gebhart/patrepeval huggingface dataset:
Cloning, expression, and purification of human cyclophilin in Escherichia coli and assessment of the catalytic role of cysteines by site-directed mutagenesis. (1990)

The cDNA encoding human cyclophilin from the Jurkat T-cell lymphoma line has been cloned by the expression cassette polymerase chain reaction and sequenced, and an expression vector has been constructed under control of the tac promoter for efficient expression in Escherichia coli. Active cyclophilin is produced at up to 40% of soluble cell protein, facilitating a one-column purification to homogeneity. Wild-type cyclophilin was characterized for binding of the potent immunosuppressant agent cyclosporin A (Kd = 46 nM) by tryptophan fluorescence enhancement and for inhibition (IC50 = 19 nM) of cyclophilin's peptidyl-prolyl cis-trans isomerase (rotamase) activity. With N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as the substrate, recombinant human cyclophilin has a high catalytic efficiency; kcat/Km is 1.4 X 10(7) M-1.S-1 at 10 degrees C. To test the prior suggestion that a cysteine residue may be essential for catalysis and immunosuppressant binding, the four cysteines at positions 52, 62, 115, and 161 were mutated individually to alanine and the purified mutant proteins were shown to retain full affinity for cyclosporin A and equivalent catalytic efficiency as a rotamase. Clearly the cysteines play no essential role in catalysis or cyclosporin A binding. These results rule out the recently proposed mechanism [Fischer, G., Wittmann-Liebold, B., Lang, K., Kiefhaber, T. & Schmid, F. X. (1989) Nature (London) 337, 476-478)] involving the formation of tetrahedral hemithioorthoamide. Whereas mechanisms that embody other tetrahedral intermediates may be operative, an alternative mechanism is considered that involves distortion of bound substrate with a twisted (90 degrees) peptidyl-prolyl amide bond.
Decomposition Property of Methylhydrazine with Titanium Nitridation at Low Temperature (1995)

We studied the thermal decomposition properties of methylhydrazine (MH) which is used in the chemical vapor deposition (CVD) of titanium‐nitride . The decomposition was carried out on the surfaces of silicon dioxide and titanium (Ti) at low pressures. The by‐products were detected by the gas chromatography mass‐spectrometry (GCMS), and surfaces were analyzed by electron spectroscopy for chemical analysis and Auger electron spectroscopy. MH decomposed on surface above 400°C, producing methane , ammonia , and monomethylamine (MMA). Above 650°C, and were predominantly generated instead of MH. The decomposition temperature on the Ti substrate was 200°C and was even lower than the temperature on . As the substrate temperature increased, Ti was converted to approaching a stoichiometric around 500°C. As a result, MMA was observed around 400°C. Due to the formation of and its poor capability for donating electrons rather than Ti, the MH decomposition rate was reduced as temperature increased above 400°C.
Autoimmune disease : aetiopathogenesis, diagnosis and treatment (1994)

Part 1: Aetiology: Focus on Autoimmune Diseases: Analysis of B Cells in Rheumatoid Inflammation by Hybridoma Clones Mechanisms Involved in Breakdown of Tolerance to Self The Human B Cell Repertoire: Is Repertoire Bias a Manifestation of Life Saver V Genes The Nature of the Antigens Driving Autoimmune Disease Part 2: Mechanisms of Pathogenesis: On the Origin of Human Autoantibodies The Regulation of Autoimmunity Through CD4+T Cells Thyroglobulin: A Model Autoantigen Cellular and Genetic Mechanisms at the Origin of SLE: A Unifying Hypothesis Cytokine Profiles in Human Diseases with Particular Attention to Rheumatoid Arthritis Part 3: Diagnosis: Diagnosis of Autoimmune Disease: Past and Present Part 4: Treatment: Antigen Receptors as Targets for Therapy in Autoimmune Diseases Reprogramming the Immune System Cyclosporin and Some New Immunosuppressive Drugs in the Treatment of Autoimmune Diseases The Potential for Antisense and Antigene Treatment of Human Disease
TREM-1 interaction with the LPS/TLR4 receptor complex (2011)

