gebhart/patrepeval huggingface dataset:
The GTP binding motif: variations on a theme (1996)

GTP binding proteins (G-proteins) have wide-ranging functions in biology, being involved in cell proliferation, signal transduction, protein synthesis, and protein targeting. Common to their functioning is that they are active in the GTP-bound form and inactive in the GDP-bound form. The protein synthesis elongation factor EF-Tu was the first G-protein whose nucleotide binding domain was solved structurally by X-ray crystallography to yield a structural definition of the GDP-bound form, but a still increasing number of new structures of G-proteins are appearing in the literature, in both GDP and GTP bound forms. A common structural core for nucleotide binding is present in all these structures, and this core has long been known to include common consensus sequence elements involved in binding of the nucleotide. Nevertheless, subtle changes in the common sequences reflect functional differences. Therefore, it becomes increasingly important to focus on how these differences are reflected in the structures, and how these structural differences are related to function. The aim of this review is to describe to what extent this structural motif for GDP/GTP binding is common to other known structures of this class of proteins. We first describe the common structural core of the G-proteins. Next, examples are based on information available on the Ras protein superfamily, the targeting protein ARF, elongation factors EF-Tu and EF-G, and the heterotrimeric G-proteins. Finally, we discuss the important structures of complexes between GTP binding proteins and their substrates that have appeared in the literature recently.
Cell-Adhesive Star Polymers Prepared by ATRP (2009)

This study presents the synthesis and evaluation of cell adhesive poly(ethylene oxide) (PEO) star polymers for potential biomedical applications. Star polymers with a size of approximately 20 nm and with relatively low polydispersities (M(w)/M(n) ≤ 1.6), containing GRGDS (Gly-Arg-Gly-Asp-Ser) segments, were prepared by atom transfer radical copolymerization of PEO methyl ether methacrylate macromonomer (MM), telechelic GRGDS-PEO-acrylate MM, and ethylene glycol dimethacrylate (EGDMA). Results from (1)H NMR spectroscopy confirmed the covalent incorporation of the peptide into the star periphery. In vitro cytotoxicity experiments showed star polymers to be cytocompatible (≥95% cell viability) and GRGDS-star hybrid hydrogels supported the attachment of MC3T3.E1 (subclone 4) cells. Hybrid hydrogels were prepared by free radical photopolymerization based on 10% (wt/v) PEO dimethacrylates M(n) = 4000 g/mol with 1% (wt/v) GRGDS-star polymers having different peptide content. Cell adhesiveness was also determined from thin film coatings prepared with GRGDS-containing star polymers on nonadherent plastic plates. After 24 h incubation, phase contrast microscopy and scanning electron microscopy (SEM) images showed uniform cell adhesion and distribution over the film containing cell-adhesive star polymers. These results confirm that incorporation of RGD ligand-binding motifs into PEO-based star polymers is required to influence substrate-cell interactions.
Nontyphoidal Salmonella infections of children in tropical Africa (2000)

GRAHAM, STEPHEN M. FRACP; MOLYNEUX, ELIZABETH M. FRCP; WALSH, AMANDA L. MIBIOL; CHEESBROUGH, JOHN S. MRCPATH*; MOLYNEUX, MALCOLM E. FRCP; HART, C. ANTHONY FRCPATH Author Information
Block of cyclic nucleotide-gated channels in salamander olfactory receptor neurons by the guanylyl cyclase inhibitor LY83583 (1995)

1. Using whole cell voltage-clamp recordings, the guanylyl cyclase inhibitor LY83583 [6-(phenylamino)-5,8-quinolinedione] is shown to act as a potent blocker of cyclic nucleotide-gated (CNG) channels in isolated olfactory receptor neurons (ORNs) of the tiger salamander. 2. Under our experimental conditions, onset of the blockade by LY83583 occurs on the time scale of seconds and is completely reversed upon wash-out of the drug. Dose-response curves reveal a Kd of 1.4 microM (at -60 mV). Other data suggest that LY83583 acts within the CNG channel pore and that the channels must be in an activated state before the drug can exert its effect. 3. It appears that LY83583 can act on both CNG channels and soluble guanylyl cyclase (sGC) and that these two effects can be distinguished by their different recovery behaviors. The LY83583-induced blockade of CNG channels activated directly by guanosine 3',5' cyclic monophosphate (cGMP) is rapidly reversible (with a recovery time constant of approximately 3 s), whereas previous results have shown that no recovery is obtained during minute-long washing periods when the channels are activated indirectly through exogenous carbon monoxide application, which acts as a stimulator of sGC in ORNs. 4. LY83583 appears to be a novel and useful agent in examining neural functions due to CNG channel responses.
Fatigue of accommodation and vergence modifies their mutual interactions. (1987)

