gebhart/patrepeval huggingface dataset:
Conformational changes in seventeen cystine disulfide bridges of bovine serum albumin proved by Raman spectroscopy (1997)

Conformational changes in cystine disulfide bridges of bovine serum albumin during acid-induced isomerization (N --> F and F --> E transitions) have been studied with Raman spectroscopy. In an X-ray crystallographic study of human serum albumin, Carter and Ho reported that all disulfide bridges of the albumin molecule are in the gauche-gauche-gauche conformation [1]. On the other hand, the solution structure of bovine serum albumin examined by Raman spectroscopy differs from its crystal structure in the conformation of some of the disulfide bridges. Two Raman bands were detected at 520 and 505 cm(-1) in the disulfide stretching mode region, suggesting that the 17 disulfide bridges in the N-form of bovine serum albumin solution take both the gauche-gauche-gauche and gauche-gauche-trans conformations. The ratio of the peak intensities at 520 and 505 cm(-1) (I505/I520) is increased from 1.6 to 2.1 and from 2.1 to 6.3 on going from the N- to the F-form and from the F- to the E-form, respectively, indicating that the gauche-gauche-trans conformation of the disulfide bridges is converted to a gauche-gauche-gauche one which is the most energetically stable form during the acid-induced isomerization. However, small amounts of gauche-gauche-trans conformation still remain even in the E-form.
Sphinganase, a new endoglycanase that cleaves specific members of the gellan family of polysaccharides (1994)

A sporeforming gram-positive aerobic bacterium was isolated from soil and shown to secrete an endoglycanase that cleaves the tetrasaccharide backbone structure of specific members within the gellan family of related bacterial exopolysaccharides. We refer to these polysaccharides as sphingans. The structures of the sphingans differ by the type and position of side groups that are attached to the backbone. The new enzyme named sphinganase degrades welan, gellan, deacylated gellan, and polysaccharides S-88, S-7, and S-198. However, the enzyme does not attack rhamsan or polysaccharide NW11. Methods for growing the bacteria, isolating the enzyme, and assaying sphinganase activity are presented, and uses for the enzyme are proposed.
Detection of immunoglobulin kappa light-chain gene rearrangement patterns by Southern blot analysis. (1994)

Immunoglobulin light-chain (IgL) gene rearrangements occur in a sequential order during normal B-cell differentiation with Ig kappa gene rearrangements prior to Ig lambda gene rearrangements. Therefore, Ig kappa producing B-cells usually retain Ig lambda genes in germline configuration, whereas the Ig kappa genes are generally deleted on one or both alleles in most Ig lambda producing B-cells. The deletion processes in the Ig kappa locus are mediated via rearrangement of the kappa deleting element (Kde), which is located approximately 24 kb downstream of the constant (C) kappa gene segment. Kde rearrangements can delete the C kappa region (including the Ig kappa enhancer) or the complete joining (J) kappa-C kappa region via rearrangements to a heptamer recombination signal sequence in the J kappa-C kappa intron (intron RSS), or via rearrangement to a variable (V) kappa gene segment, respectively. To improve the Southern blot detection of clonal Ig kappa gene rearrangements and deletions in B-lineage malignancies, we developed a new set of optimal J kappa, C kappa, and Kde probes, and made a detailed restriction map of the J kappa, C kappa, and Kde region. Extensive Southern blot studies revealed that rearrangements in the J kappa gene region are optimally detectable by use of a J kappa probe in combination with at least two appropriate restriction enzymes, i.e. BamHI, BglII, EcoRI, HindIII, and/or SacI. J kappa gene rearrangements are also detectable with the C kappa probe in BglII and BamHI digests, if no deletion of the C kappa region has occurred. The two different types of Kde-mediated J kappa and/or C kappa gene deletions are easily detectable with the Kde probe in BglII, HindIII and/or EcoRI digests. This is in contrast to the inaccurate information obtained with the J kappa and C kappa probes, because these probes can detect deletions only in the form of decreased densities of J kappa and/or C kappa germline bands in the absence of rearranged bands. Our detailed analysis of 217 B-lineage leukemias revealed that 62% (69/111) of precursor B-cell acute lymphoblastic leukemias had rearranged and/or deleted Ig kappa genes. All 53 Ig lambda+ chronic B-cell leukemias contained Ig kappa gene deletions; in 75% this concerned biallelic J kappa and/or C kappa gene deletions. Virtually all Ig kappa gene deletions appeared to be mediated via Kde rearrangements, while only 1.5% of the Ig kappa gene deletions were mediated via an alternative deletion mechanism which involved the J kappa region.
Experiments Using Stochastic Search for Text Planning (1998)

