gebhart/patrepeval huggingface dataset:
Coptisine induces autophagic cell death through down-regulation of PI3K/Akt/mTOR signaling pathway and up-regulation of ROS-mediated mitochondrial dysfunction in hepatocellular carcinoma Hep3B cells (2020)

Coptisine is isoquinoline alkaloid derived from Coptidis Rhizoma and is known to have potential anti-cancer activity toward various carcinomas. Targeting autophagy is one of the main approaches for cancer therapy, but whether the anti-cancer efficacy of coptisine involves autophagy is still unclear. Therefore, this study investigated the effect of coptisine on autophagy in hepatocellular carcinoma (HCC) Hep3B cells, and identified the underlying mechanism. Our results showed that coptisine increased cytotoxicity and autophagic vacuoles in a concentration-dependent manner. Furthermore, the expressions of light chain 3 (LC3)-I/II, Beclin-1 and autophagy genes were markedly increased by coptisine, while the expression of p62 decreased. In addition, we found that pretreatment with bafilomycin A1, an inhibitor of autophagosome-lysosome fusion, markedly reduced coptisine-mediated autophagic cell death, but 3-methyladenine, an inhibitor for autophagosome formation did not. Moreover, our results showed that although coptisine up-regulated AMP-activated protein kinase (AMPK) that partially induced LC3-I/II, coptisine-mediated AMPK signaling did not directly regulate autophagic cell death. Additionally, we found that coptisine suppressed the phosphorylation of phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR), and this effect was notably enhanced by PI3K inhibitor LY294002. Meanwhile, coptisine significantly increased both the production of mitochondrial reactive oxygen species (ROS) and the recruitment of mitophagy-regulated proteins to mitochondria. Furthermore, N-acetylcysteine, a potential ROS scavenger, substantially suppressed the expression of mitophagy-regulated proteins and LC3 puncta by coptisine. Overall, our results demonstrate that coptisine-mediated autophagic cell death was regulated by PI3K/Akt/mTOR signaling and mitochondrial ROS production associated with mitochondrial dysfunction. Taken together, these findings suggest that coptisine exerts its anti-cancer effects through induction of autophagy in HCC Hep3B cells.
Disc Replacement Adjacent to Cervical Fusion (2011)

The porous-coated motion cervical prosthesis restored the ROM of the treated level to the intact state. When the porous-coated motion prosthesis was used in a hybrid construct, the TDR response was not adversely affected. A hybrid construct seems to offer significant biomechanical advantages over two-level fusion in terms of reducing compensatory adjacent-level hypermobility and also loads required to achieve a predetermined ROM.
Tetrapotassium heptacyanidomolybdate(III) dihydrate (2009)

The asymmetric unit of the title compound, K(I) (4)[Mo(III)(CN)(7)]·2H(2)O, consists of one [Mo(CN)(7)](4-) anion, four K(+) cations, and two water mol-ecules. The [Mo(III)(CN)(7)](4-) anion has a seven-coordinated capped-trigonal-prismatic coordination geometry. The site-occupancy factors of the disordered water mol-ecules were set at 0.90, 0.60 and 0.50. The H-atom positions could not be determined for two of the water mol-ecules. The H atoms of the water with a site-occupancy factor of 0.90 were refined using O-H and H⋯H distance restraints.
Microbes mediated host innate immune response in idiopathic pulmonary fibrosis (2016)

<b>Background:</b> The host immune response to lung microbes in idiopathic pulmonary fibrosis (IPF) is unclear. <b>Objective:</b> Investigate immune pathways implicated by presence of operational taxonomic units (OTU) microbiota from bronchoscopy IPF lung samples, and if bacterial CpG-oligodeoxynucleotide (CpG-ODN) motifs mediated fibroblast TLR9 activation is involved. <b>Methods:</b> Paired gene expression arrays and 16S rDNA sequencing data of 68 IPF patients were retrieved from COMET study. R package “WGCNA” were used to construct gene co-expression modules. Each eigengene value was correlated with each trait. <b>Results:</b> Figure 1 showed 10 modules and their respective positive/negative correlation with each trait. Magenta module significantly correlated with the D<sub>L</sub>CO (<i>p</i>=0.007), species richness (<i>p</i>=5x10<sup>-6</sup>), and OTU1302 (<i>Pseudomonas</i>) (<i>p</i>=0.0001). Purple module correlated OTU1341 (<i>Prevotella</i>) (<i>p</i>=0.003) and OTU1348 (<i>Staphylococcus</i>) (<i>p</i>=0.03) and negatively correlated with CpG response (<i>p</i>=0.03). D<sub>L</sub>CO and CpG response significantly correlated with blue module with opposite directions. Canonical pathways enriched in magenta, purple, and blue modules are integrin signaling, regulation of epithelial-mesenchymal transition, and Toll-like receptor signaling, respectively. <b>CONCLUSIONS:</b> The integrated analysis of host transcriptome with lung microbiota and CpG-ODN response unveiled underlying molecular mechanism of microbes mediated host innate immune response in IPF.
Smallest lithographic marks generated by optical focusing systems (2007)

