gebhart/patrepeval huggingface dataset:
Cold Induction of Arabidopsis <i>CBF</i> Genes Involves Multiple ICE (Inducer of <i>CBF</i> Expression) Promoter Elements and a Cold-Regulatory Circuit That Is Desensitized by Low Temperature (2003)

The Arabidopsis CBF1, 2, and 3 genes (also known as DREB1b, c, and a, respectively) encode transcriptional activators that have a central role in cold tolerance. CBF1-3 are rapidly induced upon exposing plants to low temperature, followed by expression of CBF-targeted genes, the CBF regulon, resulting in an increase in plant freezing tolerance. At present, little is known about the cold-sensing mechanism that controls CBF expression. Results presented here indicate that this mechanism does not require a cold shock to bring about the accumulation of CBF transcripts, but instead, absolute temperature is monitored with a greater degree of input, i.e. lower temperature, resulting in a greater output, i.e. higher levels of CBF transcripts. Temperature-shift experiments also indicate that the cold-sensing mechanism becomes desensitized to a given low temperature, such as 4 degrees C, and that resensitization to that temperature requires between 8 and 24 h at warm temperature. Gene fusion experiments identified a 125-bp section of the CBF2 promoter that is sufficient to impart cold-responsive gene expression. Mutational analysis of this cold-responsive region identified two promoter segments that work in concert to impart robust cold-regulated gene expression. These sequences, designated ICEr1 and ICEr2 (induction of CBF expression region 1 or 2), were also shown to stimulate transcription in response to mechanical agitation and the protein synthesis inhibitor, cycloheximide.
Role of Chemical Composition in the Enhanced Catalytic Activity of Pt-Based Alloyed Ultrathin Nanowires for the Hydrogen Oxidation Reaction under Alkaline Conditions (2016)

With the increased interest in the development of hydrogen fuel cells as a plausible alternative to internal combustion engines, recent work has focused on creating alkaline fuel cells (AFC), which employ an alkaline environment. Working in alkaline as opposed to acidic media yields a number of tangible benefits, including (i) the ability to use cheaper and plentiful precious-metal-free catalysts, due to their increased stability, (ii) a reduction in the amount of degradation and corrosion of Pt-based catalysts, and (iii) a longer operational lifetime for the overall fuel cell configuration. However, in the absence of Pt, no catalyst has achieved activities similar to those of Pt. Herein, we have synthesized a number of crystalline ultrathin PtM alloy nanowires (NWs) (M = Fe, Co, Ru, Cu, Au) in order to replace a portion of the costly Pt metal without compromising on activity while simultaneously adding in metals known to exhibit favorable synergistic ligand and strain effects with respect to the host lattice. In fact, our experiments confirm theoretical insights about a clear and correlative dependence between measured activity and chemical composition. We have conclusively demonstrated that our as-synthesized alloy NW catalysts yield improved hydrogen oxidation reaction (HOR) activities as compared with a commercial Pt standard as well as with our as-synthesized Pt NWs. The Pt<sub>7</sub>Ru<sub>3</sub> NW system, in particular, quantitatively achieved an exchange current density of 0.493 mA/cm<sup>2</sup>, which is higher than the corresponding data for Pt NWs alone. In addition, the HOR activities follow the same expected trend as their calculated hydrogen binding energy (HBE) values, thereby confirming the critical importance and correlation of HBE with the observed activities.
What can readability measures really tell us about text complexity (2012)

This study presents the results of an initial phase of a project seeking to convert texts into a more accessible form for people with autism spectrum disorders by means of text simplification technologies. Random samples of Simple Wikipedia articles are compared with texts from News, Health, and Fiction genres using four standard readability indices (Kincaid, Flesch, Fog and SMOG) and sixteen linguistically motivated features. The comparison of readability indices across the four genres indicated that the Fiction genre was relatively easy whereas the News genre was relatively difficult to read. The correlation of four readability indices was measured, revealing that they are almost perfectly linearly correlated and that this correlation is not genre dependent. The correlation of the sixteen linguistic features to the readability indices was also measured. The results of these experiments indicate that some of the linguistic features are well correlated with the readability measures and that these correlations are genre dependent. The maximum correlation was observed for fiction.
CA-BINDING GLYCOPROTEINS IN MOLLUSCAN SHELLS WITH DIFFERENT TYPES OF ULTRASTRUCTURE (1990)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Managing financial risk in planning under uncertainty (2004)

