gebhart/patrepeval huggingface dataset:
Disruption of integrin function and induction of tyrosine phosphorylation by the autonomously expressed beta 1 integrin cytoplasmic domain (1994)

The cytoplasmic domains of integrin beta subunits are essential for the function of integrins in cell adhesion and signaling. A chimera combining the transmembrane and cytoplasmic domains of the beta 1 integrin subunit with an irrelevant extracellular domain derived from L3T4 (murine CD4) was tested for its ability to interfere with integrin function. Expression of this construct in cultured human embryonic kidney cells under the control of the inducible metallothionein promoter resulted in cell rounding and detachment, and blocked cell adhesion mediated by the beta 1 and alpha v beta 5 integrins. Expression of the beta 1 chimera at basal levels interfered with the tyrosine phosphorylation of a 125-kDa protein induced by antibody-induced clustering of integrins. Induced expression of the chimera resulted in sustained tyrosine phosphorylation of this protein, which could be enhanced by clustering of the chimera but was insensitive to clustering of integrins. These results demonstrate that the autonomously expressed beta 1 integrin cytoplasmic domain can act as a trans-dominant inhibitor of integrin function, presumably via competitive interactions with cytoplasmic components that are required for integrin-mediated cell adhesion and tyrosine phosphorylation.
Recent advances in engineering the central carbon metabolism of industrially important bacteria (2012)

This paper gives an overview of the recent advances in engineering the central carbon metabolism of the industrially important bacteria Escherichia coli, Bacillus subtilis, Corynobacterium glutamicum, Streptomyces spp., Lactococcus lactis and other lactic acid bacteria. All of them are established producers of important classes of products, e.g. proteins, amino acids, organic acids, antibiotics, high-value metabolites for the food industry and also, promising producers of a large number of industrially or therapeutically important chemicals. Optimization of existing or introduction of new cellular processes in these microorganisms is often achieved through manipulation of targets that reside at major points of central metabolic pathways, such as glycolysis, gluconeogenesis, the pentose phosphate pathway and the tricarboxylic acid cycle with the glyoxylate shunt. Based on the huge progress made in recent years in biochemical, genetic and regulatory studies, new fascinating engineering approaches aim at ensuring an optimal carbon and energy flow within central metabolism in order to achieve optimized metabolite production.
Microscopic effects of the bonding configuration of nitrogen-doped graphene on its reactivity toward hydrogen peroxide reduction reaction (2013)

We report a density functional theory (DFT) study of microscopic detailed effects of the bonding configuration of nitrogen-doped graphene (N-graphene) within the carbon lattice (including pyridinic, pyrrolic, and graphitic N) on the reactivity and mechanistic processes of H2O2 reduction reaction. We simulated the adsorption process of H2O2, analyzed the mechanistic processes, and calculated the reversible potential of each reaction step of the H2O2 reduction reaction on N-graphene. The results indicate that the adsorption of H2O2 on the pristine and N-doped graphene surfaces occurs via physisorption without the formation of a chemical bond. When H(+) is introduced into the system, a series of reactions can occur, including the breakage of the O-O bond, the formation of an O-C chemical bond between oxygen and graphene, and the creation of water molecules. The results also indicate a decrease in the energy of the system and a positive reversible potential for each reaction step. The calculations of the relative energy of each reaction step and the value of the onset potential for H2O2 reduction reaction suggest that the reactivity of pristine and N-doped graphene has the following order: pyridinic N-graphene > pyrrolic N-graphene > graphitic N-graphene > pristine graphene. We also proposed an explanation based on electrostatic potential calculations for this dependence of the reactivity order on the bond configuration of the doping in N-graphene. The results of this study should help in the atomic-scale understanding of the dependence of the reactivity of N-graphene on its microstructure, inspire the study of various types of heteroatom-doped graphenes to improve their catalytic efficiency, and provide a theoretical framework to analyze their reactivities.
Three Aromatic Amino Acid Residues Critical for Galactose Transport in Yeast Gal2 Transporter (2000)