We show that the combination of Bessel beams and photosensitive materials exhibiting polarization filtering properties allows one to reach the smallest mark that can be lithographically generated by focusing systems. This property is of interest in current optical data storage techniques.
Adsorption of N-Nitrosodimethylamine Precursors by Powdered and Granular Activated Carbon (2012)

Activated carbon (AC) has been shown to remove precursors of halogenated disinfection byproducts. Granular and powdered activated carbon (GAC, PAC) were investigated for their potential to adsorb N-nitrosodimethylamine (NDMA) precursors from blends of river water and effluent from a wastewater treatment plant (WWTP). At bench scale, waters were exposed to lignite or bituminous AC, either as PAC in bottle point experiments or as GAC in rapid small-scale column tests (RSSCTs). NDMA formation potential (FP) was used as a surrogate for precursor removal. NDMA FP was reduced by 37, 59, and 91% with 3, 8, and 75 mg/L of one PAC, respectively, with a 4-h contact time. In RSSCTs and in full-scale GAC contactors, NDMA FP removal always exceeded that of the bulk dissolved organic carbon (DOC) and UV absorbance at 254 nm. For example, whereas DOC breakthrough exceeded 90% of its influent concentration after 10,000 bed volumes of operation in an RSSCT, NDMA FP was less than 40% of influent concentration after the same bed life of the GAC. At full or pilot scale, high NDMA FP reduction ranging from >60 to >90% was achieved across GAC contactors, dependent upon the GAC bed life and/or use of a preoxidant (chlorine or ozone). In all experiments, NDMA formation was not reduced to zero, which suggests that although some precursors are strongly sorbed, others are not. This is among the first studies to show that AC is capable of adsorbing NDMA precursors, but further research is needed to better understand NDMA precursor chemical properties (e.g., hydrophobicity, molecular size) and evaluate how best to incorporate this finding into full-scale designs and practice.
Excited Triplet and Reduced Forms of CM (1995)

visible absorption spectra of c8429 and the reduction potentials of c8427-31 have already been reported. At least six reversible reductions have been characterized using cyclic v o l t a m r r ~ e t r y . ~ ~ ~ ~ Although distinctively different electronic properties of these two isomers were observed in electrochemical and ESR studies, the separation of the two isomers of c 8 4 has not yet been achieved. Consequently, a mixture of the two isomers has been used in this investigation. We report here, for the first time, experimental results which characterize triplet excited state properties of c84. We also report the photoelectrochemical reduction of c 8 4 in colloidal Ti02 suspension. Experimental Section Materials. Mass-pure C84 was obtained via selective solvent extraction followed by HPLC chromatography with a semipreparative Buckyclutcher column (Regis) run in recycling mode. Details of the selective solvent enrichment techniques will be published later.26a The purity of the sample was checked by surface analysis via laser ionization (SALI) mass spectrometry (MS), a technique that has been used extensively at SRI Intemational for analysis of fullerene samples.27b SALI-MS showed that the fullerene purity exceeded 99.5%, with the only impurity peaks belonging to c 8 2 and c86; in particular, no c60 or c 7 0 was present in the SALI-MS spectrum obtained. The
Slow Light Enhanced Silicon Chip Based Chem-Bio Sensors (2017)

Silicon nanophotonic waveguides and microcavities are experimentally investigated. High density lab on chip sensor integration and high sensitivity sensors enabled by engineering slow light and analyte overlap integrals are demonstrated for chemical and biosensing applications.
Defective Insulin Receptor Function in Down-Regulated HepG2 Cells* (1990)

