gebhart/patrepeval huggingface dataset:
Dynamic viscoelastic study on the gelation of 7 S globulin from soybeans (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDynamic viscoelastic study on the gelation of 7 S globulin from soybeansTakao. Nagano, Motohiko. Hirotsuka, Hiroyuki. Mori, Kaoru. Kohyama, and Katsuyoshi. NishinariCite this: J. Agric. Food Chem. 1992, 40, 6, 941–944Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://doi.org/10.1021/jf00018a004RIGHTS & PERMISSIONSArticle Views1877Altmetric-Citations348LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Kneglomeratanol, Kneglomeratanones A and B, and Related Bioactive Compounds from Knema glomerata (1994)

One new phenylalkyl phenol, kneglomeratanol [1], and two new acetophenones, kneglomeratanones A [2] and B [3], together with ten known compounds, 3-(12'-phenyldodecyl)-phenol [4], 3-(10'-phenyldecyl)-phenol [5], 5-pentadecylresorcinol [6], 5-(10'-phenyldecyl)-resorcinol [7], 5-(12'-phenyldodecyl)-resorcinol [8], 2,4-dihydroxy-6-(10'-phenyldecyl)-acetophenone [9], 2-hydroxy-6-(12'-phenyldodecyl)-benzoic acid [10], formononetin, biochanin A, and 8-O-methylretusin, have been isolated from the stem bark of Knema glomerata. Brine shrimp lethality was used for the activity-directed chromatographic fractionations. All of these compounds showed moderate but significant toxicities to three human tumor cell lines and inhibited the growth of crown gall tumors on discs of potato tubers.
A comparison of pitch prediction algorithms in forward and backward adaptive CELP systems (1992)

Compares several pitch prediction algorithms in forward and backward adaptive CELP system. Since a forward adaptation system uses the original speech signal to compute the filter parameters, while a backward adaptation system only uses the locally decoded speech which contains encoding noise, there are important differences between the two systems in the implementation of a pitch prediction algorithm. The authors investigated such pitch prediction strategies in these two systems in terms of the pitch prediction configuration, the pitch determination algorithms, and the pitch predictor adaptation technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The 64-kDa protein that associates with the platelet-derived growth factor receptor beta subunit via Tyr-1009 is the SH2-containing phosphotyrosine phosphatase Syp. (1993)

Ligand-stimulated autophosphorylation of the platelet-derived growth factor receptor (PDGFR) beta subunit creates a number of binding sites for SH2-containing proteins. One of the PDGFR-associated proteins is a 64-kDa protein of unknown identity and function. We present data indicating that the 64-kDa protein that associates with the activated PDGFR is Syp (also called SH-PTP2, PTP-1D, or SH-PTP3), the ubiquitously expressed 64-kDa SH2-containing protein-tyrosine phosphatase. Phosphorylation of Tyr-1009 in the C terminus of the PDGFR is required for the stable association of Syp, suggesting that phosphorylation of this residue creates a binding site for the Syp SH2 domains. Although Syp stably associates with the PDGFR, this event is not required for PDGF-stimulated tyrosine phosphorylation of Syp. These data raise the interesting possibility that protein-tyrosine phosphatases contribute to the intracellular relay of biological signals originating from receptor tyrosine kinases such as the PDGFR.
Plasma processing in the fabrication of amorphous silicon thin-film-transistor arrays (1999)

Plasma deposition and etching are two critical processes in the fabrication of the arrays of thin-film transistors (TFTs) in active-matrix liquid crystal displays. The processes fulfill three important production requirements: suitability for use at relatively low substrate temperatures, suitability for large substrates, and high throughput capability. We present an overview of our recent studies on the plasma-processing aspects of the fabrication of large-area arrays of TFTs in which use is made of thin films of amorphous silicon containing hydrogen (a-Si:H). Subjects covered include the plasma-enhanced chemical vapor deposition (PECVD) of a-Si:H films, SiN <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> films, and heavily phosphorus-doped Si films; the influence of the films on TFT characteristics; associated plasma-etching and edge-profile aspects; plasma-etching-induced damage to TFTs and repair of the damage; and equipment aspects.
Beyond Thermodynamic Acidity: A Perspective on the Complex‐Induced Proximity Effect (CIPE) in Deprotonation Reactions (2004)

