gebhart/patrepeval huggingface dataset:
Osimertinib (AZD9291), a Mutant-Selective EGFR Inhibitor, Reverses ABCB1-Mediated Drug Resistance in Cancer Cells (2016)

In recent years, tyrosine kinase inhibitors (TKIs) have been shown capable of inhibiting the ATP-binding cassette (ABC) transporter-mediated multidrug resistance (MDR). In this study, we determine whether osimertinib, a novel selective, irreversible EGFR (epidermal growth factor receptor) TKI, could reverse ABC transporter-mediated MDR. The results showed that, at non-toxic concentrations, osimertinib significantly sensitized both ABCB1-transfected and drug-selected cell lines to substrate anticancer drugs colchicine, paclitaxel, and vincristine. Osimertinib significantly increased the accumulation of [³H]-paclitaxel in ABCB1 overexpressing cells by blocking the efflux function of ABCB1 transporter. In contrast, no significant alteration in the expression levels and localization pattern of ABCB1 was observed when ABCB1 overexpressing cells were exposed to 0.3 µM osimertinib for 72 h. In addition, ATPase assay showed osimertinib stimulated ABCB1 ATPase activity. Molecular docking and molecular dynamic simulations showed osimertinib has strong and stable interactions at the transmembrane domain of human homology ABCB1. Taken together, our findings suggest that osimertinib, a clinically-approved third-generation EGFR TKI, can reverse ABCB1-mediated MDR, which supports the combination therapy with osimertinib and ABCB1 substrates may potentially be a novel therapeutic stategy in ABCB1-positive drug resistant cancers.
Fast mode decision algorithm for intraprediction in H.264/AVC video coding (2005)

The H.264/AVC video coding standard aims to enable significantly improved compression performance compared to all existing video coding standards. In order to achieve this, a robust rate-distortion optimization (RDO) technique is employed to select the best coding mode and reference frame for each macroblock. As a result, the complexity and computation load increase drastically. This paper presents a fast mode decision algorithm for H.264/AVC intraprediction based on local edge information. Prior to intraprediction, an edge map is created and a local edge direction histogram is then established for each subblock. Based on the distribution of the edge direction histogram, only a small part of intraprediction modes are chosen for RDO calculation. Experimental results show that the fast intraprediction mode decision scheme increases the speed of intracoding significantly with negligible loss of peak signal-to-noise ratio.
Granulocyte colony-stimulating factor after allogeneic bone marrow transplantation (1994)

Hematopoietic growth factors have been shown to be effective in reducing the period of neutropenia after autologous bone marrow transplantation (BMT). Initial concerns over potential aggravation of graft-versus-host disease (GVHD) and increase in the incidence of relapse in patients with myeloid leukemias influenced the number of studies using hematopoietic growth factors after allogeneic BMT. We report the experience with 50 patients treated at a single institution using granulocyte colony-stimulating factor (G-CSF) after allogeneic sibling (n = 30) and matched unrelated (n = 20) BMT. The time to an absolute neutrophil count > or = 500/microL was significantly faster in patients who received G-CSF and cyclosporine and prednisone for GVHD prophylaxis when compared with historical control patients receiving the same GVHD prophylaxis (10 v 13 days, P < .01). A similar accelerated myeloid engraftment was observed for those patients who received the addition of methotrexate for GVHD prophylaxis when compared with historical control patients receiving the same GVHD prophylaxis regimen (16 v 19 days, P < .05). The median time to engraftment for patients receiving a matched unrelated BMT and G-CSF was 17 days (range 13 to 26). We did not observe any increase in GVHD or early mortality in the matched related sibling BMT. The incidence of acute GVHD in the matched unrelated BMT recipients was also low at 21%; however, 9 patients (45%) died within 100 days of the date of BMT, similar to the experience reported with granulocyte-macrophage CSF. This study confirms the efficacy of G-CSF in accelerating myeloid engraftment after allogeneic matched sibling BMT. The higher early mortality associated with patients receiving matched unrelated BMT suggests that randomized controlled trials using G-CSF after allogeneic BMT should be performed.
Lactams. IX. Generation of lactam carbonyl function in 1,3-disubstituted piperidines by mercuric acetate-EDTA oxidation: Effects of hydrocarbon substituents at the 3-position. (1977)

