gebhart/patrepeval huggingface dataset:
Identification and Characterization of a Ca2+-Sensitive Nonspecific Cation Channel Underlying Prolonged Repetitive Firing inAplysiaNeurons (1996)

The afterdischarge of Aplysia bag cell neurons has served as a model system for the study of phosphorylation-mediated changes in neuronal excitability. The nature of the depolarization generating the afterdischarge, however, has remained unclear. We now have found that venom from Conus textile triggers a similar prolonged discharge, and we have identified a slow inward current and corresponding channel, the activation of which seems to contribute to the onset of the discharge. The slow inward current is voltage-dependent and Ca 2+ -sensitive, reverses at potentials slightly positive to 0 mV, exhibits a selectivity of K ≅ Na ≫ Tris &gt; N -methyl- d -glucamine (NMDG), and is blocked by high concentrations of tetrodotoxin. Comparison of these features with those observed in channel recordings provides evidence that a Ca 2+ -sensitive, nonspecific cation channel is responsible for a slow inward current that regulates spontaneous repetitive firing and suggests that modulation of the cation channel underlies prolonged changes in neuronal response properties.
Ionic Conduction and Solution Structure in LiPF6 and LiBF4 Propylene Carbonate Electrolytes (2018)

Expanding the performance limit of current Li-ion batteries requires ion–ion and ion–solvent interaction, which governs the ion transport behavior of the electrolytes, to be fully understood as a matter of crucial importance. We herein examine the ionic speciation and conduction behavior of propylene carbonate (PC) electrolytes of 0.1–3.0 M LiPF6 and LiBF4 using Raman spectroscopy, dielectric relaxation spectroscopy (DRS), and pulsed-field gradient NMR (PFG-NMR) spectroscopy. In both LiPF6–PC and LiBF4–PC, free ions and a solvent-shared ion pair (SIP) are dominant species at dilute salt concentrations (<0.8 M), and SIP becomes dominant at intermediate concentrations (0.8–1.5 M). At higher concentrations (1.5–3.0 M), the solvent-shared dimer (SSD) and contact dimer (CD) are dominant in LiPF6–PC, whereas the contact ion pair (CIP), CD, and agglomerate (AGG) prevail in LiBF4–PC. Ionic conduction in 0.1–1.5 M LiPF6–PC and LiBF4–PC is governed by the migration of free ions and SIP. Notably, above 1.5 M of the two PC electrolytes, SSD participates in ionic conduction via the migration mode as well. Furthermore, it is suggested that the large number of CIPs present in LiBF4–PC may contribute to ionic conduction via a Grotthuss-type mechanism.
Control of Minimally Persistent Leader-Remote-Follower and Coleader Formations in the Plane (2011)

This paper solves an <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> -agent formation shape control problem in the plane. The objective is to design decentralized control laws so that the agents cooperatively restore a prescribed formation shape in the presence of small perturbations from the prescribed shape. We consider two classes of directed, cyclic information architectures associated with so-called minimally persistent formations: leader-remote-follower and coleader. In our framework the formation shape is maintained by controlling certain interagent distances. Only one agent is responsible for maintaining each distance. We propose a decentralized control law where each agent executes its control using only the relative position measurements of agents to which it must maintain its distance. The resulting nonlinear closed-loop system has a manifold of equilibria, which implies that the linearized system is nonhyperbolic. We apply center manifold theory to show local exponential stability of the desired formation shape. The result circumvents the non-compactness of the equilibrium manifold. Choosing stabilizing gains is possible if a certain submatrix of the rigidity matrix has all leading principal minors nonzero, and we show that this condition holds for all minimally persistent leader-remote-follower and coleader formations with generic agent positions. Simulations are provided.
ChemInform Abstract: Facile‐Prepared Sulfonated Water‐Soluble PEPPSI‐Pd‐NHC Catalysts for Aerobic Aqueous Suzuki—Miyaura Cross‐Coupling Reactions. (2015)

