gebhart/patrepeval huggingface dataset:
Coagulation cascade proteases and tissue fibrosis (2002)

Fibrotic disorders of the liver, kidney and lung are associated with excessive deposition of extracellular matrix proteins and ongoing coagulation-cascade activity. In addition to their critical roles in blood coagulation, thrombin and the immediate upstream coagulation proteases, Factors Xa and VIIa, influence numerous cellular responses that may play critical roles in subsequent inflammatory and tissue repair processes in vascular and extravascular compartments. The cellular effects of these proteases are mediated via proteolytic activation of a novel family of cell-surface receptors, the protease-activated receptors (PAR-1, -2, -3 and -4). Although thrombin is capable of activating PAR-1, -3 and -4, there is accumulating in vitro evidence that the profibrotic effects of thrombin are predominantly mediated via PAR-1. Factor Xa is capable of activating PAR-1 and PAR-2, but its mitogenic effects for fibroblasts are similarly mediated via PAR-1. These proteases do not exert their profibrotic effects directly, but act via the induction of potent fibrogenic mediators, such as platelet-derived growth factor and connective tissue growth factor. In vivo studies using proteolytic inhibitors, PAR-1 antagonists and PAR-1-deficient mice have provided evidence that coagulation proteases play a key role in tissue inflammation and in a number of vascular pathologies associated with hyperproliferation of smooth muscle cells. More recently, coagulation proteases have also been shown to play a role in the pathogenesis of fibrosis but the relative contribution of their cellular versus their procoagulant effects awaits urgent evaluation in vivo. These studies will be informative in determining the potential application of PAR-1 antagonists as antifibrotic agents.
Contribution of IL-33 to induction and augmentation of experimental allergic conjunctivitis (2010)

IL-33, a member of the IL-1 family of cytokines, is the ligand for ST2 (IL-33Ralpha chain). IL-33 has the capacity to induce T(h)2 cytokine production from T(h)2 cells, mast cells and basophils, indicating that IL-33 has the potential to induce T(h)2 cytokine-mediated allergic inflammation of the eye. Thus, we tested the pathological role of IL-33 in allergic conjunctivitis (AC). As reported elsewhere, animals immunized with ragweed pollen (RW)/alum and boosted with RW/PBS developed AC promptly (within 15 min) and conjunctival eosinophilic inflammation after a delay (within 24 h) in response to eye drop challenge with RW. Furthermore, RW-immunized mice, when topically challenged with both RW and IL-33, developed more striking eosinophilia in their conjunctiva without exacerbation of the clinical AC score. This in vivo IL-33 treatment significantly increased the capacity of T cells in the cervical lymph nodes of RW-immunized mice to produce IL-4, IL-5 and IL-13 upon challenge with anti-CD3 and anti-CD28 antibodies in vitro. Furthermore, the infiltrating cells were largely eosinophils and a small proportion of CD4(+) T cells, both of which express ST2. We also found that even splenic eosinophils express ST2 and show increased expression in response to IL-5, granulocyte-macrophage colony-stimulating factor (GM-CSF) or IL-33. Eosinophils, stimulated with IL-5 and/or GM-CSF, are responsive to IL-33, which induces production of IL-4 and chemokines. Finally, we showed that conjunctival tissues constitutively express biologically active IL-33, suggesting that IL-33 might play a crucial role in the induction and augmentation of AC.
The Identification of Antigenic Determinants on Mycobacterium bovis Using Monoclonal Antibodies (1985)

