gebhart/patrepeval huggingface dataset:
Histone hypercitrullination mediates chromatin decondensation and neutrophil extracellular trap formation (2009)

Peripheral blood neutrophils form highly decondensed chromatin structures, termed neutrophil extracellular traps (NETs), that have been implicated in innate immune response to bacterial infection. Neutrophils express high levels of peptidylarginine deiminase 4 (PAD4), which catalyzes histone citrullination. However, whether PAD4 or histone citrullination plays a role in chromatin structure in neutrophils is unclear. In this study, we show that the hypercitrullination of histones by PAD4 mediates chromatin decondensation. Histone hypercitrullination is detected on highly decondensed chromatin in HL-60 granulocytes and blood neutrophils. The inhibition of PAD4 decreases histone hypercitrullination and the formation of NET-like structures, whereas PAD4 treatment of HL-60 cells facilitates these processes. The loss of heterochromatin and multilobular nuclear structures is detected in HL-60 granulocytes after PAD4 activation. Importantly, citrullination of biochemically defined avian nucleosome arrays inhibits their compaction by the linker histone H5 to form higher order chromatin structures. Together, these results suggest that histone hypercitrullination has important functions in chromatin decondensation in granulocytes/neutrophils.
Highly Enantioselective Ring Opening of Epoxides Catalyzed by (salen)Cr(III) Complexes (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHighly Enantioselective Ring Opening of Epoxides Catalyzed by (salen)Cr(III) ComplexesLuis E. Martinez, James L. Leighton, Douglas H. Carsten, and Eric N. JacobsenCite this: J. Am. Chem. Soc. 1995, 117, 21, 5897–5898Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/ja00126a048https://doi.org/10.1021/ja00126a048research-articleACS PublicationsRequest reuse permissionsArticle Views6756Altmetric-Citations531LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. (1984)

The GAL1 and GAL10 genes of Saccharomyces cerevisiae are divergently transcribed, with 606 base pairs of DNA separating their transcription initiation sites. These two genes are stringently coregulated: their expression is induced ca. 1,000-fold in cells growing on galactose and is repressed by growth on glucose. The nucleotide sequence of the region of DNA between these genes and the precise sites of transcription initiation are presented here. The most notable feature of the nucleotide sequence of this region is a 108-base-pair guanine-plus-cytosine-rich stretch of DNA located approximately in the middle of the region between GAL1 and GAL10. Analysis of the effects of mutations that alter the region between these two genes, constructed in vitro or selected in vivo, suggest that these guanine-plus-cytosine-rich sequences are required for the expression of both genes. The region of DNA between GAL1 and GAL10 is sufficient for regulation of expression of these genes: fusion of the region to the yeast HIS3 gene places HIS3 under GAL control.
A Planar Array of Micro-Fabricated Electrospray Emitters for Thruster Applications (2006)

This paper reports the design, fabrication, and experimental characterization of a planar array of micro-fabricated electrospray emitters intended for space propulsion applications in micro–satellites. The engine uses the ionic liquid EMI-BF <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$_4$</tex> as propellant. Electrospray engines take advantage of the electrohydrodynamic effect known as Taylor cone to produce thrust. The array is designed with an open architecture and it is composed of a set of spikes, i.e., emitters, coming out from a propellant pool. There are two configurations for the emitters: fully sharpened slender emitters, i.e., pencils, and truncated pyramidal emitters, i.e., volcanoes. The arrays have between 4 and 1024 emitters in an active area of 0.64 <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$ cm^2$</tex> . The surface of the engine (tank and emitters) is covered with “black silicon” that acts as wicking material. The micro-fabrication of the engine is described. The paper reports experimental characterization of the hydraulics system including wettability tests, current/emitter–voltage characteristics, and imprints of the exit stream on a collector. Preliminary results demonstrating the feasibility of obtaining substantially larger emission currents at the same extraction voltage by controlling the temperature are also reported. The paper compares the experimental current/emitter–voltage characteristics with relevant theories of field emission of electrons.1433
Sweetness and mechanism of picric in stevioside (2007)

