gebhart/patrepeval huggingface dataset:
Transformation of Human and Murine Fibroblasts without Viral Oncoproteins (2005)

Murine embryo fibroblasts are readily transformed by the introduction of specific combinations of oncogenes; however, the expression of those same oncogenes in human cells fails to convert such cells to tumorigenicity. Using normal human and murine embryonic fibroblasts, we show that the transformation of human cells requires several additional alterations beyond those required to transform comparable murine cells. The introduction of the c-Myc and H-RAS oncogenes in the setting of loss of p53 function efficiently transforms murine embryo fibroblasts but fails to transform human cells constitutively expressing hTERT, the catalytic subunit of telomerase. In contrast, transformation of multiple strains of human fibroblasts requires the constitutive expression of c-Myc, H-RAS, and hTERT, together with loss of function of the p53, RB, and PTEN tumor suppressor genes. These manipulations permit the development of transformed human fibroblasts with genetic alterations similar to those found associated with human cancers and define specific differences in the susceptibility of human and murine fibroblasts to experimental transformation.
Molecular motion in spin-labeled phospholipids and membranes (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular motion in spin-labeled phospholipids and membranesHarden M. McConnell and Wayne L. HubbellCite this: J. Am. Chem. Soc. 1971, 93, 2, 314–326Publication Date (Print):January 1, 1971Publication History Published online1 May 2002Published inissue 1 January 1971https://pubs.acs.org/doi/10.1021/ja00731a005https://doi.org/10.1021/ja00731a005research-articleACS PublicationsRequest reuse permissionsArticle Views1210Altmetric-Citations1236LEARN 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
Cloning and Expression in Escherichia coli of a Synthetic DNA for Hirudin, the Blood Coagulation Inhibitor in the Leech (1986)

A 235-bp DNA coding for the leech blood coagulation inhibitor, hirudin, was chemically synthesized. The synthesis involved preparation of seven long oligodeoxyribonucleotide pairs which were assembled and cloned using a rapid and simple procedure. More than half of the transformed Escherichia coli cells expressed a biosynthetic polypeptide having biological properties which were very similar to authentic hirudin from the leech Hirudo medicinalis. To achieve efficient expression, we fused the hirudin DNA to a truncated C1 repressor gene of bacteriophage lambda to create a hybrid protein. An additional methionine at the fusion point allowed the active hirudin to be cleaved off by cyanogen bromide.
Discrete multiple tone modulation with coset coding for the spectrally shaped channel (1992)

A discrete approach to multiple tone modulation is developed for digital communication channels with arbitrary intersymbol interference (ISI) and additive Gaussian noise. Multiple tone modulation is achieved through the concatenation of a finite block length modulator based on discrete Fourier transform (DFT) code vectors, and high gain coset or trellis codes. Symbol blocks from an inverse DFT (IDFT) are cyclically extended to generate ISI-free channel-output symbols that decompose the channel into a group of orthogonal and independent parallel subchannels. Asymptotic performance of this system is derived, and examples of asymptotic and finite block length coding gain performance for several channels are evaluated at different values of bits per sample. This discrete multiple tone technique is linear in both the modulation and the demodulation, and is free from the effects of error propagation that often afflict systems employing bandwidth-optimized decision feedback plus coset codes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tannic acid potently inhibits tumor cell proteasome activity, increases p27 and Bax expression, and induces G1 arrest and apoptosis. (2001)

Animal studies have demonstrated that a dietary polyphenol known as tannic acid (TA) exhibits anticarcinogenic activity in chemically induced cancers, although the involved molecular target remains unknown. In addition, proteasome inhibitors have been shown to suppress human tumor growth in nude mice. Most recently, we have reported that ester-bond-containing tea polyphenols are potent proteasome inhibitors in vitro and in vivo. We have hypothesized that TA, which contains multiple similar gallate moieties linked by ester bonds, should inhibit the proteasome activity. Here, we report that indeed TA potently and specifically inhibits the chymotrypsin-like activity of purified 20S proteasome (IC(50) = 0.06 microg/ml), 26S proteasome of Jurkat T-cell extracts, and 26S proteasome of living Jurkat cells. Inhibition of the proteasome by TA in Jurkat cells results in accumulation of two natural proteasome substrates, the cyclin-dependent kinase inhibitor p27(Kip1) and the proapoptotic protein Bax, followed by growth arrest in G1 and induction of apoptotic cell death. Our present study suggests that TA targets and inhibits the proteasome in tumor cells, which may contribute to the previously observed anticarcinogenic activity of TA.
Displacement Activation of Tantalum Diffusion Barrier Layer for Electroless Copper Deposition (2001)

