gebhart/patrepeval huggingface dataset:
Calcium-sensing receptor 20 years later (2014)

The calcium-sensing receptor (CaSR) has played an important role as a target in the treatment of a variety of disease states over the past 20 plus years. In this review, we give an overview of the receptor at the cellular level and then provide details as to how this receptor has been targeted to modulate cellular ion transport mechanisms. As a member of the G protein-coupled receptor (GPCR) family, it has a high degree of homology with a variety of other members in this class, which could explain why this receptor has been identified in so many different tissues throughout the body. This diversity of locations sets it apart from other members of the family and may explain how the receptor interacts with so many different organ systems in the body to modulate the physiology and pathophysiology. The receptor is unique in that it has two large exofacial lobes that sit in the extracellular environment and sense changes in a wide variety of environmental cues including salinity, pH, amino acid concentration, and polyamines to name just a few. It is for this reason that there has been a great deal of research associated with normal receptor physiology over the past 20 years. With the ongoing research, in more recent years a focus on the pathophysiology has emerged and the effects of receptor mutations on cellular and organ physiology have been identified. We hope that this review will enhance and update the knowledge about the importance of this receptor and stimulate future potential investigations focused around this receptor in cellular, organ, and systemic physiology and pathophysiology.
Recipe-oriented Food Logging for Nutritional Management (2022)

We propose a recipe-oriented food logging method that records food by recipe, unlike the ordinary food logging method that records food by name. We also develop an application RecipeLog for this purpose. RecipeLog can create a "skeleton recipe," which is a standardized recipe representation suitable for estimating the nutritional value of a dish. This is represented by a list of ingredients linked to a Nutrition Facts table and a flow graph consisting of cooking actions such as cutting, mixing, baking, simmering, and frying the ingredients. The recipe log allows recipes to be written with fewer operations by editing only the differences from the already registered base recipe. Experiments have confirmed that the recipe log can effectively identify differences in recipes from household to household. The future work is to construct a multimedia recipe dataset consisting of structured recipes and their images using RecipeLog.
SuppTable5 from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer (2023)

&lt;p&gt;Supplementary table 5 lists potential draggable target(s) for each tumor&lt;/p&gt;
Study of SiO2/4H-SiC interface nitridation by post-oxidation annealing in pure nitrogen gas (2015)

An alternative and effective method to perform interface nitridation for 4H-SiC metal-oxide-semiconductor (MOS) devices was developed. We found that the high-temperature post-oxidation annealing (POA) in N2 ambient was beneficial to incorporate a sufficient amount of nitrogen atoms directly into thermal SiO2/SiC interfaces. Although N2-POA was ineffective for samples with thick thermal oxide layers, interface nitridation using N2-POA was achieved under certain conditions, i.e., thin SiO2 layers (&amp;lt; 15 nm) and high annealing temperatures (&amp;gt;1350°C). Electrical characterizations of SiC-MOS capacitors treated with high-temperature N2-POA revealed the same evidence of slow trap passivation and fast trap generation that occurred in NO-treated devices fabricated with the optimized nitridation conditions.
Hepatitis C Virus Envelope Glycoprotein E1 Forms Trimers at the Surface of the Virion (2015)

HCV glycoproteins E1 and E2 play an essential role in virus entry into liver cells as well as in virion morphogenesis. In infected cells, these two proteins form a complex in which E2 interacts with cellular receptors, whereas the function of E1 remains poorly understood. However, recent structural data suggest that E1 could be the protein responsible for the process of fusion between viral and cellular membranes. Here we investigated the oligomeric state of HCV envelope glycoproteins. We demonstrate that E1 forms functional trimers after virion assembly and that in addition to the requirement for E2, a determinant for this oligomerization is present in a conserved GxxxG motif located within the E1 transmembrane domain. Taken together, these results indicate that a rearrangement of E1E2 heterodimer complexes likely occurs during the assembly of HCV particles to yield a trimeric form of the E1E2 heterodimer. Gaining structural information on this trimer will be helpful for the design of an anti-HCV vaccine.
Amortizing Garbled Circuits (2014)

