gebhart/patrepeval huggingface dataset:
Synthesis of facial cyclometalated iridium(iii) complexes triggered by tripodal ligands (2012)

The tripodal ligands composed of the 1,3,5-trisubstituted cyclohexyl moiety as a molecular scaffold and 2-phenylpyridyl moieties as a coordination site were designed. The homoleptic cyclometalated fac-Ir(C^N)(3) complexes could be obtained by the reaction of IrCl(3)·nH(2)O with the designed tripodal ligands. The single crystal X-ray structure determination confirmed the fac configuration and a distorted octahedral geometry with three intramolecular cyclometalated 2-phenylpyridyl ligands surrounding the iridium metal center. Also, the cyclohexyl scaffold was found to serve as a flexible scaffold to induce the fac configuration. The thus-obtained homoleptic cyclometalated fac-Ir(C^N)(3) complexes exhibited a broad emission band in the emission spectra at 298 K.
Effects on protein adsorption, bacterial adhesion and contact angle of grafting PEG chains to polystyrene (1993)

Abstract Poly(ethylene glycol) (PEG) has been grafted to polystyrene using branched poly(ethylene imine) (PEI) as an anchoring polymer. A dense grafting of PEG chains is obtained if a PEG-PEI adduct is first prepared by treatment of PEI with PEG epoxide and the adduct subsequently adsorbed on an oxidized polystyrene surface. Prepared in this way, the PEG-PEI adduct is irreversibly attached to the surface with the PEG chains oriented towards the aqueous phase, as shown by ellipsometry. This dense PEG coating is highly effective in preventing adsorption of fibrinogen and IgG, as well as adhesion of the oral bacterium Streptococcus mutans. Somewhat surprisingly, the degree of PEG branching, as well as the PEG molecular weight, did not markedly influence protein repelling properties. The water contact angle on polystyrene decreased in the order: untreated polystyrene > oxidized > PEI treated > PEG-PEI treated. Block copolymers of poly(ethylene glycol)/poly(propylene glycol) type attached to polystyrene showed temperature dependent protein rejecting properties. At temperatures well below the cloud point of the polymer in water, the surface is protein repellent whereas around and above the cloud point, protein adsorption occurs to a considerable extent. The block copolymer layer expands and contracts with temperature variations, as can be monitored by ellipsometry. Keywords: Hydrophilizationpolystyreneprotein adsorptionbacterial adhesionPEGellipsometryESCAcontact angle
Radiosity and Global Illumination (1994)

Radiosity &amp;amp; Global Illumination is a more theoretical coverage of global illumination. It has less code, but covers more topics than A Programmer's Perspective. In addition to the fundamental radiosity technique, this book discusses issues with control and complexity, and Monte Carlo techniques. Along with Peter Shirley's book, this provides fairly good coverage of the theory and practice of ray tracing based global illumination algorithms.
Ammonia-induced brain edema and intracranial hypertension in rats after portacaval anastomosis (1994)

Brain edema, leading to intracranial hypertension and brain herniation, is a major cause of death in fulminant liver failure. Astrocyte swelling is a prominent neuropathological feature in experimental fulminant liver failure. It has been postulated that the osmotic effects of glutamine, generated in astrocytes from ammonia and glutamate in a reaction catalyzed by glutamine synthetase, could mediate brain swelling. Normal rats and rats that received a portacaval anastomosis were infused with ammonium acetate or a sodium acetate control; brain water in cerebral cortex was measured with the gravimetry method, intracranial pressure by means of a cisterna magna catheter and cortical amino acids using high-performance liquid chromatography. Although brain edema was detected in both groups receiving ammonia, it was of a greater magnitude in portacaval anastomosis rats (80.94% + 0.17% vs. 80.24% + 0.09%, p < 0.01), resulting in the development of intracranial hypertension. When portacaval anastomosis rats were infused with ammonium acetate and pretreated with 150 mg/kg methionine-sulfoximine, an inhibitor of glutamine synthetase activity, brain edema was ameliorated and intracranial pressure did not rise. A dose-dependent reduction in brain glutamine levels was seen with increasing doses of methionine-sulfoximine; however, brain edema did not decrease beyond the 150 mg/kg dose, suggesting that the increase in brain water was not solely a result of glutamine accumulation. We conclude that brain edema of a magnitude that results in intracranial hypertension is more likely to develop in rats after portacaval anastomosis receiving a continuous ammonia infusion. The osmotic effects of glutamine appear to mediate, but only in part, the increase in brain water seen in this preparation.(ABSTRACT TRUNCATED AT 250 WORDS)
Mumps Virus V Protein Antagonizes Interferon without the Complete Degradation of STAT1 (2005)

