gebhart/patrepeval huggingface dataset:
Neutrophil Extracellular Traps Go Viral (2016)

Neutrophils are the most numerous immune cells. Their importance as the first line of defense against bacterial and fungal pathogens is well described. In contrast, the role of neutrophils in controlling viral infections is less clear. Bacterial and fungal pathogens can stimulate neutrophils extracellular traps (NETs) in a process called NETosis. Although NETosis has previously been described as a special form of programmed cell death, there are forms of NET production that do not end with the demise of neutrophils. As an end result of NETosis, genomic DNA complexed with microbicidal proteins is expelled from neutrophils. These structures can kill pathogens or at least prevent their local spread within host tissue. On the other hand, disproportionate NET formation can cause local or systemic damage. Only recently, it was recognized that viruses can also induce NETosis. In this review, we discuss the mechanisms by which NETs are produced in the context of viral infection and how this may contribute to both antiviral immunity and immunopathology. Finally, we shed light on viral immune evasion mechanisms targeting NETs.
Mutagenicity and genotoxicity of the major DNA adduct of the antitumor drug cis-diamminedichloroplatinum(II) (1993)

The mutagenicity and genotoxicity of cis-[Pt(NH3)2[d(GpG)-N7(1),-N7(2)]] (G*G*), the major DNA adduct of the antitumor drug cisplatin, has been investigated in Escherichia coli. A duplex bacteriophage M13 genome was constructed to contain the G*G* adduct at a specific site in the (-) strand. The singly platinated duplex genome exhibited a survival of 22% relative to that of the unplatinated control genomes, and this value rose to 38% in cells treated with ultraviolet light to induce the SOS response. Singly platinated single-stranded genomes were also produced. Replication of the single- and double-stranded genomes in vivo yielded SOS-dependent, targeted mutations at frequencies of 1.3% and 0.16%, respectively. The mutagenic specificity of G*G* in both single- and double-stranded DNA was striking in that 80-90% of the mutations occurred at the 5'-platinated G. Approximately 80% of the mutations were G-->T transversions at that site. A model of mutagenesis is presented to explain this mutational specificity with respect to current understanding of platinum-DNA adduct structure.
Isolation and structure of a cDNA encoding the B1 (CD20) cell-surface antigen of human B lymphocytes. (1988)

The B1 (CD20) molecule is a Mr 33,000 phosphoprotein on the surface of human B lymphocytes that may serve a central role in the humoral immune response by regulating B-cell proliferation and differentiation. In this report, a cDNA clone that encodes the B1 molecule was isolated and the amino acid sequence of B1 was determined. B-cell-specific cDNA clones were selected from a human tonsillar cDNA library by differential hybridization with labeled cDNA derived from either size-fractionated B-cell mRNA or size-fractionated T-cell mRNA. Of the 261 cDNA clones isolated, 3 cross-hybridizing cDNA clones were chosen as potential candidates for encoding B1 based on their selective hybridization to RNA from B1-positive cell lines. The longest clone, pB1-21, contained a 2.8-kilobase insert with an 891-base-pair open reading frame that encodes a protein of 33 kDa. mRNA synthesized from the pB1-21 cDNA clone in vitro was translated into a protein of the same apparent molecular weight as B1. Limited proteinase digestion of the pB1-21 translation product and B1 generated peptides of the same sizes, indicating that the pB1-21 cDNA encodes the B1 molecule. Gel blot analysis indicated that pB1-21 hybridized with two mRNA species of 2.8 and 3.4 kilobases only in B1-positive cell lines. The amino acid sequence deduced from the pB1-21 nucleotide sequence apparently lacks a signal sequence and contains three extensive hydrophobic regions. The deduced B1 amino acid sequence shows no significant homology with other known proteins.
Simultaneous measurement of gastric emptying, small bowel residence and colonic filling of a solid meal by the use of the gamma camera. (1986)

