gebhart/patrepeval huggingface dataset:
Epstein-Barr Virus Infection of Cell Lines Derived from Diffuse Large B-Cell Lymphomas Alters MicroRNA Loading of the Ago2 Complex (2018)

Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid tumor which is occasionally Epstein-Barr virus (EBV) positive and is further subtyped as activated B-cell DLBCL (ABC-DLBCL) and germinal center B-cell DLBCL (GCB-DLBCL), which has implications for prognosis and treatment. We performed Ago2 RNA immunoprecipitation followed by high-throughput RNA sequencing (Ago2-RIP-seq) to capture functionally active microRNAs (miRNAs) in EBV-negative ABC-DLBCL and GCB-DLBCL cell lines and their EBV-infected counterparts. In parallel, total miRNA profiles of these cells were determined to capture the cellular miRNA profile for comparison with the functionally active profile. Selected miRNAs with differential abundances were validated using real-time quantitative PCR (RT-qPCR) and Northern blotting. We found 6 miRNAs with differential abundances (2 upregulated and 4 downregulated miRNAs) between EBV-negative and -positive ABC-DLBCL cells and 12 miRNAs with differential abundances (3 upregulated and 9 downregulated miRNAs) between EBV-negative and -positive GCB-DLBCL cells. Eight and twelve miRNAs were confirmed using RT-qPCR in ABC-DLBCL and GCB-DLBCL cells, respectively. Selected miRNAs were analyzed in additional type I/II versus type III EBV latency DLBCL cell lines. Furthermore, upregulation of miR-221-3p and downregulation of let7c-5p in ABC-DLBCL cells and upregulation of miR-363-3p and downregulation of miR-423-5p in GCB-DLBCL cells were verified using RIP-Northern blotting. Our comprehensive sequence analysis of the DLBCL miRNA profiles identified sets of deregulated miRNAs by Ago2-RIP-seq. Our Ago2-IP-seq miRNA profile could be considered an important data set for the detection of deregulated functionally active miRNAs in DLBCLs and could possibly lead to the identification of miRNAs as biomarkers for the classification of DLBCLs or even as targets for personalized targeted treatment.<b>IMPORTANCE</b> Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive tumor of lymphoid origin which is occasionally Epstein-Barr virus (EBV) positive. MicroRNAs are found in most multicellular organisms and even in viruses such as EBV. They regulate the synthesis of proteins by binding to their cognate mRNA. MicroRNAs are tethered to their target mRNAs by "Argonaute" proteins. Here we compared the overall miRNA content of the Ago2 complex by differential loading to the overall content of miRNAs in two DLBCL cell lines and their EBV-converted counterparts. In all cell lines, the Ago2 load was different from the overall expression of miRNAs. In addition, the loading of the Ago2 complex was changed upon infection with EBV. This indicates that the virus not only changes the overall content of miRNAs but also influences the expression of proteins by affecting the Ago complexes.
An improved CO2 laser intracavity photoacoustic spectrometer for trace gas analysis (1996)

This work describes an improved CO2 laser intracavity photoacoustic spectrometer. It can detect and measure small quantities of trace gases in air. The measured absorption sensitivity of 3.3×10−10 cm−1 corresponds to a mixture of 11 pptv (volume parts per trillion) of ethene in nitrogen. The sensitivity and reliability of the instrument were enhanced by reducing the level of background signals originating from optical and acoustical sources. The sensitivity reached is comparable with the best existing continuous measuring instruments while the background signal is two orders of magnitude smaller. The improvements are described in detail and a comparison to previous work is made. A first measurement demonstrates the suitability of the apparatus for biological applications.
ChemInform Abstract: Total Syntheses of Marine Furanosesquiterpenoids, Tubipofurans. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Intelligent Transportation Systems-A Frontier for Breaking Boundaries of Traditional Academic Engineering Disciplines [Education] (2016)

