gebhart/patrepeval huggingface dataset:
Induction of cyclo‐oxygenase‐2 by cytokines in human cultured airway smooth muscle cells: novel inflammatory role of this cell type (1997)

1. Cyclo-oxygenase (COX) is the enzyme that converts arachidonic acid to prostaglandin H2 (PGH2) which can then be further metabolized to prostanoids which modulate various airway functions. COX exists in at least two isoforms. COX-1 is expressed constitutively, whereas COX-2 is expressed in response to pro-inflammatory stimuli. Prostanoids are produced under physiological and pathophysiological conditions by many cell types in the lung. However, the regulation of the different COX isoforms in human airway smooth muscle (HASM) cells has not yet been determined. 2. COX-1 and COX-2 protein were measured by Western blot analysis with specific antibodies for COX-1 and COX-2. COX-2 mRNA levels were assessed by Northern blot analysis by use of a COX-2 cDNA probe. COX activity was determined by measuring conversion of either endogenous or exogenous arachidonic acid to three metabolites, PGE2, thromboxane B2 or 6-ketoPGF1 alpha by radioimmunoassay. 3. Under control culture conditions HASM cells expressed COX-1, but not COX-2, protein. However, a mixture of cytokines (interleukin-1 beta (IL-1 beta), tumour necrosis factor alpha (TNF alpha) and interferon gamma (IFN gamma) each at 10 ng ml-1) induced COX-2 mRNA expression, which was maximal at 12 h and inhibited by dexamethasone (1 microM; added 30 min before the cytokines). Furthermore, COX-2 protein was detected 24 h after the cytokine treatment and the expression of this protein was also inhibited by dexamethasone (1 microM) and cyclohexamide (10 micrograms ml-1; added 30 min before the cytokines). 4. Untreated HASM cells released low or undetectable amounts of all COX metabolites measured over a 24 h period. Incubation of the cells with the cytokine mixture (IL-1 beta, TNF alpha, IFN gamma each at 10 ng ml-1 for 24 h) caused the accumulation of PGE2 and 6-keto-PGF1 alpha. 5. In experiments where COX-2 metabolized endogenous stores of arachidonic acid, treatment of HASM cells with IL-1 beta in combination with TNF alpha caused a similar release of PGE2 to that when the three cytokines were given in combination. 6. In other experiments designed to measure COX-2 activity directly, cells were treated with cytokines for 24 h before fresh culture medium was added containing exogenous arachidonic acid (30 microM for 15 min) after which PGE2 was measured. IL-1 beta and TNF alpha increased COX-2 activity and an additional small increase was produced by the three cytokines in combination. 7. These findings suggest that the increased expression of COX-2 is intimately involved in the exaggerated release of prostanoids from HASM cells exposed to pro-inflammatory cytokines. These data indicate a role for airway smooth muscle cells, in addition to their contractile function, as inflammatory cells involved in the production of mediators which may contribute to the inflammatory response seen in diseases such as asthma.
Role of metal ions in the tetraloop–receptor complex as analyzed by NMR (2006)

Metal ions are critical for the proper folding of RNA, and the GAAA tetraloop-receptor is necessary for the optimal folding and function of many RNAs. We have used NMR to investigate the role of metal ions in the structure of the tetraloop-receptor in solution. The NMR data indicate native tertiary structure is formed under a wide range of ionic conditions. The lack of conformational adaptation in response to very different ionic conditions argues against a structural role for divalent ions. Nuclear Overhauser effects to cobalt hexammine and paramagnetic relaxation enhancement induced by manganese ions were used to determine the NMR structures of the tetraloop receptor in association with metal ions, providing the first atomic-level view of these interactions in the solution state. Five manganese and two cobalt hexammine ions could be localized to the RNA surface. The locations of the associated metal ions are similar, but not identical to, those of previously determined crystal structures. The sites of association are in general agreement with nonlinear Poisson-Boltzmann calculations of the electrostatic surface, emphasizing the general importance of diffusely associated ions in RNA tertiary structure.
Dihematoporphyrin Ether Clearance in Primate Bladders (1986)

