gebhart/patrepeval huggingface dataset:
Human reserve pluripotent mesenchymal stem cells are present in the connective tissues of skeletal muscle and dermis derived from fetal, adult, and geriatric donors (2001)

This study details the profile of 13 cell surface cluster differentiation markers on human reserve stem cells derived from connective tissues. Stem cells were isolated from the connective tissues of dermis and skeletal muscle derived from fetal, mature, and geriatric humans. An insulin/dexamethasone phenotypic bioassay was used to determine the identity of the stem cells from each population. All populations contained lineage-committed myogenic, adipogenic, chondrogenic, and osteogenic progenitor stem cells as well as lineage-uncommitted pluripotent stem cells capable of forming muscle, adipocytes, cartilage, bone, fibroblasts, and endothelial cells. Flow cytometric analysis of adult stem cell populations revealed positive staining for CD34 and CD90 and negative staining for CD3, CD4, CD8, CD11c, CD33, CD36, CD38, CD45, CD117, Glycophorin-A, and HLA DR-II.
Vascular permeability factor: A unique regulator of blood vessel function (1991)

Vascular permeability factor (VPF), also known as vascular endothelial growth factor (VEGF), is a potent polypeptide regulator of blood vessel function. VPF promotes an array of responses in endothelium, including hyperpermeability, endothelial cell growth, angiogenesis, and enhanced glucose transport. VPF regulates the expression of tissue factor and the glucose transporter. All of the endothelial cell responses to VPF are evidently mediated by high affinity cell surface receptors. Thus, endothelial cells have a unique and specific spectrum of responses to VPF. Since each of the responses of endothelial cells to VPF are also elicited by agonists, such as bFGF, TNF, histamine and others, it remains a major challenge to determine how post-receptor signalling pathways maintain both specificity and redundancy in cellular responses to various agonists.
Identifying the Truth (2013)

Huge amounts of textual information relevant for market analysis, trending or product monitoring can be found on the Web. To exploit that knowledge a number of extraction services were proposed that extract and categorize entities from given text. Prior work showed that a combination of individual extractors can increase quality. However, so far no system exists that is fully applicable to reasonably combine real world extraction services that differ substantially in the entity types they extract and the schemata used. In this paper, we propose an aggregation system and a corresponding aggregation process that can be used for these services. We present a number of novel aggregation techniques that incorporate schema-information as well as entity extraction specific characteristics into the aggregation process. The aggregation system is broadly evaluated on six real world named entity recognition services and compared to state of the art approaches.
Expediting the Fmoc solid phase synthesis of long peptides through the application of dimethyloxazolidine dipeptides (2003)

This paper describes the step-wise Fmoc solid phase synthesis of a 95-residue peptide related to FAS death domain. Attempts to prepare this peptide employing conventional amino acid building blocks failed. However, by the judicious use of dimethyloxazolidine dipeptides of serine and threonine, the peptide could be readily prepared in remarkable purity by applying single 1 h coupling reactions.
The two sides of cytokine signaling and glaucomatous optic neuropathy (2009)

The mechanistic study of glaucoma pathogenesis has shifted to seeking to understand the effects of immune responses on retinal ganglion cell damage and protection. Cytokines are the hormonal factors that mediate most of the biological effects in both the immune and nonimmune systems. CD4-expressing T helper cells are a major source of cytokine production and regulation. Type 1 helper T (Th1) cells are characterized by the production of proinflammatory cytokines such as interferon-gamma, interleukin (IL)-2, IL-12, IL-23, and tumor necrosis factor-alpha while type 2 helper T (Th2) cells are characterized by the production of IL-4, IL-5, IL-6, and IL-10. The balance of Th1/Th2 cytokine production influences many pathological processes and plays both causative and protective roles in neuron damages. Growing evidence indicates that imbalances of Th1/Th2 cytokine production are involved in neural damage or protection in many neurological diseases. In this review, we discuss the possible roles of Th1/Th2 cytokine production and imbalance of Th1/Th2 cytokines in retina, especially glaucomatous optic neuropathy.
In vivo studies of a synthetic inhibitor of thrombin. (1982)

