gebhart/patrepeval huggingface dataset:
Synthesis of pCpCpA-3‘-NH-Phenylalanine as a Ribosomal Substrate (2002)

[reaction: see text] The trinucleotide cytidylyl(3'-->5'phosphoryl)cytidylyl(3'-->5'phosphoryl)-3'-deoxy-3'-(L-phenylalanyl) amido adenosine (CpCpA-NH-Phe) was synthesized by phosphoramidite chemistry from 3'-amino-3'-deoxyadenosine as the ribosomal substrate. The 3'-amino-3'-deoxyadenosine was first converted to 3'-(N-tert-butyloxycarbonyl-L-phenylalanine)amido-3'-deoxy-6-N,6-N,2'-O-tribenzoyl-adenosine and then coupled with cytidine phosphoramidite to produce the fully protected CpCpA-NH-Phe-Boc. The title product was obtained after removing all protection groups and then radiolabeled with (32)P to yield pCpCpA-NH-Phe, which demonstrated high activity for the peptidyl transferase reaction in the ribosome.
P072 GLPG0634, the first selective JAK1 inhibitor, shows strong activity in the mouse DSS-colitis model (2014)

Poster presentations TGF-beta, TNF-alfa, and t-TG. (3) Hp(2-20) counteracted the increase in FPR-1 and FPR-2 mRNA expression induced by TNBS. (4) FPR-1 and FPR-2 mRNA expression is up-regulated in patients with ulcerative colitis.
Overexpression of the human tissue kallikrein genes KLK4, 5, 6, and 7 increases the malignant phenotype of ovarian cancer cells (2006)

The human tissue kallikrein family of serine proteases (hK1-hK15 encoded by the genes KLK1-KLK15) is involved in several cancer-related processes. Accumulating evidence suggests that certain tissue kallikreins are part of an enzymatic cascade pathway that is activated in ovarian cancer and other malignant diseases. In the present study, OV-MZ-6 ovarian cancer cells were stably co-transfected with plasmids expressing hK4, hK5, hK6, and hK7. These cells displayed similar proliferative capacity as the vector-transfected control cells (which do not express any of the four tissue kallikreins), but showed significantly increased invasive behavior in an in vitro Matrigel invasion assay (p<0.01; Mann-Whitney U-test). For in vivo analysis, the cancer cells were inoculated into the peritoneum of nude mice. Simultaneous expression of hK4, hK5, hK6, and hK7 resulted in a remarkable 92% mean increase in tumor burden compared to the vector-control cell line. Five out of 14 mice in the 'tissue kallikrein overexpressing' group displayed a tumor/situs ratio greater than 0.198, while this weight limit was not exceeded at all in the vector control group consisting of 13 mice (p=0.017; chi2 test). Our results strongly support the view that tumor-associated overexpression of tissue kallikreins contributes to ovarian cancer progression.
Structural and enzymatic characterization of a purified prohormone-processing enzyme: secreted, soluble Kex2 protease. (1992)

The prohormone-processing Kex2 protease of the budding yeast Saccharomyces cerevisiae can be converted from an intracellular membrane protein to a soluble, secreted, and active form by deletion of the transmembrane domain and C-terminal tail. One such molecule was purified to near homogeneity from the culture medium of an overexpressing yeast strain. Amino acid sequence analysis revealed that the N terminus of mature Kex2 protease is created by a potentially autoproteolytic cleavage at Lys108-Arg109, prior to the domain homologous to subtilisin, followed by trimming of Leu-Pro and Val-Pro dipeptides by the Ste13 dipeptidyl aminopeptidase. Kinetic parameters were examined using fluorogenic peptidyl-methylcoumarin amide substrates. Initial burst titration indicated that the preparation was entirely active. Measurements of dependence of activity on pH yielded a simple curve suggesting titration of a single ionizable group. Activity was half-maximal at pH 5.7 and nearly constant from pH 6.5 to 9.5. Discrimination between substrates was as great as 360-fold in Km and 130-fold in kcat. Substrates with a Lys-Arg dipeptide preceding the cleaved bond were preferred, having kcat/Km values up to 1.1 x 10(7) sec-1.M-1. The enzyme cleaved substrates having Arg-Arg, Pro-Arg, Ala-Arg, and Thr-Arg with increased Km but with unchanged kcat. In contrast, the enzyme displayed a dramatically lower kcat for a Lys-Lys substrate with a smaller increase in Km. Thus the two residues preceding the cleaved bond may play distinct roles in the selectivity of binding and cleavage of prohormone substrates.
GENETICS OF DUCHENNE MUSCULAR DYSTROPHY (1988)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Vascular-access-port implantation for serial blood sampling in conscious swine. (1986)

