gebhart/patrepeval huggingface dataset:
Chinese Hamster Ovary (CHO) Cells May Express Six β4-Galactosyltransferases (β4GalTs) (2001)

Six beta4-galactosyltransferase (beta4GalT) genes have been cloned from mammalian sources. We show that all six genes are expressed in the Gat(-)2 line of Chinese hamster ovary cells (Gat(-)2 CHO). Two independent mutants termed Pro(-)5Lec20 and Gat(-)2Lec20, previously selected for lectin resistance, were found to have a galactosylation defect. Radiolabeled biantennary N-glycans synthesized by Pro(-)5Lec20 were proportionately less ricin-bound than similar species from parental CHO cells, and Lec20 cell extracts had a markedly reduced ability to transfer Gal to GlcNAc-terminating acceptors. Northern blot analysis revealed a severe reduction in beta4GalT-1 transcripts in Pro(-)5Lec20 cells. The Gat(-)2Lec20 mutant expressed beta4GalT-1 transcripts of reduced size due to a 311-base pair deletion in the beta4GalT-1 gene coding region. Northern analysis with probes from the remaining five beta4GalT genes revealed that Gat(-)2 CHO and Gat(-)2Lec20 cells express all six beta4GalT genes. Unexpectedly, the beta4GalT-6 gene is not expressed in either Pro(-)5 or Pro(-)5Lec20 cells. Thus, in addition to a deficiency in beta4GalT-1, Pro(-)5Lec20 cells lack beta4GalT-6. Nevertheless, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry data of N-glycans released from cellular glycoproteins showed that both the beta4GalT-1(-) (Gat(-)2Lec20) and beta4GalT-1(-)/beta4GalT-6(-) (Pro(-)5Lec20) mutants have a similar Gal deficiency, affecting neutral and sialylated bi-, tri-, and tetraantennary N-glycans. By contrast, glycolipid synthesis was normal in both mutants. Therefore, beta4GalT-1 is a key enzyme in the galactosylation of N-glycans, but is not involved in glycolipid synthesis in CHO cells. beta4GalT-6 contributes only slightly to the galactosylation of N-glycans and is also not involved in CHO cell glycolipid synthesis. These CHO glycosylation mutants provide insight into the variety of in vivo substrates of different beta4GalTs. They may be used in glycosylation engineering and in investigating roles for beta4GalT-1 and beta4GalT-6 in generating specific glycan ligands.
Read-Through Strategies for Suppression of Nonsense Mutations in Duchenne/ Becker Muscular Dystrophy: Aminoglycosides and Ataluren (PTC124) (2010)

Nucleotide changes within an exon can alter the trinucleotide normally encoding a particular amino acid, such that a new ''stop'' signal is transcribed into the mRNA open reading frame. This causes the ribosome to prematurely terminate its reading of the mRNA, leading to nonsense-mediated decay of the transcript and lack of production of a normal full-length protein. Such premature termination codon mutations occur in an estimated 10% to 15% of many genetically based disorders, including Duchenne/Becker muscular dystrophy. Therapeutic strategies have been developed to induce ribosomal read-through of nonsense mutations in mRNA and allow production of a full-length functional protein. Small-molecule drugs (aminoglycosides and ataluren [PTC124]) have been developed and are in clinical testing in patients with nonsense mutations within the dystrophin gene. Use of nonsense mutation suppression in Duchenne/Becker muscular dystrophy may offer the prospect of targeting the specific mutation causing the disease and correcting the fundamental pathophysiology.
Mechanism of cytotoxicity of anticancer platinum drugs: evidence that cis-diamminedichloroplatinum(II) and cis-diammine-(1,1-cyclobutanedicarboxylato)platinum(II) differ only in the kinetics of their interaction with DNA. (1986)

