gebhart/patrepeval huggingface dataset:
ATP‐ and glutathione‐dependent transport of chemotherapeutic drugs by the multidrug resistance protein MRP1 (1999)

The present study was performed to investigate the ability of the multidrug resistance protein (MRPI) to transport different cationic substrates in comparison with MDR1-P-glycoprotein (MDR1). Transport studies were performed with isolated membrane vesicles from in vitro selected multidrug resistant cell lines overexpressing MDR1 (A2780AD) or MRP1 (GLC4/Adr) and a MRP1-transfected cell line (S1(MRP)). As substrates we used 3H-labelled derivatives of the hydrophilic monoquaternary cation N-(4',4'-azo-in-pentyl)-21-deoxy-ajmalinium (APDA), the basic drug vincristine and the more hydrophobic basic drug daunorubicin. All three are known MDR1-substrates. MRP1 did not mediate transport of these substrates per se. In the presence of reduced glutathione (GSH), there was an ATP-dependent uptake of vincristine and daunorubicin, but not of APDA, into GLC4/Adr and S1(MRP) membrane vesicles which could be inhibited by the MRP1-inhibitor MK571. ATP- and GSH-dependent transport of daunorubicin and vincristine into GLC4/Adr membrane vesicles was inhibited by the MRP1-specific monoclonal antibody QCRL-3. MRP1-mediated daunorubicin transport rates were dependent on the concentration of GSH and were maximal at concentrations > or = 10 mM. The apparent KM value for GSH was 2.7 mM. Transport of daunorubicin in the presence of 10 mM GSH was inhibited by MK571 with an IC50 of 0.4 microM. In conclusion, these results demonstrate that MRP1 transports vincristine and daunorubicin in an ATP- and GSH-dependent manner. APDA is not a substrate for MRP1.
A β‐glucosidase gene (<i>bgl3</i>) from <i>Streptomyces</i> sp. strain QM‐B814 (1994)

A beta-glucosidase gene (bgl3) from Streptomyces sp. QM-B814 (American Type Culture Collection 11238) has been cloned by functional complementation of a beta-glucosidase-negative mutant of Streptomyces lividans. An open-reading frame of 1440 nucleotides encoding a polypeptide of 479 amino acids was found by sequencing. The encoded protein (Bgl3) shows extensive similarity (over 45% identity) with beta-glycosidases from family-1 glycosyl hydrolases. The cloned enzyme, purified following ammonium sulphate precipitation and two chromatographic steps, is monomeric with molecular mass 52.6 kDa, as determined by mass spectrometry, and an isoelectric point of pI 4.4. The enzyme appears to be a beta-glucosidase with broad substrate specificity, is active on cellooligomers, and performs transglycosylation reactions. The estimated apparent Km values for p-nitrophenyl-beta-D-glucopyranoside and cellobiose are 0.27 mM and 7.9 mM, respectively. The Ki values for glucose and delta-gluconolactone, using p-nitrophenyl-beta-D-glucopyranoside as a substrate, are 65 mM and 0.08 mM, respectively. The purified enzyme has a pH optimum of pH 6.5 and the temperature optimum for activity is 50 degrees C.
Volatile Metabolites of Pathogens: A Systematic Review (2013)

Ideally, invading bacteria are detected as early as possible in critically ill patients: the strain of morbific pathogens is identified rapidly, and antimicrobial sensitivity is known well before the start of new antimicrobial therapy. Bacteria have a distinct metabolism, part of which results in the production of bacteria-specific volatile organic compounds (VOCs), which might be used for diagnostic purposes. Volatile metabolites can be investigated directly in exhaled air, allowing for noninvasive monitoring. The aim of this review is to provide an overview of VOCs produced by the six most abundant and pathogenic bacteria in sepsis, including Staphylococcus aureus, Streptococcus pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli. Such VOCs could be used as biological markers in the diagnostic approach of critically ill patients. A systematic review of existing literature revealed 31 articles. All six bacteria of interest produce isopentanol, formaldehyde, methyl mercaptan, and trimethylamine. Since humans do not produce these VOCs, they could serve as biological markers for presence of these pathogens. The following volatile biomarkers were found for identification of specific strains: isovaleric acid and 2-methyl-butanal for Staphylococcus aureus; 1-undecene, 2,4-dimethyl-1-heptane, 2-butanone, 4-methyl-quinazoline, hydrogen cyanide, and methyl thiocyanide for Pseudomonas aeruginosa; and methanol, pentanol, ethyl acetate, and indole for Escherichia coli. Notably, several factors that may effect VOC production were not controlled for, including used culture media, bacterial growth phase, and genomic variation within bacterial strains. In conclusion, VOCs produced by bacteria may serve as biological markers for their presence. Goal-targeted studies should be performed to identify potential sets of volatile biological markers and evaluate the diagnostic accuracy of these markers in critically ill patients.
Pathways in the formation of human plasma high density lipoprotein subpopulations containing apolipoprotein A-I without apolipoprotein A-II. (1987)