Activation of substrates using a buffered oxide etch displacement solution and electroless Cu deposition have been investigated in this paper. Surface morphologies and distribution of Pd nuclei on the Ta layer were strongly dependent on the ratio of during activation as confirmed by scanning electron microscopy and atomic force microscopy surface observation. Using an activation solution with a ratio of of 3:2, electrolessly deposited Cu films with good surface coverage and low electrical resistivity were obtained. The surface coverage of electroless Cu grains on the Ta layer degraded with longer activation time and other activation solutions due to the Pd removal resulting from lateral under-substrate cut during activation. No preferred orientation of the electrolessly deposited Cu films was found from X-ray diffraction analysis. Good selectivity of electroless Cu deposition contributed to the preferred nucleation of Cu on Pd nuclei which deposited only on the Ta layer rather than on during activation. © 2001 The Electrochemical Society. All rights reserved.
Occurrence of phrenic nerve stimulation in cardiac resynchronization therapy patients: the role of left ventricular lead type and placement site (2012)

Phrenic nerve stimulation occurred in 13% of patients undergoing LV lead placement and was more common at mid-lateral/posterior, and LV apical sites. Most cases (123/139; 88%) of PNS were mitigated via electrical reprogramming, without the need for invasive intervention.
Mild Preparation of 1-Benzyloxyiminoalkylphosphonic Dichlorides: Application to the Synthesis of Cyclic Phosphonic Diesters and Cyclic Monoester Amides (1993)

1-Benzyloxyiminophosphonates (3) were converted under very mild conditions to the corresponding phosphonyl dichlorides (5). The application toward the synthesis of diastereomeric 1,3,2,-oxazaphospholidines (6/7), and diastereomeric 1,3,2-dioxaphosphorinanes (8/9) is reported. The structure of 9a was confirmed by X-ray analysis
Wound-Induced Deposition of Polyphenols in Transgenic Plants Overexpressing Peroxidase (1991)

Tobacco (Nicotiana tabacum) plants transformed with a chimeric tobacco anionic peroxidase gene have previously been shown to synthesize high levels of peroxidase in all tissues throughout the plant. One of several distinguishable phenotypes of transformed plants is the rapid browning of pith tissue upon wounding. Pith tissue from plants expressing high levels of peroxidase browned within 24 hours of wounding, while tissue from control plants did not brown as late as 7 days after wounding. A correlation between peroxidase activity and wound-induced browning was observed, whereas no relationship between polyphenol oxidase activity and browning was found. The purified tobacco anionic peroxidase was subjected to kinetic analysis with substrates which resemble the precursors of lignin or polyphenolic acid. The purified enzyme was found to readily polymerize phenolic acids in the presence of H(2)O(2) via a modified ping-pong mechanism. The percentage of lignin and lignin-related polymers in cell walls was nearly twofold greater in pith tissue isolated from peroxidase-overproducer plants compared to control plants. Lignin deposition in wounded pith tissue from control plants closely followed the induction of peroxidase activity. However, wound-induced lignification occurred 24 to 48 hours sooner in plants overexpressing the anionic peroxidase. This suggests that the availability of peroxidase rather than substrate may delay polyphenol deposition in wounded tissue.
Speech enhancement using warped discrete cosine transform (2003)

