gebhart/patrepeval huggingface dataset:
Proteomic and Computational Analysis of Bronchoalveolar Proteins during the Course of the Acute Respiratory Distress Syndrome (2008)

Proteomics and protein network analysis reveals the complex nature of lung protein interactions in ARDS. The results provide new insights about protein networks in injured lungs, and identify novel mediators that are likely to be involved in the pathogenesis and progression of acute lung injury.
The Correction of I and Q Errors in a Coherent Processor (1981)

A method is presented for correcting the gain and phase imbalances and the bias errors of the in-phase and quadrature channels of a coherent signal processor [1] by means of coefficients which are derived from measurements of a test signal. The residual errors after correction depend upon the signal-to-noise ratio (S/N) of the test signal and the degree of filtering used in deriving the correction coefficients.
Nonspectroscopic interelement interferences in inductively coupled plasma mass spectrometry (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNonspectroscopic interelement interferences in inductively coupled plasma mass spectrometryGeorge R. Gillson, Donald J. Douglas, John E. Fulford, Kenneth W. Halligan, and Scott D. TannerCite this: Anal. Chem. 1988, 60, 14, 1472–1474Publication Date (Print):July 15, 1988Publication History Published online1 May 2002Published inissue 15 July 1988https://doi.org/10.1021/ac00165a024RIGHTS & PERMISSIONSArticle Views672Altmetric-Citations208LEARN 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 InReddit PDF (406 KB) Get e-Alerts Get e-Alerts
3′ processing of eukaryotic precursor tRNAs (2010)

Biogenesis of eukaryotic tRNAs requires transcription by RNA polymerase III and subsequent processing. 5' processing of precursor tRNA occurs by a single mechanism, cleavage by RNase P, and usually occurs before 3' processing although some conditions allow observation of the 3'-first pathway. 3' processing is relatively complex and is the focus of this review. Precursor RNA 3'-end formation begins with pol III termination generating a variable length 3'-oligo(U) tract that represents an underappreciated and previously unreviewed determinant of processing. Evidence that the pol III-intrinsic 3'exonuclease activity mediated by Rpc11p affects 3'oligo(U) length is reviewed. In addition to multiple 3' nucleases, precursor tRNA(pre-tRNA) processing involves La and Lsm, distinct oligo(U)-binding proteins with proposed chaperone activities. 3' processing is performed by the endonuclease RNase Z or the exonuclease Rex1p (possibly others) along alternate pathways conditional on La. We review a Schizosaccharomyces pombe tRNA reporter system that has been used to distinguish two chaperone activities of La protein to its two conserved RNA binding motifs. Pre-tRNAs with structural impairments are degraded by a nuclear surveillance system that mediates polyadenylation by the TRAMP complex followed by 3'-digestion by the nuclear exosome which appears to compete with 3' processing. We also try to reconcile limited data on pre-tRNA processing and Lsm proteins which largely affect precursors but not mature tRNAs.A pathway is proposed in which 3' oligo(U) length is a primary determinant of La binding with subsequent steps distinguished by 3'-endo versus exo nucleases,chaperone activities, and nuclear surveillance.
A single-chip digital signal processor for voiceband applications (1980)

A single-chip digital signal processor utilizing parallel multiplier and 3μ NMOS technology will be presented. Development can implement 41 second-order digital filter sections for 8kHz sampling of voiceband signals.
Triple-Detector GPC Characterization and Processing Behavior of Long-Chain-Branched Polyethylene Prepared by Solution Polymerization With Constrained Geometry Catalyst (2004)