The kinetics of the aquation reactions of cisplatin and carboplatin and their subsequent reactions with DNA, both in vitro and in vivo, have been measured. The results have been extrapolated to indicate the expected cytotoxicity of these compounds in cells obtained from human cancer patients. Rate constants for the aquation at 37 degrees C of cisplatin and carboplatin of 8 X 10(-5) and 7.2 X 10(-7) s-1, respectively, were calculated from the half-life of these compounds in phosphate buffer, pH 7. This difference in their rate of activation was matched by their rates of binding to DNA. By use of a 14C-labeled ligand, carboplatin was shown to bind monofunctionally to DNA, after which there was a time-dependent formation of difunctional interstrand cross-links, formed from some of these initially monofunctional adducts. A similar, although faster, accumulation of cross-links was seen when cisplatin was bound to DNA. The loss of the 14C-CBDCA ligand of carboplatin was calculated to occur with a rate constant of 1.3 X 10(-5) s-1 which was similar to that for the rate of formation of interstrand cross-links and faster than that for the monofunctional reaction with DNA. It was concluded therefore that the CBDCA ligand becomes a more labile leaving group once carboplatin has been monoaquated. In contrast, both chloro-ligands of cisplatin were shown to leave at similar rates. The fact that other difunctional lesions were formed to the same extent, by equal bound doses of cisplatin or carboplatin, was indicated by the unwinding of supercoiled plasmid DNA. The effects of cisplatin and carboplatin on this DNA were the same once bound to the same extent. About a 100-fold larger dose of carboplatin was, as predicted by their rates of aquation, required to produce equivalent binding to plasmid DNA. In vivo, equal binding of the two drugs to DNA of various cell systems resulted in equal cytotoxicity. Again a much larger dose (20- to 40-fold) of carboplatin was required to produce this equal binding. In general a DNA bound platinum level of about 20 nmol/g reduced cell survival by 90%, although certain cell lines were shown to be much more sensitive to DNA bound platinum. Similar binding values, to those above, were obtained in the DNA extracted from cells of human cancer patients treated with cisplatin. It was inferred that the cytotoxic effect of this level of platinum on DNA would be (unless the cells were of a sensitive phenotype) about 90%.(ABSTRACT TRUNCATED AT 400 WORDS)
Epidermal Serine Proteases and Their Inhibitors in Atopic Dermatitis (2012)

The skin and its appendages protect the body from water loss, chemical and physical damages, UV-radiation and infection by pathogenic as well as non-pathogenic microbes. The protective function of both, the physical and the chemical barrier, is provided from epidermal keratinocytes, which are continuously dividing in the stratum basale and differentiating towards the surface Cells of the uppermost living epidermis layer, the stratum granulosum, are loosing their nuclei and other organelles at the transition zone to the stratum corneum (SC), forming now flattened polyhedrons, called corneocytes. These corneocytes contain instead of a cell membrane the cornified envelope (CE) consisting of structural proteins, which are crosslinked by glutaminases The intercellular space of the corneocytes is filled with lamellar bodyderived lipids, which make the SC more hydrophobous. This mechanism protects skin from water loss and other insults. Finally, in a tightly regulated process termed desquamation that abolishes the cohesion between corneocytes, these cells are shed into the environment by proteolysis of corneodesmosomal proteins. The formation of stratified epithelia requires a specific differentiation program, which includes a timely and spatially well coordinated proteolytic system to detach the corneocytes from each other without any disturbance of the barrier function. During the last years it became evident that this proteolytic balance is not only important for the physical barrier function of the skin but is also paving the way for immunological responses. In this chapter we want to look at the various proteases in the epidermis, their inhibitors and how they might contribute to the pathogenesis of atopic dermatitis (AD).
Defective Function of Langerhans Cells in Tumor-Bearing Animals Is the Result of Defective Maturation from Hemopoietic Progenitors (1998)

Langerhans cells (LC), the APCs in the skin, serve as a model for investigation of dendritic cell (DC) function in tissues. DC play a crucial role in the generation of antitumor immune responses. In this study, we investigated the effect of the presence of tumor in vivo on the ability of LC to take up Ag, migrate to draining lymph nodes, and stimulate primary T cell responses. In two animal models, these functions were substantially inhibited. This effect was not restricted to LC located in the skin near a tumor but was also seen at sites distant from the tumor. The duration of tumor exposure, and not its ultimate size, were found to be important, suggesting that tumors could be inhibiting the maturation of LC rather than directly inhibiting their function. Model experiments with radiation chimeras supported this hypothesis. To investigate the potential role of vascular endothelial growth factor (VEGF) in these effects we used anti-VEGF-neutralizing Ab to treat animals bearing tumors. Treatment with the Ab at a dose of 10 microg i.p. per mouse, twice a week for 4 wk, significantly improved the number and function of LC as measured by their ability to migrate to lymph nodes and stimulate primary T cell responses, even at doses that do not affect the growth of these established poorly immunogenic tumors. Thus, inhibition of VEGF signaling may improve DC function in tumor-bearing hosts and possibly serve to improve the efficacy of cancer immunotherapy.
Hemoglobin A1C separation by isoelectric focusing (1978)

