gebhart/patrepeval huggingface dataset:
Capture of a cellular transcriptional unit by a retrovirus: mode of provirus activation in embryonal carcinoma cells (1992)

The expression of murine leukemia provirus in embryonal carcinoma (EC) cells is blocked by a mechanism still incompletely understood. The blockage is not overcome by deleting a large portion of the enhancer region (in U3) in recombinant retroviruses (M-MuLVneo delta Enh). This confirms the presence of negative elements outside the viral 82-bp repeats. However, a few sites in the genomes of EC cells permit M-MuLVneo delta Enh proviral expression. One such site, identified in PCC4, PCC3, and LT, was studied. The complete analysis of the mechanism of activation by Northern (RNA) blotting, cloning, and sequencing of partial cDNA copies of the viral transcript and of the site of integration establishes that viral transcripts are initiated from an upstream host-cell promoter and are spliced from a host donor to a cryptic viral acceptor at position 542 in the Moloney murine leukemia virus (M-MuLV) genome. In consequence, the mature transcripts are host cell-virus fusion transcripts from which M-MuLV sequences, including the cis-active negative elements of the 5' long terminal repeat-containing region, are absent. The provirus integrates apparently randomly into any of the three most proximal introns of the transcriptional unit. The host cell promoter contains a TATA box and 14 potential SpI binding sites included in a 1.0-kb GC-rich island. These elements promote gene expression of recombinant vectors in EC and differentiated cells. The mechanism described points to a mechanism by which retroviruses can be transcribed from upstream nonviral elements and can acquire host genes by 5' annexation of exons.
The application of semantic classification trees to natural language understanding (1995)

This article describes a new method for building a natural language understanding (NLU) system, in which the system's rules are learnt automatically from training data. The method has been applied to design of a speech understanding (SU) system. Designers of such systems rely increasingly on robust matchers to perform the task of extracting meaning from one or several word sequence hypotheses generated by a speech recognizer. We describe a new data structure, the semantic classification tree (SCT), that learns semantic rules from training data and can be a building block for robust matchers for NLU tasks. By reducing the need for handcoding and debugging a large number of rules, this approach facilitates rapid construction of an NLU system. In the case of an SU system, the rules learned by an SCT are highly resistant to errors by the speaker or by the speech recognizer because they depend on a small number of words in each utterance. Our work shows that semantic rules can be learned automatically from training data, yielding successful NLU for a realistic application.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Pharmacokinetic/Pharmacodynamic Model of Tumor Lysis Syndrome in Chronic Lymphocytic Leukemia Patients Treated with Flavopiridol (2013)

Abstract Purpose: Flavopiridol, the first clinically evaluated cyclin-dependent kinase inhibitor, shows activity in patients with refractory chronic lymphocytic leukemia, but prevalent and unpredictable tumor lysis syndrome (TLS) presents a major barrier to its broad clinical use. The purpose of this study was to investigate the relationships between pretreatment risk factors, drug pharmacokinetics, and TLS. Experimental Design: A population pharmacokinetic/pharmacodynamic model linking drug exposure and TLS was developed. Plasma data of flavopiridol and its glucuronide metabolite (flavo-G) were obtained from 111 patients treated in early-phase trials with frequent sampling following initial and/or escalated doses. TLS grading was modeled with logistic regression as a pharmacodynamic endpoint. Demographics, baseline disease status, and blood chemistry variables were evaluated as covariates. Results: Gender was the most significant pharmacokinetic covariate, with females displaying higher flavo-G exposure than males. Glucuronide metabolite exposure was predictive of TLS occurrence, and bulky lymphadenopathy was identified as a significant covariate on TLS probability. The estimated probability of TLS occurrence in patients with baseline bulky lymphadenopathy less than 10 cm or 10 cm or more during the first 2 treatments was 0.111 (SE% 13.0%) and 0.265 (SE% 17.9%), respectively, when flavo-G area under the plasma concentration versus time curve was at its median value in whole-patient group. Conclusions: This is the first population pharmacokinetic/pharmacodynamic model of TLS. Further work is needed to explore potential mechanisms and to determine whether the associations between TLS, gender, and glucuronide metabolites are relevant in patients with chronic lymphocytic leukemia treated with other cyclin-dependent kinase inhibitors. Clin Cancer Res; 19(5); 1269–80. ©2012 AACR.
Hydrological consequences of ponded water on Mars (1993)