Mumps virus (MuV) has been shown to antagonize the antiviral effects of interferon (IFN) through proteasome-mediated complete degradation of STAT1 by using the viral V protein (T. Kubota et al., Biochem. Biophys. Res. Commun. 283:255-259, 2001). However, we found that MuV could inhibit IFN signaling and the generation of a subsequent antiviral state long before the complete degradation of cellular STAT1 in infected cells. In MuV-infected cells, nuclear translocation and phosphorylation of STAT1 and STAT2 tyrosine residue (Y) at 701 and 689, respectively, by IFN-beta were significantly inhibited but the phosphorylation of Jak1 and Tyk2 was not inhibited. The transiently expressed MuV V protein also inhibited IFN-beta-induced Y701-STAT1 and Y689-STAT2 phosphorylation, suggesting that the V protein could block IFN-beta-induced signal transduction without the aid of other viral components. Finally, a substitution of an alanine residue in place of a cysteine residue in the C-terminal V-unique region known to be required for STAT1 degradation and inhibition of anti-IFN signaling resulted in the loss of V protein function to inhibit the Y701-STAT1 and Y689-STAT2 phosphorylation.
Lipoperoxidation Is Selectively Involved in Progressive Supranuclear Palsy (2000)

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder characterized by extensive neurofibrillary tangle (NFT) formation and neuronal loss in selective neuronal populations. Currently, no clues to the biological events underlying the pathological process have emerged. In Alzheimer disease (AD), which shares with PSP the occurrence of NFTs, advanced glycation end products (AGEs) as well as oxidation adducts have been found to be increased in association with neurofibrillary pathology. The presence and the amount of lipid and protein oxidation markers, as well as of pyrraline and pentosidine. 2 major AGEs, was assessed by biochemical, immunochemical, and immunocytochemical analysis in midbrain tissue from 5 PSP cases, 6 sporadic AD cases, and 6 age-matched control cases. The levels of 4-hydroxynonenal (HNE) and thiobarbituric acid reactive substances (TBARS), 2 major products of lipid peroxidation, were significantly increased by 1.6-fold (p < 0.04) and 3.9-fold (p < 0.01), respectively, in PSP compared with control tissues, whereas in AD only TBARS were significantly increased. In PSP tissue the intensity of neuronal HNE immunoreactivity was proportional to the extent of abnormal aggregated tau protein. The amount of protein oxidation products and AGEs was instead similar in PSP and control tissues. In AD, a higher but not significant level of pyrraline and pentosidine was measured, whereas the level of carbonyl groups was doubled. These findings indicate that in PSP, unlike in AD, lipid peroxidation is selectively associated with NFT formation. The intraneuronal accumulation of toxic aldehydes may contribute to hamper tau degradation, leading to its aggregation in the PSP specific abnormal filaments.
Broadband azimuthal polarization conversion using gold nanowire enhanced step-index fiber (2016)

We show broadband azimuthal polarization state conversion using an entirely connectorized step-index fiber with a central gold nanowire. This device provides broadband polarization discrimination of the low-loss TE01 fiber mode with respect to all other modes, and converts light into the azimuthal polarization state, resulting in a high beam quality and an azimuthal conversion efficiency of 37%. The device is monolithically integrated into fiber circuitry, representing a new platform for plasmonics and fiber optics and enabling important applications in super-resolution microscopy, laser tweezing, and plasmonic superfocussing.
Intrinsic Tau Acetylation Is Coupled to Auto-Proteolytic Tau Fragmentation (2016)