A method for determining the profiles of gastric emptying, small intestinal residence, and colonic filling of a solid test meal, labelled with 250 microCi 99mTechnetium sulphur colloid has been evaluated in nine healthy volunteers and six patients with a disturbance in bowel habit. Mean small bowel transit time was determined by deconvolving the rate of colonic filling with the rate of gastric emptying. In normal subjects, the stomach appeared to empty exponentially with a half time of 1.2 +/- 0.3 hours (mean +/- SD). Food reached the colon by 2.8 +/- 1.5 hours. The mean small bowel transit time was 4.0 +/- 1.4 hours. In most normal subjects, the colon appeared to fill in a linear fashion with approximately 16% food residues entering every hour, and the profile of colonic filling in normal subjects was similar to the profile of ileal emptying observed after feeding a similar radiolabelled solid meal to 14 patients equipped with terminal ileostomies. There was a highly significant correlation between the onset of breath hydrogen excretion and the appearance of radioactivity over the caecum (r = 0.88, p less than 0.01), though in one third of subjects the increase in caecal radioactivity preceded the rise in breath hydrogen concentration by more than 20 minutes. There was also a highly significant correlation between the mean transit time and values for colonic filling but not values for gastric emptying. Patients with irritable bowel syndrome who had diarrhoea tended towards short small bowel transit and early colonic filling, whereas patients who have constipation tended towards long small bowel transit and delayed colonic filling. This method offers a novel means of assessing small bowel transit time, small bowel residence and the profile of colonic filling in man.
Binding of chylomicron remnants and beta-very low density lipoproteins to hepatic and extrahepatic lipoprotein receptors. A process independent of apolipoprotein B48. (1984)

The ability of apolipoprotein (apo-) B48 to interact with lipoprotein receptors was investigated using three different types of lipoproteins. First, canine chylomicron remnants, which contained apo-B48 as their primary apoprotein constituent, were generated by the hydrolysis of chylomicrons with milk lipoprotein lipase. These apo-B48-containing chylomicron remnants are deficient in apo-E and reacted very poorly with apo-E receptors on adult dog liver membranes and the low density lipoprotein (apo-B,E) receptors on human fibroblasts. Addition of normal human apo-E3 restored the receptor binding activity of these lipoproteins. Second, beta-very low density lipoproteins (beta-VLDL) from cholesterol-fed dogs were subfractionated into distinct classes containing apo-E along with either apo-B48 or apo-B100. Both classes bound to the apo-B,E and apo-E receptors. Their binding was almost completely mediated by apo-E, as evidenced by the ability of the anti-apo-E to inhibit the receptor interaction. Third, beta-VLDL from type III hyperlipoproteinemic patients were subfractionated by immunoaffinity chromatography into lipoproteins containing apo-E plus either apo-B48 or apo-B100. Both subfractions bound poorly to apo-B,E and apo-E receptors due to the presence of defective apo-E2. However, the residual binding of the apo-B48-containing and apo-B100-containing human beta-VLDL was inhibited by the anti-apo-E. After lipase hydrolysis, apo-B100 became a more prominant determinant responsible for mediating receptor binding to the apo-B,E receptor. By contrast, lipase hydrolysis did not increase the binding activity of the apo-B48-containing beta-VLDL. These results indicate that apo-B48 does not play a direct role in mediating the interaction of lipoproteins with receptors on fibroblasts or liver membranes.
Analysis of immunoglobulin chain secretion using hybrid myelomas (1980)

Abstract Three different approaches have been used to study nonsecreting variants of myeloma and hybrid myeloma lines. Hemolytic plaque assays were used to screen nonsecreting and light (L) chain‐secreting anti‐sheep red blood cell hybrid myeloma variants for reversion to specific antibody or immunoglobulin (Ig) production. No revert ants were detected from among 1.5 × 10 7 −4.2 × 10 7 cells of each line studied. In the absence of a heavy (H) chain, the P3 (MOPC 21) x chain is not secreted but degraded intracellularly. The nature of this secretion defect was investigated in a hybrid myeloma line that produces the P3 x chain and another L chain which is secreted without an H chain, by biochemical studies of the relative distribution of mRNA activity for the two L chains between membrane‐bound and free polysomal fractions. The mutant P3 H chain (H*) produced by the line P3‐NSII/1 is also degraded intracellularly rather than secreted. This defect was complemented by cell fusion of P 3‐NSII/1 to P1, a different Ig‐secreting myeloma line. Mutant H* chains were only secreted as part of hybrid Ig molecules with P1 L chains indicating that the defect in their secretion in the P 3‐ NSII/l line was due to lack of a complementary Ig chain. Additionally, the preferential recovery of P1 H chain loss variants from these hybrids that are producing two H chains and only one L chain, supports the idea that free intracellular H chains have an effect on cell viability and influence the type of variants recovered from hybrid myeloma lines.
Scrib Complex and Par Complex:From Apical-basal Polarity to Tumorigenesis (2010)