A modified type of isolectric focusing has been applied successfully to the separation of hemoglobin A1C (HbA1C) from HbA in normal and diabetic cell lysates. It consists of transforming a linear pH gradient into a nonlinear one, by the addition of an amphoteric substance ("separator" or "pH gradient modifier") with an isoelectric point (pI) close to the pI's of the two hemoglobins. Among the "modifiers" tested, histidine, proline, threonine, beta-alanine, 6-amino caproic acid, and 5-amino valeric acid are not useful in the hemoglobin pI range (pH 6.9--7.0). The dipeptide histidyl-glycine (pI = 6.8; pI-pK1 = 1) is very efficient in flattening the pH gradient, in the hemoglobin region. even when added in low concentrations (10--100 mM), thus affording full resolution of the two hemoglobin species.
Members of the gibberellin receptor gene family GID1 (GIBBERELLIN INSENSITIVE DWARF1) play distinct roles during Lepidium sativum and Arabidopsis thaliana seed germination (2011)

Germination of endospermic seeds is partly regulated by the micropylar endosperm, which acts as constraint to radicle protrusion. Gibberellin (GA) signalling pathways control coat-dormancy release, endosperm weakening, and organ expansion during seed germination. Three GIBBERELLIN INSENSITIVE DWARF1 (GID1) GA receptors are known in Arabidopsis thaliana: GID1a, GID1b, and GID1c. Molecular phylogenetic analysis of angiosperm GID1s reveals that they cluster into two eudicot (GID1ac, GID1b) groups and one monocot group. Eudicots have at least one gene from each of the two groups, indicating that the different GID1 receptors fulfil distinct roles during plant development. A comparative Brassicaceae approach was used, in which gid1 mutant and whole-seed transcript analyses in Arabidopsis were combined with seed-tissue-specific analyses of its close relative Lepidium sativum (garden cress), for which three GID1 orthologues were cloned. GA signalling via the GID1ac receptors is required for Arabidopsis seed germination, GID1b cannot compensate for the impaired germination of the gid1agid1c mutant. Transcript expression patterns differed temporarily, spatially, and hormonally, with GID1b being distinct from GID1ac in both species. Endosperm weakening is mediated, at least in part, through GA-induced genes encoding cell-wall-modifying proteins. A suppression subtraction hybridization (SSH) cDNA library enriched for sequences that are highly expressed during early germination in the micropylar endosperm contained expansins and xyloglucan endo-transglycosylases/hydrolases (XTHs). Their transcript expression patterns in both species strongly suggest that they are regulated by distinct GID1-mediated GA signalling pathways. The GID1ac and GID1b pathways seem to fulfil distinct regulatory roles during Brassicaceae seed germination and seem to control their downstream targets distinctly.
A comparison of uptake of metformin and phenformin mediated by hOCT1 in human hepatocytes (2009)

Metformin, a biguanide that has been used to treat type 2 diabetes mellitus, is reportedly transported into human hepatocytes by human organic cation transporter 1 (hOCT1). The objective of this study was to investigate differences in the hepatic uptake of metformin and phenformin, a biguanide derivative similar to metformin. Special focus was on the role of active transport into cells. Experiments were therefore performed using human cryopreserved hepatocytes and hOCT1 expressing oocytes. Both biguanides proved to be good substrates for hOCT1. However, phenformin exhibited a much higher affinity and transport activity, with a marked difference in uptake kinetics compared with metformin. Both biguanides were transported actively by hOCT1, with the active transport components much greater than passive transport components in both cases, suggesting that functional changes in hOCT1 might affect the transport of both compounds to the same degree. This study for the first time produced detailed comparative findings for uptake profiles of metformin and phenformin in human hepatocytes and hOCT1 expressing oocytes. It is considered that hOCT1 may not be the only key factor that determines the frequency of metformin and phenformin toxicity, considering the major contribution of this transporter to the total hepatic uptake and comparable width of their therapeutic concentrations.
Transmembrane Residues of the Parathyroid Hormone (PTH)/PTH-related Peptide Receptor That Specifically Affect Binding and Signaling by Agonist Ligands (1996)

