gebhart/patrepeval huggingface dataset:
Ceramide stimulates epidermal growth factor receptor phosphorylation in A431 human epidermoid carcinoma cells. Evidence that ceramide may mediate sphingosine action (1991)

Recent studies suggest the existence of a signal transduction pathway involving sphingomyelin and derivatives (Kolesnick, R. N. (1989) J. Biol. Chem. 264, 7617-7623). The present studies compare effects of ceramide, sphingosine, and N,N-dimethylsphingosine on epidermal growth factor (EGF) receptor phosphorylation in A431 human epidermoid carcinoma cells. To increase ceramide solubility, a ceramide containing octanoic acid at the second position (C8-cer) was synthesized. C8-cer induced time- and concentration-dependent EGF receptor phosphorylation. This event was detectable by 2 min and maximal by 10 min. As little as 0.1 microM C8-cer was effective, and 3 microM C8-cer induced maximal phosphorylation to 1.9-fold of control. EGF (20 nM) increased phosphorylation to 2.1-fold of control. Sphingosine stimulated receptor phosphorylation over the same concentration range (0.03-3 microM) and to the same extent (1.8-fold of control) as ceramide. The effects of C8-cer and sphingosine were similar by three separate criteria, phosphoamino acid analysis, anti-phosphotyrosine antibody immunoblotting, and phosphopeptide mapping by high performance liquid chromatography. Phosphorylation occurred specifically on threonine residues. N,N-Dimethylsphingosine, a potential derivative of sphingosine, was less effective. Since sphingosine and ceramide are interconvertible, the level of each compound was measured under conditions sufficient for EGF receptor phosphorylation. C8-cer (0.1-1 microM) induced dose-responsive elevation of cellular ceramide from 132 to 232 pmol.10(6) cells-1. In contrast, cellular sphingosine levels did not rise. This suggests that C8-cer acts without conversion to sphingosine. Exogenous sphingosine (0.1-1 microM) also increased cellular ceramide levels to 227 pmol.10(6) cells-1, but did not increase its own cellular level of 12 pmol.10(6) cells-1. Higher sphingosine concentrations that induced no further increase in EGF receptor phosphorylation produced very large elevations in cellular sphingosine. Hence, at effective concentrations, both compounds elevated cellular ceramide but not sphingosine levels. Additional studies performed with [3H]sphingosine demonstrated that cells contain substantially less N,N-dimethylsphingosine than free sphingosine and, during short term incubation, convert less than 5% of added sphingosine to N,N-dimethylsphingosine. These studies provide evidence that ceramide may have bioeffector properties and suggest sphingosine may act in part by conversion to ceramide.
Breathing-Mode Ceramic Element for Therapeutic Array Transducer (2011)

A new concept of piezoceramic array transducer element using breathing mode has been proposed for therapeutic application. Finite element numerical simulation showed that a concave hemispherical piezoceramic shell with a diameter slightly larger than the wavelength in water is effective for obtaining good acoustic matching with water. A hemispherical piezoceramic element with an inner diameter of 4.0 mm and a thickness of 0.2–0.4 mm produced more than several times higher acoustic power output than a conventional thickness-mode element at the same drive voltage in the simulation. Its good acoustic matching with water is considered to be accomplished by the combined resonance with the spherical bulk of water half covered by the shell, because the resonance was very sensitive to the change in sound speed of the virtual material replacing water with the same acoustic impedance in simulation.
Nonlinear averaging method to optimize the accuracy of optical tracking (2003)

In image-guided surgery, it is essential to be able to track the positions of instruments in physical space and relate these positions to preoperative or intraoperative images. The most common way of tracking the instruments is using optical tracking; a camera containing two charge-coupled devices calculates the 3D position of IR light emitting diodes, and uses this information to deduce the position and orientation of the instrument. Because the IREDs cannot be localized perfectly, the calculated pose of the instrument, and hence the overlay of the instrument on the image, undergoes continual small changes even when the instrument is stationary. This leads to the user interface of the image guidance system displaying rapid small movements of the probe; we call this phenomenon 'jitter'. Severe jitter can make the image guidance system difficult and bothersome to use and may reduce system accuracy. In this paper, we examine a novel method of overcoming the jitter problem. This method performs a nonlinear average of historical tracking information collected over a given time period. We show the disadvantages of a simpler linear averaging technique; we also use a phantom of known geometry to examine the overall effect that averaging has on system accuracy.
In Situ Space‐ and Time‐Resolved Sorption Kinetics of Anionic Dyes on Individual LDH Crystals (2005)

