gebhart/patrepeval huggingface dataset:
The ExsY Protein Is Required for Complete Formation of the Exosporium of Bacillus anthracis (2006)

ABSTRACT The outermost layer of the Bacillus anthracis spore is the exosporium, which is composed of a paracrystalline basal layer and an external hair-like nap. The filaments of the nap are formed by a collagen-like glycoprotein called BclA, while the basal layer contains several different proteins. One of the putative basal layer proteins is ExsY. In this study, we constructed a ΔexsY mutant of B. anthracis , which is devoid of ExsY, and examined the assembly of the exosporium on spores produced by this strain. Our results show that exosporium assembly on ΔexsY spores is aberrant, with assembly arrested after the formation of a cap-like fragment that covers one end of the forespore—always the end near the middle of the mother cell. The cap contains a normal hair-like nap but an irregular basal layer. The cap is retained on spores prepared on solid medium, even after spore purification, but it is lost from spores prepared in liquid medium. Microscopic inspection of ΔexsY spores prepared on solid medium revealed a fragile sac-like sublayer of the exosporium basal layer, to which caps were attached. Examination of purified ΔexsY spores devoid of exosporium showed that they lacked detectable levels of BclA and the basal layer proteins BxpB, BxpC, CotY, and inosine-uridine-preferring nucleoside hydrolase; however, these spores retained half the amount of alanine racemase presumed to be associated with the exosporium of wild-type spores. The ΔexsY mutation did not affect spore production and germination efficiencies or spore resistance but did influence the course of spore outgrowth.
Chalcogenapyrylium dyes as photochemotherapeutic agents. 2. Tumor uptake, mitochondrial targeting, and singlet-oxygen-induced inhibition of cytochrome c oxidase (1990)

Cationic selena- and tellurapyrylium dyes 1d-g and 1i were found to inhibit cytochrome c oxidase upon irradiation of isolated mitochondrial suspensions treated with 10 microM solutions of dye. The amount of inhibition by these dyes was found to be related to oxygen concentration and inversely related to the concentration of added imidazole, a singlet-oxygen trap, suggesting that singlet oxygen is responsible, at least in part, for the inhibition of the enzyme. Dyes 1d-g and 1i, containing either selenium or tellurium, produce singlet oxygen with a quantum efficiency, phi (1O2), between 0.005 and 0.09 in methanol. Dyes 1a-c, containing the lighter chalcogens oxygen and sulfur, have values of phi (1O2) that are less than 0.0008 in methanol and do not inhibit cytochrome c oxidase in irradiated mitochondrial suspensions. Dyes 1c and 1d have nearly identical spectral and redox properties. Only the selenapyrylium dye 1d inhibits the enzyme, suggesting that neither ground-state nor excited-state electron transfer is important in inhibition of the enzyme. Electron micrographs of human U251 glioma cells, treated in vitro with 1i and light, showed pronounced morphology changes in the mitochondrial membranes relative to electron micrographs of untreated cells. Epifluorescence microscopy of the treated cells showed granular yellow-green fluorescence presumably from photooxidized dye in the mitochondria.
Measurement of the group delay of laser mirrors by a Fabry–Perot interferometer (1995)

The group delay of multilayer laser mirrors was measured by determining the spectral position of transmission maxima of a Fabry–Perot interferometer formed by the mirrors to be characterized. By optimizing the spacer thickness, we obtained an accuracy of the group-delay measurement of better than 0.23 fs. To our knowledge, this is the most precise direct measuring method reported.
Speakers' Overestimation of Their Effectiveness (2002)

Successful communication depends in part on an ability to anticipate miscommunication. We investigated speakers' ability to gauge their addressees' understanding. Participants in our experiments were asked to say ambiguous sentences while attempting to convey a specific intention to their addressee. When they estimated the addressee's understanding of the intended meaning, they showed a consistent tendency to overestimate their effectiveness. They expected the addressee to understand more often than the addressee actually did. In contrast, overhearers who were informed about the speakers intention did not systematically overestimate the speakers' effectiveness. Our findings suggest that when speakers monitor their own utterances, they do not act as unbiased observers. Instead, they underestimate the ambiguity of their own utterances and overestimate the extent to which their disambiguating cues make their intention transparent. Such overestimation could be a systematic source of miscommunication in natural conversation, and should be accounted for by any theory of language production.
Metabolism of Angiotensin-(1–7) by Angiotensin-Converting Enzyme (1998)

