gebhart/patrepeval huggingface dataset:
Identification of potent P2Y‐purinoceptor agonists that are derivatives of adenosine 5′‐monophosphate (1996)

1. A series of chain-extended 2-thioether derivatives of adenosine monophosphate were synthesized and tested as agonists for activation of the phospholipase C-linked P2Y-purinoceptor of turkey erythrocyte membranes, the adenylyl cyclase-linked P2Y-purinoceptor of C6 rat glioma cells, and the cloned human P2U-receptor stably expressed in 1321N1 human astrocytoma cells. 2. Although adenosine monophosphate itself was not an agonist in the two P2Y-purinoceptor test systems, eleven different 2-thioether-substituted adenosine monophosphate analogues were full agonists. The most potent of these agonists, 2-hexylthio AMP, exhibited an EC50 value of 0.2 nM for activation of the C6 cell receptor. This potency was 16,000 fold greater than that of ATP and was only 10 fold less than the potency of 2-hexylthio ATP in the same system. 2-hexylthio adenosine was inactive. 3. Monophosphate analogues that were the most potent activators of the C6 cell P2Y-purinoceptor were also the most potent activators of the turkey erythrocyte P2Y-purinoceptor. However, agonists were in general more potent at the C6 cell receptor, and potency differences varied between 10 fold and 300 fold between the two receptors. 4. Although 2-thioether derivatives of adenosine monophosphate were potent P2Y-purinoceptor agonists no effect of these analogues on the human P2U-purinoceptor were observed. 5. These results support the view that a single monophosphate is sufficient and necessary for full agonist activity at P2Y-purinoceptors, and provide insight for strategies for development of novel P2Y-purinoceptor agonists of high potency and selectivity.
Redundant roles of EGFR ligands in the ERK activation waves during collective cell migration (2021)

Epidermal growth factor receptor (EGFR) plays a pivotal role in collective cell migration by mediating cell-to-cell propagation of extracellular signal-regulated kinase (ERK) activation. Here, we aimed to determine which EGFR ligands mediate the ERK activation waves. We found that epidermal growth factor (<i>EGF</i>)-deficient cells exhibited lower basal ERK activity than the cells deficient in heparin-binding EGF (<i>HBEGF</i>), transforming growth factor alpha (<i>TGFα</i>) or epiregulin (<i>EREG</i>), but all cell lines deficient in a single EGFR ligand retained the ERK activation waves. Surprisingly, ERK activation waves were markedly suppressed, albeit incompletely, only when all four EGFR ligands were knocked out. Re-expression of the EGFR ligands revealed that all but HBEGF could restore the ERK activation waves. Aiming at complete elimination of the ERK activation waves, we further attempted to knockout <i>NRG1</i>, a ligand for ErbB3 and ErbB4, and found that <i>NRG1</i>-deficiency induced growth arrest in the absence of all four EGFR ligand genes. Collectively, these results showed that EGFR ligands exhibit remarkable redundancy in the propagation of ERK activation waves during collective cell migration.
Microsatellite analysis and telomerase activity in archived tissue and urine samples of bladder cancer patients (1997)

We performed microsatellite analysis and tested telomerase activity in paired tissue and urine of bladder cancer patients from frozen archived samples. DNA obtained from microdissected tumor and urine sediment was analyzed and compared to peripheral lymphocytes for microsatellite alterations (loss of heterozygosity [LOH] or instability) using a panel of 20 microsatellite markers in 15 patients with transitional or squamous cell carcinoma of the urinary tract. Additionally, telomerase activity was determined in 12 microdissected tumor specimens and corresponding frozen urine pellets. Tumor cell DNA was detected by microsatellite analysis (LOH or shift) in at least one marker in 14/15 microdissected tumor specimens and in 13/15 DNA samples obtained from urine sediments. Telomerase activity was present in 11/12 tumor samples but could not be detected in any of the corresponding urine sediments. Frozen archived urine samples are useful for retrospective studies utilizing microsatellite analysis or other PCR-based approaches after DNA extraction. However, the evaluation of telomerase protein activity in stored urine samples appears to be unsuitable. Int. J. Cancer 74:625–629, 1997.© 1997 Wiley-Liss, Inc.
Sparse Three-parameter Restricted Indian Buffet Process for\n Understanding International Trade (2018)

