gebhart/patrepeval huggingface dataset:
The DNA‐binding activity of the Neisseria gonorrhoeae LexA orthologue NG1427 is modulated by oxidation (2010)

Neisseria gonorrhoeae is a human-specific organism that is not usually exposed to UV light or chemicals but is likely to encounter reactive oxygen species during infection. Exposure of N. gonorrhoeae to sublethal hydrogen peroxide revealed that the ng1427 gene was upregulated sixfold. N. gonorrhoeae was thought to lack an SOS system, although NG1427 shows amino acid sequence similarity to the SOS response regulator LexA from Escherichia coli. Similar to LexA and other S24 peptidases, NG1427 undergoes autoproteolysis in vitro, which is facilitated by either the gonococcal or E. coli RecA proteins or high pH, and autoproteolysis requires the active and cleavage site residues conserved between LexA and NG1427. NG1427 controls a three gene regulon: itself; ng1428, a Neisseria-specific, putative integral membrane protein; and recN, a DNA repair gene known to be required for oxidative damage survival. Full NG1427 regulon de-repression requires RecA following methyl methanesulphonate or mitomycin C treatment, but is largely RecA-independent following hydrogen peroxide treatment. NG1427 binds specifically to the operator regions of the genes it controls, and DNA binding is abolished by oxidation of the single cysteine residue encoded in NG1427. We propose that NG1427 is inactivated independently of RecA by oxidation.
Progress with proton pump inhibition. (1994)

The proton pump, a H+/K(+)-ATPase located on the secretory canalicular membrane of the parietal cell, forms the final pathway for gastric acid secretion. Omeprazole is concentrated in the secretory canaliculus, where it is converted to its active form, which binds covalently with the H+/K(+)-ATPase, thus inhibiting acid secretion arising from any stimulus. Meta-analysis has defined the primary determinants for peptic ulcer healing as the degree of acid suppression, the duration of suppression over 24 hours, and the length of treatment. The longer duration of acid suppression with omeprazole, particularly during the day, when food is ingested and H2-receptor antagonists are less effective, is reflected in the clinical superiority for symptom relief and ulcer healing and especially for the treatment of erosive esophagitis. Extensive clinical experience has proved omeprazole to be safe, and concerns over hypergastrinemia, ECL-cell hyperplasia, and carcinoid formation have not been substantiated in humans. Recent evidence has shown that omeprazole suppresses Helicobacter pylori and, in combination with antibiotics, can eradicate this organism in a substantial proportion of patients. This effect may result from enhancement of antibiotic bioavailability and optimizing host defense mechanisms.
Effect of Mixing Conditions on the Behavior of Lipoxygenase, Peroxidase, and Catalase in Wheat Flour Doughs (1998)

ABSTRACT The effect of mixing has been tested on the extractable activities of lipoxygenase, peroxidase, and catalase from dough after 2, 5, and 20 min of mixing, and 30 min of rest period after 20 min of mixing. Different mixing conditions have been studied including temperature, atmosphere, speed, amount of water added to the dough, buffer solutions between pH 3.6 and 7.5 added to the dough, and different additives (linoleic acid, guaiacol, hydrogen peroxide, ascorbic acid, cysteine, yeast, and sodium chloride). In all the mixing conditions tested, the dough peroxidase activity remains equivalent to the initial flour activity, whereas losses in lipoxygenase and catalase activities largely varied according to mixing conditions. The results show that a self‐destruction mechanism as well as physicochemical denaturation are responsible for these losses. Lipoxygenase losses seem mainly associated with the former mechanism, whereas catalase losses are highly increased in acidic conditions (physicochemical denaturation). Therefore, the relative impact of the three oxidoreducing enzymes may be largely modulated by mixing conditions.
Gene and other biological therapies for vascular diseases (1997)

