gebhart/patrepeval huggingface dataset:
Phenotypic Drug Resistance Patterns in Subtype A HIV-1 Clones with Nonnucleoside Reverse Transcriptase Resistance Mutations (2006)

We analyzed the nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI) susceptibility of 29 subtype A HIV-1 clones isolated from 10 Ugandan women after single-dose nevirapine (NVP) administration. Six clones had no NNRTI resistance-associated mutations ("wild type"), eight had K103N, nine had Y181C, five had G190A, and one had Y181S. Three clones displayed unexpected phenotypic drug susceptibility/resistance based on their RT genotypes. One wild-type clone had reduced susceptibility to NVP, delavirdine (DLV), and efavirenz (EFV), one clone with K103N was susceptible to all three NNRTIs, and one clone with G190A had extreme hypersusceptibility to DLV. Three unusual HIV-1 RT amino acid substitutions may have contributed to the unexpected phenotypes of the clones: I31T, N136S, and N265D. These polymorphisms were rarely detected among 47,900 HIV-1 genotypes from clinical samples of predominantly United States origin. Further studies are needed to define the genetic correlates of antiretroviral drug resistance in nonsubtype B HIV-1.
Metrinome: Continuous Monitoring and Security Validation of Distributed Systems (2014)

Abstract : Distributed enterprise systems consist of a collection of interlinked services and components that exchange information to collectively implement functionality in support of (sometimes mission critical) workflows. Systematic experimental testing and continuous runtime monitoring of these large scale distributed systems, including event interpretation and aggregation, are key to ensuring that the system s implementation functions as expected and that its security is not compromised
Poly(ADP-ribose) polymerase -14 interacts with tristetraprolin to selectively regulate tissue factor mRNA stability: a novel role for ADP-ribosylation in regulating mRNA turnover and thrombosis (2013)

Background: Targeting post-transcriptional pathways is now emerging as a promising therapeutic strategy in a wide spectrum of diseases. Monocyte-derived tissue factor (TF) plays critical roles in atherothrombosis, but little is known about its post-transcriptional regulation. Tristetraprolin (TTP) is the most widely studied mRNA-binding protein, and binds to the 3'UTR of target mRNAs and promotes decay. Poly(ADP-ribose)-polymerase-14 (PARP-14), belongs to a family of ∼17 proteins with a PARP domain that generates poly(ADP-ribose) adducts on intracellular proteins – a post-translational modification implicated in diverse cellular functions. Purpose: We sought to determine the roles for TTP and PARP-14 in regulating TF expression, and the role of ADP ribosylation in TF mRNA turnover. Methods and results: TF mRNA and protein were increased in TTP-/- vs TTP+/+ macrophages (p<0.05) with increased TF mRNA stability (t1/2=347±62min vs 82±14min,p<0.001). Similarly, TF mRNA and protein were increased in PARP14-/- vs PARP-14+/+ macrophages (p<0.05) with increased TF mRNA stability (t1/2=181±11min vs 60±5min,p<0.001). TF mRNA, activity and protein were increased in vivo (heart, lung, kidney, aorta and unfractionated circulating leukocytes) in PARP-14-/- vs PARP-14+/+ mice (p<0.05). Intravital microscopy demonstrated a 66% reduction in median arteriolar occlusion time in LPS-stimulated PARP-14-/- vs PARP-14+/+ mice (p=0.008). RNP immunoprecipitation and RNA biotin pulldown assays demonstrated an interdependency for PARP-14 and TTP to form a ternary complex with TF mRNA, where both proteins interacted within the same 3'UTR segment. Inhibition of PARP activity reduced TF mRNA stability in PARP-14+/+ macrophages (p=0.018), but not in PARP-14-/- macrophages. Interestingly, PARP-14 conferred selectivity for TTP to degrade TF mRNA, as PARP-14 had no effect on TNFα, an established target of TTP, both in vitro and in vivo. Accordingly, PARP inhibition had no effect on TNFα mRNA decay. Conclusions: These data define novel roles for TTP and PARP-14 in the selective regulation of TF mRNA turnover. PARP-14 functions as an accessory RNA-binding protein which is required for TTP to bind and degrade TF mRNA. Furthermore, inhibition of PARP-14 catalytic activity promotes TTP-mediated TF mRNA decay. These data also show for the first time how the actions of TTP may be selectively regulated. Thus selective destabilization of TF mRNA via pharmacological inhibition of PARP-14 may offer a novel therapeutic strategy in atherosclerosis and cardiovascular disease where thrombosis is linked to TF expression.
Near- and far-field investigation of dark and bright higher order resonances in square loop elements at mid-infrared wavelengths (2017)