Triggering receptor expressed on myeloid cells 1 (TREM-1) is an activating receptor expressed on neutrophils and monocytes that amplifies inflammation induced by stimulation of pattern-recognition receptors. In this study, several lines of evidence are presented that TREM-1 interacts with the toll-like receptor 4 (TLR4) receptor complex, or is a component of this complex. Blocking anti-TREM-1 antibodies specifically inhibited LPS-induced TNF-α production, while the alternative approach of blocking TLR4 by a specific inhibitor led to a down-regulation of the effects of TREM-1 cross-linking. These data are in line with the TLR4-TREM1 co-localization in human neutrophils and suggests that, at least some of the biological effects of TREM-1 may be due to its interaction with the TLR4/LPS-receptor complex.
The BH3 α-Helical Mimic BH3-M6 Disrupts Bcl-XL, Bcl-2, and MCL-1 Protein-Protein Interactions with Bax, Bak, Bad, or Bim and Induces Apoptosis in a Bax- and Bim-dependent Manner (2010)

A critical hallmark of cancer cell survival is evasion of apoptosis. This is commonly due to overexpression of anti-apoptotic proteins such as Bcl-2, Bcl-X(L), and Mcl-1, which bind to the BH3 α-helical domain of pro-apoptotic proteins such as Bax, Bak, Bad, and Bim, and inhibit their function. We designed a BH3 α-helical mimetic BH3-M6 that binds to Bcl-X(L) and Mcl-1 and prevents their binding to fluorescently labeled Bak- or Bim-BH3 peptides in vitro. Using several approaches, we demonstrate that BH3-M6 is a pan-Bcl-2 antagonist that inhibits the binding of Bcl-X(L), Bcl-2, and Mcl-1 to multi-domain Bax or Bak, or BH3-only Bim or Bad in cell-free systems and in intact human cancer cells, freeing up pro-apoptotic proteins to induce apoptosis. BH3-M6 disruption of these protein-protein interactions is associated with cytochrome c release from mitochondria, caspase-3 activation and PARP cleavage. Using caspase inhibitors and Bax and Bak siRNAs, we demonstrate that BH3-M6-induced apoptosis is caspase- and Bax-, but not Bak-dependent. Furthermore, BH3-M6 disrupts Bcl-X(L)/Bim, Bcl-2/Bim, and Mcl-1/Bim protein-protein interactions and frees up Bim to induce apoptosis in human cancer cells that depend for tumor survival on the neutralization of Bim with Bcl-X(L), Bcl-2, or Mcl-1. Finally, BH3-M6 sensitizes cells to apoptosis induced by the proteasome inhibitor CEP-1612.
Low Density Lipoprotein Receptor-related Protein (LRP1) Regulates Rac1 and RhoA Reciprocally to Control Schwann Cell Adhesion and Migration (2010)

LDL receptor-related protein (LRP1) is expressed by Schwann cells in vivo mainly after injury to the peripheral nervous system (PNS). Schwann cells in primary culture, which provide a model of Schwann cells in the injured PNS, also express abundant LRP1. Herein, we show that LRP1 gene-silencing or treatment with receptor-associated protein (RAP) promotes Schwann cell adhesion and inhibits cell migration on fibronectin. LRP1 gene-silencing also resulted in the formation of prominent focal adhesions and actin stress fibers. These changes, which were induced by loss of LRP1 expression or activity, were explained mechanistically by an increase in activated RhoA, coupled with a decrease in activated Rac1. Known LRP1 ligands, including matrix metalloprotease-9, tissue-type plasminogen activator, and alpha(2)-macroglobulin activated Rac1 in LRP1-expressing Schwann cells. An inhibitor of Rac1 activation promoted Schwann cell adhesion. Conversely, in cells in which LRP1 was silenced, a Rho kinase inhibitor promoted migration and inhibited adhesion. These results demonstrate that direct binding of ligands to LRP1 controls activation of small Rho family GTPases. The effects of LRP1 gene-silencing and RAP implicate autocrine pathways involving endogenously produced LRP1 ligands. Regulation of Schwann cell migration by LRP1 may be important in PNS injury.
DISC: Deep Image Saliency Computing via Progressive Representation Learning (2016)

