gebhart/patrepeval huggingface dataset:
Regulation of Cellular Oncosis by Uncoupling Protein 2 (2002)

Cell death can proceed through at least two distinct pathways. Apoptosis is an energy-dependent process characterized morphologically by cell shrinkage, whereas oncosis is a form of cell death induced by energy depletion and initially characterized by cell swelling. We demonstrate in HeLa cells but not in normal diploid fibroblasts that modest increases in the expression level of uncoupling protein 2 (UCP-2) leads to a rapid and dramatic fall in mitochondrial membrane potential and to a reduction of mitochondrial NADH and intracellular ATP. In HeLa cells, increased UCP-2 expression leads to a form of cell death that is not inhibited by the anti-apoptotic gene product Bcl-2 and that morphologically resembles cellular oncosis. We further describe the creation of a dominant interfering mutant of UCP-2 whose expression increases resting mitochondrial membrane potential and selectively increases the resistance to cell death following oncotic but not apoptotic stimuli. These results suggest that distinct genetic programs may regulate the cellular response to either apoptotic or oncotic stimuli.
Antitumor Alkaloids in Clinical Use or in Clinical Trials (2007)

This chapter contains sections titled: Introduction Antitumor Alkaloids in Clinical Use Vinca Alkaloids Vinblastine (VLB, 1) Vincristine (VCR, 2) Vindesine (VDS, 3) Vinorelbine (VRLB, 4) Vinflunine (VFL, 5) Camptothecin and Analogs Camptothecin (CPT, 6) Irinotecan (CPT-11) Topotecan Exatecan Gimatecan Karenitecin Lurtotecan Rubitecan (9-nitrocamptothecin) Taxanes Paclitaxel Docetaxel Antitumor Alkaloids in Clinical Trials Ecteinascidin-743 (Yondelis, Trabectedin) 7-Hydroxystaurosporine (UCN-01) Ellipticine and Analogs Acronycine and Analogs Colchicine and Analogs Ukrain Alkaloids Used for MDR Reversal Cinchona Alkaloids Dofequidar Fumarate (MS-209) Alkaloids Used for Cancer Prevention Conclusions Acknowledgments
A hitchhiker's guide to G-quadruplex ligands (2007)

Over the past decade, nucleic acid chemists have seen the spectacular emergence of molecules designed to interact efficiently and selectively with a peculiar DNA structure named G-quadruplex. Initially derived from classical DNA intercalators, these G-quadruplex ligands progressively became the focal point of new excitement since they appear to inhibit selectively the growth of cancer cells thereby opening interesting perspectives towards the development of novel anti-cancer drugs. The present article aims to help researchers enter this exciting research field, and to highlight recent advances in the design of G-quadruplex ligands.
[Complex characteristics of the alterations of oncogenes HER-2/ERBB-2, HER-1/ERBB-1, HRAS-1, C-MYC and antioncogenes p53, RB1, as well as deletions of loci of chromosome 17 in colon carcinoma]. (1993)

Abnormalities of some oncogenes, antioncogenes and losses of heterozygosity (LOH) of chromosome 11p, 17p, and 17q in colorectal carcinomas (CC) was studied. Amplification of ERBB-1/HER-1 oncogene was detected in 2 of 56 cases; ERBB-2/HER-2- in 4 of 62. There was a lack of evidence for C-MYC oncogene amplification (67 cases). LOH of chromosome 11p (HRAS-1 probe) was found in 2 of 37 informative (heterozygous) cases; such events were not accompanied by point mutations in "hot" codons (12th or 61st) in the remaining allele. Prevalence of A3 and A4 alleles of HRAS-1 oncogene (68 cases) as compared to healthy donors was noted. RB-1 (41 cases) and p53 (62 cases) suppressor genes did not show any alterations in Southern-blot analysis. LOH of chromosome 17p (YNZ-22 probe) was found in 15 of 26 heterozygous CC; 17q (THH-59 probe)--in 4 of 16. Analysis of 175th codon of p53 gene revealed only one case of mutation in 35 CC studied. Finally, we were able to detect genetic alterations in 23 of 40 (58%) CC, that were studied on each parameter using Southern-blot. We failed to find any correlation between various molecular abnormalities or clinical characteristics. The data obtained are in disagreement with the view concerning frequent involvement of p53 antioncogene in chromosome 17p deletions.
MEROPS: the peptidase database (2005)

