gebhart/patrepeval huggingface dataset:
Effective Use of Autoantibody Tests in the Diagnosis of Systemic Autoimmune Disease (2005)

Screening for disease-specific autoantibodies may be useful in asymptomatic ANA-positive individuals as a means of evaluating the risk of developing a systemic autoimmune disease such as systemic lupus erythematosus (SLE), polymyositis/dermatomyositis (PM/DM), scleroderma (SSc), Sjögren's syndrome (SS), rheumatoid arthritis (RA), or primary biliary cirrhosis (PBC) in the future. In patients with known or suspected systemic autoimmune disease, a panel of disease-specific markers may help to establish a diagnosis and to assess the prognosis. The great strides in autoantibody testing over the last 20 years make it feasible to use specific autoantibody markers to improve diagnostic accuracy in systemic autoimmune disease. New technology enabling screening for multiple autoantibodies may further enhance the clinical usefulness of autoantibody testing, making it possible to diagnose autoimmune disease in its earliest stages and to intervene before serious end organ damage occurs.
Identification of a 160-kDa polypeptide that binds to the tight junction protein ZO-1. (1991)

ZO-1 is a 210- to 220-kDa peripheral membrane protein associated with the cytoplasmic surface of the epithelial tight junction. Because ZO-1 may interact with other unidentified tight junction proteins, we have looked for other polypeptides that bind to ZO-1. A 160-kDa polypeptide was identified that coimmunoprecipitates with ZO-1 from detergent extracts of metabolically labeled Madin-Darby canine kidney (MDCK) cells. This polypeptide appears to be distinct from ZO-1, rather than a degradation product, by several criteria. It lacks ZO-1 epitopes recognized by both monoclonal antibodies and a polyclonal serum to ZO-1, since it is not detectable in immunoblots of either whole cell extracts or ZO-1 immunoprecipitates. Also, it exhibits a peptide map different from that of ZO-1 on one-dimensional "Cleveland gels." Moreover, because the kinetics of appearance of newly synthesized 160-kDa polypeptide in anti-ZO-1 immunoprecipitates is much slower than that of ZO-1, its presence in immunoprecipitates cannot be simply explained by degradation of ZO-1 during cell lysis. Like ZO-1, the 160-kDa polypeptide seems to be a cytoplasmic peripheral membrane protein. It cannot be labeled by two different cell surface labeling reagents. It can be extracted from the membrane by high salt concentration in the absence of detergents. As expected for a protein complex, the 160-kDa polypeptide and ZO-1 turn over with similar kinetics. We propose that the 160-kDa polypeptide is a component of the tight junction.
Calcium Stimulation of Ammonium Absorption in Onion (1991)

Abstract The inefficiency of N use in soils has been studied widely, producing varied suggestions for increased effectiveness. The object of this research was to examine the use of Ca 2+ as a means to increase NH + 4 absorption, using onion ( Allium cepa L.) as a test crop. Ammonium absorption in the presence of variable Ca 2+ concentrations was measured in short‐term greenhouse studies as well as longterm greenhouse studies and field‐production trials. The greenhouse 15 NH + 4 absorption study was conducted in 4‐L pots containing 3.5 kg of calcareous Gila sandy loam (coarse‐loamy, mixed, calcareous, thermic Typic Torrifluvents). The long‐term growth study was conducted in calcareous quartz sand. Irrigation solutions consisted of half‐strength nutrient solutions (5 mol m −3 in NH + 4 ) with Ca 2+ :NH + 4 molar proportions of 0, 0.25, 0.50, 1.00, and 2.00. The 15 NH + 4 absorption study was conducted during a 30‐h period on 60‐d onion. The long‐term growth experiment received the same nutrient solutions until mature onion bulbs were produced (about 5 cm in diameter). A 2‐yr field production trial used single rows on 1‐m wide beds. The soil was a calcareous Saneli silty clay loam [clayey over sandy or sandy‐skeletal, montmorillonitic (calcareous), thermic Vertic Torrifluvent]. In 15 NH + 4 studies, NH + 4 absorption increased with added Ca by as much as 189% in onion bulbs and by 67% in onion tops relative to absorption with no Ca added. These maximum increases were in association with solution Ca 2+ :NH + 4 molar proportions (MP) of 0.5 in onion bulbs and 1.0 in onion tops. Total plant dry weights with Ca added increased as much as 100% in bulbs and 25% in tops in 30‐h 15 NH + 4 absorption tests over the 0 Ca 2+ controls. In greenhouse growth tests, vegetative matter increased as much as 40% with increasing Ca 2+ concentrations at constant NH + 4 levels compared to the 0 Ca 2+ control. This translated to increased total N absorption. In 2 yr of field testing with a MP of 0.25, mature bulbs from both years increased 64% over yields with urea alone. Thus the addition of Ca 2+ with urea produced significantly improved plant N‐use efficiencies (greater plant yield at the same level of N application). These results were suggested from both the short‐term greenhouse 15 NH + 4 absorption experiment and from the long‐term greenhouse growth trial.
Chondroitinase C activity of Streptococcus intermedius (1989)