The family of q-Gaussian and q-exponential probability densities fit the statistical behavior of diverse complex self-similar nonequilibrium systems. These distributions, independently of the underlying dynamics, can rigorously be obtained by maximizing Tsallis "nonextensive" entropy under appropriate constraints, as well as from superstatistical models. In this paper we provide an alternative and complementary scheme for deriving these objects. We show that q-Gaussian and q-exponential random variables can always be expressed as a function of two statistically independent gamma random variables with the same scale parameter. Their shape index determines the complexity q parameter. This result also allows us to define an extended family of asymmetric q-Gaussian and modified q-exponential densities, which reduce to the standard ones when the shape parameters are the same. Furthermore, we demonstrate that a simple change of variables always allows relating any of these distributions with a beta stochastic variable. The extended distributions are applied in the statistical description of different complex dynamics such as log-return signals in financial markets and motion of point defects in a fluid flow.
Quantum transistors: toward nanoelectronics (2000)

Electrons that tunnel through insulating barriers and hop on and off minuscule dots are shown to be at the heart of future transistor generations.
HTLV-1 tax activation of the GM-CSF and G-CSF promoters requires the interaction of NF-kB with other transcription factor families. (1993)

The trans-activator protein, tax, from the human T leukemia virus type 1 (HTLV-1) trans-activates both viral and cellular genes. It has previously been shown that granulocyte macrophage-colony stimulating factor (GM-CSF) is constitutively expressed in HTLV-1 infected cells and in cells artificially expressing tax. We show here that the GM-CSF promoter is tax responsive in fibroblasts and T cells, whereas the granulocyte (G)-CSF promoter is tax responsive only in fibroblasts. The tax protein can activate cellular genes through a least two families of transcription factors; the NF-kB/rel and CREB/ATF families. We have used mutant tax proteins to show that the activation of NF-kB proteins is essential for tax trans-activation of both the GM-CSF and G-CSF promoters. The ability of tax to activate CREB/ATF proteins is also essential for GM-CSF transactivation. We have identified a 44 bp region of the GM-CSF promoter that contains tax responsive elements. This region contains a classical NF-kB site, a CK-1 element that can bind the NF-kB p65 protein, as well as a putative ATF binding site. The tax response of the G-CSF promoter requires not only the conserved CK-1 sequence but also an adjacent NF-IL6 binding site that may explain the cell restricted function of the G-CSF promoter.
Common Sense (2009)

Poor air quality is a global health issue, causing serious problems like asthma, cancer, and heart disease around the world. Earlier this decade, the World Health Organization estimated that three million people die each year from the effects of air pollution [6]. Unfortunately, while variations in air quality are significant, today's air quality monitors are very sparsely deployed. To address this visibility gap, the Common Sense project is developing participatory sensing systems that allow individuals to measure their personal exposure, groups to aggregate their members' exposure, and activists to mobilize grassroots community action.
Outer Membrane Vesicles Mediate Transport of Biologically Active Vibrio cholerae Cytolysin (VCC) from V. cholerae Strains (2014)

Biological assays of OMVs from the V. cholerae strain V:5/04 demonstrated that OMV-associated VCC is indeed biologically active and induces toxicity on mammalian cells and furthermore can induce autophagy.
Aerobic epoxidation of olefins with ruthenium porphyrin catalysts (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAerobic epoxidation of olefins with ruthenium porphyrin catalystsJohn T. Groves and Robert QuinnCite this: J. Am. Chem. Soc. 1985, 107, 20, 5790–5792Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/ja00306a029https://doi.org/10.1021/ja00306a029research-articleACS PublicationsRequest reuse permissionsArticle Views2419Altmetric-Citations387LEARN 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
Vitronectin Inhibits the Thrombotic Response to Arterial Injury in Mice (1999)

Vitronectin (VN) binds to plasminogen activator inhibitor-1 (PAI-1) and integrins and may play an important role in the vascular response to injury by regulating fibrinolysis and cell migration. However, the role of VN in the earliest response to vascular injury, thrombosis, is not well characterized. The purpose of this study was to test the hypothesis that variation in vitronectin expression alters the thrombotic response to arterial injury in mice. Ferric chloride (FeCl3) injury was used to induce platelet-rich thrombi in mouse carotid arteries. Wild-type (VN +/+, n = 14) and VN-deficient (VN −/−, n = 15) mice, matched for age and gender, were studied. Time to occlusion after FeCl3 injury was determined by application of a Doppler flowprobe to the carotid artery. Occlusion times of VN −/− mice were significantly shorter than those of VN +/+ mice (6.0 ± 1.2 minutesv 17.8 ± 2.3 minutes, respectively, P &amp;lt; .001). Histologic analysis of injured arterial segments showed that thrombi from VN +/+ and VN −/− mice consisted of dense platelet aggregates. In vitro studies of murine VN +/+ andVN −/− platelets showed no significant differences in ADP-induced aggregation, but a trend towards increased thrombin-induced aggregation in VN −/− platelets. Purified, denatured VN inhibited thrombin-induced platelet aggregation, whereas native VN did not. Thrombin times of plasma from VN −/− mice (20.5 ± 2.1 seconds, n = 4) were significantly shorter than those ofVN +/+ mice (34.2 ± 6.7 seconds, n = 4, P &amp;lt; .01), and the addition of purified VN to VN −/− plasma prolonged the thrombin time into the normal range, suggesting that VN inhibits thrombin-fibrinogen interactions. PAI-1-deficient mice (n = 6) did not demonstrate significantly enhanced arterial thrombosis compared with wild-type mice (n = 6), excluding a potential indirect antithrombin function of VN mediated by interactions with PAI-1 as an explanation for the accelerated thrombosis observed in VN−/− mice. These results suggest that vitronectin plays a previously unappreciated antithrombotic role at sites of arterial injury and that this activity may be mediated, at least in part, by inhibiting platelet-platelet interactions and/or thrombin procoagulant activity.
Buried asparagines determine the dimerization specificities of leucine zipper mutants (1997)

