gebhart/patrepeval huggingface dataset:
A Rapid, Sensitive, and Inexpensive Assay for Chloramphenicol Acetyltransferase (1987)

We present a rapid, sensitive enzymatic assay for chloramphenicol acetyltransferase (CAT) that does not require chromatography, HPLC, or autoradiography. The assay is based on the use of an inexpensive substrate, tritiated acetate, instead of [14C]chloramphenicol. The method is adapted from one originally used by de Crombrugghe et al. (1973) and by Shaw (1975), but with simplifications appropriate for routine use. In our hands, the method is as sensitive as the customary thin-layer chromatography assay and is far more efficient for the performance of many assays, both in terms of labor and expense.
Nucleic Acid Structure and Recognition (2002)

Abstract This book provides a detailed view of the molecular structures of DNA and RNA and how they are recognised by small molecules and proteins. Extensive source material is provided, including information on relevant web sites and computer programmes. The major methods of structural investigation for nucleic acids: X-ray crystallography, NMR, and molecular modelling are reviewed and their scope and limitations (in the context of nucleic acids) discussed. Also covered are the conformational features of nucleic acid building blocks, including a description of how base-pair morphologies are analysed; the structures of DNA double helices and helical oligonucleotides, emphasising current ideas on sequence-dependent structure; and DNA-DNA interactions, including triplexes and quadruplexes. The principles of RNA folding, ribosome, and ribozyme structure are also surveyed. Both covalent and non-covalent nucleic acid interactions with small molecules are described, with the emphasis on recognition principles and sequence specific gene recognition. The principles of protein - nucleic acid are covered, focussing on regulatory proteins. Nucleic Acid Structure and Recognition will therefore equip readers with a good understanding of all the important aspects of this major field. The Nucleic Acid Database (NDB) crystallographic and NMR structures for the nucleic acid structures described in the book are freely available through the Nucleic Acid Structure and Recognition website.
Multi-electron ionization and charge exchange in heavy ion fusion (2008)

Together with space-charge neutralization, ionization and charge exchange in the heavy ion beam fusion (HIBF) chamber can change beam quality and final focusing. Our research here supports simulation of these interactions through exploring theoretical approaches and developing improved models. This study is focused on the multi-electron processes which play an important role for these low-charged high-energy heavy ions. An improved classic trajectory Monte Carlo model and corresponding codes have been developed to simulate the heavy ion-atom collisions, which require intensive computations to solve many-body Hamiltonian Equations. Currently the results from the ion Xeq+ (q = 1-18) colliding with Xe gas show that multi-electron effects are significant, and this cross section can reach about 40% of the total. The improved code is expected to be an integral part of a plasma simulation package designed to study the atomic effects in beam transport and focusing in HIBF using plasma neutralization techniques. This should help provide improved physical insight into current HIBF experiments and future studies.
Supplementary Figure S2 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer (2023)

&lt;p&gt;The gating ancestry for the populations in the study of D2.A1 model&lt;/p&gt;
Adaptive Idle Speed Control for Internal Combustion Engines (2007)

The paper presents an application of a recently developed adaptive posicast controller for time-delay systems to the idle speed control (ISC) problem in internal combustion (IC) engines. The objective is to regulate the engine speed at a prescribed set-point in the presence of accessory load torque disturbances such as air conditioning and power steering. The adaptive controller, integrated with the existing proportional spark controller, is used to drive the electronic throttle as an actuator. We present both simulation and experimental results which demonstrate the potential of the adaptive controller to improve the performance. In addition, the reduction in calibration time and effort which can be achieved with our approach is discussed.
Comparison of two cold compression therapy protocols after tibial plateau leveling osteotomy in dogs (2017)

The reported data can be used to establish the new protocol of CCT in a clinical surrounding and to support postoperative rehabilitation of the canine patient.
The dependence of geminal hydrogen-hydrogen spin-spin coupling constants on .phi. and .psi. angles of peptides in solution (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe dependence of geminal hydrogen-hydrogen spin-spin coupling constants on .phi. and .psi. angles of peptides in solutionM. Barfield, V. J. Hruby, and J. P. MeraldiCite this: J. Am. Chem. Soc. 1976, 98, 6, 1308–1314Publication Date (Print):March 1, 1976Publication History Published online1 May 2002Published inissue 1 March 1976https://pubs.acs.org/doi/10.1021/ja00422a002https://doi.org/10.1021/ja00422a002research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-Citations59LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Simple, accurate electrostatics-based formulas for calculating ionization potentials, electron affinities, and capacitances of fullerenes (2017)