Abstract Fourteen long-chain branched (LCB) polyethylene (PE) samples were prepared by a constrained geometry catalyst. The PE samples had average branching frequencies of 0.06–0.98 branches per polymer chain, as determined by the nuclear magnetic resonance spectroscopy (13C NMR). These samples, as well as five linear PEs were characterized using a gel permeation chromatography (GPC) coupled with online three-angle laser light scattering (LS), differential refractive index (DRI), and viscosity (CV) detectors. The root mean-square radius of gyration ( 〈 r g 2 〉 1 / 2 ) , intrinsic viscosity ([η]), and molecular mass (M) of the PEs were measured for each elution fraction. Based on the comparison of the long-chain branching (LCB) PEs with their linear counterparts and the Zimm–Stockmayer equation, the distributions of long-chain branch frequency (LCBF) and density (LCBD) as function of molecular mass were estimated. It was found that although the LCBF increased with the increase of molecular mass, the LCBD showed a maximum value in the medium molecular mass range for most of the PE samples. The average LCBD data from the GPC analysis were in good agreement with the 13C NMR measurements. The rheological properties and processing behavior of these samples were also assessed. While the long chain branching showed significant effects on the modulus and viscosity, it did not improve the processing. Compared to linear PE, polymer melt flow instabilities such as sharkskin, stick-slip and gross melt fracture developed in extrusion of LCB PEs occurred at lower wall shear stresses and apparent shear rates.
Notch signaling is activated by TLR stimulation and regulates macrophage functions (2007)

Notch signaling is a well-conserved pathway involved in cell fate decisions, proliferation and apoptosis. We report on the involvement of Notch signaling in regulating gene expression in activated macrophages. Toll-like receptors (TLR) agonists such as bacterial lipopeptide, polyI:C, lipopolysaccharide and unmethylated CpG DNA all induced up-regulation of Notch1 in primary and macrophage-like cell lines. Notch1 up-regulation was dependent on the MyD88 pathway when stimulated through TLR2, but not TLR4. Activated Notch1 and expression of the Notch target genes, Hes1 and Deltex, were detected in activated macrophages, suggesting that Notch signaling was activated upon stimulation. Inhibiting processing of Notch receptor by gamma-secretase using a gamma-secretase inhibitor (GSI), the expression of Notch1 was down-regulated to basal levels. This treatment significantly modulated expression of TNF-alpha, IL-6, and IL-10. In addition, the amount of nitric oxide produced was significantly lower and the expression of MHC class II was up-regulated in GSI-treated cells. Treatment with GSI or silencing Notch1 resulted in decreased translocation of NF-kappaBp50 into nucleus upon stimulation. Taken together, stimulation of macrophages through the TLR signaling cascade triggered activation of Notch signaling, which in turn regulated gene expression patterns involved in pro-inflammatory responses, through activation of NF-kappaB.
Quantized Indexing: Background Information * (2005)

This report presents background material ‡ for the Quantized Indexing § (QI) form of enumerative coding. Following the introduction to conventional enumerative coding and its reformulation as lattice walks, the relations between arithmetic and enumerative coding are explored. In addition to examining the fundamental origins of the performance differences (in speed and output size), special emphasis was on the distinctions in the two approaches to modeling. General modeling pattern for enumerative coding (including QI) is described, along with the special cases for finite order Markov sources. This approach is compared to the arithmetic coder adaptive modeling as well as to the grammer and dictionary based modeling methods.
Effects of the position of the simian virus 40 enhancer on expression of multiple transcription units in a single plasmid. (1986)

We have examined the ability of the simian virus 40 72-base pair enhancer segment to simultaneously activate multiple transcription units with plasmids that contain one, two, or three simian virus 40-based transcription units in various arrangements. After transfection into CV1 cells, the expression of a marker gene, Ecogpt, was determined as a function of the position of that marker gene relative to the other transcription units and the position of the marker gene relative to enhancer elements on the plasmids. Two types of position effects were revealed by that analysis. The first, promoter occlusion, causes reduced transcription at a downstream promoter if transcription is initiated at a nearby upstream promoter. This effect does not involve enhancer elements directly, even though the effect is most pronounced when the downstream promoter lacks an enhancer element. The second effect stems from the ability of promoter sequences to reduce the effect of a single enhancer element on other promoters in the same plasmid. This latter effect is mediated by either promoters adjacent to the enhancer element or promoters interposed between the enhancer element and the other promoters on the plasmid.
Ferrous iron transport mutants inEscherichia coliK12 (1987)