Abstract A methodology is presented to include financial risk management in the framework of two‐stage stochastic programming for planning under uncertainty. A known probabilistic definition of financial risk is adapted to be used in this framework and its relation to downside risk is analyzed. Using these definitions, new two‐stage stochastic programming models that manage financial risk are presented. Computational issues related to these models are also discussed. © 2004 American Institute of Chemical Engineers AIChE J , 50: 963–989, 2004
Processing queries on tree-structured data efficiently (2006)

This is a survey of algorithms, complexity results, and general solution techniques for efficiently processing queries on tree-structured data. I focus on query languages that compute nodes or tuples of nodes—conjunctive queries, first-order queries, datalog, and XPath. I also point out a number of connections among previous results that have not been observed before.
An evolutionary and structural perspective on T cell antigen receptor function (2003)

After a brief overview of the themes and variations that occur in the family of receptors containing immunoreceptor tyrosine-based activation motifs (ITAMs), and of recent structural data on the ligand-binding subunits of these receptors, we use these data to revisit how information on the state and quality of occupancy of the binding site of the T cell antigen receptor (TCR) is conveyed to the proximal components of the TCR transduction cassette.
Tripodal peptides with chiral conformations stabilized by interstrand hydrogen bonds (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTripodal peptides with chiral conformations stabilized by interstrand hydrogen bondsYitzhak Tor, Jacqueline Libman, Abraham Shanzer, Clifford E. Felder, and Shneior LifsonCite this: J. Am. Chem. Soc. 1992, 114, 17, 6653–6661Publication Date (Print):August 1, 1992Publication History Published online1 May 2002Published inissue 1 August 1992https://pubs.acs.org/doi/10.1021/ja00043a007https://doi.org/10.1021/ja00043a007research-articleACS PublicationsRequest reuse permissionsArticle Views311Altmetric-Citations25LEARN 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
New<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>C</mml:mi><mml:mi>P</mml:mi></mml:math>-Violation and Preferred-Frame Tests with Polarized Electrons (2006)

We used a torsion pendulum containing approximately 9 x 10(22) polarized electrons to search for CP-violating interactions between the pendulum's electrons and unpolarized matter in the laboratory's surroundings or the Sun, and to test for preferred-frame effects that would precess the electrons about a direction fixed in inertial space. We find, /g(P)(e)g(S)(N)//(Planck's constant x c) < 1.7 x 10(-36), and /g(A)(e)g(V)(N)//(Planck's constant x c) < 4.8 x 10(-56) for lambda > 1 AU. Our preferred-frame constraints, interpreted in the Kostelecký framework, set an upper limit on the parameter /b(e)/ <or= 5.0 x 10(-21) eV that should be compared to the benchmark value m(e)(2)/M(Planck)= 2 x 10(-17) eV.
Practical Strategies for Performance Optimization of the Enhanced Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (2004)