Three different size gold square loop structures were fabricated as arrays on ZnS over a ground plane and designed to have absorptive fundamental, second order, and third order resonances at a wavelength of 10.6 µm and 60° off-normal. The angular dependent far-field spectral absorptivity was investigated over the mid-infrared for each size loop array. It was found that the second order modes were dark at normal incidence, but became excited at off-normal incidence, which is consistent with previous work for similar geometry structures. Furthermore, near-field measurements and simulations at a wavelength of 10.6 µm and 60° off-normal showed that the second order mode (quadrupolar) of the medium size loop yielded a near-field response similar in magnitude to the fundamental mode (dipolar) of the small size loop, which can be important for sensing related applications where both strong near-field enhancement and more uniform or less localized field is beneficial.
Developments in oncological positron emission tomography/computed tomography assessment. (2015)

Positron emission tomography (PET)/computed tomography (CT) using 18 F-fluorodeoxyglucose (FDG) has become a standard tool for staging and therapy monitoring in oncology. Qualitative assessment of tracer uptake has become the basis for important therapy decisions such as whether to continue or abandon radiotherapy after effective chemotherapy in advanced Hodgkin lymphoma (1,2). The tools for this PET interpretation have to be reproducible and standardized, to ensure adequate treatment for all patients (2,3). In contrast to some lymphatic malignancies, cure rates are generally lower in most advanced solid tumors. If responses to a specific treatment occur, they can easily be detected by quantitative analyses, which are more sensitive than visual criteria. Therefore, quantitative PET analyses have been introduced in solid tumor PET studies and several PET parameters have been proposed as a supplement to visual analyses to measure the patient’s response to a specific treatment (4).
Conversion of Creatinine in the Presence of Activated Carbon (1977)

Activated carbon (a.c.) coated with different types of polymer has been used as a sorbent in haemoperfusion techniques for the removal of toxic products (drug overdose, metabolites, etc). The adsorption capacity of different types of a.c. for creatinine, uric acid, etc, has to be determined to select the types of a.c. best suited for specific purposes. Dedrick et al. (1967) have studied the adsorption of uric acid onto the a.c. Columbia NXC (Union Carbide Corporation). They reported that uric acid in contact with a.c. was converted at least partially into yet unknown products. We report on the conversion of creatinine in the presence of a.c. (Norit RBX1) and oxygen.
Interpolation for non-linear Retinex-type algorithms (2007)

image processing, retinex-type algorithms, image interpolation In this paper we propose a method to speed up Retinex-type algorithms, consisting of a computationally intensive non-linear illumination estimation module followed by a relatively simple manipulation module. Speed up is obtained by way of computing the illumination on a subsampled image. The challenge is to interpolate a piece-wise smooth low resolution image. We present and analyze the trade off between two types of interpolation methods. On one hand, regular illumination interpolation, which preserves the Retinex-type output quality, however may result in artifacts. On the other hand a detail preserving interpolation which removes artifacts, however may compromise the output quality.
Redox-Active Pyocyanin Secreted by Pseudomonas aeruginosa 7NSK2 Triggers Systemic Resistance to Magnaporthe grisea but Enhances Rhizoctonia solani Susceptibility in Rice (2006)

Pseudomonas aeruginosa 7NSK2 induces resistance in dicots through a synergistic interaction of the phenazine pyocyanin and the salicylic acid-derivative pyochelin. Root inoculation of the monocot model rice with 7NSK2 partially protected leaves against blast disease (Magnaporthe grisea) but failed to consistently reduce sheath blight (Rhizoctonia solani). Only mutations interfering with pyocyanin production led to a significant decrease in induced systemic resistance (ISR) to M. grisea, and in trans complementation for pyocyanin production restored the ability to elicit ISR. Intriguingly, pyocyanin-deficient mutants, unlike the wild type, triggered ISR against R. solani. Hence, bacterial pyocyanin plays a differential role in 7NSK2-mediated ISR in rice. Application of purified pyocyanin to hydroponically grown rice seedlings increased H202 levels locally on the root surface as well as a biphasic H202 generation pattern in distal leaves. Co-application of pyocyanin and the antioxidant sodium ascorbate alleviated the opposite effects of pyocyanin on rice blast and sheath blight development, suggesting that the differential effectiveness of pyocyanin with respect to 7NSK2-triggered ISR is mediated by transiently elevated H202 levels in planta. The cumulative results suggest that reactive oxygen species act as a double-edged sword in the interaction of rice with the hemibiotroph M. grisea and the necrotroph R. solani.
Investigating the detection capability of RSNs with fMRI at a low field scanner equipped with a high-performance gradient (2023)