The concept of the complex-induced proximity effect (CIPE) in deprotonations is helpful in elucidating the mechanisms involved in carbanion chemistry and in planning organic syntheses. In this Review, the consequences of complexation of organolithium bases to functional groups of the substrates before the proton-transfer step are discussed. Experimental data from kinetic measurements and isotope-labeling experiments as well as the results of calculations in many cases point to a prelithiation complex as a reaction intermediate. Some examples from natural products synthesis illustrate how this concept can be used to obtain intermediates in a regio- or stereoselective manner. Of particular interest is the functionalization of positions that are remote from the coordination group.
Apolipoprotein A-I is a selective target for myeloperoxidase-catalyzed oxidation and functional impairment in subjects with cardiovascular disease (2004)

In recent studies we demonstrated that systemic levels of protein-bound nitrotyrosine (NO(2)Tyr) and myeloperoxidase (MPO), a protein that catalyzes generation of nitrating oxidants, serve as independent predictors of atherosclerotic risk, burden, and incident cardiac events. We now show both that apolipoprotein A-I (apoA-I), the primary protein constituent of HDL, is a selective target for MPO-catalyzed nitration and chlorination in vivo and that MPO-catalyzed oxidation of HDL and apoA-I results in selective inhibition in ABCA1-dependent cholesterol efflux from macrophages. Dramatic selective enrichment in NO(2)Tyr and chlorotyrosine (ClTyr) content within apoA-I recovered from serum and human atherosclerotic lesions is noted, and analysis of serum from sequential subjects demonstrates that the NO(2)Tyr and ClTyr contents of apoA-I are markedly higher in individuals with cardiovascular disease (CVD). Analysis of circulating HDL further reveals that higher NO(2)Tyr and ClTyr contents of the lipoprotein are each significantly associated with diminished ABCA1-dependent cholesterol efflux capacity of the lipoprotein. MPO as a likely mechanism for oxidative modification of apoA-I in vivo is apparently facilitated by MPO binding to apoA-I, as revealed by cross-immunoprecipitation studies in plasma, recovery of MPO within HDL-like particles isolated from human atheroma, and identification of a probable contact site between the apoA-I moiety of HDL and MPO. To our knowledge, the present results provide the first direct evidence for apoA-I as a selective target for MPO-catalyzed oxidative modification in human atheroma. They also suggest a potential mechanism for MPO-dependent generation of a proatherogenic dysfunctional form of HDL in vivo.
Distributed query evaluation on semistructured data (2002)

Semistructured data is modeled as a rooted, labeled graph. The simplest kinds of queries on such data are those which traverse paths described by regular path expressions. More complex queries combine several regular path expressions, with complex data restructuring, and with sub-queries. This article addresses the problem of efficient query evaluation on distributed, semistructured databases. In our setting, the nodes of the database are distributed over a fixed number of sites, and the edges are classified into local (with both ends in the same site) and cross edges (with ends in two distinct sites). Efficient evaluation in this context means that the number of communication steps is fixed (independent on the data or the query), and that the total amount of data sent depends only on the number of cross links and of the size of the query's result. We give such algorithms in three different settings. First, for the simple case of queries consisting of a single regular expression; second, for all queries in a calculus for graphs based on structural recursion which in addition to regular path expressions can perform nontrivial restructuring of the graph; and third, for a class of queries we call select-where queries that combine pattern matching and regular path expressions with data restructuring and subqueries. This article also includes a discussion on how these methods can be used to derive efficient view maintenance algorithms.
Laser cleaning of optical elements in 157-nm lithography (2000)