Loss of cell polarity is commonly observed in most human cancers derived from epithelial tissues.However,the contribution of cell polarity disruption to tumor progression has been unknown.Recently,the molecular mechanisms that control cellular polarization were gradually uncovered.Meanwhile,it was found that this molecular machinery is intimately involved in tumorigenesis.During the formation of apical-basal cell polarity,Scrib complex and Par complex antagonize reciprocally to determine the apical and basolateral membrane domains.Once the fine balance between their activities is broken due to the inhibition of Scrib complex or the activation of Par complex,cancer or other developmental disease will appear.Here we will discuss how the interactions between Scrib complex and Par complex are implicated in the establishment of apical-basal cell polarity and their contributions to tumorigenesis.
Identification of New Diterpenoids from Euphorbia calyptrata Cell Cultures (1996)

Four new diterpenoids, helioscopinolides F (2), H (4), I (5), and L (6), were isolated from three different cultured cell lines of Euphorbia calyptrata var. involucrata. Helioscopinolide B (1) and jolkinolide E (3), previously found in Euphorbia helioscopia and Euphorbia jolkini, respectively, were also isolated from the same cultures. Structures were identified by spectroscopic methods.
Cover Picture: Angew. Chem. Int. Ed. 1/2003 (2003)

The Art of Synthesis and the beauty of Nature lure so many chemists into total synthesis. The cover picture shows yellow jasmine in full bloom, from which the poisonous alkaloid gelsemine was isolated. The formula of gelsemine and important intermediates from six total syntheses are overlaid on the photograph. From these syntheses, we can learn which strategies represent the fastest and/or most efficient routes to the target. More about this fascinating compound and organic synthesis at its best can be found in the Review by S. J. Danishefsky and H. Lin on pg. 36 ff.
Development of porous silicon-based miniature fuel cells (2005)

Nowadays the rise in portable electronics requires energy sources compatible with the environmental constraints. We demonstrate, in this paper, how microfabrication techniques allow the development of low-cost miniature fuel cells fully integrated on silicon. Contrary to usual proton-conducting membranes made of ionomers ensuring the proton conductivity of proton-exchange membrane fuel cells (PEMFCs), we present here another way to proceed. It consists in the chemical grafting of molecules bearing acid groups on the pore walls of a porous silicon membrane to mimic the structure of an ionomer, such as Nafion®. We obtain an inorganic, dimensionally stable, proton-conducting membrane with many optimizable parameters such as the pore size and the pore structure of the membrane or the nature of the grafted molecules. Moreover, the use of a silicon substrate offers advantages of serial and parallel integration, the possibility of encapsulation by wafer bonding and gas feed and electrical contacts may be included into the membrane etching process, thanks to simple KOH wet etching processes and metal sputtering.
Enhanced translation of a chloroplast-expressed Rbc S gene restores small subunit levels and photosynthesis in nuclear Rbc S antisense plants (2004)