Salient object detection increasingly receives attention as an important component or step in several pattern recognition and image processing tasks. Although a variety of powerful saliency models have been intensively proposed, they usually involve heavy feature (or model) engineering based on priors (or assumptions) about the properties of objects and backgrounds. Inspired by the effectiveness of recently developed feature learning, we provide a novel deep image saliency computing (DISC) framework for fine-grained image saliency computing. In particular, we model the image saliency from both the coarse-and fine-level observations, and utilize the deep convolutional neural network (CNN) to learn the saliency representation in a progressive manner. In particular, our saliency model is built upon two stacked CNNs. The first CNN generates a coarse-level saliency map by taking the overall image as the input, roughly identifying saliency regions in the global context. Furthermore, we integrate superpixel-based local context information in the first CNN to refine the coarse-level saliency map. Guided by the coarse saliency map, the second CNN focuses on the local context to produce fine-grained and accurate saliency map while preserving object details. For a testing image, the two CNNs collaboratively conduct the saliency computing in one shot. Our DISC framework is capable of uniformly highlighting the objects of interest from complex background while preserving well object details. Extensive experiments on several standard benchmarks suggest that DISC outperforms other state-of-the-art methods and it also generalizes well across data sets without additional training. The executable version of DISC is available online: http://vision.sysu.edu.cn/projects/DISC.
Source model for transform video coder and its application. II. Variable frame rate coding (1997)

In the first part of this paper, we derived a source model describing the relationship between bits, distortion, and quantization step size for transform coders. Based on this source model, a variable frame rate coding algorithm is developed. The basic idea is to select a proper picture frame rate to ensure a minimum picture quality for every frame. Because our source model can predict approximately the number of coded bits when a certain quantization step size is used, we could predict the quality and bits of coded images without going through the entire real-coding process. Therefore, we could skip the right number of picture frames to accomplish the goal of constant image quality. Our proposed variable frame rate coding schemes are simple but quite effective as demonstrated by simulation results. The results of using another variable frame rate scheme, Test Model for H.263 (TMN-5), and the results of using a fixed frame rate coding scheme, Reference Model 8 for H.261 (RM8), are also provided for comparison.
<title>Interferometric metrology of wafer nanotopography for advanced CMOS process integration</title> (2001)

According to industry standards (SEMI M43, Guide for Reporting Wafer Nanotopography), Nanotopography is the non- planar deviation of the whole front wafer surface within a spatial wavelength range of approximately 0.2 to 20 mm and within the fixed quality area (FQA). The need for precision metrology of wafer nanotopography is being actively addressed by interferometric technology. In this paper we present an approach to mapping the whole wafer front surface nanotopography using an engineered coherence interferometer. The interferometer acquires a whole wafer raw topography map. The raw map is then filtered to remove the long spatial wavelength, high amplitude shape contributions and reveal the nanotopography in the filtered map. Filtered maps can be quantitatively analyzed in a variety of ways to enable statistical process control (SPC) of nanotopography parameters. The importance of tracking these parameters for CMOS gate level processes at 180-nm critical dimension, and below, is examined.
Skin Effect and Proximity Effect in Tubular Conductors (1922)

