gebhart/patrepeval huggingface dataset:
Triclosan-Induced Aminoglycoside-Tolerant Listeria monocytogenes Isolates Can Appear as Small-Colony Variants (2014)

Exposure of the human food-borne pathogen Listeria monocytogenes to sublethal concentrations of triclosan can cause resistance to several aminoglycosides. Aminoglycoside-resistant isolates exhibit two colony morphologies: normal-size and pinpoint colonies. The purposes of the present study were to characterize the small colonies of L. monocytogenes and to determine if specific genetic changes could explain the triclosan-induced aminoglycoside resistance in both pinpoint and normal-size isolates. Isolates from the pinpoint colonies grew poorly under aerated conditions, but growth was restored by addition of antibiotics. Pinpoint isolates had decreased hemolytic activity under stagnant conditions and a changed spectrum of carbohydrate utilization compared to the wild type and isolates from normal-size colonies. Genome sequence comparison revealed that all seven pinpoint isolates had a mutation in a heme gene, and addition of heme caused the pinpoint isolates to revert to normal colony size. Triclosan-induced gentamicin-resistant isolates had mutations in several different genes, and it cannot be directly concluded how the different mutations caused gentamicin resistance. However, since many of the mutations affected proteins involved in respiration, it seems likely that the mutations affected the active transport of the antibiotic and thereby caused resistance by decreasing the amount of aminoglycoside that enters the bacterial cell. Our study emphasizes that triclosan likely has more targets than just fabI and that exposure to triclosan can cause resistance to antibiotics that enters the cell via active transport. Further studies are needed to elucidate if L. monocytogenes pinpoint isolates could have any clinical impact, e.g., in persistent infections.
Thiol–yne coupling: revisiting old concepts as a breakthrough for up-to-date applications (2012)

Radical thiol-yne coupling (TYC) has emerged as one of the most appealing click chemistry procedures, appearing as a sound candidate for replacing/complementing other popular click reactions such as the thiol-ene coupling (TEC) and the Cu-catalysed azide-alkyne cycloaddition (CuAAC). Radical TYC is indeed a metal-free reaction suitable for biomedical applications, and its mechanistic features often make it more efficient than its TEC sister reaction and more suitable for multifaceted derivatisations in the materials chemistry and bioconjugation realms. This article reviews the fascinating results obtained in those fields in very recent years.
On the physics of electron ejection from laser-irradiated overdense plasmas (2016)

Using 1D and 2D PIC simulations, we describe and model the backward ejection of electron bunches when a laser pulse reflects off an overdense plasma with a short density gradient on its front side. The dependence on the laser intensity and gradient scale length is studied. It is found that during each laser period, the incident laser pulse generates a large charge-separation field, or plasma capacitor, which accelerates an attosecond bunch of electrons toward vacuum. This process is maximized for short gradient scale lengths and collapses when the gradient scale length is comparable to the laser wavelength. We develop a model that reproduces the electron dynamics and the dependence on laser intensity and gradient scale length. This process is shown to be strongly linked with high harmonic generation via the Relativistic Oscillating Mirror mechanism.
High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping (2015)

This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.
Disruption of LACCASE4 and 17 Results in Tissue-Specific Alterations to Lignification of Arabidopsis thaliana Stems (2011)

Peroxidases have been shown to be involved in the polymerization of lignin precursors, but it remains unclear whether laccases (EC 1.10.3.2) participate in constitutive lignification. We addressed this issue by studying laccase T-DNA insertion mutants in Arabidopsis thaliana. We identified two genes, LAC4 and LAC17, which are strongly expressed in stems. LAC17 was mainly expressed in the interfascicular fibers, whereas LAC4 was expressed in vascular bundles and interfascicular fibers. We produced two double mutants by crossing the LAC17 (lac17) mutant with two LAC4 mutants (lac4-1 and lac4-2). The single and double mutants grew normally in greenhouse conditions. The single mutants had moderately low lignin levels, whereas the stems of lac4-1 lac17 and lac4-2 lac17 mutants had lignin contents that were 20 and 40% lower than those of the control, respectively. These lower lignin levels resulted in higher saccharification yields. Thioacidolysis revealed that disrupting LAC17 principally affected the deposition of G lignin units in the interfascicular fibers and that complementation of lac17 with LAC17 restored a normal lignin profile. This study provides evidence that both LAC4 and LAC17 contribute to the constitutive lignification of Arabidopsis stems and that LAC17 is involved in the deposition of G lignin units in fibers.
Specific features of infrared absorption in films materials subjected to a magnetic field (2003)

