gebhart/patrepeval huggingface dataset:
GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation (2009)

O-GlcNAcylation is an essential, dynamic and inducible post-translational glycosylation of cytosolic proteins in metazoa and can show interplay with protein phosphorylation. Inhibition of OGA (O-GlcNAcase), the enzyme that removes O-GlcNAc from O-GlcNAcylated proteins, is a useful strategy to probe the role of this modification in a range of cellular processes. In the present study, we report the rational design and evaluation of GlcNAcstatins, a family of potent, competitive and selective inhibitors of human OGA. Kinetic experiments with recombinant human OGA reveal that the GlcNAcstatins are the most potent human OGA inhibitors reported to date, inhibiting the enzyme in the sub-nanomolar to nanomolar range. Modification of the GlcNAcstatin N-acetyl group leads to up to 160-fold selectivity against the human lysosomal hexosaminidases which employ a similar substrate-assisted catalytic mechanism. Mutagenesis studies in a bacterial OGA, guided by the structure of a GlcNAcstatin complex, provides insight into the role of conserved residues in the human OGA active site. GlcNAcstatins are cell-permeant and, at low nanomolar concentrations, effectively modulate intracellular O-GlcNAc levels through inhibition of OGA, in a range of human cell lines. Thus these compounds are potent selective tools to study the cell biology of O-GlcNAc.
A new temperature, capacitive-resistivity, and magnetic-susceptibility borehole probe for mineral exploration, groundwater, and environmental applications (2011)

A new borehole-logging probe has been developed and fi eld tested for the simultaneous recording of high-resolution temperature, capacitive-resistivity, and magnetic-susceptibility logs. The resistivity parameter is measured with a capacitive sensor. The probe was developed by the Borehole Geophysics Group at the Geological Survey of Canada in Ottawa. Applications documented in detail include mineral exploration, groundwater and environmental monitoring, and geotechnical studies. The probe is expected to soon be commercially available.
Clinical use of electronic portal imaging: Report of AAPM Radiation Therapy Committee Task Group 58 (2001)

AAPM Task Group 58 was created to provide materials to help the medical physicist and colleagues succeed in the clinical implementation of electronic portal imaging devices (EPIDs) in radiation oncology. This complex technology has matured over the past decade and is capable of being integrated into routine practice. However, the difficulties encountered during the specification, installation, and implementation process can be overwhelming. TG58 was charged with providing sufficient information to allow the users to overcome these difficulties and put EPIDs into routine clinical practice. In answering the charge, this report provides; comprehensive information about the physics and technology of currently available EPID systems; a detailed discussion of the steps required for successful clinical implementation, based on accumulated experience; a review of software tools available and clinical use protocols to enhance EPID utilization; and specific quality assurance requirements for initial and continuing clinical use of the systems. Specific recommendations are summarized to assist the reader with successful implementation and continuing use of an EPID.
Controlling the surface properties of high temperature superconductors (1997)

Molecular monolayer‐based surface modification has been used extensively for three of the four important classes of electronic materials, namely metals, semiconductors, and insulators. In this article recent progress in the application of t. is technique, which is commonly called “self‐assembly”, to the modification of the surfaces of high‐ T c superconductors (e.g. see Figure) is reviewed. magnified image
THE EFFECT OF DONOR STRAIN BLOOD PRETREATMENT ON RENAL ALLOGRAFT REJECTION IN RATS (1972)

SUMMARY In the experiments reported here, the effects of both single and multiple i.v. injections of donor strain blood have been investigated in both DA and Lewis recipients of (DA X Lewis) F1 renal allografts. The (DA X Lewis) F1 to Lewis model represented the stronger incompatibility and was characterised by vigorous unmodified rejection, ready production of lymphocytotoxins, and difficulty in induction of specific immunosuppression. In the (DA X Lewis)F1 to DA model, unmodified rejection was sometimes spontaneously reversible, lymphocytotoxin production was weak or absent, and specific immunosuppression was easily induced. In both strain combinations, the timing of single exposures to donor strain blood was critical. Exposures 1 day pregraft resulted in sensitisation in the F1 to Lewis model and no effect in the F1 to DA model. If the grafts were delayed until 7 days after exposure to blood, then immunosuppression was the result in both models, but was far more effective in F1 to DA transplants, where most recipients went on to be long-term survivors. By 4 weeks after exposure to blood, immunosuppression was still present in the F1 to DA model but had virtually disappeared in the F1 to Lewis model. Multiple exposures to blood were more effective than single exposures for the production of immunosuppression. In many experimental groups, donor-specific lymphocytotoxins induced by the blood transfusions were present at the time of grafting, but in no case was hyperacute rejection seen.
A Role for Syndecan-1 in Coupling Fascin Spike Formation by Thrombospondin-1 (2001)