Insulin receptors on the surface of down-regulated HepG2 cells were studied, and multiple defects of receptor function were demonstrated. Insulin treatment led to a 58% decrease in cell surface receptor number, and the remaining receptors exhibited a 50% decrease in insulin internalization and degradation on a per receptor basis. Down-regulated cells internalized 36% of receptors photolabeled with 125I-NAPA-insulin vs. 56% of labeled receptors in control cells, indicating a 40% decrease in ligand-mediated receptor internalization. Total cellular receptors purified from down-regulated cells by wheat germ affinity chromatography demonstrated a 20% decrease in maximal autophosphorylation. Assessment of autophosphorylation of cell surface receptors in intact cells by restimulation of cells with insulin at 12 C (a temperature nonpermissive for receptor recycling), followed by immunoblotting with antiphosphotyrosine antibodies revealed a decrease of approximately 70% in insulin-stimulated autophosphorylation compared with controls. This method also revealed a comparable decrease in insulin-stimulable tyrosine phosphorylation of pp185, a putative endogenous substrate. When receptors were stimulated to undergo autophosphorylation with 125I-NAPA-insulin in intact cells and then solubilized, only 11% of 125I-NAPA-insulin receptor complexes from down-regulated cells were immunoprecipitated with antiphosphotyrosine antibodies compared with 35% of labeled control receptors. These results indicate that treatment with high concentrations of insulin results in the accumulation on the cell surface of a population of receptors that display multiple functional abnormalities. This probably results from preferential internalization and degradation of kinase-competent insulin receptors causing an accumulation of kinase-incompetent receptors on the cell surface. These receptors may in part be responsible for the postbinding defects in insulin action observed in down-regulated cells.
Benefits of p-cycles in a mixed protection and restoration approach (2004)

There are reasons to expect that the protection switching times of p-cycles will allow them to be considered for protecting services where previously only 1+1 automatic protection switching would have been specified, for the highest speed. Here we introduce p-cycles as an option in a mixed-method environment to protect demands that do not strictly require dedicated 1+1 APS, but need a faster switching time than provided by shared backup path protection. Results show that in a mixed services environment, realizing such demands with p-cycles rather than 1+1 APS can produce a significant capacity saving. To further explore the potential of mixed-method design, we also test an approach where individual demands are not strictly assigned to be realized by a particular method. Instead, each path may be protected with any method that gives the minimum required service guarantee, but where possible or advantageous in the overall design, paths can be protected by an even faster method than required. For instance, a requirement for 200 ms, usually served by an SBPP realization, may (selectively) be realized instead with p-cycle protection at 80 ms. This optimization of the protection method selection produces a small further capacity savings, but provides a remarkable increase in the number of service paths that enjoy faster protection than strictly required by their class of service specification. When modularity is included, this new design approach provides even greater improvement in protection quality.
Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions (2008)

Our study demonstrates how a new level of integration between high throughput measurements and flux balance model predictions can improve understanding of both experimental and computational results. The added value of a joint analysis is a more reliable platform for specific testing of biological hypotheses, such as the catabolic routes of different carbon sources.
Supplementary Tables 1 - 3 from Targeting Activated Akt with GDC-0068, a Novel Selective Akt Inhibitor That Is Efficacious in Multiple Tumor Models (2023)

&lt;p&gt;XLSX file - 74K, Table S1. Enzymatic potency, selectivity and cellular potency of GDC-0068 Table S2. GDC-0068 IC50 profile on cell viability and genetic background of cancer cell lines Table S3. Maximum percent body weight changes of mice treated with GDC-0068 single agent and in combination with chemotherapeutic agents&lt;/p&gt;
Linkage analysis of chromosome 4 in families with familial pancreatic cancer (2007)

Our results do not support linkage to the 4q32-34 region in the majority of our familial pancreatic cancer kindreds. However, because multiple pancreatic cancer susceptibility genes are likely to exist, it is possible that a subset of the families in this study may be linked to this region.
Mild Solvent Extraction of Wood Waste (2003)