Polar residues within the transmembrane domains (TMs) of G protein-coupled receptors have been implicated to be important determinants of receptor function. We have identified mutations at two polar sites in the TM regions of the rat parathyroid hormone (PTH)/PTH-related peptide receptor, Arg-233 in TM 2 and Gln-451 in TM 7, that caused 17-200-fold reductions in the binding affinity of the agonist peptide PTH-(1-34) without affecting the binding affinity of the antagonist/partial agonist PTH-(3-34). When mutations at the TM 2 and TM 7 sites were combined, binding affinity for PTH-(1-34) was restored to nearly that of the wild type receptor. The double mutant receptors, however, were completely defective in signaling cAMP or inositol phosphate production in response to PTH-(1-34) agonist ligand. The results demonstrate that Arg-233 and Gln-451 have important roles in determining agonist binding affinity and transmembrane signaling. Furthermore, the finding that residues in TM 2 and TM 7 are functionally linked suggests that the TM domain topology of the PTH/PTH-related peptide receptor may resemble that of receptors in the rhodopsin/beta-adrenergic receptor family, for which structural and mutagenesis data suggest interactions between TMs 2 and 7.
Enhanced CO2absorption kinetics in lithium silicate platelets synthesized by a sol–gel approach (2014)

Platelet-shaped lithium orthosilicate particles synthesized by a sol–gel approach employing the precursors lithium nitrate and colloidal silica displayed enhanced absorption kinetics for CO2 compared to the powders prepared by a solid-state reaction process involving Li2CO3 and silica. The sol–gel samples showed a CO2 absorption capacity of 350 mg g−1 at an absorption rate of 22.5 mg g−1 min−1, a value 70% higher than the rate of 13.2 mg g−1 min−1 measured with the solid-state samples under similar conditions. The higher sorption kinetics of CO2 by the sol–gel derived lithium orthosilicate could be attributed to the unique platelet morphology of the particles, which have a very small thickness. A porous carbon mesh coated with the sol–gel based particles exhibited CO2 absorption capacity of 150 mg g−1 at an absorption rate of 37.5 mg g−1 min−1. This supported absorbent also showed stable absorption and desorption performance for the 8 cycles examined in this study. The excellent absorption characteristics of the sol–gel prepared powders, more specifically the coated strips, provide a successful pathway for the commercialisation of these materials.
Discriminant models for high‐throughput proteomics mass spectrometer data (2003)

We use several different multivariate analysis methods to discriminate between diseased and healthy patients using protein mass spectrometer data provided by Duke University. Two problems were presented by the university; one in which the responses (diseased or healthy) of the patients were not known and second, when the responses were known. In the latter case, the data can be used as a 'training' set. We attempted both problems. In particular, we use principle component analysis along with clustering methods to discriminate for the first problem set and partial least squares coupled with logistic and discriminant methods when the responses were known. In addition, we were able to detect regions of interest in the spectrum where there were differences in the protein patterns between healthy and diseased patients. There was considerable effort involved in the preprocessing of the data. We used a binning approach to reduce the number of variables rather than peak heights or peak areas. We performed a square root transformation on the data to help stabilize the variance; this in turn made a significant improvement in clustering results.
Directed Evolution of DNA Polymerases for Next‐Generation Sequencing (2010)

Speeding evolution: An activity-based phage display method was used to address the title application. A mutant of Taq DNA polymerase was identified (see scheme) that incorporates the fluorophore-labeled dA, dT, dC, and dG substrates 50 to 400-fold more efficiently into scarred primers in solution and that also demonstrates significantly improved performance under actual sequencing conditions. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Dynamic strategy selection in flexible parsing (1981)