An important role of cell matrix adhesion receptors is to mediate transmembrane coupling between extracellular matrix attachment, actin reorganization, and cell spreading. Thrombospondin (TSP)-1 is a modulatory component of matrix expressed during development, immune response, or wound repair. Cell adhesion to TSP-1 involves formation of biochemically distinct matrix contacts based on stable fascin spikes. The cell surface adhesion receptors required have not been identified. We report here that antibody clustering of syndecan-1 proteoglycan specifically transduces organization of cortical actin and fascin bundles in several cell types. Transfection of COS-7 cells with syndecan-1 is sufficient to stimulate cell spreading, fascin spike assembly, and extensive protrusive lateral ruffling on TSP-1 or on syndecan-1 antibody. The underlying molecular mechanism depends on glycosaminoglycan (GAG) modification of the syndecan-1 core protein at residues S45 or S47 for cell membrane spreading and on the VC2 region of the cytoplasmic domain for spreading and fascin spike formation. Expression of the VC2 deletion mutant or GAG-negative syndecan-1 showed that syndecan-1 is necessary in spreading and fascin spike formation by C2C12 cells on TSP-1. These results establish a novel role for syndecan-1 protein in coupling a physiological matrix ligand to formation of a specific matrix contact structure.
Lack of effects on heart rate and blood pressure in ketamine-anesthetized rats briefly exposed to ultra-wideband electromagnetic pulses (1999)

Fourteen Sprague-Dawley rats were exposed to pulses produced by a Bournlea ultra-wideband (UWB) pulse generator (rise time, 318-337 ps; maximum E field, 19-21 kV/m). Exposures at a repetition frequency of 1 kHz for 0.5 s or to repetitive pulse trains (2-s exposure periods alternating with 2 s of no exposure, for a total of 2 min) resulted in no significant changes in heart rate or mean arterial blood pressure. These results suggest that acute whole-body exposure to UWB pulses does not have a detrimental effect on the cardiovascular system.
Designing Effective Inter-Pixel Information Flow for Natural Image Matting (2017)

We present a novel, purely affinity-based natural image matting algorithm. Our method relies on carefully defined pixel-to-pixel connections that enable effective use of information available in the image and the trimap. We control the information flow from the known-opacity regions into the unknown region, as well as within the unknown region itself, by utilizing multiple definitions of pixel affinities. This way we achieve significant improvements on matte quality near challenging regions of the foreground object. Among other forms of information flow, we introduce color-mixture flow, which builds upon local linear embedding and effectively encapsulates the relation between different pixel opacities. Our resulting novel linear system formulation can be solved in closed-form and is robust against several fundamental challenges in natural matting such as holes and remote intricate structures. While our method is primarily designed as a standalone natural matting tool, we show that it can also be used for regularizing mattes obtained by various sampling-based methods. Our evaluation using the public alpha matting benchmark suggests a significant performance improvement over the state-of-the-art.
The Wolff-Parkinson-White syndrome: the cellular substrate for conduction in the accessory atrioventricular pathway (1994)