Tyr(446) in putative transmembrane segment 10 (TM10) of the yeast galactose transporter Gal2 has previously been identified as essential for galactose recognition. In the present study, alignment of the amino acid sequences of 63 sugar transporters or related proteins revealed 14 aromatic sites, including Tyr(446) of Gal2, that are conserved in >75% of these proteins. The importance of the remaining 13 conserved aromatic amino acids was examined individually by random mutagenesis using degenerate primers. Galactose transport-positive clones were identified by plate selection and subjected to DNA sequencing. For those transport-positive clones corresponding to Tyr(352), and Phe(504) mutants, all the amino acid substitutions comprised aromatic residues. The importance of the aromatic residues at these sites was further investigated by replacing them individually with each of the other 19 amino acids and measuring the galactose transport activity of the resulting mutants. Among both Tyr(352) and Phe(504) mutants, the other aromatic amino acids supported galactose transport; no other amino acids conferred high affinity transport activity. Thus, at least three aromatic sites are critical for galactose transport: one at the extracellular boundary of putative TM7 (Tyr(352)), one in the middle of putative TM10 (Tyr(446)), and one in the middle of putative TM12 (Phe(504)).
<title>Multivariate determination of blood substrates in human plasma by FT-NIR spectroscopy</title> (1992)

A spectral analysis of human EDTA plasma from 124 different patients was undertaken using an FT-NIR spectrometer. Optimized intervals of the absorbance spectra were considered for the PLS-calibrations with reference concentrations from standard clinical methods determined in triplicate. The following relative prediction errors were achieved: total protein 1.4%, cholesterol 3.8%, triglycerides 8.6%, glucose 9.1%, and urea 18.6%.
Conjunctivitis Caused by a Swine Chlamydia Trachomatis-Like Organism in Gnotobiotic Pigs (1999)

The objective of this study was to determine whether a chlamydial strain recovered from growing and finishing swine with conjunctivitis or keratoconjunctivitis could cause the same infections in gnotobiotic pigs. The strain shares biological characteristics with Chlamydia trachomatis. After propagation in Vero cells and preparation of the inoculum (10(7) inclusion-forming units/ml), chlamydial strain H7 was instilled into the ventral conjunctival sac (0.15 ml/sac) of 12 anesthetized 3-day-old gnotobiotic piglets. Four age-matched gnotobiotic piglets were anesthetized and sham infected with uninfected cell culture lysates. None of the principal piglets developed clinical symptoms of conjunctivitis or keratoconjunctivitis. Principal piglets necropsied 7 days postinfection (DPI) had histologic lesions of mild or moderate conjunctivitis; immunohistochemical evaluation revealed chlamydial antigen in conjunctival epithelium. A majority of principal piglets necropsied at 14-28 DPI had histologic lesions of mild conjunctivitis, but chlamydial antigen was not detected by immunohistochemistry. The results indicated that chlamydial strain H7 can cause mild or occasionally moderate conjunctivitis in gnotobiotic pigs, but the conjunctival infection is asymptomatic.
The nuclear protooncogenes c-jun and c-fos as regulators of DNA replication. (1991)

Polyomavirus (Py) DNA replication is regulated by its enhancer, which contains an AP1 site, c-Jun and c-Fos, the products of nuclear protooncogenes c-jun and c-fos, form the heterodimeric transcriptional activating factor AP1. Overexpression of c-fos and c-jun genes strongly stimulated Py DNA replication from the Py origin of replication as well as transcription from the Py early promoter through the AP1 binding site. The cAMP response element (CRE)-binding protein CREB stimulated only transcription, not DNA replication, through the CRE under similar conditions. The results indicate that AP1 functions as a regulator of DNA replication and that the mechanism of activation of Py DNA replication by AP1 is distinct from that of activation of transcription from the Py early promoter.
Neonatal-Onset Multisystem Inflammatory Disease Responsive to Interleukin-1β Inhibition (2006)

Daily injections of anakinra markedly improved clinical and laboratory manifestations in patients with neonatal-onset multisystem inflammatory disease, with or without CIAS1 mutations. (ClinicalTrials.gov number, NCT00069329 [ClinicalTrials.gov].).
The bisphosphonate, zoledronic acid, induces apoptosis of breast cancer cells: evidence for synergy with paclitaxel (2001)