Fluorescence spectroscopy is employed to follow the ion exchange of an emissive dye--a carboxylated perylene imide--on a layered double hydroxide. The exchange of the carboxylate ions starts at the edges of the layered double hydroxide crystals and is followed by diffusion to the basal plane. Such space-resolved observations provide a solid basis for modelling and studying the mechanisms of exchange.
Purification and characterization of the bacteriophage T7 gene 2.5 protein : a single-stranded DNA-binding protein (2021)

Bacteriophage T7 gene 2.5 protein has been purified to homogeneity from cells overexpressing its gene. Native gene 2.5 protein consists of a dimer of two identical subunits of molecular weight 25,562. Gene 2.5 protein binds specifically to single-stranded DNA with a stoichiometry of approximately 7 nucleotides bound per monomer of gene 2.5 protein; binding appears to be noncooperative. Electron microscopic analysis shows that gene 2.5 protein is able to disrupt the secondary structure of single-stranded DNA. The single-stranded DNA is extended into a chain of gene 2.5 protein dimers bound along the DNA. In fluorescence quenching and nitrocellulose filter binding assays, the binding constants of gene 2.5 protein to single-stranded DNA are 1.2 x 10(6) M-1 and 3.8 x 10(6) M-1, respectively. Escherichia coli single-stranded DNA-binding protein and phage T4 gene 32 protein bind to single-stranded DNA more tightly by a factor of 25. Fluorescence spectroscopy suggests that tyrosine residue(s), but not tryptophan residues, on gene 2.5 protein interacts with single-stranded DNA.
Development of a Zooming Analysis System using 3-dimentional Geometric Model. (1999)

This paper describes a zooming analysis system that uses a three-dimentional geometric model. A finite element analysis (FEA) using a zooming technique is needed for the estimatation of stresses in a very small area. However, it takes a long time to make an FEA mesh model and set the analysis conditions of any part of the model. We have developed a technique that automatically creates the FEA mesh model and sets the analysis conditions of any part of the model. In this system, a user inputs a geometry and analysis conditions of the entire model as well as the geometry of any part of the model and carries out a whole-model analysis and a detailed analysis of the target part. Employing this zooming technique significantly reduces the analysis time.
Combined treatment: antifungal drugs with antibodies, cytokines or drugs (2000)

To improve present results with antifungal drugs, modulation of the host immune response is being explored. Human phagocytes of various lineages work cooperatively in vitro with antifungal drugs to inhibit or kill fungal pathogens, and this activity is augmented by several recombinant cytokines. Monoclonal antibodies against the cryptococcal capsule have been shown to act as an adjunct in enhancing the outcome of cryptococcosis in animal models. This approach is now being pursued in systematic clinical trials. In experimental candidiasis, several manipulations of the immune system, via administration of cytokines, gene deletion or antibodies to cytokines, have been shown to significantly affect survival and fungal clearance in vivo. This approach has already been demonstrated to be of benefit with recombinant human granulocyte-colony stimulating factor adjunct therapy of human candidiasis. Combining antifungal drugs of different classes may enhance their therapeutic effect.
InP/InGaAsP wafer-bonded vertically coupled X-crossing multiple channel optical add-drop multiplexer (2002)

A vertically coupled InP/InGaAsP crossed waveguide optical add-drop multiplexer (OADM) has been realized through the use of wafer bonding. Designed for signals in the 1550-nm range, this novel device requires only a single epitaxial growth and illustrates the use of vertical optical interconnects for the three-dimensional routing of optical signals. To our knowledge, it is also one of the first optical vertically coupled devices with no horizontally coupled counterpart.
Abstract 4931: Biomarker discovery in a large panel of cell lines shows different sample size requirement for prediction of response across a set of compounds (2012)

