gebhart/patrepeval huggingface dataset:
Characterization of Signal Transduction Pathways in Human Bone Marrow Endothelial Cells (1997)

Human bone marrow endothelial cells immortalized with the T antigen of SV40 (TrHBMEC) have previously been characterized by us with regard to their properties that are similar to primary marrow endothelial cells and their utility as a model system. We now report that TrHBMEC express a recently discovered signal transduction molecule termed RAFTK (related adhesion focal tyrosine kinase), also called Pyk2 or CAK-beta. RAFTK, the second member of the focal adhesion kinase (FAK) family, is known to be activated in response to calcium flux in neuronal cells and integrin stimulation in megakaryocytes and B cells. We have studied the effects of cytokines on RAFTK activation in TrHBMEC. Treatment of TrHBMEC with the vascular endothelial growth factor (VEGF), as well as the VEGF-related protein (VRP), the recently identified ligand for the FLT-4 receptor, resulted in enhanced tyrosine phosphorylation of RAFTK. Similar changes in RAFTK phosphorylation were observed upon stimulation of TrHBMEC with basic fibroblast growth factor (bFGF) or oncostatin M (OSM). Stimulation of these cells with growth factors also resulted in an increase in RAFTK activity and the c-Jun NH2-terminal kinase (JNK). RAFTK coimmunoprecipitated with the cytoskeletal protein paxillin through its C-terminal proline-rich domain in TrHBMEC. These results suggest that, in marrow endothelium, activation of RAFTK by VEGF, VRP, OSM, and bFGF represents a new element in the signal transduction pathways used by these growth factors and likely acts to coordinate signaling from their surface receptors to the cytoskeleton, thereby modulating cell growth and function.
Cell quake elastography (2018)

The ability to measure the elasticity of a cell provides information about its anatomy, function, and pathological state. Many techniques have been proposed to measure mechanical properties of single cells but most need a model of the cell characteristics and the fixation of the cell on a substrate. Moreover, current measurements take seconds to hours to perform, during which biological processes can modify the cell elasticity. Here, we have developed an alternative technique by applying shear wave elastography to the micrometer scale. Elastic waves were mechanically induced in live mammalian oocytes using a vibrating actuator. These audible frequency waves were observed optically at 205,000 frames per second and tracked with an optical flow algorithm previously developed in the context of ultrasound elastography. Whole-cell elasticity was then reconstructed using an elastography method inspired by the seismology field. Using this approach we showed that the elasticity of mouse oocytes is decreased when the oocyte cytoskeleton is disrupted with cytochalasin B. The technique is fast (less than 1 ms for data acquisition), precise (spatial resolution of a few micrometers), and able to map internal cell structures. The proposed method may represent a tractable option for interrogating biomechanical properties of diverse cell types.
Room temperature blue phosphorescence: a combined experimental and theoretical study on the bis-tridentate Ir(iii) metal complexes (2016)

A series of new bis-tridentate Ir(iii) complexes (1/1b, 2/2b and 3/3b) incorporating both bis(imidazolylidene)benzene and dianionic functional pyrazolyl (or phenyl) pyridine chelates have been synthesized, among which complexes 2 and 2b exhibit intense and structural sky-blue emission in both solution and solid states. In stark contrast, 1/1b is non-emissive in solution, while 3/3b reveals highly red-shifted emission with a featureless spectral profile. This variation in photophysics is associated with the interchange of metal-chelate bonding in the selected tridentate chelate, which affects both the crystal field stabilization energy and the ππ* transition character of the resulting Ir(iii) metal complexes. In 1/1b, the stabilized metal-centered (MC) dd excited states induce a dominant radiationless channel that accounts for the lack of emission in solution. The appreciable ligand-to-ligand charge transfer (LLCT) in 3/3b rationalizes its broad and featureless emission, which is different from the dominant intraligand ππ* transition in 2/2b. The combination of experimental and theoretical approaches thus provides fundamental insight into the influence of chelates as well as the metal-chelate interaction, which is beneficial for the future design of efficient and robust Ir(iii) phosphors for OLED applications.
FGF signaling regulates Wnt ligand expression to control vulval cell lineage polarity in C. elegans (2013)