Murine hybridomas secreting monoclonal antibodies to Mycobacterium bovis were produced and three soluble antigens were identified using radioimmunoassays and immunoblotting from polyacrylamide electrophoresis gels. Antibody MB3 (IgM, k chain) reacted with 20-100 kDal antigens produced by all mycobacterial strains examined while antibody MB5 (IgG2a, k chain) identified a 29.8 kDal antigen detected in field isolates of M. bovis and M. bovis strains Vallée and AN5. There was insignificant binding to M. bovis BCG, M. tuberculosis, M. microti, M. africanum, M. avium or M. paratuberculosis. Monoclonal antibody MB17 (IgA, k chain) reacted with a 17.4 kDal antigen present in M. bovis, M. tuberculosis and M. microti. Absorption of monoclonal antibodies with antigens from different species of Mycobacterium confirmed the specificities of MB3 and MB5 but the binding of MB17 was inhibited to some extent by all the extracts examined. The antigen identified by MB3 was present in purified protein derivative (PPD) from M. bovis, M. paratuberculosis and M. avium but antigens identified by MB5 and MB17 were not detected in these reagents.
Cholinesterase Inhibitors: A New Class of Psychotropic Compounds (2000)

Acetylcholinesterase inhibitors have psychotropic effects and may play an important role in controlling neuropsychiatric and behavioral disturbances in patients with Alzheimer's disease. These agents also may contribute to the management of other disorders with cholinergic system abnormalities and neuropsychiatric symptoms. The beneficial response is most likely mediated through limbic cholinergic structures.
Metering for Exposure Stacks (2012)

Abstract When creating a High‐Dynamic‐Range (HDR) image from a sequence of differently exposed Low‐Dynamic‐Range (LDR) images, the set of LDR images is usually generated by sampling the space of exposure times with a geometric progression and without explicitly accounting for the distribution of irradiance values of the scene. We argue that this choice can produce sub‐optimal results both in terms of the number of acquired pictures and the quality of the resulting HDR image. This paper presents a method to estimate the full irradiance histogram of a scene, and a strategy to select the set of exposures that need to be acquired. Our selection usually requires a smaller or equal set of LDRs, yet produces higher quality HDR images.
Dynamic DMF Binding in MOF-5 Enables the Formation of Metastable Cobalt-Substituted MOF-5 Analogues (2015)

Multinuclear solid-state nuclear magnetic resonance, mass spectrometry, first-principles molecular dynamics simulations, and other complementary evidence reveal that the coordination environment around the Zn(2+) ions in MOF-5, one of the most iconic materials among metal-organic frameworks (MOFs), is not rigid. The Zn(2+) ions bind solvent molecules, thereby increasing their coordination number, and dynamically dissociate from the framework itself. On average, one ion in each cluster has at least one coordinated N,N-dimethylformamide (DMF) molecule, such that the formula of as-synthesized MOF-5 is defined as Zn4O(BDC)3(DMF) x (x = 1-2). Understanding the dynamic behavior of MOF-5 leads to a rational low-temperature cation exchange approach for the synthesis of metastable Zn4-x Co x O(terephthalate)3 (x > 1) materials, which have not been accessible through typical high-temperature solvothermal routes thus far.
Site-directed mutagenesis and structure-function analysis of the human apolipoprotein A-I. Relation between lecithin-cholesterol acyltransferase activation and lipid binding. (1992)

We have mutagenized the human apoA-I gene and have generated cell lines which express normal and mutant apoA-I forms. Point mutations were introduced which changed Gln-1, Gln-2 to Arg,Arg, Pro99 to His, and Pro121 to His. In addition, the following amino acid deletions (delta) were generated: delta 113-124, delta 148-186, delta 212-233, and delta 213-243. The apoA-I form isolated from the culture medium of C127 cells was analyzed for its ability to activate lecithin-cholesterol acyltransferase (LCAT) and to bind to phospholipid vesicles and high density lipoprotein (HDL). Compared with the wild type (WT) apoA-I, the relative activation of LCAT achieved by the point mutations Gln-1, Gln-2----Arg,Arg, Pro99----His, and Pro121----His were 106 +/- 7, 92 +/- 6, and 77 +/- 9%, respectively. Kinetic analysis of one mutant apoA-I form showed similar Vmax but a 15-fold increase in the Km of the mutant apoA-I form. Furthermore, the activation achieved by the internal deletion mutants delta 113-124, delta 148-186, delta 212-233, and delta 213-243 was 47 +/- 3, 0.5 +/- 0.4, 28 +/- 4 and 13 +/- 5%, respectively. Mutants deficient in their ability to activate LCAT displayed alterations in liposome and HDL binding, compared with WT as determined by density gradient ultracentrifugation analysis of the culture medium. Thus, the peak recovery (approximately 50%) of apoA-I bound to HDL was at density 1.14 g/ml for the WT apoA-I, at 1.18 g/ml for the mutants delta 113-124 and delta 148-186, and at d greater than 1.21 g/ml for the delta 212-233 and delta 213-243. Electron microscopy of the proteoliposome LCAT substrate generated by WT and mutant apoA-I forms showed that the carboxyl-terminal deletion mutants which displayed aberrant binding to HDL also displayed reduced ability to convert the spherical lecithin-cholesterol vesicles into discs compared with WT. The findings suggest that (a) the importance of the carboxyl terminus of apoA-I for LCAT activation is related to its ability to bind to lipid and/or to form discoidal substrate for LCAT, and (b) the interaction of several domains of apoA-I are required for the activation of LCAT.
Methods for Structuring Scientific Knowledge from Many Areas Related to Aging Research (2011)