Abstract A panel of more than 600 cell lines from 17 tumor types has been profiled and sensitivity to a set of FDA approved compounds with different mechanisms of action has been tested. Comparison of gene expression profiles with overlapping set of publicly available profiles showed 100% accuracy of cell line identity prediction using nearest neighbor classifier. Similar analysis of CNV data had 80% accuracy due to relatively little CNV perturbation in some of the cell lines. Significant gene expression signatures have been detected for 80% of compounds. De-novo agnostic classification based on 50% train/test split and a linear classifier resulted in significant prediction on the test set for about 40% of the compounds, such as dasatinib, 5FU, paclitaxel, but failed to produce a significant prediction for others, such as doxorubicine, irinotecan, and vinblastine. For most of the compounds, the prediction of response is complex, with multiple distinct molecular features contributing to a classification algorithm. This inherent complexity requires integration of gene expression, CNV and mutation data as well as a large cell line sets for development of accurate classification algorithms. We defined functional CNV and SNV events using gene expression based modules as a functional readout. Predictive models that incorporate prior knowledge of mechanism of action of the compounds and rely on functional SNV and CNV events out perform completely agnostic methods of prediction. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4931. doi:1538-7445.AM2012-4931
Inhomogeneity Based Characterization of Distribution Patterns on the Plasma Membrane (2016)

Cell surface protein and lipid molecules are organized in various patterns: randomly, along gradients, or clustered when segregated into discrete micro- and nano-domains. Their distribution is tightly coupled to events such as polarization, endocytosis, and intracellular signaling, but challenging to quantify using traditional techniques. Here we present a novel approach to quantify the distribution of plasma membrane proteins and lipids. This approach describes spatial patterns in degrees of inhomogeneity and incorporates an intensity-based correction to analyze images with a wide range of resolutions; we have termed it Quantitative Analysis of the Spatial distributions in Images using Mosaic segmentation and Dual parameter Optimization in Histograms (QuASIMoDOH). We tested its applicability using simulated microscopy images and images acquired by widefield microscopy, total internal reflection microscopy, structured illumination microscopy, and photoactivated localization microscopy. We validated QuASIMoDOH, successfully quantifying the distribution of protein and lipid molecules detected with several labeling techniques, in different cell model systems. We also used this method to characterize the reorganization of cell surface lipids in response to disrupted endosomal trafficking and to detect dynamic changes in the global and local organization of epidermal growth factor receptors across the cell surface. Our findings demonstrate that QuASIMoDOH can be used to assess protein and lipid patterns, quantifying distribution changes and spatial reorganization at the cell surface. An ImageJ/Fiji plugin of this analysis tool is provided.
Scalable multi-chip quantum architectures enabled by cryogenic hybrid wireless/quantum-coherent network-in-package (2023)

The grand challenge of scaling up quantum computers requires a full-stack architectural standpoint. In this position paper, we will present the vision of a new generation of scalable quantum computing architectures featuring distributed quantum cores (Qcores) interconnected via quantum-coherent qubit state transfer links and orchestrated via an integrated wireless interconnect.
Cyclization–hydrolysis of a 1,2,4-benzothiadiazine 1,1-dioxide through a diazonium intermediate (1979)

N. D. Heindel and E. G. Corley, J. Chem. Soc., Chem. Commun., 1979, 1008 DOI: 10.1039/C39790001008
Influence of media composition on the growth rate of Chlorella vulgaris and Scenedesmus acutus utilized for CO2 mitigation (2012)

Atmospheric carbon dioxide levels have increased since the industrial revolution due to the increase in combustion of fossil fuels. These elevated levels of CO2 have been cited as a significant cause of climate change. Hence, there is a well motivated need to find ways to mitigate CO2 emissions. Chemical absorption and geological storage of CO2 have high energy consumption, high capital cost and potential leakage. One possible alternative strategy is the use of microalgae for mitigation of CO2. This paper focuses on the influence of media composition on the growth rate of two microalgae strains, Chlorella vulgaris and Scenedesmus actus. A KNO3 based medium was found to work better for Chlorella, while a urea based equivalent worked better for Scenedesmus. Upon reduction of the urea concentration, the algae growth rate increased slightly, showing that the urea level was not the limiting ingredient in the medium. The urea based media investigated here resulted in growth similar to that found with previously reported KNO3 based media. This should result in an economic benefit in large scale algae cultivation for CO2 mitigation, since urea is typically less expensive than KNO3. Additional media components were tested and it was found that EDTA and vitamin B do not result in a significant increase in algae growth rate.
Hierarchical image coding with pyramid DPCM (2002)

