gebhart/patrepeval huggingface dataset:
Treatment With a Spleen Tyrosine Kinase Inhibitor Reduced Inflammation and Protected Kidney Function in Experimental Renal Allograft Rejection. (2014)

Introduction: Spleen tyrosine kinase (SYK) mediates signalling of immune receptors. We have shown that fostamatinib, a SYK inhibitor, was effective in treatment of antibody mediated experimental glomerulonephritis (JASN. 21:231, 2010). We have now studied SYK inhibition for prevention of renal allograft rejection. Method: We studied the effect of fostamatinib (from Rigel Pharmaceuticals and AstraZeneca) in a rat (Brown Norway (BN) to Lewis (LEW)) model of renal allograft rejection. In experiment 1, the left kidney of a LEW rat was replaced by a left kidney from a BN rat. This is a severe model of rejection characterised by cortical infarction by day 7. Severity of rejection was analysed after 7 days. The percentage of the cortex of the allograft with infarction was assessed by a pathologist blinded to treatment group on to the following scale: 0=0, 0-10%=1, 11-25%=2, 26-50% =3, 51-75%=4, >75%=5. In experiment 2, bilateral nephrectomy was performed in the recipient LEW rat at the time of transplantation so that transplant kidney function could be assessed by creatinine clearance (CrCl); rats were culled on day 6 for assessment of cell infiltrates before graft infarction. Treatment was given by gavage twice daily. The results are median values analysed by non-parametric tests. Results: In experiment 1, control rats (vehicle or no treatment, n=10), showed severe allograft infarction, grade 5. In the fostamatinib treated rats, there was complete prevention of allograft infarction grade 0 and 0 in rats treated with 30 mg/kg (n=7) or 20 mg/kg (n=7) respectively twice daily (p<0.001). In experiment 2, treatment was started on day 2 when the rats recovered from surgery. Treatment with 30 mg/kg of fostamatinib twice daily from day 2-6 reduced severity of tubulointerstitial injury, grade 3, in the fostamatinib treated group (n=8) v grade 5, (p<0.005) in the vehicle treated group (n=7), reduced cortical infiltration by macrophages (1.7 v 10.5 au by image analysis, p<0.005) and CD8+ cells (1.7 v 7.4 au, p<0.05) and protected renal function compared with the vehicle treatment (CrCl 4.2 v 0.1 ml/min, p<0.005). Conclusion: Treatment with a SYK inhibitor reduces the severity of experimental renal allograft rejection and protects renal function. DISCLOSURE:Masuda, E.: Employee, Rigel Pharmaceuticals, Other, Rigel Pharmaceuticals, Stock option. Tam, F.: Grant/Research Support, AstraZeneca, Other, Rigel Pharmaceuticals, Consultancy.
Novel Bioactive and Therapeutic Root Canal Sealers with Antibacterial and Remineralization Properties (2020)

According to the American Dental Association Survey of Dental Services Rendered (published in 2007), 15 million root canal treatment procedures are performed annually. Endodontic therapy relies mainly on biomechanical preparation, chemical irrigation and intracanal medicaments which play an important role in eliminating bacteria in the root canal. Furthermore, adequate obturation is essential to confine any residual bacteria within the root canal and deprive them of nutrients. However, numerous studies have shown that complete elimination of bacteria is not achieved due to the complex anatomy of the root canal system. There are several conventional antibiotic materials available in the market for endodontic use. However, the majority of these antibiotics and antiseptics provide short-term antibacterial effects, and they impose a risk of developing antibacterial resistance. The root canal is a dynamic environment, and antibacterial and antibiofilm materials with long-term effects and nonspecific mechanisms of action are highly desirable in such environments. In addition, the application of acidic solutions to the root canal wall can alter the dentin structure, resulting in a weaker and more brittle dentin. Root canal sealers with bioactive properties come in direct contact with the dentin wall and can play a positive role in bacterial elimination and strengthening of the root structure. The new generation of nanostructured, bioactive, antibacterial and remineralizing additives into polymeric resin-based root canal sealers are discussed in this review. The effects of these novel bioactive additives on the physical and sealing properties, as well as their biocompatibility, are all important factors that are presented in this article.
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles (2020)

JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR—the JASPAR CORE subcollection, which contains curated, non-redundant profiles—with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.
Polynomial approximations in the polytope model: Bringing the power of quasi-polynomials to the masses (2008)