Marcu has characterised an important and difficult problem in text planning: given a set of facts to convey and a set of rhetorical relations that can be used to link them together, how can one arrange this material so as to yield the best possible text? We describe experiments with a number of heuristic search methods for this task. 1 Introduction: Text Planning 1.1 The Task This paper presents some initial experiments using stochastic search methods for aspects of text planning. The work was motivated by the needs of the ILEX system for generating descriptions of musum artefacts (in particular, 20th Century jewellery) [Mellish et al 98]. We present results on examples semi-automatically generated from datastructures that exist within ILEX. Forming a set of facts about a piece of jewellery into a structure that yields a coherent text is a non-trivial problem. Rhetorical Structure Theory [Mann and Thompson 87] claims that a text is coherent just in case it can be analysed hierarchic...
Revealing the role of CD4+ T cells in viral immunity (2012)

Protective immunity to chronic and acute viral infection relies on both the innate and adaptive immune response. Although neutralizing antibody production by B cells and cytotoxic activity of CD8(+) T cells are well-accepted components of the adaptive immune response to viruses, identification of the specific role of CD4(+) T cells in protection has been more challenging to establish. Delineating the contribution of CD4(+) T cells has been complicated by their functional heterogeneity, breadth in antigen specificity, transient appearance in circulation, and sequestration in tissue sites of infection. In this minireview, we discuss recent progress in identifying the multiple roles of CD4(+) T cells in orchestrating and mediating the immune responses against viral pathogens. We highlight several recent reports, including one published in this issue, that have employed comprehensive and sophisticated approaches to provide new evidence for CD4(+) T cells as direct effectors in antiviral immunity.
Automatic parsing of TV soccer programs (2002)

While automatic parsing of general video images are difficult or nearly impossible, parsing a specific type of video image can be achieved if the video structure can be explicitly identified and its model can be constructed. The paper presents ongoing work on using domain knowledge to parse content of soccer video programs. The proposed system can classify a sequence of soccer frames into various play categories, such as shot at left goal, top left corner kick play in right penalty area, in midfield, etc, based on a priori model comprising four major components: a soccer court, a ball, the players and the motion vectors. Approaches in applying the model for parsing soccer programs are presented in detail. Experimental results are included to evaluate the performance of the system.
A computer program to generate two-dimensional grids about airfoils and other shapes by the use of Poisson's equation (1980)

A method for generating two dimensional finite difference grids about airfoils and other shapes by the use of the Poisson differential equation is developed. The inhomogeneous terms are automatically chosen such that two important effects are imposed on the grid at both the inner and outer boundaries. The first effect is control of the spacing between mesh points along mesh lines intersecting the boundaries. The second effect is control of the angles with which mesh lines intersect the boundaries. A FORTRAN computer program has been written to use this method. A description of the program, a discussion of the control parameters, and a set of sample cases are included.
An instant and accurate size estimation method for joins and selections in a retrieval-intensive environment (1993)

This paper proposes a novel strategy for estimating the size of the resulting relation after an equi-join and selection using a regression model. An approximating series representing the underlying data distribution and dependency is derived from the actual data. The proposed method provides an instant and accurate size estimation by performing an evaluation of the series, with no run-time overheads in page faults and space, and with negligible CPU overhead. In contrast, the popular sampling methods incur run-time overheads in page faults (for sampling), CPU time and space. These overheads of sampling methods increase the response time of processing a query. The results of a comprehensive experimental study are also reported, which demonstrate that the estimation accuracy by the proposed method is comparable with that of the sampling methods which are believed to provide the most accurate estimation. The proposed method seems ideal for retrieval-intensive database and information systems. Since the overheads involved in deriving the approximating series are fairly moderate, we believe that this method is also an extremely competent method when moderate or periodical updates are present.
Syk-dependent mTOR activation in follicular lymphoma cells (2006)