The interpretation of extracellular cues leading to the polarization of intracellular components and asymmetric cell divisions is a fundamental part of metazoan organogenesis. The Caenorhabditis elegans vulva, with its invariant cell lineage and interaction of multiple cell signaling pathways, provides an excellent model for the study of cell polarity within an organized epithelial tissue. Here, we show that the fibroblast growth factor (FGF) pathway acts in concert with the Frizzled homolog LIN-17 to influence the localization of SYS-1, a component of the Wnt/β-catenin asymmetry pathway, indirectly through the regulation of cwn-1. The source of the FGF ligand is the primary vulval precursor cell (VPC) P6.p, which controls the orientation of the neighboring secondary VPC P7.p by signaling through the sex myoblasts (SMs), activating the FGF pathway. The Wnt CWN-1 is expressed in the posterior body wall muscle of the worm as well as in the SMs, making it the only Wnt expressed on the posterior and anterior sides of P7.p at the time of the polarity decision. Both sources of cwn-1 act instructively to influence P7.p polarity in the direction of the highest Wnt signal. Using single molecule fluorescence in situ hybridization, we show that the FGF pathway regulates the expression of cwn-1 in the SMs. These results demonstrate an interaction between FGF and Wnt in C. elegans development and vulval cell lineage polarity, and highlight the promiscuous nature of Wnts and the importance of Wnt gradient directionality within C. elegans.
Trends and outcomes of modern staging of solitary plasmacytoma of bone (2012)

Over the years, the definition of solitary plasmacytoma of bone (SPB) has shifted in part due to more modern testing capabilities. We hypothesized that outcomes data based on antiquated testing would not reflect outcomes using modern staging. To address both how widely applied adequate diagnostic staging is and what the progression rates of SPB as defined with state-of-the-art staging are, we performed a retrospective chart review of those patients with a diagnosis of SPB seen at our institution over the past decade. Two groups were studied: all patients with SPB (n = 127); and those patients referred to our institution for an indication other than progression (n = 91). The median PFS for those two groups were 26 months and 42 months, respectively. At baseline, only a minority of patients had state-of-the-art staging. The 5 patients with both modern imaging and a negative bone marrow had a 21 month PFS of 100%. Patients with plasmacytoma plus, one plasmacytoma but bone marrow consistent with monoclonal gammopathy of undetermined significance, fare worse than true SPB. The use of modern testing is imperative to characterize a patient's risk for progression. PET/CT plays an important role in the diagnostic work-up.
Insights into Adsorption of Linear, Monobranched, and Dibranched Alkanes on Pure Silica STW Zeolite as a Promising Material for Their Separation (2020)

The adsorption of linear, monobranched and dibranched saturated hydrocarbons in the gasoline range has been studied on pure silica STW zeolite (Si-STW) by using pentane, hexane, and heptane isomers as model adsorbates. Experimental single-component adsorption isotherms and kinetic measurements together with configurational bias Monte Carlo (CBMC) and molecular dynamics (MD) simulations were carried out. Significant differences in both the equilibrium adsorption and especially the adsorption kinetics were found, which suggests that the separation of the quaternary-carbon dibranched isomer is feasible. The adsorption capacities and selectivities surpass those of pure silica MFI (Si-MFI), considered as reference. Altogether, Si-STW is presented as a promising adsorbent for increasing the octane number (ON) of the hydroisomerization product by selectively excluding quaternary-carbon dibranched hydrocarbons.
Generation and measurement of sub-micrometer relativistic electron beams (2018)

