gebhart/patrepeval huggingface dataset:
The Yersinia enterocolitica Ysa type III secretion system is expressed during infections both in vitro and in vivo (2013)

Yersinia enterocolitica biovar 1B maintains two type III secretion systems (T3SS) that are involved in pathogenesis, the plasmid encoded Ysc T3SS and the chromosomally encoded Ysa T3SS. In vitro, the Ysa T3SS has been shown to be expressed only at 26°C in a high-nutrient medium containing an exceptionally high concentration of salt - an artificial condition that provides no clear insight on the nature of signal that Y. enterocolitica responds to in a host. However, previous research has indicated that the Ysa system plays a role in the colonization of gastrointestinal tissues of mice. In this study, a series of Ysa promoter fusions to green fluorescent protein gene (gfp) were created to analyze the expression of this T3SS during infection. Using reporter strains, infections were carried out in vitro using HeLa cells and in vivo using the mouse model of yersiniosis. Expression of green fluorescent protein (GFP) was measured from the promoters of yspP (encoding a secreted effector protein) and orf6 (encoding a structural component of the T3SS apparatus) in vitro and in vivo. During the infection of HeLa cells GFP intensity was measured by fluorescence microscopy, while during murine infections GFP expression in tissues was measured by flow cytometry. These approaches, combined with quantification of yspP mRNA transcripts by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR), demonstrate that the Ysa system is expressed in vitro in a contact-dependent manner, and is expressed in vivo during infection of mice.
Molybdenum and Tungsten Imido Alkylidene Complexes as Efficient Olefin‐Metathesis Catalysts. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Polarimetric Control of Reflective Metasurfaces (2012)

This letter addresses the synthesis of reflective cells approaching a given desired Floquet's scattering matrix. This work is motivated by the need to obtain much finer control of reflective metasurfaces by controlling not only their copolarized reflection, but also their cross-coupling behavior. The demonstrated capability will enable more powerful design approaches-involving all field components in phase and magnitude-and consequently better performance in applications involving reflective metasurfaces. We first expose some fundamental theoretical constraints on the cell scattering parameters. Then, a successful procedure for controlling all four scattering parameters by applying parallelogram and trapezoid transformations to square patches is presented, considering both normal and oblique incidence.
Dosimetric evaluation of a Monte Carlo IMRT treatment planning system incorporating the MIMiC (2007)

The high dose per fraction delivered to lung lesions in stereotactic body radiation therapy (SBRT) demands high dose calculation and delivery accuracy. The inhomogeneous density in the thoracic region along with the small fields used typically in intensity-modulated radiation therapy (IMRT) treatments poses a challenge in the accuracy of dose calculation. In this study we dosimetrically evaluated a pre-release version of a Monte Carlo planning system (PEREGRINE 1.6b, NOMOS Corp., Cranberry Township, PA), which incorporates the modeling of serial tomotherapy IMRT treatments with the binary multileaf intensity modulating collimator (MIMiC). The aim of this study is to show the validation process of PEREGRINE 1.6b since it was used as a benchmark to investigate the accuracy of doses calculated by a finite size pencil beam (FSPB) algorithm for lung lesions treated on the SBRT dose regime via serial tomotherapy in our previous study. Doses calculated by PEREGRINE were compared against measurements in homogeneous and inhomogeneous materials carried out on a Varian 600C with a 6 MV photon beam. Phantom studies simulating various sized lesions were also carried out to explain some of the large dose discrepancies seen in the dose calculations with small lesions. Doses calculated by PEREGRINE agreed to within 2% in water and up to 3% for measurements in an inhomogeneous phantom containing lung, bone and unit density tissue.
Ultrafast capillary electrophoresis/mass spectrometry of controlled substances with optical isomer separation in about a minute (2016)

Amphetamine, cathinone, nor-mephedrone and pregabalin were separated and detected in about a minute, demonstrating the utility of the portable CE instrument for the analysis of controlled substances and their optical isomers. Copyright © 2016 John Wiley & Sons, Ltd.
A novel cyclic dinuclear gold(i) complex induces anticancer activity via an oxidative stress-mediated intrinsic apoptotic pathway in MDA-MB-231 cancer cells (2022)