Preliminary evaluation of the feasibility to perform resting state BOLD fMRI at a low field (0.5 T) MR scanners equipped with a high-performance gradient system by investing the detection capability of RSNs at lower field strengths. There was an overall deterioration in the number of detected regions within all RSNs as the tSNR decreased. However, the 0.5 Evry system that will be used for experimental studies offer a better SNR efficiency than the modelled cases considered here suggesting reasonable capability in extracting RSNs that can potentially provide clinical utility.
Trap-related delay analysis of self-aligned N-polar GaN/InAlN HEMTs with record extrinsic g<inf>m</inf> of 1105 mS/mm (2011)

Ga-polar InAlN-based charge-inducing barrier for HEMTs have been recently demonstrated as a viable technology for high frequency applications due to high polarization charge and hence, low resistance channels. In this paper, we report on MBE-grown N-polar GaN/InAlN HEMTs with excellent DC and RF performance. There exists a discrepancy in the DC and RF data for N-polar MBE InAlN devices which is explained through several measurements and analysis and possible solutions are discussed.
Fixation, Polyethylene Wear, and Pelvic Osteolysis in Primary Total Hip Replacement (1999)

A multicenter retrospective review was performed analyzing 1081 primary total hip replacements in 944 patients using the Harris Galante-I cementless acetabular component with screw fixation. All patients were followed up for a minimum of 5 years with a mean followup of 81 months. Linear polyethylene wear averaged 0.11 mm/year (range, 0-0.86 mm/year). Pelvic osteolysis was seen in 25 patients (2.3%). Migration of the acetabular component was seen in four hips. A subgroup of patients was reanalyzed at a minimum followup of 10 years. The mean linear polyethylene wear rate remained 0.11 mm/year. In this group, only one socket had migrated. There was an association between wear rate and age. On average, younger patients had higher wear rates. The risk for having pelvic osteolysis develop and the need for revision surgery also was age-related. Twenty-two percent of hip replacements (15 hips) in patients younger than 50 years of age at the time of their index operation had pelvic osteolysis develop. In contrast, for patients older than 50 years of age at the time of surgery only 7.8% (eight hips) had osteolysis of the pelvis develop. For patients older than 70 years of age at the time of primary total hip replacement, none had pelvic osteolysis develop.
Hydrophone Spatial Averaging Correction for Acoustic Exposure Measurements From Arrays—Part II: Validation for ARFI and Pulsed Doppler Waveforms (2020)

This article reports the experimental validation of a method for correcting underestimates of peak compressional pressure ( p<sub>c</sub>) , peak rarefactional pressure ( p<sub>r</sub>) , and pulse intensity integral (pii) due to hydrophone spatial averaging effects that occur during output measurement of clinical linear and phased arrays. Pressure parameters ( p<sub>c</sub> , p<sub>r</sub> , and pii), which are used to compute acoustic exposure safety indexes, such as mechanical index (MI) and thermal index (TI), are often not corrected for spatial averaging because a standardized method for doing so does not exist for linear and phased arrays. In a companion article (Part I), a novel, analytic, inverse-filter method was derived to correct for spatial averaging for linear or nonlinear pressure waves from linear and phased arrays. In the present article (Part II), the inverse filter is validated on measurements of acoustic radiation force impulse (ARFI) and pulsed Doppler waveforms. Empirical formulas are provided to enable researchers to predict and correct hydrophone spatial averaging errors for membrane-hydrophone-based acoustic output measurements. For example, for a 400- [Formula: see text] membrane hydrophone, inverse filtering reduced errors (means ± standard errors for 15 linear array/hydrophone pairs) from about 34% ( p<sub>c</sub>) , 22% ( p<sub>r</sub>) , and 45% (pii) down to within 5% for all three parameters. Inverse filtering for spatial averaging effects significantly improves the accuracy of estimates of acoustic pressure parameters for ARFI and pulsed Doppler signals.
Hole transport layer material and solar cell using hole transport layer material having high photoelectric conversion efficiency (2016)