Chondroitin 6-sulfate depolymerizing activity was examined in the culture supernatant of Streptococcus intermedius ATCC 27335. 2-Acetamido-2-deoxy-3-O-(beta-D-gluco-4-enepyranosyluronic acid)-6-O-sulfo-D-galactose was split from the substrate. The enzyme(s) was not active upon chondroitin 4-sulfate or dermatan sulfate, which indicated that the enzyme responsible for the depolymerization is chondroitinase C.
Histone Sequence Database: new histone fold family members (1998)

Searches of the major public protein databases with core and linker chicken and human histone sequences have resulted in the compilation of an annotated set of histone protein sequences. In addition, new database searches with two distinct motif search algorithms have identified several members of the histone fold family, including human DRAP1 and yeast CSE4. Database resources include information on conflicts between similar sequence entries in different source databases, multiple sequence alignments, links to the Entrez integrated information retrieval system, structures for histone and histone fold proteins, and the ability to visualize structural data through Cn3D. The database currently contains >1000 protein sequences, which are searchable by protein type, accession number, organism name, or any other free text appearing in the definition line of the entry. All sequences and alignments in this database are available through the World Wide Web at http://www.nhgri.nih. gov/DIR/GTB/HISTONES or http://www.ncbi.nlm.nih. gov/Baxevani/HISTONES
Modulating Affect, Cognition, and Behavior – Prospects of Deep Brain Stimulation for Treatment-Resistant Psychiatric Disorders (2011)

Most patients suffering from psychiatric disorders respond to combinations of psycho- and psychopharmacotherapy; however there are patients who profit little if anything even after many years of treatment. Since about a decade different modalities of targeted neuromodulation - among them most prominently - deep brain stimulation (DBS) - are being actively researched as putative approaches to very treatment-resistant forms of those disorders. Recently, promising pilot data have been reported both for major depression (MD) and obsessive-compulsive disorder (OCD). Given the fact that patients included in DBS studies had been treated unsuccessfully for many years with conventional treatment methods, renders these findings remarkable. Remarkable is the fact, that in case of the long-term studies underway for MD, patients show a stable response. This gives hope to a substantial percentage of therapy-resistant psychiatric patients requiring new therapy approaches. There are no fundamental ethic objections to its use in psychiatric disorders, but until substantial clinical data is available, mandatory standards are needed. DBS is a unique and very promising method for the treatment of therapy-resistant psychiatric patients. The method allows manipulating pathological neuronal networks in a very precise way.
Identification, cloning, and expression of a cytosolic megakaryocyte protein-tyrosine-phosphatase with sequence homology to cytoskeletal protein 4.1. (1991)

We have isolated a cDNA encoding a third type of protein-tyrosine-phosphatase. We screened human megakaryoblastic cell line (MEG-01) an umbilical vein endothelial cell cDNA libraries to obtain a 3.7-kilobase cDNA designated PTPase MEG. Northern blot analysis of MEG-01 RNA detected a 3.7-kilobase transcript, suggesting that a full-length cDNA has been identified. PTPase MEG cDNA contains an open reading frame of 926 amino acids. The cDNA has a G+C-rich 5' untranslated region of 771 nucleotides that has the potential to form stable stem-loop structures and has two upstream ATG codons. The predicted protein (Mr = 105,910) has no apparent membrane-spanning region and contains a single protein-tyrosine-phosphatase domain (amino acids 659-909) that is 35-40% identical to previously described tyrosine-phosphatase domains. The recombinant phosphatase domain possesses protein-tyrosine-phosphatase activity when expressed in Escherichia coli. The amino-terminal region (amino acids 31-367) is 45% identical to the amino terminus of human erythrocyte protein 4.1, a cytoskeletal protein. The identification of a protein-tyrosine-phosphatase that is related to cytoskeletal proteins implies that cell signaling activities reside not only in transmembrane receptors but in cytoskeletal elements as well.
Selection of DNA clones with enhancer sequences. (1994)