In-situ laser cleaning is shown to be an effective tool for removal of organic contaminants on CaF<SUB>2</SUB> windows. To study laser cleaning in a controlled fashion, CaF<SUB>2</SUB> substrates were pre-contaminated with 5 to 10 nm of poly(methyl methacrylate), poly(4-hydroxy styrene), poly(norbornene), and poly((beta) -pinene) thin films. Irradiation of all the polymer films showed similar trends. Initially, a high rate of material removal occurs, which depends on the chemistry of the polymer. During this period, the material also undergoes significant bond rearrangement, forming a more tightly bound highly conjugated network. Removal of this residual 'graphitized' film is significantly more difficult, but can be accelerated by the presence of modest levels of oxygen. For oxygen concentrations between 10-1000 ppm, the measured removal rate is approximately 3 nm/(kJ/cm<SUP>2</SUP>) ppm oxygen. No effect on removal rate was observed as pulse energy or purge gas flow rate was varied over ranges expected to be used in practical systems.
Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases (2019)

Programmable nucleases and deaminases, which include zinc-finger nucleases, transcription activator-like effector nucleases, CRISPR RNA-guided nucleases, and RNA-guided base editors, are now widely employed for the targeted modification of genomes in cells and organisms. These gene-editing tools hold tremendous promise for therapeutic applications. Importantly, these nucleases and deaminases may display off-target activity through the recognition of near-cognate DNA sequences to their target sites, resulting in collateral damage to the genome in the form of local mutagenesis or genomic rearrangements. For therapeutic genome-editing applications with these classes of programmable enzymes, it is essential to measure and limit genome-wide off-target activity. Herein, we discuss the key determinants of off-target activity for these systems. We describe various cell-based and cell-free methods for identifying genome-wide off-target sites and diverse strategies that have been developed for reducing the off-target activity of programmable gene-editing enzymes.
PAM4 enzyme immunoassay alone and in combination with CA 19‐9 for the detection of pancreatic adenocarcinoma (2012)

The PAM4 enzyme immunoassay identified approximately two-thirds of patients with stage I PDAC with high discriminatory power with respect to benign, nonneoplastic pancreatic disease. These results provide a rationale for testing patient groups considered to be at high risk for PDAC with a combined PAM4 and CA 19-9 biomarker serum assay for the detection of early stage PDAC.
Complementation of Mutation in Acyl-CoA:Cholesterol Acyltransferase (ACAT) Fails to Restore Sterol Regulation in ACAT-defective Sterol-resistant Hamster Cells (1996)

A previously described mutant line of Chinese hamster ovary cells, designated SRD-4, fails to synthesize cholesteryl esters, owing to a deficiency in the activity of acyl-CoA:cholesterol acyltransferase (ACAT). These cells also fail to suppress low density lipoprotein receptors or cholesterol synthesizing enzymes in the presence of 25-hydroxycholesterol. In the current studies we show that SRD-4 cells have three defects: 1) a point mutation in one allele at the ACAT locus that changes codon 265 from Ser to Leu, resulting in an inactive enzyme; 2) a silent allele at the other ACAT locus that does not produce detectable mRNA; and 3) a mutation, as yet undefined, that abolishes the ability of 25-hydroxycholesterol to inhibit the cleavage of both sterol regulatory element binding proteins (SREBP-1 and SREBP-2). Correction of the ACAT deficiency by transfection of a wild-type cDNA failed to restore inhibition of SREBP cleavage by 25-hydroxycholesterol, indicating that the ACAT deficiency and the sterol regulatory defect are caused by independent mutations. These data provide further insight into the interplay between ACAT activation and inhibition of SREBP cleavage by 25-hydroxycholesterol, and they indicate that these two processes can be disrupted independently by mutation.
Reservoir Management Tenets: Why They Matter to Sustainable Supplies (2005)

