gebhart/patrepeval huggingface dataset:
Abstract A7: Investigating the differential regulation of poly(ADP-ribose) polymerases in cancer (2012)

Abstract Poly(ADP-ribose) (pADPr) is an important but poorly understood post-translational modification. Poly(ADP-ribose) polymerases (PARPs) catalyze the addition of ADP-ribose onto acceptor proteins using NAD+ as a substrate. The function of pADPr has been best studied in the context of the DNA damage response where PARPs are activated by DNA damage, recruit repair machinery to the site of damage, and modify histones altering chromatin structure. Emerging evidence reveals broader roles for pADPr in other essential cellular pathways including apoptosis, inflammation, and stress responses. The role of PARPs in DNA damage has led to much interest in PARP inhibitors as chemotherapeutics, and multiple inhibitors are currently in clinical trials. The focus so far has been on using PARP inhibitors in combination with DNA damaging agents or in cancers deficient in DNA damage repair pathways (e.g., BRCA1/2 deficient cancers). Recent studies suggest that PARP inhibitors may also have utility in treating some cancers independent of DNA damage, e.g., Ewing's sarcoma. This increases the importance of understanding PARP biology and the role of pADPr in the growth and survival of cancer cells, and opens up the question of why inhibiting PARPs alone is more detrimental to some cancer cells than to others. We have developed a method for quantifying pADPr levels in cell lysates with increased sensitivity compared to previous approaches. Using this method we have found that pADPr levels vary widely between breast cancer cell lines. The differences in pADPr levels appear to be largely attributable to differences in PARP1 activity. PARP1, the most abundant family member, is primarily localized to the nucleus and is overexpressed in some cancers. We are currently investigating the mechanisms behind PARP1 activation and the implications of this finding for both basic biology and chemotherapy. Not only will this provide insight into the biological function of pADPr, but pADPr levels may be useful as an indicator of which patients will respond best to PARP inhibitors or other treatments. Citation Format: Kristin Krukenberg, Timothy Mitchison. Investigating the differential regulation of poly(ADP-ribose) polymerases in cancer [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A7.
Modeling the Effects of Crevice Former, Particulates, and the Evolving Surface Profile in Crevice Corrosion (2007)

Crevice corrosion may initiate in confined regions due to transport limitations, followed by an accumulation of a highly corrosive chemistry, capable of dissolving the metal. The metal and the crevice former surface roughness, the presence of particulates under the crevice former and the accumulation of solid corrosion products at the corroding site would significantly affect the current and potential distribution at the anode by increasing the ohmic potential drop. Most crevice corrosion models focus on a smooth walled crevice of uniform gap and do not account for the changing profile after crevice corrosion has been initiated. In this work we analyze the crevice (anodic) region and apply current and potential distribution models to examine the effects of the perturbed surface topography. The analysis focuses on three related issues: (i) the effects surface roughness of the metal and the crevice former, (ii) the effects of particulates under the crevice former, and (iii) the evolution of the crevice profile with corrosion product accumulation at the active, anodic region.
Uplink Carrier Aggregation (2012)

This chapter presents the long term evolution (LTE) uplink carrier aggregation principles. The uplink carrier aggregation is also part of the Release 10 LTE specifications, similar to the downlink carrier aggregation. The chapter then proceeds to the detailed impact on the protocols, procedures and physical layer. It also covers physical layer changes in the uplink in the resource usage within a single carrier in Release 10 with the introduction of uplink multi-cluster scheduling. The chapter deals with the uplink carrier aggregation performance investigation and the expected implementation impacts and challenges with the different uplink band combinations. The use of two uplinks causes additional considerations for the interference and some band combinations may need to be used only with the downlink carrier aggregation. The 3GPP performance work will cover first the downlink band combinations with them being simpler than the uplink ones. Controlled Vocabulary Terms aggregation; long term evolution; uplink
Modeling appendicular skeletal cartilage development with modified high-density micromass cultures of adult human bone marrow-derived mesenchymal progenitor cells (2019)

