gebhart/patrepeval huggingface dataset:
NADP<sup>+</sup> production using thermostable NAD<sup>+</sup> kinase of <i>Corynebacterium flaccumfaciens</i> AHU-1622 (1986)

A sonicate of Corynebacterium flaccumfaciens AHU-1622 had the highest NAD+ kinase activity (1.22 mU/mL culture broth) of the strains of bacteria we investigated. This enzyme was thermostable, with activity maintained at 50 degrees C for 1 h. This treatment inactivated phosphatase activity. Resting cells of the bacterium also had NAD+ kinase activity when treated at 60 degrees C for 30 min with 0.2% Triton X-100. NADP+ production was achieved using 8 mumol NAD+, 8 mumol ATP, 16 mumol MgCl2, 1.6 mumol NaN3, and 12 mU NAD+ kinase (0.1 g of permeabilized wet cells) in 2 mL of 0.1 M phosphate buffer, pH 7.5. The conversion ratio of NADP+ from NAD+ was 75% after 10 h of incubation at 50 degrees C, and the amount of accumulated NADP+ was 3 mumol/mL of reaction mixture. The NAD+ kinase activity of the permeabilized cells was stable and did not decrease after repeated use.
Resistance to Paclitaxel in a Cisplatin-Resistant Ovarian Cancer Cell Line Is Mediated by P-Glycoprotein (2012)

The IGROVCDDP cisplatin-resistant ovarian cancer cell line is also resistant to paclitaxel and models the resistance phenotype of relapsed ovarian cancer patients after first-line platinum/taxane chemotherapy. A TaqMan low-density array (TLDA) was used to characterise the expression of 380 genes associated with chemotherapy resistance in IGROVCDDP cells. Paclitaxel resistance in IGROVCDDP is mediated by gene and protein overexpression of P-glycoprotein and the protein is functionally active. Cisplatin resistance was not reversed by elacridar, confirming that cisplatin is not a P-glycoprotein substrate. Cisplatin resistance in IGROVCDDP is multifactorial and is mediated in part by the glutathione pathway and decreased accumulation of drug. Total cellular glutathione was not increased. However, the enzyme activity of GSR and GGT1 were up-regulated. The cellular localisation of copper transporter CTR1 changed from membrane associated in IGROV-1 to cytoplasmic in IGROVCDDP. This may mediate the previously reported accumulation defect. There was decreased expression of the sodium potassium pump (ATP1A), MRP1 and FBP which all have been previously associated with platinum accumulation defects in platinum-resistant cell lines. Cellular localisation of MRP1 was also altered in IGROVCDDP shifting basolaterally, compared to IGROV-1. BRCA1 was also up-regulated at the gene and protein level. The overexpression of Pglycoprotein in a resistant model developed with cisplatin is unusual. This demonstrates that P-glycoprotein can be upregulated as a generalised stress response rather than as a specific response to a substrate. Mechanisms characterised in IGROVCDDP cells may be applicable to relapsed ovarian cancer patients treated with frontline platinum/taxane chemotherapy.
Studies on the structure of yeast mannan. I. Purification and some properties of an alpha-mannosidase from an arthrobacter species. (1969)

Abstract A soil microorganism, designated Arthrobacter GJM-1, has been isolated which is capable of growing on Saccharomyces cerevisiae mannan as the carbon source. When grown on mannan, the microorganism secretes an α-mannosidase into the cultural medium. The enzyme is not found when mannose, glucose, or glycerol is substituted for mannan, but is present when oligosaccharides obtained by acetolysis of mannan are used as carbon sources. The α-mannosidase has been isolated and partially purified. It was free of contaminating glycosidase, phosphatase, and protease activities. The enzyme is active on mannans from several different yeasts and on the oligosaccharides produced by acetolysis of yeast mannans, but has a low activity on α-mannosides with aromatic or aliphatic aglycons. This is in contrast to results obtained with other α-mannosidases and may reflect the different metabolic roles of the respective enzymes. The Km values for the di-, tri-, tetra-, penta-, and hexasaccharides from S. cerevisiae mannan varied between 0.5 and 2 mm. Because of the structural heterogeneity of these oligosaccharides, it is not certain what features contribute to the differences observed. The Km value for intact mannan was 1 x 10-5 m, but this value probably reflects the higher concentration of side chains in the mannan molecule.
The Role of Equilibrium and Kinetic Properties in the Dissociation of Gd[DTPA‐bis(methylamide)] (Omniscan) at near to Physiological Conditions (2015)