Tau proteins are abnormally aggregated in a range of neurodegenerative tauopathies including Alzheimer's disease (AD). Recently, tau has emerged as an extensively post-translationally modified protein, among which lysine acetylation is critical for normal tau function and its pathological aggregation. Here, we demonstrate that tau isoforms have different propensities to undergo lysine acetylation, with auto-acetylation occurring more prominently within the lysine-rich microtubule-binding repeats. Unexpectedly, we identified a unique intrinsic property of tau in which auto-acetylation induces proteolytic tau cleavage, thereby generating distinct N- and C-terminal tau fragments. Supporting a catalytic reaction-based mechanism, mapping and mutagenesis studies showed that tau cysteines, which are required for acetyl group transfer, are also essential for auto-proteolytic tau processing. Further mass spectrometry analysis identified the C-terminal 2nd and 4th microtubule binding repeats as potential sites of auto-cleavage. The identification of acetylation-mediated auto-proteolysis provides a new biochemical mechanism for tau self-regulation and warrants further investigation into whether auto-catalytic functions of tau are implicated in AD and other tauopathies.
A novel gate-offset NAND cell (GOC-NAND) technology suitable for high-density and low-voltage-operation flash memories (2003)

This paper describes a novel scaled and low-voltage-operation NAND EEPROM technology with a G_ate-O_ffset NAND C_ell (GOC-NAND), which is free from program disturbance in a self-boosted program. In GOC-NAND, novel source/drain engineering is introduced for the first time. The program disturbance is decreased by two decades of magnitude in 0.1 /spl mu/m generation, without area penalty and additional process steps. Furthermore, the program disturbance is not increased by scaling and low voltage operation. Therefore, GOC-NAND is indispensable technology for gigabit-scaled NAND EEPROMs.
Emerging Roles of CCCH-Type Zinc Finger Proteins in Destabilizing mRNA Encoding Inflammatory Factors and Regulating Immune Responses (2015)

Posttranscriptional gene regulation is a rapid and effective way to mediate the expression of inflammatory genes. CCCH-type zinc finger proteins are nucleotide-binding molecules involved in RNA metabolism pathways such as RNA splicing, polyadenylation, and messenger RNA (mRNA) decay. Among these proteins, tristetraproline, Roquins, and Regnase-1/monocyte chemotactic protein-1-induced protein-1 have been recently reported to be responsible for mRNA instability. They bind to mRNAs harboring unique motifs and induce mRNA decay. In this review we summarize current progress regarding the specific characteristics of sequences and structures in the 3' untranslated regions of mRNAs that are recognized by tristetraproline, Roquins, and Regnase-1. The target mRNAs to be destabilized by those CCCH-type zinc finger proteins also are included. Notably, most target mRNAs encode cytokines and other inflammatory mediators, suggesting the immune regulation role of CCCH zinc finger proteins. Mice carrying a genetic null allele or modification of these genes display severe symptoms of autoimmune diseases. Taken together, data show that CCCH-type zinc finger proteins play a crucial role in regulating immune response by targeting multiple mRNAs, and including decay. Further understanding the functions of these proteins may provide new therapeutic targets for immune-related disorders in the future.
Bifunctional Inhibitors of Pepsin (1971)

Two bifunctional reagents designed to probe the active site of pepsin and other acid proteinases are described. One of these, the bisdiazoketone 1,1-bis(diazoacetyl)-2-phenylethane inactivates pepsin at pH 5.0 much more rapidly than the corresponding monodiazoketon 1-diazoacetyl-2-phenylethane, whereas the other, the bromodiazoketone dl-1-diazoacetyl-1-bromo-2-phenylethane is less effective in this regard. The inactivation is greatly accelerated by the presence of Cu(II), and the pH dependence of the process is consistent with the interaction of the enzyme with the metal complex of the carbene derived from the reagent. The bisdiazoketone appears to react stoichiometrically with pepsin in a 1:1 ratio to form a product whose apparent molecular size is the same as that of untreated pepsin. The inactivation of pepsin by the bromodiazoketone is accompanied by the release of stoichiometric amounts of bromide ions and the formation of a major product whose apparent size is similar to that of pepsin, and a minor component larger than the untreated enzyme.
Recombinant Tissue Plasminogen Activator Increases Blood-Brain Barrier Disruption in Acute Ischemic Stroke: An MR Imaging Permeability Study (2009)