Peptidases (proteolytic enzymes) and their natural, protein inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these proteins. The organizational principle of the database is a hierarchical classification in which homologous sets of proteins of interest are grouped into families and the homologous families are grouped in clans. The most important addition to the database has been newly written, concise text annotations for each peptidase family. Other forms of information recently added include highlighting of active site residues (or the replacements that render some homologues inactive) in the sequence displays and BlastP search results, dynamically generated alignments and trees at the peptidase or inhibitor level, and a curated list of human and mouse homologues that have been experimentally characterized as active. A new way to display information at taxonomic levels higher than species has been devised. In the Literature pages, references have been flagged to draw attention to particularly 'hot' topics.
Introduction of a lacZ reporter gene into the mouse int-2 locus by homologous recombination. (1990)

We demonstrate that the frequency of gene targeting is unaffected by the length of nonhomologous DNA transferred to a target chromosomal sequence. A result of this finding is that a much wider spectrum of designed genomic alterations is now feasible. As a first application, we inserted a 5.4-kilobase cassette of nonhomologous DNA into the int-2 locus in mouse embryo-derived stem cells by gene targeting. The inserted DNA contained a lacZ gene positioned to create an in-frame fusion with the int-2 protein-coding region. Upon differentiation of these cells to embryoid bodies, the int-2-lacZ fusion faithfully reproduced the expression pattern of int-2 RNA. This ability to target reporter genes, such as lacZ, to specific mouse loci, combined with the ability to move the tagged gene into different mutant backgrounds, may provide an ideal approach for analyzing interactions among genes that participate in a developmental network.
Effect of Ligand Structure on Activation Rate Constants in ATRP (2006)

Activation rate constants (kact) for Cu complexes with various nitrogen-based ligands for Cu-mediated ATRP were determined at 35 °C in acetonitrile. The ratio of kact for complexes with different ligands exceeds 1 million times. The general order of Cu complex activity for ligands is tetradentate (cyclic-bridged) > tetradentate (branched) > tetradentate (cyclic) > tetradentate (linear) > tridentate > bidentate ligands. The nature of nitrogen atoms in ligands also plays a significant role in the activity of the Cu complexes and follows the order pyridine ≥ aliphatic amine > imine.
Mesenchymal Stem Cells as Vehicles for Gene Delivery (2000)

Mesenchymal stem cells contribute to the regeneration of mesenchymal tissues such as bone, cartilage, muscle, ligament, tendon, adipose, and marrow stroma. Transduction of mesenchymal stem cells from species other than humans is required for the development of disease models in which mesenchymal stem cells-based gene delivery is evaluated. Attempts to transduce mesenchymal stem cells from some species with amphotropic retroviral vectors were unsuccessful, leading to comparative mesenchymal stem cells transductions with xenotropic and gibbon-ape leukemia virus envelope-pseudotyped retroviral vectors. Human, baboon, canine, and rat mesenchymal stem cells were transduced optimally with amphotropic vector supernatants. In contrast, sheep, goat, and pig mesenchymal stem cells showed highest transduction levels with xenotropic retroviral vector supernatant, and rabbit mesenchymal stem cells were transduced optimally with gibbon-ape-enveloped vectors. Using a myeloablative canine transplantation model and gene-marked canine mesenchymal stem cells, the biodistribution of infused and ex vivo expanded mesenchymal stem cells were examined. The majority of transduced canine mesenchymal stem cells were found in the bone marrow samples. The current study shows the use of mesenchymal stem cells as a delivery vehicle for gene transfer studies, and validates the feasibility of delivering mesenchymal stem cells to the marrow compartment for stromal regeneration after cancer-associated cytotoxic therapies.
Foresighted instruction scheduling under timing constraints (1992)

When data dependency graph arcs representing data dependency information are annotated with minimum and maximum timing information, new algorithms are required. Foresighted compaction is a list scheduling technique in which look ahead is used in making decisions. Foresighted compaction is very effective in reducing, failure inherent in greedy compaction algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Production of Gasoline and Diesel Fuels from Bio-materials (2007)

