gebhart/patrepeval huggingface dataset:
Establishment of Lipopolysaccharide-dependent Nuclear Factor κB Activation in a Cell-free System (1995)

Nuclear factor kappa B (NF-kappa B), consisting of p50 and p65, is bound to a cytoplasmic retention protein, I kappa B, in a resting state, and the stimulation of cells with a variety of inflammatory stimuli induces the dissociation of NF-kappa B from I kappa B and the nuclear translocation of NF-kappa B, thereby activating several genes involved in inflammatory responses, such as interleukin (IL)-6, IL-8, and tumor necrosis factor alpha. In order to elucidate the precise mechanism of NF-kappa B activation, we have established lipopolysaccharide (LPS)-dependent NF-kappa B activation in a cell-free system using plasma membrane-enriched, cytosol, and nuclear fractions extracted from a human monocytic cell line, THP-1, by disruption with sonication followed by a differential centrifugation. The combination of plasma membrane-enriched fraction and cytosol was sufficient to activate NF-kappa B in a LPS/CD14-dependent manner only in the presence of ATP as judged by the binding of NF-kappa B to the IL-8 gene kappa B site on an electrophoretic mobility shift assay. LPS-dependent NF-kappa B activation was inhibited by protein kinase inhibitors, such as staurosporine, herbimycin A, tyrphostin, and genistein, but not mitogen-activated protein kinase substrate, cGMP-dependent protein kinase, cAMP-dependent protein kinase, protein kinase C, and calmodulin-dependent protein kinase II inhibitory peptides, suggesting that staurosporine-sensitive kinase(s) as well as tyrosine kinase(s) are involved in LPS-mediated NF-kappa B activation. In addition, LPS induced the phosphorylation of I kappa B-alpha, starting at 5 min after the stimulation in a cell-free system. Moreover, the phosphorylation was inhibited by herbimycin A and tyrphostin, but not staurosporine, suggesting that these protein kinase inhibitors act at distinct steps of signal transmission. Establishment of ligand-dependent activation of NF-kappa B in a cell-free system will facilitate identification of protein kinase(s) and its substrate(s) involved in LPS-mediated NF-kappa B activation.
A DC-to-1GHz tunable RF &#x0394;&#x03A3; ADC achieving DR &#x003D; 74dB and BW &#x003D; 150MHz at f<inf>0</inf> &#x003D; 450MHz using 550mW (2012)

The ultimate ADC for receiver applications would be one that converts any desired RF signal directly into digital form so that the rest of the signal chain enjoys accurate and flexible digital signal processing and CMOS scaling. Flexibility in center frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ), bandwidth (BW), sampling frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</sub> ), full-scale (FS), dynamic range (DR) and power consumption (P) would allow the ADC to handle multiple standards and adapt to the RF environment [1-4]. The ADC reported in this paper is a step toward this Holy Grail of ADCs, supporting fο = 0 to 1 GHz, BW = 35 to 150MHz, f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</sub> = 2 to 4GHz and FS = -18dBm to +18dBm. At f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> = 450MHz, BW = 150MHz, f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</sub> = 4GHz and FS = +6dBm, the ADC achieves instantaneous DR = 74dB and peak SNR = 69dB with P = 550mW.
Highly Sensitive Pulse Wave Sensor with a Piezoresistive Cantilever Inside an Air Chamber (2019)