Gene transfer and antisense therapy offer novel approaches to the study and treatment of vascular diseases. The localized nature of vascular diseases like restenosis has made the application of genetic material an attractive therapeutic option. Viral and nonviral vectors have been developed to facilitate the entry of foreign DNA or RNA into cells. Vector improvement and production, demonstration of vector safety and demonstration of therapeutic efficacy are among the main present challenges. Various strategies have already been shown to be successful in preventing restenosis in animal models and include: the transfer of the herpes simplex virus thymidine kinase associated with ganciclovir: transfection of the cell cycle regulatory genes encoding for the active form of retinoblastoma gene product (Rb) or the cyclin-dependent kinase inhibitor p21, and antisense therapy. Therapeutic angiogenesis using gene transfer is a new strategy for the treatment of severe limb ischemia. Transfection of DNA encoding for the vascular endothelial growth factor has resulted in increasing collateral flow in animal models of peripheral ischemia. This approach is currently being investigated in a clinical trial in patients with distal ischemia. Other potential targets for genetic treatment in cardiovascular diseases include thrombosis, extracellular matrix synthesis and lipid metabolism.
Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity (2002)

The mechanism by which methionine relieves the growth inhibition of Escherichia coli K-12 that is caused by organic weak acid food preservatives was investigated. In the presence of 8 mM acetate the specific growth rate of E. coli Frag1 (in MacIlvaine's minimal medium pH 6.0) is reduced by 50%. Addition of methionine restores growth to 80% of that observed in untreated controls. Similar relief was seen with cultures treated with either benzoate or propionate. Mutants with an elevated intracellular methionine pool were almost completely resistant to the inhibitory effects of acetate, suggesting that the methionine pool becomes limiting for growth in acetate-treated cells. Measurement of the intracellular concentrations of pathway intermediates revealed that the homocysteine pool is increased dramatically in acetate-treated cells, suggesting that acetate inhibits a biosynthetic step downstream from this intermediate. Supplementation of the medium with homocysteine inhibits the growth of E. coli cells. Acetate inhibition of growth arises from the depletion of the intracellular methionine pool with the concomitant accumulation of the toxic intermediate homocysteine and this augments the effect of lowering cytoplasmic pH.
Identification and DNA sequence of a human apolipoprotein E cDNA clone. (1982)

cDNA clones encoding human apolipoprotein E were identified by screening an adult human liver cDNA library with an oligonucleotide probe. The probe was a mixture of synthetic 14-base long DNA oligomers constructed to correspond to all possible codons for apo-E amino acids 218-222. Plasmids from four of the 20 clones selected by this screening procedure were digested with PstI and all had five internal PstI sites with a total length of the cDNA insert of approximately 900 base pairs. DNA sequence analysis of one of these clones, designated pE-301, revealed that it corresponded to apo-E amino acids 81-299, and contained a standard termination codon, polyadenylation signal, and poly A tail. The DNA sequence examined included the known apo-E polymorphic sites at amino acids 112, 145, and 158, and the mutant apo-E phenotypes can all be explained on the basis of a single base substitution in the first position of each of these codons. This work supports the hypothesis that the apo-E polymorphism is due to mutations in the region of DNA coding for the apo-E structural gene.
Cancer Chemotherapy and Biotherapy: Principles and Practice (1996)

Clinical Strategies for Cancer Treatment: The Role of Drugs Preclinical Aspects of Cancer Drug Discovery and Development Pharmacokinetics and Clinical Monitoring Infertility after Cancer Chemotherapy Carcinogenesis: A Late Complication of Cancer Chemotherapy Steroid Hormone Therapies for Cancer Antifolates 5-Fluoropyrimidines Cytidine Analogs Purine Antimetabolites Hydroxyurea Antimicrotubule Agents Alkylating Agents Nonclassic Alkylating Agents Cisplatin and Analogs Bleomycin Antitumor Antibiotics Anthracyclines and Anthracenediones Topoisomerase II Inhibitors: Epipodophyllotoxins, Acridines, Ellipticines, and Bisdioxopiperazines Topoisomerase I Targeting Agents: The Camptothecins Enzyme Therapy: l-Asparaginase Pharmacologic Considerations in Chemotherapy for Brain Tumors Retinoids and Other Differentiating Agents Bisphosphonates Radiation Modifiers Pharmacology of Interferons:Induced Proteins, Cell Activation, and Antitumor Activity Clinical Pharmacokinetics of Interleukin 1, Interleukin 2, Interleukin 4, Tumor Necrosis Factor, Interleukin 12, and Macrophage Colony-Stimulating Factor Colony-Stimulating Factors Antibody-Based Immunotherapies for Cancer Targeted Therapy Physical Barriers to Drug Delivery Adoptive Cellular Therapy Cancer Vaccines Cytokine and Growth Factor and Receptor Database: Biologic, Molecular, and Pathophysiologic Properties of Ligand-Receptor Interactions Inhibitors of Tumor Angiogenesis Pharmacogenetics Chemokine-Chemokine Receptor Database 2001: Biologic, Molecular, and Pathophysiologic Properties of Chemokine-Receptor Interactions Index
Biological Control of Pierce's Disease in the Vineyard with Strains ofXylella fastidiosaBenign to Grapevine (2005)