The results of this study indicate that KPS is able to identify patients at higher risk of HT and may allow use of physiologic imaging rather than time from onset of symptoms to guide treatment decision.
A Global, 0.05-Degree Product of Solar-Induced Chlorophyll Fluorescence Derived from OCO-2, MODIS, and Reanalysis Data (2019)

Solar-induced chlorophyll fluorescence (SIF) brings major advancements in measuring terrestrial photosynthesis. Several recent studies have evaluated the potential of SIF retrievals from the Orbiting Carbon Observatory-2 (OCO-2) in estimating gross primary productivity (GPP) based on GPP data from eddy covariance (EC) flux towers. However, the spatially and temporally sparse nature of OCO-2 data makes it challenging to use these data for many applications from the ecosystem to the global scale. Here, we developed a new global ‘OCO-2’ SIF data set (GOSIF) with high spatial and temporal resolutions (i.e., 0.05°, 8-day) over the period 2000–2017 based on a data-driven approach. The predictive SIF model was developed based on discrete OCO-2 SIF soundings, remote sensing data from the Moderate Resolution Imaging Spectroradiometer (MODIS), and meteorological reanalysis data. Our model performed well in estimating SIF (R2 = 0.79, root mean squared error (RMSE) = 0.07 W m−2 μm−1 sr−1). The model was then used to estimate SIF for each 0.05° × 0.05° grid cell and each 8-day interval for the study period. The resulting GOSIF product has reasonable seasonal cycles, and captures the similar seasonality as both the coarse-resolution OCO-2 SIF (1°), directly aggregated from the discrete OCO-2 soundings, and tower-based GPP. Our SIF estimates are highly correlated with GPP from 91 EC flux sites (R2 = 0.73, p &lt; 0.001). They capture the expected spatial and temporal patterns and also have remarkable ability to highlight the crop areas with the highest daily productivity across the globe. Our product also allows us to examine the long-term trends in SIF globally. Compared with the coarse-resolution SIF that was directly aggregated from OCO-2 soundings, GOSIF has finer spatial resolution, globally continuous coverage, and a much longer record. Our GOSIF product is valuable for assessing terrestrial photosynthesis and ecosystem function, and benchmarking terrestrial biosphere and Earth system models.
Anti-factor VIII antibodies of hemophiliac patients are frequently directed towards nonfunctional determinants and do not exhibit isotypic restriction (1993)

Abstract A significant proportion of hemophilia A patients receiving transfusions of factor VIII (FVIII) develop a specific antibody response towards FVIII. These antibodies are usually detected by assays in which they inhibit the function of the molecule, such as the Bethesda clotting test. We have prepared anti-FVIII antibodies by specific immunoadsorption from the plasma of four hemophiliacs with stable inhibitor levels. The isotypic distribution of such antibodies was determined and their capacity to bind to insolubilized FVIII was compared with their inhibitory activity in two functional assays, namely, the Bethesda assay and a chromogenic assay. In addition, the FVIII epitope specificity was determined by competition with monoclonal antibodies for the binding to insolubilized FVIII. We show here that (1) anti-FVIII antibodies are not isotypically restricted; thus, a significant proportion of specific IgG2 was found; (2) antibodies are frequently directed towards epitopes of FVIII that are not directly involved in the function of the molecule and therefore escape detection in the Bethesda method or chromogenic assay; and (3) each patient shows a unique pattern of FVIII epitope recognition. We conclude that evaluation of anti-FVIII antibodies by a functional method does not provide an accurate evaluation of the specific antibody response. These findings have important implications for the comparison of the immunogenicity of FVIII molecules produced by different technologies and for the development of methods to control anti-FVIII antibody production.
Human endogenous retrovirus K10: expression of Gag protein and detection of antibodies in patients with seminomas (1995)

