gebhart/patrepeval huggingface dataset:
Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. (1987)

To analyze the specificity of RNA processing reactions, we constructed hybrid genes containing RNA polymerase III promoters fused to sequences that are normally transcribed by polymerase II and assessed their transcripts following transfection into human 293 cells. Transcripts derived from these chimeric constructs were analyzed by using a combined RNase H and S1 nuclease assay to test whether RNAs containing consensus 5' and 3' splicing signals could be efficiently spliced in intact cells, even though they were transcribed by RNA polymerase III. We found that polymerase III-derived RNAs are not substrates for splicing. Similarly, we were not able to detect poly(A)+ RNAs derived from genes that contained a polymerase III promoter linked to sequences that were necessary and sufficient to direct 3'-end cleavage and polyadenylation when transcribed by RNA polymerase II. Our findings are consistent with the view that in vivo splicing and polyadenylation pathways are obligatorily coupled to transcription by RNA polymerase II.
The Nucleoside Triphosphatase and Helicase Activities of Vaccinia Virus NPH-II Are Essential for Virus Replication (1998)

Vaccinia virus NPH-II is the prototypal RNA helicase of the DExH box protein family, which is defined by six shared sequence motifs. The contributions of conserved amino acids in motifs I (TGVGKTSQ), Ia (PRI), II (DExHE), and III (TAT) to enzyme activity were assessed by alanine scanning. NPH-II-Ala proteins were expressed in baculovirus-infected Sf9 cells, purified, and characterized with respect to their RNA helicase, nucleic acid-dependent ATPase, and RNA binding functions. Alanine substitutions at Lys-191 and Thr-192 (motif I), Arg-229 (motif Ia), and Glu-300 (motif II) caused severe defects in RNA unwinding that correlated with reduced rates of ATP hydrolysis. In contrast, alanine mutations at His-299 (motif II) and at Thr-326 and Thr-328 (motif III) elicited defects in RNA unwinding but spared the ATPase. None of the mutations analyzed affected the binding of NPH-II to RNA. These findings, together with previous mutational studies, indicate that NPH-II motifs I, Ia, II, and VI (QRxGRxGRxxxG) are essential for nucleoside triphosphate (NTP) hydrolysis, whereas motif III and the His moiety of the DExH-box serve to couple the NTPase and helicase activities. Wild-type and mutant NPH-II-Ala genes were tested for the ability to rescue temperature-sensitive nph2-ts viruses. NPH-II mutations that inactivated the phosphohydrolase in vitro were lethal in vivo, as judged by the failure to recover rescued viruses containing the Ala substitution. The NTPase activity was necessary, but not sufficient, to sustain virus replication, insofar as mutants for which NTPase was uncoupled from unwinding (H299A, T326A, and T328A) were also lethal. We conclude that the phosphohydrolase and helicase activities of NPH-II are essential for virus replication.
New technique for high-resolution absolute conductivity imaging using magnetic-resonance electrical impedance tomography (MR-EIT) (2001)

A novel MR-EIT imaging modality has been developed to reconstruct high-resolution conductivity images with true conductivity value. In this new technique, electrical impedance tomography (EIT) and magnetic resonance imaging (MRI) techniques are simultaneously used. Peripheral voltages are measured using EIT and magnetic flux density measurements are determined using MRI. The image reconstruction algorithm used is an iterative one, based on minimizing the difference between two current density distributions calculated from voltage and magnetic flux density measurements separately. The performance of the proposed method and the suggested reconstruction algorithm are tested on simulated data. A finite element model with 1089 nodes and 2048 triangular elements is used to generate the simulated potential and magnetic field measurements. A 16 electrode opposite drive EIT strategy is adopted. The spatial resolution is space independent and limited by either the finite element size or half the MR resolution. The worst of the two defines the spatial resolution. The rms error in reconstructed conductivity for a concentric inhomogeneity is calculated as 5.35% and this error increases to 13.22% when 10% uniformly distributed random noise is added to potential and magnetic flux density measurements. The performance of the algorithm for more complex models will also be presented.
Association of tumor necrosis factor microsatellite polymorphisms with HLA‐DRB1*04–bearing haplotypes in rheumatoid arthritis patients (1996)

