gebhart/patrepeval huggingface dataset:
Functional basis for the overlap in ligand interactions and substrate specificities of matrix metalloproteinases-9 and -2 (2005)

The MMPs (matrix metalloproteinases) MMP-9 and -2 each possess a unique CBD (collagen-binding domain) containing three fibronectin type II-like modules. The present experiments investigated whether the contributions to ligand interactions and enzymatic activities by the CBD of MMP-9 (CBD-9) corresponded to those of CBD in MMP-2 (CBD-2). The interactions of recombinant CBD-9 with a series of collagen types and extracellular matrix molecules were characterized by protein-protein binding assays. CBD-9 bound native and denatured type I, II, III, IV and V collagen, as well as Matrigel and laminin, with apparent K(d) values of (0.1-6.8)x10(-7) M, which were similar to the K(d) values for CBD-2 [(0.2-3.7)x10(-7) M]. However, CBD-9 bound neither native nor denatured type VI collagen. We also generated two modified MMPs, MMP-9(E402A) and MMP-2(E404A), by site-specific mutations in the active sites to obtain enzymes with intact ligand binding, but abrogated catalytic properties. In subsequent competitive binding assays, CBD-9 and MMP-9(E402A) inhibited the interactions of MMP-2(E404A) and, conversely, CBD-2 and MMP-2(E404A) competed with MMP-9(E402A) binding to native and denatured type I collagens, pointing to shared binding sites. Importantly, the capacity of CBD-9 to disrupt the MMP-9 and MMP-2 binding of collagen translated to inhibition of the gelatinolytic activity of the enzymes. Collectively, these results emphasize the essential contribution of CBD-9 to MMP-9 substrate binding and gelatinolysis, and demonstrate that the CBDs of MMP-9 and MMP-2 bind the same or closely positioned sites on type I collagen.
A simple synthesis of novel 2‐pyridones from chalcones (1990)

Abstract Several novel 2‐pyridones were synthesized in good yields from a simple one‐pot reaction by the condensation of different substituted chalcones and malonamide using sodium ethoxide in ethanol at room temperature. The structures of these 2‐pyridones were elucidated from their 1 H, 13 C and infrared spectral data as well as their elemental analysis. Different 2‐pyridones tautomers were obtained as the solvent of crystallization changes.
Decreased antioxidant status and increased lipid peroxidation in patients with septic shock and secondary organ dysfunction (1995)

These data indicate decreased antioxidant status in the face of enhanced free radical activity, and suggest potential therapeutic strategies involving antioxidant repletion.
The swelling of collagen in alkaline solutions. 2. Swelling in solutions of univalent bases (1950)

Research Article| May 01 1950 The swelling of collagen in alkaline solutions. 2. Swelling in solutions of univalent bases Joane H. Bowes; Joane H. Bowes 1British Leather Manufacturers' Research Association, Egham, Surrey Search for other works by this author on: This Site PubMed Google Scholar R. H. Kenten R. H. Kenten 1British Leather Manufacturers' Research Association, Egham, Surrey Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1950) 46 (5): 524–529. https://doi.org/10.1042/bj0460524 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Joane H. Bowes, R. H. Kenten; The swelling of collagen in alkaline solutions. 2. Swelling in solutions of univalent bases. Biochem J 1 May 1950; 46 (5): 524–529. doi: https://doi.org/10.1042/bj0460524 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1950 CAMBRIDGE UNIVERSITY PRESS1950 Article PDF first page preview Close Modal You do not currently have access to this content.
Properties of hexagonal ScN versus wurtzite GaN and InN (2002)

Local-density approximation calculations are performed to compare properties of hexagonal ScN with those of wurtzite GaN and InN. A nearly five-times coordinated hexagonal structure is found to be (meta)stable in ScN, unlike the wurtzite structure. Structural, dielectric, and optical properties of this stable hexagonal phase are predicted to be rather different from those of wurtzite GaN and InN. This implies that disordered hexagonal ${\mathrm{Sc}}_{1\ensuremath{-}x}{\mathrm{Ga}}_{x}\mathrm{N}$ and ${\mathrm{Sc}}_{1\ensuremath{-}x}{\mathrm{In}}_{x}\mathrm{N}$ alloys are very attractive both fundamentally and technologically.
Induction of Serotonin Transporter by Hypoxia in Pulmonary Vascular Smooth Muscle Cells (1999)