This paper addresses one issue in the polyhedral model of loop nests that limits its practical applicability. We present methods for avoiding the use of quasi-polynomials when enumerating integer points in polyhedra, by computing polynomial approximations of the quasi-polynomials and also polynomial upper and lower bounds of the quasi-polynomial. We propose two methods and different variants thereof. An evaluation on a set of systems of linear equalities generated by several compiler analyses shows that the accuracy of our more advanced method is similar to or better than the accuracy of existing techniques, while the computation is faster on difficult problems.
Consensus Guidelines for the Definition of Time-to-Event End Points in Image-guided Tumor Ablation: Results of the SIO and DATECAN Initiative (2021)

There is currently no consensus regarding preferred clinical outcome measures following image-guided tumor ablation or clear definitions of oncologic end points. This consensus document proposes standardized definitions for a broad range of oncologic outcome measures with recommendations on how to uniformly document, analyze, and report outcomes. The initiative was coordinated by the Society of Interventional Oncology in collaboration with the Definition for the Assessment of Time-to-Event End Points in Cancer Trials, or DATECAN, group. According to predefined criteria, based on experience with clinical trials, an international panel of 62 experts convened. Recommendations were developed using the validated three-step modified Delphi consensus method. Consensus was reached on when to assess outcomes per patient, per session, or per tumor; on starting and ending time and survival time definitions; and on time-to-event end points. Although no consensus was reached on the preferred classification system to report complications, quality of life, and health economics issues, the panel did agree on using the most recent version of a validated patient-reported outcome questionnaire. This article provides a framework of key opinion leader recommendations with the intent to facilitate a clear interpretation of results and standardize worldwide communication. Widespread adoption will improve reproducibility, allow for accurate comparisons, and avoid misinterpretations in the field of interventional oncology research. Published under a CC BY 4.0 license. <i>Online supplemental material is available for this article.</i> See also the editorial by Liddell in this issue.
Dense multipath depolarization in outdoor and indoor radio transmissions (2014)

The polarimetric properties of so-called Dense Multipath Components (DMC) are investigated in various outdoor and indoor environments, relying on broadband measurements and Ray-Tracing (RT) simulations. The ultimate goal is to parameterize a heuristic Diffuse Scattering model to be embedded in RT tools, in order to reproduce the experimentally observed cross-polar discrimination (XPD) characteristics.
Measuring the thermal conductivity of the GaN buffer layer in AlGaN/GaN HEMTs: Effect of carbon and iron doping (2015)

A thermal conductivity of 200±20 Wm-1K -1 has been determined for the carbon-doped (concentration of 1017 cm-3) GaN buffer layer of an AlGaN/GaN HEMT using new experimental techniques. Micro-Raman thermography combined with diamond micro-thermometry were used to measure the vertical temperature gradient through the device layers and finite element thermal simulation was fit to the measured temperatures to determine the GaN layer thermal conductivity. This technique is beneficial as it can be used on standard device wafers with no additional test structures required. Furthermore we have found that the thermal conductivity of iron-doped (concentration of 1018 cm-3) and carbon-doped (concentration of 1017 cm-3) buffer layers studied are very similar.
Type I nitroreductases in soil enterobacteria reduce TNT (2,4,6-trinitrotoluene) and RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) (2000)

Many enteric bacteria express a type I oxygen-insensitive nitroreductase, which reduces nitro groups on many different nitroaromatic compounds under aerobic conditions.Enzymatic reduction of nitramines was also docu mented in enteric bacteria under anaerobic conditions.This study indicates that nitramine reduction in enteric bacteria is carried out by the type I, or oxygen-insensitive nitroreductase, rather than a type II enzyme.The enteric bacterium Morganella morganii strain B2 with documented hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) nitroreductase activity, and Enterobacter cloacae strain 96-3 with documented 2,4,6-trinitrotoluene (TNT) nitroreductase activity, were used here to show that the explosives TNT and RDX were both reduced by a type I nitroreductase.Morganella morganii and E. cloacae exhibited RDX and TNT nitroreductase activities in whole cell assays.Type I nitroreductase, purified from E. cloacae, oxidized NADPH with TNT or RDX as substrate.When expression of the E. cloacae type I nitroreductase gene was induced in an Escherichia coli strain carrying a plasmid, a simultaneous increase in TNT and RDX nitroreductase activities was observed.In addition, neither TNT nor RDX nitroreductase activity was detected in nitrofurazone-resistant mutants of M. morganii.We conclude that a type I nitroreductase present in these two enteric bacteria was responsible for the nitroreduction of both types of explosive.
Filtered gradient algorithm for closed loop MIMO systems (2005)

This paper proposes a new adaptive beamforming algorithm for FDD MIMO systems with closed loop feedback. We base our work on recently proposed sign gradient methods [Banister, BC et al., 2003][Raghothaman, B 2003] that aim to maximize the signal to noise ratio (SNR) at the user equipment (UE) by adapting the complex baseband weights of the base station (BS) transmit antenna array, based on the quantized feedback information. The methods use simplified gradient estimates, suitable for slowly fading channels. In order to improve tracking in fast fading channels, we propose an algorithm that utilizes filtering of the gradient estimates and orthogonal stochastic search directions. Simulations show an improvement of 1 dB in uncorrelated channels at 30 km/h.
Erratum to: Resolving and assigning N-linked glycan structural isomers from ovalbumin by IMS-MS (2009)

