gebhart/patrepeval huggingface dataset:
Isolation and characterization of lymphatic microvascular endothelial cells from human tonsils (2005)

Human lymphatic endothelial cells (LECs) have isolated prevalently from human derma and tumors. As specialized lymphatic organs within the oropharynx, palatine tonsils are easily obtained and rich in lymphatic venules. Using a two-step purification method based on the sorting of endothelial cells with Ulex Europaeus Agglutinin 1 (UEA-1)-coated beads, followed by purification with monoclonal antibody D2-40, we successfully purified LECs from human palatine tonsils. The LECs were expanded on flasks coated with collagen type 1 and fibronectin for up to 8-10 passages and then analyzed for phenotypic and functional properties. Cultured cells retained the phenotypic pattern of the lymphatic endothelium of palatine tonsils and expressed functional VEGFR-3 molecules. In fact, stimulation with VEGFR-3 ligand, the vascular endothelium grow factor C, induced a marked increase in cell proliferation. Similarly to blood endothelial cells (BECs), LECs were able to form tube-like structure when seeded in Cultrex basement membrane extract. Comparative studies performed on LECs derived from palatine tonsils and iliac lymphatic vessels (ILVs), obtained with the same procedures, showed substantial discrepancies in the expression of various lymphatic markers. This points to the existence of micro- and macrovessel-derived LECs with different phenotypes, possibly involving different biological activities and functions. Palatine tonsil- and ILV-derived LECs may, therefore, represent new models for investigating function and biochemical properties of these lymphatic endothelia.
Circadian Rhythms in Cell Maturation (2014)

Circadian rhythms are of major importance in mammalian physiology and disease. In this review, we give an overview of the present knowledge on origination of circadian rhythms. We discuss the development of both master and peripheral clocks and compare the origination of circadian rhythms in utero and in vitro.
Antigen presentation by hapten-specific B lymphocytes. I. Role of surface immunoglobulin receptors. (1984)

The present study examines the ability of hapten-specific murine splenic B lymphocytes to present hapten-proteins to carrier-specific T cell hybridomas. BALB/cB cells specific for 2,4,6-trinitrophenyl (TNP) were isolated from spleens of immune mice by elution from TNP-gelatin-coated dishes. Such cells presented the TNP-modified terpolymer, GL phi, at concentrations as low as 0.1 microgram/ml, to a GL phi-specific, I-Ed-restricted, interleukin 2-producing T cell hybridoma. In contrast, the same B lymphocytes required 1,000-fold higher concentrations of unmodified GL phi to stimulate the same T cell hybridoma. The presentation of low concentrations of TNP-GL phi by TNP-specific B lymphocytes was significantly or completely blocked by anti-Ig antibody or TNP-proteins, indicating that surface Ig receptors were critically involved in this phenomenon. Finally, binding of TNP-proteins did not alter the ability of the B cells to present unrelated, unhaptenated proteins or to stimulate alloreactive T cells. These results suggest that surface Ig receptors serve to focus antigens onto specific B lymphocytes and that such cells are highly efficient at presenting linked antigenic determinants to T cells. The implications of these findings for the mechanisms of physiologic, histocompatibility-restricted T-B collaboration are discussed.
Lack of AMPA Receptor Desensitization During Basal Synaptic Transmission in the Hippocampal Slice (1999)

Excitatory postsynaptic currents in the CA1 region of rat hippocampal slices are mediated primarily by alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in response to synaptically released glutamate. Outside-out patches from pyramidal cells in this region have shown that AMPA receptors are desensitized by short (1 ms) pulses of glutamate. We have taken a number of approaches to ask whether synaptic receptors desensitize in response to synaptically released glutamate in the slice. Recordings with paired pulses and minimal stimulation conditions that are presumably activating only a single release site do not show evidence for desensitization. Furthermore, cyclothiazide, a drug that blocks desensitization, does not alter paired-pulse ratios even under conditions of high probability of release, which should maximize desensitization. These results suggest that synaptic receptors do not desensitize in response to synaptically released glutamate during basal synaptic transmission.
Changes in Human Immunodeficiency Virus Type 1 Populations after Treatment Interruption in Patients Failing Antiretroviral Therapy (2001)

Mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase and protease that confer resistance to antiretroviral agents are usually accompanied by a reduction in the viral replicative capacity under drug-free conditions. Consequently, when antiretroviral treatment is interrupted in HIV-1-infected patients harboring drug-resistant virus, resistant quasi-species appear to be most often replaced within several weeks by wild-type virus. Using a real-time PCR-based technique for the selective quantification of resistant viral sequences in plasma, we have studied the kinetics of the switch from mutant to wild-type virus and evaluated the extent to which minority populations of resistant viruses not detected by genotyping persist in these individuals. Among 12 patients with viruses expressing the V82A or L90M resistance mutation who had undergone a 3-month interruption of therapy and for whom conventional genotyping had revealed an apparent total reconversion to wild-type virus, minority populations expressing these mutations, representing 0.1 to 21% of total virus, were still detectable in 9 cases. Kinetic studies demonstrated that viruses expressing resistance mutations could be detected for >5 months after the discontinuation of treatment in some patients. Most of the minority resistant genomes detected more than 3 months after the interruption of therapy carried only part of the mutations present in the resistant viruses prior to treatment interruption and appeared to result from the emergence of existing strains selected at earlier stages in the development of drug resistance. Thus, following the interruption of treatment, viral populations containing resistance mutations can persist for several months after the time when conventional genotyping techniques detect only wild-type virus. These populations include viral strains with only some of the resistance mutations initially present, strains that presumably express better fitness under drug-free conditions.
Purification and characterization of the major allergen from Dermatophagoides pteronyssinus-antigen P1. (1980)

Abstract A purified allergen was obtained from D. pteronyssinus culture by gel filtration, block electrophoresis, and preparative isoelectricfocusing (IEF). The antigenic activity on IEF was predominantly distributed in two peaks (pI 4.7 to 5.4 and pI 6.6 to 7.1), which were completely cross-reactive on immunodiffusion and by cross-inhibition of radioimmunoassay. These fractions had the same m.w. (24,000) and a very similar amino acid composition. The common antigen in each fraction was designated Derma tophagoides pteronyssinus antigen P1. In seven, symptomatic mite allergic subjects skin test reactivity to antigen P1 and crude mite extract was closely correlated. There was also a very good correlation between IgE-binding activity (BA) for P1 measured by antigen-binding radioimmunoassay and IgE antibody (ab) to D. pteronyssinus measured by using the radioallergosorbent test (RAST) (r = 0.82, p &amp;lt; 0.001). RAST experiments showed that up to three-quarters of the IgE ab to D. pteronyssinus was directed against P1, and that IgE ab to P1 accounted for on average 12% of the total serum IgE. These data strongly suggest that P1 is the major allergen of D. pteronyssinus. By immunodiffusion, SDS-PAGE, and radioimmunoassay antigen P1 appeared to be present as a large proportion (10 to 20%) of the protein in crude mite extract. Our results support the view that the importance of an inhalant allergen is largely determined by its physical properties, and by the quantities inhaled during natural exposure.
Mass Spectrometry (1996)

ADVERTISEMENT RETURN TO ISSUEPREVReviewMass SpectrometryA. L. Burlingame, Robert K. Boyd, and Simon J. GaskellView Author Information Department of Pharmaceutical Chemistry, The Mass Spectrometry Facility and the Liver Center, University of California, San Francisco, California 94143-0446 Institute for Marine Biosciences, National Research Council, Halifax, Nova Scotia, Canada B3H 3Z1 Department of Chemistry, University of Manchester Institute of Science & Technology, Manchester, U.K. Cite this: Anal. Chem. 1996, 68, 12, 599–652Publication Date (Web):June 15, 1996Publication History Published online15 June 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/a1960021uhttps://doi.org/10.1021/a1960021ureview-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views2449Altmetric-Citations167LEARN 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 SUBJECTS:Genetics,Ionization,Ions,Mass spectrometry,Peptides and proteins Get e-Alerts
Completeness theorems for non-cryptographic fault-tolerant distributed computation (1988)

Every function of n inputs can be efficiently computed by a complete network of n processors in such a way that:
Short Term Requirements for Network Asserted Identity (2002)

A Network Asserted Identity is an identity initially derived by a Session Initiation Protocol (SIP) network intermediary as a result of an authentication process. This document describes short term requirements for the exchange of Network Asserted Identities within networks of securely interconnected trusted nodes and to User Agents securely connected to such networks.
Dynamic hierarchical Markov random fields and their application to web data extraction (2007)

Hierarchical models have been extensively studied in various domains. However, existing models assume fixed model structures or incorporate structural uncertainty generatively. In this paper, we propose Dynamic Hierarchical Markov Random Fields (DHMRFs) to incorporate structural uncertainty in a discriminative manner. DHMRFs consist of two parts -- structure model and class label model. Both are defined as exponential family distributions. Conditioned on observations, DHMRFs relax the independence assumption as made in directed models. As exact inference is intractable, a variational method is developed to learn parameters and to find the MAP model structure and label assignment. We apply the model to a real-world web data extraction task, which automatically extracts product items for sale on the Web. The results show promise.
In Vivo klotho Gene Transfer Ameliorates Angiotensin II-Induced Renal Damage (2002)