-The increased delivery of serotonin (5-hydroxytryptamine, 5-HT) to the lung aggravates the development of hypoxia-induced pulmonary hypertension in rats, possibly through stimulation of the proliferation of pulmonary artery smooth muscle cells (PA-SMCs). In cultured rat PA-SMCs, 5-HT (10(-8) to 10(-6) mol/L) induced DNA synthesis and potentiated the mitogenic effect of platelet-derived growth factor-BB (10 ng/mL). This effect was dependent on the 5-HT transporter (5-HTT), since it was prevented by the 5-HTT inhibitors fluoxetine (10(-6) mol/L) and paroxetine (10(-7) mol/L), but it was unaltered by ketanserin (10(-6) mol/L), a 5-HT2A receptor antagonist. In PA-SMCs exposed to hypoxia, the levels of 5-HTT mRNA (measured by competitive reverse transcriptase-polymerase chain reaction) increased by 240% within 2 hours, followed by a 3-fold increase in the uptake of [3H]5-HT at 24 hours. Cotransfection of the cells with a construct of human 5-HTT promoter-luciferase gene reporter and of pCMV-beta-galactosidase gene allowed the demonstration that exposure of cells to hypoxia produced a 5.5-fold increase in luciferase activity, with no change in beta-galactosidase activity. The increased expression of 5-HTT in hypoxic cells was associated with a greater mitogenic response to 5-HT (10(-8) to 10(-6) mol/L) in the absence as well as in the presence of platelet-derived growth factor-BB. 5-HTT expression assessed by quantitative reverse transcriptase-polymerase chain reaction and in situ hybridization in the lungs was found to predominate in the media of pulmonary artery, in which a marked increase was noted in rats that had been exposed to hypoxia for 15 days. These data show that in vitro and in vivo exposure to hypoxia induces, via a transcriptional mechanism, 5-HTT expression in PA-SMCs, and that this effect contributes to the stimulatory action of 5-HT on PA-SMC proliferation. In vivo expression of 5-HTT by PA-SMC may play a key role in serotonin-mediated pulmonary vascular remodeling.
Hierarchical Mobile IPv6 (HMIPv6) Mobility Management (2008)

This document introduces extensions to Mobile IPv6 and IPv6 Neighbour
Discovery to allow for local mobility handling. Hierarchical mobility
management for Mobile IPv6 is designed to reduce the amount of
signalling between the Mobile Node, its Correspondent Nodes, and its
Home Agent. The Mobility Anchor Point (MAP) described in this document
can also be used to improve the performance of Mobile IPv6 in terms of
handover speed.
An experimental demonstration of the stereochemistry of enzymic cyclization of 2,3-oxidosqualene to the protosterol system, forerunner of lanosterol and cholesterol (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn experimental demonstration of the stereochemistry of enzymic cyclization of 2,3-oxidosqualene to the protosterol system, forerunner of lanosterol and cholesterolE. J. Corey and Scott C. VirgilCite this: J. Am. Chem. Soc. 1991, 113, 10, 4025–4026Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ja00010a073https://doi.org/10.1021/ja00010a073research-articleACS PublicationsRequest reuse permissionsArticle Views724Altmetric-Citations93LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Surface Nanometer‐Scale Patterning in Realizing Large‐Scale Ordered Arrays of Metallic Nanoshells with Well‐Defined Structures and Controllable Properties (2010)

