gebhart/patrepeval huggingface dataset:
Binding of Hoechst 33258 and 4',6-diamidino-2-phenylindole to self-complementary decadeoxynucleotides with modified exocyclic base substituents (1991)

Fluorescence titrations have been carried out to determine the association constants (Ka) for binding of the dyes Hoechst 33258 and DAPI to the self-complementary decamer d(CTGAATTCAG) and nine duplex derivatives with exocyclic substituent changes in the six central base pairs. Many Ka values are in the range (2-5) x 10(8) (duplex M)-1 at 5.5 degrees C. Replacement of the leftmost adenine by 2-aminopurine in the sequence decreases Ka for Hoechst 33258 by a factor of 170. When the centermost adenine is replaced by 2-aminopurine, Ka for Hoechst 33258 and DAPI is too small to be evaluated. When the centermost adenine is replaced by purine, Ka for both dyes increases, but this very stable duplex-Hoechst 33258 complex is nonfluorescent. The measured affinities are compared to expectations derived from X-ray studies with dodecamer-dye complexes having an identical central binding sequence (Pjura et al., 1987; Teng et al., 1988; Larsen et al., 1989).
Repeated polyketide synthase modules involved in the biosynthesis of a heptaene macrolide by Streptomyces sp. FR‐008 (1994)

Genes for biosynthesis of a Streptomyces sp. FR-008 heptaene macrolide antibiotic with antifungal and mosquito larvicidal activity were cloned in Escherichia coli using heterologous DNA probes. The cloned genes were implicated in heptaene biosynthesis by gene replacement. The FR-008 antibiotic contains a 38-membered, polyketide-derived macrolide ring. Southern hybridization using probes encoding domains of the type I modular erythromycin polyketide synthase (PKS) showed that the Streptomyces sp. FR-008 PKS gene cluster contains repeated sequences spanning c. 105kb of contiguous DNA; assuming c. 5 kb for each PKS module, this is in striking agreement with the expectation for the 21-step condensation process required for synthesis of the FR-008 carbon chain. The methods developed for transformation and gene replacement in Streptomyces sp. FR-008 make it possible to genetically manipulate polyene macrolide production, and may later lead to the biosynthesis of novel polyene macrolides.
Stopped-flow fluorescence kinetics of bovine α2-antiplasmin inhibition of bovine midiplasmin (1995)

In the conversion of bovine plasminogen to bovine plasmin not only the expected urokinase-catalysed cleavage of Arg-557-Val-558, and the following autocatalytic cleavage separating the N-terminal peptide 1-77 from the heavy chain of plasmin, but also a cleavage at Arg-342-Met-343 between kringles 3 and 4 is seen. Here, kinetic studies of the interaction of bovine alpha 2-antiplasmin with bovine plasmin were performed on isolated bovine midiplasmin (lacking kringles 1-3) and on bovine plasmin containing all of the activation products from the bovine plasminogen. A series of experiments using stopped-flow fluorescence fast kinetics as well as conventional techniques suggests a reaction model in accordance with the one known for the human system. First, a tight complex (K1 in the nanomolar range) is formed in a fast reaction step; and second, a tightening of this complex occurs in a slow reaction step. The final complex is indeed so tight (Ki < or = pM), that the reaction for many practical purposes is legitimately considered irreversible. The stopped-flow method allows for the determination of reliable values of the second-order rate constant for the fast association step. At pH 7.4 and 25 degrees C, k+1 = 1.7 x 10(6) M-1 s-1 was obtained in the absence and k+1 = 0.9 x 10(6) M-1.s-1 in the presence of the kringles 1-3 domain of bovine plasmin. In contrast to this, substantial reductions of k+1 were seen in the presence of concentrations of 6-amino-hexanoic acid corresponding to lysine-binding-site interactions and far too low to be attributed to active-site interactions with the bovine plasmins (for each, Ki = 42 mM). All in all, the data indicated that the lysine-binding site(s) not of kringle 1, but of midiplasmin (those of kringles 4 and 5) are regulating the inhibition reaction.
Direct Imaging Raman Microscope Based on Tunable Wavelength Excitation and Narrow-Band Emission Detection (1993)