Bisphosphonates are well established in the management of breast-cancer-induced bone disease. Recent studies have suggested that these compounds are effective in preventing the development of bone metastases. However, it is unclear whether this reflects an indirect effect via an inhibition of bone resorption or a direct anti-tumour effect. The breast cancer cell lines, MCF-7 and MDA-MB-231 cells were treated with increasing concentrations of the bisphosphonate, zoledronic acid, for varying time periods, in the presence or absence of paclitaxel. The effects of zoledronic acid were determined by assessing cell number and rate of apoptosis by evaluating changes in nuclear morphology and using a fluorescence nick translation assay. Zoledronic acid caused a dose- and time-dependent decrease in cell number (P< 0.001) and a concomitant increase in tumour cell apoptosis (P< 0.005). Short-term exposure to zoledronic acid was sufficient to cause a significant reduction in cell number and increase in apoptosis (P< 0.05). These effects could be prevented by incubation with geranyl geraniol, suggesting that zoledronic acid-induced apoptosis is mediated by inhibiting the mevalonate pathway. Treatment with zoledronic acid and clinically achievable concentrations of paclitaxel resulted in a 4-5-fold increase in tumour cell apoptosis (P< 0.02). Isobologram analysis revealed synergistic effects on tumour cell number and apoptosis when zoledronic acid and paclitaxel were combined. Short-term treatment with zoledronic acid, which closely resembles the clinical setting, has a clear anti-tumour effect on breast cancer cells. Importantly, the commonly used anti-neoplastic agent, paclitaxel, potentiates the anti-tumour effects of zoledronic acid. These data suggest that, in addition to inhibiting bone resorption, zoledronic acid has a direct anti-tumour activity on breast cancer cells in vitro.
Redundancy identification/removal and test generation for sequential circuits using implicit state enumeration (1993)

Finite state machine (FSM) verification based on implicit state enumeration can be extended to test generation and redundancy identification. The extended method constructs the product machine of two FSMs to be compared, and reachability analysis is performed by traversing the product machine to find any difference in I/O behavior. When an output difference is detected, the information obtained by reachability analysis is used to generate a test sequence. This method is complete, and it generates one of the shortest possible test sequences for a given fault. However, applying this method indiscriminately for all faults may result in unnecessary waste of computer resources. An efficient method based on reachability analysis of the fault-free machine (three-phase ATPG) in addition to the powerful but more resource-demanding product machine traversal is presented. The application of these algorithms to the problems of generating test sequences, identifying redundancies, and removing redundancies is reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In vitro synthesis, glycosylation, and membrane insertion of the four subunits of Torpedo acetylcholine receptor. (1981)

We have characterized the early biosynthetic forms of the Torpedo electroplax acetylcholine receptor by using a cell-free protein synthesizing system. We obtained primary translation products of approximately 38, 50, 49, and 60 kilodaltons for the alpha, beta, gamma, and delta polypeptides, respectively, by using immunoprecipitation with subunit-specific antisera. These chains could each be labeled by the formylated initiator [35S]Met-tRNA. On cotranslational incubation with pancreatic rough microsomes, glycosylated forms of each subunit were obtained that had molecular weights close to those of their mature authentic counterparts. Extensive trypsinization reduced the glycosylated forms of the receptor subunits to glycosylated membrane-protected fragments of approximately 35 (alpha), 37 (beta), 45 (gamma), and 44 (delta) kilodaltons. In this system, then, each receptor chain spans the membrane at least once. This in vitro-synthesized material apparently exhibited neither oligomeric assembly nor alpha-bungarotoxin binding.
Predicting oligonucleotide affinity to nucleic acid targets (1999)