Abstract Surface patterns of nanoshell arrays play an important role in diverse applications including surface‐enhanced Raman scattering (SERS) sensors, lithium‐ion batteries, solar cells, and optical devices. This paper describes an innovative surface nanopatterning technique for realizing large‐scale ordered arrays of metallic spherical nanoshells with well‐defined structures. Ag nanoshell arrays are prepared using polystyrene sphere templates by an electrophoretic process in Ag colloidal solutions. The fabricated Ag nanoshell arrays have a high controllability of the structural parameters, including the diameter, the surface roughness, and the intershell spacing, giving rise to the tunable properties of nanoshell arrays. As an example, tunable SERS and localized surface plasmon resonance of the nanoshell arrays are demonstrated by controlling the structural parameters. The surface nanopatterning technique shown in this paper is a general fabrication process in achieving not only metallic nanoshell arrays, but also nanoshell arrays of semiconductors and metallic oxides.
Method described for using 4D seismic to track reservoir fluid movement (1995)

This is the second part of an article about the use of time-lapse 3D seismic data (4D) to analyze changes in reservoir status during production of giant Eugene Island Block 330 field in the Gulf of Mexico off Louisiana. Because of the 4D effects being observed by the partners in the LF sand reservoir, the Global Basins Research Network (GBRN) began an independent but collaborative analysis of the differences observed between the two 3D seismic datasets in this area. The authors utilized a 4D seismic analysis technique consisting of seismic imaging, feature extraction, and pattern recognition functions, coupled iteratively with high resolution, seismic forward and inverse modeling. Pattern recognition, rather than interpolation and recomputation, is used to examine similarities and differences among the seismic amplitudes of the datasets. This technique minimizes the difficulties in matching acquisition parameters, variable geometries, and technology improvements that have accompanied the development of 3D seismic methodologies over the years. The paper details the normalization techniques used, the high amplitude regions, similarities and differences, and analysis of drainage, and a seismic model.
Bacterial DNA evokes epithelial IL‐8 production by a MAPK‐dependent, NFκB‐independent pathway (2003)

ABSTRACT Recognition of bacterial products by the innate immune system is dependent on pattern‐recognition receptors: toll‐like receptor 9 (TLR‐9) in the case of bacterial DNA. We hypothesized that bacterial DNA can directly affect enteric epithelial cells. RT‐PCR revealed constitutive TLR‐9 mRNA expression in three human colonic epithelial cell lines (T84, HT‐29, Caco‐2) and THP‐1 monocytes. Epithelial cells, in six‐well culture plates or on filter supports, were exposed to E. coli DNA (1–50 µg/ml), synthetic CpG‐rich oligonucleotides, or calf thymus DNA for 6–48 h. Exposure to E. coli DNA resulted in an increase in IL‐8 mRNA, and a time‐and dose‐dependent increase in IL‐8 secretion. Also, CpG oligonucleotides induced epithelial IL‐8 production, whereas calf thymus DNA did not. Exposure to E. coli DNA resulted in phosphorylation of ERK 1/2 MAPK and inhibitors of ERK activity (PD98059, UO126) significantly reduced the evoked IL‐8 production. In contrast, inhibitors of NFκB activity (PDTC, SN50) did not block E. coli DNA‐induced IL‐8 production. Electrophoretic mobility shift assays revealed that E. coli DNA stimulated epithelial AP‐1 but not NFκB activation. The barrier (i.e., transepithelial resistance) and ion transport parameters of epithelial monolayers (assessed in Ussing chambers) were unaltered following E. coli DNA exposure. Thus model gut epithelia express TLR‐9 mRNA and, while maintaining their barrier function, can respond to E. coli DNA by increased IL‐8 production.
Secretion of Insulin-Like Growth Factor-II into Bile of Rats of Different Ages (2000)