Aging and age-related disease represents a substantial quantity of current natural, social and behavioral science research efforts. Presently, no centralized system exists for tracking aging research projects across numerous research disciplines. The multidisciplinary nature of this research complicates the understanding of underlying project categories, the establishment of project relations, and the development of a unified project classification scheme. We have developed a highly visual database, the International Aging Research Portfolio (IARP), available at AgingPortfolio.org to address this issue. The database integrates information on research grants, peer-reviewed publications, and issued patent applications from multiple sources. Additionally, the database uses flexible project classification mechanisms and tools for analyzing project associations and trends. This system enables scientists to search the centralized project database, to classify and categorize aging projects, and to analyze the funding aspects across multiple research disciplines. The IARP is designed to provide improved allocation and prioritization of scarce research funding, to reduce project overlap and improve scientific collaboration thereby accelerating scientific and medical progress in a rapidly growing area of research. Grant applications often precede publications and some grants do not result in publications, thus, this system provides utility to investigate an earlier and broader view on research activity in many research disciplines. This project is a first attempt to provide a centralized database system for research grants and to categorize aging research projects into multiple subcategories utilizing both advanced machine algorithms and a hierarchical environment for scientific collaboration.
Exploration of the influence of 5-iodo-2′-deoxyuridine incorporation on the structure of d[CACG(IDU)G] (2003)

The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5 methyl group is replaced by an I atom. The structure of the self-complementary hexamer d[CACG(IDU)G] was determined by single-crystal X-ray diffraction techniques. The orthorhombic crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 18.16, b = 30.03, c = 41.99 A. Refinement in the resolution range 20-1.3 A converged with a final R1 = 0.167, including 43 water molecules and two cobalt hexammine complexes. The incorporation of a large I atom has only minor consequences for the overall structure as is noticed in the IDU.A base pairs, which are of the common Watson-Crick type. To contribute to the still puzzling mechanism of this historically important agent, details of base stacking, helical parameters, hydration etc. have been studied. A general scheme of cobalt hexammine-binding modes in Z-DNA is provided, revealing similar binding modes for the reported structure.
Bright dual-mode green emission from selective set of dopant ions in β-Na(Y,Gd)F4:Yb,Er/β-NaGdF4:Ce,Tb core/shell nanocrystals (2012)

Bright dual-mode green-emitting core/shell nanoparticles (NPs) were synthesized by doping selective set of lanthanide ions. Up-conversion (UC) green-emitting β-NaY0.2Gd0.6F4:Yb0.18,Er0.02 NPs (8.3 nm) were used as core material. Bright down-conversion (DC) green-emitting β-NaGd0.8F4:Ce0.15,Tb0.05 NPs showed ca. 31 times higher photoluminescence (PL) intensity than β-NaGdF4:Tb NPs and they were served as shell material with their excellent PL properties. The UC/DC core/shell NPs showed bright green light under excitations of 980 nm near infrared (NIR) light and 254 nm ultraviolet (UV) light, respectively. The UC/DC core/shell NPs showed ca. 11 times higher UC PL intensity than core UCNPs. Consequently, the core/shell NPs doped with selective set of lanthanide ions showed bright dual-mode green emission under excitations of NIR light and UV light, indicating that they are promising for application to optical imaging.
Regulation of Cell Surface Polarity from Bacteria to Mammals (1992)

