gebhart/patrepeval huggingface dataset:
Identification of a Novel Inhibitor of Coactivator-associated Arginine Methyltransferase 1 (CARM1)-mediated Methylation of Histone H3 Arg-17 (2009)

Methylation of the arginine residues of histones by methyltransferases has important consequences for chromatin structure and gene regulation; however, the molecular mechanism(s) of methyltransferase regulation is still unclear, as is the biological significance of methylation at particular arginine residues. Here, we report a novel specific inhibitor of coactivator-associated arginine methyltransferase 1 (CARM1; also known as PRMT4) that selectively inhibits methylation at arginine 17 of histone H3 (H3R17). Remarkably, this plant-derived inhibitor, called TBBD (ellagic acid), binds to the substrate (histone) preferentially at the signature motif, "KAPRK," where the proline residue (Pro-16) plays a critical role for interaction and subsequent enzyme inhibition. In a promoter-specific context, inhibition of H3R17 methylation represses expression of p21, a p53-responsive gene, thus implicating a possible role for H3 Arg-17 methylation in tumor suppressor function. These data establish TBBD as a novel specific inhibitor of arginine methylation and demonstrate substrate sequence-directed inhibition of enzyme activity by a small molecule and its physiological consequence.
Patent status of histone deacetylase inhibitors (2004)

Histone deacetylase (HDAC) has emerged as an important therapeutic target for the treatment of cancer and other diseases. Several HDAC inhibitors that target class I and II HDACs are currently in clinical trials. The initial results from these studies indicate that HDAC inhibitors show great promise for the treatment of cancer. To date, more than 30 research organisations are named as applicants on published patent applications claiming structures of HDAC inhibitors. This review summarises the patent literature published from mid-2002 to early 2004 containing claims directed towards HDAC inhibitor structures, together with discussion of the related primary literature.
Analysis of the Heart Antigens (1977)

The present study has indicated the presence of 3 heart specific antigens, using homologous and heterologous antibodies produced in immunized rabbits. Two of these antigenic proteins exhibit restricted organ specificity for heart and the other one shares by heart and kidney. One of these 2 heart specific antigens reacts to both homologous and heterologous anti-heart sera absorbed with kidney, while the other reacts to only heterologous anti-heart sera. The former has an electrophoretic mobility corresponding to that of serum beta-globulin, and is found to have a molecular weight of about 175,000. The latter has the same electrophoretic mobility as that of alpha2-globulin and is found to have a molecular weight of about 50,000.
hrp gene‐dependent induction of hin1: a plant gene activated rapidly by both harpins and the avrPto gene‐mediated signal (1996)

Two classes of bacterial genes are involved in the elicitation of the plant hypersensitive response (HR) in resistant plants: hrp genes and avr genes. hrp genes have been shown to be involved in the production and secretion of a new class of bacterial virulence/avirulence proteins, including harpin of Erwinia amylovora and harpinPss of Pseudomonas syringae. The ability of avr genes in the elicitation of the HR/resistance is dependent on functional hrp genes. The relationships between harpins and avr gene products are not known. This study investigates the plant genes induced by harpins and the effect of avr genes on the expression of such plant genes. A tobacco gene highly induced by harpins was isolated by a subtractive hybridization method. Induction of hin1 by P.s. pv. syringae 61 (Pss61) was found to be dependent on functional bacterial hrp genes. P. fluorescens (a saprophyte) or hrp mutants defective in the Hrp secretion pathway did not induce hin1 significantly. A hin 1-related gene in tomato cv. Rio Grande-PtoR was found to be rapidly induced by P. s. pv. tomato T1 (a virulent bacterium on Rio Grande-PtoR) containing the avrPto gene, which mediates the elictation of the HR/resistance in a Pto plant resistance gene-dependent manner. The induction of hin1 by bacteria correlates with production of harpins in planta. The putative open reading frame of hin1 encodes a novel protein of 221 amino acids. The data suggest that harpins and the avrPto-mediated signal induce a common plant gene in the elicitation of the HR.
Effect of Earth's Rotation on the Quantum Mechanical Phase of the Neutron (1979)