Regulation of gene expression by many transcription factors is controlled by specific combinations of homo- and heterodimers through a short alpha-helical coiled-coil known as a leucine zipper. The dimer interface of a leucine zipper involves side chains of the residues at the a, d, e, and g positions of the (abcdefg)n heptad repeat. To understand the basis for the specificity of dimer formation, we characterized GCN4 leucine zipper mutants with all 16 possible permutations and combinations of isoleucines and asparagines at four a positions in the dimer interface, using a genetic test for the specificity of dimer formation by lambda repressor-leucine zipper fusions. Heterodimers were detected by loss of repressor activity in the presence of a fusion to a dominant-negative mutant form of the DNA-binding domain of repressor. Reconstruction experiments using leucine zippers from GCN4, Jun, Fos, and C/EBP showed that this assay distinguishes pairs that form heterodimers from those that do not. We found that the mutants have novel dimerization specificities determined by the positioning of buried asparagine residues at the a positions. The pattern of buried polar residues could also explain the dimerization specificities of some naturally occurring leucine zippers. The altered specificity mutants described here should be useful for the construction of artificial regulatory circuitry.
The Echo Distributed File System (1993)

Echo is an ambitious distributed file system. It was designed around a truly global name space. It uses a coherent caching algorithm. It is fault tolerant. And it is real—it was the primary file system for a large group of researchers. Its novel aspects include an extensible “junction ” mechanism for global naming; extensive write-behind with ordering semantics that allow applications to maintain invariants without resorting to synchronous writes; and fault tolerance mechanisms that are highly configurable and that tolerate network partitions. It was designed with the intention that its performance could be as good as a local file system, while supporting large numbers of clients per server. Its reliability was designed to be higher than other distributed file systems, and higher than
The Effect of the Particle Size on the Kinetics of CO Electrooxidation on High Surface Area Pt Catalysts (2005)

Using high-resolution transmission electron microscopy (TEM), infrared reflection-absorption spectroscopy (IRAS), and electrochemical (EC) measurements, platinum nanoparticles ranging in size from 1 to 30 nm are characterized and their catalytic activity for CO electrooxidation is evaluated. TEM analysis reveals that Pt crystallites are not perfect cubooctahedrons, and that large particles have "rougher" surfaces than small particles, which have some fairly smooth (111) facets. The importance of "defect" sites for the catalytic properties of nanoparticles is probed in IRAS experiments by monitoring how the vibrational frequencies of atop CO (nu(CO)) as well as the concomitant development of dissolved CO(2) are affected by the number of defects on the Pt nanoparticles. It is found that defects play a significant role in CO "clustering"on nanoparticles, causing CO to decrease/increase in local coverage, which yields to anomalous redshift/blueshift nu(CO) frequency deviations from the normal Stark-tuning behavior. The observed deviations are accompanied by CO(2) production, which increases by increasing the number of defects on the nanoparticles, that is, 1 < or = 2 < 5 << 30 nm. We suggest that the catalytic activity for CO adlayer oxidation is predominantly influenced by the ability of the surface to dissociate water and to form OH(ad) on defect sites rather than by CO energetics. These results are complemented by chronoamperometric and rotating disk electrode (RDE) data. In contrast to CO stripping experiments, we found that in the backsweep of CO bulk oxidation, the activity increases with decreasing particle size, that is, with increasing oxophilicity of the particles.
Evaluation of a Cascade Hybrid Recommendation as a Combination of One-Class Classification and Collaborative Filtering (2012)