Introduction The evolution of the modern transportation system has been instrumental in the prosperity of human civilization. Over the centuries, technological innovations have improved the performance and efficiency of transportation systems, which has in turn led us to the creation of the modern intelligent transportation system (ITS). Nonetheless, innovations in sensing, computing, analytics and communication technologies over the last few decades have vastly changed how we consume transportation services. According to the US National Academy of Engineering's report "The Engineer of 2020: Visions of Engineering in the New Century," information and communication technologies will be integrated in every process and structure in future, and these technologies will be critical to the seamless performance of every engineered product [1]. Auto makers are expected to market several vehicle models with vehicle-tovehicle (V2V) connectivity within a few years with a subsequent presence of autonomous vehicles on highways within a decade. Such breakthroughs will create new challenges for ITS professionals concerning the design and development of ITS infrastructure. Although multidisciplinary skills are essential for ITS professionals, the current pedagogy of training ITS engineers is inadequate for this new era of smart and connected transportation systems. Consequently, there is a great urgency to train a new generation of mobility professionals in traditional traffic engineering skills as well in cyberphysical systems. The focus of this article is to establish the importance of a new educational focus area in ITS at the undergraduate and graduate levels.
CHAPTER 18 Stress transfer and deformation mechanisms around diaphragm walls (2004)

Overview Numerical models and parameters Finite-difference mesh and modelling procedure Normal stress distributions behind panel Shear stress distributions behind panel Horizontal deformations Surface settlements Assessment Concluding comments
Simulated Data For "Spot-On: Robust Model-Based Analysis Of Single-Particle Tracking Experiments" (2017)

<strong>Generation of simulated data</strong> To systematically evaluate the performance of Spot-On as well as other common analysis tools such as MSD<sub>i</sub> and vbSPT, we considered a comprehensive set of 3480 realistic SPT simulations spanning the range of plausible dynamics. The simulations were performed using simSPT, which is freely available at GitLab: https://gitlab.com/tjian-darzacq-lab/simSPT. The simulation methods are described in detail at GitLab. A full description of the parameters which allows exact reproduction of the simulations is available together with the data (see Data Availability section). Briefly, we parameterized simSPT to consider that particles diffuse inside a sphere (the nucleus) of 8 µm diameter illuminated using HiLo illumination (assuming a HiLo beam width of 4 µm), with an axial detection range of ~700 nm, centered at the middle of the HiLo beam. Molecules are assumed to have a half-life of 4 frames (when inside the HiLo beam) and of 40 frames when outside the HiLo beam. The localization error was set to 25 nm and the simulation was run until 100000 in-focus trajectories were recorded. More specifically, the effect of the exposure time (1 ms, 4 ms, 7 ms, 13 ms, 20 ms), the free diffusion constant (from 0.5 µm²/s to 14.5 µm²/s in 0.5 µm²/s increments) and the fraction bound (from 0 % to 95 % in 5 % increments) were investigated, yielding a dataset consisting of 3480 simulations. The advantage of simulations is that the ground truth is known. This allows a quantitative assessment of which method works the best. <strong>Content of the archives:</strong> 170718_simSPT_simulations.zip the code and instructions to reproduce the simulations 4um.tar.bz2 simulated data inside a 4 µm nucleus 20um.tar.bz2 simulated data inside a 20 µm nucleus, in which virtually no confinement occurs. subsampled.tar.bz2 is a set of subsampled datasets, containing either 99999, 30000, 10000, 3000, 1000, 300, 100 or 30 trajectories. Each subsampling was done 50 times, yielding 50 files per subsmpling. <strong>Formats:</strong> The data is provided both in CSV and .mat formats. .mat files are provided in the following dataset: 10.5281/zenodo.835541
Propolin H from Taiwanese Propolis Induces G1 Arrest in Human Lung Carcinoma Cells (2007)

Propolis, a natural product collected by honeybee, has been reported to exert a wide spectrum of biological functions. In this study, we have isolated a novel component, namely, propolin H, and investigated its effects in human carcinoma cells. Propolin H inhibited the proliferation of human lung carcinoma cell lines in MTT assay, and a significant G1 arrest was observed to occur in a dose-dependent manner at 24 h of exposure in H460 cells. After treatment with propolin H in H460 cells, the content of the CDK inhibitor p21Waf1/Cip1 protein increased in correlation with the elevation in p53 levels. Western blot analysis of G1 regulatory proteins further revealed a decrease in cyclin-dependent kinase 2 (CDK2) and CDK4 and an increase in cyclin E. The CDKs kinase activities assay showed that propolin H has inhibited CDK2 and CDK4 kinase activities. Accordingly, coimmunoprecipitations revealed an increased association of both CDK2 and CDK4 immunoreactive protein with the p21Waf1/Cip1 protein complex under propolin H-treated conditions. Additionally, we found that propolin H enhanced the expression of p21Waf1/Cip1 in p53-mutant and p53-null lung carcinoma cell lines, following the induction of G1 arrest. Together, these findings suggest that the induction of p21Waf1/Cip1 expression occurred through p53-dependent and -independent pathways in propolin H-treated cells. Propolin H exerts its significantly growth inhibitory effects and may have therapeutic applications. Keywords: Propolis; propolin H; lung carcinoma cell; cell cycle; p21Waf1/Cip1
Water-Responsive and Mechanically Adaptive Natural Rubber Composites by in Situ Modification of Mineral Filler Structures (2019)