Aftereffects of accommodation and convergence demonstrate the adaptability of these two visual motor systems. These aftereffects were reduced after ramp tracking exercises of either accommodation or vergence, and this reduced aftereffect or fatigue was associated with an increase of accommodative vergence and vergence accommodation. When one motor system (accommodation or vergence) adapted more readily than the other, fatigue caused an increase of the cross-link interaction originating from the more adaptable motor system and a reduction of the cross-link interaction originating from the less adaptable motor system. These results suggest an inverse relationship between adaptation and the cross-link interactions between accommodation and vergence and that adaptation of tonic accommodation and tonic vergence is a process that underlies plasticity of accommodative vergence and vergence accommodation respectively.
USING INTERACTION OBJECT GRAPHS TO SPECIFY GRAPHICAL WIDGETS (1995)

This paper describes a new method for specifying widgets, the Interactive Object Graph (IOG). IOGs are an extension of statecharts designed for widget specification. They add special states which represent changes in the widget's appearance. These states enhance the readability of IOG diagrams. In addition, IOGs have the ability to represent and modify widget attributes. IOGs are described, and their use illustrated by specifying five new widgets: a range-selection slider, the AlphaSlider, a tree viewer, a treemap viewer, and a secure switch. For each widget there is a brief description of its operation and a specification. Our experience using IOGs to communicate the designs when implementing the above widgets is also described.
Begriffe, Grundgesetze, Grundaufgaben (2012)

No AccessTechnische MechanikSep 2012Begriffe, Grundgesetze, GrundaufgabenMartin MayrMartin Mayrhttps://doi.org/10.3139/9783446434011.001SectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF key 'share (en)' returned an object instead of string.FacebookTwitterEmailLinkedIn previous chapternext chapter FiguresReferencesRelatedDetails 2012Pages: 1-7Print ISBN: 978-3-446-43400-4eISBN: 978-3-446-43401-1 Copyright & Permissions© 2012 Carl Hanser Verlag GmbH & Co. KGPDF downloadLoading ...
HDNET: Exploiting HD Maps for 3D Object Detection (2020)

In this paper we show that High-Definition (HD) maps provide strong priors that can boost the performance and robustness of modern 3D object detectors. Towards this goal, we design a single stage detector that extracts geometric and semantic features from the HD maps. As maps might not be available everywhere, we also propose a map prediction module that estimates the map on the fly from raw LiDAR data. We conduct extensive experiments on KITTI as well as a large-scale 3D detection benchmark containing 1 million frames, and show that the proposed map-aware detector consistently outperforms the state-of-the-art in both mapped and un-mapped scenarios. Importantly the whole framework runs at 20 frames per second.
A Cognitive Spectrum Assignment Protocol using Distributed Conflict Graph Construction (2007)

The availability of multiple interfaces and channels in wireless devices is expected to alleviate the capacity limitations that exist in traditional single channel wireless mesh networks. Although having multiple radio interfaces and available channels can generally increase the effective throughput, a problem arises as to what is the best strategy to dynamically assign available channels to multiple radio interfaces for maximizing effective network throughput by minimizing the interference. This paper presents a distributed and localized interference-aware channel assignment framework for multi-radio wireless mesh networks in a cognitive network environment. The proposed framework uses a novel interference estimation method by utilizing distributed conflict graphs at each network interface to model the interference. Extensive simulation studies in 802.11 based multi-radio mesh networks have been performed. The results indicate that for both local and multi-hop traffic, the proposed protocol can facilitate a large increase in network throughput in comparison with a Common Channel Assignment mechanism that is used as a benchmark in the literature.
Acquired von Willebrand factor deficiency during high‐dose infusion of recombinant factor VIII (1996)

