gebhart/patrepeval huggingface dataset:
Biological indicators of response and resistance to PARP inhibition in BRCA wild-type breast cancer. (2015)

125 Background: Although PARP inhibitors are currently being tested in clinical trials in breast cancer patients, it is not well understood which subgroup of patients will best respond to such therapy or how to combine anti-PARP therapy to improve therapeutic response. Methods: We assessed the response of a panel of 8 HER2-negative breast cancer cell lines against three PARP inhibitors: veliparib, olaparib, and BMN 673. Efficacy of carboplatin as a single agent and in combination with PARP inhibitors was determined. Therapeutic response and cellular phenotype were elucidated using live-cell imaging, high-content imaging and immunofluorescence. We computed IC50 as the measure of sensitivity to each PARP inhibitor across the panel of cell lines. Cellular phenotype was ascertained by quantifying endpoints for apoptosis and DNA damage. Results: BMN 673 demonstrated the highest potency, with IC50 values in the nanomolar range, while the IC50 values of olaparib and veliparib were in the micromolar range. Drug sensitivity was independent of BRCA mutational status. Biomarkers of apoptosis and DNA damage varied with the PARP inhibitor and across different cell lines. The resistant cell lines could be classified into two groups that varied in DNA damage response and cell death due to DNA damage. A combined DNA damage – cell death (DDD) Response Score was developed and correlated strongly with IC50 values in BRCA wild-type breast cancer cell lines. The DDD Response Score identified cell lines that were highly sensitive to single-agent PARP inhibitors or carboplatin. A Response Score that identified intermediate sensitivity may predict which cell lines may benefit from the combination of anti-PARP therapy and carboplatin. Conclusions: Overall, a spectrum of response to three different PARP inhibitors was identified in a panel of eight breast cancer lines. Cellular phenotype can help classify resistant cancer cell lines. We have developed an experimental approach that may help to inform which breast cancer subtypes may benefit from PARP inhibitors and carboplatin, both as single agents, and in combination.
Antifeedant effects of plant lectins and an enzyme on the adult stage of the rice brown planthopper, Nilaparvata lugens (1995)

Abstract The feeding activity of adult rice brown planthopper, Nilaparvata lugens (Stal) on selected proteins incorporated into artificial diets was examined, based on quantitative analysis of honeydew excretion, in order to determine the mechanism of action of antimetabolic proteins towards homopteran pests. The lectins Galanthus nivalis agglutinin (GNA), wheat germ agglutinin (WGA) and the enzyme soybean lipoxygenase (LPO), previously demonstrated to be toxic to this insect, reduced honeydew excretion levels of adult Nilaparvata lugens over a 24 h period when incorporated into artificial diet at 0.1% {w:v}, indicating that these proteins acted as antifeedants. Of the proteins tested GNA was the most effective antifeedant, reducing honeydew droplet production by 96%, although after 24 h there was some recovery in the honeydew excretion levels and thus the insects appeared to tolerate the presence of the antifeedant with time. The lectin Pisum sativum agglutinin (PSA), previously demonstrated to be non‐toxic, showed no antifeedant properties.
An Overview of 5G System Accessibility Differentiation and Control (2021)

The 5G system is characterized by its ability to support a wide range of use cases and services. Supporting accessibility differentiation therefore becomes essential to preserve a stable network condition during high traffic load, while ensuring connection and service quality to prioritized devices and services. In this article, we describe some use cases and requirements that impact the 3GPP design of the 5G accessibility differentiation frame-work. We then provide an overview of the supported mechanisms for accessibility differentiation and control in 5G standalone systems, including cell barring and reservation, unified access control, paging control, random access control, and admission control. We discuss how these functionalities can be used to maintain the service quality and selectively limit the incoming traffic to the network in high load situations, leveraging different connection-type indicators and connection-priority identifiers.
DNA and the Digital Data Storage (2019)

