gebhart/patrepeval huggingface dataset:
Chromosomal Imbalances in Diffuse Large B-Cell Lymphoma Detected by Comparative Genomic Hybridization (2002)

Diffuse large B-cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma. In contrast to many other hematological malignancies, no chromosomal abnormalities with a diagnostic or prognostic value have been identified in DLBCL. Numerical chromosomal imbalances were characterized by comparative genomic hybridization (CGH) performed on 54 DLBCL tumors from a total of 40 patients. The clonal relatedness was demonstrated in 9 of 11 pairs of matched diagnostic tumors and their relapses as determined by IGH gene rearrangement analysis and/or the CGH profiles. Furthermore, immunohistochemical expression analyses of BCL2 and BCL6/LAZ3 were performed on all cases. Copy number changes were detected in 94% of the diagnostic tumor samples and in all of the relapses. Chromosomal losses in diagnostic tumors were preferentially observed at 8p22-pter (29%), 1p34-pter (26%), 6q23-qter (20%), 17p12-pter (17%) and 22q (17%), 9p23-pter (14%), whereas gains were mainly seen in Xq25-26 (43%), 13q22 (26%), 12cen-q14 (20%), 3q24-25 (11%), 7 (11%), and 18q12-21 (11%). Loss of 22q was significantly more commonly seen in the diagnostic tumor samples with more advanced clinical stage in other words, Stage III-IV compared with Stage I-II, and band 18q21 was significantly more often gained in relapses as compared to diagnostic tumors. None of the recurrent alterations were detected as a single abnormality, suggesting that other genetic lesions below the detection level of CGH may be the initiating event in the tumorigenesis of DLBCL. However, the distribution of CGH alterations support the idea of a progression of genetic events where loss of 8p and 9p and gain of 3q, 13q, and 18q would represent relatively early events because they were distributed in tumors with only two abnormalities.
Assessment of the Integrity of Poly(caprolactone)-b-poly(ethylene oxide) Micelles under Biological Conditions:  A Fluorogenic-Based Approach (2006)

The integrity of block copolymer micelles is important for their effectiveness and successful delivery of the incorporated drugs. Here we evaluate the integrity of poly(caprolactone)-b-poly(ethylene oxide) micelles in media of varying chemical complexity and in cells by using fluorogenic micelles. Fluorogenic dye fluorescein-5-carbonyl azide diacetate was covalently attached to the micelle-core-forming part of the block copolymer, poly(caprolactone). The fluorescence was not detectable unless the poly(caprolactone)21-b-poly(ethylene oxide)45 micelles were destroyed and the fluorogenic dye was activated by deesterification. The fluorescence of the activated dye from destroyed micelles was easily detectable in various media and in cells. Micelles were stable in simple media such as phosphate-buffered saline but disassembled to varying extents with increasing chemical complexity of the media and addition of serum. The integrity of the internalized micelles within the cells showed a time-dependent decrease but remained largely preserved (80%) after 20 h of incubation with cells. A proof of principle was also demonstrated in vivo in mice. The fluorogenic approach to micelle integrity assessment presented herein should lend itself to other block copolymer micelles and assessments of their integrity in complex biological systems in vitro and in vivo.
A long-term time course of colorimetric evaluation of ultraviolet light-induced skin reactions (1999)