The lecithin:cholesterol acyltransferase (LCAT)-induced transformation of two discrete species of model complexes that differ in number of apolipoprotein A-I (apoA-I) molecules per particle was investigated. One complex species (designated 3A-I(UC)-complexes) contained 3 apoA-I per particle, was discoidal (13.5 X 4.4 nm), and had a molar composition of 22:78:1 (unesterified cholesterol (UC):egg yolk phosphatidylcholine (egg yolk PC):apoA-I). The other complex species (designated 2A-I(UC)complexes) containing 2 apoA-I per particle was also discoidal (8.4 X 4.1 nm) and had a molar composition of 6:40:1. Transformation of 3A-I(UC)complexes by partially purified LCAT yielded a product (24 hr, 37 degrees C) with a cholesteryl ester (CE) core, 3 apoA-I, and a mean diameter of 9.2 nm. The 2A-I(UC)complexes were only partially transformed to a core-containing product (24 hr, 37 degrees C) which also had 3 apoA-I; this product, however, was smaller (diameter of 8.5 nm) than the product from 3A-I(UC)complexes. Transformation of 3A-I(UC)complexes appeared to result from build-up of core CE directly within the precursor complex. Transformation of 2A-I(UC)complexes, however, followed a stepwise pathway to the product with 3 apoA-I, apparently involving fusion of transforming precursors and release of one apoA-I from the fusion product. In the presence of low density lipoprotein (LDL), used as a source of additional cholesterol, conversion of 2A-I(UC)complexes to the product with 3 apoA-I was more extensive. The transformation product of 3A-I(UC)complexes in the presence of LDL also had 3 apoA-I but was considerably smaller in size (8.6 vs. 9.2 nm, diameter) and had a twofold lower molar content of PC compared with the product formed without LDL. LDL appeared to act both as a donor of UC and an acceptor of PC. Transformation products with 3 apoA-I obtained under the various experimental conditions in the present studies appear to be constrained in core CE content (between 13 to 22 CE per apoA-I; range of 9 CE molecules) but relatively flexible in content of surface PC molecules they can accommodate (between 24 to 49 PC per apoA-I; range of 25 PC molecules). The properties of the core-containing products with 3 apoA-I compare closely with those of the major subpopulation of human plasma HDL in the size range of 8.2-8.8 nm that contains the molecular weight equivalent of 3 apoA-I molecules.
The new voltage gated potassium channel KCNQ5 and neonatal convulsions (2000)

In 1998, mutations in the voltage gated potassium channel gene KCNQ2 were found to be the main cause underlying the autosomal dominant inherited syndrome of benign familial neonatal convulsions (BFNC). In one BFNC family a mutation was found in an homologous gene, KCNQ3. We have now identified another brain-expressed member of this ion channel subfamily, KCNQ5, which maps to chromosome 6q14. On the genomic level KCNQ5 is composed of 14 exons, which are coding for 897 amino acid residues. Mutation analysis made KCNQ5 unlikely as a candidate gene for benign neonatal convulsions in patients with a positive family history for neonatal or early infantile seizures, but without mutations in the KCNQ2 or KCNQ3 genes.
Histology does not influence prognosis in differentiated thyroid carcinoma when accounting for age, tumour diameter, invasive growth and metastases (2009)