The kinetics and the turnover and anticoagulant action in rabbits were studied of D-phenylalanyl-L-prolyl-L-arginyl-chloromethyl ketone (D-Phe-Pro-Arg-Ch/sub 2/Cl) (FPRMeCl), a synthetic irreversible inhibitor of thrombin. The inhibition of thrombin by FPRMeCl could be described as a two-step reaction; a reversible complex formation with a Klt. slashsub jlt. slash of 3.7 x 10/sup -8/M followed by formation of an irreversible complex with a rate constant k/sub 2/ of 0.4 sec/sup -1/. The disappearance rate from the plasma in six rabbits after intravenous injection of 1 mg of FPRMeCl could be described by a sum of two exponential terms, the first with a half-life of 0.7 min and the second with a half-life of 2.9 min. The recovery of inhibitory activity in the urine in two rabbits was 2.3% and 5.4%. After subcutaneous injection of 1 mg in six rabbits, the FPRMeCl level in plasma rose to an average value of 1 ..mu..M after 10 min and decreased gradually to 50 nM after 90 min. Intravenous injection of 0.5 mg human thrombin over 5 min in seven anesthesized rabbits resulted in death due to massive thrombosis in the right heart. Six rabbits that had received an intravenous injection of 1 mg of FPRMeCl more » just before the thrombin infusion all survived without a significant drop in fibrinogen levels. Infusion of 12 ml of a brain thromboplastin suspension over 30 min in six rabbits resulted in extensive prothrombin activation (residual prothrombin 21% +/- 1.5 of preinfusion value) and virtually complete defibrination (residual fibrinogen 14% +/- 4). Subcutaneous injection of 1 mg of FPRMeCl before and 30 to 60 min after the start of the thromboplastin infusion in four rabbits resulted in a comparable degree of prothrombin activation and a decrease of the fibrinogen level to 30% +/- 5 of its preinfusion level. « less
P-glycoprotein-mediated in vitro biliary excretion in sandwich-cultured rat hepatocytes. (2001)

Recently, sandwich-cultured (SC) rat hepatocytes have been used as an in vitro model to assess biliary excretion of drugs and xenobiotics. The purpose of the present study was to validate the use of SC rat hepatocytes for the in vitro assessment of P-glycoprotein (P-gp)-mediated biliary drug excretion. The specific and fluorescent P-gp substrate rhodamine 123 (Rh123) and the P-gp substrate digoxin were selected as model compounds. Rh123 and digoxin accumulation and Rh123 efflux under standard and Ca(2+)-free conditions were quantified in SC rat hepatocytes to determine substrate secretion into canalicular networks in vitro. The major role of P-gp in the biliary excretion of these compounds was confirmed by inhibition experiments with the potent P-gp inhibitor GF120918. Hepatocyte culture conditions, including media type and time in culture, significantly affected Rh123 biliary excretion. P-gp expression, as assessed by Western blot, was increased with culture time. Dexamethasone (an in vivo inducer of P-gp) concentrations ranging from 0.01 to 1 microM in the cell culture medium did not influence P-gp expression or Rh123 biliary excretion. Rh123 and digoxin biliary clearance values, predicted from SC rat hepatocyte data, were consistent with values reported in vivo and in isolated perfused rat liver studies. In conclusion, the results of this study demonstrate the utility of SC rat hepatocytes as an in vitro model to study and predict the biliary excretion of P-gp substrates.
γ-Hydroxybutyrate Reduces Mitogen-activated Protein Kinase Phosphorylation via GABAB Receptor Activation in Mouse Frontal Cortex and Hippocampus (2003)

gamma-Hydroxybutyrate (GHB) naturally occurs in the brain, but its exogenous administration induces profound effects on the central nervous system in animals and humans. The intracellular signaling mechanisms underlying its actions remain unclear. In the present study, the effects of GHB on the activation (phosphorylation) of mitogen-activated protein kinases (MAP kinases), extracellular signal-regulated kinase 1 and 2 (ERK1/2), were investigated. Acute administration of GHB (500 mg/kg, intraperitoneal) induced a fast and long lasting inhibition of MAP kinase phosphorylation in both frontal cortex and hippocampus. The reduced MAP kinase phosphorylation was observed in the CA1 and CA3 areas but not in the dentate gyrus. Pretreatment with the specific gamma-aminobutyric acid, type B (GABAB), receptor antagonist CGP56999A (20 mg/kg, intraperitoneal) prevented the action of GHB, and the effect of GHB was mimicked by baclofen, a selective GABAB receptor agonist, whereas the high affinity GHB receptor antagonist NCS-382 (200 mg/kg, intraperitoneal) had no effect on GHB-inhibited MAP kinase phosphorylation. Moreover, the GHB dehydrogenase inhibitor valproate (500 mg/kg, intraperitoneal), which inhibits the conversion of GHB into GABA, failed to block the effect of GHB on MAP kinase phosphorylation. Altogether, these data suggest that GHB, administered in vivo, reduces MAP kinase phosphorylation via a direct activation of GABAB receptors by GHB. In contrast, GHB (10 mm for 15 min) was found ineffective on MAP kinase phosphorylation in brain slices, indicating important differences in the conditions required for the second messenger activating action of GHB.
Crystal Structure of Recombinant Farnesyl Diphosphate Synthase at 2.6-.ANG. Resolution (1994)

