gebhart/patrepeval huggingface dataset:
Specific immune modulation of experimental colitis drives enteric alpha-synuclein accumulation and triggers age-related Parkinson-like brain pathology (2021)

<b>Background</b>: In some people with Parkinson's disease (PD), α-synuclein (αSyn) accumulation may begin in the enteric nervous system (ENS) decades before development of brain pathology and disease diagnosis. <b>Objective</b>: To determine how different types and severity of intestinal inflammation could trigger αSyn accumulation in the ENS and the subsequent development of αSyn brain pathology. <b>Methods</b>: We assessed the effects of modulating short- and long-term experimental colitis on αSyn accumulation in the gut of αSyn transgenic and wild type mice by immunostaining and gene expression analysis. To determine the long-term effect on the brain, we induced dextran sulfate sodium (DSS) colitis in young αSyn transgenic mice and aged them under normal conditions up to 9 or 21 months before tissue analyses. <b>Results</b>: A single strong or sustained mild DSS colitis triggered αSyn accumulation in the submucosal plexus of wild type and αSyn transgenic mice, while short-term mild DSS colitis or inflammation induced by lipopolysaccharide did not have such an effect. Genetic and pharmacological modulation of macrophage-associated pathways modulated the severity of enteric αSyn. Remarkably, experimental colitis at three months of age exacerbated the accumulation of aggregated phospho-Serine 129 αSyn in the midbrain (including the substantia nigra), in 21- but not 9-month-old αSyn transgenic mice. This increase in midbrain αSyn accumulation is accompanied by the loss of tyrosine hydroxylase-immunoreactive nigral neurons. <b>Conclusions</b>: Our data suggest that specific types and severity of intestinal inflammation, mediated by monocyte/macrophage signaling, could play a critical role in the initiation and progression of PD.
Stereoselective Synthesis of Bicyclic Nitrocyclopropanes by a Radical–Anion Domino Reaction (2009)

A novel one-step radical-ionic cyclopropanation was carried out to prepare aza- or oxabicyclo[3.1.0]hexane from β-nitroamides or β-nitroethers in a stereoselective manner (see scheme). The present procedure involves a higher-order domino process that includes one-electron oxidation– radical cyclization–intramolecular SN2 reaction. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Prion protein is ubiquitinated after developing protease resistance in the brains of scrapie‐infected mice (2004)

Although the key event in the pathology of prion diseases is thought to be the conversion of cellular prion protein (PrP(C)) to the protease-resistant scrapie species termed PrP(Sc), the factors that contribute to neurodegeneration in scrapie-infected animals are poorly understood. One probable determinant could be when the accumulation of PrP(Sc) in infected brain overwhelms the ubiquitin-proteasome system and triggers the degenerative cascade. In the present study, it was found that in mouse brains infected with the ME7 scrapie strain, the level of ubiquitin protein conjugates increased significantly at approximately 144 days post-infection (pi) when clinical signs first become apparent. This elevation correlated with the detection of protease-resistant PrP(Sc) and a decline in two endopeptidase activities associated with proteasome function. However, ubiquitination of PrP was only detected at the terminal stage, 3 weeks after the development of clinical symptoms (approximately 165 days pi). These results suggest that ubiquitination of PrP is a late event phenomenon and this conjugation occurs after the formation of protease-resistant PrP(Sc). Whether this post-translational modification and the impairment of proteasome function are pivotal events in the pathogenesis of prion diseases remains to be determined.
Maskless Electrochemical Patterning of Gold Films for Biosensors Using Micromachined Polyimide Probes (2006)

This paper explores the electrochemical patterning of thin metal films using a scanning probe tip as an electrode. In particular, a masking nickel film is etched to reveal a gold pattern to which biomolecules like liposomes and proteins can be attached after treatment with functionalized self assembled monolayers (SAMs) of gold-thiolate. The machining is performed by ultracomplaint polyimide micromachined probes (with tip diameter <200 nm) as the machining tool in NaCl:HCl electrolyte. These probes provide an embedded electrical lead as well as high mechanical compliance that eliminates the need for servo control, which is typically needed to maintain the proximity between the workpiece and the tool. By applying 500 ns, 2 V pulses, 3 mum wide patterns were fabricated. Experiments suggest that they can be scaled down to tens of nanometers by using 5 ns pulses. Selective adsorption of undecanethiol SAMs to the patterned gold was confirmed using XPS spectroscopy
Inventaire des Ascomycota du parc national du Mercantour. Compte rendu de la première prospection (2010)