The reflection spectra and magnetorefractive effect (MRE) of metal (Co, CoFe), semiconductor (Si, GaAs), and granular and amorphous Co30Ag70 and Co59Fe5Ni10Si11B15 films are studied in the IR spectral region at λ=2.5–25 μm. It is found that the IR optical properties of the ferromagnetic metal films can be described with regard to light absorption due to electron transitions in the two spin systems. The MRE is found to occur in both the ferromagnetic (Co, CoFe) and semiconductor (Si, GaAs) films. The amplitude and shape of the MRE are determined for the p and s polarizations of light. It is shown that, to a first approximation, the IR optical properties of the films with giant magnetoresistance can be described by the Drude theory, while the MRE is explained on the basis of a modified Hagen-Rubens relation. Variations in the IR reflection of semiconductor or amorphous metal films in the magnetic field are found to depend on the degree of polarization of localized electron states at the Fermi level.
Noncircular Inlet Duct Cross-Section to Reduce Combustion Instabilities (1990)

Abstract The unique shear-flow characteristics of a triangular jet were used to suppress longitudinal pressure oscillations in a coaxial dump combustor. The asymmetric flow configuration enhanced fine-scale mixing in the corner flow, while maintaining large-scale mixing at the flat sides, as demonstrated in air and water flows with and without forcing. In a forced annular diffusion flame it was shown that the flat-side shear layers were dominated by reacting vortices which lead to periodic heat release and possible driving of pressure oscillations, while the combustion at the corners was more intense and free of periodicity because of highly three-dimensional flow with enhanced molecular mixing between the fuel and oxidizer. For a coaxial dump, the pressure oscillations were significantly reduced with a triangular inlet duct and corner injection, compared to a triangular inlet duct with flat-side injection and to a circular inlet duct.
Focus on the Controversial Activation of Human iNKT Cells by 4-Deoxy Analogue of KRN7000 (2009)

4-Deoxy-alpha-GalCer analogues are considered weaker agonists than KRN7000 for the stimulation of human iNKT cells, but this remains strongly debated. In this work, we described a strategy toward 4-deoxy-alpha-GalCers with, as a key step, a metathesis reaction allowing sphingosine modifications from a single ethylenic alpha-galactoside precursor. The 4-deoxy-KRN7000 derivative 2, described here, induced potent cytokinic responses, comparable to those of KRN7000, both from human iNKT cells in vitro and from their murine counterpart in vivo.
Multi-Beam Spatio-Spectral Beamforming Receiver for Wideband Phased Arrays (2013)

This paper reports the first analog integrated spatio-spectral beamforming front-end. The proposed front-end allows for accurate beam steering of signals with large fractional bandwidths, thus minimizing beam squinting, and simultaneous and independent steering of multi-carrier signals. Different spatio-spectral beamforming strategies are discussed and compared. As a proof of concept, an 8 GHz 2-channel, 4-frequency phased-array beamformer is designed and implemented in 65 nm CMOS. The IF signal on each channel is frequency split using an all passive 4-point analog FFT. The orthogonal frequency outputs are then beam-steered using an all passive I-Q vector-combiner. The RF circuit draws 22.8 mA from a 1.2 V supply while the analog baseband consumes 135 μW at 120 MS/s (9 pJ/conv.).
Amides as Phase Modifiers for N,N′-Tetraalkylmalonamide Extraction of Actinides and Lanthanides from Nitric Acid Solutions (1997)