Angiotensin converting enzyme (ACE) inhibitors augment circulating levels of the vasodilator peptide angiotensin-(1-7) [Ang-(1-7)] in man and animals. Increased concentrations of the peptide may contribute to the antihypertensive effects associated with ACE inhibitors. The rise in Ang-(1-7) following ACE inhibition may result from increased production of the peptide or inhibition of the metabolism of Ang-(1-7)-similar to that observed for bradykinin. To address the latter possibility, we determined whether Ang-(1-7) is a substrate for ACE in vitro. In a pulmonary membrane preparation, the ACE inhibitor lisinopril attenuated the metabolism of low concentrations of 125I-Ang-(1-7). The primary product of 125I-Ang-(1-7) metabolism was identified as Ang-(1-5). Using affinity-purified ACE from canine lung, HPLC separation and amino acid analysis revealed that ACE functioned as a dipeptidyl carboxypeptidase cleaving Ang-(1-7) to the pentapeptide Ang-(1-5). The ACE inhibitors lisinopril and enalaprilat (1 micromol/L), as well as the chelating agents EDTA, o-phenanthroline, and DTT (0.1-1 mmol/L) abolished the generation of Ang-(1-5) and did not yield other metabolic products. Ang-(1-5) was not further hydrolyzed by ACE. Kinetic analysis of the hydrolysis of Ang-(1-7) by ACE revealed a substrate affinity of 0.81 micromol/L and maximal velocity of 0.65 micromols min(-1) mg(-1). The calculated turnover constant for the peptide was 1.8 sec(-1) with a catalytic efficiency (Kcat/Km) of 2200 sec(-1) mmol/L(-1). These findings suggest that increased levels of Ang-(1-7) following ACE inhibition may be due, in part, to decreased metabolism of the peptide.
Island rescue PCR: a rapid and efficient method for isolating transcribed sequences from yeast artificial chromosomes and cosmids. (1994)

The identification of transcripts from large genomic regions cloned in yeast artificial chromosomes (YACs) or cosmids continues to be a critical and often rate-limiting step in positional cloning of human disease genes. We have developed a PCR-based method for rapid and efficient generation of probes from YACs or cosmids that can be used for cDNA library screening. The method, which we call island rescue PCR (IRP), is based upon the observation that the 5' ends of many genes are associated with (G+C)-rich regions called CpG islands. In IRP, the YAC of interest is digested with a restriction enzyme that recognizes sequences of high CpG content, and vectorette linkers are ligated to the cleaved ends. The PCR is used to amplify the region extending from the cleaved restriction enzyme site to the nearest SINE (Alu) repeat. In many cases this product contains sequences from the 5' end of the associated gene. cDNA clones isolated with these products are then verified by mapping them back to the original YAC. The method allows rapid screening of > 500 kb of human genomic insert in one experiment, is tolerant of contaminating yeast sequences, and can also be applied to cosmid pools. In a control experiment, the method was able to identify cDNA clones for the neurofibromatosis type 1 (NF1) gene using a probe generated from a YAC in the region. Application of IRP has yielded nine other genes from YACs isolated from chromosome locations 4p16.3 and 17q21.
Complement factor H polymorphisms in Japanese population with age-related macular degeneration. (2006)

The frequencies for five haplotypes previously identified were analyzed in a Japanese population with AMD. Four previously found haplotypes were identified and one additional haplotype was found. The frequencies of each haplotype were significantly different from that in found Americans affected with AMD. Two of the haplotypes were identified as risk factors and one was considered protective.
Viruses as supramolecular self-assemblies: modelling of capsid formation and genome packaging (2008)

Viruses are considered the simplest form of live. A virus is basically composed of genomic material surrounded by a protecting capsid. Today, full molecular details of many viruses are known, and several subclasses can be discerned. In this review, we present recent advances made over the past few years obtained from theoretical considerations and model simulations to improve our understanding on two vital aspects of the physics of viruses: viz. viral capsid self-assembly and viral genome packaging. Many processes, such as the self-assembly pathway, genome packing, and ultimately the infection mechanism, differ between viruses containing double-stranded polynucleotides on one hand and single-stranded polynucleotides on the other hand. We believe that these differences to a large degree originate from the different genome flexibilities.
Comparative distribution of N‐Acetylaspartylglutamate and GAD67 in the cerebellum and precerebellar nuclei of the rat utilizing enhanced carbodiimide fixation and immunohistochemistry (1994)