Patent number: JP 2016100478 A 20160530 Reference EPFL-PATENT-221238Search for this record at the European Patent Office Record created on 2016-09-10, modified on 2017-05-12
A naphthenic jet fuel produced from an Australian marine oil shale (1987)

CSR Limited holds title to an Authority to Prospect covering the Cretaceous Julia Creek oil shale deposit, located in Queensland, Australia, approximately 600 km inland from the eastern seaboard. The shale is of marine origin, having been deposited as an anaerobic sediment in a restricted epicontinental sea. Algae are the predominant source of organic matter. Resources are estimated at 20 billion barrels of oil, approximately half in shale deposits suitable for open cut mining. Typical oil shale analyses are given. Average oil yields are 70 liters per ton. The oil has several deleterious characteristics which necessitate its upgrading at higher severity than is conventional at existing refineries. Heteroatom levels are in total significantly higher than values for petroleum crudes and the aromaticity and metal content of the oil add to its complexity and unusual nature. Two processing routes have been proposed for this oil - either the production of a syncrude by hydrostabilization of the whole oil, or alternatively, upgrading separate fractions to marketable fuels. Pilot plant studies were carried out to simulate refinery processes options. During these investigations, they were successful in the first Australian production of shale-derived jet and diesel synfuels which met all specifications. In this paper,more » they present details of the jet fuel production and describe its unusual naphthenic character.« less
Erratum to: Controlled Motion with the XL-TDR Lateral-Approach Lumbar Total Disk Replacement: In Vitro Kinematic Investigation (J Neurol Surg A Cent Eur Neurosurg 2015;76(2):133–138) (2015)

Correction to: Controlled Motion with the XL-TDR Lateral-Approach Lumbar Total Disk Replacement: In Vitro Kinematic InvestigationJ Neurol Surg A Cent Eur Neurosurg 2015; 76(02): 133-138DOI: 10.1055/s-0034-1394187
<title>Using the human eye to characterize displays</title> (2001)

Monitor characterization has taken on new importance for non-professional users, who are not usually equipped to make photometric measurements. Our purpose was to examine some of the visual judgements used in characterization schemes that have been proposed for web users. We studied adjusting brightness to set the black level, banding effects du to digitization, and gamma estimation in the light an din the dark, and a color-matching tasks in the light, on a desktop CRT and a laptop LCD. Observers demonstrated the sensitivity of the visual system for comparative judgements in black- level adjustment, banding visibility, and gamma estimation. The results of the color-matching task were ambiguous. In the brightness adjustment task, the action of the adjustment was not as presumed; however, perceptual judgements were as expected under the actual conditions. Whenthe gamma estimates of observers were compared to photometric measurements, pro9blems with the definition of gamma were identified. Information about absolute light levels that would be important for characterizing a display, given the shortcomings of gamma in measuring apparent contrast, are not measurable by eye alone. The LCD was not studied as extensively as the CRT because of viewing-angle problems, and its transfer function did not follow a power law, rendering gamma estimation meaningless.
Plant cell wall integrity maintenance and pattern-triggered immunity modulate jointly plant stress responses in Arabidopsis thaliana (2017)