The mercuric acetate-(ethylenedinitrilo) tetraacetic acid oxidation of 1-(3,4-dimethoxyphenyl)-2-(3-substituted piperidino) ethanols (7c-f), which carry the n-butyl, isopropyl, benzyl, and phenyl group as the 3-substituent in the piperidine ring, has been found to produce the corresponding 2- (8c-f) and 6-piperidones (12c-f) in good yields in ratios of 41 : 59,29 : 71,26 : 74,and 15 : 85. It is suggested that the 3-substituents exert both steric and electronic effects. The structures of the lactam alcohols (8c-f, 12c-f) have been confirmed by the chemical correlation with the known pyridones (11c-f, 15c-f) through the lactams (10c-f, 14c-f). The starting piperidinoethanols (7c-f) have been synthesized from the 3-substituted pyridines (5c-f) by quaternization with 3,4-dimethoxyphenacyl bromide followed by catalytic and sodium borohydride reductions.
Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition in vitro and identifies 2,4‐pyridine‐dicarboxylic acid as an in vitro and in cell inhibitor (2012)

Dynamic methylations and demethylations of histone lysine residues are important for gene regulation and are facilitated by histone methyltransferases and histone demethylases (HDMs). KDM5B/Jarid1B/PLU1 is an H3K4me3/me2-specific lysine demethylase belonging to the JmjC domain-containing family of histone demethylases (JHDMs). Several studies have linked KDM5B to breast, prostate and skin cancer, highlighting its potential as a drug target. However, most inhibitor studies have focused on other JHDMs, and inhibitors for KDM5B remain to be explored. Here, we report the expression, purification and characterization of the catalytic core of recombinant KDM5B (ccKDM5B, residues 1-769). We show that ccKDM5B, recombinantly expressed in insect cells, demethylates H3K4me3 and H3K4me2 in vitro. The kinetic characterization showed that ccKDM5B has an apparent Michaelis constant (K(m) (app) ) value of 0.5 μm for its trimethylated substrate H3(1-15)K4me3, a considerably increased apparent substrate affinity than reported for related HDMs. Despite the presence of a PHD domain, the catalytic activity was not affected by additional methylation at the H3K9 position, suggesting that in vitro chromatin cross-talk between H3K4 and H3K9 does not occur for ccKDM5B. Inhibition studies of ccKDM5B showed both in vitro and in cell inhibition of ccKDM5B by 2,4-pyridinedicarboxylic acid (2,4-PDCA) with a potency similar to that reported for the HDM KDM4C. Structure-guided sequence alignment indicated that the binding mode of 2,4-PDCA is conserved between KDM4A/C and KDM5B.
A relationship between the charge capacity and the hardness of neutral atoms and groups (1987)

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Leaf Area Index Estimation Using Chinese GF-1 Wide Field View Data in an Agriculture Region (2017)

Leaf area index (LAI) is an important vegetation parameter that characterizes leaf density and canopy structure, and plays an important role in global change study, land surface process simulation and agriculture monitoring. The wide field view (WFV) sensor on board the Chinese GF-1 satellite can acquire multi-spectral data with decametric spatial resolution, high temporal resolution and wide coverage, which are valuable data sources for dynamic monitoring of LAI. Therefore, an automatic LAI estimation algorithm for GF-1 WFV data was developed based on the radiative transfer model and LAI estimation accuracy of the developed algorithm was assessed in an agriculture region with maize as the dominated crop type. The radiative transfer model was firstly used to simulate the physical relationship between canopy reflectance and LAI under different soil and vegetation conditions, and then the training sample dataset was formed. Then, neural networks (NNs) were used to develop the LAI estimation algorithm using the training sample dataset. Green, red and near-infrared band reflectances of GF-1 WFV data were used as the input variables of the NNs, as well as the corresponding LAI was the output variable. The validation results using field LAI measurements in the agriculture region indicated that the LAI estimation algorithm could achieve satisfactory results (such as R² = 0.818, RMSE = 0.50). In addition, the developed LAI estimation algorithm had potential to operationally generate LAI datasets using GF-1 WFV land surface reflectance data, which could provide high spatial and temporal resolution LAI data for agriculture, ecosystem and environmental management researches.
Estimating sample sizes for binary, ordered categorical, and continuous outcomes in two group comparisons (1995)