Using a neutron interferometer of the type first developed by Bonse and Hart for x rays, we have observed the effect of Earth's rotation on the phase of the neutron wave function. This experiment is the quantum mechanical analog of the optical interferometry observations of Michelson, Gale, and Pearson.
Printing Methods and Materials for Large-Area Electronic Devices (2005)

Two digital printing methods for the fabrication of active matrix thin-film transistor (AM-TFT) backplanes for displays are described. A process using printed resists layers, referred to as digital lithography, was used to fabricate arrays of hydrogenated amorphous silicon TFTs. TFTs were also fabricated using a combination of digital lithography to pattern metals and inkjet printing to pattern and deposit a polymeric semiconducting layer. The relative performance of amorphous silicon and polymer TFTs were evaluated. The utility of digital lithographic processing was demonstrated by the fabrication of prototype reflective displays using electrophoretic media.
Overview of algorithms for estimating swing modes from measured responses (2009)

Linear-system formulations are often used to describe power-system small-signal electromechanical dynamic properties. Over the past two decades, many techniques have been developed to conduct modal analysis using only actual-system measurements. Some techniques are appropriate for transient signals, others are for ambient signal conditions, and some are for conditions where a known probing signal is exciting the system. An overview of many of the more successful analysis techniques is presented. The theoretical background for these methods is summarized as well as application properties. Examples include computer simulations and actual system experiments from the western North American power system. Analysis goals center on estimating the modal frequency and damping.
A new approach to the minimum cut problem (1996)

This paper present a new approach to finding minimum cuts in undirected graphs. The fundamental principle is simple: the edges in a graph's minimum cut form an extremely small fraction of the graph's edges. Using this idea, we give a randomized, strongly polynomial algorithm that finds the minimum cut in an arbitrarily weighted undirected graph with high probability. The algorithm runs in O(n 2 log 3 n) time, a significant improvement over the previous O˜(mn) time bounds based on maximum flows. It is simple and intuitive and uses no complex data structures. Our algorithm can be parallelized to run in RNC with n 2 processors; this gives the first proof that the minimum cut problem can be solved in RNC . The algorithm does more than find a single minimum cut; it finds all of them. With minor modifications, our algorithm solves two other problems of interest. Our algorithm finds all cuts with value within a multiplicative factor of α of the minimum cut's in expected O˜(n 2α ) time, or in RNC with n 2α processors. The problem of finding a minimum multiway cut of graph into r pieces is solved in expected O˜(n 2(r-1) ) time, or in RNC with n 2(r-1) processors. The “trace” of the algorithm's execution on these two problems forms a new compact data structure for representing all small cuts and all multiway cuts in a graph. This data structure can be efficiently transformed into the more standard cactus representing for minimum cuts.
Boron-doped carbon nanotube-supported Pt nanoparticles with improved CO tolerance for methanol electro-oxidation (2012)

Boron doping into carbon nanotubes improves the CO tolerance and increases the utilization efficiency of the supported Pt nanoparticles. Boron doping leads to a uniform deposition of Pt nanoparticles and also facilitates the removal of CO from the Pt surface, resulting in an increase in the electrocatalytic activity for methanol oxidation.
Efficient transduction of human neurons with an adeno-associated virus vector. (1996)

An adeno-associated virus vector containing a lacZ gene driven by a CMV immediate-early promoter (AAV beta-gal) was evaluated with respect to its transduction efficiency and integration ability in nondividing human NT neurons. A dose-dependent pattern in transduction efficiency of the AAV beta-gal was demonstrated immunocytochemically, with up to 100% of the neurons expressing the gene product. No neurotoxic effects of the vector were detected. Quantitative PCR analyses of high molecular weight cellular DNA from the transduced neurons indicated that the copy number of the AAV beta-gal genome increased gradually in a time dependent manner, suggesting a slow but progressive rate of vector integration over a period of approximately 1 week following transduction. Equal or greater transduction efficiency of the AAV beta-gal into NT neurons than into a standard target cell line indicated that the NT neurons were readily susceptible to AAV-mediated gene transfer. This study demonstrates that AAV-based vectors can efficiently transduce and stably express a foreign gene in post-mitotic human neurons.
RAILROAD POLICY AND INTERMODALISM: Policy Choices after Deregulation (2002)

