gebhart/patrepeval huggingface dataset:
Angiopoietin‐regulated recruitment of vascular smooth muscle cells by endothelial‐derived heparin binding EGF‐like growth factor (2003)

Recruitment of vascular smooth muscle cells (SMC) by endothelial cells (EC) is essential for angiogenesis. Endothelial-derived heparin binding EGF-like growth factor (HB-EGF) was shown to mediate this process by signaling via ErbB1 and ErbB2 receptors in SMCs. 1) Analysis of ErbB-ligands demonstrated that primary ECs expressed only HB-EGF and neuregulin-1. 2) Primary SMCs expressed ErbB1 and ErbB2, but not ErbB3 or ErbB4. 3) Consistent with their known receptor specificities, recombinant HB-EGF, but not neuregulin-1, stimulated tyrosine phosphorylation of ErbB1 and ErbB2 and migration in SMCs. 4) Neutralization of HB-EGF or inhibition of ErbB1 or ErbB2 blocked 70-90% of the potential of ECs to stimulate SMC migration. Moreover, 5) angiopoietin-1, an EC effector with a role in recruitment of SMC-like cells to vascular structures in vivo, enhanced EC-stimulated SMC migration by a mechanism involving up-regulation of endothelial HB-EGF. Finally, 6) immunohistochemical analysis of developing human tissues demonstrated that HB-EGF was expressed in vivo in ECs associated with SMCs or pericytes but not in ECs of the hyaloid vessels not associated with SMCs. These results suggest an important role for HB-EGF and ErbB receptors in the recruitment of SMCs by ECs and elaborate on the mechanism by which angiopoietins exert their vascular effects.
Presence ofermgene classes in Gram-positive bacteria of animal and human origin in Denmark (1999)

A classification of the different erm gene classes based on published sequences was performed, and specific primers to detect some of these classes designed. The presence of ermA (Tn554), ermB (class IV) and ermC (class VI) was determined by PCR in a total of 113 enterococcal, 77 streptococcal and 68 staphylococcal erythromycin resistant isolates of animal and human origin. At least one of these genes was detected in 88% of the isolates. Four isolates contained more than one erm gene. ermB dominated among the enterococci (88%) and streptococci (90%) and ermC among staphylococci (75%) with ermA (Tn554) present in some isolates (16%). Variations in the presence of the different genes when comparing staphylococcal isolates of human and animal origin were observed.
Insertion of a GFP Reporter Gene in Influenza Virus (2013)

The incorporation of a fluorescent reporter gene into a replication-competent influenza A virus (IAV) has made it possible to trace IAV infection in vivo. This protocol describes the process of inserting a green fluorescent protein (GFP) reporter into the IAV genome using the established reverse genetics system. The strategy begins with the reorganization of segment eight of the IAV genome, during which the open reading frames of nonstructural protein 1 (NS1) and the nuclear export protein (NEP) are separated to allow for GFP fusion to the NS1 protein. The NS1, GFP, and NEP open reading frames (ORF) are then cloned into the IAV rescue system backbone. Upon construction of the GFP-encoding segment eight rescue plasmid, recombinant NS1-GFP influenza virus can be rescued via co-transfection with the remaining seven rescue plasmids. The generated NS1-GFP IAV can subsequently be used to visualize infected cells, both in vitro and in vivo.
Luminal trypsin may regulate enterocytes through proteinase-activated receptor 2 (1997)

Proteinase-activated receptor 2 (PAR-2) is a recently characterized G-protein coupled receptor that is cleaved and activated by pancreatic trypsin. Trypsin is usually considered a digestive enzyme in the intestinal lumen. We examined the hypothesis that trypsin, at concentrations normally present in the lumen of the small intestine, is also a signaling molecule that specifically regulates enterocytes by activating PAR-2. PAR-2 mRNA was highly expressed in the mucosa of the small intestine and in an enterocyte cell line. Immunoreactive PAR-2 was detected at the apical membrane of enterocytes, where it could be cleaved by luminal trypsin. Physiological concentrations of pancreatic trypsin and a peptide corresponding to the tethered ligand of PAR-2, which is exposed by trypsin cleavage, stimulated generation of inositol 1,4,5-trisphosphate, arachidonic acid release, and secretion of prostaglandin E2 and F1alpha from enterocytes and a transfected cell line. Application of trypsin to the apical membrane of enterocytes and to the mucosal surface of everted sacs of jejunum also stimulated prostaglandin E2 secretion. Thus, luminal trypsin activates PAR-2 at the apical membrane of enterocytes to stimulate secretion of eicosanoids, which regulate multiple cell types in a paracrine and autocrine manner. We conclude that trypsin is a signaling molecule that specifically regulates enterocytes by triggering PAR-2.
Protein kinase C zeta isoform is critical for kappa B-dependent promoter activation by sphingomyelinase. (1994)