From molecular structure of chemistry,picric in stevioside,sweetness,the relation between sweetness,aglycone join position and join glucosyl quantity were discussed in the paper.Enzyme catalysis improve picric of total stevioside introduced and offer new technique method.
Ne mettons à l'écart ni le symbolique ni la guérison (2009)

que dans les limites des conditions générales d'utilisation du site ou, le cas échéant, des conditions générales de la licence souscrite par votre établissement.
Chimeric oligodeoxynucleotide analogues: enhanced cell uptake of structures which direct ribonuclease H with high specificity. (1993)

A previous report has demonstrated that normal phosphodiester oligodeoxynucleotides could direct extensive non-targeted ribonuclease (RNase) H-dependent effects, and that greatly enhanced specificity could be achieved upon methylphosphonodiester substitution of terminal phosphodiester residues. In this report, we extend our previous observations to show that phosphorothioate oligodeoxynucleotides also direct substantial inappropriate RNase H-mediated hydrolysis of non-targeted RNA. Chimeric methylphosphonodiester/phosphodiesters were found to be capable of efficiently directing RNase H when the central phosphodiester section was reduced to just two contiguous internucleoside linkages. Furthermore, cleavage of non-target RNA sites was found to be undetectable, or minimal in extent, when RNase H was directed by such chimeras. In addition, we show that analogue structures which contain three, or fewer, phosphodiester residues in otherwise methylphosphonodiester molecules were imported into cells via the comparatively more efficient route taken by methylphosphonates, rather than by receptor-mediated endocytosis, which is generally characteristic for polyanionic structures. Evidence is presented that the primary process responsible for enhanced uptake is an active mechanism. Nevertheless, a proportion of the applied oligodeoxynucleotide analogues, which demonstrate augmented uptake, appear to have penetrated into the cytoplasmic cellular compartment. The present results suggest that chimeric molecules of the type we describe here may show considerable utility as antisense effectors due to their increased cellular import, access to the intracellular compartments, and their highly efficient and specific direction of RNase H.
The gamma evaluation method as a routine QA procedure of IMRT (2009)

The conventional QA procedures dedicated to 3D CRT are unsatisfactory if the dMLC is in operation. In the case of IMRT not only should the dose on the beam axis, but also its distribution in the total plane perpendicular to the beam be taken under control. The comparison between the predicted and the observed fluence can be achieved using the gamma method. It takes into consideration the dose difference and the spatial displacement between analyzed points to provide a γ-index as a result of comparison. The aim of the investigation was to develop the procedure of IMRT verification based on the gamma algorithm. 700 patients have been irradiated using IMRT since 2002. Over 1500 images recorded on the film and/or EPID have been analyzed with the help of self-made software. Histograms of γ-value and the γ-images have been created for each field. The fields have been classified depending on tumour location and the method of dose delivery, to obtain an average result for each class. We have performed a comparison of γ-histograms acquired with the help of different methods of recording. We have observed a correlation between results of verification obtained with the help of the gamma algorithm and the method of intensity modulation. Gamma evaluation allows one to find local hot-spots caused by irregularities in leaf motion or the tongue-and-groove effect.
β-Turn Phe in HIV-1 Env Binding Site of CD4 and CD4 Mimetic Miniprotein Enhances Env Binding Affinity but Is Not Required for Activation of Co-Receptor/17b Site (2002)