The enhanced Gen-Probe Amplified Mycobacterium Tuberculosis Direct (MTD) test was evaluated using a combined set of 338 acid-fast smear-positive and smear-negative, respiratory and nonrespiratory clinical specimens received by the Massachusetts State Tuberculosis Laboratory from September 1999 through March 2002. Microbiological culture was used as the reference method; therefore, the sensitivity and specificity of the MTD test were calculated for culture-positive specimens only. The initial assessment indicated that the overall sensitivity, specificity, and positive and negative predictive values of the MTD test for all specimens grouped together were 62, 98, 99, and 68%, respectively. A detailed discrepancy analysis revealed that two major factors causing negative MTD results in specimens that were culture positive for M. tuberculosis complex were patient treatment with antituberculosis drugs prior to testing and the presence of inhibitory substances in the specimen. Based on these findings, a protocol for optimizing MTD test performance in this setting is proposed in which (i) specimens from patients taking antituberculosis medications are excluded from testing and (ii) all initially MTD-negative or MTD-equivocal specimens are subjected to testing for inhibitors. If this strategy was followed, the MTD test sensitivity would be at least 91%, a significant improvement over the initial sensitivity of 62%. Accordingly, the negative predictive value would increase from 68 to 91%.
The proto-oncogene product p120CBL and the adaptor proteins CRKL and c-CRK link c-ABL, p190BCR/ABL and p210BCR/ABL to the phosphatidylinositol-3' kinase pathway. (1996)

Chronic myelogenous leukemia (CML) and some acute lymphoblastic leukemias (ALL) are caused by the t(9;22) chromosome translocation, which produces the constitutively activated BCR/ABL tyrosine kinase. When introduced into factor dependent hematopoietic cell lines, BCR/ABL induces the tyrosine phosphorylation of many cellular proteins. One prominent BCR/ABL substrate is p120CBL, the cellular homolog of the v-Cbl oncoprotein. In an effort to understand the possible contribution of p120CBL to transformation by BCR/ABL, we looked for cellular proteins which associate with p120CBL in hematopoietic cell lines transformed by BCR/ABL. In addition to p210BCR/ABL and c-ABL, p120CBL coprecipitated with an 85 kDa phosphoprotein, which was identified as the p85 subunit of PI3K. Anti-p120CBL immunoprecipitates from BCR/ABL-transformed, but not from untransformed, cell lines contained PI3K lipid kinase activity. Interestingly, the adaptor proteins CRKL and c-CRK were also found in these complexes. In vitro binding studies indicated that the SH2 domains of CRKL and c-CRK bound directly to p120CBL, while the SH3 domains of c-CRK and CRKL bound to BCR/ABL and c-ABL. The N-terminal and the C-terminal SH2 and the SH3 domain of p85PI3K bound directly in vitro to p120CBL. The ABL-SH2, but not ABL-SH3, could also bind to p120CBL. These data suggest that BCR/ABL may induce the formation of multimeric complexes of signaling proteins which include p120CBL, PI3K, c-CRK or CRKL, c-ABL and BCR/ABL itself.
Structural and functional relationships of enzyme activities induced by nitrate in barley (1970)

1. Nitrate induces the development of NADH-nitrate reductase (EC 1.6.6.1), FMNH(2)-nitrate reductase and NADH-cytochrome c reductase activities in barley shoots. 2. Sucrose-density-gradient analysis shows one band of NADH-nitrate reductase (8S), one band of FMNH(2)-nitrate reductase activity (8S) and three bands of NADH-cytochrome c reductase activity (bottom layer, 8S and 3.7S). Both 8S and 3.7S NADH-cytochrome c reductase activities are inducible by nitrate, but the induction of the 8S band is much more marked. 3. The 8S NADH-cytochrome c reductase band co-sediments with both NADH-nitrate reductase activity and FMNH(2)-nitrate reductase activity. Nitrite reductase activity (4.6S) did not coincide with the activity of either the 8S or the 3.7S NADH-cytochrome c reductase. 4. FMNH(2)-nitrate reductase activity is more stable (t((1/2)) 12.5min) than either NADH-nitrate reductase activity (t((1/2)) 0.5min) or total NADH-cytochrome c reductase activity (t((1/2)) 1.5min) at 45 degrees C. 5. NADH-cytochrome c reductase and NADH-nitrate reductase activities are more sensitive to p-chloromercuribenzoate than is FMNH(2)-nitrate reductase activity. 6. Tungstate prevents the formation of NADH-nitrate reductase and FMNH(2)-nitrate reductase activities, but it causes superinduction of NADH-cytochrome c reductase activity. Molybdate overcomes the effects of tungstate. 7. The same three bands (bottom layer, 8S and 3.7S) of NADH-cytochrome c reductase activity are observed irrespective of whether induction is carried out in the presence or absence of tungstate, but only the activities in the 8S and 3.7S bands are increased. 8. The results support the idea that NADH-nitrate reductase, FMNH(2)-nitrate reductase and NADH-cytochrome c reductase are activities of the same enzyme complex, and that in the presence of tungstate the 8S enzyme complex is formed but is functional only with respect to NADH-cytochrome c reductase activity.
A Cobalt-Catalyzed Entry Into the Ergot Alkaloids: Total Syntheses of (±)-Lysergene and (±)-LSD (1994)