ADVERTISEMENT RETURN TO ISSUEPREVAdditions & Corr...Additions & CorrectionsNEXTORIGINAL ARTICLEThis notice is a correctionErratum to: Resolving and assigning N-linked glycan structural isomers from ovalbumin by IMS-MSManolo D. PlasenciaManolo D. PlasenciaMore by Manolo D. Plasencia, Dragan IsailovicDragan IsailovicMore by Dragan Isailovic, Samuel I. MerenbloomSamuel I. MerenbloomMore by Samuel I. Merenbloom, Yehia MechrefYehia MechrefMore by Yehia Mechref, Milos V. NovotnyMilos V. NovotnyMore by Milos V. Novotny, and David E. ClemmerDavid E. ClemmerMore by David E. ClemmerCite this: J Am Soc Mass Spectrom 2010, 21, 1, 191Publication Date (Web):November 22, 2011Publication History Published online22 November 2011Published inissue 1 January 2010https://pubs.acs.org/doi/10.1016/j.jasms.2009.09.021https://doi.org/10.1016/j.jasms.2009.09.021correctionACS PublicationsCopyright © 2010 © American Society for Mass Spectrometry 2010. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views29Altmetric-Citations1LEARN 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 PDF (34 KB) Get e-Alerts
Three-dimensional analysis of ion beam deflection by the magnetic field at H− ion sources for the negative-ion-based neutral beam injection (1998)

In negative-ion-based neutral beam injection (NBI) systems for the large helical device (LHD), beams must be transported over 13 m from the H− ion source to the injection port. In order to clarify beam deflection by the electron deflection magnets set in a beam extraction grid (EG) and to control beam transport direction, we analyzed beam trajectories. The physics of the beam deflection was studied with theoretical calculations and the deflection angle was estimated by 3D beam trajectory simulation. The evaluated deflection angle was 10 mrad in the opposite direction of the electron deflection when the maximum magnetic field on the beam axis was 480 G and the beam energy was 83.2 keV. The electrostatic lens effect on the beam deflection at the EG exit was estimated to be larger than the magnetic field effect. This deflection was reduced to 2 mrad by a 1.3 mm displacement of the grounded grid (GG) aperture, a result in agreement with experimental results of a 1/3-scale model for the LHD ion source. The maximum GG aperture displacement of the LHD ion source was designed as 3.4 mm to reduce the deflection and to focus multibeamlets using the simulation. We have developed the ion source with this design. The targeted performance is a production of H− beams of 40 A (40 mA/cm2), 180 keV.
Continuous Flow Synthesis of Chiral Amines in Organic Solvents: Immobilization of E. coli Cells Containing Both ω-Transaminase and PLP (2014)

E. coli cells containing overexpressed (R)-selective ω-transaminase and the cofactor PLP were immobilized on methacrylate beads suitable for continuous flow applications. The use of an organic solvent suppresses leaching of PLP from the cells; no additional cofactor was required after setting up the packed-bed reactor containing the biocatalyst (ω-TA-PLP). Non-natural ketone substrates were transformed in flow with excellent enantioselectivity (>99% ee). Features of this novel system include high-throughput (30-60 min residence time), clean production (no quench, workup, or purification required), high enzyme stability (the packed-bed reactor can be continuously operated for 1-10 days), and excellent mass recovery.
A monolithic Knudsen pump WITH 20 sccm flow rate using through-wafer ONO channels (2014)

This paper describes a lithographically microfabricated Knudsen pump for high gas flow. Knudsen pumps operate by thermal transpiration and require no moving parts. To achieve high gas flow, high-density arrays of microchannels (with over 4000 channels/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) are used in parallel. These vertically oriented microchannels have 2×120 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> openings surrounded by 0.1 μm-thick silicon oxide-nitride-oxide (ONO) sidewalls. The thin ONO sidewalls provide thermal isolation between a heat sink formed within the Si substrate, and a Cr/Pt heater that provides a temperature bias for thermal transpiration. The Knudsen pump is monolithically microfabricated on a single wafer using a four-mask process. It has a footprint of 8×10 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . It produces a measured air flow of 20 sccm (i.e., 0.8 sccm/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), with typical response times of 0.1–0.4 sec.
Genetic analysis ofEscherichia colifrom porcine postweaning diarrhoea (1993)