Report of the first field survey devoted to Ascomycota, made during June 2010 in the National Park of Mercantour (France), for the European program ATBI+M covering the biodiversity of this park
Microenvironment regulation of PRG4 phenotype of chondrocytes (2007)

Articular cartilage is a heterogeneous tissue with superficial (S), middle (M), and deep (D) zones. Chondrocytes in the S zone secrete the lubricating PRG4 protein, while chondrocytes from the M and D zones are more specialized in producing large amounts of the glycosaminoglycan (GAG) component of the extracellular matrix. Soluble and insoluble chemicals and mechanical stimuli regulate cartilage development, growth, and homeostasis; however, the mechanisms of regulation responsible for the distinct PRG4-positive and negative phenotypes of chondrocytes are unknown. The objective of this study was to determine if interaction between S and M chondrocytes regulates chondrocyte phenotype, as determined by coculture in monolayer at different ratios of S:M (100:0, 75:25, 50:50, 25:75, 0:100) and at different densities (240,000, 120,000, 60,000, and 30,000 cells/cm(2)), and by measurement of PRG4 secretion and expression, and GAG accumulation. Coculture of S and M cells resulted in significant up-regulation in PRG4 secretion and the percentage of cells expressing PRG4, with simultaneous down-regulation of GAG accumulation. Tracking M cells with PKH67 dye in coculture revealed that they maintained a PRG4-negative phenotype, and proliferated less than S cells. Taken together, these results indicate that the up-regulated PRG4 expression in coculture is a result of preferential proliferation of PRG4-expressing S cells. This finding may have practical implications for generating a large number of phenotypically normal S cells, which can be limited in source, for tissue engineering applications.
Removal of Salt-Soluble Fission Products from the Metal Product of the Electrolytic Reduction Process - 14063 (2014)

The metal product from the electrolytic reduction of oxide spent fuel in LiCl–Li2O molten salt retains about 20 wt% of electrolyte. In addition, during the electrolytic reduction, some salt-soluble fission products such as Cs, Sr, and Ba accumulate in the LiCl-Li2O salt bath as chlorides. In order to separate the residual salt from the metal product of electrolytic reduction, vacuum distillation equipment was developed. With this equipment, the LiCl was evaporated and could be recovered in a fine white powder form. The evaporation rate of the LiCl molten salt was considerably decreased by the addition of BaCl2, SrCl2, and Li2O. For LiCl and CsCl, the complete removal of the salts from the evaporator was accomplished by reducing the pressure to less than 13.3 Pa and heating to 900 ℃. However, for BaCl2 and SrCl2, only about 30% were vaporized at 900 ℃. BaCl2 and SrCl2 were not vaporized by their own single component, but could be vaporized through a co-vaporization with LiCl salt. Evaporation efficiencies of 100% were achieved by heating above 1,000 ℃.
An analytical model for predicting noise radiated by switch reluctance electric motors (2021)

Switch reluctance motors (SRM) have become a prominent alternative for electric vehicles in recent years due to their simple, high power density architecture and cost-effective manufacturability. Despite its potential, NVH problems have been one of the biggest challenges for SRM's implementation. Vibration and noise generated by the SRM are mainly caused by phase switching related torque ripple, unbalanced electromagnetic forces from air gap variations and lamination problems. Our proposed model is an analytical noise radiation prediction model which relates geometrical, material and electrical design inputs to radiated sound power. The electromagnetic part of the model is nonlinear with saturation and provides back-emf and flux linkage by receiving design inputs. The computed magnetic energy, radial and tangential rotor forces are utilized as excitation sources to a continuous shell dynamic model to obtain the steady-state vibration response. Finally, surface velocities obtained from the shell model are used to calculate sound power. Utilizing a shell structure provides axial, radial and tangential information on the casing by considering the effect of magneto-restrictive forces of laminations, torque ripples and unbalanced electromagnetic forces. The effect of air gap, lamination error, and stator and rotor geometry on sound radiation are studied through an example case study.
Pixelated resonant subwavelength grating filters for greenhouse gas monitoring (2011)

