gebhart/patrepeval huggingface dataset:
Automatic concept identification in goal-oriented conversations (2002)

We address the problem of identifying key domain concepts<br>automatically from an unannotated corpus of goal-oriented<br>human-human conversations. We examine two clustering<br>algorithms, one based on mutual information and another one<br>based on Kullback-Liebler distance. In order to compare the<br>results from both techniques quantitatively, we evaluate the<br>outcome clusters against reference concept labels using<br>precision and recall metrics adopted from the evaluation of<br>topic identification task. However, since our system allows<br>more than one cluster to associate with each concept an<br>additional metric, a singularity score, is added to better capture<br>cluster quality. Based on the proposed quality metrics, the<br>results show that Kullback-Liebler-based clustering<br>outperforms mutual information-based clustering for both the<br>optimal quality and the quality achieved using an automatic<br>stopping criterion
PD1/PDL1 inhibitors for the treatment of advanced urothelial bladder cancer (2018)

Immunotherapy has offered a glimmer of hope to patients with bladder cancer. The current landscape is rapidly evolving, with novel immunotherapy-combination trials to improve outcomes further and evaluate predictive biomarkers to help identify patients most likely to benefit from such therapies.
Ovarian Cancer Biomarkers in Urine (2006)

In this issue of Clinical Cancer Research , Ye et al. ([1][1]) have taken steps to address the pressing need for the identification of biomarkers for use in detecting ovarian cancer.

For the past 30 years, the statistics have remained the same. The majority of women who develop ovarian cancer will
Cell-free synthesis and processing of a putative precursor for mitochondrial carbamyl phosphate synthetase I of rat liver (1979)

Total RNA or poly(A)(+) RNA of rat liver was translated in a rabbit reticulocyte or wheat germ protein-synthesizing system and the carbamyl phosphate synthetase I [carbamoyl-phosphate synthetase (ammonia); carbon dioxide: ammonia ligase (ADP-forming, carbamate-phosphorylating), EC 6.3.4.16] synthesized was isolated by indirect immunoprecipitation by using antibody purified on enzyme-bound Sepharose and Staphylococcus aureus cells. The in vitro product moved on sodium dodecyl sulfate/polyacrylamide gels as a polypeptide that was about 5000 daltons larger than the subunit of the mature enzyme (160,000 daltons). The same polypeptide was also obtained by direct immunoprecipitation or by a double-antibody precipitation method. The mature enzyme competed effectively with the in vitro product for interaction with anti-carbamyl phosphate synthetase I antibody. Digestion of the in vitro product by S. aureus protease gave a pattern of peptide fragments similar to that of the mature enzyme. A mitochondrial membrane preparation from rat liver converted the in vitro product into a polypeptide that comigrated with the mature subunit on sodium dodecyl sulfate gel electrophoresis. Similar proteolytic activity was not detected in either a cytosol or a microsomal fraction of rat liver. These results indicate that the enzyme is synthesized as a larger precursor which is converted to the mature form of enzyme by posttranslational processing.
Extremely low power consumption semiconductor opticalamplifier gate for WDM applications (1997)

A polarisation insensitive semiconductor optical amplifier gate is reported. Very low current for fibre-to-fibre lossless operation (5.6–7.0 mA) and a high extinction ratio (&gt;40 dB) were obtained over a wide wavelength range (1530–1560 nm), even when lensed fibres (5 dB loss/facet) were used.
Total synthesis of 5(S),15(S)-dihydroxy-6,13-trans-8,15-cis-eicosatetraenoic acid (5,15-diHETE) and 8(S),15(S)-dihydroxy-5,11-cis-9,13-trans-eicosatetraenoic acid (8,15-DiHETE), two novel metabolites of arachidonic acid (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of 5(S),15(S)-dihydroxy-6,13-trans-8,15-cis-eicosatetraenoic acid (5,15-diHETE) and 8(S),15(S)-dihydroxy-5,11-cis-9,13-trans-eicosatetraenoic acid (8,15-DiHETE), two novel metabolites of arachidonic acidK. C. Nicolaou and S. E. WebberCite this: J. Am. Chem. Soc. 1984, 106, 19, 5734–5736Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/ja00331a058https://doi.org/10.1021/ja00331a058research-articleACS PublicationsRequest reuse permissionsArticle Views721Altmetric-Citations63LEARN 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
Micropatterning metal electrode of organic light emitting devices using rapid polydimethylsiloxane lift-off (2007)