There is no difference in tumour-specific survival between PTC and FTC when accounting for the presence of metastases, age, tumour size and the presence of extrathyroidal invasion.
The Design and Synthesis of Bis(thiourea) Ligands and Their Application in Pd‐Catalyzed Heck and Suzuki Reactions Under Aerobic Conditions (2005)

Abstract New, bulky N , N ‐disubstituted acyclic and cyclic bis(thiourea) ligands have been designed and synthesized. Their palladium(0) complexes are very stable and are active catalysts for Heck and Suzuki coupling reactions of aryl iodides and bromides under aerobic conditions. Good TONs and TOFs were achieved in the coupling reactions [for PhI, TONs up to 1000000 and TOFs up to 200000 (h –1 ); for activated aryl bromide, TONs up to 89000]. In addition, further studies were conducted to know more about the nature of these catalysts. The active catalyst was found to be the chelate complex containing the bis(thiourea) and Pd in a 1:1 ratio. However, unlike a monothiourea, further coordination can occur to give a coordinatively saturated complex when bis(thiourea) and Pd are combined in a 2:1 ratio; this complex is catalytically inactive in coupling reactions. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
[Acupuncture for treatment of depressive neurosis: a multi-center randomized controlled study]. (2008)

Acupuncture is an effective and safe therapy for depressive neurosis; therapeutic effect of acupuncture on depressive neurosis possibly is better than or similar to that of Prozac, but with less side-effects.
Ceramics Via Polymer Pyrolysis (1984)

▪ Abstract The phase-field method has recently emerged as a powerful computational approach to modeling and predicting mesoscale morphological and microstructure evolution in materials. It describes a microstructure using a set of conserved and ...Read More
Comparison of dorsal and ventral spinal root regeneration through semipermeable guidance channels (1991)

Semipermeable guidance channels have been shown to support nerve regeneration in the peripheral nervous system (PNS) possibly through interactions with the wound healing environment. This study quantitatively assesses the ability of such channels to support regeneration in the PNS segment of the spinal roots across a 4 mm gap and compares the resultant dorsal and ventral root regeneration. Acrylic copolymer guidance channels with a molecular weight (Mw) cutoff of 50,000 Da were used in a transected rat spinal root model. Cohorts of 23 animals (11 ventral, 12 dorsal) were examined at four weeks; 6 animals (3 ventral, 3 dorsal) at ten weeks; and 10 animals (5 ventral, 5 dorsal) at twenty-four weeks post-implantation. Both the dorsal and ventral roots were able to regenerate across the gap within the semipermeable channel. At all time periods, the regenerated dorsal roots contained fewer myelinated axons than found in the contralateral control root and consisted of an abundance of collagenous tissue. In contrast, by ten weeks the regenerated ventral roots contained twice the contralateral control number of myelinated axons and were composed predominantly of large, myelinated axons. At twenty-four weeks the number of unmyelinated axons was also quantified, with the regenerated dorsal root containing only one-fifth of the control number and the regenerated ventral root containing more than four times the control. Due to the proximity of the dorsal root lesion to the axonal cell bodies, the dorsal root ganglion (DRG) neuronal cell loss was investigated at four weeks post-implantation.(ABSTRACT TRUNCATED AT 250 WORDS)
The Factorized Multi-Carrier Ambiguity Resolution (FAMCAR) Approach for Efficient Carrier-Phase Ambiguity Estimation (2004)