Abstract Biomass samples were converted to charcoal and to liquid and gaseous products by pyrolysis process at different temperatures. Under pyrolysis conditions, plastic wastes can be decomposed into three fractions: gas, liquid, and solid residue. The liquid products are usually composed of higher boiling point hydrocarbons. In order to obtain useful gasoline-range hydrocarbons from the pyrolytic oil, fractional distillation is preferred for product separation. More valuable chemical raw materials including benzene, toluene, and other condensed aromatic hydrocarbons may be obtained by refining the pyrolytic oil. The vegetable oils and their soaps obtained from the vegetable oils can be pyrolyzed into hydrocarbon rich products. The yield of conversion of the sunflower oil reached the maximum 78.3% at 660 K over ZnCl2 catalyst. The maximum gasoline yield of 48 wt% from palm oil was obtained with composite micromesoporous zeolite.
Quantification of Lung Fibrosis and Emphysema in Mice Using Automated Micro-Computed Tomography (2012)

We report on a high resolution in vivo micro-computed tomography image analysis algorithm that runs fully automated and allows quantification of aerated lung volume in mice. This method is reproducible with low inherent measurement variability. We show that it is a reliable quantitative tool to investigate experimental lung fibrosis and emphysema in mice. Its non-invasive nature has the unique benefit to allow dynamic 4D evaluation of disease processes and therapeutic interventions.
Mutations in the gene encoding the adenovirus early region 1B 19,000-molecular-weight tumor antigen cause the degradation of chromosomal DNA (1984)

The adenovirus mutant Ad2ts111 has been previously shown to contain a mutation in the early region 2A gene encoding the single-stranded-DNA-binding protein that results in thermolabile replication of virus DNA and a mutation in early region 1 that causes degradation of intracellular DNA. A recombinant virus, Ad2cyt106, has been constructed which contains the Ad2ts111 early region 1 mutation and the wild-type early region 2A gene from adenovirus 5. This virus, like its parent Ad2ts111, has two temperature-independent phenotypes; first, it has the ability to cause an enhanced and unusual cytopathic effect on the host cell (cytocidal [cyt] phenotype) and second, it induces degradation of cell DNA (DNA degradation [deg] phenotype). The mutation responsible for these phenotypes is a single point mutation in the gene encoding the adenovirus early region 1B (E1B) 19,000-molecular-weight (19K) tumor antigen. This mutation causes a change from a serine to an asparagine in the 20th amino acid from the amino terminus of the protein. Three other mutants that affect the E1B 19K protein function have been examined. The mutants Ad2lp5 and Ad5dl337 have both the cytocidal and DNA degradation phenotypes (cyt deg), whereas Ad2lp3 has only the cytocidal phenotype and does not induce degradation of cell DNA (cyt deg+). Thus, the DNA degradation is not caused by the altered cell morphology. Furthermore, the mutant Ad5dl337 does not make any detectable E1B 19K protein product, suggesting that the absence of E1B 19K protein function is responsible for the mutant phenotypes. A fully functional E1B 19K protein is not absolutely required for lytic growth of adenovirus 2 in HeLa cells, and its involvement in transformation of nonpermissive cells to morphological variants is discussed.
Fertility assessment through heterospermic insemination of flow-sorted sperm in cattle1 (2003)

The ability to assess fertility of bovine sperm accurately and rapidly would be very useful for research and applications to the cattle industry. Sperm motility and other in vitro tests of sperm normality are only partially correlated with fertility, and lengthy breeding trials are expensive and time consuming. Heterospermic insemination by mixing sperm from more than one male provides an in vivo method to assess relative fertility among bulls that can be economical and rapid. Sperm that had been flow-sorted and cryopreserved from four groups of four bulls were inseminated in all combinations of three bulls within groups into nonsuperovulated heifers or superovulated heifers. Embryos were collected nonsurgically between d 13.5 and 20 following estrus and evaluated for paternity by genotyping. Following determination of paternity, a heterospermic index was created for each bull using a maximum likelihood function. These indices ranged from 0.22 +/- 0.15 to 2.43 +/- 0.43 (mean = 1.00, with a higher value indicative of greater fertility). In all four groups, either the high- or low-fertility bull was identified (P < 0.05) using a total of 25 to 36 genotypable embryos from nonsuperovulated heifers. The heterospermic rankings of bulls were similar for single and superovulated heifers for one group of bulls, but dissimilar for a second group. Heterospermic insemination followed by genotyping of embryos proved to be efficacious for rapidly ranking fertility of flow-sorted sperm from bulls when females were not superovulated, but results were less clear when females were superovulated.
Increase of Antibody Titer against Leucocytozoon caulleryi by Oral Administration of Recombinant R7 Antigen (2005)