This paper presents a Bayesian nonparametric latent feature model specially\nsuitable for exploratory analysis of high-dimensional count data. We perform a\nnon-negative doubly sparse matrix factorization that has two main advantages:\nnot only we are able to better approximate the row input distributions, but the\ninferred topics are also easier to interpret. By combining the three-parameter\nand restricted Indian buffet processes into a single prior, we increase the\nmodel flexibility, allowing for a full spectrum of sparse solutions in the\nlatent space. We demonstrate the usefulness of our approach in the analysis of\ncountries' economic structure. Compared to other approaches, empirical results\nshow our model's ability to give easy-to-interpret information and better\ncapture the underlying sparsity structure of data.\n
WiFi Overcast: Enabling True Mobility for Realtime Applications in the Enterprise (2009)

Enterprises are increasingly deploying Wireless LANs to provide mobile access to users in corporate offices. However, existing enterprise WLANs are far from being truly mobile. In particular, they do not adequately support continuous mobility, where users access the network on-the-go. Furthermore, WLANs that do provide continuous mobility support require client modifications, making them hard to deploy in practice [20]. In addition, with the growing interest in realtime applications such as voice and video, users are increasingly placing additional (QoS) demands on the network, which for inadequately designed WLANs, does not scale to large numbers of users [10]. In this paper, we propose Overcast, a novel WLAN architecture that targets scenarios demanding continuous mobility and real-time support for 802.11 clients. Overcast does not require client modifications and supports all 802.11 standards. Though Overcast borrows some features from prior WLAN designs, it improves on them by incorporating a novel RF mapping framework (proposed in [3]) for accurate online detection of RF interference. We describe the architecture of Overcast in detail and discuss our current efforts in realizing such a system on off-the-shelf commodity hardware. We also describe an example application of Overcast to highlight it’s usefulness in supporting realtime applications in continuously mobile user environments.
Modeling of annealing kinetics for hydrogenated-amorphous-silicon-based solar cells using two-component metastable defects (2006)

We propose a kinetic model for the annealing in p-i-n-type hydrogenated-amorphous-silicon (a-Si:H)-based solar cells using a combination of the fill factor and “fast” and “slow” metastable defect states in their absorbers. Reported annealing data are simulated on p-i-n-type a-Si:H-based solar cells using the proposed model in order to confirm its validity. The recovery kinetic dependence on the thermal annealing temperature, biased voltage, and phase of the absorber controlled by the hydrogen dilution ratio during deposition are reviewed. Furthermore, we suggest a recovery mechanism for the solar cells based on long range hydrogen diffusion.
[Emergent viruses: SARS-associate coronavirus and H5N1 influenza virus]. (2006)

Two viral agents with RNA genome are responsible for emerging illnesses: influenza virus A/H5N1 and Severe Acute Respiratory Syndrome virus (SARS). For the diagnosis of SARS virus infection, an epidemiological investigation is necessary to know whether the patient has been exposed to a risk in a country where the SARS virus is circulating or whether the patient had worked in a laboratory handling SARS virus. The detection of SARS virus is possible in various clinical samples (including urine) by viral culture or RT-PCR. The handling of those samples and RNA extraction must be performed in a BSL3 laboratory. The SARS virus RT-PCR is poorly sensitive, therefore the test should be performed on samples collected consecutively for several days. In front of a suspicion of A/H5N1, similar procedures are recommended. An epidemiologic investigation is necessary to specify whether the patient stayed in a country where A/H5N1 virus was circulating. Clinical samples needed for a specific diagnosis are: nasopharyngeal, throat-swab or fecal samples, cerebrospinal fluid and blood. The presence of A/H5N1 virus is confirmed by viral isolation or RNA detection by RT-PCR. RNA extraction must be performed in a BSL3 laboratory. For diagnosis of A/H5N1 virus infection, RT-PCR test amplifies specifically a fragment of H5 gene (Hemagglutinin). In french laboratories of medical virology, procedures are ready to diagnose the first case of A/H5N1 virus infection and cases of reemerging SARS virus infection.
Keywords to visual categories: Multiple-instance learning forweakly supervised object categorization (2008)