Sample size calculations are now mandatory for many research protocols, but the ones useful in common situations are not all easily accessible. This paper outlines the ways of calculating sample sizes in two group studies for binary, ordered categorical, and continuous outcomes. Formulas and worked examples are given. Maximum power is usually achieved by having equal numbers in the two groups. However, this is not always possible and calculations for unequal group sizes are given.
A Phosphatidylinositol 3-Kinase-dependent Pathway That Differentially Regulates c-Raf and A-Raf (1999)

Cytokines trigger the rapid assembly of multimolecular signaling complexes that direct the activation of downstream protein kinase cascades. Two protein kinases that have been linked to growth factor-regulated proliferation and survival are mitogen-activated protein/ERK kinase (MEK) and its downstream target Erk, a member of the mitogen-activated protein kinase family. Using complementary pharmacological and genetic approaches, we demonstrate that MEK and Erk activation requires a phosphatidylinositol 3-kinase (PI3-K)-generated signal in an interleukin (IL)-3-dependent myeloid progenitor cell line. Analysis of the upstream pathway leading to MEK activation revealed that inhibition of PI3-K did not block c-Raf activation, whereas MEK activation was effectively blocked under these conditions. Furthermore, agents that elevated cAMP suppressed IL-3-induced c-Raf activation but did not inhibit MEK activation. Because c-Raf activation and MEK activation were inversely affected by PI3-K- and cAMP-dependent pathways, we examined whether IL-3 activated the alternative Raf isoforms A-Raf and B-Raf. Although IL-3 did not activate B-Raf, A-Raf was activated by the cytokine. Moreover, A-Raf activation, like MEK activation, was blocked by inhibition of PI3-K but was insensitive to cAMP. Experiments with dominant negative mutants of the Raf isoforms showed that overexpression of dominant negative c-Raf did not prevent MEK activation. However, dominant negative A-Raf effectively blocked MEK activation, suggesting that activation of the MEK-Erk signaling cascade is mediated through A-Raf. Taken together, these results suggest that IL-3 receptors engage and activate both c-Raf and A-Raf in hemopoietic cells. However, these intermediates are differentially regulated by upstream signaling cascades and selectively coupled to downstream signaling pathways.
Immunochemical characterization of two surface polysaccharides of Bacteroides fragilis (1991)

Immunochemical analysis of the capsular polysaccharide from Bacteroides fragilis NCTC 9343 revealed a novel structure composed of two distinct polysaccharides. Immunoelectrophoresis of an extract of purified surface polysaccharide from fermenter-grown organisms showed a complex precipitin profile with varying anodal mobility. DEAE-Sephacel anion-exchange chromatography of the polysaccharide extract failed to separate the majority of this aggregate. Disaggregation of this complex was accomplished by very mild acid treatment; purification was achieved by DEAE-Sephacel anion-exchange chromatography. Polysaccharide A had a neutral charge at pH 7.3, a net negative charge at pH 8.6, and an average Mr = 110,000; chemical analysis showed it to contain galactose, galactosamine, and an unidentified amino sugar. Polysaccharide B eluted from the anion-exchange column with increased salt concentration; it had a net negative charge and an average Mr = 200,000, and contained fucose, galactose, quinovosamine, galacturonic acid, and glucosamine. Neither of these polysaccharides contained detectable 3-deoxy-D-manno-octolusonic acid, and both were recognized as distinct antigens on the basis of their reactivity with monoclonal antibodies CE3 and F10, which reacted with the complex before acid treatment. These data indicate that the capsule of B. fragilis NCTC 9343 comprises two discrete, surface-exposed polysaccharides with differing physiochemical properties that are distinct from the lipopolysaccharide of this organism. The finding of two surface polysaccharides has not been described for other bacteria pathogenic to humans.
Increased cell-substratum adhesion, and decreased gelatinase secretion and cell growth, induced by E-cadherin transfection of human colon carcinoma cells. (1995)