A method is described for selection of DNA clones that contain enhancer sequences that activate gene expression. An Escherichia coli-rodent cell shuttle vector, pPyE0, was used that contains polyoma viral DNA without the polyoma enhancer region. Replication of pPyE0 DNA in mouse cells is markedly reduced due to deletion of the polyoma enhancer region. Insertion of mouse genomic DNA fragments that contain putative enhancer sequences into pPyE0 adjacent to the polyoma origin of replication restored, to varying extents, the ability of the recombinant plasmid DNA to replicate in mouse cells. Recombinant plasmids that replicate well in mouse cells, therefore, are amplified selectively. Transfection of mouse neuroblastoma or fibroblast cells that constitutively synthesize polyoma large tumor antigen with a library of mouse genomic DNA fragments inserted in pPyE0 yielded many recombinant plasmids. DNA inserts from each of the 16 clones that were examined stimulated the expression of an enhancerless chloramphenicol acetyltransferase reporter gene. The DNA inserts from 4 clones that were studied resulted in 4- to 13-fold increases in chloramphenicol acetyltransferase mRNA in transfected mouse cells. Nucleotide sequence analysis led to the identification of 5 genomic DNA clones that were obtained by selection. All of the homologies found were to regions of DNA that are thought to be involved in the regulation of gene expression.
Extending the imaging volume for biometric iris recognition (2005)

The use of the human iris as a biometric has recently attracted significant interest in the area of security applications. The need to capture an iris without active user cooperation places demands on the optical system. Unlike a traditional optical design, in which a large imaging volume is traded off for diminished imaging resolution and capacity for collecting light, Wavefront Coded imaging is a computational imaging technology capable of expanding the imaging volume while maintaining an accurate and robust iris identification capability. We apply Wavefront Coded imaging to extend the imaging volume of the iris recognition application.
Modified RNAs in CRISPR/Cas9: An Old Trick Works Again (2016)

Old tricks, new dog: CRISPR/Cas9 is a powerful tool for gene editing that requires an endonuclease (Cas9) and RNA strands. It has been shown that chemical modification of the RNA structures, an approach that has been used to improve the efficiency of RNA interference, can also be applied to enhance the activity of CRISPR/Cas9 and reduce its off-target effects.
Induction of the Mouse Ribonucleotide Reductase R1 and R2 Genes in Response to DNA Damage by UV Light (1996)

Ribonucleotide reductase is responsible for the production of deoxyribonucleotides required for DNA synthesis and consists of two nonidentical subunits, proteins R1 and R2. Here we show that the R1 promoter can be induced up to 3-fold, and the R2 promoter is induced up to 10-fold by UV light in a dose-dependent manner. This was demonstrated using serum-starved, synchronized G0/G1 mouse fibroblast 3T3 cells stably transformed with different R1 and R2 promoter-luciferase reporter gene constructs. R2 promoter activation requires a minimal promoter, containing a TTTAAA element plus the transcription start, and either three upstream DNA-protein binding regions or one proximal, NF-Y binding region. This is different from proliferation-specific activation of the R2 promoter. Using Northern blotting we show a preferential accumulation of the minor, 1. 6-kilobase R2 transcript in irradiated cells, whereas the levels of the major 2.1-kilobase transcript are unchanged. No R2 promoter activation was observed after treatment of mouse cells with agents reported to induce the ribonucleotide reductase genes in Saccharomyces cerevisiae such as hydroxyurea or methylmethane sulfonate. This indicates that activation of ribonucleotide reductase gene expression is specific for nucleotide excision repair in mammalian cells and not part of a general response to DNA damage.
Glycoproteomics enabled by tagging sialic acid- or galactose-terminated glycans (2012)

