additional PAS-anti-PAS interaction is needed to assemble an initiation-competent and processive reverse transcription complex.
Mechanism of the reverse gate leakage in AlGaN/GaN high electron mobility transistors (2003)

The off-state gate current in AlGaN/GaN high electron mobility transistors is shown to arise from two parallel gate to substrate tunneling paths: a direct path, and a path via deep traps, which are distributed throughout the AlGaN layer and spread over an energy band. A model to calculate this current is given, which shows that trap-assisted tunneling dominates below T∼500 K, and direct tunneling (thermionic field emission) dominates at higher temperatures. A model fit to experimental results yields the following fabrication process sensitive parameters: trap concentration of ∼1013–1015 cm−3, and trap bandwidth of ∼50%–70% of the barrier height located 0.4–0.55 V below the conduction band edge.
Studies Utilizing the Portable Electromagnetic Ballistocardiograph (1953)

One hundred patients, who had survived their first episode of myocardial infarction, were studied by serial ballistocardiograms which provided a reliable index in determining myocardial functional recovery. The degree of ballistocardiographic reversion toward normal, as judged by an 18-month or longer follow-up period, has proved to be a valuable standard for prognosis.
Activation of Endoplasmic Reticulum Stress by Hyperglycemia Is Essential for Müller Cell–Derived Inflammatory Cytokine Production in Diabetes (2012)

Inflammation plays an important role in diabetes-induced retinal vascular leakage. The purpose of this study is to examine the role of endoplasmic reticulum (ER) stress and the signaling pathway of ER stress-induced activating transcription factor 4 (ATF4) in the regulation of Müller cell-derived inflammatory mediators in diabetic retinopathy. In diabetic animals, elevated ER stress markers, ATF4, and vascular endothelial growth factor (VEGF) expression were partially localized to Müller cells in the retina. In cultured Müller cells, high glucose induced a time-dependent increase of ER stress, ATF4 expression, and inflammatory factor production. Inducing ER stress or overexpressing ATF4 resulted in elevated intracellular adhesion molecule 1 and VEGF proteins in Müller cells. In contrast, alleviation of ER stress or blockade of ATF4 activity attenuated inflammatory gene expression induced by high glucose or hypoxia. Furthermore, we found that ATF4 regulated the c-Jun NH2-terminal kinase pathway resulting in VEGF upregulation. ATF4 was also required for ER stress-induced and hypoxia-inducible factor-1α activation. Finally, we showed that administration of chemical chaperone 4-phenylbutyrate or genetic inhibition of ATF4 successfully attenuated retinal VEGF expression and reduced vascular leakage in mice with STZ-induced diabetes. Taken together, our data indicate that ER stress and ATF4 play a critical role in retinal inflammatory signaling and Müller cell-derived inflammatory cytokine production in diabetes.
Effect of electrode contact resistance on electric field measurements (1985)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1985Effect of electrode contact resistance on electric field measurementsAuthors: Kenneth L. ZongeLarry J. HughesKenneth L. ZongeZonge Engineering and Research Organization, Inc. and Larry J. HughesZonge Engineering and Research Organization, Inc.https://doi.org/10.1190/1.1892703 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetailsCited byA new electronic model of seismoelectric measurements: Theory, simulations and experimental validationJournal of Applied Geophysics, Vol. 205Effect of Electrode Contact Resistance on Electrical Field Measurements21 September 2022 | Izvestiya, Physics of the Solid Earth, Vol. 58, No. 5Hybrid receiving line for broadband electric field measurement29 January 2022 | Moscow University Bulletin. Series 4. Geology, Vol. 1, No. 5A Hybrid Receiving Line for Measuring the Electric Field in a Wide Frequency Band21 February 2022 | Moscow University Geology Bulletin, Vol. 76, No. 6A novel approach for seismoelectric measurements using multielectrode arrangements – I: theory and numerical experiments4 July 2018 | Geophysical Journal International, Vol. 215, No. 1Design of Analog Front-end Circuit for Audio-frequency Magnetotelluric InstrumentYinglu Zhang, Zhenzhu Xi, Xingpeng Chen, Honglan Wei, Long Huang, and Wei Xiao1 October 2018 | Journal of Environmental and Engineering Geophysics, Vol. 23, No. 3Laboratory monitoring of CO 2 injection in saturated silica and carbonate sands using spectral induced polarization7 September 2016 | Geophysical Journal International, Vol. 207, No. 2Induced polarization response of porous media with metallic particles — Part 4: Detection of metallic and nonmetallic targets in time-domain induced polarization tomographyDeqiang Mao, André Revil, and John Hinton23 May 2016 | GEOPHYSICS, Vol. 81, No. 4Data repeatability and acquisition techniques for time-domain spectral induced polarization1 January 2013 | Near Surface Geophysics, Vol. 11, No. 4The effect of electrode contact resistance and capacitive coupling on complex resistivity measurementsThomas Ingeman‐Nielsen6 October 2006On measuring electromagnetic surface impedance-discussions with Professor James R. WaitIEEE Transactions on Antennas and Propagation, Vol. 48, No. 10 SEG Technical Program Expanded Abstracts 1985ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1985 Pages: 643 publication data© 1985 Copyright © 1985 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 07 Mar 2005 CITATION INFORMATION Kenneth L. Zonge and Larry J. Hughes, (1985), "Effect of electrode contact resistance on electric field measurements," SEG Technical Program Expanded Abstracts : 231-234. https://doi.org/10.1190/1.1892703 Plain-Language Summary PDF DownloadLoading ...
Pyramid-based texture analysis/synthesis (2002)

This paper describes a method for synthesizing images that match the texture appearance of a given digitized sample. This synthesis is completely automatic and requires only the "target" texture as input. It allows generation of as much texture as desired so that any object can be covered. The approach is based on a model of human texture perception, and has potential to be a practically useful tool for image processing and graphics applications.
Digital Memory: The Visual Recording of Mass Grave Exhumations in Contemporary Spain (2008)

Exhumations of the victims of Franco's repressive policies are cultural practices of tremendous heuristic value and allow for the analysis of the public emergence, circulation and consumption of traumatic memory in local contexts. The use of visual media to capture social action in the surroundings of the exhumations serves as both a recording and as a triggering device for this emerging social memory. In the first part of this article we shall reflect on the different forms of visual and audiovisual interventions by different social actors that shape around mass grave exhumations. In the second part we will focus on the visual methods used by social scientists, particularly the recording of video-testimony of survivors and witnesses. URN: urn:nbn:de:0114-fqs0803351