Robust natural language interpretation requires strong semantic domain models, "fail-soft" recovery heuristics, and very flexible control structures. Although single-strategy parsers have met with a measure of success, a multi-strategy approach is shown to provide a much higher degree of flexibility, redundancy, and ability to bring task-specific domain knowledge (in addition to general linguistic knowledge) to bear on both grammatical and ungrammatical input. A parsing algorithm is presented that integrates several different parsing strategies, with case-frame instantiation dominating. Each of these parsing strategies exploits different types of knowledge; and their combination provides a strong framework in which to process conjunctions, fragmentary input, and ungrammatical structures, as well as less exotic, grammatically correct input. Several specific heuristics for handling ungrammatical input are presented within this multi-strategy framework.
Human prostate‐infiltrating CD8+ T lymphocytes are oligoclonal and PD‐1+ (2009)

CD8(+) PIL appear to have undergone clonal expansion in response to an as yet unidentified antigen; however, due to the high expression of PD-1, these cells are likely incapable of mounting an effective immune response. The results provide an important basis for further efforts aimed at the identification of specific antigens involved in prostatic inflammation, and suggest that PD-1 blockade may be useful in immunotherapy for PCa.
The human interleukin‐6 (IL‐6) receptor exists as a preformed dimer in the plasma membrane (2003)

The recently solved X-ray structure of the extracellular portion of the interleukin-6 (IL-6) receptor (IL-6R) revealed an IL-6R dimer in the crystal lattice which probably represents a physiological dimer. Performing coprecipitation experiments with two differently tagged IL-6R variants expressed in COS-7 cells, we show that an IL-6R dimer exists in the plasma membrane in the absence of IL-6. Ligand binding does not seem to affect the dimerization status. When lysates of COS-7 cells expressing only one of the IL-6R variants are mixed, spontaneous dimerization occurs. Thus, the IL-6R dimer observed in the crystal structure represents a physiologically occurring phenomenon.
Security-Constrained Optimal Power Flow with Post-Contingency Corrective Rescheduling (1987)

This paper describes a mathematical framework for the solution of the economic dispatch problem with security constraints, which can take into account the system corrective capabilities after the outage has occurred. The solution algorithm is based on mathematical programming decomposition techniques that allow the iterative solution of a "base-case" economic dispatch and separate contingency analysis with generation rescheduling to eliminate constraint violations. The resulting dispatch has the same security level as the usual security-constrained dispatch, but with lower operating costs. Case studies with the IEEE 118-bus are presented. The extension of the methodology to the probabilistic case will be discussed in a forthcoming paper.
Characterization of a Circulating Subpopulation of Spontaneous Antitetanus Toxoid Antibody Producing B Cells Following in Vivo Booster Immunization (1979)

Abstract The appearance of circulating B lymphocyte subpopulations responsible for the in vitro synthesis of IgG or IgM antitetanus toxoid antibody after in vivo booster immunization has been analyzed. Before booster immunization, only background levels of IgG antitetanus toxoid antibody were synthesized by B lymphocytes alone, or in combination with T cells and pokeweed mitogen, as measured by quantitative radioimmunoassay. Within 5 days after booster immunization, a population of B lymphocytes appeared within the circulation that had the capacity to synthesize IgG antitetanus toxoid antibody in the absence of T lymphocytes or pokeweed mitogen. These cells could be detected in the circulation until 10 to 12 days after immunization, and the antibody synthesized was inhibited by the inclusion of 50 µg/ml cyclohexamide in the culture medium. At the peak of this response, between 10 and 60% of the total IgG synthesized was IgG directed against tetanus toxoid. The cells responsible had a precursor frequency of up to 10-3 in the non-E-rosetting cell fraction obtained from peripheral blood and sedimented at 1 × G with velocities ranging from 4 to 11 mm/hr. The synthesis of IgM antitetanus toxoid antibody by this cell fraction was not detected. In contrast to the above B cells, lymphocytes capable of responding to pokeweed mitogen and T lymphocytes with the synthesis of IgG antitetanus toxoid antibody did not appear in the circulation until 10 days after immunization. Limiting dilution analysis of the pokeweed mitogen responsive B lymphocytes 2 to 4 weeks after booster immunization gave a precursor frequency of 1 × 10-4. In the presence of T cells and PWM, the synthesis of IgM anti-Tet remained at constant levels before and for 3 weeks post-booster immunization. These results indicate that multiple subsets of circulating B cells can be functionally defined in humans.