A new dinuclear cyclic gold(I) complex [Au<sub>2</sub>(DCyPA)<sub>2</sub>](PF<sub>6</sub>)<sub>2</sub>, 1, based on bis[2-(dicyclohexylphosphano)ethyl]amine (DCyPA) has been synthesized and characterized by elemental analysis, IR and NMR spectroscopy, and X-ray crystallography. In the dinuclear complex cation [Au<sub>2</sub>(DCyPA)<sub>2</sub>]<sup>2+</sup>, the two gold(I) ions are bridged by the ligand bis[2-(dicyclohexylphosphano)ethyl]amine (DCyPA) giving rise to a 16-membered ring centrosymmetric metallacycle. The cytotoxicity of the complex was evaluated against the triple-negative human breast cancer cells MDA-MB-231. In order to understand the mechanism of the cytotoxic behavior, a variety of assays, including Annexin V-FITC/Propidium iodide double staining, ROS production, and mitochondrial membrane potential and migration assays were carried out. The results indicated that complex 1 induced cytotoxicity <i>via</i> an oxidative stress-mediated intrinsic apoptotic pathway in MDA-MB-231 cancer cells.
From Lab-on-a-Chip to Lab-in-the Body: Miniaturization of Diagnostic Tools (2013)

Optical molecular diagnostic tools are rapidly shrinking, enabling miniature systems that can be used to continuously monitor health in the body. We describe our work on integrated photonic systems for this purpose. Article not available.
High-Level Performance Estimation Using Simulators At Multiple Abstraction Levels (2009)

High-level simulators used in EU-MULTICUBE project, enable a multi-abstraction-level system specification and modeling framework to provide static and dynamic evaluation of the system-level performance metrics (e.g. execution time, energy consumption). These simulators are coupled with Design-Space Exploration (DSE) tools (using a common XML interface) to generate Pareto set of optimum system configurations for a specified application on a specified platform. This Pareto set (of optimum configurations) is used by a Run-Time Manager during the application run to optimize platform resource usage. Motivation for various abstraction levels of simulation: • DSE for an application running on a specific platform requires a large number of application runs (typically on platform simulator). • There is a trade-off between the accuracy of the simulation results and the time taken for simulating the application. • Using multiple simulators at various abstraction levels enables DSE to be done with faster higher-level simulators (e.g. IMEC-HLsim and MultiCube-SCoPE). The DSE end results (Pareto set of optimum points) are verified using more accurate platform simulator (i.e. cycle-accurate simulator e.g. CoWare Virtual Platform).
Efficiency of human observers relative to linear-discriminant models (1992)

In another presentation at this symposium, Myers and Wagner review the use of the Bayesian ideal observer as a model for human performance and define efficiency as the ratio of squares of detectability indices for the human and the Bayesian. Though this approach has proved very useful, especially in evaluation and optimization of medical imaging systems, the kinds of problems that can be analyzed in this manner are limited because the Bayesian observer needs to know the full probability laws for the data. In practice this restricts the Bayesian to fairly simple and often unrealistic tasks. Linear discriminants, on the other hand, can be calculated from knowledge of just the first and second-order statistics of the data; thus they are often analytically tractable when the Bayesian model is not. In this paper we briefly review the principles of this approach, summarize the circumstances where it is practical, and discuss a variety of psychophysical studies that show that a particular linear discriminant, which we refer to as the Hotelling observer, correlates well with human performance. Efficiency is then redefinied in terms of the Hotelling observer.
Reaction of Aryl Halides with π‐Allylnickel Halides: Methallylbenzene (2003)

Abstract Reaction of aryl halides with π‐allylnickel halides: methallylbenzene reactant: 50.8 g. (38.5 ml., 0.298 mole) of nickel carbonyl solvent: 250 ml. of petroleum ether product: methallylbenzene reactant: Methallyl bromide intermediate: π‐methallylnickel bromide byproduct: 1% 2,5‐dimethyl‐1,5‐hexadiene byproduct: biphenyl product: β,β‐dimethylstyrene
Piezoceramic Telescopic Actuator Quasi-Static Experimental Characterization (2003)

