gebhart/patrepeval huggingface dataset:
Generation of a Flexible Cell Line with Regulatable, High-Level Expression of HIV Gag/Pol Particles Capable of Packaging HIV-Derived Vectors (2001)

HIV-derived vectors are of potential clinical relevance due to their ability to transduce nondividing cells in vitro and in vivo. However, the generation of cell lines stably and reproducibly expressing high amounts of defined subviral particles, capable of packaging and transducing HIV-derived vectors, has been hampered by the cytotoxicity of some of the required gene products, in particular of the HIV-1 protease. The successful use of regulatable gene expression systems to overcome this problem requires that the remaining basally expressed gene product activity is below the threshold for cytotoxicity. To try to achieve this, we have consecutively introduced appropriate plasmids, encoding HIV rev and HIV gag/pol gene products, each under the control of separate ecdysone-inducible promoters, into human 293 cells. Using a protocol in which a specific HIV protease inhibitor, Saquinavir, was continuously present in the culture medium during selection, we could generate stable cell lines inducibly expressing high amounts of subviral particles. A cell line, termed 293-Rev/Gag/Pol(i), which has been characterized in more detail, inducibly releases, within 48 h postinduction, high amounts of HIV Gag/Pol particles (about 10 microg CA/ml). These HIV Gag/Pol particles can package and transduce third-generation HIV vectors to high titers. Thus, in addition to other applications, the 293-Rev/Gag/Pol(i) cell line represents a "founder" packaging cell line which, depending on the requirement, can be further modified to include specific transgene-encoding vector and targeting glycoprotein genes.
Essential operating principles for tumor spheroid growth (2008)

The finalized analogue required nine axioms. We posit that the validated analogue's operating principles are reasonable representations of those utilized by EMT6/Ro cells during tumor spheroid development.
Reducing Acrylamide in Fried Snack Products by Adding Amino Acids (2005)

ABSTRACT: The aims of this study were to develop commercial methods for reducing the acrylamide content in processed foods and apply them to commercial snacks. The formation of acrylamide in fried foods was found to depend on the composition of raw materials as well as the frying time and temperature. In potato chips, acrylamide was rapidly formed at over 160°C, with the amount proportional to the heating duration and temperature. Free amino acids were used to reduce acrylamide, with lysine, glycine, and cysteine having the greatest effects in the aqueous system. Lysine and glycine were effective at inhibiting the formation of acrylamide in wheat‐flour snacks. In potato snacks, the addition of 0.5% glycine to pallets reduced acrylamide by more than 70%. Soaking potato slices in a 3% solution of either lysine or glycine reduced the formation of acrylamide by more than 80% in potato chips fried for 1.5 min at 185°C. These results indicate that the addition of certain amino acids by soaking the uncooked products in appropriate solutions is an effective way of reducing acrylamide in processed foods.
Artificial Neural Network Model for Predicting Compressive Strength of Concrete (2009)

Compressive strength of concrete is a commonly used criterion in evaluating concrete. Although testing of the compressive strength of concrete specimens is done routinely, it is performed on the 28th day after concrete placement. Therefore, strength estimation of concrete at early time is highly desirable. This study presents the effort in applying neural network-based system identification techniques to predict the compressive strength of concrete based on concrete mix proportions, maximum aggregate size (MAS), and slump of fresh concrete. Back-propagation neural networks model is successively developed, trained, and tested using actual data sets of concrete mix proportions gathered from literature. The test of the model by un-used data within the range of input parameters shows that the maximum absolute error for model is about 20% and 88% of the output results has absolute errors less than 10%. The parametric study shows that water/cement ratio (w/c) is the most significant factor affecting the output of the model. The results showed that neural networks has strong potential as a feasible tool for predicting compressive strength of concrete.
Liposomal Membranes. V. Interaction of Zinc(II) Ion with Egg Phosphatidylcholine Liposomes (1980)