The authors demonstrate a subtractive stamping technique for patterning metal electrodes of organic light emitting devices. Patterning is achieved by placing a relief patterned polydimethylsiloxane stamp in contact with a planar metal electrode film and subsequently peeling off the stamp. A fast peel rate increases the weak adhesion energy of the stamp to the metal so that no surface treatment, pressure, or temperature control is necessary to lift-off the metal film in contact with the stamp. Patterning is dependent on metal film thickness, geometry of the features, and peel direction of stamp release. The minimum feature size patterned is 13μm wide stripes within &amp;lt;1μm in-plane edge roughness and 0.1μm height transition region of the patterned edge.
The Analytic Hierarchy Process in Medical Decision Making (1989)

The analytic hierarchy process (AHP) is a quantitative decision making technique created especially for complicated, multicriteria decision problems. This report reviews the theoretical foundations of the AHP and shows how to use it in a step-by-step fashion.
Plexin-B1/RhoGEF–mediated RhoA activation involves the receptor tyrosine kinase ErbB-2 (2004)

Plexins are widely expressed transmembrane proteins that mediate the effects of semaphorins. The molecular mechanisms of plexin-mediated signal transduction are still rather unclear. Plexin-B1 has recently been shown to mediate activation of RhoA through a stable interaction with the Rho guanine nucleotide exchange factors PDZ-RhoGEF and LARG. However, it is unclear how the activity of plexin-B1 and its downstream effectors is regulated by its ligand Sema4D. Here, we show that plexin-B family members stably associate with the receptor tyrosine kinase ErbB-2. Binding of Sema4D to plexin-B1 stimulates the intrinsic tyrosine kinase activity of ErbB-2, resulting in the phosphorylation of both plexin-B1 and ErbB-2. A dominant-negative form of ErbB-2 blocks Sema4D-induced RhoA activation as well as axonal growth cone collapse in primary hippocampal neurons. Our data indicate that ErbB-2 is an important component of the plexin-B receptor system and that ErbB-2-mediated phosphorylation of plexin-B1 is critically involved in Sema4D-induced RhoA activation, which underlies cellular phenomena downstream of plexin-B1, including axonal growth cone collapse.
A Novel Non-Synonymous Polymorphism (p.Arg240His) in C4b-Binding Protein Is Associated with Atypical Hemolytic Uremic Syndrome and Leads to Impaired Alternative Pathway Cofactor Activity (2008)

Atypical hemolytic uremic syndrome (aHUS) is a disorder characterized by hemolytic anemia, thrombocytopenia, and acute renal failure. Mutations, polymorphisms, and copy number variation in complement factors and inhibitors are associated with aHUS. In this study, we report the first functional non-synonymous polymorphism in the complement inhibitor C4b-binding protein (C4BP) alpha-chain (c.719G>A; p.Arg240His), which is associated with aHUS. This heterozygous change was found in 6/166 aHUS patients compared with 5/542 normal (chi2 = 6.021; p = 0.014), which was replicated in a second cohort of aHUS patients in which we found 5/170 carriers. The polymorphism does not decrease expression efficiency of C4BP. p.Arg240His is equally efficient as the wild type in binding and supporting degradation of C4BP but its ability to bind C3b and act as cofactor to its degradation both in fluid phase and on surfaces is impaired. This observation supports the hypothesis that dysregulation of the alternative pathway of complement is pivotal for aHUS. Three of the patients carry also mutations in membrane cofactor protein and factor H strengthening the hypothesis that individuals may carry multiple susceptibility factors with an additive effect on the risk of developing aHUS.
Anecortave Acetate: Treatment of Age‐Related Macular Degeneration Angiogenesis Inhibitor (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Cloning and analysis of the poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) biosynthesis genes of Aeromonas caviae (1997)