Abstract. We consider secure two-party computation in a multiple-execution setting, where two parties wish to securely evaluate the same circuit multiple times. We design efficient garbled-circuit-based two-party protocols secure against malicious adversaries. Recent works by Lindell (Crypto 2013) and Huang-Katz-Evans (Crypto 2013) have obtained op-timal complexity for cut-and-choose performed over garbled circuits in the single execution setting. We show that it is possible to obtain much lower amortized overhead for cut-and-choose in the multiple-execution setting. Our efficiency improvements result from a novel way to combine a recent technique of Lindell (Crypto 2013) with LEGO-based cut-and-choose techniques (TCC 2009, Eurocrypt 2013). In concrete terms, for 40-bit statistical security we obtain a 2 × improvement (per execution) in com-munication and computation for as few as 7 executions, and require only 8 garbled circuits (i.e., a 5 × improvement) per execution for as low as 3500 executions. Our results suggest the exciting possibility that secure two-party computation in the malicious setting can be less than an order of magnitude more expensive than in the semi-honest setting. 1
Graded and alloyed II-VI semiconductors for photovoltaic buffer layers grown by atomic layer deposition (ALD) (2011)

Deposition of Cd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Zn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-y</sub> was demonstrated with atomic layer deposition (ALD) using diethylzinc (DEZn), dimethylcadmium (DMCd), H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O, and H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> S as the precursors. The chemical, material, and optical properties of the films were investigated, and these properties were adjusted by varying the stoichiometry. Notably, by correlating the crystal phases to the optical constants and bandgap, strong relationships between optical and materials properties are determined. Deposition of buffer layers at 150 °C on CuInS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> absorbers was demonstrated and characterization of working devices was shown with IV curves and quantum efficiency measurement. CdS ALD buffer films behave similar to CdS chemical bath deposition (CBD) films even when slightly thinner than normal. Depositing mixed films across the Cd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Zn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-y</sub> system leads to increases in the J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SC</sub> due to decreased parasitic absorption from the increase in bandgap due to Zn.
Selenols catalyze the interchange reactions of dithiols and disulfides in water (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelenols catalyze the interchange reactions of dithiols and disulfides in waterRajeeva Singh and George M. WhitesidesCite this: J. Org. Chem. 1991, 56, 24, 6931–6933Publication Date (Print):November 1, 1991Publication History Published online1 May 2002Published inissue 1 November 1991https://pubs.acs.org/doi/10.1021/jo00024a041https://doi.org/10.1021/jo00024a041research-articleACS PublicationsRequest reuse permissionsArticle Views545Altmetric-Citations71LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Hepatic cirrhosis and hepatitis: MR imaging enhanced with superparamagnetic iron oxide. (1990)

Superparamagnetic iron oxide was applied as a reticuloendothelial contrast agent in the diagnosis of cirrhosis and hepatitis in seven patients. Three patients had compensated cirrhosis, and four had active hepatitis. T1- and T2-weighted spin-echo magnetic resonance images were obtained before and 1 hour after the administration of iron oxide. Eight patients without diffuse liver disease served as a control group. Normal liver tissue showed a 75% +/- 9% reduction in signal intensity after the administration of iron oxide, and the liver appeared homogeneously hypointense. Cirrhotic liver tissue showed a smaller response (P less than .05) to iron oxide, with a 52% +/- 13% reduction in liver signal intensity. Inhomogeneous structures could be observed in enhanced images and are thought to represent fibrous bands or regenerating nodules. Liver tissue with active hepatitis showed a markedly reduced response to iron oxide (11% +/- 2%) (P less than .05), and the parenchyma appeared homogeneous. The authors conclude that the uptake of iron oxide particles is inhomogeneously altered in cirrhosis because of structural changes and homogeneously decreased in hepatitis because of functional changes of hepatic parenchyma.
Abstract 2829: Preclinical analysis and characterization of abemaciclib using three-dimensional patient-derived colorectal cancer organoid cultures (2016)