Abstract The efficiency of encapsulation of several divalent metal ions, mainly Zn(II) ion, into egg lecithin liposomes has been investigated with particular attention to the stability of liposomal membranes against the transition metal(II) ions. The stronger interaction of metal ions to lecithins led to the less formation of liposomes. The addition of a suitable amount of nonionic detergent, 2-[ω-hydroxypentadeca(oxyethylene)-α-yl]-1,3-bis(dodecyloxy)propane (2C1215G, see text), enhanced the encapsulation of Zn(II) and Cu(II) ions in liposomes. The stoichiometric measurement for the binding of Zn(II) ion to single compartment liposomes of egg lecithin suggested that a Zn(II) ion is interacting with three or four lecithin molecules on the average in both halves of liposomal bilayers. Even under the circumstances, the bilayer structure of liposomes was certainly kept stable, which was electron micrographically visualized.
Microtubule Formation in vitro in Solutions Containing Low Calcium Concentrations (1972)

Isolated rat brain tubulin can be repolymerized in vitro in solutions containing adenosine triphosphate or guanosine triphosphate, magnesium ions, and a good calcium chelator. The extreme sensitivity of tubulin to calcium ions explains the failure of previous efforts to obtain polymerization and suggests a possible mechanism for regulation of microtubule polymerization in vivo.
Kinetics of Oxidation of Ammonia in Solutions Containing Ozone with or without Hydrogen Peroxide (1997)

This research investigates the kinetics of traditional ozonation and peroxone oxidation of ammonia in alkaline solutions. The ozonation reaction is governed by the direct oxidation of ammonia with ozone molecules, and the overall kinetics is second order, with first order each in ozone and ammonia. The reaction rate increases slightly with temperature, and at 25 °C, the overall rate constant varies from 12.3 to 27.0 1/Ms as the pH increases from 8 to 10. In the presence of hydrogen peroxide, the peroxone oxidation is controlled mainly by the formation of hydroxyl radical and its subsequent radical reactions. The depletion rate of ozone is first order with respect to both concentrations of ozone and hydrogen peroxide but is nearly independent of the ammonia concentration. The overall rate constant increases from 5860 to 133 000 1/Ms in the pH range of 8−10 at 25 °C, indicating that the rate increases with the hydroxyl ion concentration of the exponent of 0.71. The destruction rate of ammonia depends on concentrations of various species, and for wastewaters containing high concentrations of ammonia, the peroxone oxidation process can be effective and economical to achieve a high efficiency for ozone utilization.
Concurrent alkylation‐methoxylation of 4,5‐dihalopyridazin‐6‐ones and synthesis of 5‐halo‐4‐hydroxypyridazin‐6‐ones (1996)

Abstract 1‐Alkyl‐5‐halo‐4‐methoxypyridazin‐6‐ones were synthesized from 1‐alkyl‐4,5‐dihalopyridazin‐6‐ones by the concurrent alkylation‐methoxylation. 1‐Alkyl‐5‐halo‐4‐hydroxypyridazin‐6‐ones were also prepared.
Upgrading to TLS Within HTTP/1.1 (2000)

This memo explains how to use the Upgrade mechanism in HTTP/1.1 to initiate Transport Layer Security (TLS) over an existing TCP connection. This allows unsecured and secured HTTP traffic to share the same well known port (in this case, http: at 80 rather than https: at 443). It also enables "virtual hosting", so a single HTTP + TLS server can disambiguate traffic intended for several hostnames at a single IP address.
The Expression and Prognostic Impact of Immune Cytolytic Activity-Related Markers in Human Malignancies: A Comprehensive Meta-analysis (2018)

Overall, our data highlight the existence of diverse levels of CYT across different cancer types and suggest that along with the existence of complicated associations among various tumor-infiltrated immune cells, it is capable to promote or inhibit the establishment of a permissive tumor microenvironment, depending on the cancer type. High levels of immunosuppression seem to exist in several tumor types.
The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases. (1990)