A new biomimetic stimuli-responsive adaptive elastomeric material, whose mechanical properties are altered by a water treatment is reported in this paper. This material is a calcium sulphate (CaSO<sub>4</sub>) filled composite with an epoxidized natural rubber (ENR) matrix. By exploiting various phase transformation processes that arise when CaSO<sub>4</sub> is hydrated, several different crystal structures of CaSO<sub>4</sub>· xH<sub>2</sub>O can be developed in the cross-linked ENR matrix. Significant improvements in the mechanical and thermal properties are then observed in the water-treated composites. When compared with the untreated sample, there is approximately 100% increase in the dynamic modulus. The thermal stability of the composites is also improved by increasing the maximum degradation rate temperature by about 20 °C. This change in behavior results from an in situ development of hydrated crystal structures of the nanosized CaSO<sub>4</sub> particles in the ENR matrix, which has been verified using Raman spectroscopy, transmission electron microscopy, atomic force microscopy, and X-ray scattering. This work provides a promising and relatively simple pathway for the development of next generation of mechanically adaptive elastomeric materials by an eco-friendly route, which may eventually also be developed into an innovative biodegradable and biocompatible smart polymeric material.
Phosphorylated Smad2 and Smad3 signaling: Shifting between tumor suppression and fibro‐carcinogenesis in chronic hepatitis C (2013)

HCV clearance limits fibrosis and reduces HCC incidence by switching inflammation-dependent phospho-Smad signaling from fibro-carcinogenesis to tumor suppression. However, progression to HCC would occur in severely fibrotic livers if an inflammation-independent fibro-carcinogenic process has already begun before HCV clearance.
Correction: Antiviral drug discovery: preparing for the next pandemic (2021)

Correction for 'Antiviral drug discovery: preparing for the next pandemic' by Catherine S. Adamson et al., Chem. Soc. Rev., 2021, 50, 3647-3655, DOI: .
Stimulated Raman scattering: diffractive coupling in transient and steady-state regimes (1991)

A numerical study is presented of the steady-state and transient regimes in stimulated Raman scattering, including diffractive coupling of the fields and detuning of the Stokes field from resonance. In the steady-state regime, ring formation in the laser output intensity is observed as well as a ring in the Stokes output intensity when it is detuned from resonance. In the transient regime a solitonlike pulse is initiated by modulation of the phase of the input Stokes field. For Fresnel numbers between 5 and 50, we observe a simultaneous maximum of the on-axis laser and Stokes intensities after a π phase shift is introduced on the Stokes seed. At the same time the transverse profiles of the fields are narrowed and the laser intensity displays a satellite ring. It is found that the soliton remains relatively stable, although diffraction eventually leads to its decay.
Withdrawal and dip coating of an object from a yield-stress reservoir (2021)

How much fluid adheres to an object pulled out from a liquid reservoir? We re-examine this dip-coating problem for yield-stress fluids. We propose a complete description that links the yield-stress fluid case with the Newtonian case. For extreme cases, asymptotic scaling laws are provided.
Pro-inflammatory cytokines induce cell death, inflammatory responses, and endoplasmic reticulum stress in human iPSC-derived beta cells (2020)

Our data show that human iPSC-derived beta cells respond to pro-inflammatory cytokines IL-1β + IFNγ and IFNα, by activating the same pathogenic processes as adult human primary beta cells. These cells thus represent a valuable tool for future research on the pathogenesis of type 1 diabetes.
Compton scattering and the character of the hydrogen bond in ice Ih (2001)