A computer program, OligoWalk, is reported that predicts the equilibrium affinity of complementary DNA or RNA oligonucleotides to an RNA target. This program considers the predicted stability of the oligonucleotide-target helix and the competition with predicted secondary structure of both the target and the oligonucleotide. Both unimolecular and bimolecular oligonucleotide self structure are considered with a user-defined concentration. The application of OligoWalk is illustrated with three comparisons to experimental results drawn from the literature.
Does the Antibacterial Activity of Silver Nanoparticles Depend on the Shape of the Nanoparticle? A Study of the Gram-Negative Bacterium Escherichia coli (2007)

In this work we investigated the antibacterial properties of differently shaped silver nanoparticles against the gram-negative bacterium Escherichia coli, both in liquid systems and on agar plates. Energy-filtering transmission electron microscopy images revealed considerable changes in the cell membranes upon treatment, resulting in cell death. Truncated triangular silver nanoplates with a {111} lattice plane as the basal plane displayed the strongest biocidal action, compared with spherical and rod-shaped nanoparticles and with Ag(+) (in the form of AgNO(3)). It is proposed that nanoscale size and the presence of a {111} plane combine to promote this biocidal property. To our knowledge, this is the first comparative study on the bactericidal properties of silver nanoparticles of different shapes, and our results demonstrate that silver nanoparticles undergo a shape-dependent interaction with the gram-negative organism E. coli.
Neurite branching on deformable substrates (2002)

The mechanical properties of substrates underlying cells can have profound effects on cell structure and function. To examine the effect of substrate deformability on neuronal cell growth, protein-laminated polyacrylamide gels were prepared with differing amounts of bisacrylamide to generate substrates of varying deformability with elastic moduli ranging from 500 to 5500 dyne/cm. Mouse spinal cord primary neuronal cells were plated on the gels and allowed to grow and extend neurites for several weeks in culture. While neurons grew well on the gels, glia, which are normally co-cultured with the neurons, did not survive on these deformable substrates even though the chemical environment was permissive for their growth. Substrate flexibility also had a significant effect on neurite branching. Neurons grown on softer substrates formed more than three times as many branches as those grown on stiffer gels. These results show that mechanical properties of the substrate specifically direct the formation of neurite branches, which are critical for appropriate synaptic connections during development and regeneration.
Involvement of histamine H4 and H1 receptors in scratching induced by histamine receptor agonists in BalbC mice (2004)

The role of histamine H(1), H(2), H(3) and H(4) receptors in acute itch induced by histamine was investigated in female BalbC mice. Scratching was induced by intradermal injections of pruritogen into the back of the neck and "itch" assessed by quantifying the scratching evoked. Histamine (0.03-80 micromol), histamine-trifluoromethyl-toluidine (HTMT, H(1) agonist, 0.002-2 micromol), clobenpropit (H(4) agonist, H(3) antagonist, 0.002-0.6 micromol) and to a lesser extent imetit (H(3)/H(4) agonist, 0.03-3 micromol) all induced dose-dependent scratching. Dimaprit (H(2) agonist, 0.04-40 micromol) did not cause scratching. Mepyramine (H(1) antagonist, 20 mg kg(-1), i.p.) reduced scratching evoked by histamine and HTMT, but not that caused by H(3) or H(4) agonists. Thioperamide (H(3)/H(4) antagonist, 20 mg kg(-1), i.p.) reduced scratching induced by histamine, H(3) and H(4) agonists, but not that caused by HTMT. The non-sedating H(1) antagonist, terfenadine, also significantly reduced the scratching induced by the H(1) agonist, HTMT. Cimetidine (H(2) antagonist, 20 mg kg(-1), i.p.) did not affect histamine-induced scratching. These results indicate that activation of histamine H(4) receptors causes itch in mice, in addition to the previously recognised role for H(1) receptors in evoking itch. Histamine H(4) receptor antagonists therefore merit investigation as antipruritic agents.
Identification of the IgA-binding region in streptococcal protein Arp. (1994)