Many attempts have been made to quantify ultraviolet (UV) radiation-induced erythema and pigmentation. However, most of these studies were concerned with the early changes of reactions and neglected events occurring in later stages. The long-term course of skin colour changes in pigmented skin, induced by broad band UVA and UVB radiation, was evaluated in 30 Korean male volunteers by means of a tri-stimulus colorimeter for 10 weeks. The L*a*b* system recommended by the Commission International de l'Eclairage was used to measure skin colour. The L* value (luminance) gives the relative lightness ranging from total black to total white. The a* value represents the balance between red and green and the b* value the balance between yellow and blue. The mean individual typology angle of our subjects was 47.3 degrees, indicating 'light' group of constitutional skin colour category. One day after UV exposure, the L* and b* values decreased significantly, following the colour direction of persistent pigment darkening. They then changed in opposite directions persistently until week 1, when maximum tanning was obtained. Then, a shift toward the original values was observed parallel to the constitutive melanization axis. The a* index showed a significant increase toward the mean colour of haemoglobin on day 1. It returned to its original value following the pathway of constitutive melanization axis. This promising quantitative method may enable objective measurement of dermatophysiologic changes to be made, and allow evaluation of the efficacy of therapeutic modalities on skin disorders without the inherent errors associated with subjective judgement. Our results would provide standard data for long-term UV-induced skin erythema and pigmentation.
Eotaxin-3 is involved in Churg-Strauss syndrome - a serum marker closely correlating with disease activity (2008)

This study reveals the specific association of elevated eotaxin-3 expression with high disease activity and eosinophilia in CSS patients. Eotaxin-3 might thus be a pathogenic player, biomarker and potential therapeutic target in CSS.
A New Class of Chiral Bridged Metallocene:  Synthesis, Structure, and Olefin (Co)polymerization Behavior of rac- and meso-1,2-CH2CH2{4-(7-Me-indenyl)}2ZrCl2 (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA New Class of Chiral Bridged Metallocene: Synthesis, Structure, and Olefin (Co)polymerization Behavior of rac- and meso-1,2-CH2CH2{4-(7-Me-indenyl)}2ZrCl2Colin J. Schaverien, René Ernst, Peter Schut, W. Mason Skiff, Luigi Resconi, Elisabetta Barbassa, Davide Balboni, Yuri A. Dubitsky, A. Guy Orpen, Pierluigi Mercandelli, Massimo Moret, and Angelo SironiView Author Information Shell Research and Technology Centre Amsterdam Postbus 38000, 1030 BN Amsterdam, The Netherlands Montell Polyolefins, Centro Ricerche G. Natta P. le G. Donegani 12, 44100 Ferrara, Italy School of Chemistry, University of Bristol Bristol BS8 1TS, U.K. Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Universitá di Milano Via Venezian 21, 20133 Milano, Italy Cite this: J. Am. Chem. Soc. 1998, 120, 38, 9945–9946Publication Date (Web):September 11, 1998Publication History Received6 April 1998Published online11 September 1998Published inissue 1 September 1998https://pubs.acs.org/doi/10.1021/ja9811290https://doi.org/10.1021/ja9811290rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views428Altmetric-Citations18LEARN 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 SUBJECTS:Alkyls,Energy,Hydrocarbons,Molecular structure,Sandwich compounds Get e-Alerts
Analysis of protein localization by use of gene fusions with complementary properties (1990)

This report describes a new transposon designed to facilitate the combined use of beta-galactosidase and alkaline phosphatase gene fusions in the analysis of protein localization. The transposon, called TnlacZ, is a Tn5 derivative that permits the generation of gene fusions encoding hybrid proteins carrying beta-galactosidase at their C termini. In tests with plasmids, TnlacZ insertions that led to high cellular beta-galactosidase activity were restricted to sequences encoding either cytoplasmic proteins or cytoplasmic segments of a membrane protein. The fusion characteristics of TnlacZ are thus complementary to those of TnphoA, a transposon able to generate alkaline phosphatase fusions whose high-activity insertion sites generally correspond to periplasmic sequences. The structure of TnlacZ allows the conversion of a TnlacZ fusion into the corresponding TnphoA fusion (and vice versa) through recombination or in vitro manipulation in a process called fusion switching. Fusion switching was used to generate the following two types of fusions with unusual properties: a low-specific-activity beta-galactosidase-alkaline phosphatase gene fusion and two toxic periplasmic-domain serine chemoreceptor-beta-galactosidase gene fusions. The generation of both beta-galactosidase and alkaline phosphatase fusions at exactly the same site in a protein permits a comparison of the two enzyme activities in evaluating the subcellular location of the site, such as in studies of membrane protein topology. In addition, fusion switching makes it possible to generate gene fusions whose properties should facilitate the isolation of mutants defective in the export or membrane anchoring of different cell envelope proteins.
Purification and characterization of interleukin 1 receptor level antagonist proteins from THP-1 cells. (1990)