The generation of unique domains on the cell, cell surface polarity, is critical for differentiation into the diversity of cell structures and functions found in a wide variety of organisms and cells, including the bacterium Caulobacter crescentus, the budding yeast Saccharomyces cerevisiae, and mammalian polarized epithelial cells. Comparison of the mechanisms for establishing polarity in these cells indicates that restricted membrane protein distributions are generated by selective protein targeting to, and selective protein retention at, the cell surface. Initiation of these mechanisms involves reorientation of components of the cytoskeleton and protein transport pathways toward restricted sites at the cell surface and formation of a targeting patch at those sites for selective recruitment and retention of proteins.
Introduction (2005)

By the twentieth century, all major industrialized countries offered formal schooling to all of their children. When these schools took shape in the nineteenth and twentieth centuries, scientists didn't know very much about how people learn. Even by the 1920s, when schools began to become the large bureaucratic institutions that we know today, there still was no sustained study of how people learn. As a result, the schools we have today were designed around commonsense assumptions that had never been tested scientifically:
Serum Vitamin C Concentration Is Low in Peripheral Arterial Disease and Is Associated With Inflammation and Severity of Atherosclerosis (2001)

Vitamin C concentrations are lower in intermittent claudicant patients in association with higher CRP levels and severity of PAD. Future studies attempting to relate vitamin C levels to disease occurrence should include in their analysis an inflammatory marker such as CRP.
Polymer electrolyte complexes of LiCIO4 and comb polymers of siloxane with oligo‐oxyethylene side chains (1988)

Abstract Polysiloxanes with oligo‐oxyethylene side chains of the type —O(CH 2 CH 2 O) 7 CH 3 and —(CH 2 ) 3 O(CH 2 CH 2 O) n CH 3 (average n ≈ 7 and 11) were synthesized from poly(hydrogenmethylsiloxane) and characterized by 1 H n.m.r., 29 Si n.m.r., i.r. and g.p.c. Cyclic analogues were used as model compounds and synthesized from tetramethylcyclotetrasiloxane. Polymer electrolyte complexes were made from the comb polymers and LiClO 4 by solvent‐casting from THF, and their conductivities measured as a function of temperature and studied by differential scanning calorimetry and correlated with their conductivity behaviour. Maximum conductivities close to 10 −4 S cm −1 were achieved at room temperature and at ethylene oxide units to Li + ratios of about 25. Cross‐linking or blending with high molecular weight poly(oxyethylene) lowers the conductance somewhat but vastly improves the mechanical properties of the complexes, and the blends with PEO can be cast into thin, flexible and tough films with good conducting properties.
The Complete Covalent Structure of Hirudin. Localization of the Disulfide Bonds (1985)

Hirudin, the thrombin-specific inhibitor from the leech Hirudo medicinalis, is a single-chain polypeptide (65 amino-acid residues) linked by three disulfide bridges. Localization of the three disulfide bonds could be assigned on the basis of the structures of cystine peptides derived by high performance liquid chromatography separations of thermolysinolytic digest of native hirudin. By characterization of the nine major fragments by amino-acid analysis, N-terminal amino-acid determination and sequence analysis, the following disulfide linkages were identified: Cys6-Cys14, Cys16-Cys28 and Cys22-Cys39. Due to the lack of any closer sequence homology and topological structural homology to other serine proteinase inhibitor proteins, hirudin seems to be unique in its primary structure and hence designates an unknown inhibitor family.
Reduction of Coal-Based Metal Emissions by Furnace Sorbent Injection (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduction of Coal-Based Metal Emissions by Furnace Sorbent InjectionBrian K. Gullett and K. RaghunathanCite this: Energy Fuels 1994, 8, 5, 1068–1076Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/ef00047a009https://doi.org/10.1021/ef00047a009research-articleACS PublicationsRequest reuse permissionsArticle Views330Altmetric-Citations70LEARN 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
Structure and efficiency in intramolecular and enzymic catalysis. Catalysis of amide hydrolysis by the carboxy-group of substituted maleamic acids (1972)