In this study, we examined oral administration with recombinant R7 (rR7) antigen expressed in Escherichia coli using chicken leucocytozoonosis subunit vaccine (LV)-vaccinated and unvaccinated chickens. Only LV-vaccinated chickens showed re-induction of anti-second-generation schizont (2GS) antibody. Also, LV-vaccinated chickens whose anti-2GS antibody titer was middle-level showed increases of the antibody titer compared to vaccinated-control chickens (P>0.01, >0.05) after oral administration with rR7 antigen.
Molecular Cloning, Sequencing, and Expression in Escherichia coli of Human Preprourokinase cDNA (1985)

A cDNA library derived from human carcinoma cells was used to isolate a clone, pULB1000, coding for the preproenzyme form of human urokinase. This clone carries the full-length sequence coding for the signal peptide and for the A chain (157 amino acids) and B chain (253 amino acids) of urokinase in tandem. The sequence of the cDNA predicts the presence of a single lysine residue between the last amino acid of the mature A polypeptide (Phe-157) and the first amino acid of the mature B polypeptide (Ile-1). The amino acid sequence deduced from the cDNA sequence fits the published amino acid sequence data with three exceptions, the reported cysteine residue at position 131 in the A chain is a tryptophan, and glycine 366 and alanine 410 in the B chain are, respectively, a cysteine and a valine in our clone. A large Bgl I fragment (1482 bp), derived from the clone pULB1000 coding for most of the signal peptide and for the A and B chains, has been subcloned into the expression vector pCQV2. Heat induction of E. coli cells carrying the recombinant plasmid leads to the production of urokinase-like polypeptides having the expected molecular weights and being specifically recognized by antibodies raised against natural human urokinase.
Pharmacological characterization of the human vasopressin receptor subtypes stably expressed in Chinese hamster ovary cells (1998)

Three subtypes of human (h) arginine vasopressin (AVP) receptors, hV1A, hV1B and hV2, were stably expressed in Chinese hamster ovary (CHO) cells and characterized by [3H]-AVP binding studies. In addition, the coupling of the expressed receptor protein to a variety of signal transduction pathways was investigated. Scatchard analysis of saturation isotherms for the specific binding of [3H]-AVP to membranes, prepared from CHO cells transfected with hV1A, hV1B and hV2 receptors, yielded an apparent equilibrium dissociation constant (Kd) of 0.39, 0.25 and 1.21 nM and a maximum receptor density (Bmax) of 1580 fmol mg(-1) protein, 5230 fmol mg(-1) protein and 7020 fmol mg(-1) protein, respectively. Hill coefficients did not differ significantly from unity, suggesting binding to homogenous, non-interacting receptor populations. Pharmacological characterization of the transfected human AVP receptors was undertaken by measuring the relative ability of nonpeptide AVP receptor antagonists, YM087, OPC-21268, OPC-31260, SR 49059 and SR 121463A, to inhibit binding of [3H]-AVP. At hV1A receptors, the relative order of potency was SR49059>YM087>OPC-31260>SR 121463A> >OPC-21268 and at hV2 receptors, YM087=SR 121463A>OPC-31260>SR 49059> >OPC-21268. In contrast, the relative order of potency, at hV1B receptors, was SR 49059> >SR 121463A=YM087=OPC-31260=OPC-21268. In CHO cells expressing either hV1A or hV1B receptors, AVP caused a concentration-dependent increase in intracellular Ca2+ concentration ([Ca2+]i) with an EC50 value of 1.13 nM and 0.90 nM, respectively. In contrast, stimulation of CHO cells expressing hV2 receptors resulted in an accumulation of cyclic AMP with an EC50 value of 2.22 nM. The potency order of antagonists in inhibiting AVP-induced [Ca2+]i or cyclic AMP response was similar to that observed in radioligand binding assays. In conclusion, we have characterized the pharmacology of human cloned V1A, V1B and V2 receptors and used these to determine the affinity, selectivity and potency of nonpeptide AVP receptor antagonists. Thus they may prove to be a valuable tool in further examination of the physiological and pathophysiological roles of AVP.
Teratogenicity of depleted uranium aerosols: A review from an epidemiological perspective (2005)

In aggregate the human epidemiological evidence is consistent with increased risk of birth defects in offspring of persons exposed to DU.
Increased Wnt Signaling During Aging Alters Muscle Stem Cell Fate and Increases Fibrosis (2007)