We propose an approach based on the warped discrete cosine transform (WDCT) to enhance degraded speech under background noise environments. To develop an effective expression for the frequency characteristics of the input speech, we apply a variable frequency warping filter to the conventional discrete cosine transform (DCT). The frequency warping control parameter is adjusted according to an analysis of the spectral distribution in each frame. For a more accurate analysis of spectral characteristics, we employ the split-band approach while the global soft decision for speech presence is performed in each band separately. A number of tests show that the WDCT-based enhancement method yields better performance than the DCT-based algorithm.
Characterization of Porphyromonas gingivalis -Induced Degradation of Epithelial Cell Junctional Complexes (2000)

Porphyromonas gingivalis is considered among the etiological agents of human adult periodontitis. Although in vitro studies have shown that P. gingivalis has the ability to invade epithelial cell lines, its effect on the epithelial barrier junctions is not known. Immunofluorescence analysis of human gingival epithelial cells confirmed the presence of tight-junction (occludin), adherens junction (E-cadherin), and cell-extracellular matrix junction (beta1-integrin) transmembrane proteins. These transmembrane proteins are expressed in Madin-Darby canine kidney (MDCK) cells. In addition, MDCK cells polarize and therefore serve as a useful in vitro model for studies on the epithelial cell barrier. Using the MDCK cell system, we examined the effect of P. gingivalis on epithelial barrier function. Exposure of the basolateral surfaces of MDCK cells to P. gingivalis (>10(9) bacteria/ml) resulted in a decrease in transepithelial resistance. Immunofluorescence microscopy demonstrated decreases in the amounts of immunoreactive occludin, E-cadherin, and beta1-integrin at specific times which were related to a disruption of cell-cell junctions in MDCK cells exposed to basolateral P. gingivalis. Disruption of cell-cell junctions was also observed upon apical exposure to bacteria; however, the effects took longer than those seen upon basolateral exposure. Cell viability was not affected by either basolateral or apical exposure to P. gingivalis. Western blot analysis demonstrated hydrolysis of occludin, E-cadherin, and beta1-integrin in lysates derived from MDCK cells exposed to P. gingivalis. Immunoprecipitated occludin and E-cadherin molecules from MDCK cell lysates were also degraded by P. gingivalis, suggesting a bacterial protease(s) capable of cleaving these epithelial junction transmembrane proteins. Collectively, these data suggest that P. gingivalis is able to invade the deeper structures of connective tissues via a paracellular pathway by degrading epithelial cell-cell junction complexes, thus allowing the spread of the bacterium. These results also indicate the importance of a critical threshold concentration of P. gingivalis to initiate epithelial barrier destruction.
Molecularly Imprinted Polymeric Fibers for Solid-Phase Microextraction (2007)

Solid-phase microextraction (SPME) is widely used in analytical laboratories for the analysis of organic compounds, thanks to its simplicity and versatility. However, the current commercially available fibers are based on nonselective sorbents, making difficult in some cases the final determination of target compounds by chromatographic techniques. Molecularly imprinted polymers (MIPs) are stable polymers with selective molecular recognition abilities, provided by the template used during their synthesis. In the present work, a simple polymerization strategy allowing the obtainment of molecularly imprinted polymeric fibers to be used in SPME is proposed. Such a strategy is based on the direct synthesis of molecularly imprinted polymeric fibers (monoliths) using silica capillaries as molds, with silica being etched away after polymerization. The system propazine:methacrylic acid was used as a model for the preparation of molecularly imprinted fibers, and its ability to selectively rebind triazines was evaluated. Variables affecting polymer morphology (i.e., polymerization time, fiber thickness) and binding-elution of target analytes (i.e., solvents, time, temperature) were studied in detail. The imprinted fiber showing the best performance in terms of selectivity and affinity for triazines was successfully applied to the extraction of target analytes from environmental and food samples.
Combinatorial Decoding:  An Approach for Universal DNA Array Fabrication (2003)