In this paper, we present two complementary strategies for enrichment of glycoproteins on living cells that combine the desirable attributes of "robust enrichment" afforded by covalent-labeling techniques and "specificity for glycoproteins" typically provided by lectin or antibody affinity reagents. Our strategy involves the selective introduction of aldehydes either into sialic acids by periodate oxidation (periodate oxidation and aniline-catalyzed oxime ligation (PAL)) or into terminal galactose and N-acetylgalactosamine residues by galactose oxidase (galactose oxidase and aniline-catalyzed oxime ligation (GAL)), followed by aniline-catalyzed oxime ligation with aminooxy-biotin to biotinylate the glycans of glycoprotein subpopulations with high efficiency and cell viability. As expected, the two methods exhibit reciprocal tagging efficiencies when applied to fully sialylated cells compared with sialic acid-deficient cells. To assess the utility of these labeling methods for glycoproteomics, we enriched the PAL- and GAL-labeled (biotinylated) glycoproteome by adsorption onto immobilized streptavidin. Glycoprotein identities (IDs) and N-glycosylation site information were then obtained by liquid chromatography-tandem mass spectrometry on total tryptic peptides and on peptides subsequently released from N-glycans still bound to the beads using peptide N-glycosidase F. A total of 175 unique N-glycosylation sites were identified, belonging to 108 nonredundant glycoproteins. Of the 108 glycoproteins, 48 were identified by both methods of labeling and the remainder was identified using PAL on sialylated cells (40) or GAL on sialic acid-deficient cells (20). Our results demonstrate that PAL and GAL can be employed as complementary methods of chemical tagging for targeted proteomics of glycoprotein subpopulations and identification of glycosylation sites of proteins on cells with an altered sialylation status.
Assessment of Intracellular Insulin Content during All Steps of Human Islet Isolation Procedure (1998)

This study investigated the recovery of pancreatic insulin content during human islet isolation prior to and after digestion-filtration, continuous Hanks-Ficoll gradient purification ( n = 20), and 3–4 day culture at 22°C ( n = 6). The native insulin content varied in a wide range from 28.4 U to 360.8 U/pancreas. After digestion the initially measured average insulin content of 115.8 ± 20.8 U/pancreas (mean ± SEM) increased to 264.6 ± 22.8% ( p &lt; 0.001). This increase of insulin during pancreas digestion was attributed to the asymetrical distribution of insulin within the pancreas. Sampling of insulin within the pancreatic caput seemed not to be representative for the insulin content of the complete native organ, because the ratio of insulin per gram tissue within the pancreatic cauda compared to the caput ( n = 5) was 2.4 ± 0.4 ( p &lt; 0.05). After purification total insulin recovery was 55.3 ± 4.8% ( p &lt; 0.001). Because recovery of islet equivalent number (IEQ) (83.7 ± 4.4%) exceeded insulin recovery, insulin/IEQ ratio decreased from 656.8 ± 70.6 μU/IEQ before purification to 436.4 ± 58.1 μU/IEQ ( p &lt; 0.001) after purification. After 22° C culture ( n = 6) recovery of insulin and IEQ was 80.1 ± 8.1% ( p &lt; 0.05) and 92.8 ± 3.5% ( p = NS), respectively. Insulin content per IEQ decreased to 85.8 ± 6.5% ( p &lt; 0.05). This study clearly shows that most of islet insulin is lost during purification. This seems to be caused rather by an amplified insulin release than by the loss of islets itself. This release may facilitate the separation of endocrine and exocrine tissue by gradient centrifugation, but may also accelerate islet exhaustion detrimental for long-term insulin independence. © 1998 Elsevier Science Inc.
Expression of vascular endothelial growth factor C and chemokine receptor CCR7 in gastric carcinoma and their values in predicting lymph node metastasis (2004)

The expression of VEGF-C and CCR7 is related to lymph node metastasis of gastric carcinoma and both of them may become new targets for the treatment of gastric carcinoma. Furthermore, the combined examination of VEGF-C and CCR7 expression in endoscopic biopsy specimens may be useful in predicting lymph node metastasis of gastric carcinoma and deciding the extent of surgical lymph node resection.
The stimulating adventure of KRN 7000 (2011)