Abstract Proper patient-tailoring strategy and the validation of novel therapeutic targets remain enormous challenges during drug discovery processes. Patient-derived three-dimensional organoid cell culture models possess great potential to associate compound sensitivity and disease complexity in order to provide a key missing link between compound screening and clinical trials. Abemaciclib is a reversible, ATP competitive, selective inhibitor of the kinase activity of both CDK4 and CDK6 and is currently undergoing advanced clinical testing. In this study, we established and characterized three-dimensional organoid cultures from primary colorectal cancer patients and validated their use as drug sensitivity models. We aimed to explore the antitumor activity of abemaciclib in colon cancer organoid cultures by assessing markers for cell viability, proliferation, cell cycle, senescence and apoptosis. Single cell suspension of patient-derived samples were precultured for four days to allow for complete morphogenesis of three-dimensional organoid structures. Subsequently, the cultures were treated for at least two population doubling times and analyzed by luminescent cell viability, immunohistochemistry and flow cytometry assays. Our data suggest that abemaciclib treatment decreased the cell viability of patient-derived colorectal cancer organoid cultures characterized by G1 cell cycle arrest and reduced Ki-67-positive cells. Furthermore, treated cultures showed elevated levels of reactive oxygen species and increased markers for early and late apoptosis. In summary, complex organoid models have the potential to further evaluate the antitumor activity of abemaciclib in various tumor types by enabling mechanistic studies in a patient-specific preclinical setting. Citation Format: Karsten Boehnke, Bruna Calsina, Joaquín Amat, Ana Hermoso, Raquel Torres, Christoph Reinhard, Juan A. Velasco, Philip W. Iversen, Alfonso De Dios, Sean Buchanan, Richard P. Beckmann, Dirk Schumacher, Christian RA Regenbrecht, Marie-Laure Yaspo, Hans Lehrach, María José Lallena. Preclinical analysis and characterization of abemaciclib using three-dimensional patient-derived colorectal cancer organoid cultures. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2829.
Dual camera system for face detection in unconstrained environments (2004)

A system for face detection in outdoor environments for multisensor video surveillance applications is presented. The system is characterized by a combination of two pan-tilt video cameras, which cooperate in order to track and to characterize moving objects with positioning and biometric informations. The final result of the action of the system is the collection of small video shots regarding the face of humans detected in outdoor environments with a robust behavior.
Activation of Adenosine A2aReceptors Inhibits Mast Cell Degranulation and Mast Cell-Dependent Vasoconstriction (2000)

Adenosine and inosine accumulate in tissue during periods of ischemia and both molecules have been shown to degranulate mast cells in the hamster cheek pouch via activation of an A3 receptor. An A2-mediated inhibitory action of adenosine on mast cell degranulation has also been reported (16), and the objective of this research was to investigate the role of adenosine A2 receptors in modulating inosine-induced mast cell degranulation and subsequent vasoconstriction of microvessels.Cheek pouches of the Golden hamster were prepared for in vivo microscopy. Adenosine, inosine, and other agents were applied either globally in the superfusion solution or to selected regions of the tissue by pipette.Micropipette application of 10(-4) M inosine to periarteriolar mast cells caused a vasoconstriction and an associated mast cell degranulation in 71% of the arterioles tested. The average diameter reduction was 29 +/- 5%. To establish a modulatory role for the A2 receptor, low doses of adenosine (100 nM and 10 nM) were applied globally via the superfusion prior to inosine stimulation. This adenosine pretreatment resulted in a decrease in the incidence of the inosine-induced vasoconstriction (17% and 31%), as well as smaller constrictions (0.5 +/- 1% and 7 +/- 3%). Mast cell degranulation was also reduced by pretreatment with adenosine, as evidenced by a decreased number of mast cells exhibiting ruthenium red dye uptake. The inhibitory effect of adenosine could be eliminated by pretreatment with the nonselective A1/A2 antagonist 8-(p-sulfophenyl) theophylline, which restored the inosine-induced responses to control values. To demonstrate that the effect was A2 alpha-mediated, vessels were pretreated with the selective A2 alpha agonist 2-[4-(2-carboxyethyl) phenethylamino]-5'-N-ethylcarboxamidoadenosine (CGS21680). Following this treatment, constriction in response to microapplication of inosine (10(-4) M) occurred in only 11% of the vessels tested; the average constriction was reduced to 2 +/- 2% and no mast cell degranulation was observed.We conclude that mast cell degranulation can be inhibited via activation of an adenosine A2 alpha receptor; which activation occurs at a lower concentration of adenosine than stimulatory A3 receptor activation. This finding may have implications for the pathology of ischemia.
Phenylation of carbanions by .pi.-(chlorobenzene)chromium tricarbonyl (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhenylation of carbanions by .pi.-(chlorobenzene)chromium tricarbonylM. F. Semmelhack and H. T. HallCite this: J. Am. Chem. Soc. 1974, 96, 22, 7091–7092Publication Date (Print):October 1, 1974Publication History Published online1 May 2002Published inissue 1 October 1974https://pubs.acs.org/doi/10.1021/ja00829a043https://doi.org/10.1021/ja00829a043research-articleACS PublicationsRequest reuse permissionsArticle Views410Altmetric-Citations65LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
1051. Prostate Cancer-Targeted Suicide Gene Therapy Achieved Effective Tumor Destruction While Safeguarding Against Systemic Toxicity (2005)