The efficiency of intramolecular catalysis of amide hydrolysis by the carboxy-group of a series of substituted N-methylmaleamic acids is remarkably sensitive to the pattern of substitution on the carbon–carbon double bond. A single alkyl group increases the rate of hydrolysis by a factor which increases with its size. A second alkyl substituent has a disproportionately larger effect, which is sharply reduced when the two groups are joined together in a ring. The rates of hydrolysis of a series of dialkyl-N-methylmaleamic acids range over more than ten powers of ten, and the ‘effective concentration’ of the carboxy-group of the most reactive compound studied is greater than 1010M. This amide, dimethyl-N-n-propylmaleamic acid, is converted into the more stable dimethylmaleic anhydride with a half-life of less than 1s at 39 °C below pH 3. The mechanism of catalysis, and the factors responsible for this extremely high reactivity, are discussed.
Orthoquinone complexes of vanadium and their reactions with molecular oxygen (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrthoquinone complexes of vanadium and their reactions with molecular oxygenMarion E. Cass, David L. Green, Robert M. Buchanan, and Cortlandt G. PierpontCite this: J. Am. Chem. Soc. 1983, 105, 9, 2680–2686Publication Date (Print):May 1, 1983Publication History Published online1 May 2002Published inissue 1 May 1983https://pubs.acs.org/doi/10.1021/ja00347a027https://doi.org/10.1021/ja00347a027research-articleACS PublicationsRequest reuse permissionsArticle Views370Altmetric-Citations62LEARN 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
Nanoscopic recombination processes in InGaN/GaN quantum wells emitting violet, blue, and green spectra (2008)

We investigated correlations between nanoscopic optical and structural properties in violet-emitting, blue-emitting, and green-emitting ${\text{In}}_{x}{\text{Ga}}_{1\ensuremath{-}x}\text{N}/\text{GaN}$ quantum wells (QWs) by means of scanning near-field optical microscopy (SNOM) and atomic force microscopy. Only in the blue-emitting QW, threading dislocations were not major nonradiative recombination centers (NRCs). SNOM data indicated that NRCs in the blue-emitting QW are surrounded by energy levels higher than those for radiative recombination. Such potential distributions realize ``antilocalization'' of carriers to NRCs, which is the cause of high emission quantum efficiencies in blue emitters.
Epidermal Growth Factor Increases Undifferentiated Pancreatic Embryonic Cells In Vitro (2001)

During embryonic life, the development of a proper mass of mature pancreatic tissue is thought to require the proliferation of precursor cells, followed by their differentiation into endocrine or acinar cells. We investigated whether perturbing the proliferation of precursor cells in vitro could modify the final mass of endocrine tissue that develops. For that purpose, we used activators or inhibitors of signals mediated by receptor tyrosine kinases. We demonstrated that when embryonic day 13.5 rat pancreatic epithelium is cultured in the presence of PD98059, an inhibitor of the mitogen-activated protein (MAP) kinase, epithelial cell proliferation is decreased, whereas endocrine cell differentiation is activated. On the other hand, in the presence of epidermal growth factor (EGF), an activator of the MAP kinase pathway, the mass of tissue that develops is increased, whereas the absolute number of endocrine cells that develops is decreased. Under this last condition, a large number of epithelial cells proliferate but remain undifferentiated. In a second step, when EGF is removed from the pool of immature pancreatic epithelial cells, the cells differentiate en masse into insulin-expressing cells. The total number of insulin-expressing cells that develop can thus be increased by first activating the proliferation of immature epithelial cells with growth factors, thus allowing an increase in the pool of precursor cells, and next allowing their differentiation into endocrine cells by removing the growth factor. This strategy suggests a possible tissue engineering approach to expanding beta-cells.