Abstract The generation of low-emittance electron beams has received significant interest in recent years. Driven by the requirements of X-ray-free electron lasers, the emittance of photocathode injectors has been reduced significantly, with corresponding increase in beam brightness. This has put increasingly stringent requirements on the instrumentation to measure the beam size. These requirements are even more stringent for novel accelerator developments, such as laser-driven accelerators based on dielectric structures or on a plasma. We present here the generation and measurement of a sub-micrometer electron beam, at a particle energy of 330 MeV, and a bunch charge below 1 pC. An electron-beam optics with a vertical β -function of a few millimeters has been setup. The beam is characterized through a wire scanner that employs a 1 μm wide metallic structure fabricated using the electron-beam lithography. The smallest (rms) transverse beam size presented here is &lt;500 nm.
Enhancing the translational capacity of E. coli by resolving the codon bias (2018)

Abstract Escherichia coli is a well-established, and popular host for heterologous expression of proteins. The preference in the choice of synonymous codons (codon bias), however, might differ for the host and the original source of the recombinant protein, constituting a potential bottleneck in production. Codon choice affects the efficiency of translation by a complex and poorly understood mechanism. The availability of certain tRNA species is one of the factors that may curtail the capacity of translation. Here we provide a tRNA-overexpressing strategy that allows the resolution of the codon bias, and boosts the translational capacity of the popular host BL21(DE3) when rare codons are encountered. In BL21(DE3)-derived strain, called SixPack, copies of the genes corresponding to the six least abundant tRNA species have been assembled in a synthetic fragment and inserted into a ribosomal RNA operon. This arrangement, while not interfering with the growth properties of the new strain, allows dynamic control of the transcription of the extra tRNA genes, providing significantly elevated levels of the rare tRNAs in exponential growth phase. Results from expression assays of a panel of heterologous proteins of diverse origin and codon composition showed that the performance of SixPack surpassed that of the parental BL21(DE3) or a related strain equipped with a rare tRNA-expressing plasmid. Importance Codon composition not fitting the codon bias of the expression host frequently compromises the efficient production of foreign proteins in E. coli . Various attempts to remedy the problem (codon optimization by gene synthesis, expression of rare tRNAs from a plasmid) proved to be unsatisfying. Our new approach, adjusting the tRNA pool by co-expressing extra copies of rare tRNA genes with ribosomal RNA genes, does not affect normal cell physiology, and seems to be a superior solution in terms of simplicity, cost, and yield.
THz Band Channel Measurements and Statistical Modeling for Urban D2D Environments (2021)

THz band is envisioned to be used in 6G systems to meet the ever-increasing demand for data rate. However, before an eventual system design and deployment can proceed, detailed channel sounding measurements are required to understand key channel characteristics. In this paper, we present a first extensive set of channel measurements for urban outdoor environments that are ultra-wideband (1 GHz 3dB bandwidth), and double-directional where both the transmitter and receiver are at the same height. In all, we present measurements at 38 Tx/Rx location pairs, consisting of a total of nearly 50,000 impulse responses, at both line-of-sight (LoS) and non-line-of-sight (NLoS) cases in the 1-100 m range. We provide modeling for path loss, shadowing, delay spread, angular spread and multipath component (MPC) power distribution. We find, among other things, that outdoor communication over tens of meters is feasible in this frequency range even in NLoS scenarios, that omni-directional delay spreads of up to 100 ns, and directional delay spreads of up to 10 ns are observed, while angular spreads are also quite significant, and a surprisingly large number of MPCs are observed for 1 GHz bandwidth and 13 degree beamwidth. These results constitute an important first step towards better understanding the wireless channel in the THz band.
Fibre orientation anisotropy profile over the thickness of a headbox jet (2004)