Cancer gene therapy based on tissue-restricted expression of cytotoxic gene should achieve superior therapeutic index over an unrestricted method. This study compared the therapeutic effects of a highly augmented, prostate-specific gene expression method to a strong constitutive promoter-driven approach. Molecular imaging was coupled to gene therapy to ascertain real-time therapeutic activity. The imaging reporter gene (luciferase) and the cytotoxic gene (herpes simplex thymidine kinase) were delivered by adenoviral vectors injected directly into human prostate tumors grafted in SCID mice. Serial bioluminescence imaging, positron emission tomography (PET) and computed tomography (CT) revealed restriction of gene expression to the tumors when prostate-specific vector was employed. In contrast, administration of constitutive active vector resulted in strong signals in the liver. Liver serology, tissue histology, and frail condition of animals confirmed liver toxicity suffered by the constitutive active cohorts, while the prostate-targeted group was unaffected. The extent of tumor killing was analyzed by apoptotic staining and human prostate marker (PSA). Overall, the augmented prostate-specific expression system was superior to the constitutive approach in safeguarding against systemic toxicity, while achieving effective tumor-killing. Integrating non-invasive imaging into cytotoxic gene therapy will provide a useful strategy to monitor gene expression and therapeutic efficacy in future clinical protocols.
Morphogenesis of calcitic sponge spicules: a role for specialized proteins interacting with growing crystals (1995)

Crystals formed in biological tissues often adopt remarkable morphologies that are thought to be determined mainly by the shapes of the confined spaces in which they grow. Another possible way of controlling crystal shape, demonstrated only in vitro, is by means of specialized proteins preferentially interacting with certain crystal faces. In so doing, they reduce the rate of growth in these directions and consequently change the overall crystal shape. In an X-ray diffraction study of the distribution of defects within the lattice of calcite crystals produced by certain sponges, we show that a remarkable correlation exists between the defect patterns or crystal texture and the macroscopic morphology of the spicules. This was observed in two cases in which proteins are present within the spicule crystal, but not in a third case where such intracrystalline proteins are absent. Furthermore, one of the spicules exhibited marked differences in texture even within families of structurally identical crystal planes, demonstrating that the organisms exert exquisite control over the microenvironment in which crystals grow. We conclude that highly controlled intercalation of specialized proteins inside the crystals is an additional means by which organisms control spicule growth.
Accelerated Battery Lifetime Simulations Using Adaptive Inter-Cycle Extrapolation Algorithm (2021)

We propose algorithms to speed up physics-based battery lifetime simulations by one to two orders of magnitude compared to the state-of-the-art. First, we propose a reformulation of the Single Particle Model with side reactions to remove algebraic equations and hence reduce stiffness, with 3x speed-up in simulation time (intra-cycle reformulation). Second, we introduce an algorithm that makes use of the difference between the “fast” timescale of battery cycling and the “slow” timescale of battery degradation by adaptively selecting and simulating representative cycles, skipping other cycles, and hence requires fewer cycle simulations to simulate the entire lifetime (adaptive inter-cycle extrapolation). This algorithm is demonstrated with a specific degradation mechanism but can be applied to various models of aging phenomena. In the particular case study considered, simulations of the entire lifetime are performed in under 5 s. This opens the possibility for much faster and more accurate model development, testing, and comparison with experimental data.
Stereology‐based quantitative characterization of dispersion from TEM micrographs of polymer–clay nanocomposites (2010)

Abstract Quantitative characterization of the state of dispersion and extent of exfoliation is critical in developing processing structure–property relationships in polymer–clay nanocomposites. Quantification of dispersion, exfoliation, and nanostructure in polymer–clay nanocomposites by 3D stereological parameters using image analysis of 2D transmission electron microscopy (TEM) micrographs were recently proposed. The 3D dispersion quantifying parameters are designed such that they are free of the bias associated with not sampling the true particle diameter in a 2D TEM section. In this article, the ability of the proposed 3D dispersion quantifying parameters to describe the dispersion over the entire possible range of exfoliation, and to capture independent aspects of dispersion are demonstrated by quantifying several sets of samples that were designed using a polypropylene (PP)/maleated PP/clay system. The details of the image analysis procedure, the underlying challenges, and errors involved in the segmentation process are also discussed. The 3D dispersion quantifying parameters, exfoliation number and inter‐particle distance, were critically compared against the standard 2D dispersion quantifying parameters, such as mean length, thickness, and aspect ratio. In all cases examined in this study, the sensitivity and resolution of the 3D parameters in terms of quantifying the dispersion of the nanostructure appeared comparable if not better than the standard 2D parameters. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011