A ferrous iron transport system in &lt;it&gt;Escherichia coli&lt;/it&gt; is described. Mutants in this transport system were isolated using the antibiotic streptonigrin. The gene locus &lt;it&gt;feo&lt;/it&gt; (for &lt;it&gt;fe&lt;/it&gt;rr&lt;it&gt;o&lt;/it&gt;us iron transport) was mapped near &lt;it&gt;pncA&lt;/it&gt; at 38.5 min on the genetic map of &lt;it&gt;E. coli&lt;/it&gt; K12. The transport of ferrous iron was regulated by &lt;it&gt;fur&lt;/it&gt; as the siderophore transport systems.
Anti-epidermal growth factor receptor monoclonal antibodies may inhibit A431 tumor cell proliferation by blocking an autocrine pathway. (1987)

Monoclonal antibodies which bind to the EGF receptor have the capacity to inhibit EGF-induced effects upon proliferation and biochemical functions in cultured human cells. Some EGF receptor-bearing tumor cells are prevented from growth by treatment with antireceptor antibody. Evidence is presented which suggests that antibody-mediated antiproliferative activity may result from effects upon growth factor-dependent processes in the receptor-bearing cells.
Isolation and amino acid sequence of a glutamic acid specific endopeptidase from Bacillus licheniformis (1992)

An endopeptidase cleaving specifically at the carboxyl side of acidic amino acid residues, preferentially at glutamic acid, has been isolated from a commercial extract obtained by fermentation with Bacillus licheniformis. Using ion-exchange chromatography and affinity chromatography on bacitracin-Sepharose, it was possible, from 100 ml commercial extract, to isolate 100 mg homogeneous enzyme in a yield of 50%. It is the first description of a large-scale isolation of a Glu/Asp-specific enzyme. The preparation was essentially free of contaminating activities. The isolated enzyme consists of one peptide chain of 222 amino acid residues and has a calculated molecular mass of 23,589 Da. The determined amino acid sequence shows similarity to the Glu/Asp-specific enzymes previously isolated from Staphylococcus aureus V8, Actinomyces sp. and Streptomyces thermovulgaris. The substrate preference of the enzyme has been investigated. Although non-specific cleavages were observed after prolonged hydrolysis at high enzyme concentrations the enzyme appears to be essentially specific for Glu-Xaa and Asp-Xaa, with strong preference for the former. The isolated enzyme exhibits a bell-shaped pH/activity profile with an optimum at pH 7.5-8.0. The activity is adversely affected by high ionic strength and beneficially affected by the inclusion of calcium ions in the assay medium. The enzyme is completely inhibited by diisopropylfluorophosphate, suggesting that it is a serine endopeptidase. It is partially inhibited by EDTA.
Tumour-derived exosomes and their role in cancer-associated T-cell signalling defects (2005)

Dendritic and lymphoid 'exosomes' regulate immune activation. Tumours release membranous material mimicking these 'exosomes,' resulting in deletion of reactive lymphocytes. Tumour-derived 'exosomes' have recently been explored as vaccines, without analysis of their immunologic consequences. This investigation examines the composition of tumour-derived 'exosomes' and their effects on T lymphocytes. Membranous materials were isolated from ascites of ovarian cancer patients (n=6) and Western immunoblotting was performed for markers associated with 'exosomes.' Using cultured T cells, 'exosomes' were evaluated for suppression of CD3-zeta and JAK 3 expressions and induction of apoptosis, measured by DNA fragmentation. 'Exosome' components mediating suppression of CD3-zeta were isolated by continuous eluting electrophoresis and examined by Western immunoblotting. 'Exosomes' were shown to be identical with previously characterised shed membrane vesicles by protein staining and TSG101 expression. 'Exosomes' expressed class I MHC, placental alkaline phosphatase, B23/nucleophosmin, and FasL. 'Exosomes' suppressed expression of T-cell activation signalling components, CD3-zeta and JAK 3 and induced apoptosis. CD3-zeta suppression was mediated by two components: 26 and 42 kDa. Only the 42 kDa component reacted with anti-FasL antibody. These results indicate that, while 'exosomes' express tumour antigens, leading to their proposed utility as tumour vaccines, they also can suppress T-cell signalling molecules and induce apoptosis.
A Core/Satellite Multifunctional Nanotheranostic for in Vivo Imaging and Tumor Eradication by Radiation/Photothermal Synergistic Therapy (2013)