Culture medium conditioned by phorbol 12-myristate 13-acetate-differentiated THP-1 cells contained interleukin 1 (IL-1) antagonist activity as measured by inhibition of both IL-1 beta binding to receptors on YT cells and inhibition of IL-1/phytohemagglutinin-stimulated IL-2 synthesis by LBRM-33-1A5 T cells. Based on their ability to compete for 125I-IL-1 beta binding to receptors on YT cells, four distinct antagonist proteins were purified from THP-1 cell conditioned medium using a combination of ion-exchange, hydrophobic interaction, and size exclusion chromatographies. The four proteins had different isoelectric points with molecular masses in the range 22-26 kDa and had similar specific activities for inhibition of IL-1 beta binding to cell surface receptors (Ki values 0.33-0.64 nM) and for inhibition of IL-1/phytohemagglutinin-stimulated IL-2 synthesis by 1A5 cells (IC50 values 25-100 pM). Amino-terminal sequence analysis of the two major forms (25 kDa/pI 5.1 and 22 kDa/pI 5.8) revealed complete identity for the first 27 residues in both forms. Based on the results of peptide mapping, amino acid compositional analysis and immune blotting, all of the forms were deduced to be variants of a common protein. Deglycosylation of the antagonist proteins with N-glycanase converted them to a common form (22 kDa/pI 5.8), indicating that the four isoforms represent glycosylation variants of a common protein and that asparagine-linked oligosaccharides are responsible for the observed size and charge heterogeneity.
Kinematics of a novel three DOF translational platform (2002)

A novel 3-DOF parallel manipulator is presented that employs only revolute joints and constrains the manipulator output to translational motion. Closed-form solutions are developed for both the inverse and forward kinematics. The inverse kinematics produces four solutions for each leg of the manipulator. In general, the four solutions are realized in only two unique leg configurations. The forward kinematic solution is reduced to a quadratic equation. So that in general, there are two poses the manipulator can assume for a given set of input joint angles.
TheSalmonella entericaSerovar TyphitsxGene, Encoding a Nucleoside-Specific Porin, Is Essential for Prototrophic Growth in the Absence of Nucleosides (2005)

The Salmonella enterica serovar Typhi tsx gene encodes a porin that facilitates the import of nucleosides. When serovar Typhi is grown under anaerobic conditions, Tsx is among the outer membrane proteins whose expression increases dramatically. This increase in expression is due, at least in part, to increased transcription and is dependent on Fnr but not on ArcA. A mutant derivative of serovar Typhi strain STH2370 with a deletion of the tsx gene is an auxotroph that requires either adenosine or thymidine for growth on minimal medium. In contrast, an otherwise isogenic nupG nupC double mutant, defective in the inner membrane nucleoside permeases, is a prototroph. Because anaerobic growth enhances the virulence of serovar Typhi in vitro, we assessed the role that the tsx gene plays in pathogenicity and found that the serovar Typhi STH2370 Deltatsx mutant is defective in survival within human macrophage-like U937 cells. To understand why the Deltatsx mutant is an auxotroph, we selected for insertions of minitransposon T-POP in the Deltatsx genetic background that restored prototrophy. One T-POP insertion that suppressed the Deltatsx mutation in the presence of the inducer tetracycline was located upstream of the pyrD gene. The results of reverse transcription-PCR analysis showed that addition of the inducer decreased the rate of pyrD transcription. These results suggest that the Tsx porin and the balance of products of the tsx and pyrD genes play critical roles in membrane assembly and integrity and thus in the virulence of serovar Typhi.
Identification of the Soluble Starch Synthase Activities of Maize Endosperm1 (1999)