Naturally occurring strains of Xylella fastidiosa Wells et al. that were weakly virulent or aviru-lent to grapevine were inoculated into the lower internodes of Vitis vinifera L. cv. Carignane plants in the greenhouse and challenge inoculated with pathogenic strains 2 weeks later. Several strains provided some reduction in symptom development. Most effective in preventing or slowing the development of Pierce's disease in the greenhouse tests were a strain from sycamore and two from elderberry. In a 2-year test on 'Himrod' grape in the vineyard, strain Syc86-1 (from sycamore), but not strain PD-1 (from grapevine), was effective in limiting the development of Pierce's disease. In tests on new vineyard plantings of 'Flame Seedless' and 'Cabernet Sauvi-gnon', six strains of X. fastidiosa were evaluated for biological control of the natural progression of Pierce's disease. Only strain EB92-1 (from elderberry) provided good control of the disease in both Flame Seedless and Cabernet Sauvignon. Strain Syc86-1 was ineffective in these vineyard tests. Grape strain PD95-6 did lower disease severity in Flame Seedless when compared with nontreated vines, and grape strain PD91-2 delayed symptoms in Cabernet Sauvignon for 12 to 18 months. Biological control by inoculation of susceptible grapevines with benign strains of X. fastidiosa, especially strain EB92-1, appears to have the potential to control Pierce's disease in commercial vineyards in Florida and other areas where the disease occurs.
Evidence of a long QT founder gene with varying phenotypic expression in South African families. (1996)

We report five South African families of northern European descent (pedigrees 161, 162, 163, 164, and 166) in whom Romano-Ward long QT syndrome (LQT) segregates. The disease mapped to a group of linked markers on chromosome 11p15.5, with maximum combined two point lod scores, all generated at theta = 0, of 15.43 for the D11S922, 10.51 for the D11S1318, and 14.29 for the tyrosine hydroxylase (TH) loci. Recent studies have shown that LQT is caused by an Ala212Val mutation in a potassium channel gene (KVLQT1) in pedigrees 161 to 164. We report that the same mutation is responsible for the disease in pedigree 166. Haplotype construction showed that all the families shared a common haplotype, suggesting a founder gene effect. DNA based identification of gene carriers allowed assessment of the clinical spectrum of LQT. The QTc interval was significantly shorter in both carriers and non-carriers in pedigree 161 (0.48 s and 0.39 s, respectively) than the same two groups in pedigree 161 (0.52 s and 0.42 s, respectively). The spectrum of clinical symptoms appeared more severe in pedigree 162. The possible influence of modulating genetic factors, such as HLA status and sex of family members, on the expression of an LQT founder gene is discussed.
Iloprost has potent anti‐inflammatory properties on human monocyte‐derived dendritic cells (2010)

In summary, our results provide evidence that iloprost profoundly affects the function of human myeloid DCs. Therefore, iloprost might also be a new therapeutical option for the treatment of asthma in humans.
Deep-UV patterning of commercial grade PMMA for low-cost, large-scale microfluidics (2008)

Although PMMA can be exposed using a variety of exposure sources, deep-UV at 254 nm is of interest because it is relatively inexpensive. Additionally, deep-UV sources can be readily scaled to large area exposures. Moreover, this paper will show that depths of over 100µm can be created in commercial grade PMMA using an uncollimated source. These depths are sufficient for creating microfluidic channels. This paper will provide measurements of the dissolution depth of commercial grade PMMA as a function of the exposure dose and etch time, using an IPA:H2O developer. Additionally, experiments were run to characterize the dependence of the dissolution rate on temperature and agitation. The patterned substrates were thermally bonded to blank PMMA pieces to enclose the channels and ports were drilled into the reservoirs. The resulting fluidic systems were then tested for leakage. The work herein presents the patterning, development and system behaviour of a complete microfluidics system based on commercial grade PMMA.
Insect Cells as a Factory to Produce Adeno-Associated Virus Type 2 Vectors (2002)