The proposed addition of a third carrier to the modernized GPS as well as the implementation of three carriers in the planned Galileo system will boost the performance of carrier-phase based positioning within the next decade. In principle, highly-reliable instantaneous (one-epoch) ambiguity resolution becomes feasible for a broad range of applications. Beyond the system level developments - regarding the frequency allocation and signal structure - the proposal of three and four carrier frequencies enables new approaches at the processing level. The Factorized Multi-Carrier Ambiguity Resolution (FAMCAR) algorithm introduces a number of new independent linear combinations of carrier-phase observations as well as of carrier-phase and pseudo-range observations. The combinations include the minimumerror geometric carrier-phase combination, the minimumerror ionosphere combination, the new Quintessence combinations and the code-carrier combinations. From these individual estimates, the full floating solution for all carriers is derived. This paper provides a detailed derivation of the approach and the statistical properties of these new linear combinations. Existing standard techniques for multi-carrier ambiguity determination usually apply one big Kalman filter to estimate all unknowns (e.g. position, ambiguities, ionosphere and multipath). The factorization enables the stepwise modeling of each error component and leads therefore to a bank of significantly smaller filters. This approach results in distinct higher computational efficiency for the Kalman filter sets (i.e. float solution) und a better knowledge of each error component for the individual measurements. In addition to the efficient processing of three and four carrier data the new approach is already applicable to a dual-frequency system. Furthermore the decreased computational load enables the use of smaller processor components and therefore provides a significant cost reduction.
Detecting and segmenting objects for mobile manipulation (2009)

This paper proposes a novel 3D scene interpretation approach for robots in mobile manipulation scenarios using a set of 3D point features (Fast Point Feature Histograms) and probabilistic graphical methods (Conditional Random Fields). Our system uses real time stereo with textured light to obtain dense depth maps in the robot's manipulators working space. For the purposes of manipulation, we want to interpret the planar supporting surfaces of the scene, recognize and segment the object classes into their primitive parts in 6 degrees of freedom (6DOF) so that the robot knows what it is attempting to use and where it may be handled. The scene interpretation algorithm uses a two-layer classification scheme: (i) we estimate Fast Point Feature Histograms (FPFH) as local 3D point features to segment the objects of interest into geometric primitives; and (ii) we learn and categorize object classes using a novel Global Fast Point Feature Histogram (GFPFH) scheme which uses the previously estimated primitives at each point. To show the validity of our approach, we analyze the proposed system for the problem of recognizing the object class of 20 objects in 500 table settings scenarios. Our algorithm identifies the planar surfaces, decomposes the scene and objects into geometric primitives with 98.27% accuracy and uses the geometric primitives to identify the object's class with an accuracy of 96.69%.
Two strategies for advanced nitrogen elimination in vertical flow constructed wetlands (1997)

Since 1991 the institute for water provision has run two vertical flow constructed wetlands for domestic wastewater treatment at two farm houses (8 p.e.) in Upper Austria. The systems are designed for elimination of organic compounds and for nitrification which was no problem even under winter conditions. In 1995 two methods were tested to achieve denitrification also in both systems. System A is a one-stage system, system B has two stages operated in series. The approach to the one-stage system consisted in pumping a part of the nitrified effluent from the soil filter back to the settling tank of the influent, where the raw wastewater mixes with the nitrified effluent-water. The approach to the two-stage system B consisted in adding an external carbon source (methanol) into the second, water saturated stage. The research was undertaken during several experimental stages to test the influence of the recirculation ratio (system A) respectively of the feeding (system B; intermittent, continuous, batch). The highest elimination rates could be achieved with system B (dosage of methanol) during experimental stage 1 (intermittent loading four times a day). The mean elimination rates were 82% for Ninorg and 78% for TN. The TN elimination performance of system A was only a little lower (72%). The elimination of COD, BOD5 and TOC was no problem throughout the whole experimental period (effluent concentrations of both systems were well below the Austrian standards).
Two‐dimensional RPLC‐RPLC system with different pH in two dimensions for separation of alkaloids from <i>Corydalis yanhusuo </i>W. T. Wang (2009)

An effective method utilizing the same RP chromatographic column with different pH in first and second LC dimensions has been developed for separation of the basic compounds from traditional Chinese medicines (TCMs). In this work, the alkaloids in Corydalis yanhusuo which is an important TCM were selected as a model to develop the method. The additives and pH values of the mobile phase were optimized in this work. To investigate the feasibility of this method, off-line mode separation was performed in the experiments. According to the UV-absorption intensity, there were eight fractions collected in acidic conditions. All the fractions were analyzed in basic conditions. The results showed that the chromatographic selectivities were significantly different in the separations performed with acidic and alkaline elution systems. Complementary separation was achieved in this work. It is demonstrated that this method would be an effective tool for alkaloids research. Based on the different pH of the mobile phase in this method, it could also be suitable to analyze compounds which were sensible to the pH of the solution.
Histamine and Cytokine Therapy: Paper presented at the annual meeting of the Swedish Oncology Society, Stockholm, 1997 (1998)