The most prevalent peptide in the nervous system, N-acetylaspartylglutamate (NAAG), specifically activates N-methyl D-aspartate (NMDA) receptors and a subclass of metabotropic glutamate receptors. One action of this peptide may be to modulate the release of other neurotransmitters, including gamma-aminobutyric acid (GABA). The present study describes the cellular distribution of NAAG, relative to GABA, in the cerebellum and precerebellar nuclei as a foundation for further physiological investigations. Numerous cells of origin for mossy fibers, including many of the larger neurons of the pontine nuclei, lateral reticular nuclei, vestibular nuclei, reticulotegmental nuclei, and spinal grey, were moderately to strongly stained for NAAG. Many NAAG-labeled fibers were clearly visible in the cerebellar peduncles and central white matter. Mossy fibers and mossy endings were among the most prominent NAAG-immunoreactive elements in the cerebellar cortex. Most neurons in the inferior olive were not stained for NAAG, and only sparse, lightly immunoreactive, climbing fiber-like endings could be identified in restricted regions of the cortical molecular layer. Purkinje neurons ranged from nonreactive to moderately positive, with the great majority being unstained. Cerebellar granule cells did not exhibit any NAAG immunoreactivity. A population of neurons in the deep cerebellar nuclei was highly immunoreactive for NAAG. Additionally, many neurons of the red nucleus were intensely stained for NAAG. Comparisons with staining for the 67 kD form of glutamic acid decarboxylase in serial sections revealed complementary distributions, with NAAG in excitatory pathways and cell groups, and glutamic acid decarboxylase in inhibitory systems. These findings suggest a significant functional involvement of NAAG in the excitatory afferent and efferent projection systems and provide an anatomical basis for investigations into the interactions of NAAG and GABA in the cerebellum.
Assays to measure the activation of membrane tyrosine kinase receptors: focus on cellular methods. (2003)

Many methods have been explored as means to measure the activation and inhibition of tyrosine kinase receptors, in vitro using the isolated kinase domain, and in living cells. Kinase activity has been measured in enzyme assays using a peptide substrate, but with different detection systems. These include the radioactive FlashPlate assay, the fluorescent resonance energy transfer (FRET) assay, the dissociation-enhance lanthanide fluorescence immunoassay (DELFIA) and other formats. These methods have successfully identified inhibitors of receptor activity. Cell-based assays have recently emerged to measure receptor activation and inhibition. When membrane tyrosine kinase receptors become activated, they increase their state of phosphorylation. This phosphorylation may lead to an increase in tyrosine kinase-specific activity. Methods have been developed that take advantage of these properties. These include measuring the ligand-stimulated total tyrosine phosphorylation of the receptor using a DELFIA or an ELISA assay, measuring ligand-stimulated enzyme activation of the receptor by quantifying enzyme activity, and dimerization of the activated receptor using bioluminescence resonance energy transfer (BRET). Although cell-based assays are still in their infancy, these techniques may prove a valuable addition to the receptor screening strategy.
Repetitive Zn2+-binding domains in the protein transcription factor IIIA from Xenopus oocytes (1986)

Conference Article| April 01 1986 Repetitive Zn2+-binding domains in the protein transcription factor IIIA from Xenopus oocytes A. KLUG; A. KLUG 1M.R.C. Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K. Search for other works by this author on: This Site PubMed Google Scholar J. MILLER; J. MILLER 1M.R.C. Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K. Search for other works by this author on: This Site PubMed Google Scholar A. D. McLACHLAN A. D. McLACHLAN 1M.R.C. Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1986) 14 (2): 221. https://doi.org/10.1042/bst0140221a Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation A. KLUG, J. MILLER, A. D. McLACHLAN; Repetitive Zn2+-binding domains in the protein transcription factor IIIA from Xenopus oocytes. Biochem Soc Trans 1 April 1986; 14 (2): 221. doi: https://doi.org/10.1042/bst0140221a Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1986 Biochemical Society1986 Article PDF first page preview Close Modal You do not currently have access to this content.
Enzymatic removal and disinfection of bacterial biofilms (1997)

Model biofilms of Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas fluorescens, and Pseudomonas aeruginosa were made on steel and polypropylene substrata. Plaque-resembling biofilms of Streptococcus mutans, Actinomyces viscosus, and Fusobacterium nucleatum were made on saliva-coated hydroxyapatite. The activity of enzymes against bacterial cells in biofilm was measured by fluorescence microscopy and an indirect conductance test in which evolution of carbon dioxide was measured. Glucose oxidase combined with lactoperoxidase was bactericidal against biofilm bacteria but did not remove the biofilm from the substrata. A complex mixture of polysaccharide-hydrolyzing enzymes was able to remove bacterial biofilm from steel and polypropylene substrata but did not have a significant bactericidal activity. Combining oxidoreductases with polysaccharide-hydrolyzing enzymes resulted in bactericidal activity as well as removal of the biofilm.
Ligand Tuning in Asymmetric Catalysis:  Mono- and Bis-Phospholanes for a Prototypical Pd-Catalyzed Asymmetric Allylation Reaction (2000)