A fiber optic microsphere-based oligonucleotide array is described that employs the sequence of the oligonucleotide probe attached to each microsphere as positional identifiers. Each microsphere serves as an immobilized array feature, functionalized with a unique single-stranded oligonucleotide sequence and randomly distributed into an array of microwells. To determine the sequences attached to individual microspheres, a series of fluorescently labeled combinatorial-pooled oligonucleotide target solutions was designed. Each combinatorial decoding solution is intended to identify the nucleotide at a particular position on every microsphere in the array. The combinatorial target solutions were synthesized by linking the four possible nucleotides at each position to four different fluorescent reporter dyes. As such, when the solutions were hybridized to the array, one of four possible fluorescent responses was generated for each position on a microsphere probe sequence. Adjusting the stringency of hybridization enabled single-base mismatch discrimination, and the signal with the highest intensity corresponded to the perfect nucleotide match. By consecutively exposing the array to a series of combinatorial decoding pool solutions, it was possible to simultaneously determine the sequence of every randomly positioned oligonucleotide-functionalized microsphere in the array. Once mapped, the microsphere array can be used for any typical genomic microarray experiment.
The effect of circuit topology on radiation-induced latchup (1989)

Topological factors that affect latchup were investigated using test structures fabricated in two different CMOS foundries. The geometry of isolation well contacts was found to have a large effect on photocurrent responses because of the effect of the lateral resistance of the well. Experiments that delayed the application of bias until time periods long after the radiation pulse subsided showed that latchup would still occur, with relatively small increases in the radiation intensity required to induce latchup until the delays exceeded several microseconds. This shows that the fast transition of the radiation pulse is not required to trigger latchup, and it also shows how latchup can occur at high intensities after internal voltages collapse to near zero at short times. Latchup tests of a 64K SRAM (static random-access memory) revealed a latchup window that was caused by the presence of two different internal latchup paths with different radiation triggering levels and holding voltages. Data on this device and several MSI devices show how the power-supply current-surge characteristics can be used to select radiation test levels to minimize interference from latchup windows.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Preparation of Low-Temperature Fired PZT Thick Films on Si by Screen Printing (2003)

Piezoelectric powder with the composition of PbTiO<TEX>$_3$</TEX>-PbZrO<TEX>$_3$</TEX>-Pb(Mn<TEX>$\_$</TEX>1/3/Nb<TEX>$\_$</TEX>2/3/)O<TEX>$_3$</TEX> and small particle size of 0.3 <TEX>$\mu\textrm{m}$</TEX> was investigated for low-temperature firing of PZT thick films. PbTiO<TEX>$_3$</TEX>-PbZrO<TEX>$_3$</TEX>-Pb(Mn<TEX>$\_$</TEX>1/3/Nb<TEX>$\_$</TEX>2/3)O<TEX>$_3$</TEX> ceramics showed dense microstructure and superior piezoelectric properties, electromechanical coupling factor (k<TEX>$\_$</TEX>p/) of 0.501 and piezoelectric constant (d<TEX>$\_$</TEX>33/) of 224. The PZT paste was made of the powder and organic vehicles, and screen-printed on Pt(450nm)/YSZ(110nm)/SiO<TEX>$_2$</TEX>(300nm)/Si substrates and fired at 800∼900<TEX>$^{\circ}C$</TEX>. Any interface reaction between the PZT thick film and the bottom electrode was not observed in the PZT thick films. The PZT thick film fired at 800<TEX>$^{\circ}C$</TEX> showed moderate electrical properties, the remanent polarization(p<TEX>$\_$</TEX>r/) of 16.0 <TEX>${\mu}$</TEX>C/<TEX>$\textrm{cm}^2$</TEX>, the coercive field(E<TEX>$\_$</TEX>c/) of 36.7 ㎸/cm, and dielectric constant (<TEX>$\varepsilon$</TEX><TEX>$\_$</TEX>r/) of 531. Low-temperature sinterable piezoelectric composition and high activity of fine particles reduced the sintering temperature of the thick film. This PZT thick film could be utilized for piezoelectric microactuators or microsensors that require Si micromachining technology.
Improvements on the purification of mannan-binding lectin and demonstration of its Ca2+-independent association with a C1s-like serine protease (1996)

