gebhart/patrepeval huggingface dataset:
Islet Regeneration During the Reversal of Autoimmune Diabetes in NOD Mice (2003)

Nonobese diabetic (NOD) mice are a model for type 1 diabetes in humans. Treatment of NOD mice with end-stage disease by injection of donor splenocytes and complete Freund's adjuvant eliminates autoimmunity and permanently restores normoglycemia. The return of endogenous insulin secretion is accompanied by the reappearance of pancreatic beta cells. We now show that live donor male or labeled splenocytes administered to diabetic NOD females contain cells that rapidly differentiate into islet and ductal epithelial cells within the pancreas. Treatment with irradiated splenocytes is also followed by islet regeneration, but at a slower rate. The islets generated in both instances are persistent, functional, and apparent in all NOD hosts with permanent disease reversal.
On the performance of integrated interleaving coding schemes (2004)

The correction of errors in bursty channels commonly utilizes interleaved blocks of codewords. Integrated Interleaving coding schemes [1] uses nonuniform redundancy in the interleaves that can be adjusted on-the-fly according to the error statistics of the channel. This gives greater flexibility in the designing of the code and achieves higher reliability for the same code rate. We give a different and substantially tighter theoretical evaluation on the performance of the Integrated Interleaving code than [1]. Based on the tighter theoretical evaluation, we formulate a closed-form analytical expression for its performance in terms of the word-error probability. We also propose a modified decoding algorithm of the Integrated Interleaving codes which achieves a significant gain in performance. We optimize the performance of this scheme within a given class of codes.
Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional 13C labeling of common amino acids (2001)

Aerobic and anaerobic central metabolism of Saccharomyces cerevisiae cells was explored in batch cultures on a minimal medium containing glucose as the sole carbon source, using biosynthetic fractional (13)C labeling of proteinogenic amino acids. This allowed, firstly, unravelling of the network of active central pathways in cytosol and mitochondria, secondly, determination of flux ratios characterizing glycolysis, pentose phosphate cycle, tricarboxylic acid cycle and C1-metabolism, and thirdly, assessment of intercompartmental transport fluxes of pyruvate, acetyl-CoA, oxaloacetate and glycine. The data also revealed that alanine aminotransferase is located in the mitochondria, and that amino acids are synthesized according to documented pathways. In both the aerobic and the anaerobic regime: (a) the mitochondrial glycine cleavage pathway is active, and efflux of glycine into the cytosol is observed; (b) the pentose phosphate pathways serve for biosynthesis only, i.e. phosphoenolpyruvate is entirely generated via glycolysis; (c) the majority of the cytosolic oxaloacetate is synthesized via anaplerotic carboxylation of pyruvate; (d) the malic enzyme plays a key role for mitochondrial pyruvate metabolism; (e) the transfer of oxaloacetate from the cytosol to the mitochondria is largely unidirectional, and the activity of the malate-aspartate shuttle and the succinate-fumarate carrier is low; (e) a large fraction of the mitochondrial pyruvate is imported from the cytosol; and (f) the glyoxylate cycle is inactive. In the aerobic regime, 75% of mitochondrial oxaloacetate arises from anaplerotic carboxylation of pyruvate, while in the anaerobic regime, the tricarboxylic acid cycle is operating in a branched fashion to fulfill biosynthetic demands only. The present study shows that fractional (13)C labeling of amino acids represents a powerful approach to study compartmented eukaryotic systems.
Earliest cardiac toxicity induced by iron overload selectively inhibits electrical conduction (2002)