Piezoceramic telescopic actuators capitalize upon an internally-leveraged amplification technique consisting of interconnected concentric, cascaded cylinders that telescope out when activated. The building-block nature of the telescopic design makes it an efficient, densely packed actuator that yields high work output for a given volume. As with any actuator, once fabricated, there are factors that lead to losses in performance that are not captured in most predictive models. To identify these and gain insight into the overall device behavior, this paper presents an experimental investigation of the quasi-static force-deflection performance. For a broader perspective, three unique telescopic prototypes were fabricated and experimentally tested, each manufactured using different techniques, materials, and geometries. As expected, discrepancies between the experimental and modeled behavior were observed. Therefore, to accurately predict the observed behavior of this architecture, a full three-dimensional numerical model was constructed for each prototype and was used to revise a previously derived analytical model accounting for the complex actuator behavior observed in the experiments and improving the characterization of the loss mechanisms in the telescopic actuation architecture.
Deoxyribonuclease I (2005)

This chapter focuses on the biochemical properties; clinical use, pharmacological aspects, and production of recombinant human deoxyribonuclease (rhDNase) I. Deoxyribonucleases (DNases) are phosphodiesterases that catalyze the hydrolysis of deoxyribonucleic acid (DNA). The three-dimensional X-ray crystallographic structure of rhDNase I is very similar to the bovine form of DNase I. DNase I shows a strong preference for double-stranded DNA, and it degrades DNA in the presence of divalent cations by introducing single-stranded nicks through hydrolysis of P–O'3-bonds. Extremely sensitive DNase I assays have been developed using fluorescent DNA and fluorescent probes. RhDNase I can be used in conjunction with standard cystic fibrosis (CF) therapies, but it should not be used in patients with known hypersensitivity to rhDNase I and Chinese hamster ovary products. A gradual deamidation of rhDNase I also occur during storage in vials and am the major cause of its short shelf life. Different, well-designed clinical trials have demonstrated the effectiveness of rhDNase I in CF patients.
Effects of electron heating on the current driven electrostatic ion cyclotron instability and plasma transport processes along auroral field lines (1988)

Fluid simulations of the plasma along auroral field lines in the return current region have been performed to show that the onset of electrostatic ion cyclotron (EIC) related anomalous resistivity and the consequent heating of electrons leads to much higher transverse ion temperature than the current driven EIC instability (CDICI) alone would produce. Anomalous resistivity enhances ion heating in two ways: (1) by inhibiting the growth of the critical electron‐ion drift velocity, V cH , which must be exceeded to excite the EIC instability and (2) by increasing the relative drift velocity between the electrons and the ions, V D , through the formation of density cavities due to increased ambipolar electric field. The anomalous resistivity associated with the turbulence is limited by electron heating, so that CDICI eventually saturates, but at a substantially higher transverse temperature than would be the case in the absence of resistivity. This process demonstrates a positive feedback loop in the interaction between CDICI, anomalous resistivity, and parallel large scale dynamics in the topside ionosphere.
Leakage control with efficient use of transistor stacks in single threshold CMOS (1999)

Article Free Access Share on Leakage control with efficient use of transistor stacks in single threshold CMOS Authors: Mark C. Johnson Rose-Hulman Institute of Technology, 5500 Wabash Avenue, Terre Haute, IN Rose-Hulman Institute of Technology, 5500 Wabash Avenue, Terre Haute, INView Profile , Dinesh Somasekhar Purdue University, 1285 EE Building, West Lafayette, IN Purdue University, 1285 EE Building, West Lafayette, INView Profile , Kaushik Roy Purdue University, 1285 EE Building, West Lafayette, IN Purdue University, 1285 EE Building, West Lafayette, INView Profile Authors Info & Claims DAC '99: Proceedings of the 36th annual ACM/IEEE Design Automation ConferenceJune 1999 Pages 442–445https://doi.org/10.1145/309847.309976Published:01 June 1999Publication History 24citation620DownloadsMetricsTotal Citations24Total Downloads620Last 12 Months40Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Preclinical efficacy of GPR4 antagonist in a short-term mouse emphysema-exacerbation model (2019)