Conventional supervised methods for image categorization rely on manually annotated (labeled) examples to learn good object models, which means their generality and scalability depends heavily on the amount of human effort available to help train them. We propose an unsupervised approach to construct discriminative models for categories specified simply by their names. We show that multiple-instance learning enables the recovery of robust category models from images returned by keyword-based search engines. By incorporating constraints that reflect the expected sparsity of true positive examples into a large-margin objective function, our approach remains accurate even when the available text annotations are imperfect and ambiguous. In addition, we show how to iteratively improve the learned classifier by automatically refining the representation of the ambiguously labeled examples. We demonstrate our method with benchmark datasets, and show that it performs well relative to both state-of-the-art unsupervised approaches and traditional fully supervised techniques.
Unraveling The Effects of siRNA Carrier Systems on Cell Physiology: A Multiparametric Approach Demonstrated on Dextran Nanogels (2013)

This methodology shows that current toxicity assays such as the 3-(4,5-dimethylthiazol-2yl-)-2,5-diphenyl tetrazolium bromide assay are not adequate to assess the full spectrum of cell-nanoparticle interactions and more in-depth studies are required.
Degradation and stabilization of cosmetic polyetherurethane in alcoholic solution (2003)

Abstract A polyetherurethane (PEU) was synthesized for potential cosmetic applications by coupling poly(tetramethylene oxide) (PTMO, M n = 2000 g mol −1 ) and poly(ethylene oxide) (PEO, M n = 2000 g mol −1 ) with 4,4′‐diphenylmethane diisocyanate (MDI), without using a chain extender. The PEU polymer, synthesized with PEO and PTMO in the ratio of 1:3 by weight, was soluble in ethanol–water mixed solvents. The solution formed a thin film in situ on the skin by coating, which was flexible and elastomeric with appropriate skin adhesiveness. However, PEU was susceptible to degradation when it was exposed to an ethanol–water (80/20 v/v %) mixed solvent and stored in an air‐filled and sealed bottle at 60°C for 4 weeks. These conditions resulted in deterioration of PEU molecular weight ( M n ), viscosity, and mechanical properties. Peak analysis of the Fourier transform infrared spectrum of the aged PEU revealed that &gt;97% of the urethane carbonyl bonds remained, whereas ether bonds were significantly reduced (∼82% of initial value). The degraded PEU contained ester bonds, which were confirmed by proton and carbon‐13 nuclear magnetic resonance spectroscopy. This observation suggests that oxidative chain cleavage rather than hydrolysis was the dominant reaction in the degradation process. Two approaches were adopted to minimize oxidative degradation of PEU dissolved in an ethanol–water (80/20 v/v %) mixed solvent; they were, applying a nitrogen environment and adding an antioxidant (1.8 wt % dry PEU). The results indicate that reduction of oxidative degradation produced a synergistic effect. Vitamin E was a more effective antioxidant than butylated hydroxytoluene (BHT), which is a typical antioxidant for commercial polyurethanes. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2270–2276, 2003
Cannabinoids Exacerbate Alcohol Teratogenesis by a CB1-Hedgehog Interaction (2019)

We tested whether cannabinoids (CBs) potentiate alcohol-induced birth defects in mice and zebrafish, and explored the underlying pathogenic mechanisms on Sonic Hedgehog (Shh) signaling. The CBs, Δ<sup>9</sup>-THC, cannabidiol, HU-210, and CP 55,940 caused alcohol-like effects on craniofacial and brain development, phenocopying Shh mutations. Combined exposure to even low doses of alcohol with THC, HU-210, or CP 55,940 caused a greater incidence of birth defects, particularly of the eyes, than did either treatment alone. Consistent with the hypothesis that these defects are caused by deficient Shh, we found that CBs reduced Shh signaling by inhibiting Smoothened (Smo), while Shh mRNA or a CB1 receptor antagonist attenuated CB-induced birth defects. Proximity ligation experiments identified novel CB1-Smo heteromers, suggesting allosteric CB1-Smo interactions. In addition to raising concerns about the safety of cannabinoid and alcohol exposure during early embryonic development, this study establishes a novel link between two distinct signaling pathways and has widespread implications for development, as well as diseases such as addiction and cancer.
3Rs friendly study designs facilitate rat liver and blood micronucleus assays and Pig‐a gene mutation assessments: Proof‐of‐concept with 13 reference chemicals (2019)