We describe the design of pixelated filter arrays for hyperspectral monitoring of CO<sub>2</sub> and H<sub>2</sub>O absorption in the midwave infrared (centered at 4.25&mu;m and 5.15&mu;m, respectively) using resonant subwavelength gratings (RSGs), also called guided-mode resonant filters (GMRFs). For each gas, a hyperspectral filter array of very narrowband filters is designed that spans the absorption band on a single substrate. A pixelated geometry allows for direct registration of filter pixels to focal plane array (FPA) sensor pixels and for non-scanning data collection. The design process for narrowband, low-sideband reflective and transmissive filters within fabrication limitations will be discussed.
Supplementary Methods, Figure Legends, Table 1 from Adoptive Transfer of MART-1 T-Cell Receptor Transgenic Lymphocytes and Dendritic Cell Vaccination in Patients with Metastatic Melanoma (2023)

&lt;p&gt;PDF file - 148KB, Supplementary Table 1. Toxicities and response to therapy with the subsequent protocol amendments.&lt;/p&gt;
Exploring the Potential of Iminosugars as Antivirals for Crimean-Congo Haemorrhagic Fever Virus, Using the Surrogate Hazara Virus: Liquid-Chromatography-Based Mapping of Viral N-Glycosylation and In Vitro Antiviral Assays (2023)

Crimean-Congo haemorrhagic fever virus (CCHFV) is a pathogen of increasing public health concern, being a widely distributed arbovirus and the causative agent of the potentially fatal Crimean-Congo haemorrhagic fever. Hazara virus (HAZV) is a genetically and serologically related virus that has been proposed as a surrogate for antiviral and vaccine testing for CCHFV. Glycosylation analysis of HAZV has been limited; first, we confirmed for the first time the occupation of two N-glycosylation sites in the HAZV glycoprotein. Despite this, there was no apparent antiviral efficacy of a panel of iminosugars against HAZV, as determined by quantification of the total secretion and infectious virus titres produced following infection of SW13 and Vero cells. This lack of efficacy was not due to an inability of deoxynojirimycin (DNJ)-derivative iminosugars to access and inhibit endoplasmic reticulum α-glucosidases, as demonstrated by free oligosaccharide analysis in uninfected and infected SW13 and uninfected Vero cells. Even so, iminosugars may yet have potential as antivirals for CCHFV since the positions and importance of N-linked glycans may differ between the viruses, a hypothesis requiring further evaluation.
Design and Evaluation of Complex Moving HIFU Treatment Protocols (2005)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Steven G. Kargl, Marilee A. Andrew, Peter J. Kaczkowski, Andrew A. Brayman, Lawrence A. Crum; Design and Evaluation of Complex Moving HIFU Treatment Protocols. AIP Conf. Proc. 28 March 2005; 754 (1): 140–142. https://doi.org/10.1063/1.1901621 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Supplementary Figure S2 from Preclinical Activity of SAR408701: A Novel Anti-CEACAM5–maytansinoid Antibody–drug Conjugate for the Treatment of CEACAM5-positive Epithelial Tumors (2023)

&lt;p&gt;Supplementary Figure S2&lt;/p&gt;
Power-scalable 157 μm mode-locked semiconductor disk laser using wafer fusion (2009)

We report the first (to our knowledge) wafer-fused high-power passively mode-locked semiconductor disk laser operating at 1.57 microm wavelength. An InP-based active medium was fused with GaAs/AlGaAs distributed Bragg reflector on a 2 inch wafer level, resulting in an integrated monolithic gain mirror. An intracavity wedged diamond heat-spreader capillary bonded to the gain chip provides efficient heat removal from the gain structure without disturbing the spectrum of the mode-locked laser. The laser produces over 0.6 W of average output power at 15 degrees C with 16 ps pulse width. The total output power accounting for all output beams emerging from the cavity was 0.86 W. The results reveal an essential advantage of wafer fusion processing of disparate materials over monolithically grown InP-based gain structures and demonstrate the high potential of this technique for power scaling of long-wavelength semiconductor disk lasers.
Dominance of macrophage derived IFN-γ in atheromatous lesions (35.3) (2010)