Nowadays, most of current digital data are mainly stored on magnetic and optical media. At the explosive era of digital data, the digital data are generated every day and increased at an exponential rate. These traditional media cannot meet the urgent requirement of big digital data storage. With such advantages as high density, high replication efficiency, long-term durability and long-term stability, deoxyribonucleic acid (DNA) is expected as a novel and potential data storage medium. For the new DNA data storage, the files or any data readable will be converted to binary and then encoded to DNA sequences consisting of Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). The data-carrying DNA sequences will be synthesized and stored until data retrieval one day. Once data retrieval, the unique data-carrying DNA fragments will be amplified, sequenced and analyzed. The DNA-based data information will then be decoded into binary and eventually converted to the information readable. Currently, the application of DNA data storage is limited due to such disadvantages as high cost, time-consuming, lack of random access ability. We still need to face serial tough challenges. However, the seen advances in DNA sequencing technology positively shine the future of DNA digital data storage.
Near‐Surface Geophysics Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science (2022)

Abstract Pointing to the Integrated, Coordinated, Open, Networked Findability, Accessibility, Interoperability, and Reusability (ICON‐FAIR) principles, we have determined several opportunities for implementation within the realm of near‐surface geophysics (NSG), representing a broad range of data acquisition and processing technologies. Our work explores the multifaceted community‐driven nature of NSG and, by applying ICON‐FAIR principles, we identify three key strategic objectives: (i) the development of an approach to integrating NSG into other geoscience data collection projects, (ii) the creation of coordinated and open standardized NSG data, and (iii) the networking of post‐secondary institutions to foster an equipment sharing consortium. The precedence within the geoscientific community demonstrates that there are significant opportunities for advancing interdisciplinary applications of NSG through the implementation of structural change within the ICON‐FAIR framework.
Delayed Time-to-Treatment of an Antisense Morpholino Oligomer Is Effective against Lethal Marburg Virus Infection in Cynomolgus Macaques (2016)

Marburg virus (MARV) is an Ebola-like virus in the family Filovirdae that causes sporadic outbreaks of severe hemorrhagic fever with a case fatality rate as high as 90%. AVI-7288, a positively charged antisense phosphorodiamidate morpholino oligomer (PMOplus) targeting the viral nucleoprotein gene, was evaluated as a potential therapeutic intervention for MARV infection following delayed treatment of 1, 24, 48, and 96 h post-infection (PI) in a nonhuman primate lethal challenge model. A total of 30 cynomolgus macaques were divided into 5 groups of 6 and infected with 1,830 plaque forming units of MARV subcutaneously. AVI-7288 was administered by bolus infusion daily for 14 days at 15 mg/kg body weight. Survival was the primary endpoint of the study. While none (0 of 6) of the saline group survived, 83-100% of infected monkeys survived when treatment was initiated 1, 24, 48, or 96 h post-infection (PI). The antisense treatment also reduced serum viremia and inflammatory cytokines in all treatment groups compared to vehicle controls. The antibody immune response to virus was preserved and tissue viral antigen was cleared in AVI-7288 treated animals. These data show that AVI-7288 protects NHPs against an otherwise lethal MARV infection when treatment is initiated up to 96 h PI.
Ultra-fast dynamic control of the Q factor in a photonic crystal nanocavity (2008)

High-quality (Q) factor photonic-crystal nanocavities are currently the focus of much interest because they can strongly confine photons in a tiny space. Nanocavities with ultrahigh Q factors of up to 2,500,000 and modal volumes of a cubic wavelength have been realized. If the Q factor could be dynamically controlled within the lifetime of a photon, significant advances would be expected in areas of physics and engineering such as the slowing and/or stopping of light and quantum-information processing. Here, we review the demonstration of dynamic control of the Q factor, by constructing a system composed of a nanocavity, a waveguide with nonlinear optical response and a photonic-crystal heterointerface mirror. The Q factor of the nanocavity was successfully changed from 3,800 to 22,000 within picoseconds.
Model-Based Real-Time Head Tracking (2002)