A method to simplify serial venous blood sampling in miniature pigs was developed. Jugular vein Vascular-Access-Ports (VAP) were implanted in four animals. The mean functional lifetime of these ports was 37.7 +/- 23.0 (S.D.) days with a range of 17 to 77 days. The VAP allowed easy serial blood sampling and intravenous drug administration. Use of these ports in animals restrained in a sling was simple and effective and caused no undue stress to the animal over a 6 to 8 hour experiment. The VAPs were implanted easily and required minimal maintenance. Subcutaneous location of the entire apparatus allowed for group housing of the pigs and decreased the susceptibility of postoperative infection and/or damage. Provided that proper maintenance and careful aseptic sampling techniques are used, the VAP is a relatively easy, safe and reliable alternative to conventional methods of serial blood sampling in swine.
Isolation and characterization of the human stearoyl-CoA desaturase gene promoter: requirement of a conserved CCAAT cis-element (2001)

Stearoyl-CoA desaturase is the rate-limiting enzyme in the production of mono-unsaturated fatty acids. We have recently cloned and characterized the human Scd cDNA and SCD (the stearoyl-CoA desaturase structural gene) on chromosome 10, as well as the non-transcribed pseudogene on chromosome 17. In order to further define SCD regulation and function, we have isolated and characterized the promoter of the structural gene. Screening of chromosome-10-specific libraries resulted in the isolation of 4.1kb of SCD sequence upstream of the translation start site. Binding sites for transcription factors critical for mouse Scd1 and Scd2 promoter activity, such as sterol-regulated-element-binding protein and nuclear factor Y, were present in the human SCD promoter (Scd is the mouse stearoyl-CoA desaturase gene). Deletion analysis in HaCaT keratinocytes identified a critical region for promoter activity between nts 496–609 upstream of the translation start site. Site-directed mutagenesis of binding sites in this region identified the CCAAT box as the critical cis-element for SCD promoter activity. An electrophoretic mobility-shift assay confirmed that this element binds nuclear proteins from HaCaT keratinocytes. The polyunsaturated-fatty-acid (PUFA) response element, previously identified in the promoters of mouse Scd1 and Scd2, was found to be conserved in the human SCD promoter, and contained the critical CCAAT cis-element. A minimal promoter construct including this region was responsive to fatty acids, with oleate and linoleate decreasing transcription and stearate increasing it. These studies indicate that CCAAT-box-binding proteins activate SCD transcription in cultured keratinocytes and that fatty acids modulate transcription, most likely through the conserved PUFA response element.
Lower Endogenous Androgen Levels and Dyslipidemia in Men with Non-Insulin-Dependent Diabetes Mellitus (1992)

Lower levels of endogenous androgens are seen in older diabetic men, and low androgen levels are associated with diabetic dyslipidemia.
Information flow in entangled quantum systems (2000)

All information in quantum systems is, notwithstanding Bell's theorem, localized. Measuring or otherwise interacting with a quantum system S has no effect on distant systems from which S is dynamically isolated, even if they are entangled with S. Using the Heisenberg picture to analyse quantum information processing makes this locality explicit, and reveals that under some circumstances (in particular, in Einstein–Podolsky–Rosen experiments and in quantum teleportation), quantum information is transmitted through ‘classical’ (i.e. decoherent) information channels.
A Hydrophobic Surface Is Essential To Inhibit the Aggregation of a Tau-Protein-Derived Hexapeptide (2013)

This paper seeks to understand how a macrocyclic β-sheet peptide inhibits the aggregation of the tau-protein-derived peptide Ac-VQIVYK-NH2 (AcPHF6). Previous studies established that macrocyclic β-sheet peptide 1 inhibits AcPHF6 aggregation, while the sequence isomer in which the lysine and leucine residues at positions R6 and R7 are swapped has little effect on AcPHF6 aggregation. The current studies find that positions R1, R3, and R7 are especially sensitive to mutations. Reducing hydrophobicity at these positions substantially diminishes inhibition. Although position R5 is not sensitive to mutations that reduce hydrophobicity, it is sensitive to mutations that increase hydrophobicity. Enhanced hydrophobicity at this position substantially enhances inhibition. These studies establish that the hydrophobic surface comprising residues R1, R3, and R7 is crucial to the inhibition process and that the residue R5, which shares this surface, is also important. Collectively, these findings demonstrate that hydrophobic surfaces between β-sheet layers are important in inhibiting amyloid aggregation.
Measuring high-bandwidth signals in CMOS circuits (1993)