The regenerative potential of skeletal muscle declines with age, and this impairment is associated with an increase in tissue fibrosis. We show that muscle stem cells (satellite cells) from aged mice tend to convert from a myogenic to a fibrogenic lineage as they begin to proliferate and that this conversion is mediated by factors in the systemic environment of the old animals. We also show that this lineage conversion is associated with an activation of the canonical Wnt signaling pathway in aged myogenic progenitors and can be suppressed by Wnt inhibitors. Furthermore, components of serum from aged mice that bind to the Frizzled family of proteins, which are Wnt receptors, may account for the elevated Wnt signaling in aged cells. These results indicate that the Wnt signaling pathway may play a critical role in tissue-specific stem cell aging and an increase in tissue fibrosis with age.
The Role of PDGF Receptor Inhibitors and PI3-Kinase Signaling in the Pathogenesis of Corneal Neovascularization (2006)

Inhibition of the PDGF signal pathway results in loss of pericytes and a reduction in vessel density in the neovascularized cornea that correlates with reduced expression of PDGF, ang1/2, and VEGF mRNA. Furthermore, PI3-K was shown to be involved in the regulation of VEGF, ang1, and PDGF, as the PI3-K inhibitors wortmannin or LY294002 had similar effects. Because PDGF is a known stimulus for PI3-K activation, it can be postulated that the observed decrease in VEGF, ang1/2, and PDGF mRNA levels on administration of the PDGF inhibitor is caused by the decreased activation of the PI3-K signaling cascade.
Muscarinic acetylcholine receptor inhibition in transgenic Alzheimer‐like Tg2576 mice by scopolamine favours the amyloidogenic route of processing of amyloid precursor protein (2006)

The molecular mechanisms of the interrelationship between cholinergic neurotransmission, processing of amyloid precursor protein (APP) and beta-amyloid (Abeta) production in vivo are still less understood. To reveal any effect of cholinergic dysfunction on APP processing in vivo, 11-month-old transgenic Tg2576 mice with Abeta plaque pathology received intraperitoneal injections of scopolamine at a daily dosage of 2mg/kg body weight for 14 days in order to suppress cortical cholinergic transmission by chronic inhibition of muscarinic acetylcholine receptors. Scopolamine treatment of transgenic Tg2576 mice resulted in increased levels of fibrillar Abeta(1-40) and Abeta(1-42), while the soluble, SDS-extractable Abeta level remained unchanged as compared to vehicle-injected Tg2576 mice. alpha-Secretase activity determined in cortical tissue from scopolamine-treated Tg2576 mice was lower by about 30% as compared to that assayed in control mice, while beta-secretase activity and BACE1 protein expression appeared unaffected by scopolamine treatment. The amount of sAPPalpha, the product secreted by alpha-secretase-mediated APP cleavage, and the unprocessed APP were assayed in the soluble and membrane fraction, respectively, of cortical tissue preparations from treated and control mice by Western blotting. Using the anti antibody 6E10 which specifically labels human sAPPalpha and full length APP in transgenic Tg2576, an enhanced APP level was detected in the membrane fraction from treated mice as compared to controls, while in the soluble fraction scopolamine treatment did not affect the protein level of sAPPalpha. These data indicate an accumulation of APP in cortical membrane fraction in scopolamine-treated Tg2576 mice presumably due to the decreased level of alpha-secretase-mediated APP cleavage, and further suggest that chronic suppression of cortical muscarinic cholinergic transmission may alter the balance between alpha- and beta-secretory APP processing by favouring the amyloidogenic route.
Time-resolved photoluminescence studies of annealed 1.3-μm GaInNAsSb quantum wells (2014)

Time-resolved photoluminescence (PL) was applied to study the dynamics of carrier recombination in GaInNAsSb quantum wells (QWs) emitting near 1.3 μm and annealed at various temperatures. It was observed that the annealing temperature has a strong influence on the PL decay time, and hence, it influences the optical quality of GaInNAsSb QWs. At low temperatures, the PL decay time exhibits energy dependence (i.e., the decay times change for different energies of emitted photons), which can be explained by the presence of localized states. This energy dependence of PL decay times was fitted by a phenomenological formula, and the average value of E0, which describes the energy distribution of localized states, was extracted from this fit and found to be smallest (E0 = 6 meV) for the QW annealed at 700°C. In addition, the value of PL decay time at the peak energy was compared for all samples. The longest PL decay time (600 ps) was observed for the sample annealed at 700°C. It means that based on the PL dynamics, the optimal annealing temperature for this QW is approximately 700°C.