This paper reports a sensor that can measure blood pulse waves with high sensitivity. The sensor has a piezoresistive cantilever which is designed to measure the pressure change of an air chamber covered with a thin membrane. Since the cantilever is highly sensitive to differential pressure, it can measure the pulse waves by only placing the sensor on the skin. Moreover, because the cantilever itself is able to eliminate the static pressing force physically, the effect of the pressing force on the measurement result is small. Finally, we demonstrate that the sensor can be used to measure pulse wave velocity (PWV).
Data from A Phase I Open-Label Study to Identify a Dosing Regimen of the Pan-AKT Inhibitor AZD5363 for Evaluation in Solid Tumors and in <i>PIK3CA</i>-Mutated Breast and Gynecologic Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; This phase I, open-label study (Study 1, D3610C00001; NCT01226316) was the first-in-human evaluation of oral AZD5363, a selective pan-AKT inhibitor, in patients with advanced solid malignancies. The objectives were to investigate the safety, tolerability, and pharmacokinetics of AZD5363, define a recommended dosing schedule, and evaluate preliminary clinical activity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patients were aged ≥18 years with World Health Organization (WHO) performance status of 0 to 1. Dose escalation was conducted within separate continuous and intermittent [4 days/week (4/7) or 2 days/week (2/7)] schedules with safety, pharmacokinetic, and pharmacodynamic analyses. Expansion cohorts of approximately 20 patients each explored AZD5363 activity in &lt;i&gt;PIK3CA&lt;/i&gt;-mutant breast and gynecologic cancers.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; MTDs were 320, 480, and 640 mg for continuous (&lt;i&gt;n&lt;/i&gt; = 47), 4/7 (&lt;i&gt;n&lt;/i&gt; = 21), and 2/7 (&lt;i&gt;n&lt;/i&gt; = 22) schedules, respectively. Dose-limiting toxicities were rash and diarrhea for continuous, hyperglycemia for 2/7, and none for 4/7. Common adverse events were diarrhea (78%) and nausea (49%) and, for Common Terminology Criteria for Adverse Events grade ≥3 events, hyperglycemia (20%). The recommended phase II dose (480 mg bid, 4/7 intermittent) was assessed in &lt;i&gt;PIK3CA&lt;/i&gt;-mutant breast and gynecologic expansion cohorts: 46% and 56% of patients, respectively, showed a reduction in tumor size, with RECIST responses of 4% and 8%. These responses were less than the prespecified 20% response rate; therefore, the criteria to stop further recruitment to the &lt;i&gt;PIK3CA&lt;/i&gt;-mutant cohort were met.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; At the recommended phase II dose, AZD5363 was well tolerated and achieved plasma levels and robust target modulation in tumors. Proof-of-concept responses were observed in patients with &lt;i&gt;PIK3CA&lt;/i&gt;-mutant cancers treated with AZD5363. &lt;i&gt;Clin Cancer Res; 24(9); 2050–9. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Costa and Bosch, p. 2029&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Mix-loss trained bias-removed blind image denoising network (2022)

We studied the modern deep convolutional neural networks used for image denoising, where RGB input images are transformed into RGB output images via feed-forward convolutional neural networks that use a loss defined in the RGB color space. Considering the difference between human visual perception and objective evaluation metrics such as PSNR or SSIM, we propose a data augmentation technique and demonstrate that it is equivalent to defining a perceptual loss function. We trained a network based on this and obtained visually pleasing denoised results. We also combine an unsupervised design and the bias-free network to deal with the overfitting due to the absence of clean images, and improve performance when the noise level exceeds the training range.
Supplementary Tables 1 - 7 from Genetically Defined Subsets of Human Pancreatic Cancer Show Unique <i>In Vitro</i> Chemosensitivity (2023)

&lt;p&gt;PDF file, 72K, S1 Characteristics of human pancreatic cancer cell lines used in this study; S2 Characteristics of human DPC4/SMAD4 isogenic pancreatic cancer cell lines; S3 Characteristics of human TP53 isogenic colon cancer cell lines; S4 IC50 values (nM) of Gemcitabine, Triptolide, Docetaxel, MMC, Cisplatin, Irinotecan, Parp1 inhibitor and Artemisinin for human PC cell lines; S5 IC50 values (nM) of Gemcitabine, Triptolide, Docetaxel, MMC, Cisplatin, Irinotecan, Parp1 inhibitor and Artemisinin for human pancreatic cancer cell lines; S6 Correlation analysis between chemosensitivity and somatic mutations alone, homozygous deletion alone or both in pancreatic cancer cells identified in the discovery and prevalence screen arranged by drugs.&lt;/p&gt;
Imaging of inflammation with granulocytes labelled in vivo (1988)

We have looked for inflammatory lesions in 37 patients using granulocytes labelled in vivo. For the purpose of cell labelling we used a monoclonal murine antibody reacting with NCA and carcinoembryonic antigen (CEA) (BW 250/183) labelled with 99Tcm. All abscesses and other inflammatory lesions were visualized with excellent quality scintigrams between 2 and 6 h after the injection. As the antibody can be stored in a freeze-dried form and labelled at any time in any department of nuclear medicine with 99Tcm without cell separation being necessary, the method appears to be suitable even for use in acute diagnosis. No side effects have so far been found.
Development of a Recombinant Escherichia coli Strain for Overproduction of the Plant Pigment Anthocyanin (2015)