The cytochrome o complex is one of two ubiquinol oxidases in the aerobic respiratory system of Escherichia coli. This enzyme catalyzes the two-electron oxidation of ubiquinol-8 which is located in the cytoplasmic membrane, and the four-electron reduction of molecular oxygen to water. The purified oxidase contains at least four subunits by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and has been shown to couple electron flux to the generation of a proton motive force across the membrane. In this paper, the DNA sequence of the cyo operon, containing the structural genes for the oxidase, is reported. This operon is shown to encode five open reading frames, cyoABCDE. The gene products of three of these, cyoA, cyoB, and cyoC, are clearly related to subunits II, I, and III, respectively, of the eukaryotic and prokaryotic aa3-type cytochrome c oxidases. This family of cytochrome c oxidases contain heme a and copper as prosthetic groups, whereas the E. coli enzyme contains heme b (protoheme IX) and copper. The most striking sequence similarities relate the large subunits (I) of both the E. coli quinol oxidase and the cytochrome c oxidases. It is likely that the sequence similarities reflect a common molecular architecture of the two heme binding sites and of a copper binding site in these enzymes. In addition, the cyoE open reading frame is closely related to a gene denoted ORF1 from Paracoccus dentrificans which is located in between the genes encoding subunits II and III of the cytochrome c oxidase of this organism. The function of the ORF1 gene product is not known. These sequence relationships define a superfamily of membrane-bound respiratory oxidases which share structural features but which have different functions. The E. coli cytochrome o complex oxidizes ubiquinol but has no ability to catalyze the oxidation of reduced cytochrome c. Nevertheless, it is clear that the E. coli oxidase and the aa3-type cytochrome c oxidases must have very similar structures, at least in the vicinity of the catalytic centers, and they are very likely to have similar mechanisms for bioenergetic coupling (proton pumping).
In vitro stimulation of megakaryocyte maturation by megakaryocyte stimulatory factor. (1987)

Counterflow centrifugal elutriation and Percoll density gradient centrifugation were employed to prepare cell populations from rat bone marrow that were selectively enriched in the cytoplasmically immature megakaryocytes and depleted of the most mature megakaryocytes. The incorporation of [14C]leucine into the platelet-specific alpha-granule protein, platelet factor 4, as well as the incorporation of [35S]sulfate into platelet proteoglycans synthesized by the maturing megakaryocytes were monitored as markers of cytoplasmic maturation. Rat platelet factor 4 was specifically isolated and characterized by its high affinity for heparin-Sepharose and its amino-terminal sequence homology to human and rabbit platelet factor 4. The [35S]sulfate-labeled proteoglycans were primarily composed of chondroitin 4-sulfate glycosaminoglycans and were identified as platelet granule components by their ability to be secreted by megakaryocytes in response to thrombin or A23187. The production of both components was increased as much as 3-fold in a dose-dependent manner by the addition of picomolar concentrations of purified megakaryocyte stimulatory factor, without a concomitant increase in general protein synthesis. The above results suggest that the megakaryocyte stimulatory factor may regulate the synthesis of platelet granule components by megakaryocytes and hence control the rate and/or extent of cytoplasmic maturation during megakaryocyte development.
Human Oct3 gene family: cDNA sequences, alternative splicing, gene organization, chromosomal location, and expression at low levels in adult tissues (1992)

Transcription factors containing the POU-domain have been shown to be important regulators of tissue-specific gene expression in the pituitary and lymphoid cells. Using a polymerase chain reaction (PCR)-based strategy, we have searched for similar factors that may be expressed in adult human pancreatic islets. This approach resulted in the amplification of sequences encoding the octamer binding proteins Oct1 and Oct3 (also called Oct4). The isolation of cDNAs encoding Oct3 revealed the expression of two isoforms of this transcription factor termed Oct3A and Oct3B that are generated by alternative splicing. Human Oct3A and Oct3B are composed of 360 and 265 amino acids, respectively, of which the 225 amino acids at the COOH-termini are identical. The sequence of human Oct3A shows 87% amino acid identity with mouse Oct3. Reverse-transcriptase PCR showed low levels of expression of both Oct3A and Oct3B mRNA in all adult human tissues examined. We also isolated and characterized the human Oct3 gene (OTF3) and a related gene, OTF3C. The human Oct3 gene, localized to human chromosome 6 in the region of the MHC complex, spans about 7 kb and consists of five exons. The Oct3-related gene, OTF3C, is a retroposon and has been localized to human chromosome 8. Southern blotting and PCR amplification of human DNA indicated the presence of other OTF3-related genes as has been previously noted in the mouse. Two polymorphisms which can be typed using PCR were identified in OTF3 which will facilitate genetic studies of this gene.
Protein-tyrosine Phosphatase PCP-2 Inhibits β-Catenin Signaling and Increases E-cadherin-dependent Cell Adhesion (2006)