ABSTRACT Intermodalism is widely viewed as a promising recent development in transportation. This article examines the role played by railroads in intermodal freight transportation and the framework of public policies around whic intermodal freight movement has evolved. Intermodalism emerged because of technological, organizational, and public policy developments that contributed to its rapid growth. Deregulation of the rail industry since 1980 has led to significant restructuring through mergers and direct contracts between railroads and customers. As intermodal shipments become more important to the overall transportation system in the United States, attention will need to be given to ways in which intermodal concerns are addressed in surface transportation programs.
FabG Mediates Polyhydroxyalkanoate Production from Both Related and Nonrelated Carbon Sources in Recombinant Escherichia coli LS5218 (2008)

Polyhydroxyalkanoates (PHAs) composed of a mixture of short-chain-length-medium-chain-length (SCL-MCL) hydroxyacyl monomers are biologically produced polyesters that have properties ranging from thermoplastic to elastomeric, dependent on the molar ratio of SCL to MCL monomers incorporated into the copolymer. Because of the potential wide range of properties and applications for SCL-MCL PHA copolymers, it is important to develop and characterize novel metabolic pathways for SCL-MCL PHA production. The current study shows that coexpression of fabG genes from either E. coli or Pseudomonas sp. 61-3 with fabH(F87T) and PHA synthase genes enhances the production of SCL-MCL PHA copolymer from both related and nonrelated carbon sources in Escherichia coli LS5218, indicating the flexibility of FabG as a monomer-supplying enzyme for biological PHA production.
Mantle–circulation models with sequential data assimilation: inferring present–day mantle structure from plate–motion histories (2002)

Data assimilation is an approach to studying geodynamic models consistent simultaneously with observables and the governing equations of mantle flow. Such an approach is essential in mantle circulation models, where we seek to constrain an unknown initial condition some time in the past, and thus cannot hope to use first-principles convection calculations to infer the flow history of the mantle. One of the most important observables for mantle-flow history comes from models of Mesozoic and Cenozoic plate motion that provide constraints not only on the surface velocity of the mantle but also on the evolution of internal mantle-buoyancy forces due to subducted oceanic slabs. Here we present five mantle circulation models with an assimilated plate-motion history spanning the past 120 Myr, a time period for which reliable plate-motion reconstructions are available. All models agree well with upper- and mid-mantle heterogeneity imaged by seismic tomography. A simple standard model of whole-mantle convection, including a factor 40 viscosity increase from the upper to the lower mantle and predominantly internal heat generation, reveals downwellings related to Farallon and Tethys subduction. Adding 35% bottom heating from the core has the predictable effect of producing prominent high-temperature anomalies and a strong thermal boundary layer at the base of the mantle. Significantly delaying mantle flow through the transition zone either by modelling the dynamic effects of an endothermic phase reaction or by including a steep, factor 100, viscosity rise from the upper to the lower mantle results in substantial transition-zone heterogeneity, enhanced by the effects of trench migration implicit in the assimilated plate-motion history. An expected result is the failure to account for heterogeneity structure in the deepest mantle below 1500 km, which is influenced by Jurassic plate motions and thus cannot be modelled from sequential assimilation of plate motion histories limited in age to the Cretaceous. This result implies that sequential assimilation of past plate-motion models is ineffective in studying the temporal evolution of core-mantle-boundary heterogeneity, and that a method for extrapolating present-day information backwards in time is required. For short time periods (of the order of perhaps a few tens of Myr) such a method exists in the form of crude 'backward' convection calculations. For longer time periods (of the order of a mantle overturn), a rigorous approach to extrapolating information back in time exists in the form of iterative nonlinear optimization methods that carry assimilated information into the past through the use of an adjoint mantle convection model.
CpG and TpA frequencies in the plant system (1987)