Metastasis of colon carcinomas is assumed to be caused by multiple steps, which include a loss of cell adhesion that results in the release of carcinoma cells from the original tumor tissue. A human colon carcinoma cell line COKFu was established from a poorly differentiated metastatic adenocarcinoma without cell-cell adhesion and without expression of E-cadherin mRNA and protein. This cell line was co-transfected with mouse E-cadherin cDNA in an expression vector and a neomycin-resistant gene. The parental carcinoma cells had a spindle shape and were scattered, whereas the transfected cells, which expressed exogenous E-cadherin gene, showed a more compact shape with strong cell-cell adhesion and with increased adhesiveness to collagen gel. These cells showed a significantly low anchorage independency (2-7%) and decreased invasiveness (30%) compared to the parental cells. Growth rate of transfectants was decreased both in vitro and in the subcutis of nude mice, with decreased lymphnode metastasis in the case of intravenous injection. It was additionally found that activity of 62 kd gelatinase, secreted from parental cells, was lost or decreased in E-cadherin-transfected cells. These results suggest that E-cadherin is not only involved in the cell-cell adhesion of colon carcinomas, it also has a wider effect, including cell-substratum adhesion and the regulation of proteinase secretion from the cells, resulting in partial suppression of invasiveness and tumorigenic growth.
A general transesterification method for the synthesis of mixed trialkyl phosphates (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA general transesterification method for the synthesis of mixed trialkyl phosphatesKelvin K. Ogilvie, Serge L. Beaucage, Nicole Theriault, and Douglas W. EntwistleCite this: J. Am. Chem. Soc. 1977, 99, 4, 1277–1278Publication Date (Print):February 1, 1977Publication History Published online1 May 2002Published inissue 1 February 1977https://pubs.acs.org/doi/10.1021/ja00446a057https://doi.org/10.1021/ja00446a057research-articleACS PublicationsRequest reuse permissionsArticle Views312Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Dermal regeneration in full‐thickness wounds in Yucatan miniature pigs using a biodegradable copolymer (1998)

The aim of this study was to assess the performance of a biodegradable dermal substrate in deep dermal skin defects. The substrate consisted of a synthetic biodegradable matrix called Polyactive, which is an elastomeric poly (ether)/ poly (ester) block copolymer. This matrix was manufactured either as a porous substrate, with gradually changing pore size (BISKIN-M), or as a bilayer consisting of a porous underlayer with a fully dense surface layer (BISKIN). Cell-free matrices and matrices seeded with autologous or allogeneic porcine fibroblasts were applied to full-thickness skin wounds in Yucatan miniature pigs. Biopsies were taken at different time intervals up to 24-months post-transplantation. Although all BISKIN substrates showed little or no adherence to the wound bed, the adherence of the BISKIN-M substrates to the underlying wound was achieved within minutes after application. Therefore, only BISKIN-M Polyactive substrates were further evaluated. Wound contraction was inhibited by both cell-free and fibroblast-populated substrates. All substrates showed extensive neovascular and fibrous tissue ingrowth within 2-weeks post-transplantation. Furthermore, during this time period, matrix degradation was observed, starting with the fragmentation of the polymers into particles, which were phagocytized by macrophages. These processes occurred actively up to 3 months and ceased thereafter. Cell-free substrates degraded faster, and also, the collagen deposition was lower as compared with cell-seeded substrates. The tissue surrounding the remnants of the Polyactive substrates after 24-months post-transplantation consisted of a mature connective tissue. The newly formed collagen had the same distribution pattern as observed in normal native dermis. We conclude therefore that treatment of full-thickness skin defects with fibroblast-populated BISKIN-M Polyactive substrates leads to satisfactory dermal regeneration.
Activity of immunotoxins constructed with modified Pseudomonas exotoxin A lacking the cell recognition domain. (1988)