Cocyclization of 4-ethynyl-3-indoleacetonitriles with alkynes in the presence of CpCo(CO)2 gives rise to the ergoline derivatives 6-9, two of which were transformed into racemic lysergene and LSD, respectively.
TEM Pseudoelliptic-Function Bandstop Filters Using Noncommensurate Lines (1976)

A synthesis procedure for distributed bandstop filters that approximate an elliptic-function response is described. Existing tables of lumped constant elliptic-function filters are used together with an approximate transform that exchanges commensurate Foster sections for noncommensurate pairs of stubs or coupled lines. The method is usable for all bandwidths up to about 100 percent, providing that networks with a relative bandwidth of more than 50 percent are considered to be pseudo-low-pass.
Frequent Phosphodiesterase 11A Gene (<i>PDE11A</i>) Defects in Patients with Carney Complex (CNC) Caused by<i>PRKAR1A</i>Mutations:<i>PDE11A</i>May Contribute to Adrenal and Testicular Tumors in CNC as a Modifier of the Phenotype (2010)

We demonstrate, in a large cohort of CNC patients, a high frequency of PDE11A variants, suggesting that PDE11A is a genetic modifying factor for the development of testicular and adrenal tumors in patients with germline PRKAR1A mutation.
Kinetics of the hydrolysis of ethyl acetate catalysed by cation‐exchange resin (1978)

Abstract The mechanism of the hydrolysis of ethyl acetate, catalysed by Dowex 50 W resins, was studied using a batch reactor. The effects of resin cross‐linkage and initial reactant ratio on the conversion were investigated. At the high stirring speed used, the film diffusional resistance was found to be insignificant. The results were analysed using the Langmuir‐Hinshelwood models. It was found that the irreversible surface reaction between ethyl acetate and water in the adsorbed state (dual site mechanism) was the most plausible rate‐controlling step. The rate data were best denoted by the model: where a 1 denotes the activity of the species i.
Autoencoding Variational Inference For Topic Models (2017)

Topic models are one of the most popular methods for learning representations of text, but a major challenge is that any change to the topic model requires mathematically deriving a new inference algorithm. A promising approach to address this problem is autoencoding variational Bayes (AEVB), but it has proven diffi- cult to apply to topic models in practice. We present what is to our knowledge the first effective AEVB based inference method for latent Dirichlet allocation (LDA), which we call Autoencoded Variational Inference For Topic Model (AVITM). This model tackles the problems caused for AEVB by the Dirichlet prior and by component collapsing. We find that AVITM matches traditional methods in accuracy with much better inference time. Indeed, because of the inference network, we find that it is unnecessary to pay the computational cost of running variational optimization on test data. Because AVITM is black box, it is readily applied to new topic models. As a dramatic illustration of this, we present a new topic model called ProdLDA, that replaces the mixture model in LDA with a product of experts. By changing only one line of code from LDA, we find that ProdLDA yields much more interpretable topics, even if LDA is trained via collapsed Gibbs sampling.
Circular Electric Wave Transmission Through Serpentine Bends (1957)