To integrate photothermal ablation (PTA) with radiotherapy (RT) for improved cancer therapy, we constructed a novel multifunctional core/satellite nanotheranostic (CSNT) by decorating ultrasmall CuS nanoparticles onto the surface of a silica-coated rare earth upconversion nanoparticle. These CSNTs could not only convert near-infrared light into heat for effective thermal ablation but also induce a highly localized radiation dose boost to trigger substantially enhanced radiation damage both in vitro and in vivo. With the synergistic interaction between PTA and the enhanced RT, the tumor could be eradicated without visible recurrence in 120 days. Notably, hematological analysis and histological examination unambiguously revealed their negligible toxicity to the mice within a month. Moreover, the novel CSNTs facilitate excellent upconversion luminescence/magnetic resonance/computer tomography trimodal imagings. This multifunctional nanocomposite is believed to be capable of playing a vital role in future oncotherapy by the synergistic effects between enhanced RT and PTA under the potential trimodal imaging guidance.
SEEDbodies: fusion proteins based on strand-exchange engineered domain (SEED) CH3 heterodimers in an Fc analogue platform for asymmetric binders or immunofusions and bispecific antibodies† (2010)

Bispecific antibodies and asymmetric Fc fusion proteins offer opportunities for important advances in therapeutics. Bivalent IgG depends upon in vivo dimerization of its heavy chains, mediated by homodimeric association of its C(H)3 domains. We have developed a heterodimeric Fc platform that supports the design of bispecific and asymmetric fusion proteins by devising strand-exchange engineered domain (SEED) C(H)3 heterodimers. These derivatives of human IgG and IgA C(H)3 domains create complementary human SEED C(H)3 heterodimers that are composed of alternating segments of human IgA and IgG C(H)3 sequences. The resulting pair of SEED C(H)3 domains preferentially associates to form heterodimers when expressed in mammalian cells. SEEDbody (Sb) fusion proteins consist of [IgG1 hinge]-C(H)2-[SEED C(H)3], that may be genetically linked to one or more fusion partners. This investigation reports on the generation of mono-Fab-Sb and Sb-IL2 monocytokine as models. They were expressed at high levels in NS/0 cells, purified on recombinant protein A resin and were well-behaved in solution. When administered intravenously to mice, Sb pharmacokinetics exhibited the long serum half-life extensions typical of comparable Fc-containing immunofusion and IgG1 controls.
Stereospecific alkylation of menthyl phenylphosphinate (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecific alkylation of menthyl phenylphosphinateWilliam B. Farnham, Roger Kenneth Murray Jr., and Kurt MislowCite this: J. Am. Chem. Soc. 1970, 92, 19, 5809–5810Publication Date (Print):September 1, 1970Publication History Published online1 May 2002Published inissue 1 September 1970https://pubs.acs.org/doi/10.1021/ja00722a083https://doi.org/10.1021/ja00722a083research-articleACS PublicationsRequest reuse permissionsArticle Views822Altmetric-Citations81LEARN 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-Alertsclose Get e-Alerts
BRCA1 interacts with components of the histone deacetylase complex (1999)

Germ-line mutations in the BRCA1 tumor-suppressor gene are associated with an increased susceptibility to breast and ovarian cancer. BRCA1 contains a carboxyl-terminal domain (BRCT) that is shared with several other proteins involved in maintaining genome integrity. In an effort to understand the function of BRCA1, we sought to isolate proteins that interact with the BRCT domain. Purified BRCT polypeptide was used as a probe to screen a human placenta cDNA expression library by Far Western analysis. Here we report that BRCA1 interacts in vivo and in vitro with the Rb-binding proteins, RbAp46 and RbAp48, as well as with Rb. Moreover, the BRCT domain associates with the histone deacetylases HDAC1 and HDAC2. These results demonstrate that BRCA1 interacts with components of the histone deacetylase complex, and therefore may explain the involvement of BRCA1 in multiple processes such as transcription, DNA repair, and recombination.
Friendship and Desire in the Lysis (1990)