A set of simple analytic formulas is derived via electrostatics-based methods to accurately calculate the values of electron affinities ${A}_{n}$ and ionization potentials ${I}_{n}$ for $n$-carbon icosahedral fullerene molecules as a function of their average radii ${R}_{n}$. These formulas reproduce with accuracy the values of ${A}_{n}, {I}_{n}$, and their scalings with $1/{R}_{n}$ that were determined previously in detailed, computationally intensive density functional theory calculations. The formula for ${A}_{n}$ is derived from an enhanced image-charge model that treats the valence region of the icosahedral system as a quasispherical conductor of radius $({R}_{n}+\ensuremath{\delta})$, where $\ensuremath{\delta}=1/4{W}_{\ensuremath{\infty}}$ is a small constant distance determined from the work function ${W}_{\ensuremath{\infty}}$ of graphene. Using this model, though, a formula for ${I}_{n}$ that includes only electrostatics-like terms does not exhibit accuracy similar to the analogous formula for ${A}_{n}$. To make it accurate, a term must be added to account for the large symmetry-induced quantum energy gap in the valence energy levels (i.e., the HOMO-LUMO gap). An elementary two-state model based upon a quantum rotor succeeds in producing a simple expression that evaluates the energy gap as an explicit function of ${A}_{n}$. Adding this to the electrostatics-like formula for ${I}_{n}$ gives a simple quantum equation that yields accurate values for ${I}_{n}$ and expresses them as a function of ${A}_{n}$. Further, the simple equations for ${A}_{n}$ and ${I}_{n}$ yield significant insight into both the physics of electron detachment in the fullerenes and the scaling with ${R}_{n}$ of their quantum capacitances ${C}_{n}=1/({I}_{n}\ensuremath{-}{A}_{n})$.
How we manage Bing–Neel syndrome (2019)

Bing-Neel syndrome (BNS) is an uncommon presentation of Waldenström macroglobulinaemia (WM), seen during the course of the disease in about 1% of patients. BNS occurs when WM cells gain access to the central nervous system (CNS) causing neurological deficits. The diagnosis of BNS is suggested by the presence of radiological abnormalities, such as leptomeningeal enhancement on magnetic resonance imaging and confirmed by the presence of clonal lymphoplasmacytic cells and MYD88 L265P in the cerebrospinal fluid. The treatment of BNS requires agents with good penetration into the CNS, such as fludarabine, methotrexate and cytarabine. The novel Bruton Tyrosine Kinase inhibitor ibrutinib has shown CNS-penetrating properties, and recent data suggest a therapeutic role in BNS. In this review, we will discuss the clinical and pathological features, diagnostic criteria, treatment options and outcomes of patients with BNS.
Transport of Gold Nanoparticles by Vascular Endothelium from Different Human Tissues (2016)

The selective entry of nanoparticles into target tissues is the key factor which determines their tissue distribution. Entry is primarily controlled by microvascular endothelial cells, which have tissue-specific properties. This study investigated the cellular properties involved in selective transport of gold nanoparticles (<5 nm) coated with PEG-amine/galactose in two different human vascular endothelia. Kidney endothelium (ciGENC) showed higher uptake of these nanoparticles than brain endothelium (hCMEC/D3), reflecting their biodistribution in vivo. Nanoparticle uptake and subcellular localisation was quantified by transmission electron microscopy. The rate of internalisation was approximately 4x higher in kidney endothelium than brain endothelium. Vesicular endocytosis was approximately 4x greater than cytosolic uptake in both cell types, and endocytosis was blocked by metabolic inhibition, whereas cytosolic uptake was energy-independent. The cellular basis for the different rates of internalisation was investigated. Morphologically, both endothelia had similar profiles of vesicles and cell volumes. However, the rate of endocytosis was higher in kidney endothelium. Moreover, the glycocalyces of the endothelia differed, as determined by lectin-binding, and partial removal of the glycocalyx reduced nanoparticle uptake by kidney endothelium, but not brain endothelium. This study identifies tissue-specific properties of vascular endothelium that affects their interaction with nanoparticles and rate of transport.
Co3O4 Nanosheets with In-Plane Pores and Highly Active {112} Exposed Facets for High Performance Lithium Storage (2017)

Recently, two-dimensional transition metal oxide nanomaterials have been extensively investigated as promising candidates for the lithium-ion battery anode materials due to their elastic volume change, efficient ion/electrical pathways, and additional interfacial lithium storage sites. Herein, we report a simple wet-chemical method followed by thermal treatment to synthesize Co3O4 nanosheets with the in-plane pores. The as-prepared nanosheets are found to selectively expose the highly active {112} facets as the dominant surfaces. When fabricated into the anode configuration, a specific capacity of 1717 mA h g–1 can be reliably retained after 100 cycles at a current density of 200 mA g–1. While increasing the current density to 1 A g–1 and prolonging the cycle life to 400 cycles, the nanosheets can still deliver a capacity of 1090 mA h g–1 with a Coulombic efficiency of 99.5%. This excellent electrochemical performance can be attributed to the unique morphological structures of our porous nanosheets for the shortened lithium ion diffusion pathway, alleviated volume expansion, and enhanced active sites, indicating the technological potency of the nanosheets for high-performance lithium storage.
Improving the Efficiency, Ease, and Efficacy of Endoscopic Abdominoplasty (1997)