The authors apply DPCM (differential pulse code modulation) to pyramid coding strategy, and show that, for practical quantizers, lower bit rates than regular DPCM are required for high-quality resulting images. The pyramid DPCM is relatively simple, feasible, and allows a processing interval between samples that is longer than the sampling interval. A blockwise scheme for multiresolution which could largely decrease the coding bit rate is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pioglitazone Decreases Hepatitis C Viral Load in Overweight, Treatment Naïve, Genotype 4 Infected-Patients: A Pilot Study (2012)

ClinicalTrials.gov NCT01157975.
Influence of Oxides on the Stress Evolution and Reversibility during SnOx Conversion and Li‐Sn Alloying Reactions (2014)

The effect of varying the oxygen content in Sn and SnO x films during potential dependent SnO x conversion reactions and Li y Sn alloying relevant to Li ion battery anodes is examined. For metallic Sn films, the stresses and stability of the films are controlled by Li alloying reactions. Small, non‐contacting separated Sn particles exhibit higher electrochemical stability relative to more continuous polycrystalline films with larger particles. Metallic Sn particles develop tensile stress during Li y Sn de‐alloying as porous structures are formed. The amount of stress associated with lithiation and delithiation of well‐separated metallic particles decreases as a porous, easy to lithiate, material forms with cycling. During the lithiation of oxides, conversion reactions (SnO x → Sn) and the lithiation of the metallic Sn control the stress responses of the films, leading to highly potential‐dependent stress development. In particular, evidence for a multistep electrochemical mechanism, in which partially reversible lithiation of the oxygen‐containing phases is conjoined with a fully reversible lithiation of the metallic phases of the Sn, is found. The electrochemical stress analysis provides new insight into these mechanisms and delineates the extent of the reversibility of lithiation and conversion reactions of oxides.
Channel Estimation and Equalization in the Presence of Timing Offset in MB-OFDM Systems (2007)

This paper presents low-complexity preamble-based channel estimation and one-tap frequency-domain equalization for zero-padded MB-OFDM based UWB systems. The required circular convolution property of the received signal is obtained by means of an overlap-add method. The proposed low-complexity channel estimator for each band is developed by first averaging the over-lap-added received preamble symbols within the same band and then applying time-domain least-squares method followed by the discrete Fourier transform. By using the probability density functions of the UWB channel path delays, we also derive the statistics of the UWB channel models, and utilizing them we present several optimization criteria for our proposed channel estimation and equalization in the presence of timing offset. The effectiveness of our proposed methods and optimization criteria are confirmed by computer simulation results.
Single-mode, narrowband thermal emitters based on quantum wells and photonic crystals (2013)

We demonstrate thermal emitters based on quantum wells and photonic crystals that have a single emission peak with a quality factor over 100. Our results will have potential applications to environmental sensors and thermo-photovoltaic systems.
Photomixer with superconductor detector for sub-THz generator (2004)

A new type of optical-microwave conversion system has been proposed as high-stabilized oscillators and optical interfaces for superconducing circuits. The photomixer with heterodyne mixing of two lasers was applied to generate the electromagnetic waves and high-T<sub>C</sub> grain boundary Josephson junction detector was used to monitor the frequency of electromagnetic waves in real time. The current-voltage properties of Josephson junction detector were examined and the system operation up to 50 GHz was demonstrated. We also described in detail the two types of optical-microwave conversion system.
Clinical performance of implantable cardioverter-defibrillator lead monitoring diagnostics (2021)

ClinicalTrials.gov identifier: NCT02277990.
Inhibition of Mitochondrial Matrix Chaperones and Antiapoptotic Bcl-2 Family Proteins Empower Antitumor Therapeutic Responses (2017)