Constant infusion of factor VIII (FVIII) into patients with haemophilia A after major surgery has been recommended as optimal treatment to avoid peaks and valleys in the circulating levels of FVIII and to allow the use of much lower doses of FVIII than are historically required. One of our young patients with severe (< 0.01 U/ml FVIII) haemophilia suffered a subdural haematoma for which he received treatment with 815190 recombinant FVIII (rFVIII) units over a period of 52d. 2 weeks after admission, because of low FVIII levels and the presence of FVIII inhibitors, the infusion rate was increased to > 100 U/kg/h for 14d. During this time the FVIII level fluctuated between 0.6 and 4.2 U/ml. For some period it was not possible to detect ristocetin co-factor activity in this patient's plasma and the von Willebrand factor (VWF) level and VWF multimer pattern resembled those of a patient with von Willebrand's disease. Subsequently, when the rFVIII dose was increased 2-fold, this was not reflected by the plasma level of FVIII although antibodies were not detected. The data suggest that the prolonged infusion of very high levels of rFVIII which is deficient in von Willebrand factor can result in depletion of VWF from existing stores, producing a laboratory picture which is consistent with the diagnosis of von Willebrand's disease. Further, in the absence of complexing with VWF, FVIII appears to be cleared from the circulation at an increased rate. This is expensive and potentially compromising. Therefore, when administering very high doses of FVIII concentrates devoid of VWF for prolonged periods of time, ristocetin cofactor and VWF levels should be monitored.
Optimized triangle mesh compression using prediction trees (2002)

Recently, a wealth of algorithms for the efficient coding of 3D triangle meshes have been published. All these focus on achieving the most compact code for the connectivity data. The geometric data, i.e. the vertex coordinates, are then coded in an order induced by the connectivity code, which is probably not optimal. This is a pity, as the geometric portion of the data set dominates the code. We propose a way to optimize the geometry code without sacrificing too much in the connectivity code. In our approach, we achieve approximately two bits/triangle for the connectivity before entropy coding, which is not as good as other published algorithms but certainly not significantly worse. Our approach is based on the parallelogram prediction method for mesh geometry. This method is based on the observation that two adjacent triangles in a typical mesh tend to form a shape similar to a parallelogram. If an algorithm uses a parallelogram prediction method then it should build a traversal structure of triangles covering all vertices. The vertex coordinates are then predicted as the structure is traversed. The cost of this code is then the entropy of the distribution of the vertex prediction errors. Since this entropy is hard to manipulate, the accepted practice is to measure the code's effectiveness in the approximation sense, i.e. as the sum of the lengths of the vertex prediction error vectors. The full version of this paper is available at <http://www.cs.technion.ac.il//spl sim/gotsman/pubs/kronrod1.zip>.
N‐Terminal Protein Modification through a Biomimetic Transamination Reaction (2006)

One hit wonder: A biomimetic transamination reaction has been developed that employs pyridoxal-5-phosphate to modify the N terminus of proteins and peptides under mild conditions. This technique introduces a uniquely reactive carbonyl group in a single location (see scheme), thus allowing further elaboration through oxime or hydrazone formation. This modification strategy is also compatible with proteins containing a free cysteine residue.
Mucosal Delivery of Inactivated Influenza Vaccine Induces B-Cell-Dependent Heterosubtypic Cross-Protection against Lethal Influenza A H5N1 Virus Infection (2001)