A total of 79 Australian isolates of beta-haemolytic Escherichia coli from cases of porcine postweaning diarrhoea (PWD), and 18 isolates of serotype O 149:K91:K88 (F4) from unweaned pigs from Australia, Indonesia and Denmark, were examined by multilocus enzyme electrophoresis. These were divided into 57 electrophoretic types (ETs), with an overall mean genetic diversity per enzyme locus of 0.466. This value closely resembled that previously recorded for the whole species. Not only was the collection diverse, but there was considerable genetic heterogeneity amongst PWD isolates of the same serogroup. Isolates from serogroups O 8 and O 138 were most varied, whilst many from serogroups O 141 and O 149 were more closely related. In contrast, the isolates from the unweaned pigs all belonged to only one ET.
Immunity of six-port measurement techniques to the AM-PM noise of the microwave signal generator (2002)

This paper presents a study of the influence of AM-PM noise present in a microwave source on the precision of six-port measurements. It has been found that a noisy microwave signal source does not degrade the precision of the measurements. Experimental validation on passive and active devices was carried out and confirm the immunity of six-port measurement techniques to the AM-PM noise of the microwave signal generator.
ChemInform Abstract: Oxalyl Chloride as a Practical Carbon Monoxide Source for Carbonylation Reactions. (2015)

Abstract This describes a variety of Pd‐catalyzed carbonylation reactions performed with ex‐situ‐generated carbon monoxide.
Using Scan Side Channel to Detect IP Theft (2017)

In the growing heterogeneous Internet of Things market, which embraces a plurality of vendors and service providers, IP protection plays a central role. This paper proposes a process for the detection of IP theft in VLSI devices that exploits the internal test scan chains, designed for production test automation. The scan chains supply direct access to the internal registers in the device, enabling combinational analysis of the device logic. By using Boolean function learning methods, the learner creates a partial dependence graph of the internal flip-flops. The graph is further partitioned using the shared nearest neighbors graph clustering method, and individual blocks of combinational logic are isolated. These blocks can be matched with known building blocks that compose the original function. This enables reconstruction of the function implementation to the level of pipeline structure. The IP owner can compare the resulting structure with his own implementation to confirm whether an IP violation has occurred. We demonstrate the power of the presented approach with a test case of an open source Bitcoin SHA-256 accelerator, containing more than 80 000 registers. With the presented method, we discover the microarchitecture of the module, locate all the main components of the SHA-256 algorithm, and learn the module's flow control. In addition to the direct recognition of the IP content, we also demonstrate a combination of reverse engineering and watermark methods. We define a new watermark structure-pipeline-associated watermark (PAW), combined with pipeline stages that can be detected with the scan-based reverse engineering method.
What experimental approaches (eg, in vivo, in vitro, tissue retrieval) are effective in investigating the biologic effects of particles? (2008)

Understanding the complex cellular and tissue mechanisms and interactions resulting in periprosthetic osteolysis requires a number of experimental approaches, each of which has its own set of advantages and limitations. In vitro models allow for the isolation of individual cell populations and have furthered our understanding of particle-cell interactions; however, they are limited because they do not mimic the complex tissue environment in which multiple cell interactions occur. In vivo animal models investigate the tissue interactions associated with periprosthetic osteolysis, but the choice of species and whether the implant system is subjected to mechanical load or to unloaded conditions are critical in assessing whether these models can be extrapolated to the clinical condition. Rigid analysis of retrieved tissue from clinical cases of osteolysis offers a different approach to studying the biologic process of osteolysis, but it is limited in that the tissue analyzed represents the end-stage of this process and, thus, may not reflect this process adequately.
Effects of surface chemical potentials on cation segregation (2020)

The presence of gas molecules alters the surface cation segregation process on perovskites.
Polyvalent DNA-Nanoparticle Conjugates Stabilize Nucleic Acids* (2020)

Polyvalent oligonucleotide gold nanoparticle conjugates have unique fundamental properties including distance-dependent plasmon coupling, enhanced binding affinity, and the ability to enter cells and resist enzymatic degradation. In this chapter, the authors quantify the enhanced stability of polyvalent gold oligonucleotide nanoparticle conjugates with respect to enzyme-catalyzed hydrolysis of DNA and present evidence that the negatively charged surfaces of the nanoparticles and resultant high local salt concentrations are responsible for enhanced stability. They examine the stability of the DNA on a nanoparticle surface as a function of surface coverage and provide an explanation for why these structures resist enzymatic degradation. Enzyme-catalyzed DNA degradation can be modeled as a 2-step reaction that involves the association of the enzyme with the substrate, and the hydrolysis of the nucleic acids. The enhanced stability observed for DNA-gold nanoparticles could result from a decrease in rate of either of these two steps.