HIV-1 enters a host cell after an initial interaction between viral envelope glycoprotein gp120 and cell surface receptor CD4, followed by a second interaction between gp120 and a cell surface chemokine receptor. CD4 residue Phe43 makes a significant contribution to the high-affinity interaction between CD4 and env. We and others have used scorpion toxin scaffolds to display and examine CD4 epitopes used for gp120 recognition. These peptides, which have a beta-turn Phe that acts as a Phe43 surrogate, compete with CD4 for gp120 binding and enhance the binding of gp120 to 17b, an antibody that binds near the co-receptor-binding site. In the current study, a scyllatoxin-scaffolded peptide, identified via phage epitope randomization and lacking a beta-turn Phe (indeed, containing no aromatic residues), was shown to behave in a distinctly CD4-like manner. This peptide, denoted [20EGLV23]ST, not only competed with CD4 for gp120 binding, but also enhanced the binding of gp120 to 17b. Quantitatively, an [20EGLV23]ST-gp120 complex exhibited the same 17b binding on-rate as a complex of gp120 with [20AGSF23]ST, a scyllatoxin-based CD4 mimetic peptide containing a beta-turn Phe. In view of this result, we examined the role of Phe43 in CD4 itself by comparing F43V D1D2 sCD4 versus D1D2 sCD4. Like the peptides, a close similarity was observed for both Phe43 and Phe43-less D1D2 sCD4s in enhancing gp120 binding to 17b. Further, when examined for their ability to enhance binding of gp120 to CCR5+ cells, [20EGLV23]ST and [20AGSF23]ST were found to have the same efficacy, after correcting for the difference in their gp120 affinities. These results show that, although Phe43 is important in maintaining high affinity in gp120 ligands, the aromatic residue is not necessary for triggering the conformational isomerization in gp120 that results in formation or exposure of the binding sites for the 17b antibody and the CCR5 receptor.
STAT-1 Signaling in Human Lung Fibroblasts Is Induced by Vanadium Pentoxide through an IFN-β Autocrine Loop (2008)

The inhalation of vanadium pentoxide (V(2)O(5)) results in bronchitis and airway fibrosis. The lung fibrotic response to V(2)O(5) partially resolves where fibroblasts first proliferate and deposit collagen, but then undergo growth arrest and apoptosis. STAT-1 mediates fibroblast growth arrest and apoptosis. We previously reported that STAT-1 is a protective factor and mice lacking STAT-1 are more susceptible to lung fibrosis. We also reported that V(2)O(5)-induced STAT-1 phosphorylation in lung fibroblasts requires H(2)O(2) and de novo protein synthesis. In this study, we identified IFN-beta as the protein that mediates STAT-1 activation by V(2)O(5) in normal human lung fibroblasts and identified NADPH and xanthine oxidase systems as sources of H(2)O(2) that drive IFN-beta gene expression. STAT-1 phosphorylation was decreased with neutralizing Abs to IFN-beta as well as an inhibitor of JAK. V(2)O(5) also increased transcription of an IFN-inducible and STAT-1-dependent chemokine, CXCL10. Inhibition of H(2)O(2)-generating enzyme systems NADPH oxidase by apocynin and xanthine oxidase by allopurinol individually reduced STAT-1 phosphorylation. Apocynin and allopurinol also decreased V(2)O(5)-induced IFN-beta mRNA levels and CXCL10 expression. IFN-alpha transcription was inhibited only by allopurinol. Taken together, these data indicate that fibroblasts play a role in the innate immune response to vanadium-induced oxidative stress by synthesizing IFN-beta and activating STAT-1 to cause growth arrest and increase levels of CXCL10, a potent antifibrotic factor. This mechanism is postulated to counterbalance profibrogenic mechanisms that follow V(2)O(5) injury.
Software defined optical network (2012)

Software define network, which has good potential for packet-switched IP network, is currently not available on circuit-switched transport network. This paper introduces the concept of software define optical network that applies SDN-like features to optical transport network, and reviews key enabling technologies at various layers, such as variable transponder, flexible switching node, control applications, and open interface with circuit extension.
Clinical features and prognosis of hepatocellular carcinoma with reference to serum alpha-fetoprotein levels. Analysis of 606 patients (1989)