The synthesis of farnesyl diphosphate (FPP), a key intermediate in the isoprenoid biosynthetic pathway required for the synthesis of cholesterol and in the formation of prenylated proteins, is catalyzed by the enzyme farnesyl diphosphate synthase (FPS). The crystal structure of avian recombinant FPS, the first three-dimensional structure for any prenyltransferase, was determined to 2.6-A resolution. The enzyme exhibits a novel fold composed entirely of alpha-helices joined by connecting loops. The enzyme's most prominent structural feature is the arrangement of 10 core helices around a large central cavity. Two aspartate-rich sequences that are highly conserved among the isoprenyl diphosphate synthase family of prenyltransferases, and are essential for enzymatic activity, were found on opposite walls of this cavity, with the aspartate side chains approximately 12 A apart and facing each other. The location and metal ion binding properties of these sequences suggest that the conserved aspartate residues participate in substrate binding of catalysis.
N‐terminal glycine‐specific protein conjugation catalyzed by microbial transglutaminase (2005)

Here, we report the N-terminal glycine (Gly) residue of a target protein can be a candidate primary amine for site-specific protein conjugation catalyzed by microbial transglutaminase (MTG) from Streptomyces mobaraensis. Gly5-enhanced green fluorescent protein (EGFP) (EGFP with five additional Gly residues at its N-terminus) was cross-linked with Myc-dihydrofolate reductase (DHFR) (DHFR with the myc epitope sequence at its N-terminus) to yield DHFR-EGFP heterodimers. The reactivities of additional peptidyl linkers were investigated and the results obtained suggested that at least three additional Gly residues at the N-terminus were required to yield the EGFP-DHFR heterodimeric form. Site-directed mutagenesis analysis revealed marked preference of MTG for amino acids adjacent to the N-terminal Gly residue involved in the protein conjugation. In addition, peptide-protein conjugation was demonstrated by MTG-catalyzed N-terminal Gly-specific modification of a target protein with the myc epitope peptide.
Homophilic binding of PTP mu, a receptor-type protein tyrosine phosphatase, can mediate cell-cell aggregation (1993)

The receptor-like protein tyrosine phosphatase, PTPmu, displays structural similarity to cell-cell adhesion molecules of the immunoglobulin superfamily. We have investigated the ability of human PTPmu to function in such a capacity. Expression of PTPmu, with or without the PTPase domains, by recombinant baculovirus infection of Sf9 cells induced their aggregation. However, neither a chimeric form of PTPmu, containing the extracellular and transmembrane segments of the EGF receptor and the intracellular segment of PTPmu, nor the intracellular segment of PTPmu expressed as a soluble protein induced aggregation. PTPmu mediates aggregation via a homophilic mechanism, as judged by lack of incorporation of uninfected Sf9 cells into aggregates of PTPmu-expressing cells. Homophilic binding has been demonstrated between PTPmu-coated fluorescent beads (Covaspheres) and endogenously expressed PTPmu on MvLu cells. Additionally the PTPmu-coated beads specifically bound to a bacterially expressed glutathione-S-transferase fusion protein containing the extracellular segment of PTPmu (GST/PTPmu) adsorbed to petri dishes. Covaspheres coated with the GST/PTPmu fusion protein aggregated in vitro and also bound to PTPmu expressed endogenously on MvLu cells. These results suggest that the ligand for this transmembrane PTPase is another PTPmu molecule on an adjacent cell. Thus homophilic binding interactions may be an important component of the function of PTPmu in vivo.
Excited-state proton-transfer reactions of naphthylammonium ion-18-crown-6 complexes (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExcited-state proton-transfer reactions of naphthylammonium ion-18-crown-6 complexesHaruo Shizuka, Kosei Kameta, and Tsutomu ShinozakiCite this: J. Am. Chem. Soc. 1985, 107, 13, 3956–3963Publication Date (Print):June 1, 1985Publication History Published online1 May 2002Published inissue 1 June 1985https://pubs.acs.org/doi/10.1021/ja00299a035https://doi.org/10.1021/ja00299a035research-articleACS PublicationsRequest reuse permissionsArticle Views124Altmetric-Citations19LEARN 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
Vascular Injury, Repair, and Restenosis After Percutaneous Transluminal Angioplasty in the Atherosclerotic Rabbit (1995)

Restenosis in an atherosclerotic artery results from a variable combination of intimal proliferation, vascular remodeling/wound contraction, and recoil of the normal section of the artery. The variability of an atherosclerotic artery to PTA injury results from variable dissection, thrombus formation, and cellular response to injury as well as variable scar contraction and elastic recoil.
Separation of Single-Walled Carbon Nanotubes on Silica Gel. Materials Morphology and Raman Excitation Wavelength Affect Data Interpretation (2005)