TNF microsatellites found to be associated with RA do not appear to be independent of class II HLA associations.
Quantitative patterns of stylistic influence in the evolution of literature (2012)

Literature is a form of expression whose temporal structure, both in content and style, provides a historical record of the evolution of culture. In this work we take on a quantitative analysis of literary style and conduct the first large-scale temporal stylometric study of literature by using the vast holdings in the Project Gutenberg Digital Library corpus. We find temporal stylistic localization among authors through the analysis of the similarity structure in feature vectors derived from content-free word usage, nonhomogeneous decay rates of stylistic influence, and an accelerating rate of decay of influence among modern authors. Within a given time period we also find evidence for stylistic coherence with a given literary topic, such that writers in different fields adopt different literary styles. This study gives quantitative support to the notion of a literary "style of a time" with a strong trend toward increasingly contemporaneous stylistic influence.
Application of hierarchical neural-network-based control to transient stabilization of interconnected power systems (2002)

Flexible AC Transmission Systems (FACTS) research is aimed at increasing transmission capabilities of existing power systems. FACTS devices provide means to dynamically control parameters of the transmission lines. In particular thyristor-controlled series capacitors have been proposed to increase inter-area transient stability margins. Design of a suitable control algorithm for adjusting capacitor compensation level is a challenging task. The power system dynamics, particularly during transients caused by severe faults, are highly nonlinear. A series capacitor affects the system dynamics in nonlinear fashion, further increasing the difficulty of applying traditional linear control. There is also an inherent system uncertainty due to fluctuations of operating conditions and to sudden structural changes caused by faults. A successful controller should be robust with respect to these uncertainties and must accommodate the nonlinear dynamics of the system. The above issues are addressed here using neural-network methodology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Anchoring discussions in lecture (1999)

Collaborative environments typically provide a medium for realizing or capturing discussion. While valuable, the discussion is often decontextualized from the situation in which it makes sense. Anchored collaboration environments provide a mechanism for connecting collaboration to digital media content, such as Web-based syllabi and assignment descriptions. The most significant learning context in most classes is still the face-to-face whole class lecture or discussion. The Classroom 2000 project at Georgia Tech is capturing classroom experiences in multiple media: audio, video, presenter's slides, presenter's whiteboard markings, and students' notes. By connecting the Classroom 2000 captured lectures to a persistent collaboration space, we provide (a) a mechanism for asynchronous collaboration that is anchored in class contexts and (b) a means for treating class activity as persistent learning medium for later comment and collaborative extension. This paper describes a pilot study to create a collaborative discussion space anchored in captured classroom lectures.
Full-wavefield inversion for acoustic wave velocity and attenuation (2013)

Recovering viscoacoustic parameters from seismic data has the potential to improve our knowledge of subsurface physical properties such as fluid saturation and can lead to better reservoir characterization. Simultaneously reconstructing attenuation and wave velocity parameters has already been pursued in frequency-domain full-wavefield inversion methods where complex-valued velocities can direclty account for attenuation effects in the wave equation. In this work, we discuss a timedomain full-wavefield inversion method for simultaneously recovering seismic wave velocities and Q-factors by minimizing a regularized L1 norm of the misfit between measured and simulated wavefields.
Stroke identification system on the mobile based CT scan image (2015)

A stroke occurs if the flow of oxygen-rich blood to a portion of the brain is blocked. Without oxygen, brain cells start to die after a few minutes. Sudden bleeding in the brain also can cause a stroke if it damages brain cells. Stroke is a harmful disease in which most of the cases of this disease bring an effect of the physical defect on patients. One of the methods of examining this disease is by means of head CT scan. However, there is a weakness of head CT scan for consisting of some unclear or invisible parts. Hence, it needs a technique for improving the image quality to again emerge the invisible parts. Adaptive histogram equalization (AHE) is a technique that can cope with the weakness of HE by enhancing the contrast in local area. The contrast enhancement, however, can be excessive sometimes. Using the contrast limited adaptive histogram equalization (CLAHE), the excessive contrast enhancement in AHE can be coped with by giving the limit value on histogram. In this research, a stroke identification system has been built comprising image enhancement with CLAHE, feature extraction statistically with the mean value, deviation standard, skewness, kurtosis, and segmentation using the statistical region merging method. The result then showed that the method of image processing significantly conducted was able to be used as a tool to identify the stroke disease in order to distinguish the type of CT scan to the normal or sick state.
Cell-specific Expression and Regulation of a Glucokinase Gene Locus Transgene (1997)