The techniques of in vivo tissue fluorescence photometry and chemical extractions of DHE, which have been recently developed in our laboratory, were employed to study DHE uptake and clearance in the primate bladders. Data show these techniques are readily applicable in studying porphyrin uptake and clearance in primate bladders. Quantitatively a correlation between fluorescence values and tissue extracted DHE values is found. Serum clearance and bladder clearance of DHE appeared phasic, but bladder clearance was slower than serum. The significance of these two methods lies in their applications in determination of drug dosimetry and optimum time for photoactivation in clinical photodynamic therapy.
Degradable dUMP Outer Primers in Merged Tandem (M/T)-Nested PCR: Low- and Single-Copy DNA Target Amplification (1998)

PCR amplification of DNA from a single initiating genomic molecule or low-copy template often requires two sequential amplification reactions with nested primer pairs to achieve the necessary specificity and sensitivity. Residual outer primers can result in undesired primer activity during the inner nested cycles. To circumvent this problem, we have used dU-containing primers for first round amplification and then uracil N-glycosylase (UNG) to degrade them and the ends of their dU-primer-containing amplified DNA products. We have applied this method to the detection of an exon 11 mutation in the HEXA gene. We have merged the step of a single-tube PCR amplification with outer dU primers with a tandem amplification using non-dU-nested primers (hence, the term merged tandem-nested or M/T-nested PCR). Serial dilutions of genomic DNA showed that this method could amplify a specific target from as few as three haploid genome equivalents of template DNA. Specific products were obtained from the DNA of single cells in 19 of 20 replicates, using 12 outer and 28 inner nested PCR cycles, with an intervening UNG digestion step. When coupled with heteroduplex mutational analysis, this method reliably distinguished mutant versus wild-type HEXA gene fragments amplified from single cells without primer artifact.
Some Common Issues in the Use of Antiepileptic Drugs (2002)

Since 1993, eight new antiepileptic drugs (AEDs) have become available in the United States for the treatment of epilepsy: felbamate, gabapentin, lamotrigine, topiramate, tiagabine, levetiracetam, oxcarbazepine, and zonisamide. Of the older AEDs, six continue to be widely used: phenobarbital, phenytoin, primidone, ethosuximide, carbamazepine, and valproate. As a result, there is a relatively large number of alternative AEDs for the treatment of any given type of epilepsy. This has been particularly beneficial for patients with generalized epilepsies, both idiopathic and symptomatic. Given the wide availability of effective agents, the toxicity and pharmacokinetic profile of an AED have become major factors in the selection process. A number of common clinical situations may benefit from the abundance of AEDs. Chronic toxicity observed with some of the older AEDs such as osteoporosis, gingival hyperplasia, or alterations in reproductive endocrine function may be avoided with the use of the newer agents. The obese patient with epilepsy may benefit from the use of AEDs such as topiramate or zonisamide, which have a tendency to produce weight loss. In patients with a history of drug-induced skin rash, AEDs such as valproate, gabapentin, topiramate, tiagabine, and levetiracetam carry a lower risk of cross-reactivity. In patients sensitive to cognitive dysfunction, drugs with a favorable profile include gabapentin, tiagabine, lamotrigine, oxcarbazepine, and levetiracetam. A more favorable pharmacokinetic profile is observed in the majority of the newer AEDs in contraposition to the classic agents. Good absorption, linear kinetics, and low drug-drug interaction potential make these drugs easier to use. The newer AEDs are eliminated through different combinations of liver metabolism and direct renal excretion, thus providing a wider variety of choices in patients with failure of one of these organs. Some specific problems have been found with some of the newer AEDs. Hyponatremia, known to occur rarely with carbamazepine use, appears to be more common with oxcarbazepine. Felbamate has been associated with a high incidence of aplastic anemia and liver failure and should be used exceptionally. Acute angle closure glaucoma has been observed with the use of topiramate. This complication occurs early in the course of therapy and reverses rapidly with discontinuation of the drug, so physician and patient awareness of this problem is very important. In this article several common clinical situations in the management of patients with epilepsy are presented in the form of case studies. These cases illustrate some current aspects of the use of the AEDs and will give some guidelines to help the treating physician in the increasingly complex process of AED selection.
Nuclei and subnuclear components (2008)