Pseudomonas exotoxin (PE) contains three domains whose functions are cell recognition, membrane translocation, and ADP ribosylation of elongation factor 2. PE40 is a form of PE which is missing the cell recognition domain. To study the properties of PE40, it was expressed in Escherichia coli using a vector which contains a T7 phage promoter, an OmpA signal sequence, and that portion of the PE gene encoding PE40. Upon induction with isopropyl-1-thio-beta-D-galactopyranoside, large amounts of PE40 were secreted, and highly purified PE40 was prepared from the culture medium. PE40 was chemically coupled to different monoclonal antibodies, and protein synthesis inhibition activities of these immunotoxins was assessed on various cell lines. These activities were compared with the activities of the corresponding immunotoxins made with native PE. These data indicate that PE40 may be useful in the construction of certain immunotoxins.
Prolonged in Vivo Residence Times of Antibody Fragments Associated with Albumin (2001)

Antibody fragments can be expressed at a high level in microbial systems, but they may have limited therapeutic value because they are rapidly eliminated from the body. We demonstrate here that site-specific conjugation or binding of bacterially derived Fab' to the long-lived protein serum albumin allows full retention of the antibody's binding characteristics while imparting the albumin's longevity in vivo. In rats the area under the curve for Fab' conjugated to rat serum albumin was 17-fold greater than for the control of Fab' conjugated to cysteine. Again, a bispecific F(ab')(2) with specificity for rat serum albumin showed an area under the curve about 8-fold greater than did a F(ab')(2) without specificity to albumin. Genetic fusions of scFv to albumin were similarly long-lived and could be expressed in yeast to provide the basis of a cost-effective production system.
Experimental verification and characterization of sub-harmonic traveling wave on an ultrasonic micromotor (2010)

In this paper, we studied the nonlinear subharmonic traveling resonant modes which generate the rotational motion on the surface-macromachined ultrasonic micromotors. Actuated by a die-attached PZT plate, when the resonant frequency of the one of the stator's vibration mode is close to PZT plate's thickness mode resonance (~4.2MHz), rotating wave is generated on the stator. Driven at 3.78MHz, the rotating wave on the stator with 820μm diameter is optically detected and spatially characterized with an optical microscope. Together with laser interferometer measurements, two subharmonic modes are obtained, (1, 13) traveling mode at 1.78MHz and (0, 20) standing mode at 2MHz. The experimental results are further verified with finite element simulation. The traveling wave is acoustically coupled to the rotor without sliding to generate motor rotation. To study motor rotation control, signal bursts with various number of cycles are applied to the motor, and rotation rate of 2 degree per thousand cycles with angular control of as little as 0.1 degree is achieved.
An extension of command shaping methods for controlling residual vibration using frequency sampling (2003)

The authors present an extension to the impulse shaping technique for commanding machines to move with reduced residual vibration. The extension, called frequency sampling, is a method for generating constraints that are used to obtain shaping sequences which minimize residual vibration in systems such as robots whose resonant frequencies change during motion. The authors present a review of impulse shaping methods, a development of the proposed extension, and a comparison of results of tests conducted on a simple model of the Space Shuttle robot arm. Frequency shaping provides a method for minimizing the impulse sequence duration required to give the desired insensitivity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heme Oxygenase-1 (2002)

Organisms on our planet have evolved in an oxidizing environment that is intrinsically inimical to life, and cells have been forced to devise means of protecting themselves. One of the defenses used most widely in nature is the enzyme heme oxygenase-1 (HO-1). This enzyme performs the seemingly lackluster function of catabolizing heme to generate bilirubin, carbon monoxide, and free iron. Remarkably, however, the activity of this enzyme results in profound changes in cells' abilities to protect themselves against oxidative injury. HO-1 has been shown to have anti-inflammatory, antiapoptotic, and antiproliferative effects, and it is now known to have salutary effects in diseases as diverse as atherosclerosis and sepsis. The mechanism by which HO-1 confers its protective effect is as yet poorly understood, but this area of invetsigation is active and rapidly evolving. This review highlights current information on the function of HO-1 and its relevance to specific pulmonary and cardiovascular diseases.