Transgenic mice containing one or more extra copies of the entire glucokinase (GK) gene locus were generated and characterized. The GK transgene, an 83-kilobase pair mouse genomic DNA fragment containing both promoter regions, was expressed and regulated in a cell-specific manner, and rescued GK null lethality when crossed into mice bearing a targeted mutation of the endogenous GK gene. Livers from the transgenic mice had elevated GK mRNA, protein, and activity levels, compared with controls, and the transgene was regulated in liver by dietary manipulations. The amount of GK immunoreactivity in hepatocyte nuclei, where GK binds to the GK regulatory protein, was also increased. Pancreatic islets displayed increased GK immunoreactivity and NAD(P)H responses to glucose, but only when isolated and cultured in 20 mM glucose, as a result of the hypoglycemic phenotype of these mice (Niswender, K. D., Shiota, M., Postic, C., Cherrington, A. D., and Magnuson, M. A. (1997) J. Biol. Chem. 272, 22604-22609). Together, these results indicate that the region of the gene from -55 to +28 kilobase pairs (relative to the liver GK transcription start site) contains all the regulatory sequences necessary for expression of both GK isoforms, thereby placing an upper limit on the size of the GK gene locus.
A homeobox gene, <i>PRESSED FLOWER</i> , regulates lateral axis-dependent development of <i>Arabidopsis</i> flowers (2001)

It is postulated that the symmetric organization of plant lateral organs is based on two crossed axes, the abaxial-adaxial and the lateral axes. The PRESSED FLOWER (PRS) gene, the expression and function of which are dependent on the lateral axis, is reported in this study. In the prs mutant, growth of the lateral sepals is repressed, and although the size and shape of the abaxial and adaxial sepals are normal, the cell files at the lateral margins are missing. Double-mutant analyses showed that the PRS gene functions independently of the determinations of both floral organ identity and floral meristem size. The PRS gene, encoding a putative transcriptional factor with a homeodomain, was shown to be required for cell proliferation. PRS gene expression is spatially and temporally unique and is expressed in a restricted number of L1 cells at the lateral regions of flower primordia, floral organ primordia, and young leaf primordia. Our study strongly suggests that the PRS gene is involved in the molecular mechanism of lateral axis-dependent development of lateral organs in Arabidopsis.
Role of the pineal gland in immunity. III. Melatonin antagonizes the immunosuppressive effect of acute stress via an opiatergic mechanism. (1988)

We have recently demonstrated that the pineal neurohormone melatonin exerts important immunoregulatory functions. We now report that exogenous melatonin counteracts completely the effect of acute anxiety-restraint stress on thymus weight and antibody response to sheep red blood cells (SRBC). In addition, administration of melatonin in the evening prevented paralysis and death of mice infected with sublethal doses of encephalomyocarditis virus (EMCV) after acute stress. The anti-stress activity of melatonin was present in mice injected with T-dependent antigens, and it was abolished by the contemporary administration of the specific opioid-antagonist naltrexone. This suggests that melatonin exerts its remarkable anti-stress effect on antigen-activated cells via an opiatergic mechanism. These findings have important implications at both basic and clinical levels. They provide a new approach to a possible physiological 'up-regulation' of the immune response under virus- and/or stress-related immunosuppression.
ChemInform Abstract: RESEARCH ON ACYL GROUP CARRIERS. XIII. NEW METHOD OF SYNTHESIS OF D‐(+)‐S‐SULFOPANTETHEINE AND ITS CONVERSION TO COENZYME FORMS OF VITAMIN B3 IN ANIMALS (1979)

Abstract Gibt man zu einer methanolischen Lösung von Ethylenimin (I) und Natriumthiosulfat (II) tropfenweise Salzsäure, so erhält man nach 7‐stündigem Kochen das S‐Sulfo‐cysteamin (III).
Single-particle measurements of electrochemical kinetics in NMC and NCA cathodes for Li-ion batteries (2018)