I. THE INTRANUCLEAR ENVIRONMENT 1. The intranuclear environment. Santiago Schnell and Ronald Hancock II. ISOLATION OF NUCLEI 2. Purification of Nuclei and Preparation of Nuclear Envelopes from Skeletal Muscle. Gavin S. Wilkie and Eric C. Schirmer 3. Isolation of Highly Purified Yeast Nuclei for Nuclease Mapping of Chromatin Structure. Joseph C. Reese, Hesheng Zhang and Zhengjian Zhang 4. Working with oocyte nuclei: cytological preparations of active chromatin and nuclear bodies from amphibian germinal vesicles. Garry T. Morgan. 5. Preparation of Arabidopsis Nuclei and Nucleoli. Peter McKeown, Alison F. Pendle and Peter J. Shaw 6. High-Yield Isolation and Subcellular Proteomic Characterization of Nuclear and Subnuclear Structures from Trypanosomes. Jeffrey A. DeGrasse, Brian T. Chait, Mark C. Field and Michael P. Rout 7. Methods for studying the nuclei and chromosomes of dinoflagellates. Marie-Odile Soyer-Gobillard III. THE NUCLEOLUS 8. Isolation of nucleoli from Ehrlich ascites tumor cells and dynamics of nascent RNA within isolated nucleoli. Marc Thiry and Dominique Ploton 9. Time-lapse microscopy and FRET to analyze the dynamics and interactions of nucleolar proteins in living cells. Emilie Louvet, Marc Tramier, Nicole Angelier and Daniele Hernandez-Verdun 10. Three-Dimensional Reconstruction of Nucleolar Components by Electron Microscope Tomography. Pavel Tchelidze, Herve Kaplan, Adrien Beorchia, Marie-Francoise O'Donohue, Helene Bobichon, Nathalie Lalun, Laurence Wortham and Dominique Ploton IV : INTRANUCLEAR STRUCTURES 11. The perinucleolar compartment (PNC): detection by immunohistochemistry. Alicja Slusarczyk and Sui Huang 12.Isolation of the Constitutive Heterochromatin from Mouse Liver Nuclei. Olga V. Zatsepina, Oxana O. Zharskaya and Andrei N. Prusov 13. Isolation of pathology-associated intranuclear inclusions. Christine Iwahashi and Paul J Hagerman 14. The nuclear ubiquitin-proteasome system: visualization of proteasomes, protein aggregates and proteolysis in the cell nucleus. Anna von Mikecz, Min Chen, Thomas Rockel and Andrea Scharf V: INTERPHASE CHROMOSOMES 15. Multicolor 3D-FISH for imaging interphase chromosomes. M. Cremer, F. Grasser, C. Lanctot, S. Muller, M. Neusser, I. Solovei, R. Zinner and T. Cremer 16. Fluorescent transgenes to study interphase chromosomes in living plants. Antonius J.M. Matzke, Bruno Huettel, Johannes van der Winden and Marjori Matzke 17. Analysis of telomeres and telomerase . Jiri Fajkus, Martina Dvorackova and Eva Sykorova 18. Combined immunofluorescence, RNA FISH, and DNA FISH to study chromatin changes, transcriptional activity, nuclear organization, and X-chromosome inactivation. Julie Chaumeil, Sandrine Augui, Jennifer C. Chow and Edith Heard 19. Analysis of the mobility of DNA double-strand break-containing chromosome domains in living mammalian cells. P.M. Krawczyk, J. Stap, R.A. Hoebe, C.H. van Oven, R. Kanaar, and J.A. Aten
Software export from developing nations (1993)