Associated with the CD1d protein, KRN 7000, a potent synthetic α-galactosylceramide, is known to activate the invariant NKT immune cells. This stimulation then leads to the production of different cytokines modulating a T(H)1/T(H)2 immune response balance involved in protection against several pathologies such as autoimmune diseases and cancers. Various efforts have been made toward the synthesis of simple and more functionalized analogues in order to selectively induce T(H)1 or T(H)2-type cytokine production. Since the discovery of KRN 7000, structure-activity relationships, crystallographic and modelling studies have pointed to the potential of several GalCer analogues in term of selective bioactivity, and have highlighted interesting elements in order to better understand the recognition and activation mechanisms of immune iNKT cells. By presenting an up-to-date library of analogues, collecting recent breakthroughs done in crystallography and molecular modelling, and relating them to the available biological results, we hope that this review will highlight and help the scientific community in their KRN research.
The C‐terminal region of NELL1 mediates osteoblastic cell adhesion through integrin α3β1 (2012)

NELL1 is a secretory osteogenic protein containing several structural motifs that suggest that it functions as an extracellular matrix component. To determine the mechanisms underlying NELL1-induced osteoblast differentiation, we examined the cell-adhesive activity of NELL1 using a series of recombinant NELL1 proteins. We demonstrated that NELL1 promoted osteoblastic cell adhesion through at least three cell-binding domains located in the C-terminal region of NELL1. Adhesion of cells to NELL1 was strongly inhibited by function-blocking antibodies against integrin α3 and β1 subunits, suggesting that osteoblastic cells adhered to NELL1 through integrin α3β1. Further, focal adhesion kinase activation is involved in NELL1 signaling.
The origin of vibrational mode couplings in various secondary structural motifs of polypeptides (2004)

Electrostatic (through-space) and covalent (through-bond) contributions to couplings involving the C[double bond]O and C[bond]N vibrational stretching modes of the amide group in the alpha-helix and the parallel and antiparallel beta-sheet structures of alanine polypeptides are analyzed. Coupling constants computed at the density functional theory level are compared with the transition dipole coupling model and the complete electrostatic interaction between transition densities. We find that the transition densities of C[double bond]O modes are localized, and the electrostatic mechanism then holds. In contrast, the C[bond]N mode transition densities are delocalized, and covalent contributions to the coupling are significant.
IV. Some 3,6-Unsymmetrically Disubstituted 1,2,4,5-Tetrazines1a,b,c (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIV. Some 3,6-Unsymmetrically Disubstituted 1,2,4,5-Tetrazines1a,b,cVytautas A. Grakauskas, Arthur J. Tomasewski, and J. P. HorwitzCite this: J. Am. Chem. Soc. 1958, 80, 12, 3155–3159Publication Date (Print):June 1, 1958Publication History Published online1 May 2002Published inissue 1 June 1958https://pubs.acs.org/doi/10.1021/ja01545a060https://doi.org/10.1021/ja01545a060research-articleACS PublicationsRequest reuse permissionsArticle Views430Altmetric-Citations31LEARN 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
Effect of externally applied focused acoustic energy on clot disruption in vitro (1999)

Application of low-frequency ultrasound for clot disruption has been suggested as a potential therapy to enhance thrombus dissolution, but the optimal mode for delivery of ultrasound with clot-disruptive properties has not yet been extensively explored. Target-specific effects are desirable and may be accomplished by focusing the ultrasound. Adequate focusing, however, requires a short wavelength. The aim of this study was to compare the clot-disruptive effects of different modalities of focused acoustic energy. An in vitro model (10 blood clots for each modality) was used to test the clot-disruptive capacity of (i) shock waves generated in an electrohydraulic lithotriptor; (ii) focused continuous ultrasound of frequency 1.1 MHz, delivered from a specially constructed piezoelectric transducer; and (iii) focused pulse-modulated ultrasound of frequency 1.1 MHz delivered from the same transducer. Exposure to 30 s of focused pulse-modulated ultrasound caused a marked reduction (99+/-2%) in clot weight compared with 30 shock waves (11+/-5%) or 30 s exposure to focused continuous wave ultrasound (11+/-6%) (P<0.0001). The observed marked and rapid disruptive effect on blood clots of focused high-frequency ultrasound indicates an alternative approach for external ultrasound-mediated thrombus destruction in vivo. The focused pulse-modulated technique has potential to exhibit the desired effect in a well-defined target volume and provides the means for control of the average power.