The mammalian target of rapamycin (mTOR) is emerging as a promising target for antitumor therapy. However, the mechanism that contributes to its regulation in B lymphomas remains unknown. This study shows that in follicular lymphoma (FL) cells, mTOR is active because the cells displayed rapamycin-sensitive phosphorylation of p70S6 kinase and 4E-BP1. Moreover, immunohistochemistry applied on lymph node tissue sections obtained from patients with FL revealed that, in most cases, p70S6 kinase was highly phosphorylated compared to normal tonsillar tissue. In FL cells, mTOR was under control of both phospholipase D (PLD) and phosphatidylinositol 3-kinase (PI3K). Moreover, we demonstrated that Syk plays a central role in mTOR activation because we found that both expression and activity are elevated compared to normal or chronic lymphocytic leukemia B cells. We also provide evidence that Syk operates through PLD- and PI3K-independent pathways. Finally, Syk inhibition by piceatannol or by siRNA plasmids resulted in a potent inhibition of mTOR activity in FL cells, as well as in mantle cell lymphoma, Burkitt lymphoma, and diffuse large B-cell lymphoma. These findings suggest that the Syk-mTOR pathway has a critical function in FL survival, and therefore, that Syk could be a promising new target for B-lymphoma therapy.
Adenosine-induced bronchoconstriction in asthma. Antagonism by inhaled theophylline. (1984)

Inhaled adenosine causes bronchoconstriction in asthmatic patients. Antagonism of the bronchoconstrictor effect of endogenous adenosine has been proposed as a possible mechanism of action of theophylline in asthma. To directly investigate this, we have compared the airway responses to inhaled adenosine and histamine, with and without the prior administration of inhaled theophylline in 8 allergic asthmatic subjects. Airway response was measured both as forced expiratory volume in one second (FEV1) and as specific airway conductance (SGaw). Inhaled adenosine was less potent than histamine in producing bronchoconstriction, with geometric mean concentrations required to produce a 20% fall of FEV1 (PCf20) and a 40% fall of SGaw (PCs40) being 0.27 and 0.25 mg/ml for adenosine and 0.10 and 0.09 mg/ml for histamine. In a total nebulized dose of 37.5 mg, inhaled theophylline was a weak bronchodilator that caused maximal increases in FEV1 of 2 +/- 2% (mean +/- SE, p less than 0.05) and in SGaw of 8 +/- 4% (p greater than 0.05). However, theophylline significantly inhibited adenosine-induced bronchoconstriction, increasing the PCf20 and PCs40 values for adenosine to 1.66 (p less than 0.001) and 2.34 (p less than 0.005) mg/ml, respectively. Inhibition of histamine-induced bronchoconstriction was less marked, with PCf20 and PCs40 values of 0.19 (p greater than 0.05) and 0.21 (p less than 0.05) mg/ml. Thus, adenosine is a bronchoconstrictor in asthma whose effects are preferentially antagonized by concentrations of theophylline that cause little change in baseline airway caliber.(ABSTRACT TRUNCATED AT 250 WORDS)
Capsular polysaccharide serotyping scheme for Staphylococcus epidermidis (1992)

A scheme for the capsular typing of Staphylococcus epidermidis that is based on direct slide agglutination between proteinase-treated bacterial cells and specific antisera is described. Antisera were prepared from serum from rabbits immunized with two selected strains of encapsulated S. epidermidis isolated from bacteremic patients. Antisera were shown to be type specific and designated type 1 and type 2. Blood isolates of S. epidermidis from hospitals in different locations within the United States and Europe were serotyped, and it was found that over 90% of all strains were of type 1 or type 2. Type-specific antibodies mediated type-specific opsonophagocytosis and killing of S. epidermidis. The specificity was shown to be due to two distinct capsular polysaccharides. The data presented in this report may open a new window on the pathogenesis of S. epidermidis which could lead to the development of new vaccines and therapies.
Quantitative determination of H2, HD, and D2 internal-state distributions by (2+1) resonance-enhanced multiphoton ionization (1991)