In COPD, airway acidification is a common phenomenon associated with decreased antibacterial activity and persistent bacterial colonization. GPR4 is a proton sensing G protein-coupled receptor highly expressed on endothelial cells that induces a signaling cascade via coupling to Gs/cAMP formation and serves as an important interface between airway acidification and inflammation. Here we present the characterization of a short-term mouse model that mimics several of the pathophysiological features observed in bacterial COPD exacerbations in humans, rendering it very useful for pharmacological studies. Additionally, we report that inhibition of GPR4 by a small molecule antagonist (Miltz et al., 2017) rescues some of these manifestations. Mice received porcine pancreatic elastase (0.4U) intratracheally (i.t.) at day 0 to induce emphysema. After 10 days to allow resolution of acute inflammation, lipopolysaccharide (2mg/kg) was administrated i.t. to mimic acute bacterial exacerbation. Treatment with the GPR4 inhibitor started 1 day later (twice daily for 4 days, 100mg/kg, per os). Our emphysema-exacerbation model recapitulates many hallmarks of human COPD exacerbation within 2 weeks e.g. small airway remodeling, increased mucus production, lung permeability and edema, induced cytokines and proteases release and significant airway obstruction (FEV100ms/FVC). In this model, GPR4 inhibition significantly reduced lung permeability, immune cells influx, pro-inflammatory cytokines, detrimental mucin MUC5AC and proteases MMP9/12. To conclude, we characterized a short-term mouse model of emphysema-exacerbation with useful properties for pharmacological research; moreover, we show that GPR4 inhibition is a promising approach for reducing severity of acute COPD exacerbations.
Aquarius—Enable Fast, Scalable, Data-Driven Service Management in the Cloud (2022)

In order to dynamically manage and update networking policies in cloud data centers, Virtual Network Functions (VNFs) use, and therefore actively collect, networking state information - and in the process, incur additional control signaling and management overhead, especially in larger data centers. In the meantime, VNFs in production prefer distributed and straightforward heuristics over advanced learning algorithms to avoid intractable additional processing latency under high-performance and low-latency networking constraints. This paper identifies the challenges of deploying learning algorithms in the context of cloud data centers, and proposes Aquarius to bridge the application of machine learning (ML) techniques on distributed systems and service management. Aquarius passively yet efficiently gathers reliable observations, and enables the use of ML techniques to collect, infer, and supply accurate networking state information—without incurring additional signaling and management overhead. It offers fine-grained and programmable visibility to distributed VNFs, and enables both open- and close-loop control over networking systems. This paper illustrates the use of Aquarius with a traffic classifier, an auto-scaling system, and a load balancer—and demonstrates the use of three different ML paradigms—unsupervised, supervised, and reinforcement learning, within Aquarius, for network state inference and service management. Testbed evaluations show that Aquarius suitably improves network state visibility and brings notable performance gains for various scenarios with low overhead.
Disc Height and Sagittal Alignment in Operated and Non-Operated Levels in the Lumbar Spine at Long-Term Follow-Up: A Case-Control Study (2013)

Lumbar disc degeneration increased at all measured levels independent of fusion and correlated poorly with clinical outcome.
Synthesis of naphthoquinone antibiotics: conjugate addition/electrophile trapping with acylnickel carbonylate anions (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of naphthoquinone antibiotics: conjugate addition/electrophile trapping with acylnickel carbonylate anionsM. F. Semmelhack, Leonard Keller, Tadahisa Sato, and E. SpiessCite this: J. Org. Chem. 1982, 47, 22, 4382–4384Publication Date (Print):October 1, 1982Publication History Published online1 May 2002Published inissue 1 October 1982https://pubs.acs.org/doi/10.1021/jo00143a055https://doi.org/10.1021/jo00143a055research-articleACS PublicationsRequest reuse permissionsArticle Views308Altmetric-Citations42LEARN 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
Calling Out Bluff: Attacking the Robustness of Automatic Scoring Systems with Simple Adversarial Testing. (2020)