In this Letter we present a technique to measure details of the shape of high-bandwidth signals in CMOS circuits. This technique allows us to study quantities in the subnanosecond range as, for instance, the rise time of a clock edge or the detailed shape of noise pulses.
PCR protocols for emerging infectious diseases : a supplement to Diagnostic molecular microbiology: principles and applications (1996)

Part I. Molecular Diagnostic Applications for Emerging Infections Molecular Methods for Pathogen Identification Genotype Detection of Antimicrobial Resistance Nucleic Acid Sequencing Studies of Microbial Pathogens: Insights into Epidemiology, Virulence, Drug Resistance, and Diversity Part II. Selected Protocols for Emerging Infections Detection of Sin Nombre Hantavirus by Reverse Transcriptase-PCR Genus- and Species-level Identification of Ehrlichia Species by Using PCR and Sequencing Detection of the Agent of Human Granulocytic Ehrlichiosis by PCR Detection of Rifampin Resistance Mutations in Mycobacterium tuberculosis by Dideoxy Fingerprinting PCR-Heteroduplex Detection of Rifampin-Resistant Mycobacterium tuberculosis Detection of Mycobacteria Resistance to Streptomycin and Clarithromycin Detection of Fluroquinolone Resistance Mutations in Mycobacterium tuberculosis PCR-RFLP Detection of Point Mutations in the Catalase-Peroxidase Gene (katG) of Mycobacterium tuberculosis Associated with Isoniazid Resistance Detection of Enterococcal Vancomycin Resistance by Multiplex PCR Genetic Detection of the Streptococcal Pyrogenic Exotoxin Gene by PCR Detection of Cryptosporium Parvum by PCR Detection of Cyclospora
<title>DocBrowse: a system for information retrieval from document image data</title> (1996)

This paper presents the software architecture for DocBrowse: a system for mixed text/graphics document image analysis and retrieval. DocBrowse is an open and extensible environment that permits the user to visually manage and perform queries on highly degraded document image databases. DocBrowse also serves as a research environment for developing document image analysis and query by image example (QBIE) algorithms. The system consists of a user interface, an object-relational document database and a variety of document image analysis engines. Using DocBrowse, it is possible to perform queries that retrieve documents based on both graphical and textual content. We describe the graphical user interface and visual image browser that is used to perform such queries. We also describe our approach to QBIE, the database structure, and the analysis engines incorporated in DocBrowse.
Differential Effects of Immunosuppressants and Antibiotics on Human Monoclonal Antibody Production in SCID Mouse Ascites by Five Heterohybridomas (1998)

SCID mice were inoculated with five human-mouse heterohybridomas derived by fusion of human lymph node lymphocytes from lung cancer patients with murine myeloma cells or human-mouse heteromyeloma cells, and the production of their human monoclonal antibodies (MAb) in the mouse ascites was investigated. In a comparison of the effects of pretreatment by i.p. (intraperitoneal) injection of pristane and anti-asialo GM1 serum on the antibody production of three of the hybridomas, pristane pretreatment resulted in substantial antibody production by all three, and pretreatment with anti-asialo GM1 serum resulted in similar or slightly lower levels of antibody production by two of the hybridomas but none by the third. In a second series of experiments using four of the hybridomas with pristane pretreatment, the co-injection of either penicillin G and streptomycin or kanamycin together with the hybridoma at the time of i.p. inoculation resulted in enhanced MAb production by the two heterohybridomas that had been propagated in medium containing hypoxanthine-aminopterin-thymidine (HAT) but not by the two that had been propagated in HAT-free medium.
Trends in Temperature and Precipitation Extremes over Circum-Bohai-Sea Region, China (2012)

在从 1961 ～ 2008 的温度和降水极端的趋势在 Circum-Bohai-Sea 区域，用每日的温度的中国和 63 个气象学的车站的降水数据上被调查了。至多驻扎的结果表演，温暖的天的年度频率有重要增加并且在冷天的年度频率温暖夜里，以及重要减少，冷夜里，霜天，并且年度日报温度范围(数据终端就绪) 。他们的地区性的平均变化是 2.06 d/10yr， 3.95 d/10yr， 1.88 d/10yr， 4.27 d/10yr， 4.21 d/10yr 并且 0.20
Endovascular occlusion of intracranial aneurysms with electrically detachable coils: correlation of aneurysm neck size and treatment results. (1994)