This study identified the complement of soluble starch synthases (SSs) present in developing maize (Zea mays) endosperm. The product of the du1 gene, DU1, was shown to be one of the two major soluble SSs. The C-terminal 450 residues of DU1 comprise eight sequence blocks conserved in 28 known or predicted glucan synthases. This region of DU1 was expressed in Escherichia coli and shown to possess SS activity. DU1-specific antisera detected a soluble endosperm protein of more than 200 kD that was lacking in du1- mutants. These antisera eliminated 20% to 30% of the soluble SS activity from kernel extracts. Antiserum against the isozyme zSSI eliminated approximately 60% of the total soluble SS, and immunodepletion of du1- mutant extracts with this antiserum nearly eliminated SS activity. Two soluble SS activities were identified by electrophoretic fractionation, each of which correlated specifically with zSSI or DU1. Thus, DU1 and zSSI accounted for the great majority of soluble SS activity present in developing endosperm. The relative activity of the two isozymes did not change significantly during the starch biosynthetic period. DU1 and zSSI may be interdependent, because mutant extracts lacking DU1 exhibited a significant stimulation of the remaining SS activity.
Parallel inactivation of multipleGALpathway genes and ecological diversification in yeasts (2004)

Understanding the evolutionary relationship between genome content and ecological niche is one of the fundamental challenges of biology. The distinct physiologies of yeast species provide a window into how genomes evolve in concert with niche. Although the enzymes of the well studied yeast galactose utilization pathway are present in all domains of life, we have found that multiple genes of the GAL pathway are absent from four yeast species that cannot use galactose. Whereas three species lack any trace of the pathway except a single gene, Saccharomyces kudriavzevii, a close relative of Saccharomyces cerevisiae, retains remnants of all seven dedicated GAL genes as syntenic pseudogenes, providing a rare glimpse of an entire pathway in the process of degeneration. An estimate of the timing of gene inactivation suggests that pathway degeneration began early in the lineage and proceeded rapidly. S. kudriavzevii exhibits several other divergent physiological properties that are associated with a shift in ecological niche. These results suggest that rapid and irreversible gene inactivation and pathway degeneration are associated with adaptation to new ecological niches in natural populations. Inactivated genes may generally serve as markers of specific functions made dispensable by recent adaptive shifts.
Platelets and Factor XI Bypass the Contact System of Blood Coagulation (1999)

Introduction Factor XI is a plasma glycoprotein (concentration ∼30 nM) that was first identified by Rosenthal et al1 as a plasma coagulation factor deficiency in patients with abnormal hemostasis, particularly common among Ashkenazi Jews.2,3 In spite of recent advances in our understanding of the structure of factor XI and its gene, the structure-function relationships of the protein, and the molecular genetics of factor XI deficiency, considerable confusion about the physiologic role and clinical relevance of factor XI has arisen from both clinical and biochemical observations. One problem arises from the fact that, until recently, the only known pathway for activation of factor XI involved proteolytic activation by factor XIIa and interactions with coagulation proteins of the contact phase of blood coagulation.4-7 The problem arose from the clinical observation that patients with deficiencies of factor XI are subject to bleeding complications, whereas patients with deficiencies of the contact proteins are not.2,3,8-13 A related unanswered question concerns the lack of correlation in many reported patients between plasma levels of factor XI and the severity of clinical bleeding manifestations.2,3,8,9,13-15 In addition, some patients with severe factor XI deficiency experience significant bleeding complications, whereas others appear to be hemostatically normal. These clinical and biochemical observations have motivated investigations focused on alternative mechanisms for activation of factor XI independent of contact phase protein.19-22 Additional studies have focused on the identification and characterization of platelet factor XI, which is postulated to be an alternative splicing product of the factor XI gene. Platelet factor XI is present in platelet membranes and might substitute for plasma factor XI in hemostasis and account for the absence of bleeding complications in some patients with severe plasma factor XI deficiency.14,16-18,23-26 Studies addressing these two important and related problems are presented and discussed in this chapter.
A model for the current–voltage characteristics and the quantum efficiency of single-layer organic light emitting diodes (1997)