A new type of imaging Raman microscope is described. First the advantages and disadvantages of the two possible approaches to Raman microscopy based on signal detection by means of a charge-coupled-device camera (i.e., direct imaging and image reconstruction) are discussed. Arguments are given to show that in most cases direct imaging is to be preferred over image reconstruction, because it provides the desired information in less time. In the direct imaging Raman microscope presented in this communication, detection of scattered light occurs in a narrow interval around a fixed wavelength. Selection of the Raman wavenumber shift at which an image is recorded is established by tuning the wavelength of the exciting laser light in such a way that the wavelength of the Raman scattered light with the desired Raman shift coincides with the detected wavelength. The microscope has been incorporated in a Raman microspectrometer in a way that enables easy switching between the imaging and the multichannel spectroscopy modes of operation. Bright field, fluorescence, and Raman microscopic images can be obtained.
The human N-formylpeptide receptor. Characterization of two cDNA isolates and evidence for a new subfamily of G-protein-coupled receptors (1990)

Two variants of the human N-formylpeptide chemoattractant receptor have been isolated from a CDM8 expression library prepared from mRNA of human myeloid HL-60 cells differentiated to the granulocyte phenotype with Bt2cAMP. Both recombinant receptors, fMLP-R26 and fMLP-R98, are 350 amino acids long (Mr 38,420); they differ from each other by two residue changes at positions 101 and 346 and by significant differences in the 5' and 3' untranslated regions. Both clones were able to transfer to COS-7 cells the capacity to specifically bind a new and highly efficient hydrophilic derivative of N-formyl-Met-Leu-Phe-Lys, referred to as fMLPK-Pep12. Photolabeling experiments revealed that the glycosylated form of the fMLP receptor in COS cells has a molecular weight (Mr 50,000-70,000) similar to that observed for the native receptor in differentiated HL-60 cells. Northern blot analysis revealed a major transcript of 1.6-1.7 kb and two minor hybridization signals of 2.3 and 3.1 kb, suggesting a related family of receptors. The complex hybridization pattern obtained with restricted genomic DNA was consistent with either two genes encoding fMLP receptor isoforms or a single gene with at least one intron in the coding sequence. Sequence comparison established that the fMLP receptor belongs to the G-protein-coupled receptor superfamily. The structural similarities observed with RDC1, a receptor isolated from a dog thyroid cDNA library, which shares weak homologies with other members of the family, suggests that the fMLP receptor is representative of a new subfamily.
Aspect Ratio Dependence of the Enhanced Fluorescence Intensity of Gold Nanorods:  Experimental and Simulation Study (2005)

Experimental observations and theoretical treatments are carried out for the band shape and relative intensity of the emission from gold nanorods of various aspect ratios in the range between 2.25 (1.5 theory) and 6.0 (9 theory). The calculation of the fluorescence spectra requires knowledge of the nanorod size distribution, the enhancement factors, and the shape of the unenhanced fluorescence spectrum. The size distribution is determined from the fit of the observed absorption spectrum for each value of aspect ratio studied to the theoretical model of Gans. The theory by Boyd and Shen is used for calculating the enhancement of the fluorescence spectrum of the previously observed weak emission of bulk gold, which originates from the interband transition. This is carried out for nanorods of different aspect ratios. To compare theory to the observed nanorod fluorescence spectra, which suffer from self-absorption, the calculated nanorod fluorescence spectra are corrected for this effect using the observed absorption spectra. The comparison between the observed and the calculated fluorescence band shapes is found to be good. The calculated changes in the relative intensities upon changing the aspect ratios are found to be much greater than that observed. This is due to the fact that for the observed emission of all the nanorods studied nonradiative processes dominate the relaxation mechanism of the excited state, a fact that was not included in the theoretical treatments.
Sulfhydryl content of bovine eye lens leucine aminopeptidase. Determination of the reactivity of the sulfhydryl groups of the zinc metalloenzyme, of the enzyme activated by Mg2+, Mn2+, and Co2+, and of the metal-free apoenzyme. (1982)