The growing global demand for energy and, in particular, crude supplies has brought into focus the twin issues of production sustainability and reliability. The question “What are the constituent elements that determine the sustainability of a set target from a typical field?” resonates with new urgency. A school of thought within the industry views reservoir attributes as the sole controlling factor in the equation. But there might be another element, often taken for granted, that could prove to be the critical link—prudent governance in the form of reservoir management tenets. Stated differently, underachievement of expected production levels or ultimate recoveries may often reflect unintended, although predictable, consequences of management practices unconstrained by due-diligence provisions. The tenets described in this article have played a definitive role in Saudi Aramco’s experience with its fields and may offer a useful platform for discussion. The case here is not to argue that the noted tenets are universally applicable. Instead, the intent is to point to their indispensable business value as a framework for all. What Is Different About Today’s Subsurface Three issues rise above all others in matters involving the subsurface: reserves, cost management, and sustainability and reliability of production. A meaningful discussion of these items, however, calls for a close look at the emerging characteristics of the subsurface and what they portend for tomorrow. There is a confluence of trends, namely increasing complexity of well architectures, higher levels of well intelligence, and the arrival of real-time information in well-placement and field operations. The latter two events, artifacts of global information technology advances, have two predictable consequences for our industry: an exponential increase in availability of real-time data and the heightened expectation of commensurate speed and accuracy in decision making and forecasting. The question that begs to be raised is, “How do we transform the massive volumes of data into intelligent decision making with business value?” Do we need a process or a formalized framework to influence the outcomes emerging from fields in terms of expected ultimate recoveries, costs, and sustainability? In their insightful article “Delusions of Success,” Lovallo and Kahneman argue that business and project failures stem from consequences of flawed decision making and specifically from a lack of an objective perspective (regarding underlying project assumptions). In this context, how can we ensure that the appropriate level of “objective perspective” is injected into field performance forecasts?
Systemic monotherapy vs combination therapy for CTCL: rationale and future strategies. (2007)

There are few approved therapies for cutaneous T-cell lymphoma (CTCL). The retinoids are the major biologic response modifiers used in CTCL, producing good response rates but few complete responses. For patients with early-stage disease, the oral retinoids can be combined with other therapies, such as psoralen plus ultraviolet A or interferon alpha, to improve response rates. Combined-modality therapy with oral retinoids, combined chemotherapy, electron-beam therapy, and topical mustargen has also proved effective. For the treatment of advanced-stage disease, the targeted therapy denileukin diftitox (Ontak) provides a nonimmunosuppressive alternative to conventional chemotherapy or radiation therapy. Of the conventional chemotherapies that have been tested in CTCL, gemcitabine (Gemzar) has demonstrated good efficacy in producing responses, particularly in patients with tumors. This agent can be used in combination with a maintenance therapy of bexarotene (Targretin) to manage the plaques and patches of mycosis fungoides. Several other targeted therapies are now also in testing, for example, alemtuzumab (CamPath), HuMax-CD4, several histone deacetylase inhibitors, and the transition-state inhibitor forodesine. These drugs, in combination with currently used therapies, may increase the number and combinations of therapies available for the treatment of this chronic condition to optimize long-lasting responses in CTCL.
Mutants of Eukaryotic Initiation Factor eIF-4E with Altered mRNA Cap Binding Specificity Reprogram mRNA Selection by Ribosomes in Saccharomyces cerevisiae (1996)