[Gd(DTPA-BMA)] is the principal constituent of Omniscan, a magnetic resonance imaging (MRI) contrast agent. In body fluids, endogenous ions (Zn(2+), Cu(2+), and Ca(2+)) may displace the Gd(3+). To assess the extent of displacement at equilibrium, the stability constants of DTPA-BMA(3-) complexes of Gd(3+), Ca(2+), Zn(2+), and Cu(2+) have been determined at 37 °C in 0.15 M NaCl. The order of these stability constants is as follows: GdL≈CuL>ZnL≫CaL. Applying a simplified blood plasma model, the extent of dissociation of Omniscan (0.35 mM [Gd(DTPA-BMA)]) was found to be 17% by the formation of Gd(PO4), [Zn(DTPA-BMA)](-) (2.4%), [Cu(DTPA-BMA)](-) (0.2%), and [Ca(DTPA-BMA)](-) (17.7%). By capillary electrophoresis, the formation of [Ca(DTPA-BMA)](-) has been detected in human serum spiked with [Gd(DTPA-BMA)] (2.0 mM) at pH 7.4. Transmetallation reactions between [Gd(DTPA-BMA)] and Cu(2+) at 37 °C in the presence of citrate, phosphate, and bicarbonate ions occur by dissociation of the complex assisted by the endogenous ligands. At physiological concentrations of citrate, phosphate, and bicarbonate ions, the half-life of dissociation of [Gd(DTPA-BMA)] was calculated to be 9.3 h at pH 7.4. Considering the rates of distribution and dissociation of [Gd(DTPA-BMA)] in the extracellular space of the body, an open two-compartment model has been developed, which allows prediction of the extent of dissociation of the Gd(III) complex in body fluids depending on the rate of elimination of the contrast agent.
2-D scanning mirror using plastically deformed angular vertical comb drive actuator (2005)

We have demonstrated microfabricated, monolithic two degrees of freedom (2D) electrostatic torsional mirrors using a 3-mask process on SOI wafer with a single plastic deformation step. The mirror operated independently in two orthogonal directions as controlled by two sets of self-aligned angular vertical combs. The measured dynamic performance showed resonant frequencies of 10.56 kHz and 1.54 kHz with optical scanning angles up to 27 degrees and 20 degrees in the two orthogonal axes respectively, under driving voltages of 20V/sub dc/ plus 15V/sub pp/. A reliability test of 90-day continuous mirror operation that corresponds to peak resonance of 80- and 12.1-billion cycles on the two orthogonal axes showed negligible performance variations.
Nuclear Receptors as Targets for Drug Development: Molecular Mechanisms for Regulation of Obesity and Insulin Resistance by Peroxisome Proliferator-Activated Receptor γ, CREB-Binding Protein, and Adiponectin (2005)

Obesity is defined as increased mass of adipose tissue, conferring a higher risk of cardiovascular and metabolic disorders such as diabetes, hyperlipidemia, and coronary heart disease. To investigate the role of transcriptional factors, which are involved in adipocytes differentiation and adiposity, we have generated peroxisome proliferator-activated receptor (PPAR) gamma or CREB-binding protein (CBP)-deficient mice by gene targeting. Heterozygous PPARgamma-deficient mice were protected from the development of insulin resistance due to adipocyte hypertrophy under a high-fat diet. Heterozygous CBP-deficient mice showed increased insulin sensitivity and were completely protected from body weight gain induced by a high-fat diet. PPARgamma or CBP deficiency results in increased effects of hormones such as adiponectin and leptin. Adiponectin was decreased in obesity and lipoatrophy, and replenishment of adiponectin ameliorated insulin resistance. Moreover, adiponectin-deficient mice showed insulin resistance and atherogenic phenotype. Finally, cDNA encoding adiponectin receptors (AdipoR1/R2) have been identified by expression cloning. The expression of AdipoR1/R2 appears to be inversely regulated by insulin in physiological and pathophysiological states such as fasting/refeeding, insulin deficiency, and hyperinsulinemia models, and it is correlated with adiponectin sensitivity. These results facilitate the understanding of molecular mechanisms of adiponectin actions and obesity-linked diseases such as diabetes and atherosclerosis and propose the molecular targets for anti-diabetic and anti-atherogenic drugs.
Efficient Near-Infrared Light-Driven Hydrogen Evolution Catalyzed by a Saddle-Distorted Porphyrin as a Photocatalyst (2020)