Recent evidence demonstrates that the protein kinase C zeta (zeta PKC) isoform is required for the activation of nuclear factor kappa B (NF-kappa B) and mitogenic signaling in Xenopus oocytes and mammalian cells. The mechanism whereby zeta PKC regulates NF-kappa B most probably involves the activation of a putative I kappa B kinase of molecular mass approximately 50 kDa, which phosphorylates and inactivates I kappa B. Tumor necrosis factor alpha (TNF alpha) and interleukin-1, besides activating the phospholipase C-mediated breakdown of phosphatidylcholine, also generate ceramide, which is produced by stimulation of sphingomyelin hydrolysis. We show here that exogenous addition of sphingomyelinase (SMase) to NIH-3T3 fibroblasts transactivates a kappa B-dependent chloramphenicol acetyltransferase reporter plasmid, to an extent similar to that produced by TNF alpha or phosphatidylcholine/phospholipase C. More importantly, the ability of SMase to stimulate this parameter is severely impaired by transfection of a zeta PKC kinase-defective dominant negative mutant, which suggests a critical role of zeta PKC in SMase signaling. In keeping with this notion, we also demonstrate here that zeta PKC is activated in vitro by ceramide and in vivo by treatment of NIH-3T3 fibroblasts with SMase.
Molecular Self-Assembly in the Solid State. The Combined Use of Solid-State NMR and Differential Scanning Calorimetry for the Determination of Phase Constitution (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Self-Assembly in the Solid State. The Combined Use of Solid-State NMR and Differential Scanning Calorimetry for the Determination of Phase ConstitutionDonna Guarrera, Lloyd D. Taylor, and John C. WarnerCite this: Chem. Mater. 1994, 6, 8, 1293–1296Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/cm00044a028https://doi.org/10.1021/cm00044a028research-articleACS PublicationsRequest reuse permissionsArticle Views154Altmetric-Citations16LEARN 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
Increased lysyl oxidase activity in blood vessels of hypertensive rats and effect of .BETA.-aminopropionitrile on arteriosclerosis. (1978)

The activity of lysyl oxidase which catalyzes the initial step of cross-linking of collagen and elastin polypeptides was measured in blood vessels of the hypertensive rat. The enzyme activity was increased in the aorta and mesenteric artery when hypertension was induced in 8-week-old rats with administration of deoxycorticosterone acetate (DOCA) and 1% saline. Reserpine diminished this increase in vascular lysyl oxidase activity concomitant with reduction in blood pressure. When beta-aminopropionitrile, a specific inhibitor of lysyl oxidase, was administered before the onset of DOCA-salt hypertension, the aortic collagen content was reduced markedly. Concomitant with reduction in the aortic collagen content, the development of hypertension and arteriosclerotic changes in the kidney was partially prevented. These results would indicate that hypertension increases the amount and the degree of cross-linking of vascular collagen and that the deposition of excess collagen in the vascular wall contributes to the development of hypertension and arteriosclerosis.
Clinical exome sequencing: results from 2819 samples reflecting 1000 families (2016)

We report our results of 1000 diagnostic WES cases based on 2819 sequenced samples from 54 countries with a wide phenotypic spectrum. Clinical information given by the requesting physicians was translated to HPO terms. WES processes were performed according to standardized settings. We identified the underlying pathogenic or likely pathogenic variants in 307 families (30.7%). In further 253 families (25.3%) a variant of unknown significance, possibly explaining the clinical symptoms of the index patient was identified. WES enabled timely diagnosing of genetic diseases, validation of causality of specific genetic disorders of PTPN23, KCTD3, SCN3A, PPOX, FRMPD4, and SCN1B, and setting dual diagnoses by detecting two causative variants in distinct genes in the same patient. We observed a better diagnostic yield in consanguineous families, in severe and in syndromic phenotypes. Our results suggest that WES has a better yield in patients that present with several symptoms, rather than an isolated abnormality. We also validate the clinical benefit of WES as an effective diagnostic tool, particularly in nonspecific or heterogeneous phenotypes. We recommend WES as a first-line diagnostic in all cases without a clear differential diagnosis, to facilitate personal medical care.
Oxaloacetic Acid Supplementation as a Mimic of Calorie Restriction (2009)