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a key enzyme that converts atmospheric carbon to food and supports life on this planet. Its low catalytic activity and specificity for oxygen leads to photorespiration, severely limiting photosynthesis and crop productivity. Consequently, Rubisco is a primary target for genetic engineering. Separate localization of the genes in the nuclear and chloroplast genomes and a complex assembly process resulting in a very low catalytic activity of hybrid Rubisco enzymes have rendered several earlier attempts of Rubisco engineering unsuccessful. Here we demonstrate that the RbcS gene, when integrated at a transcriptionally active spacer region of the chloroplast genome, in a nuclear RbcS antisense line and expressed under the regulation of heterologous (gene 10) or native (psbA) UTRs, results in the assembly of a functional holoenzyme and normal plant growth under ambient CO(2) conditions, fully shortcircuiting nuclear control of gene regulation. There was approximately 150-fold more RbcS transcript in chloroplast transgenic lines when compared with the nuclear RbcS antisense line, whereas the wild type has 7-fold more transcript. The small subunit protein levels in the gene 10/RbcS and psbA/RbcS plants were 60% and 106%, respectively, of the wild type. Photosynthesis of gene 10/RbcS plants was approximately double that of the antisense plants, whereas that of psbA/RbcS plants was restored almost completely to the wild-type rates. These results have opened an avenue for using chloroplast engineering for the evaluation of foreign Rubisco genes in planta that eventually can result in achieving efficient photosynthesis and increased crop productivity.
DNA methylation markers: a versatile diagnostic tool for routine clinical use. (2007)

In recent years, several new options have been introduced for the treatment of various neoplasias. Biomarkers are urgently needed to improve diagnosis and treatment selection. DNA metlhylation biomarkers unite these desirable characteristics because they relate to key aspects of tumor biology and can be measured reliably on routinely available patient specimens. Recent improvements in DNA methylation marker discovery and efforts to transfer these into routine clinical use are summarized in this review.
Recognition and Killing of Brain Tumor Stem-Like Initiating Cells by CD8+ Cytolytic T Cells (2009)

Solid tumors contain a subset of stem-like cells that are resistant to the cytotoxic effects of chemotherapy/radiotherapy, but their susceptibility to cytolytic T lymphocyte (CTL) effector mechanisms has not been well characterized. Using a panel of early-passage human brain tumor stem/initiating cell (BTSC) lines derived from high-grade gliomas, we show that BTSCs are subject to immunologic recognition and elimination by CD8(+) CTLs. Compared with serum-differentiated CD133(low) tumor cells and established glioma cell lines, BTSCs are equivalent with respect to expression levels of HLA class I and ICAM-1, similar in their ability to trigger degranulation and cytokine synthesis by antigen-specific CTLs, and equally susceptible to perforin-dependent CTL-mediated cytolysis. BTSCs are also competent in the processing and presentation of antigens as evidenced by the killing of these cells by CTL when antigen is endogenously expressed. Moreover, we show that CTLs can eliminate all BTSCs with tumor-initiating activity in an antigen-specific manner in vivo. Current models predict that curative therapies for many cancers will require the elimination of the stem/initiating population, and these studies lay the foundation for developing immunotherapeutic approaches to eradicate this tumor population.
Why Is Trehalose an Exceptional Protein Stabilizer? (2003)

Trehalose, a naturally occurring osmolyte, is known to be an exceptional stabilizer of proteins and helps retain the activity of enzymes in solution as well as in the freeze-dried state. To understand the mechanism of action of trehalose in detail, we have conducted a thorough investigation of its effect on the thermal stability in aqueous solutions of five well characterized proteins differing in their various physico-chemical properties. Among them, RNase A has been used as a model enzyme to investigate the effect of trehalose on the retention of enzymatic activity upon incubation at high temperatures. 2 m trehalose was observed to raise the transition temperature, Tm of RNase A by as much as 18 degrees C and Gibbs free energy by 4.8 kcal mol-1 at pH 2.5. There is a decrease in the heat capacity of protein denaturation (DeltaCp) in trehalose solutions for all the studied proteins. An increase in the DeltaG and a decrease in the DeltaCp values for all the proteins points toward a general mechanism of stabilization due to the elevation and broadening of the stability curve (DeltaG versus T). A direct correlation of the surface tension of trehalose solutions and the thermal stability of various proteins has been observed. Wyman linkage analysis indicates that at 1.5 m concentration 4-7 molecules of trehalose are excluded from the vicinity of protein molecules upon denaturation. We further show that an increase in the stability of proteins in the presence of trehalose depends upon the length of the polypeptide chain. The pH dependence data suggest that even though the charge status of a protein contributes significantly, trehalose can be expected to work as a universal stabilizer of protein conformation due to its exceptional effect on the structure and properties of solvent water compared with other sugars and polyols.
Structure and mechanism of non‐histone protein acetyltransferase enzymes (2013)