Compton scattering is an experimental technique which probes the electron momentum density. Here we present a method which allows the calculation of the Compton profile using the formalism of the maximally localized Wannier functions. We applied this method to analyze recent experimental measurements of the anisotropy component of the Compton profile which have been interpreted as the signature of the partial covalent character of the hydrogen bond in ice Ih. We are able to reproduce well the experimental results, however we do not find evidence of a covalent nature of the hydrogen bond. In fact our analysis shows that, although the wave functions in ice Ih have a quantum-mechanical, multicenter character, this gives rise to an antibonding, repulsive interaction between neighboring water molecules. Application to our technique to other, nonhydrogen bonded systems, and analysis of the corresponding Compton scattering profile anisotropy, gives further support to our interpretation.
Tolerances for combining high gain antennas (2002)

Coherently combining high gain antennas to obtain increased gain is sometimes proposed. Coherent combining produces grating lobes in the overall antenna pattern limiting combining efficiency in the signal direction. Requirements for narrow bandwidth phase matching and wider bandwidth time delay matching are presented. >
Detection of Hostile Intent by Spatial Movements (2021)

Early identification of threats based on movement characteristics alone is likely to be difficult, but particularly so when adversaries employ some level of uncertainty to mask their intentions. These findings highlight the need to develop decision aids to support human performance.
Formal C−H Carboxylation of Unactivated Arenes (2020)

A formal C-H carboxylation of unactivated arenes using CO<sub>2</sub> in green solvents is described. The present strategy combines a sterically controlled Ir-catalyzed C-H borylation followed by a Cu-catalyzed carboxylation of the in situ generated organoboronates. The reaction is highly regioselective for the C-H carboxylation of 1,3-disubstituted and 1,2,3-trisubstituted benzenes, 1,2- or 1,4-symmetrically substituted benzenes, fluorinated benzenes and different heterocycles. The developed methodology was applied to the late-stage C-H carboxylation of commercial drugs and ligands.
Effect of Tocopherols on the Anti‐Polymerization Activity of Oryzanol and Corn Steryl Ferulates in Soybean Oil (2013)

Abstract Steryl ferulates (SFs) are ferulic acid esters of phytosterols and/or triterpene alcohols which have potential as frying oil antioxidants. The objective of this study was to evaluate the anti‐polymerization and antioxidant activity at frying temperatures of corn steryl ferulates (CSFs), rice steryl ferulates (oryzanol), and a mixture of CSFs with oryzanol, alone and with tocopherols. Antioxidant activity was measured by the reduction of polymerized triacylglycerol formation, and loss of olefinic and bisallylic protons from fatty acid double bonds by 1 H NMR. CSFs and oryzanol slowed the oxidation and polymerization of soybean oil triacylglycerols heated to 180 °C more effectively than a mixture of alpha and gamma tocopherols. CSFs were more effective at preventing polymerization than oryzanol, but when oryzanol was combined with tocopherols, they all had similar antioxidant activity. In addition, tocopherols had a protective effect on SFs. Corn SFs were degraded more quickly during heating than oryzanol, however, the phytosterol constituents of corn SFs, sitostanol and campestanol, were actually more resistant to degradation compared to the phytosterol constituents of rice SFs. Results demonstrate that corn and rice SFs may be effective antioxidants for use in frying oils, and that their activity is enhanced in the presence of tocopherols.
System management of a wind-energy converter (2001)

Wind energy converters are commonly used in converting wind energy into useful mechanical and electrical energies. But the problems of smooth start, tower effect and oscillations caused by aerodynamic forces acting on the rotor cause fluctuations in its power output. A system management was designed to reduce these effects. It consists of a microcontroller. This was verified with the help of laboratory test bench model of a wind energy converter driving an asynchronous generator. The model was a direct replication of a real wind energy converter and was designed with the help of a wind rotor simulator program. The aerodynamic data for the test were obtained from the rotor blade profile of real equipment (Ventis 100). The microcontroller was programmed with a selected power control method. The test showed that the system management compensates the power fluctuations and enables the smooth start of the wind energy converter. Furthermore, it quickly shuts off the wind energy converter in stormy and calm periods.
Analysis of heterokaryon incompatibility between heterokaryon-compatibility (h-c) groups R and GL provides evidence that at least eight het loci control somatic incompatibility in Aspergillus nidulans (1993)