Abstract IFN-γ activates macrophages that are abundant in atheromas, periodontal lesions, and other sites of chronic inflammation. It is thought that the IFN-γ present in athromas is derived from Th-1 cells. However, macrophages dominate the inflammatory infiltrate in atheromas and macrophages can produce IFN-γ prompting the hypothesis that macrophages are the source of a significant proportion of IFN-γ in established atherosclerotic lesions. To test this, CD14+, CD3+, and CD14- &amp; 3- cells were isolated from endarterectomy tissue and examined for spontaneous production of IFN-γ, IL-1β, IL-6, and TNF-α in supernatant fluids from 48 hr cell cultures. The CD14+ macrophages, including foam cells, were responsible not only for the TNF-α, IL-1β &amp; IL-6 but also for the vast majority of the IFN-γ produced in culture. Moreover, this spontaneous macrophage IFN-γ response was maintained in culture for over two weeks. IL-12 induced IFN-γ responses in macrophages and IL-12 was induced by incubating DCs with A. actinomycetemcomitans and far more dramatically by opsonized A. actinomycetemcomitans. In short, engagement of DCs in the intima of the arterial wall with opsonized microorganisms from the blood could trigger IL-12 production, and the released IL-12 could induce a sustained IFN-γ response by macrophages. This macrophage INF-γ response induced by DC-IL-12 bypasses a need for T cells to produce IFN-γ in established atheromas.
Abstract P141: Aging in Mice Enhances Microvascular Reactive Oxygen Species (ROS) That Impair the Anti-Contractile Actions of Perivascular Adipose Tissue (PVAT) (2018)

Background: Reactive oxygen species (ROS) contribute to oxidative stress and aging that predicts cardiovascular disease (CVD). Perivascular adipose tissue (PVAT) enhances endothelial function and reduces contractility of normal vessels. We tested the hypothesis that ROS and age impair PVAT signaling using mesenteric arterioles (MAs) from young and old wild type (Wt) and superoxide dismutase 3 knockout mice (KO). Methods and Results: MAs were isolated with and without PVAT from young (3 – 4 months; n = 5 – 7) and old (23 – 24 months; n = 5 – 7) wild-type (Wt) and superoxide dismutase 3 knockout (-/-) mice (to create oxidative stress). Contractions were assessed on an isometric myograph and ROS and mitochondrial ROS by fluorescence microscopy in MAs loaded with dihydroethidium or MitoSOX Red. The increase in ROS and mitochondrial ROS signals with 10 -7 mol·l -1 endothelin 1 (ET1) were increased in MAs from Wt old vs young mice (0.21 ± 0.05 vs 0.11 ± 0.04 units; P&lt;0.05 and 0.15 ± 0.04 vs 0.08 ± 0.04 units; P&lt;0.05 respectively). Amongst Wt mice, the effect of PVAT to reduce contractions to 10 -6 mol·l -1 U-46,619 was reduced in old vs young mice (15 ± 1 vs 45 ± 6% reduction; P&lt;0.005) with similarly reduced effects of PVAT in vessels from old mice on contractions to 10 -7 mol·l -1 endothelin 1 (ET1: 15 ± 4 vs 34 ± 3% reduction; P&lt;0.005). Compared to young Wt mice, MAs from young SOD3 -/- mice had reduced protection by PVAT from contractions to U-46,619 (25 ± 3 vs 45 ± 6% reduction; P&lt;0.01) or to ET1 (3 ± 2 vs 34 ± 8% reduction; P&lt;0.005). The effects of oxidative stress to lessen the protective effects of PVAT were lessened in old mice where the reductions in contractions mediated by PVAT to U-46,619 were no longer different in SOD +/+ vs -/- mouse MAs (12 ± 1 vs 15 ± 1% reduction; NS) while contractions to ET1 remained somewhat protected by PVAT (8 ± 2 vs 15 ± 4% reduced; P&lt;0.05). Conclusions: Aging enhances ROS generation by mesenteric arterioles that impairs the beneficial effects of PVAT to protect vessels from contractions with thromboxane and endothelin. This discloses a novel mechanism for age-related cardiovascular disease.
PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis (2019)