A model for the current–voltage characteristics and the quantum efficiency of single-layer organic light emitting diodes is presented. With variables such as the electric field, the hole, and electron carrier densities, a set of coupled nonlinear differential equations is derived by using classical electrostatics and by assuming Fowler–Nordheim injection. Numerical calculations for different carrier mobility and barrier height conditions show that low barrier height at both electrodes leads to higher efficiency and higher carrier mobility leads to higher brightness. We find that for applications that require high current injection such as lasers, materials with high mobility are desired to reduce space charge effects.
Optically active N-protected .alpha.-amino aldehydes in organic synthesis (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptically active N-protected .alpha.-amino aldehydes in organic synthesisJanusz Jurczak and Adam GolebiowskiCite this: Chem. Rev. 1989, 89, 1, 149–164Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/cr00091a004https://doi.org/10.1021/cr00091a004research-articleACS PublicationsRequest reuse permissionsArticle Views2394Altmetric-Citations429LEARN 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
Complete exon-intron organization of the human leukocyte common antigen (CD45) gene. (1988)

Ten genomic DNA clones encoding the human leukocyte common Ag (LCA, CD45) gene were isolated by screening human genomic DNA libraries with LCA cDNA probes. One genomic DNA clone contains the promoter region and the first two exons, as determined by primer extension analyses and S1 nuclease protection studies as well as nucleotide sequence determination. The first exon does not encode a peptide, while the second exon contains the initiation ATG codon and encodes the signal peptide. The other nine genomic DNA clones, which are separated from the first genomic clone by an unknown distance, are connected and span a total of 73 kb. The nine connected genomic clones encode a total of 31 exons. The 33 exons encoded by these 10 genomic clones account for the entire cDNA sequences including the 5' and 3' untranslated sequences. Exon 3 and exons 7 through 15 encode the extracellular domain sequences that are common to all LCA isoforms. Differential usage of exons 4, 5, and 6, generates at least five distinct LCA isoforms. Exon 16 encodes the transmembrane peptide. The cytoplasmic region of the leukocyte common antigens is composed of two homologous domains. Exons 17 through 24 encode the first domain, and exons 25 through 32 encode the second domain. The comparison of these exons indicated that the homologous domains were generated by duplication of several exons. The most 3' exon (exon 33) encodes the carboxy terminus of the LCA molecules and includes the entire 3' untranslated sequence.
Synthesis, characterization, biodegradation, and drug delivery application of biodegradable lactic/glycolic acid polymers. Part II: Biodegradation (2001)

A series of previously-synthesized lactic/glycolic acid polymers (PLGA) with various molar ratios of lactic to glycolic acid and various molecular weights were further studied with regard to their biodegradation behavior, and in particular, the factors affecting the biodegradation rate. The biodegradation of PLGA is affected by many factors including polymer composition, molecular weight, and nature of the incubating media. The biodegradation rate of PLGA containing higher content of lactic acid moiety is lower than those containing a lower content of lactic acid moiety. PLGAs with a higher molecular weight, degrade faster than those with a lower molecular weight, i.e. the molecular weight decreases more rapidly for higher molecular weight PLGAs than their lower molecular weight counterparts. Nature or properties of the hydrolysis/incubating media may have an effect on the biodegradation of PLGAs. A basic medium may slow down the biodegradation of PLGA in comparison with samples in an acidic medium. The rate of pH reduction for the incubating medium can be divided into three deferent phases, giving an inverted S-type pH profile for the non-buffered incubating media.