A 5.0-kbp EcoRV-EcoRI restriction fragment was cloned and analyzed from genomic DNA of Aeromonas caviae, a bacterium producing a copolyester of (R)-3-hydroxybutyrate (3HB) and (R)-3-hydroxyhexanoate (3HHx) [P(3HB-co-3HHx)] from alkanoic acids or oils. The nucleotide sequence of this region showed a 1,782-bp poly (3-hydroxyalkanoate) (PHA) synthase gene (phaC(Ac) [i.e., the phaC gene from A. caviae]) together with four open reading frames (ORF1, -3, -4, and -5) and one putative promoter region. The cloned fragments could not only complement PHA-negative mutants of Alcaligenes eutrophus and Pseudomonas putida, but also confer the ability to synthesize P(3HB-co-3HHx) from octanoate or hexanoate on the mutants' hosts. Furthermore, coexpression of ORF1 and ORF3 genes with phaC(Ac) in the A. eutrophus mutant resulted in a decrease in the polyester content of the cells. Escherichia coli expressing ORF3 showed (R)-enoyl-coenzyme A (CoA) hydratase activity, suggesting that (R)-3-hydroxyacyl-CoA monomer units are supplied via the (R)-specific hydration of enoyl-CoA in A. caviae. The transconjugant of the A. eutrophus mutant expressing only phaC(Ac) effectively accumulated P(3HB-co-3HHx) up to 96 wt% of the cellular dry weight from octanoate in one-step cultivation.
흰쥐 간에서 용량별 초오전탕액의 약물대사효소 Cytochrome P450 발현에 대한 연구 (2004)

Objective: Wild Aconiti Tuber is known as a toxic herb and used for anti-arthritic, analgesic, and so on. This study was carried out to evaluate the effects of different Dosage of Wild Aconiti Tuber Decoction on rat liver Cytochrome P450 expression. Methods: A clinical dosage, 0.4g/kg/day oral administrations of Wild Aconiti Tuber Decoction was investigated. Rats were given 2 weeks of clinical dosage p.o. group, Aconitine i.p. group and control. Also, high dosage of 1, 5, 10 g/kg/day for 3 days p.o. group was investigated. CytochromeP450 induction/inhibition were tested by competitive RT-PCR in each group. Results. The amounts of aconitine in the methanol extract of Wild Aconiti Tuber was . But aconitine was not detected in the water decoction of Wild Aconiti Tuber. Among several CYP450 isozymes, Wild Aconiti Tuber 0.4g/kg/day for 2 weeks p.o. group showed induction of 3A2, aconitine for 2 weeks i.p. group showed inhibition of 2E1. While 1, 5, 10 g/kg/day for 3days p.o. group showed induction of lA2, 2El, 3Al, 3A2, 4A1. Conclusions: According to the results, though aconitine was not detected in the Wild Aconiti Tuber decoction, 0.4g/kg/day for 2 weeks p.o. (clinical dosage) group showed CYP450 3A2 induction and high dose group showed general induction of CYP450 isozymes.
Iran - Tehran Sewerage Project : environmental assessment (1999)

This is the environmental assessment for the Tehran Sewerage Project, which builds a piped sewerage system, sewage and sludge treatment facilities, and a sewerage drainage system. Measures to minimize negative environmental impacts include the following: During construction and operation, reduce noise levels by suitable dampening; screening plant air compressors and de-watering pumps with sandbags; restrict work to daytime where possible; issue workers equipment to protect hearing; and restrict construction traffic during nighttime. Mitigate vibration impacts by limiting the use of percussive equipment when excavating sewer trenches and tunnel shafts; and using dead-weight rather than vibration compaction plant. Dust problems will be alleviated by spraying water, covering stockpiles of excavated material with tarpaulins; providing workers with masks to keep from inhaling dust. Noisome odors will be controlled by covering containers and equipment, and designating the area surrounding the site as a greenbelt. Disposal of solid waste in the municipal landfill has been designed to prevent groundwater or surface runoff from contaminating the site. To ensure the health and safety of workers and the public, access to sewage treatment plant effluent will be restricted by installing a fence; a regular eradication program will use biodegradable pesticides for pest control; and other safety measures, such as barriers, flags, and bollards, will be used.
Controlling molecular transport through nanopores (2011)

Nanopores are emerging as powerful tools for the detection and identification of macromolecules in aqueous solution. In this review, we discuss the recent development of active and passive controls over molecular transport through nanopores with emphasis on biosensing applications. We give an overview of the solutions developed to enhance the sensitivity and specificity of the resistive-pulse technique based on biological and solid-state nanopores.
Photothermal coagulation of blood vessels: a comparison of high-speed optical coherence tomography and numerical modelling (2001)