Clinical features of hepatocellular carcinoma (HCC) with normal serum alpha-fetoprotein (AFP) levels were compared with those of AFP-positive cases. A total of 606 patients were divided into four groups based on their serum AFP levels at the time of diagnosis: group 1 (less than or equal to 20 ng/ml, N = 125), group 2 (20-1000 g/ml, N = 256), group 3 (1000-10000 ng/ml, N = 149), and group 4 (greater than 10000 ng/ml, N = 76). Increasing prevalence of group 1 patients and decreasing prevalence of group 4 were noted during the last 9 years. The proportion of hepatitis B virus-positive cases was significantly lower in group 1 than in group 4. The serum glutamic oxaloacetic transaminase/serum glutamic pyruvic transaminase ratio was found to be significantly higher in group 4 than in group 1 regardless of the size of the tumors. The survival rates were compared among the four groups in size matched cases since the size of the tumor significantly influenced their prognosis. The median survival in relatively small HCC patients (less than or equal to 5 cm in diameter, N = 199) were 24.6 months for group 1, 20.6 months for group 2, and 13.7 months for group 3 patients; and those in large HCC (greater than 50% in the proportion of the tumor area, N = 200) were 15.1 months for group 1, 6.3 months for group 2, 5.8 months for group 3, and 5.2 months for group 4. Thus, serum AFP values at the time of presentation are not only of diagnostic value, but also of prognostic significance in patients with HCC.
Multiplex epitope mapping using bacterial surface display reveals both linear and conformational epitopes (2012)

As antibody-based diagnosis and therapy grow at an increased pace, there is a need for methods which rapidly and accurately determine antibody-antigen interactions. Here, we report a method for the multiplex determination of antibody epitopes using bacterial cell-surface display. A protein-fragment library with 10(7) cell clones, covering 60 clinically-relevant protein targets, was created and characterized with massively parallel sequencing. Using this multi-target fragment library we determined simultaneously epitopes of commercial monoclonal and polyclonal antibodies targeting PSMA, EGFR, and VEGF. Off-target binding was observed for one of the antibodies, which demonstrates the methods ability to reveal cross-reactivity. We exemplify the detection of structural epitopes by mapping the therapeutic antibody Avastin. Based on our findings we suggest this method to be suitable for mapping linear and structural epitopes of monoclonal and polyclonal antibodies in a multiplex fashion and could find applicability in serum profiling as well as other protein-protein interaction studies.
Alloying effects on superionic conductivity in lithium indium halides for all-solid-state batteries (2018)

Alloying of anions is a promising engineering strategy for tuning ionic conductivity in halide-based inorganic solid electrolytes. We explain the alloying effects in Li3InBr6−xClx, in terms of strain, chemistry, and microstructure, using first-principles molecular dynamics simulations and electronic structure analysis. We find that strain and bond chemistry can be tuned through alloying and affect the activation energy and maximum diffusivity coefficient. The similar conductivities of the x = 3 and x = 6 compositions can be understood by assuming that the alloy separates into Br-rich and Cl-rich regions. Phase-separation increases diffusivity at the interface and in the expanded Cl-region, suggesting microstructure effects are critical. Similarities with other halide superionic conductors are highlighted.
Quantisation Techniques for Prototype Waveforms (1996)

Speech coders based on Prototype Waveform techniques can produce speech at rates as low as 2.4kbIs. These coders represent the speech residual by a series of pitch length characteristic or prototype waveform which are aligned and interpolated to rcumstruct the excitation at the receiver. The Prototype Waveforms can be decomposed into noisy and periodic components for quantisation. This paper examines the different quantisation requirements of these two distinct, variable-length vector components and describes codebook solutions leading to near-Toll quality Multi-Rototype Waveform coders at bit-rates from 2.4 to4kbIs.
Time management in distributed factory simulation, a case study using HLA (2005)

DAistributed simulation is attractive for modeling large scale manufacturing systems. However, synchronization requirements present distinct challenges in designing and implementing a suitable modeling structure. Our experience in building a distributed simulation model for 300mm wafer fab using the High Level Architecture (HLA) shows that time management should be considered at both the design and the implementation stages. This paper proposes an optimistic-conservative synchronization scheme by using model specific information at the implementation stage. Computational results are then presented to show that properly implemented distributed factory simulation can achieve significant reduction in model execution time.
Molecular Recognition of Sialic Acid End Groups by Phenylboronates (2005)