Anthocyanins are water-soluble colored pigments found in terrestrial plants and are responsible for the red, blue, and purple coloration of many flowers and fruits. In addition to the plethora of health benefits associated with anthocyanins (cardioprotective, anti-inflammatory, antioxidant, and antiaging properties), these compounds have attracted widespread attention due to their promising potential as natural food colorants. Previously, we reported the biotransformation of anthocyanin, specifically cyanidin 3-O-glucoside (C3G), from the substrate (+)-catechin in Escherichia coli. In the present work, we set out to systematically improve C3G titers by enhancing substrate and precursor availability, balancing gene expression level, and optimizing cultivation and induction parameters. We first identified E. coli transporter proteins that are responsible for the uptake of catechin and secretion of C3G. We then improved the expression of the heterologous pathway enzymes anthocyanidin synthase (ANS) and 3-O-glycosyltransferase (3GT) using a bicistronic expression cassette. Next, we augmented the intracellular availability of the critical precursor UDP-glucose, which has been known as the rate-limiting precursor to produce glucoside compounds. Further optimization of culture and induction conditions led to a final titer of 350 mg/liter of C3G. We also developed a convenient colorimetric assay for easy screening of C3G overproducers. The work reported here constitutes a promising foundation to develop a cost-effective process for large-scale production of plant-derived anthocyanin from recombinant microorganisms.
Enhanced Uniformity and Area Scaling in Carbon Nanotube–Fullerene Bulk‐Heterojunction Solar Cells Enabled by Solvent Additives (2015)

Single‐walled carbon nanotube (SWCNT) fullerene solar cells have recently attracted attention due to their low‐cost processing, high environmental stability, and near‐infrared absorption. While SWCNT–fullerene bulk‐heterojunction photovoltaics employing an inverted architecture and polychiral SWCNTs have achieved efficiencies exceeding 3% over device areas of ≈1 mm 2 , large‐area SWCNT solar cells have not yet been demonstrated. In particular, with increasing device area, spatial inhomogeneities in the SWCNT film have limited overall device performance. Here, 1,8‐diiodooctane (DIO) is utilized as a solvent additive to reduce fullerene domain size and to improve SWCNT–fullerene bulk‐heterojunction morphology. Under optimized conditions, DIO elucidates the influence of SWCNT chiral distribution on overall device performance, revealing a tradeoff between short‐circuit current density and fill factor as a function of the chirality distribution present. The combination of SWCNT chirality distribution engineering and improved spatial homogeneity via solvent additives enables area‐scaling of SWCNT–fullerene solar cells with performance comparable to small‐area cells.
Service-level agreements and commercial grids (2003)

Service-level agreements impose unique requirements on commercial grid infrastructures - specifically, they emphasize the need for a dynamic offload infrastructure.
Stackless Multi‐BVH Traversal for CPU, MIC and GPU Ray Tracing (2013)

Abstract Stackless traversal algorithms for ray tracing acceleration structures require significantly less storage per ray than ordinary stack‐based ones. This advantage is important for massively parallel rendering methods, where there are many rays in flight. On SIMD architectures, a commonly used acceleration structure is the MBVH, which has multiple bounding boxes per node for improved parallelism. It scales to branching factors higher than two, for which, however, only stack‐based traversal methods have been proposed so far. In this paper, we introduce a novel stackless traversal algorithm for MBVHs with up to four‐way branching. Our approach replaces the stack with a small bitmask, supports dynamic ordered traversal, and has a low computation overhead. We also present efficient implementation techniques for recent CPU, MIC (Intel Xeon Phi) and GPU (NVIDIA Kepler) architectures.
Expression of the carboxypeptidase T gene fromThermoactinomyces vulgarisin stable protoplast type L-forms ofProteus mirabilis (1998)

The structural gene of the carboxypeptidase T (cpt) was successfully expressed in cell wall-less L-form cells of Proteus mirabilis. The DNA sequence encoding the PhoA leader peptide was fused with a truncated cpt gene encoding the mature enzyme. The modified gene in a pUC-based kanamycin resistance vector under the control of the lac promoter was transformed into L-form cells of P. mirabilis. They were able to produce the recombinant CpT both as a secretory and as a cell-bound insoluble form. The co-secretory processing of the PhoA leader peptide was quite efficient. The yield of the secreted CpT was not less than 20 mg l-1 and should be improvable.
ArchiMed: A Data Management System for Clinical Research in Imaging (2016)