Electrochemical kinetics of Li-ion battery cathodes are measured at single-particle level and combined with transmission X-ray microscopy to elucidate behavior during use.
Deletion of the Heptosyltransferase Genes <i>rfaC</i> and <i>rfaF</i> in <i>Escherichia Coli</i> K‐12 Results in an Re‐Type Lipopolysaccharide with a High Degree of 2‐Aminoethanol Phosphate Substitution (1997)

The chromosomal genes rfaC and rfaF of Escherichia coli W3110 were inactivated by allelic-replacement mutagenesis to generate a defined strain lacking both heptosyltransferases which catalyze in lipopolysaccharide (LPS) biosynthesis the transfer of the first two L-glycero-D-manno-heptose (Hep) residues to 3-deoxy-D-manno-2-octulosonic acid (Kdo). The LPS of the mutant was isolated and its chemical structure was investigated by compositional analysis and nuclear magnetic resonance spectroscopy of isolated, deacylated oligosaccharide phosphates. The basic structure was a tetrasaccharide alpha-Kdo-(2-->4)-alpha-Kdo-(2-->6)-beta-D-GlcN4P-(1-->6)-alpha-D- GlcN1P which in LPS was substituted at position 07 of Kdo II by 2-aminoethanol phosphate in non-stoichiometric amounts. 2-Aminoethanol was cleaved during deacylation of the LPS by successive hydrazinolysis and KOH treatment and, in addition, phosphate migration from 07 to 08 of Kdo II occurred. Thus, the oligosaccharides alpha-Kdo7P-(2-->4)-alpha-Kdo-(2-->6)-beta-D-GlcN4P-(1-->6)- alpha-D-GlcN1P and alpha-Kdo8P-(2-->4)-alpha-Kdo-(2-->6)-beta-D-GlcN4P-(1-->6)- alpha-D-GlcN1P could be isolated. KOH treatment of the two trisphosphates and authentic methyl 3-deoxy-D-manno-octulopyranoside 7-(2-acetamidoethyl phosphate) proved that phosphate migration only took place when the phosphate group was substituted with 2-aminoethanol. Complementation studies with plasmid-encoded rfaC and rfaF genes revealed that the mutant strain can be used in combination with LPS-specific antibodies for the cloning and characterization of heptosytransferases which glycosylate Kdo residues of the inner core region of LPS.
Combined Neuroprotection by Xenon and Dexmedetomidine in vitro (2004)

s: 32nd Annual Meeting of the Society of Neurosurgical Anesthesia and Critical Care, Las Vegas, Nevada, October 22, 2004: CEREBRAL PROTECTION/PHARMACOLOGY
Polymer transistors fabricated by painting of metallic nanoparticles (2006)

In this letter the authors describe the fabrication of high performance polymer thin film transistors using an aqueous based silver colloid to form source and drain electrodes patterned by brush painting. The electrode dimensions were controlled by a surface energy pattern defined by soft contact printing of a self-assembled monolayer 1H,1H,2H,2H-perfluorodecyl-trichlorosilane on a SiO2 surface which acted as a dewetting layer for the painted silver particle suspension. Another self-assembled monolayer of 1H,1H,2H,2H-perfluorodecanethiol was also used to increase the work function of the patterned silver electrodes in order to decrease the barrier for charge injection into the polymer semiconductor. The field-effect mobility of the thin film transistors fabricated by this method approached 0.02cm2V−1s−1 with an on/off current ratio of 105. The relative high mobility may be influenced by the ordering of the poly(3-hexylthiophene) semiconductor layer by the self-assembled monolayer used to define the source and drain electrodes.
Measurement-Based Evaluation of Vertical Separation MIMO Antennas for Base Station (2012)

It is worth noting that the use of vertical separation antenna configuration provides an easy way to form large separation on a single pole. In this letter, the effect of vertical separation multiple-input-multiple-output (MIMO) antenna configurations for base station is investigated by field drive tests. The results show that vertical separation antenna configurations can meet the requirement of spatial multiplexing and provide good MIMO performance. Furthermore, measurements of MIMO antenna arrays were conducted to evaluate the performance of radiation patterns with interaction between antennas. The results show that vertical separation antenna configurations can reduce or avoid mutual coupling between antennas and improve the performance of antenna radiation patterns.
Allosteric Modulators: The New Generation of Receptor Antagonist (2004)