The klotho gene, originally identified by insertional mutagenesis in mice, suppresses the expression of multiple aging-associated phenotypes. This gene is predominantly expressed in the kidney. Recent studies have shown that expression of renal klotho gene is regulated in animal models of metabolic diseases and in humans with chronic renal failure. However, little is known about the mechanisms and the physiological relevance of the regulation of the expression of the klotho gene in the kidney in some diseased conditions. In the present study, we first investigated the role of angiotensin II in the regulation of renal klotho gene expression. Long-term infusion of angiotensin II downregulated renal klotho gene expression at both the mRNA and protein levels. This angiotensin II-induced renal klotho downregulation was an angiotensin type 1 receptor-dependent but pressor-independent event. Adenovirus harboring mouse klotho gene (ad-klotho, 3.3x10(10) plaque forming units) was also intravenously administered immediately before starting angiotensin II infusion in some rats. This resulted in a robust induction of Klotho protein in the liver at day 4, which was still detectable 14 days after the gene transfer. Ad-klotho gene transfer, but not ad-lacZ gene transfer, caused an improvement of creatinine clearance, decrease in urinary protein excretion, and amelioration of histologically demonstrated tubulointerstitial damage induced by angiotensin II administration. Our data suggest that downregulation of the renal klotho gene may have an aggravative role in the development of renal damage induced by angiotensin II, and that induction of the klotho gene may have therapeutic possibilities in treating angiotensin II-induced end organ damage.
Distribution and Abundance of Insertion Sequences Among Natural Isolates of Escherichia coli (1987)

A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS1, IS2, IS3, IS4, IS5 and IS30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with regard to their fit of the observed distributions. No single model fits all copy number distributions. The best models incorporate no regulation of transposition and a moderate to strong decrease in fitness with increasing copy number for IS1 and IS5, strong regulation of transposition and a negligible to weak decrease in fitness with increasing copy number for IS3, and less than strong regulation of transposition for IS2, IS4 and IS30.
Theranostic near-infrared fluorescent nanoplatform for imaging and systemic siRNA delivery to metastatic anaplastic thyroid cancer (2016)

Anaplastic thyroid cancer (ATC), one of the most aggressive solid tumors, is characterized by rapid tumor growth and severe metastasis to other organs. Owing to the lack of effective treatment options, ATC has a mortality rate of ∼100% and median survival of less than 5 months. RNAi nanotechnology represents a promising strategy for cancer therapy through nanoparticle (NP) -mediated delivery of RNAi agents (e.g., siRNA) to solid tumors for specific silencing of target genes driving growth and/or metastasis. Nevertheless, the clinical success of RNAi cancer nanotherapies remains elusive in large part because of the suboptimal systemic siRNA NP delivery to tumors and the fact that tumor heterogeneity produces variable NP accumulation and thus, therapeutic response. To address these challenges, we here present an innovative theranostic NP platform composed of a near-infrared (NIR) fluorescent polymer for effective in vivo siRNA delivery to ATC tumors and simultaneous tracking of the tumor accumulation by noninvasive NIR imaging. The NIR polymeric NPs are small (∼50 nm), show long blood circulation and high tumor accumulation, and facilitate tumor imaging. Systemic siRNA delivery using these NPs efficiently silences the expression of V-Raf murine sarcoma viral oncogene homolog B (BRAF) in tumor tissues and significantly suppresses tumor growth and metastasis in an orthotopic mouse model of ATC. These results suggest that this theranostic NP system could become an effective tool for NIR imaging-guided siRNA delivery for personalized treatment of advanced malignancies.
Activation-dependent Exposure of the Inter-EGF Sequence Leu83-Leu88 in Factor Xa Mediates Ligand Binding to Effector Cell Protease Receptor-1 (1997)

Binding of factor Xa to human umbilical vein endothelial cells (HUVEC) is contributed by effector cell protease receptor-1 (EPR-1). The structural requirements of this recognition were investigated. Factor Xa or catalytically inactive 5-dimethylaminonaphthalene-1sulfonyl (dansyl) Glu-Gly-Arg-(DEGR)-chloromethylketone-factor Xa bound indistinguishably to HUVEC and EPR-1 transfectants, and inhibited equally well the binding of 125I-factor Xa to these cells. Similarly, factor Xa active site inhibitors TAP or NAP5 did not reduce ligand binding to EPR-1. A factor X peptide duplicating the inter-EGF sequence Leu83-Phe84-Thr85-Arg86-Lys87-Leu88- (Gly) inhibited factor V/Va-independent prothrombin activation by HUVEC and blocked binding of 125I-factor Xa to these cells in a dose-dependent manner (IC50 approximately 20-40 microM). In contrast, none of the other factor X peptides tested or a control peptide with the inter-EGF sequence in scrambled order was effective. A recombinant chimeric molecule expressing the factor X sequence Leu83-Leu88 within a factor IX backbone inhibited binding of 125I-factor Xa to HUVEC and EPR-1 transfectants in a dose-dependent fashion, while recombinant factor IX or plasma IXa had no effect. An antibody generated against the factor X peptide 83-88, and designated JC15, inhibited 125I-factor Xa binding to HUVEC. The JC15 antibody bound to factor Xa and the recombinant IX/X83-88 chimera in a concentration dependent manner, while no specific reactivity with factors X or IXa was observed. Furthermore, binding of 125I-factor Xa to immobilized JC15 was inhibited by molar excess of unlabeled factor Xa, but not by comparable concentrations of factors X or IXa. These findings identify the inter-EGF sequence Leu83-Leu88 in factor Xa as a novel recognition site for EPR-1, and suggest its potential role as a protease activation-dependent neo-epitope. This interacting motif may help elucidate the contribution of factor Xa to cellular assembly of coagulation and vascular injury.
Derivation of Dihedral Angles from CH–CH Dipolar–Dipolar Cross‐Correlated Relaxation Rates: A C–C Torsion Involving a Quaternary Carbon Atom in Epothilone A Bound to Tubulin (2003)