Optical-thermal models that can accurately predict temperature rise and damage in blood vessels and surrounding tissue may be used to improve the treatment of vascular disorders. Verification of these models has been hampered by the lack of time- and depth-resolved experimental data. In this preliminary study, an optical coherence tomography system operating at 4-30 frames per second was used to visualize laser irradiation of cutaneous (hamster dorsal skin flap) blood vessels. An argon laser was utilized with the following parameters: pulse duration 0.1-2.0 s, spot size 0.1-1.0 mm, power 100-400 mW. Video microscopy images were obtained before and after irradiations, and optical-thermal modelling was performed on two irradiation cases. Time-resolved optical coherence tomography and still images were compared with predictions of temperature rise and damage using Monte Carlo and finite difference techniques. In general, predicted damage agreed with the actual blood vessel and surrounding tissue coagulation seen in images. However, limitations of current optical-thermal models were identified, such as the inability to model the dynamic changes in blood vessel diameter that were seen in the optical coherence tomography images.
Conditional inactivation of mRNA capping enzyme affects yeast pre-mRNA splicing in vivo. (1996)

Acquisition of the 5'cap is the earliest modification event during eukaryotic mRNA synthesis. The cap is thought to facilitate later processing steps, such as pre-mRNA splicing. If this is so, then a defect in cap synthesis should impact on splicing in vivo. We tested this hypothesis by examining the consequences of conditional inactivation of the Saccharomyces cerevisiae CEG1 gene, which encodes mRNA guanylyltransferase (capping enzyme). Two different ceg1-ts mutants, Y66A and C354Y, displayed a pre-mRNA processing (prp) defect, characterized by an increase in the amount of unspliced pre-mRNA after shift to nonpermissive temperature and a decrease in the amount of mature mRNA. The guanylyltransferase activities of the Y66A and C354Y proteins were thermolabile, suggesting that defective capping in vivo was contributory to the prp phenotype. Although these results provide the first genetic link between capping and splicing in vivo, we were unable to demonstrate a role for either the cap or the capping enzyme during yeast pre-mRNA splicing in vitro.
Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups (2007)

The alpha-proteobacteria-specific proteins and indels described here provide novel and powerful means for the taxonomic, biochemical and molecular biological studies on these bacteria. Their functional studies should prove helpful in identifying novel biochemical and physiological characteristics that are unique to these bacteria.
A Stereoselective Synthesis of (+)-Gonyautoxin 3 (2008)

An asymmetric synthesis of the paralytic shellfish poison (PSP), (+)-gonyautoxin 3, is described. A unique, Rh-catalyzed amination reaction provides rapid access to the heteratom-rich, tricyclic core of the toxin, which is common to more than 30 related natural products. The completed route should facilitate the preparation of other naturally occurring PSPs and designed analogues thereof.
Biologic and Biochemical Analyses of p16INK4a Mutations From Primary Tumors (1999)

Among 16 mutants analyzed, nine had detectable functional defects. Three mutants (D84V, D84G, and R87P) had defects in CDK binding, kinase inhibition, and cell cycle arrest. The corresponding mutations are located in the third ankyrin repeat in a highly conserved region believed to form the CDK binding cleft. Three mutants (P48L, D74N, and R87L) had defects in kinase inhibition and cell cycle arrest. Among the 10 mutants with normal CDK binding and inhibitory activity, three mutants (N71S, R80L, and H83Y) had defects only in their ability to induce cell cycle arrest. Thus, p16 mutant proteins that retain CDK4 and CDK6 binding may have more subtle functional defects. All nine mutations leading to functional impairments mapped to the central portion of the p16 protein. Ankyrin repeats II and III appear more critical to p16 function, and mutations in ankyrin repeats I and IV are less likely to disrupt p16 function.
Evidence for a Plasma Membrane-Mediated Permeability Barrier to Tat Basic Domain in Well-Differentiated Epithelial Cells: Lack of Correlation with Heparan Sulfate (2002)