MOTIVATION: Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e., precision, recall, false positive rate, and correlation) in comparison with three leading tools (rMATS, SUPPA2, and Whippet). RESULTS: PSI-Sigma outperformed these tools, especially in the case of AS events with multiple alternative exons and intron-retention events. We also briefly evaluated its performance in long-read RNA-seq analysis, by sequencing a mixture of human RNAs and RNA Sequins with nanopore long-read sequencers. AVAILABILITY: PSI-Sigma is implemented is available at https://github.com/wososa/PSI-Sigma.
The added value of quantitative ultrasound to shear wave elastography for assessment of steatohepatitis in a rat model (2019)

Non-alcoholic fatty liver disease is a highly prevalent condition, which may progress to non-alcoholic steatohepatitis (NASH), an advanced form found in 3 to 5% of the population. As liver biopsy is invasive, there is a need for a non-invasive technique for the assessment of NASH. Due to promising results of shear wave elastography (SWE) in staging this disease, there is a high interest in developing a multi-parametric approach for assessment of liver steatosis within the same ultrasound (US) examination. The goal of this study was to assess the added value of quantitative US (QUS) parameters to SWE, based on random forest classifiers and areas under the ROC curve (AUC). Sixty male Sprague-Dawley rats were either fed a standard chow or a methionine- and choline-deficient diet. Using a research US system (model V1, Verasonics Inc.), SWE measurements were performed while rats were under anesthesia. To generate shear wavefronts within the liver, a linear array US transducer (ATL L7-4, Philips) was used to induce three 40-V 125-μs long radiation force pushes 4 mm apart. For SW tracking, the same transducer was used to acquire plane wave radiofrequency data at a frame rate of 4 kHz; images were reconstructed using the f-k migration algorithm. QUS acquisitions were performed using the same system and transducer. One hundred frames were acquired, migrated, and the echo envelope was obtained with Hilbert transforms. The image post-processing yielded 4 homodyned-K parametric maps within the region-of-interest (ROI), from which 8 features were extracted. The local attenuation coefficient slope within the ROI was also computed using the spectral shift method. QUS parameters improved the classification accuracy of steatohepatitis, liver steatosis, inflammation, and fibrosis compared to SWE alone. For detection of liver steatosis grades 0 vs ≥ 1, ≤ 1 vs ≥ 2, ≤ 2 vs 3, respectively, AUCs increased from 0.70, 0.65, and 0.69 to 0.78, 0.78, and 0.75 (p <; 0.001).
Microbial synthesis of natural products by employing methyltransferases (2020)

Methyltransferases (MTs) constitute a large group of enzymes that catalyze the transfer of a methyl moiety most frequently from S-adenosyl-L-methionine to their substrates. It plays an essential role in regulation of genes expression and synthesis of many natural compounds. Owing to its broad substrate spectrum, MTs make important contributions to diversify the spectrum of products through methylation modifications. Recently, employment of MTs for biosynthesis of natural products has made great progress but have not been detailed and informative viewed so far. In this article, we summary the recent advances in application of MTs for microbial synthesis of various natural products including phenylpropane compounds, fragrances, hormones and antibiotics. We put emphasis on the applied metabolic engineering strategies for efficient production of those chemicals and for expanding the diversity of the products. Then, we present the current challenges and future perspectives in utilization of MTs for efficient production of more diverse natural products in microorganisms.
Filterbank Multicarrier Reflectometry for Cognitive Live Wire Testing (2009)

Multicarrier reflectometry (MCR) for locating faults on live wires has recently been proposed. This paper studies the use of filterbanks for generation/synthesis of MCR test signals and also for signal analysis for fault identification and location. We note that the test signals have to be confined to the portion(s) of the frequency band that is (are) free of signals already on the wires in order to avoid interfering with them. Moreover, for effective analysis of the reflected waves, optimal filters that separate the test signal tones and also minimize leakage from the existing signals on the wires should be designed. We discuss the criteria necessary to design effective MCR systems and develop the relevant filterbank design procedures. We also introduce the novel idea of cognitive live wire testing, where the tester first measures the live wire signal activities and then decides on which part of the spectrum should be used for testing.