Ferraro, Frank J. M.D.; Zavitsanos, George P. M.D.; Van Buskirk, Eric R. M.D.; Rehnke, Robert D. M.D.; Ruff, Gregory L. M.D.; Ritter, Edmond F. M.D. Author Information
Alignment Properties of Liquid Crystal Molecules with Negative Dielectric Anisotropy on Hydrogenated Silicon Carbide Films (2008)

We study the alignment properties of liquid crystals (LCs) with a negative dielectric anisotropy on a hydrogenated silicon carbide (SiC:H) film, which is an alternative alignment material. SiC:H layers align LC molecules with a negative dielectric anisotropy via ion beam (IB) irradiation and control the pretilt angle in a range from 90 to 75° depending on the change of IB irradiation angle. Also, when they are exposed to high temperatures for a long time, they show robust properties without degradation. We conclude that although the SiC:H alignment layers are not sensitive to IB irradiation compared with the SiC layers, they show a potential as alternative LC alignment layers for IB irradiation method.
Nanosecond Repetitively Pulsed (NRP) Plasmas: Relationship Between Induced Flow and Plasma Characteristics at Atmospheric Pressure (Final Technical Report) (2023)

The local flow fields induced by plasma discharges at atmospheric pressure can play a critical role in aerodynamic flow and combustion control and have significant implications for plasma-based technologies in medicine and environmental engineering. However, the coupling between the plasma characteristics, the geometry and the induced flow field is not well understood. The primary goal of this work is to determine the relationship between the plasma characteristics and the induced flow field for nanosecond pulsed discharges at atmospheric pressure. A comprehensive experimental investigation of plasmas produced by nanosecond high-voltage pulses in a pin-to-pin electrode configuration was conducted, employing several measurement techniques including microwave and laser Rayleigh scattering, optical emission spectroscopy, and high-speed imaging. The flow field induced by the nanosecond plasma was measured and characterized using measurements of the velocity (particle image velocimetry) and density (background oriented schlieren) with unprecedented spatiotemporal resolution. The experimental measurements were complemented by development of a one-dimensional model of the plasma discharge and a high-fidelity computational fluid dynamics (CFD) simulation of the subsequent plasma-induced flow field.
Effects of translation on degradation of mRNA segments transcribed from the polycistronic puf operon of Rhodobacter capsulatus (1991)

Previous work has shown that expression of genes within the polycistronic puf operon of Rhodobacter capsulatus is regulated in part by differential degradation of segments of puf transcripts. To understand the role of ribosome coverage in the differential stability of puf mRNA segments, we have studied the effects of mutations that alter translation of specific puf transcript segments on puf mRNA decay. Our results show that stopping translation either within the light-harvesting I (LHI) genes or near the 5' end of the reaction center (RC)-coding region decreased the stability of puf transcript segments downstream from a hairpin loop structure located between the LHI and RC genes but failed to affect the upstream sequences so long as the loop was present. Mutations that allowed translation to proceed through the hairpin structure reduced its ability to protect upstream sequences from accelerated decay. Introduction of translation stops more than 107 bp into the RC-coding region, but still 5' to an mRNA segment containing decay-promoting endonuclease cleavage sites, had no effect on puf mRNA stability. The divergent and location-dependent consequences of translation stops imply that different mechanisms are responsible for the degradation of different puf mRNA segments and indicate that coverage of puf mRNA sequences by ribosomes is insufficient and may in some cases be unnecessary to protect these sequences from degradation.
An Efficient Method to Enhance the Quality of Ultrasound Medical Images (2021)

Today, non-invasive imaging has become one of the popular and prevalent methods in medical applications. Ultrasound imaging is a popular imaging modality as it avoids harmless radiation, has low computation cost, can operate in real time and be implemented in low-cost instruments. However, the image quality decreases due to diverse noise sources. In this paper, a new method based on CEEMDAN to Speckle denoise of the ultrasound images is introduced. The results show an improvement in SSIM and PSNR of 14% and 29%, respectively. In addition, this method can enhance the image quality by adding weights to the primary modes, which increases the sharpness and contrast by 56% and 22%, respectively.
Evaluation of Anisotropic Biaxial Stress in Thin Strained-SiGe Layer Using Surface Enhanced Raman Spectroscopy (2014)

We applied surface-enhanced Raman spectroscopy (SERS) to the excitation of transversal optical (TO) phonos in strained SiGe. The SERS technique can greatly enhance the Raman signal owing to metal-surface plasmon resonance. Furthermore, the electrical field includes a large amount of z-polarization, which can excite TO phonons. In this study, we evaluated anisotropic biaxial stress state in thin strained-SiGe layer on a Si substrate with the SERS technique.
Gender in end-user software engineering (2008)