It is shown that software export is an attainable goal for developing nations, especially when government policies are favorable, and that the industrialized nations dominating the worldwide market can expect some serious competition. Examples of the efforts of developing nations to export software to North America and Europe are cited.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure, Function and Networks of Transcription Factors Involved in Abiotic Stress Responses (2013)

Transcription factors (TFs) are master regulators of abiotic stress responses in plants. This review focuses on TFs from seven major TF families, known to play functional roles in response to abiotic stresses, including drought, high salinity, high osmolarity, temperature extremes and the phytohormone ABA. Although ectopic expression of several TFs has improved abiotic stress tolerance in plants, fine-tuning of TF expression and protein levels remains a challenge to avoid crop yield loss. To further our understanding of TFs in abiotic stress responses, emerging gene regulatory networks based on TFs and their direct targets genes are presented. These revealed components shared between ABA-dependent and independent signaling as well as abiotic and biotic stress signaling. Protein structure analysis suggested that TFs hubs of large interactomes have extended regions with protein intrinsic disorder (ID), referring to their lack of fixed tertiary structures. ID is now an emerging topic in plant science. Furthermore, the importance of the ubiquitin-proteasome protein degradation systems and modification by sumoylation is also apparent from the interactomes. Therefore; TF interaction partners such as E3 ubiquitin ligases and TF regions with ID represent future targets for engineering improved abiotic stress tolerance in crops.
Wetting and Capillary Phenomena of Water on Mica (1998)

The structure of water films on mica was locally modified by contact with the tip of an atomic force microscope (AFM) in a humid environment. The subsequent evolution of the film was studied by noncontact scanning polarization force microscopy. At high relative humidity (>20%), capillary condensation caused water to form droplets and two-dimensional islands around the contact point. The droplets evaporated in a short period of time, but the islands remained for much longer periods (hours). At low relative humidity (<20%), the tip contact produced a circular depression in the local polarizability. None of these structures could be observed in contact AFM images which revealed only the usual atomically flat mica surface.
Allelic imbalance and microsatellite instability in prostatic adenocarcinoma. (1996)

Although prostate cancer is one of the most common malignancies of males in Western countries, relatively little is known about the molecular mechanisms involved in tumor initiation and progression. Allelic loss studies have suggested the involvement of multiple tumor suppressor genes (TSGs), but few detailed studies of all chromosomes have been performed. In an effort to localize and identify candidate TSGs, we performed allelic imbalance (AI) studies on 55 prostate cancers, using 135 polymorphic microsatellite markers. For the entire chromosome. AI ranged from a low of 0% on chromosomes 14 and 20 to a high of 71% on chromosome 8. Chromosomal regions demonstrating at least twice the background frequency of AI (ranging from 20 to 69%) included 5q, 6q, 7q, 8p, 13, l6q, l8q, and 21. In addition, AI was examined for association with a number of clinicopathological parameters. AI on chromosomes 7 and 16 were each associated with greater age at diagnosis (P = 0.009 and 0.001, respectively), and AI on chromosomes 10, 16, and 18 was associated with aneuploidy/tetraploidy (P = 0.037, 0.013, and 0.054, respectively). Furthermore, AI on chromosome 5 was associated with a higher pathological stage (P = 0.021) and on chromosome 8 and 16 with a higher Gleason score (P = 0.027 and 0.041, respectively). No tumor exhibited a phenotype of widespread microsatellite instability. These results indicate that there likely exist multiple sites harboring candidate TSG in prostate cancer, some of which may have important clinical implications, and which argue against widespread microsatellite instability.
Competitive interaction of cyclosporins with the Vinca alkaloid-binding site of P-glycoprotein in multidrug-resistant cells. (1990)