Recognition of the 5'-end of eukaryotic mRNA by the ribosomal 43 S preinitiation complex involves the eukaryotic translation initiation factor eIF-4E (eIF-4alpha). Deletion mutants of the eIF-4E gene of Saccharomyces cerevisiae (CDC33) encoded proteins with reduced affinity for the 5'-cap. One of these mutant proteins lacked any detectable binding to a cap analogue binding column, yet was still able to support cell growth. More than 17% of the total eIF-4E amino acid sequence could be removed without fully inactivating this factor. At least 30 of the N-terminal amino acids are not essential for function. The minimal functional eIF-4E protein segment therefore comprises at most 176 amino acids. The translation and growth defects of the deletion mutants could be at least partially compensated by increases in eIF-4E synthesis, possibly due to a mass-action effect on mRNA binding. Electroporation of yeast spheroplasts with in vitro synthesized mRNA allowed us to characterize the ability of eIF-4E mutant strains to distinguish between capped and uncapped mRNAs in vivo. Our data show that the cap specificity of eIF-4E determines to what extent the translational apparatus differentiates between capped and uncapped mRNAs and indicate the minimum relative mRNA (cap) binding activity of eIF-4E required for yeast cell viability.
Role of heavy water in biological sciences with an emphasis on thermostabilization of vaccines (2009)

Preservation of vaccines, viruses and other biologicals is one of the onerous tasks in maintaining the quality of the products from manufacture until they reach the end users. Live-attenuated viral vaccines, serum immunoglobulins, plasma fractions and clinical samples, including tissues and body fluids, are all materials that usually require cold-chain maintenance during storage and distribution. A number of stabilizers are currently used to help retain the quality of these materials, in particular vaccines, during transit. Deuterium oxide (heavy water; D(2)O) has previously been reported to have a protective effect on biomolecules (proteins and nucleic acids), cells and simple multicellular organisms against thermal shock. Of late, the potential of D(2)O has been demonstrated in stabilization of the oral polio and yellow fever 17D vaccines. This review is the outcome of a thorough search and scan of the literature in a quest to explore the potential use of heavy water in the stabilization of veterinary biologicals. The literature search revealed this potential of heavy water as exemplified by successful stabilization of oral polio and yellow fever vaccines. Through this review, the authors wish to inform animal health researchers and disseminate their knowledge on the use of heavy water in biomolecule stabilization and its potential application in the stabilization of veterinary vaccines and other biologicals.
Identification of the trans-acting Rep proteins of adeno-associated virus by antibodies to a synthetic oligopeptide (1986)

Prior genetic analysis provided evidence for trans-acting regulatory proteins (Rep) coded by the left-hand open reading frame (orf-1) of adeno-associated virus (AAV). We have used immunoblotting analysis to identify four protein products of orf-1. Antibodies elicited against an oligopeptide encoded by orf-1 were reacted with extracts of cells that were infected with AAV or transfected with AAV recombinant vectors in the presence or absence of helper adenovirus. The antibody recognized four polypeptides with apparent molecular weights of 78,000, 68,000, 52,000, and 40,000. The 78,000-dalton (78K) (Rep78) and 68K (Rep68) proteins appear to be encoded by the unspliced 4.2-kilobase (kb) and spliced 3.9-kb mRNAs, respectively, transcribed from the p5 promoter. The 52K (Rep52) and 40K (Rep40) proteins appear to be the products of the unspliced 3.6-kb and the spliced 3.3-kb mRNAs, respectively, transcribed from the p19 promoter. Rigorous identification of Rep68 as an AAV-coded protein is compromised by a cross-reacting cellular protein of similar size. All four proteins were expressed in the human cell lines 293, HeLa, HT29, and A549 infected with AAV together with adenovirus. Rep78 and Rep52 were detected at lower levels in cells infected with AAV at high multiplicity in the absence of adenovirus. Human 293 cells transfected with a recombinant AAV vector (pAV2) also expressed Rep proteins in the presence or absence of adenovirus. Mutations introduced into the Rep region of pAV2 further identified the Rep proteins. The amount of each Rep protein varied between nuclear and cytoplasmic extracts, but all four proteins accumulated during the lytic cycle of the viral infection. Other studies have indicated that the Rep proteins have independent trans-acting functions in viral DNA replication and negative and positive regulation of gene expression. Correlation of each trans-acting function with individual Rep proteins will be facilitated with the antibodies described herein.