The reduction in dietary intake leads to changes in metabolism and gene expression that increase lifespan, reduce the incidence of heart disease, kidney disease, Alzheimer's disease, type-2 diabetes and cancer. While all the molecular pathways which result in extended lifespan as a result of calorie restriction are not fully understood, some of these pathways that have resulted in lifespan expansion have been identified. Three molecular pathways activated by calorie restriction are also shown to be activated by supplementing the diet with the metabolite oxaloacetic acid. Animal studies supplementing oxaloacetic acid show an increase in lifespan and other substantial health benefits including mitochondrial DNA protection, and protection of retinal, neural and pancreatic tissues. Human studies indicate a substantial reduction in fasting glucose levels and improvement in insulin resistance. Supplementation with oxaloacetic acid may be a safer method to mimic calorie restriction than the use of traditional diabetes drugs.
Functional characterization of highly purified human hematopoietic repopulating cells isolated according to aldehyde dehydrogenase activity (2004)

Human hematopoietic stem cells (HSCs) are commonly purified by the expression of cell surface markers such as CD34. Because cell phenotype can be altered by cell cycle progression or ex vivo culture, purification on the basis of conserved stem cell function may represent a more reliable way to isolate various stem cell populations. We have purified primitive HSCs from human umbilical cord blood (UCB) by lineage depletion (Lin(-)) followed by selection of cells with high aldehyde dehydrogenase (ALDH) activity. ALDH(hi)Lin(-) cells contained 22.6% +/- 3.0% of the Lin(-) population and highly coexpressed primitive HSC phenotypes (CD34(+) CD38(-) and CD34(+)CD133(+)). In vitro hematopoietic progenitor function was enriched in the ALDH(hi)Lin(-) population, compared with ALDH(lo)Lin(-) cells. Multilineage human hematopoietic repopulation was observed exclusively after transplantation of ALDH(hi)Lin(-) cells. Direct comparison of repopulation with use of the nonobese diabetic/severe combined immunodeficient (NOD/SCID) and NOD/SCID beta2 microglobulin (beta2M) null models demonstrated that 10-fold greater numbers of ALDH(hi)-Lin(-) cells were needed to engraft the NOD/SCID mouse as compared with the more permissive NOD/SCID beta2M null mouse, suggesting that the ALDH(hi)Lin(-) population contained committed progenitors as well as primitive repopulating cells. Cell fractionation according to lineage depletion and ALDH activity provides a viable and prospective purification of HSCs on the basis of cell function rather than cell surface phenotype.
Growth of high optical and electrical quality GaN layers using low-pressure metalorganic chemical vapor deposition (1991)

We report on the low-pressure metalorganic chemical vapor deposition of high quality single-crystal GaN layers over basal plane sapphire substrates. Optimization of growth conditions resulted in material with carrier densities of 1017 /cm3 at room temperature and corresponding mobilities around 350 cm2 /V s. The photoluminescence linewidths improved from 160 meV [full width at half maximum (FWHM)] to 25 meV (FWHM). With improved material quality we were able to observe the polar optical mode and the ionized impurity scattering regimes in the mobility versus temperature data. Good quality Schottky barriers were formed on the as-grown material using a tungsten probe and an alloyed indium contact. Our observations indicate a direct correlation between electrical and optical characteristics of good material and strongly question nitrogen vacancies as the sole explanation for the high carrier densities observed in poor quality GaN growths.
Recombinant Mycobacterium bovis Bacillus Calmette-Guérin Secreting Merozoite Surface Protein 1 (MSP1) Induces Protection against Rodent Malaria Parasite Infection Depending on MSP1-stimulated Interferon γ and Parasite-specific Antibodies (1998)

The merozoite surface protein 1 (MSP1) has emerged as a leading malaria vaccine candidate at the erythrocytic stage. Recombinant bacillus Calmette-Guérin (rBCG), which expressed a COOH-terminal 15-kD fragment of MSP1 of Plasmodium yoelii (MSP1-15) as a fusion protein with a secretory protein of Mycobacterium kansasii, was constructed. Immunization of mice with this rBCG induced a higher degree of protection against blood-stage parasite infection than with recombinant MSP1-15 in the RIBI adjuvant (RIBI ImmunoChem Research, Inc., Hamilton, MT) or incomplete Freund's adjuvant systems. We studied the mechanism of protection induced by MSP1-15, and found that interferon (IFN)-gamma had a major role in protection in all adjuvant systems we examined. Mice that produced low amounts of MSP1-15 stimulated IFN-gamma and could not control parasite infection. The antibody against MSP1-15 did not play a major role in protection in this system. After parasite infection, immunoglobulin G2a antibodies, which had been produced by IFN-gamma stimulation, were induced and subsequently played an important role in eradicating parasites. Thus, both cellular and humoral immune responses were essential for protection from malaria disease. These data revealed that BCG is a powerful adjuvant to induce such a protective immune response against malaria parasites.
Induced pluripotent stem cells: will they be safe? (2009)