Abstract The N,N′-tetraalkylmalonamides are a class of compounds under development for transuranic (TRU) separations under high nitric acid conditions. There are several issues that challenge the further development of these ligands. One is the development of improved synthetic procedures that lend themselves to commercial scale-up. Another major issue is the third-phase formation that occurs when the N,N′-tetraalkylmalonamides are contacted with medium-to-high nitric acid concentrations in hydrocarbon solvents. To address the synthesis issue we have developed a new synthetic approach for preparing these materials. Third-phase formation can be eliminated by addition of diluent modifiers such as tributylphosphate (TBP). TBP is inappropriate if a nonphosphate-containing process stream is required. Amides have been proposed as alternatives for TBP in a variety of applications because of their ease of synthesis and the variety of substituents that can be generated. We have been able to develop an amide phase-modified system that extends the working process range of alkylmalonamides (0.5 M) in dodecane (unbranched hydrocarbon) from 3.5 M to 7.5 M nitric acid and in Isopar H (branched hydrocarbon) from 4.0 M to 10.0 M nitric acid using 1.0 M di-2-ethylhexylacetamide/0.5 M alkylmalonamide. The Kd values were comparable to extraction with alkylmalonamide in Isopar H or hydrogenated tetrapropylene (TPH) solvents. The overall extraction system was more robust than the phase-unmodified system allowing for greater temperature and acid concentration fluctuations without third-phase formation.
Evidence of excess oxygen accommodation in yttria partially-stabilized zirconia (2019)

Yttria partially stabilized zirconia (ZrO2)x(Y2O3)½-x has been investigated to understand accommodation of excess oxygen into its structure. ZrO2 powder with 8 wt% Y2O3 additions was treated in 30 vol% H2O2 solution to promote oxidation of the material. A new Raman peak was observed after treatment at 840 cm−1, consistent with previous reports of solid state peroxide ions (O22−). This was corroborated using atomic scale simulation based on density functional theory; these also highlighted the near-zero solution enthalpy for excess oxygen in the monoclinic structure via the formation of a peroxide ion defect.
THz time domain spectroscopy system using 1.55 &#x00B5;m laser pulses and phase modulation detection in DAST crystal (2010)

We report terahertz time-domain spectroscopy system based on Er:fiber laser at 1.55 μm wavelength. Ion-irradiated In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> As photoconductive antenna is used as emitter. The detection is based on a phase modulation detection scheme in DAST electro-optic sensor.
A687V EZH2 is a gain‐of‐function mutation found in lymphoma patients (2012)

Heterozygous point mutations at Y641 and A677 in the EZH2 SET domain are prevalent in about 10-24% of Non-Hodgkin lymphomas (NHL). Previous studies indicate that these are gain-of-function mutations leading to the hypertrimethylation of H3K27. These EZH2 mutations may drive the proliferation of lymphoma and make EZH2 a molecular target for patients harboring these mutations. Here, another EZH2 SET domain point mutation, A687V, occurring in about 1-2% of lymphoma patients, is also shown to be a gain-of-function mutation that greatly enhances its ability to perform dimethylation relative to wild-type EZH2 and is equally proficient at catalyzing trimethylation. We propose that A687V EZH2 also leads to hypertrimethylation of H3K27 and may thus be a driver mutation in NHL.
Phosphatidylcholine catabolism in the MCF-7 cell cycle (2006)

The catabolism of phosphatidylcholine (PtdCho) appears to play a key role in regulating the net accumulation of the lipid in the cell cycle. Current protocols for measuring the degradation of PtdCho at specific cell-cycle phases require prolonged periods of incubation with radiolabelled choline. To measure the degradation of PtdCho at the S and G2 phases in the MCF-7 cell cycle, protocols were developed with radiolabelled lysophosphatidylcholine (lysoPtdCho), which reduces the labelling period and minimizes the recycling of labelled components. Although most of the incubated lysoPtdCho was hydrolyzed to glycerophosphocholine (GroPCho) in the medium, the kinetics of the incorporation of label into PtdCho suggests that the labelled GroPCho did not contribute significantly to cellular PtdCho formation. A protocol which involved exposing the cells twice to hydroxyurea, was also developed to produce highly synchronized MCF-7 cells with a profile of G1:S:G2/M of 90:5:5. An analysis of PtdCho catabolism in the synchronized cells following labelling with lysoPtdCho revealed that there was increased degradation of PtdCho in early to mid-S phase, which was attenuated in the G2/M phase. The results suggest that the net accumulation of PtdCho in MCF-7 cells may occur in the G2 phase of the cell cycle.
A new multicast technique supporting source mobility for future vision delivery service (2004)