Abstract The catalyst is shown to be active for the Suzuki—Miyaura cross‐coupling reaction.
Hypotheses ranking for robust domain classification and tracking in dialogue systems (2014)

We present a novel application of hypothesis ranking (HR) for the task of domain detection in a multi-domain, multiturn dialog system. Alternate, domain dependent, semantic frames from a spoken language understanding (SLU) analysis are ranked using a gradient boosted decision trees (GBDT) ranker to determine the most likely domain. The ranker, trained using Lambda Rank, makes use of a range of signals derived from the SLU and previous turn context to improve domain detection. On a multi-turn corpus we show that this approach offers accuracy improvements of 3.2% absolute (25.6% relative) compared to relying solely on upfront non-contextual SLU domain models and 2.9% (24.5% relative) improvement even with contextual SLU domain models. We also show that HR can be trained to be robust to changes in the SLU.
A Statistical Framework for the Analysis of ChIP-Seq Data (2011)

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has revolutionalized experiments for genome-wide profiling of DNA-binding proteins, histone modifications, and nucleosome occupancy. As the cost of sequencing is decreasing, many researchers are switching from microarray-based technologies (ChIP-chip) to ChIP-Seq for genome-wide study of transcriptional regulation. Despite its increasing and well-deserved popularity, there is little work that investigates and accounts for sources of biases in the ChIP-Seq technology. These biases typically arise from both the standard pre-processing protocol and the underlying DNA sequence of the generated data. We study data from a naked DNA sequencing experiment, which sequences non-cross-linked DNA after deproteinizing and shearing, to understand factors affecting background distribution of data generated in a ChIP-Seq experiment. We introduce a background model that accounts for apparent sources of biases such as mappability and GC content and develop a flexible mixture model named MOSAiCS for detecting peaks in both one- and two-sample analyses of ChIP-Seq data. We illustrate that our model fits observed ChIP-Seq data well and further demonstrate advantages of MOSAiCS over commonly used tools for ChIP-Seq data analysis with several case studies.
Visual evaluation of text features for document summarization and analysis (2008)

Thanks to the Web-related and other advanced technologies, textual information is increasingly being stored in digital form and posted online. Automatic methods to analyze such textual information are becoming inevitable. Many of those methods are based on quantitative text features. Analysts face the challenge to choose the most appropriate features for their tasks. This requires effective approaches for evaluation and feature-engineering.
Nonreciprocal charge transport in topological superconductor candidate Bi2Te3/PdTe2 heterostructure (2022)

Abstract In a hybrid system of topological insulator (TI)/superconductor (SC), the proximity-induced topological superconductivity is expected to appear at the interface. Here we propose and demonstrate that a TI/SC hybrid Bi 2 Te 3 /PdTe 2 heterostructure serves as a platform for exploring topological superconductivity with various features: all made of tellurium compounds, epitaxial growth, and a small charge transfer interface. In the Bi 2 Te 3 /PdTe 2 heterostructure films, we observe large nonreciprocal charge transport near the superconducting transition temperature under a transverse in-plane magnetic field. The observation indicates the interplay between the topological surface state and superconductivity, suggesting that the Bi 2 Te 3 /PdTe 2 heterostructure is a candidate for a topological superconductor. Also observed is an unexpected sign reversal of the nonreciprocal coefficient when the in-plane magnetic field is slightly tilted toward the out-of-plane direction. The analysis reveals that the sign reversal occurs with the change of dominant vortex type, that is, the change from spontaneous vortices to external-field induced ones.
Short-term magnesium deficiency upregulates ceramide synthase in cardiovascular tissues and cells: cross-talk among cytokines, Mg2+, NF-κB, and de novo ceramide (2011)