This paper treats real-time tracking of a human head using an analysis by synthesis approach. The work is based on the Structure from Motion (SfM) algorithm from Azarbayejani and Pentland (1995). We will analyze the convergence properties of the SfM algorithm for planar objects, and extend it to handle new points. The extended algorithm is then used for head tracking. The system tracks feature points in the image using a texture mapped three-dimensional model of the head. The texture is updated adaptively so that points in the ear region can be tracked when the user′s head is rotated far, allowing out-of-plane rotation of up to without losing track. The covariance of the - and the -coordinates are estimated and forwarded to the Kalman filter, making the tracker robust to occlusion. The system automatically detects tracking failure and reinitializes the algorithm using information gathered in the original initialization process.
Aqueous medium induced optical transitions in cerium oxide nanoparticles (2015)

Experimental and theoretical investigations were performed to investigate the effect of water on optical properties of nanoceria as a function of Ce(3+) concentration. Theoretical studies based on density functional plane-wave calculations reveal that the indirect optical transitions in bare ceria nanoparticles are red-shifted with an increase in the concentration of Ce(3+). However, ceria nanoparticles model with adsorbed water molecules show a blue shift in the indirect optical spectra under identical conditions. Direct optical transitions are almost independent of Ce(3+) concentration but show a pronounced blue shift in the aqueous environment relative to the bare nanoparticles. The theoretical study is consistent with our experimental observation in difference of shift behaviour in bare and aqueous suspended ceria nanoparticles. This change from red- to blue-shift in indirect optical transitions is associated with the polarization effect of water molecules on f-electron states.
Cannabis Use and Plasma Human Immunodeficiency Virus (HIV) RNA Levels in Patients Coinfected With HIV and Hepatitis C Virus Receiving Antiretroviral Therapy: Data From the ANRS CO13 HEPAVIH Cohort (2020)

International audience
Cross-regulation of TNF and IFN-α in autoimmune diseases (2005)

Cytokines, most particularly TNF and type I IFN (IFN-alphabeta), have been long considered essential elements in the development of autoimmunity. Identification of TNF in the pathogenesis of rheumatoid arthritis and TNF antagonist therapy represent successes of immunology. IFN-alphabeta plays a major role in systemic lupus erythematosus (SLE), a prototype autoimmune disease characterized by a break of tolerance to nuclear components. Here, we show that TNF regulates IFN-alpha production in vitro at two levels. First, it inhibits the generation of plasmacytoid dendritic cells (pDCs), a major producer of IFN-alphabeta, from CD34+ hematopoietic progenitors. Second, it inhibits IFN-alpha release by immature pDCs exposed to influenza virus. Neutralization of endogenous TNF sustains IFN-alpha secretion by pDCs. These findings are clinically relevant, as five of five patients with systemic juvenile arthritis treated with TNF antagonists display overexpression of IFN-alpha-regulated genes in their blood leukocytes. These results, therefore, might provide a mechanistic explanation for the development of anti-dsDNA antibodies and lupus-like syndrome in patients undergoing anti-TNF therapy.
Advanced Scanning Electrochemical Microscope System for High-Resolution imaging and Electrochemical Applications (2017)

We developed three modes of high resolution scanning probe microscope system based on electrochemical principles, scanning ion conductance microscopy (SICM), scanning electrochemical microscopy-scanning ion conductance microscopy (SECM-SICM), and scanning electrochemical cell microscopy (SECCM). Firstly, a developed SICM system was constructed with a nanopipette filled with electrolyte solution as a probe. High resolution topographic images of NanoCulture®Plate with hexagonal chambers with 2 µm-width banks, electrodeposited PEDOT (poly(3,4-ethylenedioxythiophane)) film, and fixed human squamous cell carcinoma were captured by the SICM. Second, SECM-SICM was performed with a double-barrel carbon nanoprobe. The one barrel of the nanoprobe was filled with carbon and used for SECM apparatus, the other barrel was filled with electrolyte for SICM configurations. Using the SECM-SICM system, simultaneous topographic and electrochemical images of micro-band electrodes with 10 µm-width line and space, and a cathode site of corrosion in the aluminum die gusto with submicron spatial resolution were obtained. Thirdly, the SECCM featuring a nanopipette probe filled with LiCl electrolyte was applied for obtaining topographies and images of current activity of a LiFePO4 electrode.
A new approach to modularity in rule-based programming (2002)