The relationship between quantum-state populations and ion signals in (2+1) resonance-enhanced multiphoton ionization (REMPI) detection of H2, HD, and D2 via the E, F 1Σ+g (v′E=0, J′=J″)–X 1Σ+g (v″,J″) transition is determined by calibration against a thermal effusive source. Correction factors are obtained for 102 rovibrational levels for v″=0, 1, and 2 and J″ ranging from 0 to 17. Within a given v″, rotational correction factors are nearly unity except for the highest J″ levels. The vibrational correction factors vary with v″; (2+1) REMPI detection is 2–3 times more sensitive to v″=1 and 2 than to v″=0. Experimental correction factors are compared with those derived from a theoretical calculation of the two-photon transition moments by Huo et al. [J. Chem. Phys. 95, xxxx (1991)]. In general, the agreement is excellent, which suggests that theoretical correction factors may be used when experimental ones are unavailable.
Evidence for a role of angiopoietin-like 7 (ANGPTL7) in extracellular matrix formation of the human trabecular meshwork: implications for glaucoma (2010)

The trabecular meshwork tissue controls the drainage of the aqueous humor of the eye. A dysfunctional trabecular meshwork leads to an altered fluid resistance, which results in increased intraocular pressure (IOP). IOP is the major risk factor of glaucoma, the second-leading cause of blindness in the developed world. In the search for genes altered by glaucomatous insults, we identified angiopoietin-like7 (ANGPTL7), a member of the ANGPTL family. Although structurally related to the angiopoietins, ANGPTL7's function is poorly understood. Because ANGPTL7 is secreted and because extracellular matrix (ECM) deposition and organization is critical for aqueous humor resistance, we investigated the effect of ANGPTL7 on relevant trabecular meshwork ECM genes and proteins. We find that overexpression of ANGPTL7 in primary human trabecular meshwork cells altered the expression of fibronectin, collagens type I, IV & V, myocilin, versican, and MMP1. ANGPTL7 also interfered with the fibrillar assembly of fibronectin. Finally, we find that silencing ANGPTL7 during the glucocorticoid insult significantly affected the expression of other steroid-responsive proteins. These results indicate that ANGPTL7 modulates the trabecular meshwork's ECM as well as the response of this tissue to steroids. Together with previous findings, these properties strengthen ANGPTL7's candidacy for the regulation of IOP and glaucoma.
Bidding in Simultaneous Auctions with a Constraint on Exposure (1977)

We consider the problem of determining a profit maximizing set of sealed bids in simultaneous auctions that are independent except for a restriction on the total of all bids. Although the objective function is not concave, we show that a Lagrangian approach will often yield an optimal answer and, when it does not, will yield a good solution and a bound on possible further improvements. Characteristics of optimal sets of bids are proven. The methodology employed will be generally attractive for any problem that involves allocating a single resource among a large number of competing activities with convex-concave profit functions.
Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA (1994)

We have characterized the copy number, organization, and genomic modification of DNA sequences within and flanking several maize genes. We found that highly repetitive DNA sequences were tightly linked to most of these genes. The highly repetitive sequences were not found within the coding regions but could be found within 6 kb either 3' or 5' to the structural genes. These highly repetitive regions were each composed of unique combinations of different short repetitive sequences. Highly repetitive DNA blocks were not interrupted by any detected single copy DNA. The 13 classes of highly repetitive DNA identified were found to vary little between diverse Zea isolates. The level of DNA methylation in and near these genes was determined by scoring the digestibility of 63 recognition/cleavage sites with restriction enzymes that were sensitive to 5-methylation of cytosines in the sequences 5'-CG-3' and 5'-CNG-3'. All but four of these sites were digestible in chromosomal DNA. The four undigested sites were localized to extragenic DNA within or near highly repetitive DNA, while the other 59 sites were in low copy number DNAs. Pulsed field gel analysis indicated that the majority of cytosine modified tracts range from 20 to 200 kb in size. Single copy sequences hybridized to the unmodified domains, while highly repetitive sequences hybridized to the modified regions. Middle repetitive sequences were found in both domains.
Parkinson's disease and dementia (1987)