The reactivity of the sulfhydryl groups of leucine aminopeptidase from bovine eye lens has been studied by carboxymethylation with iodoacetate of the native enzyme (Zn2+-Zn2+), of the enzyme activated with magnesium (Zn+-Mg2+) or manganese (Zn2+-Mn2+), the enzyme incubated with cobalt (CO2+-Co2+), and the metal-free apoenzyme. The reactivity of the sulfhydryl groups was also determined in the presence of denaturing agents with or without reducing agents. All seven half-cystines per leucine aminopeptidase subunit are in the sulfhydryl form. In the native and the Zn2+-Mn2+ enzyme, only one of the cysteines (residue 344) reacts readily with iodoacetate. In the Zn2+-Mg2+ enzyme, two cysteines react (residues 344 and 412) and in the Co2+-incubated enzyme only one (residue 412). The metal-free apoenzyme has at least three reactive cysteines (residues 344, 412, and 429). The data suggest that sulfhydryl groups are involved in the binding of metal ions.
Cutting Edge: High Molecular Weight Hyaluronan Promotes the Suppressive Effects of CD4+CD25+ Regulatory T Cells (2007)

Hyaluronan is a glycosaminoglycan present in the extracellular matrix. When hyaluronan is degraded during infection and injury, low m.w. forms are generated whose interactions influence inflammation and angiogenesis. Intact high m.w. hyaluronan, conversely, conveys anti-inflammatory signals. We demonstrate that high m.w. hyaluronan enhances human CD4(+)CD25(+) regulatory T cell functional suppression of responder cell proliferation, whereas low m.w. hyaluronan does not. High m.w. hyaluronan also up-regulates the transcription factor FOXP3 on CD4(+)CD25(+) regulatory T cells. These effects are only seen with activated CD4(+)CD25(+) regulatory T cells and are associated with the expression of CD44 isomers that more highly bind high m.w. hyaluronan. At higher concentrations, high m.w. hyaluronan also has direct suppressive effects on T cells. We propose that the state of HA in the matrix environment provides contextual cues to CD4(+)CD25(+) regulatory T cells and T cells, thereby providing a link between the innate inflammatory network and the regulation of adaptive immune responses.
RADIAL BASIS FUNCTION NETWORK DEPENDENT EXCLUSIVE MUTUAL INTERPOLATION FOR MISSING VALUE IMPUTATION (2013)

The success of data mining relies on the purity of the data set. Before performing the data mining, the data has to be cleaned. An unprocessed data set may contain noisy or missing values which is a critical research issue in the pre-processing stage. Imputation methods are being used to solve the missing value problems. In this proposed work, a machine learning based imputation method is proposed by using the mutual information by exclusively interpolating two different section of the same dataset. For designing the proposed model, a radial basis function based neural network has been used. The performance of the proposed algorithm has been measured with respect to different rate or percentage of missing values in the data set and the results has been compared with existing simple and efficient imputation methods also. To evaluate the performance, the standard WDBC data set has been used. The proposed algorithm performs well and was able to impute the missing values even in the worst cases with more than 50% of missing values. Instead of using simple quality measure such as Mean Square Error (MSE) to evaluate the imputed data quality, in this study, the quality is measured in terms of classification performance. The results arrived were more significant and comparable.
Large-Scale Optical Phased Arrays Enabled by Silicon Photonics (2013)

The largest (up to 64×64) optical phased arrays to date are demonstrated with silicon photonics, including passive arrays generating intricate far-field patterns and an active array for dynamic beam steering and shaping.
Enhanced time-resolved imaging with a diffusion model of photon transport (1994)