Membrane permeation peptides, such as Tat basic domain, have emerged as useful membrane transduction agents with potential utility in therapeutic delivery and diagnostic imaging. While generally thought to universally permeate all cells by a nonselective process, the mechanism of membrane transduction remains poorly characterized. To examine vectorial transport properties of Tat basic domain in well-differentiated epithelial cells possessing tight junctions, L and D stereoisomers of Tat(48-57) peptide conjugates labeled with (99m)Tc were quantitatively analyzed in confluent monolayers of MDCK renal epithelial and CaCo-2 colonic carcinoma cells grown in transwell configurations. In both cell lines, vectorial transepithelial apparent permeability coefficients (P(app)) for L- and D-[(99m)Tc]Tat-peptides ranged from 30 to 70 nm/s, comparable to values for the macromolecular impermeant marker inulin in both apical-to-basolateral and basolateral-to-apical directions, but 100-fold less than the P(app) values for propranolol, a highly permeable control compound. Upon direct instillation of [(99m)Tc]Tat-peptide into the urinary bladder of living rats in vivo, no transepithelial permeation into other tissues was identified. Furthermore, MDCK and CaCo-2 cells showed a complete lack of intracellular accumulation of fluorescein conjugated Tat-peptide. However, translocation into cells was induced by treatment with plasma membrane permeabilizing agents such as digitonin and acetone/methanol, while cholesterol depletion with beta-methyl-cyclodextrin and metabolic inhibition with CCCP or 4 degrees C showed no effect. By contrast, in Hela and KB 3-1 cells, epithelial lines that do not form tight junctions in monolayer culture, baseline cytoplasmic and nucleolar accumulation was readily observed. Because all four cell lines expressed heparan sulfate proteoglycans, putative receptors for Tat basic peptides, we found no correlation between heparan sulfate and the permeation barrier observed in MDCK and CaCo-2 cells. The unanticipated presence of a permeation barrier to Tat-peptides in well-differentiated epithelial cells suggests the existence of cell-specific mechanisms for mediated translocation of these permeation peptides.
Identification of Functional Domains of the Aryl Hydrocarbon Receptor Nuclear Translocator Protein (ARNT) (1994)

The activated aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) bind DNA as a heterodimer. Both proteins represent a novel class of basic helix-loop-helix (bHLH)-containing transcription factors in that (i) activation of AHR requires the binding of ligand (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD]), (ii) the xenobiotic responsive element (XRE) recognized by the AHR/ARNT heterodimer differs from the recognition sequence for nearly all other bHLH proteins, and (iii) both proteins contain a PAS homology region, which in the Drosophila PER and SIM proteins functions as a dimerization domain. A cDNA for mouse ARNT has been cloned, and potential functional domains of ARNT were investigated by deletion analysis. A mutant lacking all regions of ARNT other than the bHLH and PAS regions is unimpaired in TCDD-dependent dimerization and subsequent XRE binding and only modestly reduced in ability to complement an ARNT-deficient mutant cell line, c4, in vivo. Both the first and second alpha helices of the bHLH region are required for dimerization. The basic region is required for XRE binding but not for dimerization. Deletion of either the A or B segments of the PAS region slightly affects TCDD-induced heterodimerization, while deletion of the complete PAS region severely affects (but does not eliminate) dimerization. Thus, ARNT possesses multiple domains required for maximal heterodimerization. Mutants deleted for PAS A, PAS B, and the complete PAS region all retain some degree of XRE binding, yet none can rescue the c4 mutant. Therefore, both the PAS A and PAS B segments, besides contributing to dimerization, apparently fulfill additional, unknown functions required for biological activity of ARNT.
Algorithms on strings, trees, and sequences (1997)

Linear-Time Construction of Suffix Trees We will present two methods for constructing suffix trees in detail, Ukkonen’s method and Weiner’s method. Weiner was the first to show that suffix trees can be built in linear time, and his method is presented both for its historical importance and for some different technical ideas that it contains. However, lJkkonen’s method is equally fast and uses far less space (i.e., memory) in practice than Weiner’s method Hence Ukkonen is the method of choice for most problems requiring the construction of a suffix tree. We also believe that Ukkonen’s method is easier to understand. Therefore, it will be presented first A reader who wishes to study only one method is advised to concentrate on it. However, our development of Weiner’s method does not depend on understanding Ukkonen’s algorithm, and the two algorithms can be read independently (with one small shared section noted in the description of Weiner’s method).