Rational therapeutic approaches based on synthetic lethality may improve cancer management. On the basis of a high-throughput drug screen, we provide preclinical proof of concept that targeting the mitochondrial Hsp90 chaperone network (mtHsp90) and inhibition of Bcl-2, Bcl-xL, and Mcl-1 is sufficient to elicit synthetic lethality in tumors recalcitrant to therapy. Our analyses focused on BH3 mimetics that are broad acting (ABT263 and obatoclax) or selective (ABT199, WEHI-539, and A1210477), along with the established mitochondrial matrix chaperone inhibitor gamitrinib-TPP. Drug combinations were tested in various therapy-resistant tumors <i>in vitro</i> and <i>in vivo</i> in murine model systems of melanoma, triple-negative breast cancer, and patient-derived orthotopic xenografts (PDX) of human glioblastoma. We found that combining BH3 mimetics and gamitrinib-TPP blunted cellular proliferation in a synergistic manner by massive activation of intrinsic apoptosis. In like manner, suppressing either Bcl-2, Bcl-xL, or Mcl-1 recapitulated the effects of BH3 mimetics and enhanced the effects of gamitrinib-TPP. Mechanistic investigations revealed that gamitrinib-TPP activated a PERK-dependent integrated stress response, which activated the proapoptotic BH3 protein Noxa and its downstream targets Usp9X and Mcl-1. Notably, in the PDX glioblastoma and BRAFi-resistant melanoma models, this drug combination safely and significantly extended host survival. Our results show how combining mitochondrial chaperone and Bcl-2 family inhibitors can synergize to safely degrade the growth of tumors recalcitrant to other treatments. <i>Cancer Res; 77(13); 3513-26. ©2017 AACR</i>.
Supplementary Figure 1 from Combinations with Allosteric SHP2 Inhibitor TNO155 to Block Receptor Tyrosine Kinase Signaling (2023)

&lt;p&gt;Identification of the feedback activated RTK and the synergy in anti-proliferation effect by the combination of respective RTK inhibitors and dabrafenib plus trametinib in RKO and MDST8 cells.&lt;/p&gt;
Ultrathin Sb2S3nanowires and nanoplatelets (2007)

Ultrathin (thickness < 2.2 nm) colloidal Sb2S3nanowires and nanoplatelets were synthesized via a simple solution synthesis. The nanowires and platelets were stable in solution for months and were characterized viaSAED, XRD, UV-VIS spectroscopy, SAXS, XPS and EDAX.
Securing Model-C Inter-Provider VPNs with Label Hopping and TicToc (2013)

In certain models of inter-provider Multi- Protocol Label Switching
(MPLS) based Virtual Private Networks (VPNs) spoofing attack against
VPN sites is a key concern. For example, MPLS-based VPN inter-
provider model C for VPLS, or any L2 VPN purpose is not favoured,
owing to security concerns in the dataplane, even though it can scale
with respect to maintenance of routing state. Since the inner labels
associated with VPN sites are not encrypted during transmission, a
man-in-the-middle attacker can spoof packets to a specific L2 VPN
site. In this paper, we propose a label-hopping technique which uses a
set of randomized labels and a method for hopping amongst these labels
using the time instant the packet leaves the port from a sending
Provider Edge Router. To prevent the attacker from identifying the
labels in polynomial time, we also use an additional label. The
proposed technique can be applied to other variants of inter-provider
MPLS based VPNs where Multi-Protocol exterior-BGP (MP- eBGP) multi-hop
is used. As we address a key security concern, we can make a case for
the deployment of MPLS based L2 VPN inter-provider model C.
Specifically we use the TicToc based Precision Time Protocol LSP to
provide the timing for determining the time instant at which the
packet is sent from the remote end Provider Edge Router and hence
calculating when it must have left that peer at the Provider Edge
Router in the near / receiving end. This version of the document
suggests a better method for gaining more finely granular time slices.
This is done by running the PTP LSP between the ASBRs in the ASes that
are providing the inter-AS L3VPN service.
Raman Spectroscopic Analysis of Living Cells and Tissues and its Potential (2019)

To observe cells and tissues in thei‘r native’ states is a great challenge for researchers in biomedical fields. Development of a non-invasive and non-labeling analytical method for cells and tissues is eagerly anticipated. Raman spectroscopic measurement is a good candidate because it provides information on biomolecules of cells and tissues in their natural conditions. This technique has high potential not only for medical application such as diagnosis but also for biological research. In this paper, we introduce our basic researches into Raman spectroscopic measurement for biomedical applications.