Female guinea pigs were injected intraperitoneally with 0.083 g/kg iron dextran (Fe-D) to achieve progressively increasing levels of iron load; controls received dextran. Delayed and blocked cardiac conductivity at the Purkinje fiber-papillary muscle junction was initially observed with Fe-D loads of 0.33 g/kg. Serial magnetic resonance relaxation time measurements obtained from livers of live animals showed a decrease (8.1 +/- 0.86 vs. 14.8 +/- 1.03 ms in controls, P < 0.001) that was first observed in animals loaded with 0.25 g/kg Fe-D. Iron concentrations in hearts and livers were significantly increased (P < 0.001). Left ventricular pressure measurements on 1.5 g/kg Fe-D animals failed to demonstrate a defect in contractility, but 27% (9/33) (P < 0.050) of the animals died without warning signs. We conclude that 1) initial decreases in liver magnetic resonance-relaxation time occur in the same range of iron excess as the threshold of iron load that induces delay or blockade of cardiac conduction and 2) a high incidence of sudden death, presumably from cardiac arrhythmias, was observed with large doses of iron that did not decrease left ventricular contractility.
Adhesion Measurement of Thin Films (1976)

A critical and comprehensive review of the various methods for the measurement of adhesion of thin films is presented. Emphasis has been placed on the techniques used for thin films (&lt;1 μ m) but consideration has also been extended to methods which have proved successful in case of relatively thicker coatings and are potentially applicable in the study of thin films. Most of the methods catalogued in this review have been harnessed in measuring the adhesion of thin evaporated or sputtered metallic films on an assortment of substrates; the literature references to the study of thin polymeric films are extremely meager. The methods of determination of adhesion are discussed under three headings: Nucleation Methods, Mechanical Methods and Miscellaneous Techniques. Furthermore, the mechanical methods are categorized depending upon the mode of application of the force to disrupt the interface. Although the emphasis is on the quantitative methods of measuring adhesion, but for completeness qualitative as well as the methods which are still in a state of infancy have been included. Requirements for the ideal adhesion test are outlined and, apparently, there does not exist any test which fulfils all the virtues. Many of the techniques may not provide absolute quantitative values of adhesion strength but these can profitably be used to follow relative changes in adhesion strength due to process variables, ageing weathering, etc. The principle, merits, potentialities, and limitations of each technique are outlined, and the difficulties associated with measuring adhesion strengths and their relationship to “basic adhesion” are discussed.
Chromosome Alignment and Segregation Regulated by Ubiquitination of Survivin (2005)

Proper chromosome segregation requires the attachment of sister kinetochores to microtubules from opposite spindle poles to form bi-oriented chromosomes on the metaphase spindle. The chromosome passenger complex containing Survivin and the kinase Aurora B regulates this process from the centromeres. We report that a de-ubiquitinating enzyme, hFAM, regulates chromosome alignment and segregation by controlling both the dynamic association of Survivin with centromeres and the proper targeting of Survivin and Aurora B to centromeres. Survivin is ubiquitinated in mitosis through both Lys(48) and Lys(63) ubiquitin linkages. Lys(63) de-ubiquitination mediated by hFAM is required for the dissociation of Survivin from centromeres, whereas Lys(63) ubiquitination mediated by the ubiquitin binding protein Ufd1 is required for the association of Survivin with centromeres. Thus, ubiquitinaton regulates dynamic protein-protein interactions and chromosome segregation independently of protein degradation.
Numerical simulations of particulate suspensions via a discretized Boltzmann equation. Part 1. Theoretical foundation (1994)

A new and very general technique for simulating solid–fluid suspensions is described; its most important feature is that the computational cost scales linearly with the number of particles. The method combines Newtonian dynamics of the solid particles with a discretized Boltzmann equation for the fluid phase; the many-body hydrodynamic interactions are fully accounted for, both in the creeping-flow regime and at higher Reynolds numbers. Brownian motion of the solid particles arises spontaneously from stochastic fluctuations in the fluid stress tensor, rather than from random forces or displacements applied directly to the particles. In this paper, the theoretical foundations of the technique are laid out, illustrated by simple analytical and numerical examples; in a companion paper (Part 2), extensive numerical tests of the method, for stationary flows, time-dependent flows, and finite-Reynolds-number flows, are reported.
Inhibit a Phosphodiesterase to Treat Heart Failure? (2018)