We describe a purely declarative method for introducing modularity into forward-chaining, rule-based languages and its embodiment in the Venus rule language. The method is enforced by the syntax of the language and includes the ability to parameterize the rule groups. Drawing from two of three Venus applications developed to date, we illustrate how this form of modularity contributes directly to the resolution of certain software engineering problems associated with rule languages.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The broad-band Wiener solution for Griffiths-Jim beamformers (1992)

The authors treat the problem of finding the Wiener filters for a wideband adaptive beamformer. Explicit expressions are given for the filters and error power spectrum in the frequency domain. The expressions are simple to program and give the possibility of investigating superresolution for wideband signals and of determining sufficient lengths of the finite-impulse-response filters in adaptive arrays. The major results are an analytical expression for the broadband array Wiener solution given for an arbitrary spectrum for target, interference, and noise and an approximate analytic expression for the angular 3-dB beamwidth for broadband signals.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Software defined radio - 20 years later: Part 1 [Guest Editorial] (2015)

It has been two decades since the publication of the seminal tutorial "The Software Radio Architecture" in IEEE Communications Magazine. The evolution of Software Defined Radio (SDR) systems had profound impact both in military and multi-standard commercial space. The intent of the feature topic is to capture key elements of the evolution of the enabling technologies as well as SDR solutions for flexible and reconfigurable wireless platforms.
Analysis of the Surface Chemical Structure of Copolymers of Poly(sebacic anhydride) with Ricinoleic Acid Maleate Using XPS and ToF−SIMS (1998)

X-ray photoelectron spectrocopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF−SIMS) have been used to characterize the surface chemistry of copolymers of poly(sebacic anhydride) with ricinoleic acid maleate. ToF−SIMS analysis yielded fragmentation patterns consisting of ions diagnostic of both monomers. Across the copolymer series, relative peak intensities of these diagnostic ions showed a good comparison between surface and bulk composition, in accordance with the XPS analysis. ToF−SIMS data also indicated that these copolymers consisted of either random or block sections.
A cluster of genes located in 1p36 are down-regulated in neuroblastomas with poor prognosis, but not due to CpG island methylation. (2005)

The genes UBE4B, KIF1B, PGD, APITD1, DFFA and PEX14 are down-regulated in high stage NB tumours, a feature that can not be explained by CpG island methylation.
Segmentation of Confocal Raman Microspectroscopic Imaging Data Using Edge-Preserving Denoising and Clustering (2013)

Over the past decade, confocal Raman microspectroscopic (CRM) imaging has matured into a useful analytical tool to obtain spatially resolved chemical information on the molecular composition of biological samples and has found its way into histopathology, cytology, and microbiology. A CRM imaging data set is a hyperspectral image in which Raman intensities are represented as a function of three coordinates: a spectral coordinate λ encoding the wavelength and two spatial coordinates x and y. Understanding CRM imaging data is challenging because of its complexity, size, and moderate signal-to-noise ratio. Spatial segmentation of CRM imaging data is a way to reveal regions of interest and is traditionally performed using nonsupervised clustering which relies on spectral domain-only information with the main drawback being the high sensitivity to noise. We present a new pipeline for spatial segmentation of CRM imaging data which combines preprocessing in the spectral and spatial domains with k-means clustering. Its core is the preprocessing routine in the spatial domain, edge-preserving denoising (EPD), which exploits the spatial relationships between Raman intensities acquired at neighboring pixels. Additionally, we propose to use both spatial correlation to identify Raman spectral features colocalized with defined spatial regions and confidence maps to assess the quality of spatial segmentation. For CRM data acquired from midsagittal Syrian hamster ( Mesocricetus auratus ) brain cryosections, we show how our pipeline benefits from the complex spatial-spectral relationships inherent in the CRM imaging data. EPD significantly improves the quality of spatial segmentation that allows us to extract the underlying structural and compositional information contained in the Raman microspectra.
New Insight into the Binding Mode of Peptide Ligands at Urotensin-II Receptor: Structure−Activity Relationships Study on P5U and Urantide (2009)