Development of a near-infrared (NIR) light-induced hydrogen (H2) evolution system is indispensable for constructing a sustainable society wherein the utilization of solar energy is maximized. Here, we report NIR light-driven H2 evolution catalyzed by a combination of a diprotonated saddle-distorted porphyrin as a photosensitizer and platinum nanoparticles as a H2-evolving catalyst. The quantum yield at 710 nm was determined to be 17%, which is the highest value among photocatalytic H2-evolution systems ever reported.
Persistence of Avian Influenza Virus (H5N1) in Feathers Detached from Bodies of Infected Domestic Ducks (2010)

Asian lineage highly pathogenic avian influenza virus (H5N1) continues to cause mortality in poultry and wild bird populations at a panzootic scale. However, little is known about its persistence in contaminated tissues derived from infected birds. We investigated avian influenza virus (H5N1) persistence in feathers detached from bodies of infected ducks to evaluate their potential risk for environmental contamination. Four-week-old domestic ducks were inoculated with different clades of avian influenza virus (H5N1). Feathers, drinking water, and feces were collected on day 3 postinoculation and stored at 4 degrees C or 20 degrees C. Viral persistence in samples was investigated for 360 days by virus isolation and reverse transcription-PCR. Infectious viruses persisted for the longest period in feathers, compared with drinking water and feces, at both 4 degrees C and 20 degrees C. Viral infectivity persisted in the feathers for 160 days at 4 degrees C and for 15 days at 20 degrees C. Viral titers of 10(4.3) 50% egg infectious doses/ml or greater were detected for 120 days in feathers stored at 4 degrees C. Viral RNA in feathers was more stable than the infectivity. These results indicate that feathers detached from domestic ducks infected with highly pathogenic avian influenza virus (H5N1) can be a source of environmental contamination and may function as fomites with high viral loads in the environment.
Structural basis and specificity of human otubain 1-mediated deubiquitination (2008)

OTUB (otubain) 1 is a human deubiquitinating enzyme that is implicated in mediating lymphocyte antigen responsiveness, but whose molecular function is generally not well defined. A structural analysis of OTUB1 shows differences in accessibility to the active site and in surface properties of the substrate-binding regions when compared with its close homologue, OTUB2, suggesting variations in regulatory mechanisms and substrate specificity. Biochemical analysis reveals that OTUB1 has a preference for cleaving Lys(48)-linked polyubiquitin chains over Lys(63)-linked polyubiquitin chains, and it is capable of cleaving NEDD8 (neural-precursor-cell-expressed developmentally down-regulated 8), but not SUMO (small ubiquitin-related modifier) 1/2/3 and ISG15 (interferon-stimulated gene 15) conjugates. A functional comparison of OTUB1 and OTUB2 indicated a differential reactivity towards ubiquitin-based active-site probes carrying a vinyl methyl ester, a 2-chloroethyl or a 2-bromoethyl group at the C-terminus. Mutational analysis suggested that a narrow P1' site, as observed in OTUB1, correlates with its ability to preferentially cleave Lys(48)-linked ubiquitin chains. Analysis of cellular interaction partners of OTUB1 by co-immunoprecipitation and MS/MS (tandem mass spectrometry) experiments demonstrated that FUS [fusion involved in t(12;6) in malignant liposarcoma; also known as TLS (translocation in liposarcoma) or CHOP (CCAAT/enhancer-binding protein homologous protein)] and RACK1 [receptor for activated kinase 1; also known as GNB2L1 (guanine-nucleotide-binding protein beta polypeptide 2-like 1)] are part of OTUB1-containing complexes, pointing towards a molecular function of this deubiquitinating enzyme in RNA processing and cell adhesion/morphology.
Soluble TREM2 induces inflammatory responses and enhances microglial survival (2017)

Triggering receptor expressed on myeloid cells 2 (TREM2) is an innate immune receptor expressed in microglia in the brain. A soluble form of TREM2 (sTREM2) derived from proteolytic cleavage of the cell surface receptor is increased in the preclinical stages of AD and positively correlates with the amounts of total and phosphorylated tau in the cerebrospinal fluid. However, the physiological and pathological functions of sTREM2 remain unknown. Here, we show that sTREM2 promotes microglial survival in a PI3K/Akt-dependent manner and stimulates the production of inflammatory cytokines depending on NF-κB. Variants of sTREM2 carrying AD risk-associated mutations were less potent in both suppressing apoptosis and triggering inflammatory responses. Importantly, sTREM2 delivered to the hippocampi of both wild-type and <i>Trem2</i>-knockout mice elevated the expression of inflammatory cytokines and induced morphological changes of microglia. Collectively, these data indicate that sTREM2 triggers microglial activation inducing inflammatory responses and promoting survival. This study has implications for the pathogenesis of AD and provides insights into targeting sTREM2 pathway for AD therapy.
Scatter Correction of Transmission Near-Infrared Spectra by Photon Migration Data: Quantitative Analysis of Solids (2005)