The longstanding quest for the anatomical basis of the Wolff-Parkinson-White syndrome has left many unanswered questions. The ultrastructural morphology of the myocytes comprising accessory atrioventricular pathways, which are capable of rapid and variable conduction, is central to understanding the development and behaviour of this congenital anomaly, but remains unknown. Examination of three surgically resected pathways was performed to determine their underlying cellular morphology and the pattern of intercellular coupling, by correlative light microscopy, electron microscopy and confocal scanning laser microscopy combined with immunohistochemical localization of the cardiac gap-junctional protein, connexin43. Two left-sided pathways were composed of myocardium of 'normal working ventricular' type. The right-sided pathway was composed almost entirely of highly abnormal myocytes characterized by aberrant myofibril organisation, with a lack of A-band material and abnormal mitochondria, but normal intact intercalated disks no different from those seen in left-sided pathways. The gap junctions of all pathways were composed of connexin43 distributed as in ventricular myocardium, and not as found in atrial or atrioventricular nodal tissues. While myocytes of abnormal structure were present in one of the accessory atrioventricular pathways examined, all pathways had morphologically normal gap junctions, the structures responsible for efficient intercellular coupling, with a pattern of distribution suggestive of working ventricular myocardium.
Efficient intra-mode decision algorithm for inter-frames in H.264/AVC video coding (2011)

An efficient intra-mode search algorithm is proposed to reduce the computational complexity of inter-frames for the H.264/AVC video encoding system. Each intra-mode search procedure usually causes a high degree of complexity in an inter-frame because of the inter-frame prediction modes that operate with the inter-mode decision procedure. To decrease this computational burden, the authors propose an adaptive thresholding algorithm based on distribution characteristics of the sum of the absolute differences (SAD) of the best inter-mode when the intra-mode is the final coding mode. The authors also include a simple refinement process by using the spatial correlation between neighbouring macro-blocks (MBs) and the current MB. The performance of the proposed algorithm is verified through comparative analysis of encoding time, loss of quality and the bit increment.
Cloning and expression of human ciliary neurotrophic factor (1991)

Ciliary neurotrophic factor (CNTF) is a survival factor for avian ciliary ganglion neurons and a variety of other neuronal cell types in vitro. We report here the cloning of the entire genomic sequence encoding human CNTF and its primary structure. Biologically active CNTF has been expressed in Chinese hamster ovary cells from a human genomic DNA clone. Human CNTF has no significant sequence similarity to any previously reported protein, although approximately 84% similarity exists compared with rat and rabbit CNTF. The lack of both an N-terminal signal sequence and consensus sequences for glycosylation or hydrophobic regions, and the fact that active CNTF is expressed but not released into the culture medium of transfected cells, argue in favour of human CNTF as a cytosolic protein. These data provide a basis for understanding the role of CNTF in nervous system physiology and pathology.
A regional broadcast-centric education system (2002)

Argues that a broadcast-centric solution can be enabled to provide educational services, in particular distance learning, to an entire region. This solution can provide equity access to resources for all schools in a large region, or access for undergraduate and postgraduate students to an open regional university. The approach described includes a combination of broadcast delivery and local redistribution of content and/or direct and interactive access to the content over the broadcast infrastructure. It requires that special consideration be given to the organization of content for distribution in this manner, therefore those issues are discussed. Enabling technologies are described.
Effects of repeated morphine on locomotion, place preference and dopamine in heterozygous glial cell line‐derived neurotrophic factor knockout mice (2006)

Glial cell line-derived neurotrophic factor (GDNF) has been shown to be involved in the maintenance of striatal dopaminergic neurons. Neurotrophic factors are crucial for the plasticity of central nervous system and may be involved in long-term responses to drug exposure. To study the effects of reduced GDNF on dopaminergic behaviour related to addiction, we compared the effects of morphine on locomotor activity, conditioned place preference (CPP) and extracellular accumbal dopamine in heterozygous GDNF knockout mice (GDNF+/-) with those in their wild-type (Wt) littermates. When morphine 30 mg/kg was administered daily for 4 days, tolerance developed towards its locomotor stimulatory action only in the GDNF+/- mice. A morphine 5 mg/kg challenge dose stimulated locomotor activity only in the GDNF+/- mice withdrawn for 96 h from repeated morphine treatment, whereas clear and similar sensitization of the locomotor response was seen after a 10 mg/kg challenge dose in mice of both genotypes. Morphine-induced CPP developed initially similarly in Wt and GDNF+/- mice, but it lasted longer in the Wt mice. The small challenge dose of morphine increased accumbal dopamine output slightly more in the GDNF+/- mice than in the Wt mice, but doubling the challenge dose caused a dose-dependent response only in the Wt mice. In addition, repeated morphine treatment counteracted the increase in the accumbal extracellular dopamine concentration we previously found in drug-naive GDNF+/- mice. Thus, reduced endogenous GDNF level alters the dopaminergic behavioural effects to repeatedly administered morphine, emphasizing the involvement of GDNF in the neuroplastic changes related to long-term effects of drugs of abuse.
Hb G Makassar (beta 6:Glu-Ala) in a Thai family. (2002)