Recent developments in stem cell research have enabled the reprogramming of somatic cells to a pluripotent state using exogenous factors. Induced pluripotent stem (iPS) cells have the potential to differentiate into any cell type, and are being used to elucidate the molecular events that permit the conversion of one cell type to another. iPS cells have potential uses in in vitro disease modeling and toxicology screening, and as cellular therapies and regenerative medicine; however, various safety concerns exist that must be resolved before iPS cell therapy becomes a reality. Potential risks are related to the delivery of the endogenous factors, alterations in target cells, the cellular effects of the expression and reactivation of the factors that induce pluripotency, and safety issues related to the incorrect characterization and incomplete differentiation of the reprogrammed cells. In this review, the technique used to generate iPS cells is described, followed by a discussion of the safety concerns and how these concerns are currently being addressed.
A model to evaluate mild analgesics in oral surgery outpatients (1976)

A model was developed to evaluate mild analgesics in an oral surgery outpatient clinic population. On a report form, patients recorded starting pain and then pain intensities, relief responses, and side effects hourly for 3 hr after drug administration. The treatments were randomly allocated to patients on a single-dose-only basis, and the double-blind technique was used. The first of two studies compared codeine 30 mg, aspirin 650 mg, codeine 30 mg with aspirin 650 mg, and placebo in 128 subjects. The second study compared codeine 60 mg, acetaminophen 600 mg, and codeine 60 mg with acetaminophen 600 mg and placebo in 160 subjects. Time-effect curves were generated for both pain relief and pain relief and pain intensity difference (PID). First-hour scores, peak scores, and total scores were statistically analyzed by parametric and nonparametric factorial analysis. Both aspirin 650 mg and acetaminophen 600 mg proved superior to placebo (p less than 0.01) for all measures of effect with both parametric or nonparametric analyses, while codeine 30 mg was not significantly superior to placebo in any analysis. Codeine 60 mg proved significantly superior to placebo for certain measures of effect when analyzed with the nonparametric model. There was no significant interaction between either aspirin or acetaminophen and codeine.
Polymer Support Oligonucleotide Synthesis XX: Synthesis of a Henhectacosa Deoxynucleotide by Use of a Dimeric Phosphoramidite Synthon (1986)

Abstract The dimeric phosphoramidite synthon (4) has been prepared by solution synthesis. Incorporation of (4) and the monomeric phosphoramidite (5) into a polymer supported synthesis on controlled pore glass (CPG) lead to the synthesis of a model oligodeoxynucleotide containing 101 nucleotide units.
Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics (2004)

Liver cirrhosis is a worldwide health problem. Reliable, noninvasive methods for early detection of liver cirrhosis are not available. Using a three-step approach, we classified sera from rats with liver cirrhosis following different treatment insults. The approach consisted of: (i) protein profiling using surface-enhanced laser desorption/ionization (SELDI) technology; (ii) selection of a statistically significant serum biomarker set using machine learning algorithms; and (iii) identification of selected serum biomarkers by peptide sequencing. We generated serum protein profiles from three groups of rats: (i) normal (n=8), (ii) thioacetamide-induced liver cirrhosis (n=22), and (iii) bile duct ligation-induced liver fibrosis (n=5) using a weak cation exchanger surface. Profiling data were further analyzed by a recursive support vector machine algorithm to select a panel of statistically significant biomarkers for class prediction. Sensitivity and specificity of classification using the selected protein marker set were higher than 92%. A consistently down-regulated 3495 Da protein in cirrhosis samples was one of the selected significant biomarkers. This 3495 Da protein was purified on-chip and trypsin digested. Further structural characterization of this biomarkers candidate was done by using cross-platform matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) peptide mass fingerprinting (PMF) and matrix-assisted laser desorption/ionization time of flight/time of flight (MALDI-TOF/TOF) tandem mass spectrometry (MS/MS). Combined data from PMF and MS/MS spectra of two tryptic peptides suggested that this 3495 Da protein shared homology to a histidine-rich glycoprotein. These results demonstrated a novel approach to discovery of new biomarkers for early detection of liver cirrhosis and classification of liver diseases.
Experimental Bit Commitment Based on Quantum Communication and Special Relativity (2013)

Bit commitment is a fundamental cryptographic primitive in which Bob wishes to commit a secret bit to Alice. Perfectly secure bit commitment between two mistrustful parties is impossible through asynchronous exchange of quantum information. Perfect security is however possible when Alice and Bob split into several agents exchanging classical and quantum information at times and locations suitably chosen to satisfy specific relativistic constraints. Here we report on an implementation of a bit commitment protocol using quantum communication and special relativity. Our protocol is based on [A. Kent, Phys. Rev. Lett. 109, 130501 (2012)] and has the advantage that it is practically feasible with arbitrary large separations between the agents in order to maximize the commitment time. By positioning agents in Geneva and Singapore, we obtain a commitment time of 15 ms. A security analysis considering experimental imperfections and finite statistics is presented.