Mild solvent extraction (MSE) is an extractive process that has been previously used todirectly convert coal to liquid products, gases, and solid chars. The MSE of white oak flour wasinvestigated at three temperatures 300, 350, and 425 C and of red oak particles at a singletemperature, 350 C. For white oak, the intermediate temperature of 350 C achieved a biomassconversion of 99%, producing 189 g of pitch from a biomass charge of 298 g, with a solvent loss of29%. MSE of the red oak particles at the same temperature achieved a biomass conversion of 94%,producing 338 g of pitch with a solvent loss of 37%. These results indicate that this process can beutilized with a biomass feedstock, where performance will depend on biomass characteristics,processing temperature, and particle size. Future studies will focus on the optimization of productyield and distribution, while minimizing solvent loss.
Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ (2023)

A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.
Enhancing the Therapeutic Potential of Sulfamidase for the Treatment of Mucopolysaccharidosis IIIA (2019)

Mucopolysaccharidosis type IIIA (MPS-IIIA) is a lysosomal storage disorder (LSD) caused by inherited defect of sulfamidase, a lysosomal sulfatase. MPS-IIIA is one of the most common and severe forms of LSDs with CNS involvement. Presently there is no cure. Here we have developed a new gene delivery approach for the treatment of MPS-IIIA based on the use of a modified version of sulfamidase expression cassette. This cassette encodes both a chimeric sulfamidase containing an alternative signal peptide (sp) to improve enzyme secretion and sulfatase-modifying factor 1 (SUMF1) to increase sulfamidase post-translational activation rate. We demonstrate that improved secretion and increased activation of sulfamidase act synergistically to enhance enzyme biodistribution in wild-type (WT) pigs upon intrathecal adeno-associated virus serotype 9 (AAV9)-mediated gene delivery. Translating such gene delivery strategy to a mouse model of MPS-IIIA results in a rescue of brain pathology, including memory deficit, as well as improvement in somatic tissues. These data may pave the way for developing effective gene delivery replacement protocols for the treatment of MPS-IIIA patients.
AMT1;1 transgenic rice plants with enhanced NH4+ permeability show superior growth and higher yield under optimal and suboptimal NH4+ conditions (2014)

The major source of nitrogen for rice (Oryza sativa L.) is ammonium (NH4\n+). The NH4\n+ uptake of roots is mainly governed by membrane transporters, with OsAMT1;1 being a prominent member of the OsAMT1 gene family that is known to be involved in NH4\n+ transport in rice plants. However, little is known about its involvement in NH4\n+ uptake in rice roots and subsequent effects on NH4\n+ assimilation. This study shows that OsAMT1;1 is a constitutively expressed, nitrogen-responsive gene, and its protein product is localized in the plasma membrane. Its expression level is under the control of circadian rhythm. Transgenic rice lines (L-2 and L-3) overexpressing the OsAMT1;1 gene had the same root structure as the wild type (WT). However, they had 2-fold greater NH4\n+ permeability than the WT, whereas OsAMT1;1 gene expression was 20-fold higher than in the WT. Analogous to the expression, transgenic lines had a higher NH4\n+ content in the shoots and roots than the WT. Direct NH4\n+ fluxes in the xylem showed that the transgenic lines had significantly greater uptake rates than the WT. Higher NH4\n+ contents also promoted higher expression levels of genes in the nitrogen assimilation pathway, resulting in greater nitrogen assimilates, chlorophyll, starch, sugars, and grain yield in transgenic lines than in the WT under suboptimal and optimal nitrogen conditions. OsAMT1;1 also enhanced overall plant growth, especially under suboptimal NH4\n+ levels. These results suggest that OsAMT1;1 has the potential for improving nitrogen use efficiency, plant growth, and grain yield under both suboptimal and optimal nitrogen fertilizer conditions.
ChemInform Abstract: CHEMISTRY, STRUCTURE, AND MOLECULAR DYNAMICS OF THE TETRAHYDROBORATOTETRACARBONYLMOLYBDATE(1‐) ANION, MO(CO)4BH4‐ (1978)

Abstract Die Verbindung (III) mit dem Titelanion wird aus der Reaktion des Iodomolybdats (I) mit dem Hydridoborat (II) durch Metathese erhalten.
2‐Mercaptobenzothiazole protected Au and Ag clusters (2000)