International audience
Aberrant expression during two‐stage mouse skin carcinogenesis of a type 147‐kDa keratin, k13, normally associated with terminal differentiation of internal stratified epithelia (1988)

Specific keratin cDNA probes and monospecific antikeratin antisera were used to analyze mouse epidermis and epidermal tumors for the expression of a type I 47-kDa keratin, K13, normally associated with terminal differentiation of internal stratified epithelia. We demonstrated that this keratin was virtually absent from the entire body epidermis at various stages of development. Also, it was not detected in various forms of acute and chronic epidermal hyperproliferation or in epidermal cells cultured under conditions that favored either cell proliferation or in vitro differentiation. In contrast, K13 was consistently expressed in squamous cell carcinomas of the skin induced by 7,12-dimethylbenz[a]anthracene and 12-O-tetradecanoylphorbol-13-acetate (TPA), whereas papillomas obtained by the same two-stage protocol were distinctly heterogeneous with regard to the expression of this keratin. These findings were true for two different strains of mice (NMRI and Sencar). Papillomas collected from Sencar mice after 12 wk or from NMRI mice after 15 wk of promotion with TPA were either negative for K13 or elicited variable amounts of this keratin. In all cases of positive expression of K13 in tumors, as in normal stratified internal epithelia, both the keratin protein and its mRNA invariably occurred in the differentiating cell compartments. In contrast to what we found in internal stratified epithelia, however, K13 was expressed without its commonly encountered type II 57-kDa partner, K4. Papillomas negative for the K13 protein were also devoid of K13 transcripts. This indicates that the aberrant K13 expression in tumors is regulated at the level of transcription. Our results suggest that K13 may provide a marker for malignant conversion in the mouse two-stage skin carcinogenesis model and may be especially suited for studies of gene expression regulation.
Identification of MARPP-58, a morphine- and cyclic AMP-regulated phosphoprotein of 58 kDa, as tyrosine hydroxylase: evidence for regulation of its expression by chronic morphine in the rat locus coeruleus (1990)

Previously, we have identified a number of morphine- and cyclic AMP-regulated phosphoproteins (MARPPs) in the rat locus coeruleus (LC) and other brain regions. We now show that one of these phosphoproteins, a 58 kDa protein designated MARPP-58, is tyrosine hydroxylase. First, MARPP-58 comigrates with immunolabeled, immunoprecipitated, and purified tyrosine hydroxylase on 1- and 2-dimensional electrophoresis. Second, MARPP-58, immunoprecipitated tyrosine hydroxylase, and purified tyrosine hydroxylase yield identical 1-dimensional phosphopeptide maps. Third, MARPP-58 exhibits a regional and subcellular distribution in brain consistent with tyrosine hydroxylase. Identification of MARPP-58 as tyrosine hydroxylase made it possible to determine whether increases in MARPP-58 phosphorylation induced by chronic morphine in the LC reported previously are associated with alterations in enzyme activity and expression in this brain region. We show that chronic treatment of rats with morphine increases levels of tyrosine hydroxylase activity, immunoreactivity, and mRNA in the LC. Induction of the enzyme by chronic morphine was blocked by concomitant treatment of rats with the opiate receptor antagonist naltrexone, indicating that morphine produces this effect through the activation of opiate receptors. Consistent with previous observations that the chronic morphine-induced change in MARPP-58 phosphorylation is specific to the LC, changes observed in enzyme activity, immunoreactivity, and mRNA were not observed in a number of other brain regions studied. The results indicate that chronic morphine regulates the expression of tyrosine hydroxylase specifically in the LC and suggest that such regulation reflects long-term adaptations of LC neurons to chronic morphine at the level of gene expression.
STERIC EFFECTS OF CHIRAL LIGANDS IN A NEW TYPE OF ALDOL CONDENSATIONS CATALYZED BY ZINC(II) COMPLEXES OF α-AMINO ACID ESTERS (1985)