Higher plant nuclear sequences reveal avoidance of CpG and TpA doublets. Chloroplast sequences avoid the TpA doublet in all codon positions. The chloroplast genome is not methylated but codon positions II-III and untranslated regions avoid CpG. The mitochondrial genome, also unmethylated, avoids CpG in all codon positions. We therefore deduce that methylation is not sufficient to explain CpG avoidance in the higher plant systems. Other factors must be taken into account such as amino acid composition, codon choices and perhaps stability of the DNA helix.
Mass spectrometry imaging as a tool for surgical decision‐making (2013)

Despite significant advances in image-guided therapy, surgeons are still too often left with uncertainty when deciding to remove tissue. This binary decision between removing and leaving tissue during surgery implies that the surgeon should be able to distinguish tumor from healthy tissue. In neurosurgery, current image-guidance approaches such as magnetic resonance imaging (MRI) combined with neuronavigation offer a map as to where the tumor should be, but the only definitive method to characterize the tissue at stake is histopathology. Although extremely valuable information is derived from this gold standard approach, it is limited to very few samples during surgery and is not practically used for the delineation of tumor margins. The development and implementation of faster, comprehensive, and complementary approaches for tissue characterization are required to support surgical decision-making--an incremental and iterative process with tumor removed in multiple and often minute biopsies. The development of atmospheric pressure ionization sources makes it possible to analyze tissue specimens with little to no sample preparation. Here, we highlight the value of desorption electrospray ionization as one of many available approaches for the analysis of surgical tissue. Twelve surgical samples resected from a patient during surgery were analyzed and diagnosed as glioblastoma tumor or necrotic tissue by standard histopathology, and mass spectrometry results were further correlated to histopathology for critical validation of the approach. The use of a robust statistical approach reiterated results from the qualitative detection of potential biomarkers of these tissue types. The correlation of the mass spectrometry and histopathology results to MRI brings significant insight into tumor presentation that could not only serve to guide tumor resection, but that is also worthy of more detailed studies on our understanding of tumor presentation on MRI.
SAMP1/YitFc mouse strain: A spontaneous model of Crohnʼs disease-like ileitis (2011)

The SAMP1/YitFc mouse strain represents a model of Crohn's disease (CD)-like ileitis that is ideal for investigating the pathogenesis of chronic intestinal inflammation. Different from the vast majority of animal models of colitis, the ileal-specific phenotype characteristic of SAMP1/YitFc mice occurs spontaneously, without genetic, chemical, or immunological manipulation. In addition, SAMP1/YitFc mice possess remarkable similarities to the human condition with regard to disease location, histologic features, incidence of extraintestinal manifestations, and response to conventional therapies. SAMP1/YitFc mice also display a well-defined time course of a predisease state and phases of acute and chronic ileitis. As such, the SAMP1/YitFc model is particularly suitable for elucidating pathways that precede the clinical phenotype that may lead to preventive, and therefore more efficacious, intervention with the natural course of disease, or alternatively, for the development of therapeutic strategies directed against chronic, established ileitis. In this review we summarize important contributions made by our group and others that uncover potential mechanisms in the pathogenesis of CD using this unique murine model of chronic intestinal inflammation.
Subgroup analysis by baseline pain intensity (BPI) and analgesic use (BAU) in NAPOLI-1: A phase III study of liposomal irinotecan (nal IRI)±5-fluorouracil/ leucovorin (5-FU/LV) in patients (pts) with metastatic pancreatic ductal adenocarcinoma (mPDAC) previously treated with gemcitabine-based therapy. (2018)