Imaging through highly scattering media with transmitted photons with the shortest flight times is limited ultimately by the available number of photons with sufficiently short paths. A method is described that enhances the performance of the time-resolved imaging technique. A least-squares fit was obtained between the measured temporal distributions of transmitted light and a model of photon transport based on the diffusion approximation to the radiative transfer theory. Images constructed from the model estimates of short-path-length photon intensities provide information on internal structure, with a significantly improved signal-to-noise ratio compared with those that would be obtained directly from the data.
New Drug Shows Promise in Monkeys (1995)

In experiments reported in this issue (p. p. 1197 ), a new AIDS drug called PMPA protected monkeys from being infected by SIV, the simian counterpart of the AIDS virus. Preliminary results presented at a meeting last week also indicate that the drug slows the onset of symptoms when it is given after SIV infection is established
Tissue factor pathway inhibitor-2 is a novel inhibitor of matrix metalloproteinases with implications for atherosclerosis (2001)

Degradation of ECM, particularly interstitial collagen, promotes plaque instability, rendering atheroma prone to rupture. Previous studies implicated matrix metalloproteinases (MMPs) in these processes, suggesting that dysregulated MMP activity, probably due to imbalance with endogenous inhibitors, promotes complications of atherosclerosis. We report here that the serine proteinase inhibitor tissue factor pathway inhibitor-2 (TFPI-2) can function as an MMP inhibitor. TFPI-2 diminished the ability of the interstitial collagenases MMP-1 and MMP-13 to degrade triple-helical collagen, the primary load-bearing molecule of the ECM within human atheroma. In addition, TFPI-2 also reduced the activity of the gelatinases MMP-2 and MMP-9. In contrast to the "classical" tissue inhibitors of MMPs (TIMPs), TFPI-2 expression in situ correlated inversely with MMP levels in human atheroma. TFPI-2 colocalized primarily with smooth muscle cells in the normal media as well as the plaque's fibrous cap. Conversely, the macrophage-enriched shoulder region, the prototypical site of matrix degradation and plaque rupture, stained only weakly for TFPI-2 but intensely for gelatinases and interstitial collagenases. Evidently, human mononuclear phagocytes, an abundant source of MMPs within human atheroma, lost their ability to express this inhibitor during differentiation in vitro. These findings establish a new, anti-inflammatory function of TFPI-2 of potential pathophysiological significance for human diseases, including atherosclerosis.
Discovery of Novel and Selective SIRT6 Inhibitors (2014)

SIRT6 is an NAD(+)-dependent deacetylase with a role in the transcriptional control of metabolism and aging but also in genome stability and inflammation. Broad therapeutic applications are foreseen for SIRT6 inhibitors, including uses in diabetes, immune-mediated disorders, and cancer. Here we report on the identification of the first selective SIRT6 inhibitors by in silico screening. The most promising leads show micromolar IC50s, have significant selectivity for SIRT6 versus SIRT1 and SIRT2, and are active in cells, as shown by increased acetylation at SIRT6 target lysines on histone 3, reduced TNF-α secretion, GLUT-1 upregulation, and increased glucose uptake. Taken together, these results show the value of these compounds as starting leads for the development of new SIRT6-targeting therapeutic agents.
Variations on a Theme: Cataloging Human DNA Sequence Variation (1997)

New methods for the discovery and scoring of single-nucleotide polymorphisms (SNPs) offer the potential for considerably improved methods for genetic analysis of complex biological phenomena, particularly common diseases. In this Policy Forum, the authors call for a publicly supported effort to discover a large number of SNPs and to place the information in public databases. Participation in this public effort by the private sector would be particularly desirable.
Differentiation of cultured Friend leukemia cells induced by short-chain fatty acids. (1975)