Nous avons analyse l'anisotropie de l'orientation des fibres a divers niveaux du jet d'une caisse d'arrivee modele dotee d'une aube au centre. Une teneur extremement faible en fibres de nylon a ete utilisee afin que la partie interieure du jet soit visible et qu'il n'y ait aucune formation de flocs. Des parois paralleles transparentes contenaient le jet. Une mince pellicule laser illuminait le jet lateralement et une camera video capturait la lumiere reflechie perpendiculairement. L'orientation des fibres a ete evaluee a l'aide de l'analyse d'images. Les couches limitrophes, aux parois de la caisse d'arrivee et a la surface de l'aube, ont reduit localement l'anisotropie de l'orientation des fibres. L'anisotropie pourrait aussi etre reduite si l'arete de l'aube etait plus epaisse et plus arrondie. En general, l'anisotropie de l'orientation des fibres a ete legerement touchee par les changements de vitesse d'ecoulement et elle dependait fortement du coefficient de contraction dans la buse. Une faible vitesse et de grandes contractions ont produit davantage d'orientations anisotropiques.
Temporal and spatial design of x-ray pulses based on free-electron–crystal interaction (2021)

Tunable x-ray radiation sources are of wide importance for imaging and spectroscopy in fundamental science, medicine, and industry. The growing demand for highly tunable, high-brightness lab-scale x-ray sources motivates research of new mechanisms of x-ray generation. Parametric x-ray radiation (PXR) is a mechanism for tunable x-ray radiation from free electrons traversing crystalline materials. Although PXR has been investigated over decades, it remained limited in usages due to the low flux and strict dependence on fixed crystal properties. Here, we find new effects hiding in the PXR mechanisms, which provide control over the radiation polarization and spatial and temporal distribution. The radiation can form ultrashort pulses and delta-pulse trains, which makes the new effects fundamentally different from all conventional mechanisms of x-ray generation. We show how these new effects can be created from free-electron interactions with van der Waals materials. Furthermore, we consider free electrons traversing near material edges, which provides an additional degree of tunability in angular distribution and polarization of PXR. Our findings enable us to utilize recent breakthroughs in the atomic-scale design of 2D material heterostructures to provide platforms for creating tunable x-ray pulses.
Thermosensitive Micelle-Forming Block Copolymers of Poly(ethylene glycol) and Poly(N-isopropylacrylamide) (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTThermosensitive Micelle-Forming Block Copolymers of Poly(ethylene glycol) and Poly(N-isopropylacrylamide)M. D. C. Topp, P. J. Dijkstra, H. Talsma, and J. FeijenView Author Information Department of Chemical Technology and Institute for Biomedical Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Pharmacy, University of Utrecht, P.O. Box 80 082, 3508 TB Utrecht, The Netherlands Cite this: Macromolecules 1997, 30, 26, 8518–8520Publication Date (Web):December 29, 1997Publication History Received18 July 1997Revised4 November 1997Published online29 December 1997Published inissue 1 December 1997https://doi.org/10.1021/ma9710803Copyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views3593Altmetric-Citations274LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (61 KB) Get e-AlertsSUBJECTS:Copolymerization,Copolymers,Micelles,Micellization,Thermoresponsive polymers Get e-Alerts
Wow Detection and Compensation Employing Spectral Processing of Audio (2004)

The engineered algorithms are presented for the detection of parasitic frequency modulation in audio originating from irregularities of sound carrier velocity. The algorithms were developed with special regard to non-periodic frequency modulation effects found in old movie sound tracks. The proposed algorithms consider the influence of the wow disturbance on the location of formants in time-frequency representation. The dynamic analysis of formant structures behavior underlies discriminating between parasitic frequency changes and natural frequency fluctuations. The compensation of the detected wow-related frequency modulation is accomplished basing on the non-uniform resampling algorithm, driven by the discerned parasite modulation patterns. The details of the proposed wow detection and compensation techniques are presented and achieved results are discussed.
Zero-Echo-Time and Dixon Deep Pseudo-CT (ZeDD CT): Direct Generation of Pseudo-CT Images for Pelvic PET/MRI Attenuation Correction Using Deep Convolutional Neural Networks with Multiparametric MRI (2017)