The human endogenous retrovirus K10 (HERV-K10) has been identified in the human genome by its homology to retroviruses of other vertebrates (M. Ono, T. Yasunaga, T. Miyata, and H. Ushikubo, J. Virol. 60:589-598, 1986). Using PCR amplification, DNA cloning, sequencing, and procaryotic expression, we were able to demonstrate that HERV-K10 encodes a 73-kDa protein which was processed by a HERV-K10-encoded protease to yield proteins p22/p26, p30, and p15/16. Analysis of the teratocarcinoma cell line Tera 1 or tumor tissues by immunoblotting demonstrated that the 80-kDa polyprotein of HERV-K10 gag and a processed protein of 39 kDa were expressed. In addition, a major protein of 39 kDa and additional species of 30, 22, 19, and 17 kDa could be detected in the supernatant of Tera 1 cells, suggesting that HERV-K10 Gag proteins are either secreted or processed to probably incomplete viral particles. In addition, the gag gene of HERV-K10 was expressed in the baculovirus system. Using this recombinant system to test antisera from patients with different diseases and healthy individuals, we were able to detect antibodies against the N-terminal part of HERV-K10 Gag in 2 to 4% of groups of tumor patients with titers ranging between 1:80 and 1:640, while approximately 0.1 to 0.5% of healthy individuals exhibited antibodies with lower titers. In contrast, patients with seminoma had antibody titers in the range of 1:2,560 at the time when the tumor was detected. Immunohistochemistry using specific rabbit sera or monoclonal antibodies against HERV-K10 Gag revealed that the Gag protein is expressed in the cytoplasm of the tumor cells. Furthermore, an 80-kDa protein corresponding to the HERV-K10 Gag polyprotein could be detected in tumor biopsies. For the first time, these data indicate that HERV-K10 Gag proteins are synthesized in seminoma cells and tumors exhibit relatively high antibody titers against Gag. So far, no information on which role HERV-K10 plays in the development of this tumor exists.
Increase in the stability of avidin produced by binding of biotin. Differential scanning calorimetric study of denaturation by heat (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIncrease in the stability of avidin produced by binding of biotin. Differential scanning calorimetric study of denaturation by heatJohn W. Donovan and Kenneth D. RossCite this: Biochemistry 1973, 12, 3, 512–517Publication Date (Print):January 1, 1973Publication History Published online1 May 2002Published inissue 1 January 1973https://pubs.acs.org/doi/10.1021/bi00727a024https://doi.org/10.1021/bi00727a024research-articleACS PublicationsRequest reuse permissionsArticle Views508Altmetric-Citations104LEARN 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
Direct and crossover PCR amplification to facilitate Tn5supF-based sequencing of λ phage clones (1991)

The 264 bp mini-transposon Tn5supF was constructed to sequence DNAs cloned in phage lambda without extensive shotgun subcloning or primer walking. Unique sequences near each transposon end serve as primer binding sites, and a supF gene is used to select transposition to lambda. We describe here PCR methods that facilitate Tn5supF-based sequencing. In a first pass, insertions are mapped relative to the ends of the cloned fragment using pairs of primers specific for vector DNA next to the cloning site and for a Tn5supF end. Most insertions not mapped in this step are near the center of the cloned fragment or in the vector arms, and are then mapped relative to the two innermost insertions by 'crossover' PCR. This involves amplification from primers on different DNA molecules, and generates hybrid DNA products whose lengths correspond to the distances between the two insertions. We routinely amplified more than 6 kb in direct PCR and 3 kb in crossover PCR; at the limit we amplified up to approximately 10 kb in direct PCR and approximately 6 kb in crossover PCR, but not reproducibly. Crossover PCR products were also obtained with insertions separated by only 200 bp, indicating that no rare sites are needed to switch templates. PCR products were purified by adsorption and then elution from glass slurry, and sequenced directly. Ladders of more than 400 bp were obtained from primer sites on each DNA strand; 2 kb was read from crossover PCR products, and showed that they were amplified with fidelity. In conclusion, direct and crossover PCR methods expedite transposon insertion mapping, and yield templates for accurate sequencing of both DNA strands.