The present study tested the hypotheses that 1) short-term dietary deficiency (MgD) of magnesium (21 days) would result in the upregulation of ceramide synthase (CS) in left ventricular (LV), right ventricular, atrial, and aortic smooth muscle, as well as induce a synthesis/release of select cytokines and chemokines into the LV and aortic smooth muscle and serum; 2) exposure of primary cultured vascular smooth muscle cells (VSMCs) to low extracellular Mg concentration would lead to the synthesis/release of select cytokines/chemokines, activation of N-SMase, and the de novo synthesis of ceramide; and 3) inhibition of CS by fumonisin B1 (FB1) or inhibition of neutral sphingomyelinase (N-SMase) by scyphostatin (SCY) in VSMCs exposed to low Mg would result in reductions in the levels of the cytokines/chemokines and lowered levels of ceramide concomitant with inhibition of NF-κB activation. The data indicated that short-term MgD (10% normal dietary intake) resulted in the upregulation of CS in ventricular, atrial, and aortic smooth muscles coupled to the synthesis/release of 12 different cytokines/chemokines, as well as activation of NF-κB in the LV and aortic smooth muscle and sera; even very low levels of water-borne Mg (e.g., 15 mg·l(-1)·day(-1)) either prevented or ameliorated the upregulation and synthesis of the cytokines/chemokines. Our experiments also showed that VSMCs exposed to low extracellular Mg resulted in the synthesis of 5 different cytokines and chemokines concomitant with synthesis/release of ceramide. However, inhibition of the synthesis and release of ceramide by either FB1 or SCY attenuated, markedly , the generation of ceramide, release of the cytokines/chemokines, and activation of NF-κB (as measured by activated p65 and cRel).
Metabolic engineering of the anaerobic central metabolic pathway in Escherichia coli for the simultaneous anaerobic production of isoamyl acetate and succinic acid (2009)

An in vivo method of producing isoamyl acetate and succinate simultaneously has been developed in Escherichia coli to maximize yields of both high value compounds as well as maintain the proper redox balance between NADH and NAD(+). Previous attempts at producing the ester isoamyl acetate anaerobically did not produce the compound in high concentrations because of competing pathways and the need for NAD(+) regeneration. The objective of this study is to produce succinate as an example of a reduced coproduct to balance the ratio of NADH/NAD(+) as a way of maximizing isoamyl acetate production. Because the volatility of the two compounds differs greatly, the two could be easily separated in an industrial setting. An ldhA, adhE double mutant strain (SBS110MG) served as the control strain to test the effect of an additional ackA-pta mutation as found in SBS990MG. Both strains overexpressed the two heterologous genes pyruvate carboxylase and alcohol acetyltransferase (for ester production). The triple mutant SBS990MG was found to produce higher levels of both isoamyl acetate and succinate. At the optimal condition of 25 degrees C, the culture produced 9.4 mM isoamyl acetate and 45.5 mM succinate. SBS990MG produced 36% more ester and over 700% more succinate than SBS110MG. In addition, this study demonstrated that a significantly higher isoamyl acetate concentration can be attained by simultaneously balancing the carbon and cofactor flow; the isoamyl acetate concentration of 9.4 mM is more than seven times higher than an earlier report of about 1.2 mM.
GluN2A-Selective Pyridopyrimidinone Series of NMDAR Positive Allosteric Modulators with an Improved in Vivo Profile (2016)

The <i>N</i>-methyl-d-aspartate receptor (NMDAR) is an ionotropic glutamate receptor, gated by the endogenous coagonists glutamate and glycine, permeable to Ca<sup>2+</sup> and Na<sup>+</sup>. NMDAR dysfunction is associated with numerous neurological and psychiatric disorders, including schizophrenia, depression, and Alzheimer's disease. Recently, we have disclosed GNE-0723 (<b>1</b>), a GluN2A subunit-selective and brain-penetrant positive allosteric modulator (PAM) of NMDARs. This work highlights the discovery of a related pyridopyrimidinone core with distinct structure-activity relationships, despite the structural similarity to GNE-0723. GNE-5729 (<b>13</b>), a pyridopyrimidinone-based NMDAR PAM, was identified with both an improved pharmacokinetic profile and increased selectivity against AMPARs. We also include X-ray structure analysis and modeling to propose hypotheses for the activity and selectivity differences.
The Role of Microenvironment Stromal Cells in Regenerative Medicine (2010)