This book shows that the different approaches in Lysis is reflective and fertile, well-conceived in theory and pregnant in practice; to respond to it briskly with the cliches of modern thought is to prefer the pleasures of the parrot to the pains of the philosophers. For Socrates, when talking about Lysis, the topic is simply friendship and the conclusion is failure. On the other hand, for Aristotle, he takes Lysis as the starting point, and takes over from it not only points of detail, but general presuppositions that locate his own conclusions, which are aporetic, in the same conceptual region. If Socrates' failure in the Lysis is wholly misconceived, so is Aristotle's success in his Ethics.
Designing Workscape (1994)

Article Designing Workscape: an interdisciplinary experience Share on Author: Joseph M. Ballay MAYA Design Group, Inc., 2100 Wharton Street, Suite 702, Pittsburgh, PA MAYA Design Group, Inc., 2100 Wharton Street, Suite 702, Pittsburgh, PAView Profile Authors Info & Claims CHI '94: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsApril 1994 Pages 10–15https://doi.org/10.1145/191666.191676Published:24 April 1994 19citation486DownloadsMetricsTotal Citations19Total Downloads486Last 12 Months11Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Complete Inhibition of Anisomycin and UV Radiation but Not Cytokine Induced JNK and p38 Activation by an Aryl-substituted Dihydropyrrolopyrazole Quinoline and Mixed Lineage Kinase 7 Small Interfering RNA (2005)

Mixed lineage kinase 7 (MLK7) is a mitogen-activated protein kinase kinase kinase (MAPKKK) that activates the pro-apoptotic signaling pathways p38 and JNK. A library of potential kinase inhibitors was screened, and a series of dihydropyrrolopyrazole quinolines was identified as highly potent inhibitors of MLK7 in vitro catalytic activity. Of this series, an aryl-substituted dihydropyrrolopyrazole quinoline (DHP-2) demonstrated an IC50 of 70 nM for inhibition of pJNK formation in COS-7 cell MLK7/JNK co-transfection assays. In stimulated cells, DHP-2 at 200 nM or MLK7 small interfering RNA completely blocked anisomycin and UV induced but had no effect on interleukin-1beta or tumor necrosis factor-alpha-induced p38 and JNK activation. Additionally, the compound blocked anisomycin and UV-induced apoptosis in COS-7 cells. Heart tissue homogenates from MLK7 transgenic mice treated with DHP-2 at 30 mg/kg had reduced JNK and p38 activation with no apparent effect on ERK activation, demonstrating that this compound can be used to block MLK7-driven MAPK pathway activation in vivo. Taken together, these data demonstrate that MLK7 is the MAPKKK required for modulation of the stress-activated MAPKs downstream of anisomycin and UV stimulation and that DHP-2 can be used to block MLK7 pathway activation in cells as well as in vivo.
A Neurodegeneration-Specific Gene-Expression Signature of Acutely Isolated Microglia from an Amyotrophic Lateral Sclerosis Mouse Model (2013)

Microglia are resident immune cells of the CNS that are activated by infection, neuronal injury, and inflammation. Here, we utilize flow cytometry and deep RNA sequencing of acutely isolated spinal cord microglia to define their activation in vivo. Analysis of resting microglia identified 29 genes that distinguish microglia from other CNS cells and peripheral macrophages/monocytes. We then analyzed molecular changes in microglia during neurodegenerative disease activation using the SOD1(G93A) mouse model of amyotrophic lateral sclerosis (ALS). We found that SOD1(G93A) microglia are not derived from infiltrating monocytes, and that both potentially neuroprotective and toxic factors, including Alzheimer's disease genes, are concurrently upregulated. Mutant microglia differed from SOD1(WT), lipopolysaccharide-activated microglia, and M1/M2 macrophages, defining an ALS-specific phenotype. Concurrent messenger RNA/fluorescence-activated cell sorting analysis revealed posttranscriptional regulation of microglia surface receptors and T cell-associated changes in the transcriptome. These results provide insights into microglia biology and establish a resource for future studies of neuroinflammation.