Accurate quantification of uptake on PET images depends on accurate attenuation correction in reconstruction. Current MR-based attenuation correction methods for body PET use a fat and water map derived from a 2-echo Dixon MRI sequence in which bone is neglected. Ultrashort-echo-time or zero-echo-time (ZTE) pulse sequences can capture bone information. We propose the use of patient-specific multiparametric MRI consisting of Dixon MRI and proton-density-weighted ZTE MRI to directly synthesize pseudo-CT images with a deep learning model: we call this method ZTE and Dixon deep pseudo-CT (ZeDD CT). <b>Methods:</b> Twenty-six patients were scanned using an integrated 3-T time-of-flight PET/MRI system. Helical CT images of the patients were acquired separately. A deep convolutional neural network was trained to transform ZTE and Dixon MR images into pseudo-CT images. Ten patients were used for model training, and 16 patients were used for evaluation. Bone and soft-tissue lesions were identified, and the SUV<sub>max</sub> was measured. The root-mean-squared error (RMSE) was used to compare the MR-based attenuation correction with the ground-truth CT attenuation correction. <b>Results:</b> In total, 30 bone lesions and 60 soft-tissue lesions were evaluated. The RMSE in PET quantification was reduced by a factor of 4 for bone lesions (10.24% for Dixon PET and 2.68% for ZeDD PET) and by a factor of 1.5 for soft-tissue lesions (6.24% for Dixon PET and 4.07% for ZeDD PET). <b>Conclusion:</b> ZeDD CT produces natural-looking and quantitatively accurate pseudo-CT images and reduces error in pelvic PET/MRI attenuation correction compared with standard methods.
Persistence and fidelity of phase singularities in optical random waves (2016)

The existing quantitative phase imaging method Multifilter Phase Imaging with Partially Coherent light (MFPI-PC) has been extended to nonparaxial case. Its improved accuracy has been verified using simulations and microlens experimental measurements.
Recurrent Scattering and Memory Effect at the Anderson Localization Transition (2014)

We report on ultrasonic measurements of the propagation operator in a strongly scattering mesoglass. The backscattered field is shown to display a deterministic spatial coherence due to a remarkably large memory effect induced by long recurrent trajectories. Investigation of the recurrent scattering contribution directly yields the probability for a wave to come back close to its starting spot. The decay of this quantity with time is shown to change dramatically near the Anderson localization transition. The singular value decomposition of the propagation operator reveals the dominance of very intense recurrent scattering paths near the mobility edge.
Interactions of TPA and insulin on Na+ transport across frog skin (1989)

The phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA) activates protein kinase C (PKC) and produces an early stimulation of Na+ transport across frog skin. The ionic basis for this stimulation was studied with combined transepithelial and intracellular electrical measurements. In an initial series of experiments, TPA approximately doubled the amiloride-sensitive short-circuit current (ISC), apical Na+ permeability (PapNa), and apical membrane conductance without affecting the basolateral membrane conductance. The apical effects led to a marked depolarization of the short-circuited skin and a small increase in intracellular Na+ concentration. TPAs increase of PapNa was sufficient to explain the stimulation of basolateral Na+ transport when both the voltage and substrate dependence of the pump were taken into account. After the early stimulation, TPA later depressed ISC. Added at this point (congruent to 1-2 h after TPA administration), insulin had no effect on ISC, whereas a partial response to vasopressin was still observed. Measured either early or late after TPA addition, the phorbol ester reduced insulin binding by congruent to 40%. Insofar as 60% of the specific binding is retained, the abolishment of insulin's natriferic response is unlikely to result from the TPA-induced reduction in hormonal binding. The data provide further support for the concept that activation of PKC produces an early stimulation of Na+ transport by increasing apical Na+ permeability, and that part of insulin's natriferic effect may be mediated by PKC activation.