Regenerative medicines offer the potential for treatment and possibly cure of debilitating diseases including heart disease, diabetes, Parkinson’s disease and liver failure. Approaches using stem cells from various sources are in pre clinical and clinical testing. The goal of these studies is to deliver cellular products capable of replacing damaged tissue and/or cells. However, the balance between cellular proliferation and differentiation is a carefully controlled process involving a range of growth factors and cytokines produced in large part by tissue stromal cells. These stromal cells make up the tissue microenvironment and appear to be essential for normal homeostasis. We hypothesize that tissue damage in many instances involves damage to the microenvironment resulting in a lack of signals through growth factor networks necessary to maintain survival and proliferation of tissue specific stem cells and progenitor cells. Therefore, optimal repair of disease tissue must account for the damage to the stromal environment. We propose that optimal cellular therapies for regenerative medicine will require combination cellular products consisting of a stromal cell population to reconstitute the microenvironment and to support the survival, proliferation and differentiation of the tissue specific stem cells or progenitor cells.
AMD 3DNow! technology: architecture and implementations (1999)

The AMD-K6-2 microprocessor is the first implementation of AMD 3DNow!, a technology innovation for the x86 architecture that drives today's personal computers. 3DNow! technology is a set of 21 new instructions designed to open the traditional processing bottlenecks for floating-point-intensive and multimedia applications. Using these instructions, applications can implement more powerful solutions to create a more entertaining and productive PC platform. Examples of the type of improvements that 3DNow! technology enables are faster frame rates on high-resolution scenes, better physical modeling of real-world environments, sharper and more detailed 3D imaging, smoother video playback, and near theater-quality audio. Future AMD processors such as the AMD-K7, designed to operate at frequencies greater than 500 MHz, should provide even higher performance implementations of 3DNow! technology.
A multigroup method for ion slowing down with velocity diffucion (1981)

Significant thrombus formation on angioplasty guide wires was a frequent finding, occurring in 48% of cases. Resistance to thrombus formation was very dissimilar among coatings, with only the Biocompatibles phosphorylcholine-coated guide wires showing no thrombus formation at all. Whether subclinical thromboembolization occurred in some patients is unknown, and the clinical implications of this study remain to be defined.
ORIGINAL ARTICLE: Towards an understanding of the Holocene distribution of Fagus sylvatica L. (2006)

Abstract Aim Understanding the driving forces and mechanisms of changes in past plant distribution and abundance will help assess the biological consequences of future climate change scenarios. The aim of this paper is to investigate whether modelled patterns of climate parameters 6000 years ago can account for the European distribution of Fagus sylvatica at that time. Consideration is also given to the role of non‐climatic parameters as driving forces of the Holocene spread and population expansion of F. sylvatica . Location Europe. Methods European distributions were simulated using a physiologically‐based bioclimatic model (STASH) driven by three different atmospheric general circulation model (AGCM) outputs for 6000 years ago. Results The three simulations generally showed F. sylvatica to have potentially been as widespread 6000 years ago as it is today, which gives a profound mismatch with pollen‐based reconstructions of the F. sylvatica distribution at that time. The results indicate that drier conditions during the growing season 6000 years ago could have caused a restriction of the range in the south. Poorer growth conditions with consequently reduced competitive ability were modelled for large parts of France. Main conclusions Consideration of the entire European range of F. sylvatica showed that no single driving force could account for the observed distributional limits 6000 years ago, or the pattern of spread during the Holocene. Climatic factors, particularly drought during the growing season, are the likely major determinants of the potential range. Climatic factors are regionally moderated by competition, disturbance effects and the intrinsically slow rate of population increase of F. sylvatica . Dynamic vegetation modelling is needed to account for potentially important competitive interactions and their relationship with changing climate. We identify uncertainties in the climate and pollen data, as well as the bioclimatic model, which suggest that the current study does not identify whether or not climate determined the distribution of F. sylvatica 6000 years ago. Pollen data are better suited for comparison with relative abundance gradients rather than absolute distributional limits. These uncertainties from a study of the past, where we have information about plant distribution and abundance, argue for extreme caution in making forecasts for the future using equilibrium models.
Random unitaries give quantum expanders (2007)