C–C torsion angles in HC-CCH3 moieties can be measured by a new NMR experiment based on the measurement of CH–CH dipolar–dipolar cross-correlated relaxation rates and is demonstrated on a mixture of 13C-labeled epothilone (1) and tubulin. The new pulse sequence is broadly applicable to any HC-CCH3 moiety and therefore to a number of amino acid side chains in proteins.
Epigenetic Editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes (2012)

Despite significant advances made in epigenetic research in recent decades, many questions remain unresolved, especially concerning cause and consequence of epigenetic marks with respect to gene expression modulation (GEM). Technologies allowing the targeting of epigenetic enzymes to predetermined DNA sequences are uniquely suited to answer such questions and could provide potent (bio)medical tools. Toward the goal of gene-specific GEM by overwriting epigenetic marks (Epigenetic Editing, EGE), instructive epigenetic marks need to be identified and their writers/erasers should then be fused to gene-specific DNA binding domains. The appropriate epigenetic mark(s) to change in order to efficiently modulate gene expression might have to be validated for any given chromatin context and should be (mitotically) stable. Various insights in such issues have been obtained by sequence-specific targeting of epigenetic enzymes, as is presented in this review. Features of such studies provide critical aspects for further improving EGE. An example of this is the direct effect of the edited mark versus the indirect effect of recruited secondary proteins by targeting epigenetic enzymes (or their domains). Proof-of-concept of expression modulation of an endogenous target gene is emerging from the few EGE studies reported. Apart from its promise in correcting disease-associated epi-mutations, EGE represents a powerful tool to address fundamental epigenetic questions.
Pegvaliase for the treatment of phenylketonuria: Results of a long-term phase 3 clinical trial program (PRISM) (2018)

Results from the PRISM Phase 3 program support the efficacy of pegvaliase for the treatment of adults with PKU, with a manageable safety profile in most participants. The PRISM-2 extension study will continue to assess the long-term effects of pegvaliase treatment.
SA2RAGE: A new sequence for fast B1+‐mapping (2011)

At high magnetic field strengths (≥ 3T), the radiofrequency wavelength used in MRI is of the same order of magnitude of (or smaller than) the typical sample size, making transmit magnetic field (B1+) inhomogeneities more prominent. Methods such as radiofrequency-shimming and transmit SENSE have been proposed to mitigate these undesirable effects. A prerequisite for such approaches is an accurate and rapid characterization of the B1+ field in the organ of interest. In this work, a new phase-sensitive three-dimensional B1+-mapping technique is introduced that allows the acquisition of a 64 × 64 × 8 B1+-map in ≈ 20 s, yielding an accurate mapping of the relative B1+ with a 10-fold dynamic range (0.2-2 times the nominal B1+). Moreover, the predominant use of low flip angle excitations in the presented sequence minimizes specific absorption rate, which is an important asset for in vivo B1+-shimming procedures at high magnetic fields. The proposed methodology was validated in phantom experiments and demonstrated good results in phantom and human B1+-shimming using an 8-channel transmit-receive array.
Resistance to Race 2 of Peronospora parasitica in U.S. Plant Introductions of Brassica oleracea var. capitata (1992)

Evaluations for resistance against race 2 of downy mildew, incited by Peronosporu parasitica Pers. ex Fr., were conducted on 325 U.S. Plant Introductions (PI) classified as Brassicu oleracea var. capitata L. (cabbage). A disease index (DI) was calculated for each entry. In 77 of the tested PIs, from 2% to 100% of the plants had reaction phenotypes ≥ 3. The DIs for 24 PIs were significantly lower than the DI for the most resistant cabbage control, `Headstart' (DI = 5.9). Eight of these PIs were highly resistant, because all plants had a reaction phenotype ≥ 3. However, most of these eight are apparently misclassified as B. oleracea var. capitata.