beta-Catenin is a key molecule involved in both cell adhesion and Wnt signaling pathway. However, the exact relationship between these two roles has not been clearly elucidated. Tyrosine phosphorylation of beta-catenin was shown to decrease its binding to E-cadherin, leading to decreased cell adhesion and increased beta-catenin signaling. We have previously shown that receptor-like protein-tyrosine phosphatase PCP-2 localizes to the adherens junctions and directly binds and dephosphorylates beta-catenin, suggesting that PCP-2 might regulate the balance between signaling and adhesive beta-catenin. Here we demonstrate that PCP-2 can inhibit both the wild-type and constitutively active forms of beta-catenin in activating target genes such as c-myc. The phosphatase activity of PCP-2 is required for this effect since loss of catalytic activity attenuates its inhibitory effect on beta-catenin activation. Expression of PCP-2 in SW480 colon cancer cells can lead to stabilization of cytosolic pools of beta-catenin perhaps, by virtue of their physical interaction. PCP-2 expression also leads to increased membrane-bound E-cadherin and greater stabilization of adherens junctions by dephosphorylation of beta-catenin, which could further sequester cytosolic beta-catenin and thus inhibit beta-catenin mediated nuclear signaling. Furthermore, SW480 cells stably expressing PCP-2 have a reduced ability to proliferate and migrate. Thus, PCP-2 may play an important role in the maintenance of epithelial integrity, and a loss of its regulatory function may be an alternative mechanism for activating beta-catenin signaling.
Effect of dietary supplementation with n-3 fatty acids on clinical manifestations of psoriasis (1988)

In a double-blind, block randomized study we investigated the effect of dietary supplementation with eicosapentaenoic acid in patients with psoriasis. The experimental group received 10 g of fish oil daily containing approximately 1.8 g eicosapentaenoic acid, while the controls were given an isoenergetic amount of olive oil. We found no significant change in the clinical manifestations of psoriasis in either group after 8 weeks of treatment. In the experimental group, the amount of n-3 fatty acids in serum phospholipids was significantly increased at the end of trial as compared to pre-treatment values, whereas the level of n-6 fatty acids was decreased.
Deep Water Running Physiologic Responses (1997)

This study differentiated by gender the physiologic responses to deep water running (DWR) and compared them to treadmill running (TM) at matched running cadences (RC) in 24 young adults (12 M, 12 F). DWR consisted of tethered subjects progressively increasing RC until they could no longer perform DWR at the desired cadence. At that point O2, peak was recorded. The TM test involved TM speeds matched to DWR RC for each stage. Once the last DWR RC was reached, TM grade was increased 5% every 2 min until O2, max. Statistical analyses employed multiple linear regression with dummy coded discrete variables. Full and restricted models tested for main effects and interactions. Significant gender differences averaged across all stages of DWR were evident for E,O2 L·min−1 and O2 ml · kg−1 · min−1, but not for HR, O2 ml · kgLBM−1 · min−1, or RER. There were no significant gender differences during TM. Significant DWR vs TM differences averaged across all stages were evident for HR, E,O2 L · min−1, O2 ml · kg−1 · min−1, O2 ml · kgLBM−1 · min−1 and RER. These data suggest that women perform DWR with less physiologic stress than men and that, compared with TM at matched RC, physiologic responses during DWR are significantly greater.
A novel marker glycoprotein for the microvillus membrane of surface colonocytes of rat large intestine and its presence in small-intestinal crypt cells. (1988)