The effective a-c. resistance of tubular conductors is required to be predetermined by designers, for radio installations, for large underground cables with non-magnetic cores, and for electric furnace circuits. (See Examples I to IV). For the above purpose, sets of curves are given in this paper. The skin effect ratio for isolated tubes is shown in Fig. 1. For stranded conductors, the resistance must be multiplied also by a ratio for the spirality effect, as is approximately indicated in Fig. 2. When the return conductor is near, a ratio for the proximity effect, as indicated in Fig. 3, is also to be used. A calculation for the proximity effect ratio for thin tubes is made, and the results are compared with tests in Fig. 3. Some of the requirements for future research work on skin effect are discussed. The conclusion is expressed that it seems scarcely worth while providing a non-magnetic core with a 2,000,000 cir. mil, 25-cycle cable in order to reduce the skin effect, but with the other cases considered, the tubular form seems very advantageous.
Electron Mobility and Injection Dynamics in Mesoporous ZnO, SnO2, and TiO2 Films Used in Dye-Sensitized Solar Cells (2011)

High-performance dye-sensitized solar cells are usually fabricated using nanostructured TiO(2) as a thin-film electron-collecting material. However, alternative metal-oxides are currently being explored that may offer advantages through ease of processing, higher electron mobility, or interface band energetics. We present here a comparative study of electron mobility and injection dynamics in thin films of TiO(2), ZnO, and SnO(2) nanoparticles sensitized with Z907 ruthenium dye. Using time-resolved terahertz photoconductivity measurements, we show that, for ZnO and SnO(2) nanoporous films, electron injection from the sensitizer has substantial slow components lasting over tens to hundreds of picoseconds, while for TiO(2), the process is predominantly concluded within a few picoseconds. These results correlate well with the overall electron injection efficiencies we determine from photovoltaic cells fabricated from identical nanoporous films, suggesting that such slow components limit the overall photocurrent generated by the solar cell. We conclude that these injection dynamics are not substantially influenced by bulk energy level offsets but rather by the local environment of the dye-nanoparticle interface that is governed by dye binding modes and densities of states available for injection, both of which may vary from site to site. In addition, we have extracted the electron mobility in the three nanoporous metal-oxide films at early time after excitation from terahertz conductivity measurements and compared these with the time-averaged, long-range mobility determined for devices based on identical films. Comparison with established values for single-crystal Hall mobilities of the three materials shows that, while electron mobility values for nanoporous TiO(2) films are approaching theoretical maximum values, both early time, short distance and interparticle electron mobility in nanoporous ZnO or SnO(2) films offer considerable scope for improvement.
Phosphonate-containing inhibitors of tyrosine-specific protein kinases (1991)

Tyrosine-specific protein kinases (TPK) are important signal transducing enzymes involved in normal cellular growth and differentiation and have been implicated in the etiology of a number of human neoplastic processes. Efforts to develop agents which inhibit the function of these enzymes by interfering with the binding of substrate have been limited by the lack of detailed three-dimensional structural data. Many inhibitors of substrate binding share a common styrene nucleus 1 which has been postulated to function as a conformationally constrained analogue of tyrosine. In an effort to develop high-affinity compounds based on this hypothesis, a number of derivatives were synthesized in which either methylphosphonate (4a-c) or (hydroxymethyl)phosphonate (3a-c) were appended to the aromatic 4-position of styrene-containing moieties. The intent of this approach was to prepare hydrolytically stable analogues which expressed additional enzyme recognition features present during the phosphorylation of tyrosine itself. None of the analogues showed inhibitory activity up to the maximum concentration tested (1000 microM) when assayed against autophosphorylation of A-431-derived epidermal growth factor receptor (EGFR) or p56lck (autophosphorylation and transphosphorylation of rabbit muscle enolase). Additionally, a series of naphthalene-based inhibitors including (1-naphthalenylhydroxymethyl)phosphonic acid (14), its known 2-positional isomer 16, and sulfonate (19, 20) and phosphate derivatives (17, 18) were also tested under similar conditions. Only (2-naphthalenyl-hydroxymethyl)phosphonic acid (16) showed activity (IC50 = 250 microM in EGFR, in agreement with the reported literature value). These results suggest that the interaction of styrene-based inhibitors with the substrate binding domain of TPKS may not occur in a manner analogous to the interaction of tyrosine with this domain.
Human antibodies from phage libraries: neutralizing activity against human immunodeficiency virus type 1 equally improved after expression as Fab and IgG in mammalian cells (1996)