Bile from rats of different ages (suckling 10-12 days; weanling 30-33 days, and adult 60-70 days) was collected and studied for the presence of immuno- and receptor-assayable insulin-like growth factor-II (IGF-II) concentrations. Concentrations of RIA IGF-II in bile were highest in suckling rats (230 +/- 38 ng/ml) and lowest in adults (47 +/- 7 ng/ml). These concentrations were approximately twice those of the bile IGF-I concentration in sucklings, as measured in a previous study. Selected bile samples were also assayed using a competitive binding assay with a crude preparation of adult rat liver membranes bearing the IGF-II receptor. These studies confirmed the presence of receptor- (as well as immuno-) active IGF-II in bile. Since bile flow rates increased dramatically after the suckling period, bile delivery rates of IGF-II were normalized as picograms per gram body weight per hour. When such calculations were done, bile IGF-II delivery rates to the small intestine were highest in sucklings and weanlings in comparison to adult rats. Thus non-enterically derived (milk- and bile-borne) IGF-II delivery to the suckling small intestine can be approximated at roughly 1 microg/day. Unlike IGF-I, intravenously injected IGF-II could not be detected in suckling bile, suggesting a predominantly hepatic origin. From this study we conclude that there exists a significant delivery of receptor-active IGF-II to the gastrointestinal tract of rats of all ages.
Enhancement of aromatase activity by D-aspartic acid in the ovary of the lizard Podarcis s. sicula (2001)

The present study investigated the role of D-aspartic acid (D-Asp) in ovarian steroidogenesis and its effect on aromatase activity in the lizard, Podarcis s. sicula. It was determined that D-Asp concentrations vary significantly during phases of the reproductive cycle: they vary inversely with testosterone concentrations and directly with oestradiol concentrations in the ovary and plasma. Experimental treatment showed that administration of D-Asp induces a decrease in testosterone and an increase in oestradiol, and that treatment with other amino acids (L-Asp, D-Glu and D-Ala) instead of D-Asp has no effects. Experiments in vitro confirmed these results. Furthermore, these experiments showed an increase in aromatase activity, as the addition of D-Asp either to fresh ovarian tissue homogenate or to acetonic powder of ovarian follicles induced a significant increase in the conversion of testosterone to oestradiol. Aromatase activity is four times greater in the presence of D-Asp than in its absence. However, almost equivalent values of the two K(m) values (both approximately 25 nmol l(-1)) indicate that aromatase has the same catalytic properties in both cases.
Fur and iron transport proteins in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius (1999)

The Brazilian purpuric fever (BPF) clone of Haemophilus influenzae biogroup aegyptius causes a fatal septicaemic disease, resembling fulminant meningococcal sepsis, in children. When isolate F3031 was grown under iron-limiting conditions, the presence of several iron-regulated proteins of 38-110 kDa was revealed by electrophoretic analysis and a Fur homologue was shown by immunoblotting. Dot-blot assays and immunoblotting indicated that BPF cells bound human transferrin and contained transferrin-binding proteins in the outer membrane. However, the binding activity and the biosynthesis of these proteins were detected even under iron-rich conditions. Immunoblot analysis demonstrated the presence of a periplasmic protein related to the ferric iron-binding protein A (FbpA), the major iron-binding protein described in Neisseria spp. However, the FbpA homologue in strain F3031 was constitutively expressed and was smaller than the periplasmic protein detected in H. influenzae type b strain Eagan. The periplasm of strain F3031 also contained a protein related to the Streptococcus parasanguis FimA protein which recently has been shown to be involved in iron acquisition in Yersinia pestis. Although the Eagan and F3031 FimA homologues had a similar mol. wt, of 31 kDa, the expression of the BPF fimA-like gene was not regulated by the iron concentration of the culture medium.
Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis (1997)

Our phylogenetic analysis based on 16S ribosomal DNA (rDNA) sequences and chemotaxonomic analyses showed that Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 are more closely related to the genus Rhodococcus, especially Rhodococcus erythropolis, than to the genus Nocardioides. N. simplex ATCC 13260 and N. simplex ATCC 19565 and ATCC 19566 exhibited levels of 16S rDNA similarity of 99.4 and 100%, respectively, to R. erythropolis DSM 43066T. Strains ATCC 13260, ATCC 19565, and ATCC 19566 had mesodiaminopimelic acid in their peptidoglycan and MK-8(H2) as their predominant menaquinone. These three strains produced cellular fatty acid patterns similar to those of R. erythropolis strains rather than those of Nocardioides species. Therefore, N. simplex ATCC 13260, ATCC 19565, and ATCC 19566 should be reclassified as strains of R. erythropolis Gray and Thornton 1928.
The optimum level of music listened to in the presence of noise. (1982)