Accurate angiographic measurements of neck diameter can be obtained in most aneurysms. The size of an aneurysm neck correlates well with the results of the endovascular treatment. Small-necked aneurysms can be satisfactorily occluded with this technique. In wide-necked aneurysms this technique should be reserved for lesions having a high surgical risk.
ULTRAFILTRATION OF SOYBEAN WATER EXTRACTS: PROCESSING CHARACTERISTICS AND YIELDS (1979)

ABSTRACT Water extracts of whole soybeans were obtained as described previously (JFS 43: 354) and processed in a hollow fiber ultrafiltration unit equipped with the XM‐50 membrane. Protein and fat concentration increased linearly with volume concentration ratio (VCR) as expected for rejected components, although some losses were evident probably due to membrane adsorption. Amount of ash in retentate was reduced by 55%, indicating some binding with proteins. Protein coefficients of 0.9 or better could be easily obtained. Trypsin inhibitor activity of final product was reduced by 79%, mostly due to heat treatments during extraction. Final product assayed typically 60% protein, 34% fat, 2.8% ash (dry basis) and was very low in oligosaccharides and phytic acid.
Comparative dual label study of first and second generation antitumor-associated glycoprotein-72 monoclonal antibodies in colorectal cancer patients. (1993)

Radiolabeled first-generation anti-tumor-associated glycoprotein-72 (TAG-72) monoclonal antibody (MAb), B72.3, has proven useful in detecting primary and secondary colorectal carcinoma. It has been anticipated that the development of second-generation, higher affinity, anti-TAG-72 MAbs, CC49 and CC83, would be of greater use in cancer detection and of value in radioimmunotherapy of human cancer. We compared the pharmacokinetics, biodistribution, and immune responses of 131I-labeled CC49 and CC83 to 125I-labeled B72.3 by preoperatively coninjecting dual-labeled MAbs into 16 colorectal cancer patients. The imaging properties of radiolabeled CC49 and CC83 were also assessed. Pharmacokinetics of all three MAbs were identical, and there were no differences in the uptake of any of three MAbs in tumor and normal tissues. Maximum tumor uptake was 0.0041% of the injected dose/g for 125I-B72.3, 0.0024% for 131I-CC49, and 0.0029% for 131I-CC83. Radiolabeled CC49 and CC83 detected most known tumor sites on scintigrams without any clear advantage for either MAb. Nonspecific splenic and testicular uptake was frequently observed. Anti-idiotypic human anti-mouse antibody responses were seen more frequently with B72.3 than with CC49 or CC83. We conclude that higher affinity, radiolabeled anti-TAG-72 MAbs can detect colorectal cancer but do not penetrate these tumors more effectively than B72.3. Improvements in tumor detection and radioimmunotherapeutic strategies will likely require the administration of smaller fragments of MAb molecules or novel delivery systems rather than the continued development of higher affinity MAbs.
The Effect of Recombinant Human Bone Morphogenetic Protein-2 (rhBMP-2) on the Healing of Full-Thickness Defects of Articular Cartilage* (1997)

Articular cartilage has a limited capacity for repair. We investigated the effect of rhBMP-2 (recombinant human bone morphogenetic protein-2) on the healing of full-thickness osteochondral defects in adult New Zealand White rabbits. A single defect, three millimeters wide by three millimeters deep, was created in the trochlear groove of the right femur in eighty-nine rabbits. The defect was either left empty, filled with a plain collagen sponge, or filled with a collagen sponge impregnated with five micrograms of rhBMP-2. The animals were killed at four, eight, or twenty-four weeks, and the repair tissue was examined histologically and evaluated with use of a grading scale. The defects also were examined immunohistochemically for the presence of type-II collagen at four and eight weeks. The rate of bone repair was evaluated with fluorescent labeling of bone at two and four weeks and with use of fluorescence microscopy at eight weeks. Treatment with rhBMP-2 greatly accelerated the formation of new subchondral bone and improved the histological appearance of the overlying articular surface. At twenty-four weeks, the thickness of the repair cartilage was 70 per cent that of the normal adjacent cartilage and a new tidemark usually had formed between the repair cartilage and the underlying subchondral bone. The average total scores on the histological grading scale were significantly better (p < 0.01) for the defects treated with rhBMP-2 than for the untreated defects (those left empty or filled with a plain collagen sponge) at all time-points. Immunostaining with an antibody against type-II collagen showed the diffuse presence of this cartilage-specific collagen throughout the repair cartilage in the treated defects. The untreated defects demonstrated minimum staining with this antibody.
Insights into Regulation and Function of the Major Stress-Induced hsp70 Molecular Chaperone In Vivo: Analysis of Mice with Targeted Gene Disruption of the hsp70.1 orhsp70.3 Gene (2001)