Human antibodies against HIV-1 have been sought to study neutralization events on the molecular level, and for possible use in passive immune intervention. The development of phage display techniques has opened the possibility of rapidly generating human monoclonal antibodies with desired specificities. We and others have isolated human HIV-1 neutralizing antibody fragments using this technique. Bacterial expression of isolated clones does, however, differ broadly both in expression levels and functional activity. In addition, intact IgG cannot be expressed in bacteria. By transferring the genes of isolated Fab clones to a mammalian expression system we could perform a comparison of functional activity between Fab expressed in bacterial and mammalian cells, as well as Fab and whole IgG. Fab fragments expressed in mammalian cells showed increased virus neutralizing activity compared to the same Fab clones expressed in Escherichia coli, underlining the inefficiency of procaryotic expression. No difference in HIV-1 neutralizing capacity was detected between monovalent (Fab) and divalent (whole antibody) reagents expressed in CHO cells. Thus, bivalency does not always confer improved neutralization efficacy.
Akt-Mediated Phosphorylation of EZH2 Suppresses Methylation of Lysine 27 in Histone H3 (2005)

Enhancer of Zeste homolog 2 (EZH2) is a methyltransferase that plays an important role in many biological processes through its ability to trimethylate lysine 27 in histone H3. Here, we show that Akt phosphorylates EZH2 at serine 21 and suppresses its methyltransferase activity by impeding EZH2 binding to histone H3, which results in a decrease of lysine 27 trimethylation and derepression of silenced genes. Our results imply that Akt regulates the methylation activity, through phosphorylation of EZH2, which may contribute to oncogenesis.
G4 motifs correlate with promoter-proximal transcriptional pausing in human genes (2011)

The RNA Pol II transcription complex pauses just downstream of the promoter in a significant fraction of human genes. The local features of genomic structure that contribute to pausing have not been defined. Here, we show that genes that pause are more G-rich within the region flanking the transcription start site (TSS) than RefSeq genes or non-paused genes. We show that enrichment of binding motifs for common transcription factors, such as SP1, may account for G-richness upstream but not downstream of the TSS. We further show that pausing correlates with the presence of a GrIn1 element, an element bearing one or more G4 motifs at the 5'-end of the first intron, on the non-template DNA strand. These results suggest potential roles for dynamic G4 DNA and G4 RNA structures in cis-regulation of pausing, and thus genome-wide regulation of gene expression, in human cells.
Regulation Of Gene Expression In Higher Plants (1987)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
Total Synthesis and Biological Evaluation of Amaryllidaceae Alkaloids:  Narciclasine, ent-7-Deoxypancratistatin, Regioisomer of 7-Deoxypancratistatin, 10b-epi-Deoxypancratistatin, and Truncated Derivatives. (2003)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionTotal Synthesis and Biological Evaluation of Amaryllidaceae Alkaloids: Narciclasine, ent-7-Deoxypancratistatin, Regioisomer of 7-Deoxypancratistatin, 10b-epi-Deoxypancratistatin, and Truncated Derivatives.Tomas Hudlicky, Uwe Rinner, David Gonzalez, Hulya Akgun, Stefan Schilling, Peter Siengalewicz, Theodore A. Martinot, and George R. PettitCite this: J. Org. Chem. 2003, 68, 2, 674Publication Date (Web):January 1, 2003Publication History Published online1 January 2003Published inissue 1 January 2003https://pubs.acs.org/doi/10.1021/jo0235930https://doi.org/10.1021/jo0235930correctionACS PublicationsCopyright © 2003 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views664Altmetric-Citations2LEARN 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 PDF (15 KB) Get e-Alertsclose Get e-Alerts