Norepinephrine, 3-methoxy 4-hydroxyphenylethyleneglycol and homovanillic acid levels were similar in the locus ceruleus of 13 controls and 8 parkinsonian patients with no intellectual deterioration, but were decreased in 7 demented patients. The concentration of dopamine was similarly diminished in non-demented and demented parkinsonians, and binding of 3H-desmethylimipramine and 3H-rauwolscine was not abnormal in parkinsonians. These data indicate that norepinephrine metabolism in the locus ceruleus is subnormal only in demented parkinsonians.
Supertriptycene, C104H62 (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSupertriptycene, C104H62Khalil Shahlai and Harold HartCite this: J. Am. Chem. Soc. 1990, 112, 9, 3687–3688Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ja00165a080https://doi.org/10.1021/ja00165a080research-articleACS PublicationsRequest reuse permissionsArticle Views298Altmetric-Citations28LEARN 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
Differential Role of Th1 and Th2 Cytokines in Autotoxicity Driven by CD19-Specific Second-Generation Chimeric Antigen Receptor T Cells in a Mouse Model (2014)

T cells engrafted with chimeric AgRs (CAR) are showing exciting potential for targeting B cell malignancies in early-phase clinical trials. To determine whether the second-generation CAR was essential for optimal antitumor activity, two CD28-based CAR constructs targeting CD19 were tested for their ability to redirect mouse T cell function against established B cell lymphoma in a BALB/c syngeneic model system. T cells armed with either CAR eliminated A20 B cell lymphoma in vivo; however, one construct induced a T cell dose-dependent acute toxicity associated with a raised serum Th1 type cytokine profile on transfer into preconditioned mice. Moreover, a chronic toxicity manifested as granuloma-like formation in spleen, liver, and lymph nodes was observed in animals receiving T cells bearing either CD28 CAR, albeit with different kinetics dependent upon the specific receptor used. This phenotype was associated with an expansion of CD4+ CAR+ T cells and CD11b+ Gr-1(+) myeloid cells and increased serum Th2-type cytokines, including IL-10 and IL-13. Mouse T cells engrafted with a first-generation CAR failed to develop such autotoxicity, whereas toxicity was not apparent when T cells bearing the same receptors were transferred into C57BL/6 or C3H animals. In summary, the adoptive transfer of second-generation CD19-specific CAR T cells can result in a cell dose-dependent acute toxicity, whereas the prolonged secretion of high levels of Th2 cytokines from these CAR T cells in vivo drives a granulomatous reaction resulting in chronic toxicity. Strategies that prevent a prolonged Th2-cytokine biased CAR T cell response are clearly warranted.
1996 Off-Label Drug Scorecard (1996)

Click to increase image sizeClick to decrease image size Additional informationNotes on contributorsJamie YoungJamie Young is ACCC director for state societies and government relations.
Renal Production, Uptake, and Handling of Circulating αKlotho (2015)

αKlotho is a multifunctional protein highly expressed in the kidney. Soluble αKlotho is released through cleavage of the extracellular domain from membrane αKlotho by secretases to function as an endocrine/paracrine substance. The role of the kidney in circulating αKlotho production and handling is incompletely understood, however. Here, we found higher αKlotho concentration in suprarenal compared with infrarenal inferior vena cava in both rats and humans. In rats, serum αKlotho concentration dropped precipitously after bilateral nephrectomy or upon treatment with inhibitors of αKlotho extracellular domain shedding. Furthermore, the serum half-life of exogenous αKlotho in anephric rats was four- to five-fold longer than that in normal rats, and exogenously injected labeled recombinant αKlotho was detected in the kidney and in urine of rats. Both in vivo (micropuncture) and in vitro (proximal tubule cell line) studies showed that αKlotho traffics from the basal to the apical side of the proximal tubule via transcytosis. Thus, we conclude that the kidney has dual roles in αKlotho homeostasis, producing and releasing αKlotho into the circulation and clearing αKlotho from the blood into the urinary lumen.