A multinuclear NMR study of the interaction between phenylboronic acid (PBA) and sialic acid (Neu5 Ac) has been performed. The latter compound is known to be overexpressed on the cell surface of tumor cells. The results of this investigation suggest that the binding of PBA to sialic acid is pH dependent. 17O NMR experiments with glycolic acid as the model compound prove that an interaction at the alpha-hydroxycarboxylate occurs at pH < 9, while a study with threonic and erythronic acids shows that the PBA group interacts selectively with the vicinal diol functions at higher pH. Similarly, Neu5 Ac binds PBA through its alpha-hydroxycarboxylate at low pH (< 9) and through its glycerol side chain at higher pH values. The conditional stability constant of the phenylboronate ester at pH 7.4 is 11.4. On cell surfaces, sialic acid is connected to the neighboring sugar unit through the 2-hydroxy group. To mimic this the 2-alpha-O-methyl derivative of Neu5 Ac was included in this study. The erythro configuration of the hydroxy substituents prevents stable-complex formation at positions C7 and C8 and, consequently, the strongest interaction is observed at positions C8 and C9, leading to a five-membered 2-boron-1,3-dioxalate. In addition, a relatively small amount of the C7-C9 six-membered complex was observed. Molecular modeling studies confirm that the C8-C9 boronate complex has the lowest energy.
Activity of purified QscR, a Pseudomonas aeruginosa orphan quorum‐sensing transcription factor (2005)

The opportunistic pathogen Pseudomonas aeruginosa has two acyl-homoserine lactone (acyl-HSL) signalling systems, LasR-I and RhlR-I. LasI catalyses the synthesis of N-3-oxododecanoyl homoserine lactone (3OC12) and LasR is a transcription factor that requires 3OC12 as a ligand. RhlI catalyses the synthesis of N-butanoyl homoserine lactone (C4) and RhlR is a transcription factor that responds to C4. LasR and RhlR control the transcription of hundreds of P. aeruginosa genes. There is a third P. aeruginosa LasR-RhlR homologue encoded by qscR for which there is no cognate acyl-HSL synthase gene. To test the hypothesis that QscR functions by direct control of specific promoters in an acyl-HSL-dependent manner we purified QscR and characterized QscR activity in vitro. We also studied QscR activity in recombinant Escherichia coli. QscR binds to promoters that have elements similar in sequence to those found in LasR- or RhlR-dependent promoters but QscR does not bind to the LasR- or RhlR-specific promoters we examined. QscR binding to DNA requires 3OC12, but QscR exhibits a relaxed acyl-HSL specificity compared with the 3OC12-cognate signal receptor LasR. Our results support the hypothesis that there is a specific QscR-dependent regulon. We show that QscR controls genes in this regulon directly and that regulation is dependent on an acyl-HSL produced by LasI. Because of its relaxed signal specificity QscR may also respond to acyl-HSLs made by other bacteria in mixed bacterial communities.
[Investigation of the level of genetical safety of urban population]. (2006)

As it is universally recognized, the population is a sound criteria of the environment quality. The most reliable method to evaluate genetic processes in a population under the condition of the environmental pollution is genetic monitoring, a survey of dynamic parameters of genetic load. An evaluation of genetical safety of an urbanized area of a city is represented in this article. The parameters of genetic load like congenital malformations and multifactorial diseases have been used in the models of monitoring. The analysis and comparison of disease frequencies in Kharkiv Dzerzhinsky District, in other European populations and in regional rural districts with various levels of production have been made.
MTBP Is Overexpressed in Triple-Negative Breast Cancer and Contributes to Its Growth and Survival (2014)

MTBP significantly contributes to breast cancer survival and is a potential novel therapeutic target in TNBC.