Abstract Plant cells are surrounded by walls, which must often meet opposing functional requirements during plant growth and defense. The cells meet them by modifying wall structure and composition in a tightly controlled and adaptive manner. The modifications seem to be mediated by a dedicated cell wall integrity (CWI) maintenance mechanism. Currently the mode of action of the mechanism is not understood and it is unclear how its activity is coordinated with established plant defense signaling. We investigated responses to induced cell wall damage (CWD) impairing CWI and the underlying mechanism in Arabidopsis thaliana. Interestingly inhibitor- and enzyme-derived CWD induced similar, turgor-sensitive stress responses. Genetic analysis showed that the receptor-like kinase (RLK) FEI2 and the mechano-sensitive, plasma membrane-localized Ca 2+ - channel MCA1 function downstream of the THE1 RLK in CWD perception. Phenotypic clustering with 27 genotypes identified a core group of RLKs and ion channels, required for activation of CWD responses. By contrast, the responses were repressed by pattern-triggered immune (PTI) signaling components including PEPR1 and 2, the receptors for the immune signaling peptide At Pep1. Interestingly At Pep1 application repressed CWD-induced phytohormone accumulation in a PEPR1/2 -dependent manner. These results suggest that PTI suppresses CWD-induced defense responses through elicitor peptide-mediated signaling during defense response activation. If PTI is impaired, the suppression of CWD-induced responses is alleviated, thus compensating for defective PTI. Significance statement Stress resistance and plant growth determine food crop yield and efficiency of bioenergy production from ligno-cellulosic biomass. Plant cell walls are essential elements of the biological processes, therefore functional integrity of the cell walls must be maintained throughout. Here we investigate the plant cell wall integrity maintenance mechanism. We characterize its mode of action, identify essential signaling components and show that the At Pep1 signaling peptide apparently coordinates pattern triggered immunity (PTI) and cell wall integrity maintenance in plants. These results suggest how PTI and cell wall modification coordinately regulate biotic stress responses with plants possibly compensating for PTI impairment through enhanced activation of stress responses regulated by the CWI maintenance mechanism.
Mechanism of Catalytic Oxidation of Styrenes with Hydrogen Peroxide in the Presence of Cationic Palladium(II) Complexes (2017)

Kinetic studies, isotope labeling, and in situ high-resolution mass spectrometry are used to elucidate the mechanism for the catalytic oxidation of styrenes using aqueous hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and the cationic palladium(II) compound, [(PBO)Pd(NCMe)<sub>2</sub>][OTf]<sub>2</sub> (PBO = 2-(pyridin-2-yl)benzoxazole). Previous studies have shown that this reaction yields acetophenones with high selectivity. We find that H<sub>2</sub>O<sub>2</sub> binds to Pd(II) followed by styrene binding to generate a Pd-alkylperoxide that liberates acetophenone by at least two competitive processes, one of which involves a palladium enolate intermediate that has not been previously observed in olefin oxidation reactions. We suggest that acetophenone is formed from the palladium enolate intermediate by protonation from H<sub>2</sub>O<sub>2</sub>. We replaced hydrogen peroxide with t-butyl hydroperoxide and found that, although the palladium enolate intermediate was observed, it was not on the major product-generating pathway, indicating that the form of the oxidant plays a key role in the reaction mechanism.
Multiplex Immunoassay for Serological Diagnosis of Mycobacterium bovis Infection in Cattle (2008)

Efforts to develop a better diagnostic assay for bovine tuberculosis have shown that the sensitivity and specificity of an assay can be improved by the use of two or more antigens. As reported here, we developed a multiplex chemiluminescent immunoassay that can simultaneously detect antibody activity to 25 antigens in a single well in a 96-well plate array format. The chemiluminescent signal is captured with a digital imaging system and analyzed with a macro program that tracks each serum for its pattern of antibody activity for Mycobacterium bovis antigens. The comparison of sera from 522 infected and 1,489 uninfected animals showed that a sensitivity of 93.1% and a specificity of 98.4% can be achieved with a combination of antigens. The assay system is rapid and can be automated for use in a centralized laboratory.
Quick Response Fuel Injector for Direct-Injection Gasoline Engines (2012)

We developed a new injector for direct injection gasoline engines that reduce the exhaust emissions and help to reduce fuel consumption. The newly developed actuator in this injector has two features. One is a bounceless valve closing mechanism, and the second is quick response moving parts. The first feature, the bounceless valve closing mechanism, can prevent ejecting a coarse droplet, which causes unburned gas emission. The new actuation mechanism realizes the bounceless valve closing. We analyzed the valve motion and injection behavior. The second feature, the quick-response actuator, achieves a smaller minimum injection quantity. This feature assists in reducing the fuel consumption under low load engine conditions. The closing delay time of the needle valve is the dominant factor of the minimum injection quantity because the injection quantity is controlled by the duration time of the valve opening. The new actuator movements can be operated with a shorter closing delay time. The closing delay time is caused by a magnetic delay and kinematic delay. A compact magnetic circuit of the actuator reduces the closing delay time by 26%. In addition, the kinematic delay was improved when the hydraulic resistance was reduced by 9%. As a result, the new injector realizes reduction of the minimum injection quantity by 25% compared to a conventional injector.