Allosteric antagonists modulate the affinity and/or efficacy of agonists for receptors. Although the manner in which this modulation can occur can mimic that of simple competitive antagonists, allosteric antagonists possess unique properties that can present seemingly capricious profiles of antagonism. These unique properties also offer potentially useful patterns for therapeutic utility. This review summarizes methods to detect allosteric antagonism and some special properties of these receptor modulators.
Variational Learning in Nonlinear Gaussian Belief Networks (1999)

We view perceptual tasks such as vision and speech recognition as inference problems where the goal is to estimate the posterior distribution over latent variables (e.g., depth in stereo vision) given the sensory input. The recent flurry of research in independent component analysis exemplifies the importance of inferring the continuous-valued latent variables of input data. The latent variables found by this method are linearly related to the input, but perception requires nonlinear inferences such as classification and depth estimation. In this article, we present a unifying framework for stochastic neural networks with nonlinear latent variables. Nonlinear units are obtained by passing the outputs of linear gaussian units through various nonlinearities. We present a general variational method that maximizes a lower bound on the likelihood of a training set and give results on two visual feature extraction problems. We also show how the variational method can be used for pattern classification and compare the performance of these nonlinear networks with other methods on the problem of handwritten digit recognition.
Grain Structure Analysis in Rolled 1050 Al Alloy Sheets Using EBSD (2001)

The effect of cryogenic heavy rolling method on grain refinement has been studied and compared with those obtained by previous methods of cryogenic rolling and heavy rolling developed separately. Both grain structure and grain size were analyzed using electron back scattered diffraction (EBSD), which can distinguish grains each other by means of crystallographic misorientations between them. The cryogenic rolling and heavy rolling exhibit reduction in grain size of 39% and 87%, respectively, and the cryogenic heavy rolling shows reduced grain size similar to that observed in the heavy rolling. The heavy rolling was proved more effective in grain size refinement than the cryogenic rolling.
Shot-based similarity measure for content-based video summarization (2008)

The rapid development of multimedia applications over the past decade requires efficient methods for video browsing. In this paper, we present an algorithm for video summarization with shot comparison. We analyze video content in the shot level, and we calculate the shot distance using the advanced Hausdorff distance. The advanced Hausdorff distance combines the Hausdorff distance and Boolean model, and it could compare two shots from the global view. When the shot similarity matrix is obtained, we group these video shots into several clusters using the affinity propagation cluster method to remove redundant video content. Performance evaluation on ten video sequences are given to illustrate the proposed algorithm.
Metaplasia. An overview. (1984)

Metaplastic changes are common lesions found at widespread locations, occurring in both reactive and neoplastic tissues. Metaplasia has the following characteristics: (1) it can arise not only as a proliferation and transformation of immature (stem) cells, but also as a direct or indirect transformation of mature cells; (2) through metaplasia, a given cell may exhibit epithelial, mesothelial, or mesenchymal characteristics, regardless of the tissue of origin; and (3) its importance lies in that metaplastic changes can often be symptomatic and may simulate tumors clinically, grossly, or histologically.
A Basis for Reduced Chemical Library Inhibition of Firefly Luciferase Obtained from Directed Evolution (2009)

We measured the "druggability" of the ATP-dependent luciferase derived from the firefly Photuris pennsylvanica that was optimized using directed evolution (Ultra-Glo, Promega). Quantitative high-throughput screening (qHTS) was used to determine IC(50)s of 198899 samples against a formulation of Ultra-Glo luciferase (Kinase-Glo). We found that only 0.1% of the Kinase-Glo inhibitors showed an IC(50) < 10 microM compared to 0.9% found from a previous qHTS against the firefly luciferase from Photinus pyralis (lucPpy). Further, the maximum affinity identified in the lucPpy qHTS was 50 nM, while for Kinase-Glo this value increased to 600 nM. Compounds with interactions stretching outside the luciferin binding pocket were largely lost with Ultra-Glo luciferase. Therefore, Ultra-Glo luciferase will show less compound interference when used as an ATP sensor compared to lucPpy. This study demonstrates the power of large-scale quantitative analysis of structure-activity relationships (>100K compounds) in addressing important questions such as a target's druggability.