An otherwise straight waveguide line with equally spaced discrete supports may deform elastically into a serpentine bend under its own weight. The TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</inf> wave couples in such bends to the TM <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</inf> and TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1n</inf> waves. The general solution of coupled lines with varying coupling coefficient is applied to a serpentine bend by an iterative process, and evaluated for the elastic curve resulting from a periodically supported line. TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</inf> -TM <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</inf> coupling causes only a small increase in TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</inf> attenuation. Mode conversion to TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1n</inf> waves can become seriously high at certain critical frequencies when the supporting distance is a multiple of the beat wavelength. In a copper pipe of 2⅜ inch O.D. and 2 inch I.D., the mode conversion to the TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</inf> wave at critical frequencies near 5-mm wavelength causes a TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</inf> attenuation increase of 90 per cent and a spurious mode level of −7 db. These mode conversion effects can be controlled effectively by inserting mode filters.
Spatial distribution of intermodulation products in active phased array antennas (1973)

In an active phased array (i.e., an array that has amplifiers in each element) transmitting multiple beams, the intermodulation products generated by the amplifier amplitude nonlinearities form beams that, in general, radiate in directions different from the principal beam directions. In effect, the phased array antenna spatially filters the intermodulation products formed by signals from different beams. In a communications application this effect can be used to reduce the signal-to-intermodulation interference ratio. A description of this phenomenon is given and examples are presented that illustrate the mainbeam directions of beams formed by third- and fifth-order intermodulation products. An experiment that was performed to demonstrate this effect is described. The spatial filtering effect for beams with amplitude modulated signals is also treated, with an improvement in carrier-to-intermodulation ratio theoretically demonstrated.
Selective inhibition of activin receptor–like kinase 5 signaling blocks profibrotic transforming growth factor β responses in skin fibroblasts (2004)

The results indicate that SB431542 is a potent inhibitor of intracellular TGFbeta signaling in normal fibroblasts through selective interference with ALK-5-mediated Smad activation and Smad-dependent transcriptional responses. Therefore, SB431542 is useful as a novel experimental tool for gaining a detailed understanding of normal and aberrant TGFbeta signaling in SSc. Furthermore, as an anti-TGFbeta agent, SB431542 may represent a potential new approach to the treatment of fibrosis.
Fast replanning for navigation in unknown terrain (2005)

Mobile robots often operate in domains that are only incompletely known, for example, when they have to move from given start coordinates to given goal coordinates in unknown terrain. In this case, they need to be able to replan quickly as their knowledge of the terrain changes. Stentz' Focussed Dynamic A/sup */ (D/sup */) is a heuristic search method that repeatedly determines a shortest path from the current robot coordinates to the goal coordinates while the robot moves along the path. It is able to replan faster than planning from scratch since it modifies its previous search results locally. Consequently, it has been extensively used in mobile robotics. In this article, we introduce an alternative to D/sup */ that determines the same paths and thus moves the robot in the same way but is algorithmically different. D/sup */ Lite is simple, can be rigorously analyzed, extendible in multiple ways, and is at least as efficient as D/sup */. We believe that our results will make D/sup */-like replanning methods even more popular and enable robotics researchers to adapt them to additional applications.
The influence of specimen refractive index, detector signal integration, and non‐uniform scan speed on the imaging properties in confocal microscopy (1991)

SUMMARY Refraction of light in a specimen volume may cause aberrations that influence the imaging properties in confocal microscopy. In this paper the influence on three‐dimensional resolution and geometry is experimentally investigated for a uniform specimen volume. It is found that the depth resolution is more severely affected than the lateral resolution. This is unfortunate, because even under ideal conditions the depth resolution is lower than the lateral resolution. Lateral image geometry is little affected by the specimen refractive index, whereas the depth scale can be considerably elongated or compressed. The influence of a finite detector integration time is also considered. This can give a noticeable, but not particularly severe effect on the image resolution in the line‐scan direction. Because the integration time can be accurately controlled, a shorter integration time can be used when maximum resolution is essential, albeit at the price of a higher noise level. In scanning fluorescence microscopy a non‐uniform scan speed may give large variations in bleaching over the specimen surface. Experiments illustrate how serious such non‐uniform bleaching effects can be when a specimen area is repeatedly scanned, for example when recording optical serial sections.