Short-chain fatty acids as sodium salts (pH 7.0) induced hemoglobin synthesis in cultured Friend leukemia cells (T-3-Cl-1) in concentrations of 0.5 mM butyrate, 6mM isobutyrate, 2mM propionate, and 30mM acetate. Relative number of cells decreased by the addition of these fatty acids. Addition of 0.5mM butyrate to culture medium resulted in the highest hemoglobin synthesis as found by the extracted hemoglobin content by spectrophotometry. The activity of delta-aminolevulinic acid synthetase increased on day 4 by the addition of any of these fatty acids into the medium. Hemoglobin synthesis was initiated on day 3 of culture by the addition of either butyrate or isobutyrate, and on day 4 by the addition of dimethyl sulfoxide. Hemoglobin accumulation reached the maximum on day 5 of culture in all cases when the fatty acid was added. Reasonably similar values were obtained for hemoglobin synthesis determined by either benzidine staining or hemoglobin quantitation. Formate, succinate, and citrate were ineffective for the induction.
Dysregulation of TGF-β1 receptor activation leads to abnormal lung development and emphysema-like phenotype in core fucose-deficient mice (2005)

The core fucosylation (alpha1,6-fucosylation) of glycoproteins is widely distributed in mammalian tissues, and is altered under pathological conditions. To investigate physiological functions of the core fucose, we generated alpha1,6-fucosyltransferase (Fut8)-null mice and found that disruption of Fut8 induces severe growth retardation and death during postnatal development. Histopathological analysis revealed that Fut8(-/-) mice showed emphysema-like changes in the lung, verified by a physiological compliance analysis. Biochemical studies indicated that lungs from Fut8(-/-) mice exhibit a marked overexpression of matrix metalloproteinases (MMPs), such as MMP-12 and MMP-13, highly associated with lung-destructive phenotypes, and a down-regulation of extracellular matrix (ECM) proteins such as elastin, as well as retarded alveolar epithelia cell differentiation. These changes should be consistent with a deficiency in TGF-beta1 signaling, a pleiotropic factor that controls ECM homeostasis by down-regulating MMP expression and inducing ECM protein components. In fact, Fut8(-/-) mice have a marked dysregulation of TGF-beta1 receptor activation and signaling, as assessed by TGF-beta1 binding assays and Smad2 phosphorylation analysis. We also show that these TGF-beta1 receptor defects found in Fut8(-/-) cells can be rescued by reintroducing Fut8 into Fut8(-/-) cells. Furthermore, exogenous TGF-beta1 potentially rescued emphysema-like phenotype and concomitantly reduced MMP expression in Fut8(-/-) lung. We propose that the lack of core fucosylation of TGF-beta1 receptors is crucial for a developmental and progressive/destructive emphysema, suggesting that perturbation of this function could underlie certain cases of human emphysema.
I- + CH3I SN2反応系における微視的溶媒効果の研究 (2010)

第4回分子科学討論会, 2010年9月14日-17日, 大阪大学豊中キャンパス(大阪), 4A10
Deuterium and carbon-13 kinetic isotope effects for the isomerization of 5,5-dimethylbicyclo[2.1.0]pent-2-ene to 5,5-dimethylcyclopentadiene (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDeuterium and carbon-13 kinetic isotope effects for the isomerization of 5,5-dimethylbicyclo[2.1.0]pent-2-ene to 5,5-dimethylcyclopentadieneJohn E. Baldwin and Naresh D. GhatliaCite this: J. Am. Chem. Soc. 1989, 111, 9, 3319–3325Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://pubs.acs.org/doi/10.1021/ja00191a032https://doi.org/10.1021/ja00191a032research-articleACS PublicationsRequest reuse permissionsArticle Views417Altmetric-Citations13LEARN 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
Solvent-free cation-conducting polysiloxane electrolytes with pendant oligo(oxyethylene) and sulfonate groups (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolvent-free cation-conducting polysiloxane electrolytes with pendant oligo(oxyethylene) and sulfonate groupsGuang Bin Zhou, Ishrat M. Khan, and Johannes SmidCite this: Macromolecules 1993, 26, 9, 2202–2208Publication Date (Print):April 1, 1993Publication History Published online1 May 2002Published inissue 1 April 1993https://pubs.acs.org/doi/10.1021/ma00061a010https://doi.org/10.1021/ma00061a010research-articleACS PublicationsRequest reuse permissionsArticle Views598Altmetric-Citations74LEARN 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