Mannan-binding lectin (MBL), previously called 'mannan-binding protein' or MBP, is a plasma C-type lectin which, upon binding to carbohydrate structures on micro-organisms, activates the classical pathway of complement. Purification of MBL relies on its Ca(2+)-dependent affinity for carbohydrate, but existing methods are susceptible to contamination by anti-carbohydrate antibodies. In the present study a sequential-sugar-elution method has been developed which can achieve a preparation of virtually pure MBL and its associated serine protease (MBL-associated serine protease, MASP) by two steps of affinity chromatography. In further separation of MASP from MBL, it was found that activated MASP was associated with MBL independent of Ca2+. Since MBL was found to bind to underivatized Sepharose 4B, the MBL-MASP complex was purified using Sepharose 4B and protease inhibitors were included to purify the complex with MASP in its proenzyme form. Analysis of thus-purified MBL-MASP complex by gel filtration on a Sephacryl S-300 column at pH 7.8 showed that the proenzyme MASP was also associated with MBL independently of Ca2+, but that the complex could be disrupted at a low pH (5.0). Therefore the mechanism of MBL-MASP-mediated complement activation appears to be significantly different from the C1-mediated classical pathway.
Selective Inhibitors of Aldo-Keto Reductases AKR1C1 and AKR1C3 Discovered by Virtual Screening of a Fragment Library (2012)

Human aldo-keto reductases 1C1-1C4 (AKR1C1-AKR1C4) function in vivo as 3-keto-, 17-keto-, and 20-ketosteroid reductases and regulate the activity of androgens, estrogens, and progesterone and the occupancy and transactivation of their corresponding receptors. Aberrant expression and action of AKR1C enzymes can lead to different pathophysiological conditions. AKR1C enzymes thus represent important targets for development of new drugs. We performed a virtual high-throughput screen of a fragment library that was followed by biochemical evaluation on AKR1C1-AKR1C4 enzymes. Twenty-four structurally diverse compounds were discovered with low μM K(i) values for AKR1C1, AKR1C3, or both. Two structural series included the salicylates and the N-phenylanthranilic acids, and additionally a series of inhibitors with completely novel scaffolds was discovered. Two of the best selective AKR1C3 inhibitors had K(i) values of 0.1 and 2.7 μM, exceeding expected activity for fragments. The compounds identified represent an excellent starting point for further hit-to-lead development.
Detection and analysis of microRNAs using LNA (locked nucleic acid)-modified probes (2007)

MicroRNAs (miRNAs) are an abundant class of short endogenous RNAs that act as post-transcriptional regulators of gene expression by base-pairing with their target mRNAs. To date more than 3500 microRNAs have been annotated in vertebrates, invertebrates and plants according to the miRBase microRNA database release 8.0 in February 2006 (Griffiths-Jones, 2004; Griffiths-Jones et al., 2006), and many miRNAs that correspond to putative genes have also been identified. The miRNAs identified to date represent most likely the tip of the iceberg, and the number of miRNAs might turn out to be very large. Recent bioinformatic predictions combined with array analyses, small RNA cloning and Northern blot validation indicate that the total number of miRNAs in vertebrate genomes is significantly higher than previously estimated and maybe as many as 1000 (Bentwich et al., 2005; Berezikov et al., 2005; Xie et al., 2005). An increasing body of research shows that animal miRNAs play fundamental biological roles in cell growth and apoptosis (Brennecke et al., 2003), hematopoietic lineage differentiation (Chen et al., 2004), life-span regulation (Boehm and Slack, 2005), photoreceptor differentiation (Li and Carthew, 2005), homeobox gene regulation (Yekta et al., 2004; Hornstein et al., 2005), neuronal asymmetry (Johnston and Hobert, 2003), insulin secretion (Poy et al., 2004), brain morphogenesis (Giraldez et al., 2005), muscle proliferation and differentiation (Chan et al., 2005; Kwon et al., 2005; Sokol and Ambros, 2005), cardiogenesis (Zhao et al., 2005) and late embryonic development in vertebrates (Wienholds et al., 2005).