Recombinant adeno-associated viruses (rAAV) are produced transiently in mammalian cells usually by cotransfecting two or three plasmids containing AAV genes, adenovirus helper genes, and a vector genome. Expansion and transfection of adherent cells limit the scale of rAAV production. Efficient transfection is performed with cells on solid support media such as tissue culture plates. A large animal study or a human clinical trial may require 10(15) particles of vector, depending on dose. To generate this quantity of rAAV by transfection, more than 10(11) HEK293 cells may be needed, which would require about 5000 x 175 cm(2) flasks. The ability to scale up rAAV production by these methods severely restricts the commercialization and use of AAV vectors. A recombinant baculovirus derived from the Autographa californica nuclear polyhedrosis virus is widely employed for large-scale production of heterologous proteins in cultured insect cells and may provide an attractive alternative. Toward this goal, we have explored the production of rAAV in invertebrate cells. Sf9 cells may be coinfected in suspension cultures with three recombinant baculoviruses (a Rep-baculovirus, a VP-baculovirus, and an AAV ITR vector genome baculovirus) and, 3 days later, rAAV is recovered. The particles produced are indistinguishable from 293 cell-produced rAAV, as determined on the basis of physical properties and biologic activities. Particles produced by either method were composed of similar proteins and nucleic acid. The yield of genome-containing particles produced per Sf9 cell approached 5 x 10(4), thus, 1000 ml of cultured Sf9 cells produced the equivalent of between 500 to 1000 x 175 cm(2) flasks of 293 cells. This robust system provides a simple, cost-effective method for AAV vector production.
Integrated Metabonomic Analysis of the Multiorgan Effects of Hydrazine Toxicity in the Rat (2005)

Hydrazine is a model toxin that induces both hepatotoxic and neurotoxic effects in experimental animals. The direct biochemical effects of hydrazine in kidney, liver, and brain tissue were assessed in male Sprague-Dawley rats using magic angle spinning nuclear magnetic resonance (NMR) spectroscopy. A single dose of hydrazine (90 mg/kg) resulted in changes to the biochemical composition of the liver after 24 h including an increase in triglycerides and beta-alanine, together with a decrease in hepatic glycogen, glucose, choline, taurine, and trimethylamine-N-oxide (TMAO). From histopathology measurements of liver tissue, minimal to mild hepatocyte alteration was observed in all animals at 24 h. The NMR spectra of the renal cortex at 24 h after dosing were dominated by a marked increase in the tissue concentration of 2-aminoadipate (2-AA) and beta-alanine, concomitant with depletions in TMAO, myo-inositol, choline, taurine, glutamate, and lysine. No alteration to the NMR spectral profile of the substantia nigra was observed after hydrazine administration, but perturbations to the relative concentrations of creatine, aspartate, myo-inositol, and N-acetyl aspartate were apparent in the hippocampus of hydrazine-treated animals at 24 h postdose. No overt signs of histopathological toxicity were observed in either the kidney or the brain regions examined. Elevated alanine levels were observed in all tissues indicative of a general inhibition of alanine transaminase activity. By 168 h postdose, NMR spectral profiles of treated rats appeared similar to those of matched controls for all tissue types indicative of recovery from toxic insult.
Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases. (1987)

A synthetic procedure has been developed by which stable abasic sites are introduced into oligodeoxynucleotides at any desired position in the sequence. A modified tetrahydrofuran moiety, isosteric with 2'-deoxyribofuranose, serves as a structural analog of the natural apurinic/apyrimidinic site. We have also prepared oligodeoxynucleotides that lack cyclic structure at the abasic site but retain the carbon atoms of the phosphodiester backbone. These synthetic oligodeoxynucleotides are cleaved on the 5' side of the abasic site by endonuclease IV and by exonuclease III; they serve also as templates for avian myeloblastosis virus reverse transcriptase, Escherichia coli DNA polymerase I (Klenow fragment), and calf thymus DNA polymerase-alpha. Extension of primed templates by these DNA polymerases is blocked initially at the position immediately 3' to the abasic site; nucleoside monophosphates are subsequently incorporated opposite the lesion. The nucleotide most frequently incorporated opposite all abasic sites, regardless of structure, is dAMP. Significant "readthrough" at the abasic site was observed in experiments using avian myeloblastosis virus reverse transcriptase and DNA polymerase-alpha and, to a much lesser degree, with DNA polymerase I. We conclude that a modified tetrahydrofuran group can serve as a stable structural analog of 2'-deoxyribose in the apurinic/apyrimidinic site. These modified oligodeoxynucleotides should prove useful for studies of chemical mutagenesis.
A 16-week comparison of the novel insulin analog insulin glargine (HOE 901) and NPH human insulin used with insulin lispro in patients with type 1 diabetes. (2000)