Abstract The aldol condensations of p-nitrobenzaldehyde with acetone have been found to be catalyzed by Zn2+ complexes of α-amino acid esters under mild and neutral conditions to afford enantiomeric excess aldol type product along with some of the dehydrated product. The complexes with ligands containing benzene ring such as esters of Phe, Tyr, and Trp are much more effective both on catalytic activity and asymmetric induction.
Purification and Properties of Poly(ADP‐ribose) Polymerase from Pig‐Thymus Nuclei (1978)

The nuclear enzyme poly(ADP-ribose) polymerase has been purified about 9200-fold from pig thymus nuclei with a 46% yield. An aqueous organic solvent system was used for the isolation of the polymerase from nuclei and for its purification by chromatography at sub-zero temperatures. Electrophoretic analysis under both denaturing and non-denaturing conditions revealed a single protein band suggesting that the preparation was homogeneous and that the enzyme is composed of one polypeptide chain. The molecular weight estimated from sodium dodecyl sulphate-/polyacrylamide gel electrophoresis was 63 500 and from gel filtration through columns of Sephadex G-100, 58 000. The enzyme preparation was free from poly(ADP-ribose)-degrading enzymes and from DNA. The purified polymerase showed an absolute requirement for both DNA and histones. The maximal specific activity of the homogeneous preparation measured by the standardized assay, was 20.7 mu mol NAD+ incorporated x min-1 x mg-1 of protein at 37 degree C. Amino-terminal group analysis with dansyl chloride did not reveal a terminal amino acid suggesting that the amino-terminal group may be blocked. In the presence of histones, the Km for NAD+ was 23 micrometer.
A novel human airway mucin cDNA encodes a protein with unique tandem-repeat organization (1994)

Highly specific affinity-purified polyclonal antibodies against deglycosylated human tracheobronchial mucin was used to select immunoreactive clones from a Uni-ZAP cDNA expression library prepared from normal human tracheal mRNA. The largest of three positive clones, designated pAM1, which reacted strongly with the polyclonal antibodies, was further characterized. Sequence analyses revealed a partial 941 bp cDNA that encoded a 313-amino-acid polypeptide. Bases 3-892 consisted of imperfect 41-nucleotide tandem repeats (CCAGGAGGGGACACCGGGTTCACGAGCTGCCCACGCCCTCT) that encoded a unique polypeptide with two types of consensus repeats, TSCPRPLQEGTRV and TSCPRPLQEGTPGSRAAHALSRRGHRVHELPTSSPGGDTGF. The overall composition of the deduced amino acid sequence matched that expected for a mucin protein core and is rich in serine, threonine, proline, glycine and alanine (approximately 51%). Northern blots probed with the mucin cDNA exhibited intense polydisperse hybridization bands with RNA isolated from normal human trachea and cystic-fibrosis bronchus. The data indicate that mucin encoded by clone pAM1 represents a unique type of peptide organization which has not been described in mucin cDNAs reported thus far.
Mechanism of Transmembrane Signaling:  Insulin Binding and the Insulin Receptor (2000)

Transmembrane signaling via receptor tyrosine kinases generally requires oligomerization of receptor monomers, with the formation of ligand-induced dimers or higher multimers of the extracellular domains of the receptors. Such formations are expected to juxtapose the intracellular kinase domains at the correct distances and orientations for transphosphorylation. For receptors of the insulin receptor family that are constitutively dimeric, or those that form noncovalent dimers without ligands, the mechanism must be more complex. For these, the conformation must be changed by the ligand from one that prevents activation to one that is permissive for kinase phosphorylation. How the insulin ligand accomplishes this action has remained a puzzle since the discovery of the insulin receptor over 2 decades ago, primarily because membrane proteins in general have been refractory to structure determination by crystallography. However, high-resolution structural evidence on individual separate subdomains of the insulin receptor and of analogous proteins has been obtained. The recently solved quaternary structure of the complete dimeric insulin receptor in the presence of insulin has now served as the structural envelope into which such individual domains were fitted. The combined structure has provided answers on the details of insulin/receptor interactions in the binding site and on the mechanism of transmembrane signaling of this covalent dimer. The structure explains many observations on the behavior of the receptor, from greater or lesser binding of insulin and its variants, point and deletion mutants of the receptor, to antibody-binding patterns, and to the effects on basal and insulin-stimulated autophosphorylation under mild reducing conditions.
A Low-Noise RF Voltage-Controlled Oscillator Using On-Chip High-Q Three-Dimensional Coil Inductor and Micromachined Variable Capacitor (1998)