A significant progress has been made in deep-learning based Automatic Essay Scoring (AES) systems in the past two decades. The performance commonly measured by the standard performance metrics like Quadratic Weighted Kappa (QWK), and accuracy points to the same. However, testing on common-sense adversarial examples of these AES systems reveal their lack of natural language understanding capability. Inspired by common student behaviour during examinations, we propose a task agnostic adversarial evaluation scheme for AES systems to test their natural language understanding capabilities and overall robustness.
Axl, Immune Checkpoint Molecules and HIF Inhibitors from the Culture Broth of Lepista luscina (2022)

Two compounds <b>1</b> and <b>2</b> were isolated from the culture broth of <i>Lepista luscina</i>. This is the first time that compound <b>1</b> was isolated from a natural source. The structure of compound <b>1</b> was identified via 1D and 2D NMR and HRESIMS data. Compounds <b>1</b> and <b>2</b> along with 8-nitrotryptanthrin (<b>4</b>) were evaluated for their biological activities using the A549 lung cancer cell line. As a result, <b>1</b> and <b>2</b> inhibited the expression of Axl and immune checkpoint molecules. In addition, compounds <b>1</b>, <b>2</b> and <b>4</b> were tested for HIF inhibitory activity. Compound <b>2</b> demonstrated statistically significant HIF inhibitory effects on NIH3T3 cells and <b>1</b> and <b>2</b> against ARPE19 cells.
Over-Testing for Suspected Pulmonary Embolism in American Emergency Departments (2020)

Over-testing for PE in American EDs remains a major public health problem. Centers with higher D-dimer ordering had higher yield of PE on CTPA. These data suggest the potential for implementation of D-dimer based protocols to reduce low-yield CTPA ordering.
Fluorescence and two-photon absorption of push—pull aryl(bi)thiophenes: structure—property relationships (2012)

Photophysical and TPA properties of series of push-pull aryl(bi)thiophene chromophores bearing electron-donating (D) and electron-withdrawing (A) end-groups of increasing strength are presented. All compounds show an intense intramolecular charge transfer (ICT) absorption band in the visible region. Increasing the D and/or A strength as well as the length of the conjugated path induces bathochromic and hyperchromic shifts of the absorption band as reported for analogous push-pull polyenes. Yet, in contrast with corresponding push-pull polyenes, a significant increase in fluorescence is observed. In particular, chromophores built from a phenyl-bithienyl conjugated path and bearing strong D and A end-groups were found to combine very large one and two-photon brightness as well as strong emission in the red/NIR region. These molecules hold promise as biphotonic fluorescent probes for bioimaging.
Growth of p-type and n-type m-plane GaN by molecular beam epitaxy (2006)

Plasma-assisted molecular beam epitaxial growth of Mg-doped, p-type and Si-doped, n-type m-plane GaN on 6H m-plane SiC is demonstrated. Phase-pure, m-plane GaN films exhibiting a large anisotropy in film mosaic (∼0.2° full width at half maximum, x-ray rocking curve scan taken parallel to [112¯0] versus ∼2° parallel to [0001]) were grown on m-plane SiC substrates. Maximum hole concentrations of ∼7×1018cm−3 were achieved with p-type conductivities as high as ∼5Ω−1cm−1 without the presence of Mg-rich inclusions or inversion domains as viewed by cross-section transmission electron microscopy. Temperature dependent Hall effect measurements indicate that the Mg-related acceptor state in m-plane GaN is the same as that exhibited in c-plane GaN. Free electron concentrations as high as ∼4×1018cm−3 were measured in the Si-doped m-plane GaN with corresponding mobilities of ∼500cm2∕Vs measured parallel to the [112¯0] direction.