This paper decomposes the problem of recommendation into a two level cascade recommendation scheme which benefits from both content-based and collaborative filtering methodologies. The first level utilizes the content-based features of items in order to incorporate the individualized (subjective) user preferences within the recommendation process. This is achieved through the exploitation of the one-class classification paradigm which provides the means in order to filter out user specific undesirable items. The second level, on the other hand, serves the purpose of assigning particular rating degrees to the user-specific desirable items identified by the first level. The combination of two approaches in a cascade form, mimics the social process when someone has selected some items according to his preferences and asks for opinions about these by others, in order to achieve the best selection. Our experimentation provides significant evidence on the recommendation efficiency of the adapted hybrid approach which outperforms pure content-based and pure collaborative techniques.
Mode Conversion Caused by Surface Imperfections of a Dielectric Slab Waveguide (1969)

This paper contains a perturbation theory which is applicable to the scattering losses suffered by guided modes of a dielectric slab waveguide as a consequence of imperfections of the waveguide wall. The development of the theory occupies the bulk of the paper. Numerical results appear in Sections VI and VIII to which a reader less interested in the theory is referred. The theory allows us to conclude that random deviations of the waveguide wall in the order of 1 percent, for guides designed to guide an optical wave of Λ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</inf> = 1μ wavelength, can cause scattering losses of 10 percent per centimeter or 0.46 dB per centimeter. A systematic sinusoidal deviation of the waveguide wall can cause total exchange of energy from the lowest order to the first order guided mode in a distance of approximately 1 cm if the amplitude of the sinusoidal deviation from perfect straightness is only 0.5 percent of the thickness of the guide. An rms deviation of one of the waveguide walls of 9Å causes a radiation loss of 10 dB per kilometer (index difference 1 percent, guide width 2.5μ).
Genetic mapping of the Escherichia coli leader (signal) peptidase gene (lep): a new approach for determining the map position of a cloned gene (1983)

The gene for leader peptidase, termed lep, was mapped to the region between purI and nadB at min 54 to 55 on the Escherichia coli chromosome. Mapping involved (i) cloning the gene into the plasmid pBR322, (ii) transforming the plasmid into a polA strain where it cannot replicate autonomously, (iii) selecting by ampicillin resistance the rare cell in which the plasmid had recombined into the chromosome, and (iv) mapping the chromosomal site of drug resistance (and thus plasmid integration) by Hfr matings and P1 transduction. The map position was confirmed by an assay of the enzyme content of cells bearing an F' factor which covered that region of the chromosome.
Using the Principles of ORGANIC CHEMISTRY to Explore CELL BIOLOGY (1992)

RETURN TO ISSUEPREVNewsNEXTUsing the Principles of ORGANIC CHEMISTRY to Explore CELL BIOLOGYSTUART L. SCHREIBERView Author Information Harvard UniversityCite this: Chem. Eng. News 1992, 70, 43, 22–32Publication Date (Print):October 26, 1992Publication History Published online10 November 2010Published inissue 26 October 1992https://pubs.acs.org/doi/10.1021/cen-v070n043.p022https://doi.org/10.1021/cen-v070n043.p022newsACS PublicationsCopyright © 1992 American Chemical SocietyArticle Views66Altmetric-Citations30LEARN 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 options SUBJECTS:Biology,Cells Get e-Alerts
Unified Synthesis of C1–C19 Building Blocks of Halichondrins via Selective Activation/Coupling of Polyhalogenated Nucleophiles in (Ni)/Cr-Mediated Reactions (2015)

A unified synthesis of the C1-C19 building blocks 8-10 of halichondrins A-C was developed from the common synthetic intermediates 26a,b. Acetylenic ketones 26a,b were in turn synthesized via selective activation/coupling of polyhalogenated nucleophiles 23a,b with aldehyde 11 in a (Ni)/Cr-mediated coupling reaction. Compared with Ni/Cr-mediated couplings of vinyl iodides and aldehydes, this (Ni)/Cr-mediated coupling exhibited two unique features. First, the coupling was found to proceed with a trace amount or no added Ni-catalyst. Second, TES-Cl, a dissociating agent to regenerate the Cr-catalyst, was found to give a better yield than Zr(Cp)2Cl2. An adjustment of the oxidation state was required to transform acetylenic ketones 26a,b into C1-C19 building blocks 8 and 9 of halichondrins A and B, respectively. In the halichondrin B series, a hydroxyl-directed (Me)4NBH(OAc)3 reduction of E- and Z-β-alkoxy-enones 30 was found cleanly to achieve the required transformation, whereas a DMDO oxidation of E-vinylogous ester 27 allowed to introduce the C13 hydroxyl group with a high stereoselectivity in the halichondrin A series. In the halichondrin C series, Hf(OTf)4 was used to convert the double oxy-Michael product 28 into C1-C19 building block 10.