Hemoglobin G Makassar was identified in a family of Thai origin, which was found to share identical properties with hemoglobin S in routine hemoglobin separation both by cellulose acetate electrophoresis and cation-exchange HPLC. It is, therefore, subjects with hemoglobin G Makassar and hemoglobin S who may sometimes be mistakenly identified for each other. In this study, identification of hemoglobin G Makassar was achieved by DNA sequence analysis, which revealed a single nucleotide substitution GAG-->GCG at codon 6 of the beta-globin gene. The hemoglobin variant was hemoglobin G Makassar [beta 6:Glu-->Ala]. This is the first report of hemoglobin G Makassar in Thailand.
A Novel Fluorescent Probe That Is Brain Permeable and Selectively Binds to Myelin (2006)

Myelin is a multilayered glial cell membrane that forms segmented sheaths around large-caliber axons of both the central nervous system (CNS) and peripheral nervous system (PNS). Myelin covering insures rapid and efficient transmission of nerve impulses. Direct visual assessment of local changes of myelin content in vivo could greatly facilitate diagnosis and therapeutic treatments of myelin-related diseases. Current histologic probes for the visualization of myelin are based on antibodies or charged histochemical reagents that do not enter the brain. We have developed a series of chemical compounds including (E,E)-1,4-bis(4'-aminostyryl)-2-dimethoxy-benzene termed BDB and the subject of this report, which readily penetrates the blood-brain barrier and selectively binds to the myelin sheath in brain. BDB selectively stains intact myelinated regions in wild-type mouse brain, which allows for delineation of cuprizone-induced demyelinating lesions in mouse brain. BDB can be injected IV into the brain and selectively detect demyelinating lesions in cuprizone-treated mice in situ. These studies justified further investigation of BDB as a potential myelin-imaging probe to monitor myelin pathology in vivo.
Purification, cloning, and molecular characterization of a high molecular weight hemorrhagic metalloprotease, jararhagin, from Bothrops jararaca venom. Insights into the disintegrin gene family (1992)

A large hemorrhagin, jararhagin, has been cloned from a Bothrops jararaca venom gland cDNA expression library. The cDNA sequence predicts a 421-amino acid residue molecule with strong amino acid sequence homology and similar domain structure to HR1B, a high molecular weight hemorrhagic metalloprotease isolated from Trimeresurus flavoviridis (Habu) venom. Like HR1B, jararhagin contains enzyme, disintegrin, and cysteine-rich carboxyl-terminal regions. In the disintegrin region, the Arg-Gly-Asp sequence is replaced by Glu-Cys-Asp, as found in non-Arg-Gly-Asp disintegrin regions of HR1B and a guinea pig sperm fusion protein PH-30 beta. The cDNA sequence of jararhagin predicts a precursor protein (proprotein) with striking similarity to cryptic regions in precursors of the disintegrin peptides trigramin and rhodostomin. Comparison of jararhagin with disintegrin precursors highlights the modular arrangement of proprotein, metalloprotease, and disintegrin domains in the metalloprotease/disintegrin family and provides an insight into their biosynthesis and evolution.
Decoder side motion vector derivation for inter frame video coding (2008)