Context: There is a great need in clinical research with imaging to collect, to store, to organize and to process large amount of varied data according to legal requirements and research obligations. In practice, many laboratories or clinical research centers working in imaging domain have to manage innumerous images and their associated data without having sufficient IT (Information Technology) skills and resources to develop and to maintain a robust software solution. Since conventional infrastructure and data storage systems for medical image such as “Picture Archiving and Communication System” (PACS) may not be compatible with research needs, we propose a solution: ArchiMed, a complete storage and visualization solution developed for clinical research. Material and methods: ArchiMed is a service oriented server application written in Java EETM which is integrated into local clinical environments (imaging devices, post-processing workstations, others devices...) and allows to safely collect data from other collaborative centers. It ensures all kinds of imaging data storage with a “study centered” approach, quality control and interfacing with mainstream image analysis research tools. Results: With more than 10 millions of archived files for about 4TB stored with 116 studies, ArchiMed, in function for 5 years at CIC-IT of Nancy-France, is used every day by about 60 persons, among whom are engineers, researchers, clinicians and clinical trial project managers.
Epigenetic regulation of protein phosphatase 2A (PP2A), Lymphotactin (XCL1) and estrogen receptor alpha (ER) expression in human breast cancer cells (2004)

Absence of the estrogen receptor alpha (ER) in human breast cancer cells is an indicator of poor prognosis, and predictive of lack of response to hormonal therapy. Previous studies in our laboratory and others have shown that epigenetic regulation, including DNA methylation and histone deacetylation, are common mechanisms leading to ER gene silencing. Through the use of pharmacologic inhibitors, 5-aza 2'deoxycytidine (AZA) and Trichostatin A (TSA), we have shown that alterations in both of these mechanisms results in synergistic reexpression of ER mRNA and functional protein. These alterations may play a larger role in stimulation of cell signaling pathways leading to ER expression. We have utilized newly developed genome wide screening microarray techniques to identify gene(s) contributing to the hormone independent phenotype and AZA/TSA mediated ER expression. From this screen, we identified and confirmed expression of 4 candidate genes (PP2A, XCL1, THY1 and NBC4) as potential regulators of the hormone independent phenotype. Expression of two genes, XCL1 and PP2A, appeared to be correlated with ER expression. PP2A expression was not changed with ER degradation using ICI 182,780 whereas XCL1 expression decreased in the presence of AZA/TSA and ICI 182,780. This suggests that PP2A may be a determinant of ER expression while XCL1 appears to be ER responsive and downstream of ER expression. These gene products may be novel targets to be further explored in the development of new therapeutics for ER negative breast cancer.
Suppression of excess oxygen for environmentally stable amorphous In-Si-O thin-film transistors (2015)

We discuss the environmental instability of amorphous indium oxide (InOx)-based thin-film transistors (TFTs) in terms of the excess oxygen in the semiconductor films. A comparison between amorphous InOx doped with low and high concentrations of oxygen binder (SiO2) showed that out-diffusion of oxygen molecules causes drastic changes in the film conductivity and TFT turn-on voltages. Incorporation of sufficient SiO2 could suppress fluctuations in excess oxygen because of the high oxygen bond-dissociation energy and low Gibbs free energy. Consequently, the TFT operation became rather stable. The results would be useful for the design of reliable oxide TFTs with stable electrical properties.
In situ template synthesis of one-dimensional gold nanoparticle arrays in organic nanowires (2013)

Well-defined one-dimensional arrays of gold nanoparticles dispersed in triphenylphosphine nanowires were obtained by annealing of chloro(triphenylphosphine) gold(I) complexes in a porous alumina template. The obtained nanocomposite wires exhibit strong surface plasmon coupling due to the close proximity of adjacent gold nanoparticles.
Pyrolysis of Acetaldehyde: a Fleeting Glimpse of Vinylidene (2011)

Author Institution: Department of Chemistry, University of Colorado, Boulder, CO, 80303; Chemical Sciences Division, Lawrence Berkeley National Laboratory,Berkeley, CA 94720; Sandia National Laboratories, Livermore, CA 94551; Department of Mechanical Engineering, University of Colorado, Boulder, CO 80302; Center for Renewable Chemical Technologies and Materials, NREL, Golden, CO 80401; Department of Chemistry and Biochemistry; University of Texas at Austin, Austin, TX 78712
A Broadly Applicable Strategy for Entry into Homogeneous Nickel(0) Catalysts from Air-Stable Nickel(II) Complexes (2014)