The murine hsp70 gene family includes the evolutionarily conserved hsp70.1 and hsp70.3 genes, which are the major proteins induced by heat and other stress stimuli. hsp70.1 and hsp70.3 encode identical proteins which protect cells and facilitate their recovery from stress-induced damage. While the hsp70 gene family has been widely studied and the roles of the proteins it encodes as molecular chaperones in a range of human pathologies are appreciated, little is known about the developmental regulation of hsp70.1 and hsp70.3 expression and the in vivo biological function of their products. To directly study the physiological role of these proteins in vivo, we have generated mice deficient in heat shock protein 70 (hsp70) by replacing the hsp70.1 or hsp70.3 gene with an in-frame beta-galactosidase sequence. We report here that the expression of hsp70.1 and hsp70.3 is developmentally regulated at the transcriptional level, and an overlapping expression pattern for both genes is observed during embryo development and in the tissues of adult mice. hsp70.1-/- or hsp70.3-/- mice are viable and fertile, with no obvious morphological abnormalities. In late embryonic stage and adult mice, both genes are expressed constitutively in tissues exposed directly to the environment (the epidermis and cornea) and in certain internal organs (the epithelium of the tongue, esophagus, and forestomach, and the kidney, bladder, and hippocampus). Exposure of mice to thermal stress results in the rapid induction and expression of hsp70, especially in organs not constitutively expressing hsp70 (the liver, pancreas, heart, lung, adrenal cortex, and intestine). Despite functional compensation in the single-gene-deficient mice by the intact homologous gene (i.e., hsp70.3 in hsp70.1-/- mice and vice versa), a marked reduction in hsp70 protein expression was observed in tissues under both normal and heat stress conditions. At the cellular level, inactivation of hsp70.1 or hsp70.3 resulted in deficient maintenance of acquired thermotolerance and increased sensitivity to heat stress-induced apoptosis. The additive or synergistic effects exhibited by coexpression of both hsp70 genes, and the evolutionary significance of the presence of both hsp70 genes, is hence underlined.
The human leukocyte adhesion glycoprotein Mac-1 (complement receptor type 3, CD11b) alpha subunit. Cloning, primary structure, and relation to the integrins, von Willebrand factor and factor B. (1988)

Mac-1 (CD 11b/CD18) is a leukocyte adhesion heterodimeric glycoprotein which functions both as a receptor for iC3b (CR3) and in several cell-cell and cell-substrate adhesive interactions. We describe full-length cDNA clones for the alpha subunit of Mac-1. Mac-1 alpha subunit message was detected in blood monocytes and phorbol-12-myristate acetate-induced myeloid cell lines, but not in cells of the T or B lineages, correlating with Mac-1 protein surface expression. The alpha subunit of Mac-1 is a transmembrane protein of 1137 residues with a long extracellular domain (1092 residues) and a 19-amino acid cytoplasmic tail. The extracellular domain contains three putative divalent cation-binding sequences and 19 potential N-glycosylation sites. The amino acid sequence of Mac-1 alpha shows that it is a member of the integrin superfamily; Mac-1 alpha shows 63% identity to the alpha subunit of the leukocyte adhesion glycoprotein p150.95 and 25% to the alpha subunits of the extracellular matrix receptors platelet glycoprotein IIb/IIIa, the fibronectin receptor, and the vitronectin receptor. The Mac-1 alpha subunit putative divalent cation-binding sites and the flanking regions exhibit a high degree of identity both to the p150.95 alpha subunit (87% identity at the amino acid level) and to the rest of the integrin alpha subunits (38%). The alpha subunit of Mac-1, like the p150.95 alpha subunit, contains a domain of 187 amino acids in the extracellular region which is absent in other integrins. This leukocyte or "L" domain is homologous to the A domains of von Willebrand factor, which in turn are homologous to regions of the C3-binding proteins factor B and C2. These findings draw attention to this region of Mac-1 as a potential binding site for iC3b.
Structural-phase transformations in bentonite after acid treatment (2003)

The methods of X-ray diffraction, Fourier transform infra-red spectroscopy (FTIR), X-ray microanalysis, electron microscopy, BET and cation exchange capacity (CEC) were used for investigation of the structural-phase transformations in bentonite under the influence of hydrochloric acid and temperature treatment (100-800?C). It is established that in HCl medium during temperature treatment, dehydration and dehydroxilation of montmorillonite occur. The presence of gypsum and barium chloride results in an intercalation of interlayer space of montmorillonite by Ca and Ba ions Temperature treatment of intercalated montmorillonite leads to the formation of pores.