Cell surface proteins that bind to the Fc part of human IgA are expressed by different species of pathogenic streptococci. The most extensively characterized streptococcal IgA-binding protein is the Streptococcus pyogenes protein Arp4, a member of the M protein family. Here we describe work that identifies the IgA-binding region in this streptococcal protein. A comparison of the amino acid sequences of protein Arp4 and four other IgA-binding proteins of S. pyogenes first made possible the identification of a putative IgA-binding region. Site-specific mutagenesis and generation of deletions were then used to show that Arp4 derivatives lacking different parts of the putative IgA-binding region had lost the ability to bind IgA. Conclusive evidence for the localization of the IgA-binding region was obtained through the characterization of a chimeric protein, in which the putative IgA-binding region of Arp4 had been introduced into another S. pyogenes cell surface protein that does not bind IgA. Our data show that a region comprising 29-amino acid residues in the N-terminal part of Arp4 is necessary and sufficient for IgA-binding capacity. Competitive inhibition experiments with synthetic peptides indicated that the C-terminal half of this 29 residue region may be most important for the IgA-binding property of Arp4. These results identify, for the first time, the ligand-binding region in an Fc alpha binding protein.
Efficient Refolding of Aggregation-prone Citrate Synthase by Polyol Osmolytes (2005)

Efficient refolding of proteins and prevention of their aggregation during folding are of vital importance in recombinant protein production and in finding cures for several diseases. We have used citrate synthase (CS) as a model to understand the mechanism of aggregation during refolding and its prevention using several known structure-stabilizing cosolvent additives of the polyol series. Interestingly, no parallel correlation between the folding effect and the general stabilizing effect exerted by polyols was observed. Although increasing concentrations of polyols increased protein stability in general, the refolding yields for CS decreased at higher polyol concentrations, with erythritol reducing the folding yields at all concentrations tested. Among the various polyols used, glycerol was the most effective in enhancing the CS refolding yield, and a complete recovery of enzymatic activity was obtained at 7 m glycerol and 10 mug/ml protein, a result superior to the action of the molecular chaperones GroEL and GroES in vitro. A good correlation between the refolding yields and the suppression of protein aggregation by glycerol was observed, with no aggregation detected at 7 m. The polyols prevented the aggregation of CS depending on the number of hydroxyl groups in them. Stopped-flow fluorescence kinetics experiments suggested that polyols, including glycerol, act very early in the refolding process, as no fast and slow phases were detectable. The results conclusively demonstrate that both the thermodynamic and kinetic aspects are critical in the folding process and that all structure-stabilizing molecules need not always help in productive folding to the native state. These findings are important for the rational design of small molecules for efficient refolding of various aggregation-prone proteins of commercial and medical relevance.
54. Synthetical approaches to the pristimerin chromophore (1965)

J. A. Hill, A. W. Johnson, T. J. King, S. Natori and S. W. Tam, J. Chem. Soc., 1965, 361 DOI: 10.1039/JR9650000361
Composite Nanospheres of PAA/silica Controlled by Anionic Polymer (2009)

The anionic polymer,poly(acrylic acid)(PAA),was used to synthesize composite nanospheres of PAA/silica with 3-aminopropyltrimethoxysilane(APMS)and tetraethyl orthosilicate(TEOS)as silica source.In the synthesis,the assembly of PAA,APMS and TEOS follows the mechanism of the anionic surfactant templated mesoporous silica(AMS)through a S-N+-I-pathway,where S stands for the anionic PAA,I stands for inorganic precursors(TEOS)and N stands for co-structure-directing agent(APMS).The results of SEM,TEM,TG and FTIR show that the average size of composite nanospheres of PAA/silica is 80 nm.Furthermore,it was proved that addition of organic solvent such as THF could tune the size of the composite spheres.
SYNTHESES OF 7-SUBSTITUTED INDOLINE DERIVATIVES1, 2 (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSYNTHESES OF 7-SUBSTITUTED INDOLINE DERIVATIVES1, 2W. G. GALL, B. D. ASTILL, and V. BOEKELHEIDECite this: J. Org. Chem. 1955, 20, 11, 1538–1544Publication Date (Print):November 1, 1955Publication History Published online1 May 2002Published inissue 1 November 1955https://pubs.acs.org/doi/10.1021/jo01128a012https://doi.org/10.1021/jo01128a012research-articleACS PublicationsRequest reuse permissionsArticle Views414Altmetric-Citations25LEARN 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