Influenza vaccines that induce greater cross-reactive or heterosubtypic immunity (Het-I) may overcome limitations in vaccine efficacy imposed by the antigenic variability of influenza A viruses. We have compared mucosal versus traditional parenteral administration of inactivated influenza vaccine for the ability to induce Het-I in BALB/c mice and evaluated a modified Escherichia coli heat-labile enterotoxin adjuvant, LT(R192G), for augmentation of Het-I. Mice that received three intranasal (i.n.) immunizations of H3N2 vaccine in the presence of LT(R192G) were completely protected against lethal challenge with a highly pathogenic human H5N1 virus and had nasal and lung viral titers that were at least 2,500-fold lower than those of control mice receiving LT(R192G) alone. In contrast, mice that received three vaccinations of H3N2 vaccine subcutaneously in the presence or absence of LT(R192G) or incomplete Freund's adjuvant were not protected against lethal challenge and had no significant reductions in tissue virus titers observed on day 5 post-H5N1 virus challenge. Mice that were i.n. administered H3N2 vaccine alone, without LT(R192G), displayed partial protection against heterosubtypic challenge. The immune mediators of Het-I were investigated. The functional role of B and CD8+ T cells in Het-I were evaluated by using gene-targeted B-cell (IgH-6(-/-))- or beta2-microglobulin (beta2m(-/-))-deficient mice, respectively. beta2m(-/-) but not IgH-6(-/-) vaccinated mice were protected by Het-I and survived a lethal infection with H5N1, suggesting that B cells, but not CD8+ T cells, were vital for protection of mice against heterosubtypic challenge. Nevertheless, CD8+ T cells contributed to viral clearance in the lungs and brain tissues of heterotypically immune mice. Mucosal but not parenteral vaccination induced subtype cross-reactive lung immunoglobulin G (IgG), IgA, and serum IgG anti-hemagglutinin antibodies, suggesting the presence of a common cross-reactive epitope in the hemagglutinins of H3 and H5. These results suggest a strategy of mucosal vaccination that stimulates cross-protection against multiple influenza virus subtypes, including viruses with pandemic potential.
Phase I Trial of 177Lutetium-Labeled J591, a Monoclonal Antibody to Prostate-Specific Membrane Antigen, in Patients With Androgen-Independent Prostate Cancer (2005)

The MTD of (177)Lu-J591 is 70 mCi/m(2). Multiple doses of 30 mCi/m(2) are well tolerated. Acceptable toxicity, excellent targeting of known sites of PC metastases, and biologic activity in patients with androgen-independent PC warrant further investigation.
A new decoding algorithm for correcting both erasures and errors of reed-solomon codes (2003)

In this paper, a high efficient decoding algorithm is developed here in order to correct both erasures and errors for Reed-Solomon (RS) codes based on the Euclidean algorithm together with the Berlekamp-Massey (BM) algorithm. The new decoding algorithm computes the errata locator polynomial and the errata evaluator polynomial simultaneously without performing polynomial divisions, and there is no need for the computation of the discrepancies and the field element inversions. Also, the separate computation of the Forney syndrome needed in the decoder is completely avoided. As a consequence, the complexity of this new decoding algorithm is dramatically reduced. Finally, the new algorithm has been verified through a software simulation using C/sup ++/ language. An illustrative example of (255,239) RS code using this program shows that the speed of the decoding process is approximately three times faster than that of the inverse-free Berlekamp-Massey algorithm.
Multifunctional host defense peptides: intracellular‐targeting antimicrobial peptides (2009)

There is widespread acceptance that cationic antimicrobial peptides, apart from their membrane-permeabilizing/disrupting properties, also operate through interactions with intracellular targets, or disruption of key cellular processes. Examples of intracellular activity include inhibition of DNA and protein synthesis, inhibition of chaperone-assisted protein folding and enzymatic activity, and inhibition of cytoplasmic membrane septum formation and cell wall synthesis. The purpose of this minireview is to question some widely held views about intracellular-targeting antimicrobial peptides. In particular, I focus on the relative contributions of intracellular targeting and membrane disruption to the overall killing strategy of antimicrobial peptides, as well as on mechanisms whereby some peptides are able to translocate spontaneously across the plasma membrane. Currently, there are no more than three peptides that have been convincingly demonstrated to enter microbial cells without the involvement of stereospecific interactions with a receptor/docking molecule and, once in the cell, to interfere with cellular functions. From the limited data currently available, it seems unlikely that this property, which is isolated in particular peptide families, is also shared by the hundreds of naturally occurring antimicrobial peptides that differ in length, amino acid composition, sequence, hydrophobicity, amphipathicity, and membrane-bound conformation. Microbial cell entry and/or membrane damage associated with membrane phase/transient pore or long-lived transitions could be a feature common to intracellular-targeting antimicrobial peptides and mammalian cell-penetrating peptides that have an overrepresentation of one or two amino acids, i.e. Trp and Pro, His, or Arg. Differences in membrane lipid composition, as well as differential lipid recruitment by peptides, may provide a basis for microbial cell killing on one hand, and mammalian cell passage on the other.
Line scan proton spin imaging in biological structures by NMR (1976)