Protoplast fusion was used to hybridize strains 99-6 (h-cR) and 7-141 (h-cGL) in the Birmingham collection of Aspergillus nidulans. A sparsely conidiating, brown-pigmented diploid strain (MA7) was isolated. Inocula from MA7 were haploidized on medium containing Benlate and a haploid progeny sample collected. Heterokaryon compatibility testing of selected progeny strains assayed each linkage group in turn and established that h-cR and h-cGL were hetero-allelic for heterokaryon incompatibility (het) loci located on linkage groups III and V. Two selected MA7 progeny strains were sexually crossed to an h-cGL strain. Compatibility classification of the progenies of these crosses indicated that three het genes were located on linkage group III and two on linkage group V. Combination of these results with previous work using h-c groups A, B and Q in comparison with h-cGL indicates that a minimum number of eight and a maximum number of 18 het loci, spread over five linkage groups, are necessary to explain the compatibility relationships among these five h-c groups.
Activating Azides and Alkynes for the Click Reaction with [Cu(aNHC)2I] or [Cu(aNHC)2]+ (aNHC = Triazole‐Derived Abnormal Carbenes): Structural Characterization and Catalytic Properties (2013)

Abstract Neutral, iodido‐containing copper(I) complexes [Cu( a NHC) 2 I] { a NHC = 1‐benzyl‐3‐methyl‐4‐phenyl‐1,2,3‐triazol‐5‐ylidene (for 6 ) and 3‐methyl‐1‐[2‐(methylthio)phenyl]‐4‐phenyl‐1,2,3‐triazol‐5‐ylidene (for 7 )} and cationic, halide‐free copper(I) complexes [Cu( a NHC) 2 ](BF 4 ) { a NHC = 1‐benzyl‐3‐methyl‐4‐phenyl‐1,2,3‐triazol‐5‐ylidene (for 8 ), 3‐methyl‐1,4‐diphenyl‐1,2,3‐triazol‐5‐ylidene (for 9 ), 3‐methyl‐1‐[2‐(methylthio)phenyl]‐4‐phenyl‐1,2,3‐triazol‐5‐ylidene (for 10 ), and 1‐mesityl‐3‐methyl‐4‐phenyl‐1,2,3‐triazol‐5‐ylidene (for 11 )}, both containing two monodentate abnormal‐carbene ligands ( a NHC), were synthesized from [Cu(CH 3 CN) 4 ](BF 4 ) and the corresponding triazolium salts. It was possible to selectively synthesize both kinds of complexes by simply variing the counter‐anion of the triazolium salts and keeping the metal precursor the same. All complexes were characterized by elemental analysis and spectroscopic methods. 6 and 11 were studied with single‐crystal X‐ray diffraction analyses. In 6 , the copper(I) center is tricoordinated, and its geometry is in between trigonal planar and T‐shaped. In halide‐free 11 , the copper(I) center is linearly coordinated by two abnormal‐carbene ligands. All complexes were tested as catalysts in the Huisgen [3+2] cycloaddition reaction between azides and alkynes, and they showed excellent efficiencies under neat conditions. A comparison between the efficiencies of the halide‐containing complexes 6 and 7 and the halide‐free cases 8 – 11 , shows that the halide‐free Cu– a NHC complexes are significantly more efficient than their halide‐containing counterparts. The best catalyst was used for a substrate screening by utilizing a variety of azides and a couple of alkynes. The efficiency of the catalyst was maintained with loadings as low as 0.005 mol‐%. Mechanistic studies were carried out as well.
Controlled Synthesis of Mesoporous Carbon Nanostructures via a “Silica-Assisted” Strategy (2012)

We have established a facile and generalizable "silica-assisted" synthesis for diverse carbon spheres-a category that covers mesoporous carbon nanospheres, hollow mesoporous carbon nanospheres, and yolk-shell mesoporous carbon nanospheres-by using phenolic resols as a polymer precursor, silicate oligomers as an inorganic precursor, and hexadecyl trimethylammoniumchloride as a template. The particle sizes of the carbon nanospheres are uniform and easily controlled in a wide range of 180-850 nm by simply varying the ethanol concentrations. All three types of mesoporous carbon nanospheres have high surface areas and large pore volumes and exhibit promising properties for supercapacitors with high capacitance and favorable capacitance retention.
Randomized Comparison of Strategies for Reducing Treatment in Mild Persistent Asthma (2007)

Patients with asthma that is well controlled with the use of twice-daily inhaled fluticasone can be switched to once-daily fluticasone plus salmeterol without increased rates of treatment failure. A switch to montelukast results in an increased rate of treatment failure and decreased asthma control; however, patients taking montelukast remained free of symptoms on 78.7% of treatment days. (ClinicalTrials.gov number, NCT00156819 [ClinicalTrials.gov].).