Regulatory guidance documents stress the value of assessing the most appropriate endpoints in multiple tissues when evaluating the in vivo genotoxic potential of chemicals. However, conducting several independent studies to evaluate multiple endpoints and/or tissue compartments is resource intensive. Furthermore, when dependent on visual detection, conventional approaches for scoring genotoxicity endpoints can be slow, tedious, and less objective than the ideal. To address these issues with current practices we attempted to (1) devise resource sparing treatment and harvest schedules that are compatible with liver and blood micronucleus endpoints, as well as the Pig-a gene mutation assay, and (2) utilize flow cytometry-based methods to score each of these genotoxicity biomarkers. Proof-of-principle experiments were performed with 4-week-old male and female Crl:CD(SD) rats exposed to aristolochic acids I/II, benzo[a]pyrene, cisplatin, cyclophosphamide, diethylnitrosamine, 1,2-dimethylhydrazine, dimethylnitrosamine, 2,6-dinitrotoluene, hydroxyurea, melphalan, temozolomide, quinoline, or vinblastine. These 13 chemicals were each tested in two treatment regimens: one 3-day exposure cycle, and three 3-day exposure cycles. Each exposure, blood collection, and liver harvest was accomplished during a standard Monday-Friday workweek. Key findings are that even these well-studied, relatively potent genotoxicants were not active in both tissues and all assays (indeed only cisplatin was clearly positive in all three assays); and whereas the sensitivity of the Pig-a assay clearly benefitted from three versus one treatment cycle, micronucleus assays yielded qualitatively similar results across both study designs. Collectively, these results suggest it is possible to significantly reduce animal and other resource requirements while improving assessments of in vivo genotoxicity potential by simultaneously evaluating three endpoints and two important tissue compartments using fit-for-purpose study designs in conjunction with flow cytometric scoring approaches. Environ. Mol. Mutagen., 60:704-739, 2019. © 2019 Wiley Periodicals, Inc.
Exploring Approaches for Heterogeneous Transfer Learning in Dynamic Networks (2022)

Maintaining machine-learning models for prediction of service performance is challenging, especially in dynamic network and cloud environments where route changes occur, and execution environments can be scaled and migrated. Recently, transfer learning has been proposed as an approach for leveraging already learned knowledge in a new environment. The challenge is that the new environment may be significantly different from the one the model is trained in, and transferred from, with respect to data distributions and dimensionality.In this paper, we introduce heterogeneous transfer learning in the context of dynamic environments and show its efficiency in predicting service performance. We propose two heterogeneous transfer-learning approaches and evaluate them on several neural-network architectures and scenarios. The scenarios are a natural consequence of network and cloud infrastructure reorchestration. We quantify the transfer gain, and empirically show positive gain in a majority of cases for both approaches. Furthermore, we study the impact of neural-network configurations on the transfer gain, providing tradeoff insights. The evaluation of the approaches is performed using data traces collected from a cloud testbed that runs two services under multiple realistic load conditions.
A Large-Number and Multilayer Quantum Walk using Silicon Nano-photonic Chip (2018)

We experimentally demonstrated 2D quantum walks in a Si3N4 chip and study how different parameters affect light distribution. Such scalable quantum device will have a promising application in the field of quantum communication and simulation.
Development of a Sustainable Procedure for the Recovery of Hydroxytyrosol from Table Olive Processing Wastewater Using Adsorption Resin Technology and Centrifugal Partition Chromatography (2015)