In this paper, we propose an innovative information delivery service on intelligent transport systems (ITS), which enables users to see their future vision delivered from users at further points along the route. This service requires special multicast and mobile routing schemes. We have developed a source mobility support multicast (SMM) technique that guarantees consecutive communication in high-speed mobile environments and minimizes the overhead in reconstructing multicast trees, which is caused by a source movement. SMM is based on a new concept where multicast tree is constructed over cellular IP network according to A. G. Valko (1999), in which a source point tree and a rendezvous point tree are combined into one multicast tree. SMM provides wide operability by partitioning the network and confining protocol uniqueness and topological constraints within the local access networks. This paper shows our design of SMM architecture and its detail protocols.
O2‐12‐01: MITOCHONDRIA AND DEATH RECEPTORS: KEY TARGETS FOR AMYLOID TOXICITY IN THE CEREBRAL VASCULATURE (2014)

The vascular deposition of amyloid, known as Cerebral Amyloid Angiopathy (CAA), is an age-associated condition featured in about 90% of Alzheimer's disease cases. CAA compromises cerebral blood flow and can cause cerebral hemorrhage and cognitive impairment. Very little is known about the mechanisms initiating the amyloid beta (Abeta)-dependent degeneration of cerebral endothelial cells in CAA. Here, we aim to identify the molecular events underlying the apoptotic cascade generated by Abeta in cerebrovascular cells and to identify new targets for drug discovery. Human brain microvascular endothelial cells were challenged with vasculotropic Abeta variants associated with cerebrovascular deposition and hemorrhagic clinical outcome, and the resulting apoptotic pathways were analysed. The in vitro findings were validated in vivo in mice subjected to intrahippocampal Abeta injections and confirmed in human CAA cases. Data revealed activation of caspase-8 and -9, together with mitochondrial dysfunction and release of cytochromeC (CytC). Signaling cascades typical of the extrinsic apoptotic pathway were activated. The involvement of membrane death receptors was confirmed by an overexpression of the TRAIL (TNF-related apoptosis inducing ligand) death receptors DR4 and DR5. The same receptors colocalized with Abeta on the cell membrane upon amyloid challenge, and specifically immunoprecipitated in vitro with oligomers of different Abeta variants. Both siRNAs targeting DR4 and DR5 and compounds targeting the release of CytC from the mitochondria significantly diminished Abeta mediated apoptosis in endothelial cells. In vivo experiments in mice injected with vasculotropic Abeta peptide and in human CAA cases confirmed the upregulation of the receptors, their colocalization with Abeta on the cerebral vasculature, and the activation of caspases, which could be prevented by inhibitors of CytC release. Overall, our data suggests a primary contribution of TRAIL death-receptors and mitochondrial dysfunction in Abeta-induced vascular cell death, unveiling new cellular targets for therapeutic intervention.
Thermal Stability of MAX Phases (2014)

The susceptibility of MAX phases to thermal dissociation at 1300-1550 °C in high vacuum has been studied using in-situ neutron diffraction. Above 1400 °C, MAX phases decomposed to binary carbide (e.g. TiC x ) or binary nitride (e.g. TiN x ), primarily through the sublimation of A-elements such as Al or Si, which results in a porous surface layer of MX x being formed. Positive activation energies were determined for decomposed MAX phases with coarse pores but a negative activation energy when the pore size was less than 1.0 μm. The insights for tailor-design of MAX phases with controlled thermal stability and intercalated MXenes for energy storage are addressed.
Intravital 2P-imaging reveals anti-viral CTL mediate fatal pathology by recruiting myelomonocytic cells (137.17) (2010)