The scope of this work is a new methodology to correct conventional near-infrared (NIR) data for scattering effects. The technique aims at measuring the absorption coefficient of the samples rather than the total attenuation measured in conventional NIR spectroscopy. The main advantage of this is that the absorption coefficient is independent of the path length of the light inside the sample and therefore independent of the scattering effects. The method is based on time-resolved spectroscopy and modeling of light transport by diffusion theory. This provides an independent measure of the scattering properties of the samples and therefore of the path length of light. This yields a clear advantage over other preprocessing techniques, where scattering effects are estimated and corrected for by using the shape of the measured spectrum only. Partial least squares (PLS) calibration models show that, by using the proposed evaluation scheme, the predictive ability is improved by 50% as compared to a model based on conventional NIR data alone. The method also makes it possible to predict the concentration of active substance in samples with other physical properties than the samples included in the calibration model.
A new solid acid catalyst: the first phosphonate and phosphonic acid functionalised microporous polysilsesquioxanes (2001)

A novel microporous solid acid, the phosphonic acid modified polysilsesquioxane [(HO)SiCH2CHPO(OH)2- CH2CH2SiO2(OH)]n P2, from the new single precursor compound [(EtO)3SiCH2CHPO(OCH2CH3) 2CH2CH2- Si(OEt)3] 1, is reported, along with the catalytic activity of P2 for the pinacol–pinacolone rearrangement.
Review article: the diagnosis of non‐alcoholic fatty liver disease – availability and accuracy of non‐invasive methods (2012)

Different non-invasive parameters are available for the accurate diagnosis and prognostic stratification of non-alcoholic fatty liver disease which, if employed in a sequential algorithm, may lead to a reduced use of invasive methods, i.e. liver biopsy.
The Value of Intraoperative Near-Infrared Fluorescence Imaging Based on Enhanced Permeability and Retention of Indocyanine Green: Feasibility and False-Positives in Ovarian Cancer (2015)

ISRCTN Registry ISRCTN16945066.
Cryogenic All Solid-State Millimeter-Wave Receivers for Airborne Radiometry (1983)

Cryogenic receiver modules for 90 and 140 GHz have been developed that are part of an airborne imaging system. They consist of Schottky-barrier mixers followed by GaAs-FET IF amplifiers. The DSB receiver noise temperatures are 210 K for the 90-GW and 250 K for the 140-GHz system. The instantaneous bandwidth is 2.5 GHz for both front ends. Results of some flight tests are presented.
A Novel Ternary Complex of Europium(III) for Eletroluminescent Device (2002)

Introduction Since Tang［1］and Adachi et al.［2］reported their double and triplelayered devices, organic electroluminescent(EL) devices have attracted a great interest due to their efficient emission in the visible region and their possible application to flat panel full color display.
Generation of Predictive Pharmacophore Models for CCR5 Antagonists:  Study with Piperidine- and Piperazine-Based Compounds as a New Class of HIV-1 Entry Inhibitors (2003)

Predictive pharmacophore models were developed for a large series of piperidine- and piperazine-based CCR5 antagonists as anti-HIV-1 agents reported by Schering-Plough Research Institute in recent years. The pharmacophore models were generated using a training set consisting of 25 carefully selected antagonists based on well documented criteria. The activity spread, expressed in K(i), of training set molecules was from 0.1 to 1300 nM. The most predictive pharmacophore model (hypothesis 1), consisting of five features, namely, two hydrogen bond acceptors and three hydrophobic, had a correlation (r) of 0.920 and a root mean square of 0.879, and the cost difference between null cost and fixed cost was 44.46 bits. The model was cross-validated by randomizing the data using the CatScramble technique. The results confirmed that the pharmacophore models generated from the test set were not due to chance correlation. The best model (hypothesis 1) was validated using test set molecules (total of 78) and performed well in classifying active and inactive molecules correctly. The model was further validated by mapping onto it a diverse set of six CCR5 antagonists identified by five different pharmaceutical companies. The best model correctly predicted these compounds as being highly active. These multiple validation approaches provide confidence in the utility of the predictive pharmacophore model developed in this study as a 3D query tool in virtual screening to retrieve new chemical entities as potent CCR5 antagonists. The model can also be used in predicting biological activities of compounds prior to undertaking their costly synthesis.
The effect of selective and non‐selective phosphodiesterase inhibitors on allergen‐ and leukotriene C<sub>4</sub>‐induced contractions in passively sensitized human airways (2000)