ADVERTISEMENT RETURN TO ISSUEPREVAdditions & Corr...Additions & CorrectionsORIGINAL ARTICLEThis notice is a correctionLigand Tuning in Asymmetric Catalysis: Mono- and Bis-Phospholanes for a Prototypical Pd-Catalyzed Asymmetric Allylation ReactionYuan-Yong Yan and T. V. RajanBabuCite this: Org. Lett. 2000, 2, 4, 569Publication Date (Web):February 4, 2000Publication History Published online4 February 2000Published inissue 1 February 2000https://pubs.acs.org/doi/10.1021/ol005588thttps://doi.org/10.1021/ol005588tcorrectionACS PublicationsCopyright © 2000 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 Views395Altmetric-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 (4 KB) Get e-AlertscloseSUBJECTS:Allylation,Carbon,Ligands Get e-Alerts
Chemical Etching of Germanium (1988)

Epitaxial germanium is an important material for the fabrication of tandem solar cells and long wavelength photodetectors. The polishing of germanium substrates, prior to germanium epitaxy, is thus an important step. A series of etching experiments have been conducted to evaluate chemical etches for this approach. It is found that the most satisfactory surfaces are obtained with a 2–3 min treatment in in a 18:8:5 ratio by volume.
Seven-hour fluorescence in situ hybridization technique for enumeration of Enterobacteriaceae in food and environmental water sample (2003)

A fluorescent in situ hybridization (FISH) technique using an Enterobacteriaceae-specific probe (probe D) to target 16S rRNA was improved in order to enumerate, within a single working day, Enterobacteriaceae present in food and environmental water samples.In order to minimize the time required for the FISH procedure, each step of FISH with probe D was re-evaluated using cultured Escherichia coli. Five minutes of ethanol treatment for cell fixation and hybridization were sufficient to visualize cultured E. coli, and FISH could be performed within 1 h. Because of the difficulties in detecting low levels of bacterial cells by FISH without cultivation, a FISH technique for detecting microcolonies on membrane filters was investigated to improve the bacterial detection limit. FISH with probe D following 6 h of cultivation to grow microcolonies on a 13 mm diameter membrane filter was performed, and whole Enterobacteriaceae microcolonies on the filter were then detected and enumerated by manual epifluorescence microscopic scanning at magnification of x100 in ca 5 min. The total time for FISH with probe D following cultivation (FISHFC) was reduced to within 7 h. FISHFC can be applied to enumerate cultivable Enterobacteriaceae in food (above 100 cells g-1) and environmental water samples (above 1 cell ml-1).Cultivable Enterobacteriaceae in food and water samples were enumerated accurately within 7 h using the FISHFC method.A FISHFC method capable of evaluating Enterobacteriaceae contamination in food and environmental water within a single working day was developed.
Probucol inhibits neointimal thickening and macrophage accumulation after balloon injury in the cholesterol-fed rabbit. (1992)

Restenosis is a frequent long-term complication after balloon angioplasty. Although smooth muscle cells form the major constituent of the occluding lesion, macrophage-derived foam cells are usually also present in high abundance. The latter have the potential to accelerate the rate of reocclusion because they elaborate many potent cytokines and growth factors, which may act to either recruit cells into the neointima or cause neointimal cell proliferation. Macrophage-derived foam-cell formation depends upon the uptake of modified low density lipoprotein via a scavenger receptor-mediated pathway. Foam-cell formation is accompanied by the release of smooth muscle cell mitogens and chemoattractants. We have examined the effects of probucol, a lipid-soluble antioxidant, in the balloon-catheterized carotid artery of the cholesterol-fed rabbit to evaluate the importance of oxidative processes in restenosis. After 5 weeks, serum cholesterol levels were 32% lower (P < 0.05) in rabbits fed 1% probucol with 2% cholesterol, compared with those receiving cholesterol alone. Probucol inhibited neointimal macrophage accumulation by 68% (P < 0.001), reduced absolute intimal size by 51% (P < 0.05), and reduced the intima/media thickness ratio by 51%. These inhibitory effects were directly related to serum probucol concentrations and appeared to be unrelated to probucol's hypocholesterolemic activity. These data suggest that reactive oxygen species may be involved in the intimal response to injury and that antioxidants, such as probucol, may be therapeutically useful as inhibitors of restenosis.
Tacotron: Towards End-to-End Speech Synthesis (2017)

A text-to-speech synthesis system typically consists of multiple stages, such as a text analysis frontend, an acoustic model and an audio synthesis module. Building these components often requires extensive domain expertise and may contain brittle design choices. In this paper, we present Tacotron, an end-to-end generative text-to-speech model that synthesizes speech directly from characters. Given pairs, the model can be trained completely from scratch with random initialization. We present several key techniques to make the sequence-to-sequence framework perform well for this challenging task. Tacotron achieves a 3.82 subjective 5-scale mean opinion score on US English, outperforming a production parametric system in terms of naturalness. In addition, since Tacotron generates speech at the frame level, it's substantially faster than sample-level autoregressive methods.