In this paper, a decoder side motion vector derivation scheme for inter frame video coding is proposed. Using a template matching algorithm, motion information is derived at the decoder instead of explicitly coding the information into the bitstream. Based on Lagrangian rate-distortion optimisation, the encoder locally signals whether motion derivation or forward motion coding is used. While our method exploits multiple reference pictures for improved prediction performance and bitrate reduction, only a small template matching search range is required. Derived motion information is reused to improve the performance of predictive motion vector coding in subsequent blocks. An efficient conditional signalling scheme for motion derivation in Skip blocks is employed. The motion vector derivation method has been implemented as an extension to H.264/AVC. Simulation results show that a bitrate reduction of up to 10.4% over H.264/AVC is achieved by the proposed scheme.
New mre genes mreC and mreD, responsible for formation of the rod shape of Escherichia coli cells (1989)

New shape-determining genes in the mre cluster at 71 min on the Escherichia coli chromosome map, named mreC and mreD, were identified by complementation experiments using delta mre-678 mutant cells, which have a 5-kilobase-pair deletion encompassing the mre region, and by DNA sequencing. The delta mre-678 mutant cells required three genes, the previously reported mreB gene and the two new genes, to restore the normal rod shape of the cells and normal sensitivity of growth to mecillinam. The mreC gene is preceded by the mreB gene and by a 65-base-pair spacing sequence containing a palindrome sequence and a possible Shine-Dalgarno sequence. The deduced amino acid sequence of the MreC protein consists of 367 amino acid residues with a molecular weight of 39,530. The initiation codon of the mreD gene overlaps the termination codon of the mreC gene by one nucleotide residue. The deduced amino acid sequence of the MreD protein consists of 162 amino acid residues with a molecular weight of 18,755. In vitro, the coding frames of mreC and mreD produced proteins with Mrs of 40,000 and 15,000, respectively, as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Modeling Studies of Binding of Sea Raven Type II Antifreeze Protein to Ice (1997)

Certain plants, insects, and fish living in cold environments prevent tissue damage due to freezing by producing antifreeze proteins or antifreeze glycoproteins that inhibit ice growth below the normal equilibrium freezing point of water in a noncolligative fashion. In polar fish these macromolecules, taking into account their structural characteristics, are grouped into three broad classes, namely Type I, Type II, and Type III. In this paper we report the results of our studies on the stereospecific binding of sea raven, a Type II antifreeze protein (AFP) to (111) hexagonal bipyramidal faces of ice. Earlier studies of Type I and Type III AFPs have shown that stereospecific binding of these proteins, recognizing specific planes of ice, is essential for their noncolligative antifreeze point depression. Moreover, as it has been shown for the AFT of Type I, this binding also occurs along specific vectors on these planes and also is enantioselective, distinguishing between the mirror related directions. In this study we will show, by using molecular modeling, that the fold of Type II AFP could facilitate a stereospecific mode of interaction with (111) planes of ice. Similar to Type I AFP, preferential directionality of binding was also observed in the simulations.
Parkinson's disease-associated mutations in LRRK2 link enhanced GTP-binding and kinase activities to neuronal toxicity (2007)

Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) cause late-onset Parkinson's disease indistinguishable from idiopathic disease. The mechanisms whereby missense alterations in the LRRK2 gene initiate neurodegeneration remain unknown. Here, we demonstrate that seven of 10 suspected familial-linked mutations result in increased kinase activity. Functional and disease-associated mutations in conserved residues reveal the critical link between intrinsic guanosine triphosphatase (GTPase) activity and downstream kinase activity. LRRK2 kinase activity requires GTPase activity, whereas GTPase activity functions independently of kinase activity. Both LRRK2 kinase and GTPase activity are required for neurotoxicity and potentiate peroxide-induced cell death, although LRRK2 does not function as a canonical MAP-kinase-kinase-kinase. These results suggest a link between LRRK2 kinase activity and pathogenic mechanisms relating to neurodegeneration, further supporting a gain-of-function role for LRRK2 mutations.
Tracing ray differentials (1999)

Antialiasing of ray traced images is typically performed by supersampling the image plane. While this type of filtering works well for many algorithms, it is much more efficient to perform filtering locally on a surface for algorithms such as texture mapping. In order to perform this type of filtering, one must not only trace the ray passing through the pixel, but also have some approximation of the distance to neighboring rays hitting the surface (i.e., a ray's footprint). In this paper, we present a fast, simple, robust scheme for tracking such a quantity based on ray differentials, derivatives of the ray with respect to the image plane.