In this paper, we describe research that reports gender differences in usage of software engineering tools by end-user programmers. We connect these findings with possible explanations based on theories from other disciplines, and then add to that our recent results that these differences go deeper than software engineering tool usage to software engineering strategies. We enumerate the strategies that work better for males and the ones that work better for females, and discuss implications and possible directions for follow-up.
Efficient topological exploration (2003)

We consider the robot exploration of a planar graph-like world. The robot's goal is to build a complete map of its environment. The environment is modeled as an arbitrary undirected planar graph which is initially unknown to the robot. The robot cannot distinguish vertices and edges that it has explored from the unexplored ones. The robot is assumed to be able to autonomously traverse graph edges, recognize when it has reached a vertex, and enumerate edges incident upon the current vertex. The robot cannot measure distances nor does it have a compass, but it is equipped with a single marker that it can leave at a vertex and sense if the marker is present at a newly visited vertex. The total number of edges traversed while constructing a map of a graph is used as a measure of performance. We present an efficient algorithm for learning an unknown, undirected planar graph by a robot equipped with one marker. Experimental results obtained by running a large collection of example worlds are presented.
Soundfield Reconstruction in Reverberant Environments Using Higher-order Microphones and Impulse Response Measurements (2019)

This paper addresses the problem of soundfield reconstruction over a large area using a distributed array of higher-order microphones. Given an area enclosed by the array, one can distinguish between two components of the soundfield: the interior soundfield generated by sources outside of the enclosed area and the exterior soundfield generated by sources inside the enclosed area. These components form an indistinguishable mixture and, despite the existence of theoretical solutions to separate them, practical implementation is challenging due to high number of microphones needed for large regions and high frequencies. In this work, we consider a scenario where the interior soundfield is characterized by reverberation and show how a set of RIR measurements can be used to parametrize the interior component as a function of the exterior component, effectively reducing the unknowns of the problem.
Regeneration of Burnt Bridges on a DNA Catenane Walker (2020)

DNA walkers are molecular machines that can move with high precision onthe nanoscale due to their structural and functional programmability. Despite recent advances in the field that allow exploring different energy sources, stimuli, and mechanisms of action for these nanomachines, the continuous operation and reusability of DNA walkers remains challenging because in most cases the steps, once taken by the walker, cannot be taken again. Herein we report the path regeneration of a burnt-bridges DNA catenane walker using RNase A. This walker uses a T7RNA polymerase that produces long RNA transcripts to hybridize to the path and move forward while the RNA remains hybridized to the path and blocks it for an additional walking cycle. We show that RNA degradation triggered by RNase A restores the path and returns the walker to the initial position. RNase inhibition restarts the function of the walker.
EXTENT OF TUMOR NECROSIS IS AN INDEPENDENT PROGNOSTIC FACTOR FOR PAPILLARY RENAL CELL CARCINOMA (2009)

You have accessJournal of Urology1 Apr 2009EXTENT OF TUMOR NECROSIS IS AN INDEPENDENT PROGNOSTIC FACTOR FOR PAPILLARY RENAL CELL CARCINOMA Tobias Klatte, Mesut Remzi, Jonathan W Said, Andrea Haitel, Fairooz Kabbinavar, Matthias Waldert, Michela de Martino, Michael Marberger, Arie S Belldegrun, and Allan J Pantuck Tobias KlatteTobias Klatte More articles by this author , Mesut RemziMesut Remzi More articles by this author , Jonathan W SaidJonathan W Said More articles by this author , Andrea HaitelAndrea Haitel More articles by this author , Fairooz KabbinavarFairooz Kabbinavar More articles by this author , Matthias WaldertMatthias Waldert More articles by this author , Michela de MartinoMichela de Martino More articles by this author , Michael MarbergerMichael Marberger More articles by this author , Arie S BelldegrunArie S Belldegrun More articles by this author , and Allan J PantuckAllan J Pantuck More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(09)61000-4AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "EXTENT OF TUMOR NECROSIS IS AN INDEPENDENT PROGNOSTIC FACTOR FOR PAPILLARY RENAL CELL CARCINOMA." The Journal of Urology, 181(4S), p. 352 © 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 4SApril 2009Page: 352 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetricsAuthor Information Tobias Klatte More articles by this author Mesut Remzi More articles by this author Jonathan W Said More articles by this author Andrea Haitel More articles by this author Fairooz Kabbinavar More articles by this author Matthias Waldert More articles by this author Michela de Martino More articles by this author Michael Marberger More articles by this author Arie S Belldegrun More articles by this author Allan J Pantuck More articles by this author Expand All Advertisement PDF DownloadLoading ...