In this report, procedures are discussed for the enrichment of single-walled carbon nanotube (SWNT) types by simple filtration of the functionalized SWNTs through silica gel. This separation uses nanotube sidewall functionalization employing two different strategies. In the first approach, a crude mixture of metallic and semiconducting SWNTs was heavily functionalized with 4-tert-butylphenyl addends to impart solubility to the entire sample of SWNTs. Two major polarity fractions were rapidly filtered through silica gel, with the solvent being removed in vacuo, heated to 700 degrees C to remove the addends, and analyzed spectroscopically. The second approach uses two different aryldiazonium salts (one with a polar grafting group and one nonpolar), appended selectively onto the different SWNTs by means of titration and monitoring by UV analysis throughout the functionalization process. The different addends accentuate the polarity differences between the band-gap-based types permitting their partial separation on silica gel. Thermal treatment regenerated pristine SWNTs in enriched fractions. The processed samples were analyzed and characterized by Raman spectroscopy. A controlled functionalization method using 4-fluorophenyl and 4-iodophenyl addends was performed, and XPS analyses yielded data on the degree of functionalization needed to affect the van Hove singularities in the UV/vis/NIR spectra. Finally, we demonstrate that relative peak intensity changes in Raman spectra can be caused by morphological changes in SWNT bundling based on differing flocculation or deposition methods. Therefore a misleading impression of separations can result, underscoring the care needed in assessing efficacies in SWNT enrichment and the prerequisite use of multiple excitation wavelengths and similar flocculation or deposition methods in comparative analyses.
DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells (2019)

Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of complex cell populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single-cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.
Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging (2019)

Whole-genome bisulfite sequencing (WGBS) is the current gold standard of methylome analysis. Post-bisulfite adaptor tagging (PBAT) is an increasingly popular WGBS protocol because of high sensitivity and low bias. PBAT originally relied on two rounds of random priming for adaptor-tagging of single-stranded DNA (ssDNA) to attain high efficiency but at a cost of library insert length. To overcome this limitation, we developed terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate connector-mediated ssDNA (TACS) ligation as an alternative to random priming. In this method, TdT attaches adenylates to the 3'-end of input ssDNA, which are then utilized by RNA ligase as an efficient connector to the ssDNA adaptor. A protocol that uses TACS ligation instead of the second random priming step substantially increased the lengths of PBAT library fragments. Moreover, we devised a dual-library strategy that splits the input DNA to prepare two libraries with reciprocal adaptor polarity, combining them prior to sequencing. This strategy ensured an ideal base-color balance to eliminate the need for DNA spike-in for color compensation, further improving the throughput and quality of WGBS. Adopting the above strategies to the HiSeq X Ten and NovaSeq 6000 platforms, we established a cost-effective, high-quality WGBS, which should accelerate various methylome analyses.
Differential tissue-specific protein markers of vaginal carcinoma (2009)

The objective was to identify proteins differentially expressed in vaginal cancer to elucidate relevant cancer-related proteins. A total of 16 fresh-frozen tissue biopsies, consisting of 5 biopsies from normal vaginal epithelium, 6 from primary vaginal carcinomas and 5 from primary cervical carcinomas, were analysed using two-dimensional gel electrophoresis (2-DE) and MALDI-TOF mass spectrometry. Of the 43 proteins identified with significant alterations in protein expression between non-tumourous and tumourous tissue, 26 were upregulated and 17 were downregulated. Some were similarly altered in vaginal and cervical carcinoma, including cytoskeletal proteins, tumour suppressor proteins, oncoproteins implicated in apoptosis and proteins in the ubiquitin-proteasome pathway. Three proteins were uniquely altered in vaginal carcinoma (DDX48, erbB3-binding protein and biliverdin reductase) and five in cervical carcinoma (peroxiredoxin 2, annexin A2, sarcomeric tropomyosin kappa, human ribonuclease inhibitor and prolyl-4-hydrolase beta). The identified proteins imply involvement of multiple different cellular pathways in the carcinogenesis of vaginal carcinoma. Similar protein alterations were found between vaginal and cervical carcinoma suggesting common tumourigenesis. However, the expression level of some of these proteins markedly differs among the three tissue specimens indicating that they might be useful molecular markers.
Application of Artificial Neural Networks to Combinatorial Catalysis: Modeling and Predicting ODHE Catalysts (2002)

This paper shows how artificial neural networks are useful for modeling catalytic data from combinatorial catalysis and for predicting new potential catalyst compositions for the oxidative dehydrogenation of ethane (ODHE). The training and testing sets of data used for the neural network studies were obtained by means of a combinatorial approach search, which employs an evolutionary optimization strategy. Input and output variables of the neural network include the molar composition of thirteen different elements presented in the catalyst and five catalytic performances (C2H6 and O2 conversion, C2H4 yield, and C2H4, CO2, and CO selectivity). The fitting results indicate that neural networks can be useful in high-dimensional data management within combinatorial catalysis search procedures, since neural networks allow the ab initio evaluation of the reactivity of multicomponent catalysts.