379 Background: We report an exploratory, post hoc subgroup analysis in pts with BPI and BAU data receiving nal-IRI+5-FU/LV, nal-IRI or 5-FU/LV in NAPOLI-1 (NCT01494506). In this pivotal trial, nal-IRI+5-FU/LV improved median OS (mOS) vs. 5-FU/LV (6.1 vs. 4.2 mo [HR=0.67; p=0.012]). Methods: BPI/BAU included an average of 3-7 days pt-recorded data before randomisation. Greater values indicated greater pain for BPI using a 100 mm visual analogue scale. BAU was converted to morphine equivalent mg/day. Results: Of 417 ITT pts, 295 had BPI and 299 had BAU data. Mean and median BPI were 28.6 and 25.0, respectively, and BAU were 33.3 and 8.1 mg/day, respectively. The percentage of pts with KPS ≥ 80 was higher in ≤ mean/≤ median (n=159/148) BPI groups vs. &gt; mean/&gt; median (n=136/147) BPI groups (96-97 vs. 83%) and in ≤mean/≤median (n=207/150) BAU groups vs. &gt; mean/&gt; median (n=92/149) BAU groups (95-97 vs. 82-85%). mOS and median PFS (mPFS) were higher for nal-IRI+5-FU/LV vs 5-FU/LV in all groups, with ≤ mean/≤ median BPI or BAU showing better outcomes vs. &gt; mean/&gt; median BPI or BAU (Table). Conclusions: BPI and BAU appear to have a prognostic effect on outcomes in mPDAC pts in the NAPOLI-1 study. No predictive effect was observed, with nal-IRI+5-FU/LV showing higher mOS vs. 5-FU/LV in all groups. Clinical trial information: NCT01494506. [Table: see text]
Synthesis and Characterization of Second-Generation Dialkylphenacylsulfonium Salt Photoinitiators (2000)

A new, simplified method for the synthesis of dialkylphenacylsulfonium salt cationic photoinitiators has been developed. This novel method was successfully used for the preparation of dialkylphenacylsulfonium salts bearing a wide variation in the length and structure of the alkyl chains as well as the light absorbing aryl ketone chromophores and the anions. Modification of the lengths of the alkyl chains permits the design of compatible photoinitiators for highly nonpolar monomers and oligomers such as epoxy functional silicones, epoxidized polybutadiene and vegetable oils. This article describes the synthesis and characterization of these photoinitiators.
Catechol‐Mediated Reversible Binding of Multivalent Cations in Eumelanin Half‐Cells (2014)

Electrochemical storage systems that utilize divalent cations such as Mg2+ can improve the volumetric charge storage capacities compared to those that use monovalent ions. Here, a cathode based on naturally derived melanin pigments is used in secondary Mg2+ batteries. Redox active catechol groups in melanins permit efficient and reversible exchange of divalent Mg2+ cations to preserve charge storage capacity in biopolymer cathodes for more than 500 cycles.
Molecular Simulation for Flexibility of a Single Clay Layer (2001)

Molecular dynamics (MD) simulations have been performed to study the flexibility of smectite clay minerals. We aim at the quantitative understanding of the mechanical behavior of a single clay layer in a completely exfoliated state. The repeating unit of a clay layer is taken to be ao = 0.52 nm and bo = 0.902 nm with formula of 2Na1/3 Al2[Si11/3Al1/3]O10(OH)2 which corresponds to that of beidellite. When the size of the basic cell (A = 9.3 nm, B = 2.6 nm, and C = 5 nm) (denoted by A-type cell) is reduced by 3−40% in the A-direction, the stationary structure of a clay layer is obtained as a curved sheet with a 2:1 smectite-type layer structure. In such a curved state, the layer experiences a stress of 0.5−0.7 GPa. The layer structure of a clay fractures when the size of the same basic cell is reduced by more than 40%. The bending constant is estimated for a curved layer by plotting the inverse of the average radius against stress. The similar calculations are performed by reducing the size of the basic cell (A = 3.1 nm, B = 10.7 nm, and C = 5 nm) (denoted by B-type cell) in the B-direction. The clay layer is found to be more flexible along the A-axis direction than along the B-axis direction. When the microscopic structure of a curved clay layer is examined, it is concluded that the main origin of flexibility lies in the change of Si−O−Si angles in the silicate tetrahedral sheets rather than in the change of bond lengths.
Reaction between Urea and Gypsum (1933)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction between Urea and GypsumColin W. Whittaker, Frank O. Lundstrom, and Streling B. HendricksCite this: Ind. Eng. Chem. 1933, 25, 11, 1280–1282Publication Date (Print):November 1, 1933Publication History Published online1 May 2002Published inissue 1 November 1933https://pubs.acs.org/doi/10.1021/ie50287a022https://doi.org/10.1021/ie50287a022research-articleACS PublicationsRequest reuse permissionsArticle Views287Altmetric-Citations9LEARN 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 Get e-Alerts