Interleukin-2 (IL-2) and interferon-alpha (IFN-alpha) are potent activators of natural killer (NK) cells and other anti-tumor effector cells, but the results obtained in clinical trials with these cytokines have proved disappointing in many forms of cancer. It may be that IL-2 and IFN-alpha are often not sufficiently effective because intratumoral monocytes/macrophages (MO) inhibit the cytokine-induced activation of cytotoxic effector lymphocytes such as NK-cells at the site of tumor growth. An essential part of this inhibitory signal is conveyed by MO-derived reactive oxygen species (ROS), which potently inhibit NK-cell-related functions, including the constitutive and cytokine-induced cytotoxicity against tumor cells. Histamine, a biogenic amine, inhibits ROS formation in MO; thereby, histamine synergizes with IL-2 and with IFN-alpha to induce killing of NK-cell-sensitive human tumor cells in vitro. Furthermore, treatment of tumor-bearing mice with histamine potentiates cytokine-induced killing of NK-cell-sensitive murine tumor cells in vivo. In ongoing clinical trials, histamine has been added to IL-2 or IFN-alpha in immunotherapy of human neoplastic disease. The results of two pilot trials in metastatic melanoma suggest that the addition of histamine to IL-2/IFN-alpha prolongs survival time and induces regression of tumors, such as liver melanoma, which are considered refractory to immunotherapy with IL-2 or IFN-alpha. In acute myelogenous leukemia (AML), histamine and IL-2 have been given in order to protect patients in remission against relapse of leukemic disease. The potential benefit of histamine therapy in melanoma and AML will be evaluated in randomized trials.
Enhancing the affinity of SEB‐binding peptides by repeating their sequence (2011)

The utilization of peptide ligands in biosensors and bioassays is dependent on achieving high affinity of these peptides toward their targets. In a previous report, we identified 12-mer peptides that could selectively bind to Staphylococcal enterotoxin B (SEB) using a phage-display library. In this study, we explore for new modification approaches to enhance the affinity of two different SEB-binding peptides. In order to identify the binding regions of selected peptides, the charged residues and the ones, critical for the structure of peptide, were replaced with alanine. However, a specific binding region could not be suggested as all mutant peptides have lost their affinities toward SEB completely. The modifications for the affinity enhancement were done by repeating the 12-mer peptide sequences. A 10-fold increase was observed in the binding affinity of one of the two-repeated peptides, while this modification did not affect the affinity of the other tested peptide. The peptide, with enhanced affinity, was further modified as three repeats; however the affinity of the peptide decreased. The structural basis of the affinity difference between modified peptides was examined by molecular dynamics simulation. The results showed that the conformational differences hold the key for affinity of peptides modified by repeating the sequence. This high affinity peptide with increased affinity is a promising molecular recognition agent to be used in the detection of SEB to be utilized in biosensing systems.
ChemInform Abstract: γ‐AApeptides as a New Class of Peptidomimetics (2016)

Abstract Review: research outcomes of γ‐AApeptides and a future perspective; 26 refs.
Interactive editing tools for image-based rendering systems (1998)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and, Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1998.
<i>In vitro</i>, <i>in vivo</i> and <i>ex vivo</i> characterization of ibrutinib: a potent inhibitor of the efflux function of the transporter <scp>MRP1</scp> (2014)

Our results indicated that ibrutinib significantly increased the efficacy of the chemotherapeutic agents which were MRP1 substrates, in MRP1-overexpressing cells, in vitro, in vivo and ex vivo. These findings will lead to further studies on the effects of a combination of ibrutinib with chemotherapeutic agents in cancer patients overexpressing MRP1.
Differential Contributions of<i>BRCA1</i>and<i>BRCA2</i>to Early-Onset Breast Cancer (1997)

Germ-line mutations in BRCA2 contribute to fewer cases of breast cancer among young women than do mutations in BRCA1. Carriers of BRCA2 mutations may have a smaller increase in the risk of early-onset breast cancer.