The mechanism of reversal of resistance to Vinca alkaloids by cyclosporins is unclear. We investigated the molecular mechanism of reversal of Vinca alkaloid resistance by cyclosporin A (CsA) and its nonimmunosuppressive analog O-acetyl C9(1) CsA (SDZ 33-243) in multidrug resistant DC-3F/VCRd-5L Chinese hamster cells. CsA at 3 microM increased vincristine (VCR) sensitivity and almost totally reversed VCR resistance. SDZ 33-243 at 1 microM reduced the IC50 for VCR in resistant cells from 62.0 to 0.00062 microM. CsA and SDZ 33-243 at 10 microM increased [3H]vinblastine (VBL) accumulation in DC-3F/VCRd-5L cells by 27- and 22-fold, respectively. At 10 microM, these compounds also increased [3H]VCR accumulation by 3.5- and 4.0-fold, respectively. [3H]VCR uptake by membrane vesicles from DC-3F/VCRd-5L cells showed high and low affinity components with Michaelis-Menten kinetics, and apparent Km values were 0.140 +/- 0.0523 and 24.8 +/- 6.67 microM, respectively. Kinetic analysis of [3H]VCR uptake in membrane vesicles in the presence of 0.2 microM CsA revealed that CsA competitively inhibited the high affinity [3H]VCR uptake with an apparent inhibition constant (Ki) of 0.126 +/- 0.0173 microM. In addition, CsA and SDZ 33-243 inhibited VBL photoaffinity labeling of P-glycoprotein in a dose-dependent manner, with half-maximum inhibition at 0.5 and 0.4 microM, respectively, compared with that of VBL at 0.6 microM. These data confirm that cyclosporins modulate Vinca alkaloid resistance at least partially through interaction with P-glycoprotein.
Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library (2016)

The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (T<sub>m</sub> of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation.
Characterization of capsid and noncapsid proteins of B19 parvovirus propagated in human erythroid bone marrow cell cultures (1987)

The major capsid and noncapsid proteins of the pathogenic parvovirus B19, propagated in vitro, were detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, immunoprecipitation, and immunoblot of the erythroid fraction of infected human bone marrow cell cultures. There were two capsid proteins of 58 kilodaltons (kDa; the major species) and 84 kDa (the minor species). Newly synthesized capsid viral proteins were present in the supernatants of infected cultures. The major noncapsid protein of 77 kDa was localized to the nucleus.
Estimating Slip Distribution for the Izmit Mainshock from Coseismic GPS, ERS-1, RADARSAT, and SPOT Measurements (2002)

We use four geodetic satellite systems (Global Positioning System [GPS], European Remote Sensing [ERS], RADARSAT, and Satellite Pour l9Observation de la Terre [SPOT]) to measure the permanent deformation field produced by the Izmit earthquake of 17 August 1999. We emphasize measurements from interferometric analysis of synthetic aperture radar (SAR) images acquired by ERS and RADARSAT and their geodetic uncertainties. The primary seismological use of these data is to determine earthquake source parameters, such as the distribution of slip and the fault geometry. After accounting for one month9s postseismic deformation, tropospheric delay, and orbital gradients, we use these data to estimate the distribution of slip at the time of the Izmit mainshock. The different data sets resolve different aspects of the distribution of slip at depth. Although these estimates agree to first order with those derived from surface faulting, teleseismic recordings, and strong motion, careful comparison reveals differences of 40% in seismic moment. We assume smooth parameterization for the fault geometry and a standard elastic dislocation model. The root mean square residual scatter is 25 mm and 11 mm for the ERS and RADARSAT range changes, respectively. Our estimate of the moment from a joint inversion of the four geodetic data sets is M 0 = 1.84 × 10 20 N m, a moment magnitude of M w 7.50. These values are lower than other estimates using more realistic layered earth models. Given the differences between the various models, we conclude that the real errors in the estimated slip distributions are at the level of 1 m. The prudent geophysical conclusion is that coseismic slip during the Izmit earthquake tapers gradually from approximately 2 m under the Hersek delta to 1 m at a point 10 km west of it. We infer that the Yalova segment west of the Hersek delta may remain capable of significant slip in a future earthquake.