The present endeavor aims to establish a novel procedure, applicable to the extraction and isolation of hydroxytyrosol from table olive processing wastewater. A two-step chromatographic separation is presented using non-ionic absorbent resin for the recovery of its phenolic content, followed by purification of hydroxytyrosol with centrifugal partition chromatography. Two table olive processing wastewaters, obtained from Kalamon and Amfissis olive varieties, were used. In the extracts obtained after resin treatment, the hydroxytyrosol content was determined by high-performance liquid chromatography with diode-array detection to be 4.05% and 10.10%, respectively. The extract from Amfissis table olive processing wastewater was further processed with preparative centrifugal partition chromatography for the purification of hydroxytyrosol. High-performance liquid chromatography analysis revealed that the isolated compound was >95% purity.
Preparation and flame retardancy of flax fabric/polybenzoxazine laminates (2020)

Summary Driven by the need to reduce the carbon footprint of materials, natural fibres reinforced composites are increasingly used. Today, their level of maturity allows to consider their applications in fields where high performance such as flame retardancy are required. This article compares the fire retardant properties of flax laminates based on two thermosets resins, a bio‐based polybenzoxazine and a petroleum‐based epoxy, both considered for aeronautical applications. The effect of alkaline and silane surface modifications of the fibres on the properties of the composites was investigated. The treatments of the flax were proven to allow a better impregnation of the fibres by the matrices but at the same time more defects were observed. Regarding the fire behaviour of the composites, no difference of flammability was highlighted between the treated and untreated materials. The burnthrough resistance evaluation was performed using a small‐scale aeronautical test. The better performance of the epoxy‐based composite compare to the polybenzoxazine one was shown whereas charring is favoured for polybenzoxazine. The low deformability of the char formed when polybenzoxazine decomposes leads to the formation of cracks with the subsequent failure of the test.
Microfluidic sieve valves (2023)

Sieve valves for use in microfluidic device are provided. The valves are useful for impeding the flow of particles, such as chromatography beads or cells, in a microfluidic channel while allowing liquid solution to pass through the valve. The valves find particular use in making microfluidic chromatography modules.
Generic Substitution Rates of Oral Contraceptives and Associated Out-of-Pocket Cost Savings Between January 2010 and December 2014 (2018)

baseline characteristics. Adequate covariate balance was attained in all models.
Mechanical Strain Induces Specific Changes in the Synthesis and Organization of Proteoglycans by Vascular Smooth Muscle Cells (2001)

In the mechanically active environment of the artery, cells sense mechanical stimuli and regulate extracellular matrix structure. In this study, we explored the changes in synthesis of proteoglycans by vascular smooth muscle cells in response to precisely controlled mechanical strains. Strain increased mRNA for versican (3.2-fold), biglycan (2.0-fold), and perlecan (2.0-fold), whereas decorin mRNA levels decreased to a third of control levels. Strain also increased versican, biglycan, and perlecan core proteins, with a concomitant decrease in decorin core protein. Deformation did not alter the hydrodynamic size of proteoglycans as evidenced by molecular sieve chromatography but increased sulfate incorporation in both chondroitin/dermatan sulfate proteoglycans and heparan sulfate proteoglycans (p < 0.05 for both). Using DNA microarrays, we also identified the gene for the hyaluronan-linking protein TSG6 as mechanically induced in smooth muscle cells. Northern analysis confirmed a 4.0-fold increase in steady state mRNA for TSG6 following deformation. Size exclusion chromatography under associative conditions showed that versican-hyaluronan aggregation was enhanced following deformation. These data demonstrate that mechanical deformation increases specific vascular smooth muscle cell proteoglycan synthesis and aggregation, indicating a highly coordinated extracellular matrix response to biomechanical stimulation.
Assessment of a Nutritional Rehabilitation Model in Two Modern Broilers and Their Jungle Fowl Ancestor (2018)

Inclusion of rye in poultry diets induces a nutritional deficit that leads to increased bacterial translocation, intestinal viscosity, and decreased bone mineralization. However, the effect of diet on developmental stage or genetic strain is unclear. Therefore, the objective of this chapter is to evaluate the effects of a well-established rye model diet during either the early or the late phase of development on performance, bone mineralization, and morphometric analysis. Furthermore, intestinal integrity evaluated by liver bacterial translocation, leakage of FITC-d, and gene expression of tight junctions across three diverse genetic backgrounds Modern 2015 (Cobb 500) broiler chicken, 1995 Cobb broiler chicken, and the Giant Jungle Fowl are also discussed.