Abstract Many viruses can cause severe neurological complications in the central nervous system (CNS) through initiation of immunopathology. A case in point is the fatal meningitis induced by lymphocytic choriomeningitis virus (LCMV) - a disease associated with vascular breakdown and seizures. Although LCMV-specific CNS-infiltrating cytotoxic lymphocytes (CTL) are essential for disease, it is not known precisely how CTL mediate fatal immunopathology. Recently, it has become possible to directly observe immunity and immunopathology using two photon laser scanning microscopy (TPLSM). We initiated our real time studies of LCMV-induced meningitis by visualizing LCMV-specific CTL dynamics in the meninges during the onset of symptoms. Our findings yielded a novel and unexpected mode of pathogenesis defined by CTL trafficking into the meningeal space followed by a massive secondary recruitment of pathogenic myelomonocytic cells (i.e., monocytes and neutrophils). Importantly, myelomonocytic cells were responsible for severe vascular leakage and rapid onset disease during meningitis, and CTL directly participated in their recruitment by releasing myelomonocytic cell chemoattractants. Our results demonstrate that a CD8+ T cell dependent disorder can proceed in the absence of CTL effector mechanisms and rely instead on secondarily recruited myelomonocytic cells.
Efficient estimation of 3D Euclidean distance fields from 2D range images (2002)

Several existing algorithms for reconstructing 3D models from range data first approximate the object's 3D distance field to provide an implicit representation of the scanned object and then construct a surface model of the object using this distance field. In these existing approaches, computing and storing 3D distance values from range data contribute significantly to the computational and storage requirements. This paper presents an efficient method for estimating the 3D Euclidean distance field from 2D range images that can be used by any of these algorithms. The proposed method uses Adaptively Sampled Distance Fields to minimize the number of distance evaluations and significantly reduce storage requirements of the sampled distance field. The method is fast because much of the computation required to convert the line-of-sight range distances to Euclidean distances can be done during a pre-processing step in the 2D coordinate space of each range image.
Development of an HIV vaccine using a vesicular stomatitis virus vector expressing designer HIV-1 envelope glycoproteins to enhance humoral responses (2017)

Vesicular stomatitis virus (VSV), like many other Rhabdoviruses, have become the focus of intense research over the past couple of decades based on their suitability as vaccine vectors, transient gene delivery systems, and as oncolytic viruses for cancer therapy. VSV as a vaccine vector platform has multiple advantages over more traditional viral vectors including low level, non-pathogenic replication in diverse cell types, ability to induce both humoral and cell-mediate immune responses, and the remarkable expression of foreign proteins cloned into multiple intergenic sites in the VSV genome. The utility and safety of VSV as a vaccine vector was recently demonstrated near the end of the recent Ebola outbreak in West Africa where VSV pseudotyped with the Ebola virus (EBOV) glycoprotein was proven safe in humans and provided protective efficacy against EBOV in a human phase III clinical trial. A team of Canadian scientists, led by Dr. Gary Kobinger, is now working with International AIDS Vaccine Initiative (IAVI) in developing a VSV-based HIV vaccine that will combine unique Canadian research on the HIV-1 Env glycoprotein and on the VSV vaccine vector. The goal of this collaboration is to develop a vaccine with a robust and potent anti-HIV immune response with an emphasis on generating quality antibodies to protect against HIV challenges.
A real time pixel-level based image fusion via adaptive weight averaging (2000)

A novel pixel-level image fusion scheme for thermal and visual images is presented. The image fusion technique rests on physical characteristics of targets deemed of interest in a surveillance scenario. Each picture element (pixel), in both the thermal and visual images, is assigned a weight proportional to the interest associated with it. Interest is defined as "not natural" or "man-made". A weighted average of the intensity images representing the thermal and visual modalities is then performed for every corresponding pair of visual and thermal picture elements to obtain the fused image. For the thermal images, elements that are warmer or cooler than their environment (background) are deemed to be of "interest". To this end, the thermal weights are associated with the divergence of the intensity of these pixels from the image mean intensity. For the visual images, the facts that the "targets of interest" are usually larger than the instantaneous field of view (IFOV) of the visual sensor and have a reflection behaviour that is more specular are used. The visual weight determination is based on the local variance in space and time of the intensity of the visual pixels, The performance of this technique is compared to a number of existing techniques in the literature. The results reveal that the proposed technique performs better than those in the literature. In addition, it also reveals that the proposed technique is more robust than those in the literature.