The optimum level of music listened to in the presence of noise is studied and discussed from the point of masked loudness. By carrying out an experiment with five pieces of music, it is revealed that the increase in the optimum level of music is about 3dB against 10dBA noise level increment if the noise level lies between 55dBA and 75dBA. The increment of the optimum music level is less as compared with the above value for a lower noise level than 55dBA, and greater for a higher noise level than 75dBA. Even if the signal is radio news instead of music, this rate of increase seems to be unchanged. This tendency of the consistency of the optimum level may be attributable to the subjects' judgement that they intend to keep the masked loudness of music constant against the change of noise level. Selecting a standard signal, we carried out a simulation test to derive the standard equal loudness contour for the signal against various noise levels. Since these contours well simulate the experimental curves, they can be used as the standard for designing an automatic level controller such as that assembled in the playback system used in the presence of noise.
The influence of electron delocalization upon the stability and structure of potential N-heterocyclic carbene precursors with 1,3-diaryl-imidazolidine-4,5-dione skeletons (2010)

Targeting N-heterocyclic carbenes (NHCs) with increased π-acceptor character featuring N-fluorophenyl substituents, the molecular 2-chloro-1,3-bis(fluorophenyl)imidazolidine-4,5-diones (1a–c) were isolated from the condensation of the corresponding formamidine with oxalyl chloride. These formal adducts of NHCs with hydrogen chloride demonstrated reactivity akin to that of alkyl halides: 1,3,1′,3′-tetrakis(2,6-dimethylphenyl)-[2,2′]diimidazolidinyl-4,5,4′,5′-tetraone (2b) was formed via the reductive coupling of 1b, while 1,3-bis(2,6-diisopropylphenyl)-4,5-dioxoimidazolidin-2-yl acetate (3c) was formed as the result of a metathesis reaction with mercury(II) acetate. Chloride abstraction resulted in the formation of imidazolium-4,5-dione salts (4a–c) that decomposed rapidly, except in the case of the kinetically-stabilized 1,3-bis(2,6-diisopropylphenyl)imidazolium-4,5-dione hexafluorophosphate 4c. All imidazolium-4,5-dione hexafluorophosphate salts decomposed to neutral 2-fluoro-1,3-bis(aryl)imidazolidine-4,5-diones (5a–c) via fluoride abstraction. 2-Methoxy-1,3-di(aryl)imidazolidine-4,5-diones (6a–c) were also prepared and they failed to undergo thermolysis and yield the free NHCs. Computational analyses revealed that the instability of NHCs with an oxalamide skeleton, as well as that of imidazolium-4,5-diones, results from a π-framework which extends over both carbonyl moieties and gives rise to a very low energy LUMO, rendering the compounds in question highly electrophilic.
Hydrogen Storage Systems for Transportation Application (2005)

This report describes proposed research which attempted to improve the state of understanding of the adsorption/desorption mechanism for hydrogen in carbon nanostructures. This would then lead to an improvement in the estimate of the hydrogen storage capacity of carbon nanostructures. The authors address hydrogen binding energies, apply the hydrogen binding energies to adsorption/desorption dynamics, and begin an engineering design for a practical storage device based on these binding energies.
Methods for Trend Estimation from Summarized Dose-Response Data, with Applications to Meta-Analysis (1992)

Meta-analysis often requires pooling of correlated estimates to compute regression slopes (trends) across different exposure or treatment levels. The authors propose two methods that account for the correlations but require only the summary estimates and marginal data from the studies. These methods provide more efficient estimates of regression slope, more accurate variance estimates, and more valid heterogeneity tests than those previously available. One method also allows estimation of nonlinear trend components, such as quadratic effects. The authors illustrate these methods in a meta-analysis of alcohol use and breast cancer.