Urotensin II (U-II) is a disulfide bridged peptide hormone identified as the ligand of a G protein-coupled receptor. Human U-II (H-Glu-Thr-Pro-Asp-c[Cys-Phe-Trp-Lys-Tyr-Cys]-Val-OH) has been described as the most potent vasoconstrictor compound identified to date. We have recently identified both a superagonist of hU-II termed P5U (H-Asp-c[Pen-Phe-Trp-Lys-Tyr-Cys]-Val-OH) and the compound termed urantide (H-Asp-c[Pen-Phe-DTrp-Orn-Tyr-Cys]-Val-OH), which is the most potent UT receptor peptide antagonist described to date. In the present study, we have synthesized several analogues of P5U and urantide in which the Asp(4) residue in N-terminus position was replaced with coded and noncoded amino acids. The replacement of the Asp(4) residue by Tic led to an analogue, compound 14, more potent as antagonist (pK(B) = 8.94) compared to urantide. Furthermore, a different SAR was observed for the P5U compared to the urantide analogues. NMR and docking studies revealed a different binding mode for the agonist and antagonist ligands which could explain the observed SAR.
Mechanisms of ATP Release, the Enabling Step in Purinergic Dynamics (2011)

The only effective intervention to slow onset and progression of glaucomatous blindness is to lower intraocular pressure (IOP). Among other modulators, adenosine receptors (ARs) exert complex regulation of IOP. Agonists of A(3)ARs in the ciliary epithelium activate Cl(-) channels, favoring increased formation of aqueous humor and elevated IOP. In contrast, stimulating A(1)ARs in the trabecular outflow pathway enhances release of matrix metalloproteinases (MMPs) from trabecular meshwork (TM) cells, reducing resistance to outflow of aqueous humor to lower IOP. These opposing actions are thought to be initiated by cellular release of ATP and its ectoenzymatic conversion to adenosine. This view is now supported by our identification of six ectoATPases in trabecular meshwork (TM) cells and by our observation that external ATP enhances TM-cell secretion of MMPs through ectoenzymatic formation of adenosine. ATP release is enhanced by cell swelling and stretch. Also, enhanced ATP release and downstream MMP secretion is one mediator of the action of actin depolymerization to reduce outflow resistance. Inflow and outflow cells share pannexin-1 and connexin hemichannel pathways for ATP release. However, vesicular release and P2X(7) release pathways were functionally limited to inflow and outflow cells, respectively, suggesting that blocking exocytosis might selectively inhibit inflow, lowering IOP.
ACTIONS OF GROWTH HORMONE-RELEASE INHIBITING HORMONE (SOMATOSTATIN) ON THE RENIN ALDOSTERONE SYSTEM (1976)

Administration of growth hormone-release inhibiting hormone (GH-RIH, somatostatin), as a 90 minute infusion (10 mug/min), to 3 healthy young men under conditons of active renin secretion acheived by pretreatment with furosemide (80 mg daily for 5 days), caused a mean 30% fall in plasma renin activity, which returned to basal levels immediately after stopping the GH-RIH infusion. Plasma aldosterone levels were not affected during the course of this experiment.
A PPG Readout Integrated With RPTT Estimation in Analog For Blood Pressure Measurement (2023)

This study proposed a Photoplethysmography (PPG) readout system to estimate the reflective pulse transit time (RPTT) in analog domain for the blood pressure measurement. The proposed photodetector readout consists of a sensing circuit, an amplification circuit, and peak-sensing circuits. The designed circuit is fabricated by TSMC <tex>$0.18\mu \mathrm{m}$</tex> 1P6M 1.8V mixed-signal CMOS process. The measurement results show that the design chip consume <tex>$50\mu \mathrm{W}$</tex> and the measured dynamic range is 100 dB. Experimental verification shows that the obtained RPTT from the designed chip is 99.9% correlated with the RPTT obtained after the pre-signal processing of the PPG signal and the measured average difference in RPTT measurement is 15.73 msec. The obtained performance in terms of SBP and DBP shows that the accuracy satisfies the requirement of the AAMI under <tex>$\pm 8$</tex> mmHg.