Nanometer sized gold and silver clusters protected with 2-mercaptobenzothiazole monolayers have been prepared and characterized by various spectroscopic methods. Optical absorption spectra show features assigned to charge-transfer excitation between the monolayer and the cluster, in addition to a red shifting and reduction of plasmon absorption. The monolayers on clusters are compared with the corresponding 2D-monolayers investigated previously. The dominant adsorbate geometries on these clusters are different. Whereas the temperature dependent dynamics are minimal for 2D-SAMs, they are significant for monolayers on 3D surfaces, which is attributed to the decreased packing density on the cluster surfaces. The thermal stability of these monolayers is high and comparable to that of alkanethiolate monolayers. The monolayers undergo irreversible structural changes upon heating, which have been studied by differential scanning calorimetry and IR spectroscopy.
Verification of the Correlation between Human Vibration Characteristic and Discomfort in Low-Frequency Band (2011)

Recently, the riding comfort of passenger cars has become important, as well as driving performance and control stability. To improve riding comfort performance, it is necessary to evaluate comfort quantitatively and take discomfort-decreasing measures. In this study, using acceleration magnitude, frequency (below 3 Hz), phase difference, and acceleration amplitude ratio as the input parameters, the characteristics of vibratory sensibility were surveyed with driving posture in a shaking experiment to identify the parameters that affect sensation. A vibration experiment was conducted using the standing wave of two axes, X (fore and aft)-Z (vertical) and Y (lateral)-Z (vertical). As a result, the riding sensation tends to depend on the frequency and the amplitude ratio. Next, the human body response was measured using an input condition in which the difference of sensation appeared notably in the experimental results of grasping the sensibility characteristics. Measurement points were the pre-head, occipital, chest, pelvis, and ischium. Moreover, we analyzed human vibration responses by observing the relative movements of body parts from the side-view and rear-view. We verified the correlation between these responses and sensations. As a result, this study shows that riding comfort can be improved by decreasing lateral vibration at the chest and pelvis.
Synthesis of N‐Diphenylphosphinoylimines Using the Kresze Reaction (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Genetic Variants Influencing Circulating Lipid Levels and Risk of Coronary Artery Disease (2010)

We have identified 4 novel loci associated with circulating lipids. We also show that in addition to those that are largely associated with LDL-C, genetic loci mainly associated with circulating triglycerides and HDL-C are also associated with risk of CAD. These findings potentially provide new insights into the biological mechanisms underlying lipid metabolism and CAD risk.
Folded MEMS Pyramid Inertial Measurement Unit (2011)

This paper reports a new approach for design and fabrication of chip-level inertial measurement units (IMUs). The method utilizes a 3-D foldable silicon-on-insulator (SOI) backbone with in-situ fabricated high-aspect-ratio sensors. A planar multisensor unit was fabricated and subsequently folded in a pyramidal shape, forming a compact IMU. Inertial characterization of the sensors integrated on the IMU pyramid was performed at atmospheric pressure. Structural rigidity and sensor axis alignment stability of the folded IMUs have been characterized under various environmental conditions, including vibration, thermal loading, thermal shock, and constant acceleration. The maximum angular misalignment due to variation in environmental conditions between IMU pyramid sidewalls was shown to be less than 4 and 0.2 mrad for epoxy and solder reinforced structures, respectively. Vibration testing revealed no resonances up to 10 kHz in the assembled 3-D structures. Our results confirm feasibility of the fabrication approach.
Exploring the Effect of Surface Functionality on the Self‐Assembly of Polyoxopalladate Macroions (2015)

The solution behavior of the two polyoxo-13-palladates(II) ([Pd(II) 13 As(V) 8 O34 (OH)6 ](8-) and [Pd(II) 13 (As(V) Ph)8 O32 ](6-) ) was studied in detail. We discovered that the countercation-mediated attraction is the driving force for their self-assembly into larger architectures. However, the presence of phenyl groups in the periphery of [Pd(II) 13 (As(V) Ph)8 O32 ](6-) results in an enhanced attraction among these polyanions through hydrophobic interactions, which leads to completely different trends of assembly size for these two very similar clusters when decreasing solvent polarity. An increase of assembly size with increasing solvent polarity was observed for [Pd(II) 13 (As(V) Ph)8 O32 ](6-) , whereas for [Pd(II) 13 As (V) 8 O34 (OH)6 ](8-) it was the opposite, due to the absence of hydrophobic interactions.