Fast scan spin imaging has been used to produce representations of static distributions of the free water (fat or oil) contained in various biological specimens. It is believed that NMR imaging will be a valuable medical diagnostic aid in man as well as a useful tool for the biologist and botanist.
Galectin-3 promotes HIV-1 budding via association with Alix and Gag p6 (2014)

Galectin-3 has been reported to regulate the functions of a number of immune cell types. We previously reported that galectin-3 is translocated to immunological synapses in T cells upon T-cell receptor engagement, where it associates with ALG-2-interacting protein X (Alix). Alix is known to coordinate with the endosomal sorting complex required for transport (ESCRT) to promote human immunodeficiency virus (HIV)-1 virion release. We hypothesized that galectin-3 plays a role in HIV-1 viral budding. Cotransfection of cells of the Jurkat T line with galectin-3 and HIV-1 plasmids resulted in increased HIV-1 budding, and suppression of galectin-3 expression by RNAi in Hut78 and primary CD4+ T cells led to reduced HIV-1 budding. We used immunofluorescence microscopy to observe the partial colocalization of galectin-3, Alix and Gag in HIV-1-infected cells. Results from co-immunoprecipitation experiments indicate that galectin-3 expression promotes Alix-Gag p6 association, whereas the results of Alix knockdown suggest that galectin-3 promotes HIV-1 budding through Alix. HIV-1 particles released from galectin-3-expressing cells acquire the galectin-3 protein in an Alix-dependent manner, with proteins primarily residing inside the virions. We also found that the galectin-3 N-terminal domain interacts with the proline-rich region of Alix. Collectively, these results suggest that endogenous galectin-3 facilitates HIV-1 budding by promoting the Alix-Gag p6 association.
On-chip high-throughput manipulation of particles in a dielectrophoresis-active hydrophoretic focuser (2014)

This paper proposes a novel concept of dielectrophoresis (DEP)-active hydrophoretic focusing of micro-particles and murine erythroleukemia (MEL) cells. The DEP-active hydrophoretic platform consists of crescent shaped grooves and interdigitated electrodes that generate lateral pressure gradients. These embedded electrodes exert a negative DEP force onto the particles by pushing them into a narrow space in the channel where the particle to groove interaction is intensive and hydrophoretic ordering occurs. Particles passing through the microfluidic device are directed towards the sidewalls of the channel. The critical limitation of DEP operating at a low flow rate and the specific hydrophoretic device for focusing particles of given sizes were overcome with the proposed microfluidic device. The focusing pattern can be modulated by varying the voltage. High throughput was achieved (maximum flow rate ~150 μL min(-1)) with good focusing performance. The non-spherical MEL cells were utilised to verify the effectiveness of the DEP-active hydrophoretic device.
Genetic and pharmacological disruption of the TEAD–YAP complex suppresses the oncogenic activity of YAP (2012)

The Drosophila TEAD ortholog Scalloped is required for Yki-mediated overgrowth but is largely dispensable for normal tissue growth, suggesting that its mammalian counterpart may be exploited for selective inhibition of oncogenic growth driven by YAP hyperactivation. Here we test this hypothesis genetically and pharmacologically. We show that a dominant-negative TEAD molecule does not perturb normal liver growth but potently suppresses hepatomegaly/tumorigenesis resulting from YAP overexpression or Neurofibromin 2 (NF2)/Merlin inactivation. We further identify verteporfin as a small molecule that inhibits TEAD-YAP association and YAP-induced liver overgrowth. These findings provide proof of principle that inhibiting TEAD-YAP interactions is a pharmacologically viable strategy against the YAP oncoprotein.
Self organizing neural networks with a split/merge algorithm (1990)

In this paper we present a new learning algorithm for Artificial Neural Networks (ANN) using a split/merge technique. An ANN model with the new algorithm has been developed and tested on a PC. The model detects the similarity between the input patterns, and identifies the number of categories present in the input samples. The algorithm is similar to a competitive learning algorithm. Unlike the competitive learning algorithm, in this algorithm we use two types of weights: long term weights (LTWs) and short term weights (STWs). The network stability is provided by the LTWs, whereas the network plasticity is provided by STWs. As an illustration, the model is used to categorize pixels in a multispectral image. The categorization is based on the observed spectral signature at each pixel.