Murine mAbs were produced against purified microvillus membranes of rat colonocytes in order to establish a marker protein for this membrane. The majority of antibodies binding to the colonic microvillus membrane recognized a single protein with a mean apparent Mr of 120 kD in both proximal and distal colon samples. The antigen is membrane bound as probed by phase-partitioning studies using Triton X-114 and by the sodium carbonate extraction procedure and is extensively glycosylated as assessed by endoglycosidase F digestion. Localization studies in adult rats by light and electron microscopy revealed the microvillus membrane of surface colonocytes as the principal site of the immunoreaction. The antigen was not detectable in kidney or liver by immunoprecipitation but was present in the small intestine, where it was predominantly confined to the apical membrane of crypt cells and much less to the microvillus membrane of differentiated enterocytes. During fetal development, the antigen appears first in the colon at day 15 and 1-2 d later in the small intestine. In both segments, it initially covers the whole luminal surface but an adult-like localization pattern develops soon after birth. The antibodies were also used to develop a radiometric assay for the quantification of the antigen in subcellular fractions of colonocytes in order to assess the validity of a previously developed method for the purification of colonic brush-border membranes (Stieger, B., A. Marxer, and H.P. Hauri. 1986. J. Membr. Biol. 91:19-31.). The results suggest that we have identified a valuable marker glycoprotein for the colonic microvillus membrane, which in adult rats may also serve as a marker for early differentiation of enterocyte progenitor cells in small-intestinal crypt cells.
Metabolic liver disease of obesity and role of adipose tissue in the pathogenesis of nonalcoholic fatty liver disease (2007)

Nonalcoholic fatty liver disease (NAFLD) is an increasingly recognized cause of liver-related morbidity and mortality. It can develop secondary to numerous causes but a great majority of NAFLD cases occur in patients who are obese or present with other components of metabolic syndrome (hypertension, dyslipidemia, diabetes). This is called primary NAFLD and insulin resistance plays a key role in its pathogenesis. Obesity is characterized by expanded adipose tissue, which is under a state of chronic inflammation. This disturbs the normal storage and endocrine functions of adipose tissue. In obesity, the secretome (adipokines, cytokines, free fatty acids and other lipid moieties) of fatty tissue is amplified, which through its autocrine, paracrine actions in fat tissue and systemic effects especially in the liver leads to an altered metabolic state with insulin resistance (IR). IR leads to hyperglycemia and reactive hyperinsulinemia, which stimulates lipid-accumulating processes and impairs hepatic lipid metabolism. IR enhances free fatty acid delivery to liver from the adipose tissue storage due to uninhibited lipolysis. These changes result in hepatic abnormal fat accumulation, which may initiate the hepatic IR and further aggravate the altered metabolic state of whole body. Hepatic steatosis can also be explained by the fact that there is enhanced dietary fat delivery and physical inactivity. IR and NAFLD are also seen in various lipodystrophic states in contrary to popular belief that these problems only occur due to excessive adiposity in obesity. Hence, altered physiology of adipose tissue is central to development of IR, metabolic syndrome and NAFLD.
Mechanisms of Real-Time, Proximal Sample Processing during Ambient Ionization Mass Spectrometry (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMechanisms of Real-Time, Proximal Sample Processing during Ambient Ionization Mass SpectrometryAndre R. Venter*†, Kevin A. Douglass†, Jacob T. Shelley‡, Gregg Hasman, Jr.†, and Elahe Honarvar†View Author Information† Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States‡ Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States*E-mail: [email protected]Cite this: Anal. Chem. 2014, 86, 1, 233–249Publication Date (Web):December 5, 2013Publication History Received27 November 2013Published online16 December 2013Published inissue 7 January 2014https://pubs.acs.org/doi/10.1021/ac4038569https://doi.org/10.1021/ac4038569review-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views3741Altmetric-Citations128LEARN 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 SUBJECTS:Desorption,Ionization,Ions,Liquids,Solvents Get e-Alerts