Basal insulin therapy with insulin glargine once a day appears to be as safe and at least as effective as using NPH insulin once or twice a day in maintaining glycemic control in patients with type 1 diabetes receiving basal-bolus insulin treatment with insulin lispro.
Proteolysis in the maturation of avian retroviruses does not require calcium (1992)

After budding from the plasma membrane, retrovirus particles undergo a process of maturation, which includes changes in morphology caused by several proteolytic cleavages of the precursor of the internal structural proteins, products of the gag gene. Cleavage is mediated by the viral protease, PR. The fact that in most systems cleavage appears to occur only after assembly is complete, suggests that PR may become enzymatically active as a consequence of release of the virion from the cell. Using avian leukosis virus as a model system, we tested the hypothesis that leakage of calcium ions into newly budded virions plays a role in their maturation. We found that in both quail Qt35 cells and monkey COS-1 cells, maturation occurred normally in calcium-free medium and in the presence of EGTA. A calcium ionophore also did not affect maturation. We conclude that calcium influx does not act as a trigger for PR-mediated maturation.
Active Oxygen Species and the Functions of Phagocytic Leukocytes (1980)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Hepatocyte transplantation for liver‐based metabolic disorders (2006)

Hepatocyte transplantation is being investigated as an alternative to orthotopic liver transplantation in patients with liver-based metabolic disorders. The progress made in this field to date is reviewed. Protocols have been developed using collagenase perfusion to isolate human hepatocytes from unused donor liver tissue. Hepatocytes with a high viability can often be obtained and can be cryopreserved for later use, though with loss of function on thawing. For clinical use, hepatocytes must be prepared in clean GMP conditions with cells meeting criteria of function and lack of microbial contamination before patient use. Hepatocytes are infused intraportally into the patient's liver, where a proportion of cells will engraft and replace the deficient metabolic function without the need for major surgery. Twenty patients have now received hepatocyte transplantation, including eight children at King's College Hospital. There was a range of aetiologies of liver disease: familial hypercholesterolaemia, Crigler-Najjar syndrome type 1, urea cycle defects, infantile Refsum disease, glycogen storage disease type Ia, inherited factor VII deficiency and progressive familial intrahepatic cholestasis type 2. Clinical improvement and partial correction of the metabolic abnormality was observed in most cases. Considerable progress has been made in developing the technique, but hepatocyte transplantation is limited by the available supply of liver tissue. Hepatocytes derived from stem cells could provide alternative sources of cells in the future.
Kinesin Movement on Glutaraldehyde-Fixed Microtubules (1996)

Glutaraldehyde-cross-linked microtubules were investigated as substrates for kinesin motility. Microtubules, formed in vitro from chicken brain tubulin, were stabilized with Taxol and chemically fixed with glutaraldehyde. The degree of tubulin monomer cross-linking as a function of time and glutaraldehyde concentration was characterized using polyacrylamide gel electrophoresis. Atomic force microscopy of fixed microtubules indicated that the cross-linking is sufficient to stabilize the gross structure of the microtubules against air drying or a distilled water challenge. Kinesin movement on immobilized, fixed microtubules was determined using a kinesin-coated bead motility assay observed with differential interference contrast microscopy. Within measurement error, kinesin bead movement velocities were independent of the degree of microtubule cross-linking. Binding affinity, however, decreased with increased cross-linking. Although air- and water-challenged microtubules did not support kinesin motility, a dilute suspension of glutaraldehyde-fixed microtubules in buffer supported kinesin motility for at least 2 days without any substantial degradation of activity. Fixed microtubules may be useful for several applications, including affinity purification of microtubule-associated proteins and motility measurements under extreme conditions of temperature and other variables.