Post-translational modification of proteins is ubiquitous and mediates many cellular processes, including intracellular localization, protein-protein interactions, enzyme activity, transcriptional regulation and protein stability. While the role of phosphorylation as a key post-translational modification has been well studied, the more evolutionarily conserved post-translational modification acetylation has only recently attracted attention as a key regulator of cellular events. Protein acetylation has been largely studied in the context of its role in histone modification and gene regulation, where histones are modified by histone acetyltransferases to promote transcription. However, more recent acetylomic and biochemical studies have revealed that acetylation is mediated by a broader family of protein acetyltransferases. The recent structure determination of several protein acetyltransferases has provided a wealth of molecular information regarding structural features of protein acetyltransferases, their enzymatic mechanisms, their mode of substrate-specific recognition and their regulatory elements. In this review, we briefly describe what is known about non-histone protein substrates, but mainly focus on a few recent structures of protein acetyltransferases to compare and contrast them with histone acetyltransferases to better understand the molecular basis for protein recognition and modification by this family of protein modification enzymes.
Ultrasonic Metal Welding of Aluminium Sheets to Carbon Fibre Reinforced Thermoplastic Composites (2009)

The ultrasonic welding technology is an innovative method to produce hybrid joints for multi-material components. The investigations described in this paper were carried out using the ultrasonic metal welding technique for joining carbon fibre reinforced thermoplastic composites (CFRP) with sheet metals like aluminium alloys or aluminium-plated steels. The achievable mechanical properties as a function of the process parameters are presented. Additionally, microscopic investigations of the bonding zone are discussed. One important advantage of ultrasonic metal welding is the possibility to realise a direct contact between the load bearing fibres of the reinforced composite and the metallic surface without destroying the carbon fibres.
Physiologically Active Compounds. VI. Cyclic Amino Thiolesters of Substituted Chloroacetic, Benzilic, and Glycolic Acids1,2 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhysiologically Active Compounds. VI. Cyclic Amino Thiolesters of Substituted Chloroacetic, Benzilic, and Glycolic Acids1,2Calvin A. Buehler, Shelby F. Thames, L. G. Abood, and J. H. BielCite this: J. Med. Chem. 1965, 8, 5, 643–647Publication Date (Print):September 1, 1965Publication History Published online1 May 2002Published inissue 1 September 1965https://doi.org/10.1021/jm00329a018RIGHTS & PERMISSIONSArticle Views99Altmetric-Citations7LEARN 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 InReddit PDF (628 KB) Get e-Alerts Get e-Alerts
A widely tunable fiber Bragg grating with a wavelength tunability over 40 nm (2001)

We have fabricated and demonstrated a 40nm widely tunable fiber Bragg grating designed for operation over Erbium band. This device is simple, low-cost and will have great potential for applications in optical communication and sensing.
Revisiting Oxford and Paris: Large-Scale Image Retrieval Benchmarking (2018)

In this paper we address issues with image retrieval benchmarking on standard and popular Oxford 5k and Paris 6k datasets. In particular, annotation errors, the size of the dataset, and the level of challenge are addressed: new annotation for both datasets is created with an extra attention to the reliability of the ground truth. Three new protocols of varying difficulty are introduced. The protocols allow fair comparison between different methods, including those using a dataset pre-processing stage. For each dataset, 15 new challenging queries are introduced. Finally, a new set of 1M hard, semi-automatically cleaned distractors is selected. An extensive comparison of the state-of-the-art methods is performed on the new benchmark. Different types of methods are evaluated, ranging from local-feature-based to modern CNN based methods. The best results are achieved by taking the best of the two worlds. Most importantly, image retrieval appears far from being solved.