A RF voltage-controlled oscillator (VCO) employs an on chip, high-Q, three-dimensional (3-D) coil inductor and micro machined variable capacitor for frequency tuning. Unlike con ventional spiral inductors, the 3-D inductor minimizes the substrate loss and achieves a record Q of 30 at 1 GHz. The micromachined variable capacitor achieves a 15% tuning range with a nominal 2pF capacitance and a Q value above 60 at 1 GHz. Both passive components are fabricated on silicon sub strates and thus amenable to monolithic integration with stan dard IC processes. The prototype VCO exhibits a phase-noise of -136 dBc/Hz at 3 MHz offset frequency from the carrier, suit able for most wireless communication applications, in particular GSM [l]. The VCO is tunable from 855 MHz to 863 MHz under 3V, limited by the test setup.
Specific, high-efficiency, triple-helix-mediated cross-linking to duplex DNA (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpecific, high-efficiency, triple-helix-mediated cross-linking to duplex DNAJeng Pyng Shaw, John Milligan, Steven H. Krawczyk, and Mark MatteucciCite this: J. Am. Chem. Soc. 1991, 113, 20, 7765–7766Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://pubs.acs.org/doi/10.1021/ja00020a051https://doi.org/10.1021/ja00020a051research-articleACS PublicationsRequest reuse permissionsArticle Views89Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Hyperoxia-induced Apoptosis Does Not Require Mitochondrial Reactive Oxygen Species and Is Regulated by Bcl-2 Proteins (2002)

Exposure of animals to hyperoxia results in lung injury that is characterized by apoptosis and necrosis of the alveolar epithelium and endothelium. The mechanism by which hyperoxia results in cell death, however, remains unclear. We sought to test the hypothesis that exposure to hyperoxia causes mitochondria-dependent apoptosis that requires the generation of reactive oxygen species from mitochondrial electron transport. Rat1a cells exposed to hyperoxia underwent apoptosis characterized by the release of cytochrome c, activation of caspase-9, and nuclear fragmentation that was prevented by the overexpression of Bcl-X(L.) Murine embryonic fibroblasts from bax(-/-) bak(-/-) mice were resistant to hyperoxia-induced cell death. The administration of the antioxidants manganese (III) tetrakis (4-benzoic acid) porphyrin, ebselen, and N-acetylcysteine failed to prevent cell death following exposure to hyperoxia. Human fibrosarcoma cells (HT1080) lacking mitochondrial DNA (rho(0) cells) that failed to generate reactive oxygen species during exposure to hyperoxia were not protected against cell death following exposure to hyperoxia. We conclude that exposure to hyperoxia results in apoptosis that requires Bax or Bak and can be prevented by the overexpression of Bcl-X(L). The mitochondrial generation of reactive oxygen species is not required for cell death following exposure to hyperoxia.
Fast data-locality profiling of native execution (2005)

Performance tools based on hardware counters can efficiently profile the cache behavior of an application and help software developers improve its cache utilization. Simulator-based tools can potentially provide more insights and flexibility and model many different cache configurations, but have the drawback of large run-time overhead.We present StatCache, a performance tool based on a statistical cache model. It has a small run-time overhead while providing much of the flexibility of simulator-based tools. A monitor process running in the background collects sparse memory access statistics about the analyzed application running natively on a host computer. Generic locality information is derived and presented in a code-centric and/or data-centric view.We evaluate the accuracy and performance of the tool using ten SPEC CPU2000 benchmarks. We also exemplify how the flexibility of the tool can be used to better understand the characteristics of cache-related performance problems.