A series of air-stable nickel complexes of the form L[subscript 2]Ni(aryl) X (L = monodentate phosphine, X = Cl, Br) and LNi(aryl)X (L = bis-phosphine) have been synthesized and are presented as a library of precatalysts suitable for a wide variety of nickel-catalyzed transformations. These complexes are easily synthesized from low-cost NiCl[subscript 2]·6H[subscript 2]O or NiBr[subscript 2]·3H[subscript 2]O and the desired ligand followed by addition of 1 equiv of Grignard reagent. A selection of these complexes were characterized by single-crystal X-ray diffraction, and an analysis of their structural features is provided. A case study of their use as precatalysts for the nickel-catalyzed carbonyl-ene reaction is presented, showing superior reactivity in comparison to reactions using Ni(cod)[subscript 2]. Furthermore, as the precatalysts are all stable to air, no glovebox or inert-atmosphere techniques are required to make use of these complexes for nickel-catalyzed reactions.
Targeting Transcriptional and Epigenetic Reprogramming in Stromal Cells in Fibrosis and Cancer (2015)

The basis of many human diseases arises from both genetic and epigenetic regulation. Recent advances in the understanding of the mechanisms underlying transcriptional and epigenetic regulation and their prevalence as contributors to a diverse range of human diseases have led us to focus on transcription and epigenetic changes in a variety of human disease conditions. Specifically, our recent studies in liver fibrosis and pancreatic cancer have demonstrated that the epigenetic regulation in hepatic stellate cells (HSCs) and pancreatic stellate cells (PSCs) significantly contributes to the progress in such diseases and presents great therapeutic potential. We show that the vitamin D receptor (VDR) acts as a master genomic suppressor in both HSC and PSC activation. The studies also have demonstrated that the VDR ligand reduces fibrosis and inflammation in a murine liver fibrosis and pancreatitis model. Although our current studies focus on characterizing the roles of VDR and regulatory regions within gene promoters and regulatory enhancers, we have expanded our effort to epigenetic mechanisms as major determinants of gene activation and repression in order to develop potential therapeutics to modulate stroma-associated pathologies including inflammation, fibrosis, and cancer.
Welcome to EMBC 2013 in Osaka [Guest Editorial] (2013)

Presents an opening message from the 2013 IEEE Engineering in Medicine and Biology Conference that will be held in Osaka, Japan.
Extracellular matrix controls tubulin monomer levels in hepatocytes by regulating protein turnover. (1994)

Cells have evolved an autoregulatory mechanism to dampen variations in the concentration of tubulin monomer that is available to polymerize into microtubules (MTs), a process that is known as tubulin autoregulation. However, thermodynamic analysis of MT polymerization predicts that the concentration of free tubulin monomer must vary if MTs are to remain stable under different mechanical loads that result from changes in cell adhesion to the extracellular matrix (ECM). To determine how these seemingly contradictory regulatory mechanisms coexist in cells, we measured changes in the masses of tubulin monomer and polymer that resulted from altering cell-ECM contacts. Primary rat hepatocytes were cultured in chemically defined medium on bacteriological petri dishes that were precoated with different densities of laminin (LM). Increasing the LM density from low to high (1-1000 ng/cm2), promoted cell spreading (average projected cell area increased from 1200 to 6000 microns2) and resulted in formation of a greatly extended MT network. Nevertheless, the steady-state mass of tubulin polymer was similar at 48 h, regardless of cell shape or ECM density. In contrast, round hepatocytes on low LM contained a threefold higher mass of tubulin monomer when compared with spread cells on high LM. Furthermore, similar results were obtained whether LM, fibronectin, or type I collagen were used for cell attachment. Tubulin autoregulation appeared to function normally in these cells because tubulin mRNA levels and protein synthetic rates were greatly depressed in round cells that contained the highest level of free tubulin monomer. However, the rate of tubulin protein degradation slowed, causing the tubulin half-life to increase from approximately 24 to 55 h as the LM density was lowered from high to low and cell rounding was promoted. These results indicate that the set-point for the tubulin monomer mass in hepatocytes can be regulated by altering the density of ECM contacts and changing cell shape. This finding is consistent with a mechanism of MT regulation in which the ECM stabilizes MTs by both accepting transfer of mechanical loads and altering tubulin degradation in cells that continue to autoregulate tubulin synthesis.