Non-selective inhibitors of cyclic nucleotide phosphodiesterase (PDE) block allergen-induced contraction of passively sensitized human airways in vitro by a dual mechanism involving a direct relaxant effect on smooth muscle and inhibition of histamine and cysteinyl leukotriene (LT) release from airways. We investigated the effects of non-selective PDE inhibitors and selective inhibitors of PDE3 and PDE4 in order to determine the involvement of PDE isoenzymes in the suppression of allergic bronchoconstriction. Macroscopically normal airways from 76 patients were sensitized with IgE-rich sera (>250 u ml(-1)) containing specific antibodies against allergen (Dermatophagoides farinae). Contractile responses of bronchial rings were assessed using standard organ bath techniques. Passive sensitization caused increased contractile responses to allergen, histamine and LTC(4). Non-selective PDE inhibitors (theophylline, 3-isobutyl-1-methylxanthine [IBMX]), a PDE3-selective inhibitor (motapizone), PDE4-selective inhibitors (RP73401, rolipram, AWD 12-281) and a mixed PDE3/4 inhibitor (zardaverine) all significantly relaxed inherent bronchial tone at resting tension and to a similar degree. Theophylline, IBMX, zardaverine and the combination of motapizone and RP73401 inhibited the contractile responses to allergen and LTC(4). Pre-treatment with motapizone, RP73401, rolipram or the methylxanthine adenosine receptor antagonist, 8-phenyltheophylline, did not significantly decrease responses to either allergen or LTC(4). We conclude that combined inhibition of PDE3 and PDE4, but not selective inhibition of either isoenzyme or antagonism of adenosine receptors, is effective in suppressing allergen-induced contractions of passively sensitized human airways. The relationship between allergen- and LTC(4)-induced responses suggests that PDE inhibitors with PDE3 and PDE4 selectivity are likely to act in part through inhibition of mediator release and not simply through direct relaxant actions on airway smooth muscle.
Ductular reaction after submassive necrosis in humans. Special emphasis on analysis of ductular hepatocytes. (1996)

The ductular reaction to acute submassive necrosis was studied in human livers removed at the time of orthotopic liver transplantation. Single, double, and triple immunohistochemical labeling in combination with morphometry was used to analyze the phenotype and proliferative and apoptotic rates of various epithelial cell compartments. These were divided on the basis of immunohistochemistry and morphology into three subtypes: 1) CK19+/AE1+ mature bile duct epithelium, 2) HEP-PAR+ mature hepatocytes (HEPs), and 3) CK19+/AE1+ ductular hepatocyte (DH) cells lying at the interface between the portal tract connective tissue and the hepatic lobules. Cycling cells were defined as those showing Ki-67+ (MIB-1) nuclear labeling. Apoptotic cells were identified with in situ labeling using the terminal deoxynucleotidyl transferase-mediated dUTP-digoxigenin nick end labeling assay. Special emphasis was placed on DHs that appeared at the interface between the portal tracts and hepatic lobules. During the recovery phase from submassive hepatic necrosis, subtraction of the rate of cell death from the proliferative index shows that all of the epithelial compartments experience a net increase in the number of cells. The highest proliferation rate occurs in the DHs, which is significantly (P < 0.0001) higher than the proliferation rate seen in either the HEP or bile duct epithelium compartments. Immunohistochemical analysis of the highly proliferative DH compartment shows it to be a heterogeneous population with unique phenotypic features. Like epithelial cells in the ductal plate of fetal liver and cholangiocarcinomas, DHs are positioned on a laminin-rich matrix and focally express vimentin and Lewis(x) and show up-regulation of bcl-2 and type IV collagenase. However, unlike ductal plate cells, DHs are CD34 and alpha-fetoprotein negative. Although a subpopulation of DHs share phenotypic features with mature bile duct epithelium (AE1/cytokeratin 19 and type IV collagenase positive) or HEP (HEP-PAR, albumin, and alpha-1-antitrypsin positive), they are also clearly separate from both populations; DHs are negative or only weakly stain for glutathione-S-transferase-pi and are type IV collagenase positive. Moreover, occasional DHs also co-expressed HEP-PAR or alpha-1-antitrypsin and AE1, indicative of both hepatocyte and ductular differentiation. These findings suggest that DHs seen in human livers after submassive necrosis may represent a transient amplifying population arising from a progenitor population located in or near the canals of Herring. In addition, injured hepatocytes can express cytokeratin 19 and AE1, which normally are biliary intermediate filaments.