We show that randomly choosing the matrices in a completely positive map from the unitary group gives a quantum expander. We consider Hermitian and non-Hermitian cases, and we provide asymptotically tight bounds in the Hermitian case on the typical value of the second largest eigenvalue. The key idea is the use of Schwinger-Dyson equations from lattice gauge theory to efficiently compute averages over the unitary group.
Corrections to Discovery and Clinical Evaluation of 1-{N-[2-(Amidinoaminooxy)ethyl]amino}carbonylmethyl-6-methyl-3-[2,2-difluoro-2-phenylethylamino]pyrazinone (RWJ-671818), a Thrombin Inhibitor with an Oxyguanidine P1 Motif (2010)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrections to Discovery and Clinical Evaluation of 1-{N-[2-(Amidinoaminooxy)ethyl]amino}carbonylmethyl-6-methyl-3-[2,2-difluoro-2-phenylethylamino]pyrazinone (RWJ-671818), a Thrombin Inhibitor with an Oxyguanidine P1 MotifTianbao Lu, Thomas Markotan, Shelley K. Ballentine, Edward C. Giardino, John Spurlino, Carl S. Crysler, Kathryn Brown, Bruce E. Maryanoff, Bruce E. Tomczuk, Bruce P. Damiano, Umesh Shukla, David End, Patricia Andrade-Gordon, Roger F. Bone, and Mark R. Player*Cite this: J. Med. Chem. 2010, 53, 8, 3422Publication Date (Web):March 24, 2010Publication History Published online24 March 2010Published inissue 22 April 2010https://doi.org/10.1021/jm100354sCopyright © 2010 American Chemical SocietyRequest reuse permissions This publication is free to access through this site. Learn MoreArticle Views550Altmetric-Citations-LEARN 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 InReddit PDF (548 KB) Get e-AlertscloseSUBJECTS:Anatomy,Inhibitors Get e-Alerts
Modulation of Roquin Function in Myeloid Cells Reduces Mycobacterium tuberculosis–Induced Inflammation (2017)

Damaging inflammation is a hallmark of <i>Mycobacterium tuberculosis</i> infection, and understanding how this is regulated is important for the development of new therapies to limit excessive inflammation. The E3 ubiquitin ligase, Roquin, is involved in immune regulation; however, its role in immunity to <i>M. tuberculosis</i> is unknown. To address this, we infected mice with a point mutation in <i>Roquin1/Rc3h1</i> (<i>sanroque</i>). Aerosol-infected <i>sanroque</i> mice showed enhanced control of <i>M. tuberculosis</i> infection associated with delayed bacterial dissemination and upregulated TNF production in the lungs after 2 wk. However, this early control of infection was not maintained, and by 8 wk postinfection <i>sanroque</i> mice demonstrated an increased bacterial burden and dysregulated inflammation in the lungs. As the inflammation in the lungs of the <i>sanroque</i> mice could have been influenced by emerging autoimmune conditions that are characteristic of the mice aging, the function of Roquin was examined in immune cell subsets in the absence of autoimmune complications. <i>M. bovis</i> bacillus Calmette-Guérin-primed <i>sanroque</i> T cells transferred into <i>Rag1<sup>-/-</sup></i> mice provided equivalent protection in the spleen and liver. Interestingly, the transfer of mycobacteria-specific (P25 CD4<sup>+</sup> TCR transgenic) wild-type spleen cells into <i>sanroque</i><i>Rag1</i><sup>-/-</sup> mice actually led to enhanced protection with reduced bacterial load, decreased chemokine expression, and reduced inflammation in the lungs compared with transfers into <i>Rag1<sup>-</sup></i><sup>/-</sup> mice expressing intact Roquin. These studies suggest that modulation of Roquin in myeloid cells may reduce both inflammation and bacterial growth during the chronic phase of <i>M. tuberculosis</i> infection.