The modified hBM-MPC micromass culture system described here represents a reproducible and controlled model for analyzing mechanisms of human skeletal development that may later be applied to pharmacological and environmental toxicity studies.
Toward Synthesized Environments: A Survey of Analysis and Synthesis Methods for Sound Designers and Composers (2009)

We present an overview of digital audio analysis and synthesis methods for sound design and composition. The sonic landscape available to us contains a multitude of sounds, ranging from artificial to natural, purely musical to purely “real-world. ” To take full advantage of this diversity, it is helpful to have a comprehensive knowledge of the tools with which we can create and manipulate different types of sounds. We offer a summary of existing techniques organized by their underlying technology and source material, as well as by the kinds of sounds for which they are known to be effective. Our survey aims to support the synthesis of rich sound scenes and environments by facilitating the selection of the most appropriate tools for each component sound. A full toolbox means the whole world need not look like a nail! 1.
Fire Bench for Extreme fire scenario from Experimental to Simulation (2018)

The objective of this study is (i) to develop a small scale test allowing to recreate at the lab scale extreme conditions (heat flux varying from 150kW/m² to 300KW/m²), (ii) to simulate the test following a finite element method, (iii) to compare the simulation and the experimental results. For the simulation, the methodology is to develop, in one hand a model of the bench with turbulent flow and on the other hand a model of the burner with the combustion of the propane. The final aim is to couple the two models to simulate the bench in the operating conditions.
Feasibility of free-breathing quantitative myocardial perfusion using multi-echo Dixon magnetic resonance imaging (2020)

Dynamic contrast-enhanced quantitative first-pass perfusion using magnetic resonance imaging enables non-invasive objective assessment of myocardial ischemia without ionizing radiation. However, quantification of perfusion is challenging due to the non-linearity between the magnetic resonance signal intensity and contrast agent concentration. Furthermore, respiratory motion during data acquisition precludes quantification of perfusion. While motion correction techniques have been proposed, they have been hampered by the challenge of accounting for dramatic contrast changes during the bolus and long execution times. In this work we investigate the use of a novel free-breathing multi-echo Dixon technique for quantitative myocardial perfusion. The Dixon fat images, unaffected by the dynamic contrast-enhancement, are used to efficiently estimate rigid-body respiratory motion and the computed transformations are applied to the corresponding diagnostic water images. This is followed by a second non-linear correction step using the Dixon water images to remove residual motion. The proposed Dixon motion correction technique was compared to the state-of-the-art technique (spatiotemporal based registration). We demonstrate that the proposed method performs comparably to the state-of-the-art but is significantly faster to execute. Furthermore, the proposed technique can be used to correct for the decay of signal due to T2* effects to improve quantification and additionally, yields fat-free diagnostic images.
Nuclear Localization of Diacylglycerol Kinase Alpha in K562 Cells Is Involved in Cell Cycle Progression (2016)

Phosphatidylinositol (PI) signaling is an essential regulator of cell motility and proliferation. A portion of PI metabolism and signaling takes place in the nuclear compartment of eukaryotic cells, where an array of kinases and phosphatases localize and modulate PI. Among these, Diacylglycerol Kinases (DGKs) are a class of phosphotransferases that phosphorylate diacylglycerol and induce the synthesis of phosphatidic acid. Nuclear DGKalpha modulates cell cycle progression, and its activity or expression can lead to changes in the phosphorylated status of the Retinoblastoma protein, thus, impairing G1/S transition and, subsequently, inducing cell cycle arrest, which is often uncoupled with apoptosis or autophagy induction. Here we report for the first time not only that the DGKalpha isoform is highly expressed in the nuclei of human erythroleukemia cell line K562, but also that its nuclear activity drives K562 cells through the G1/S transition during cell cycle progression. J. Cell. Physiol. 232: 2550-2557, 2017. © 2016 Wiley Periodicals, Inc.
High Rate of Aminoglycoside Resistance among Staphylococci Causing Prosthetic Joint Infection (2005)

Gentamicin and tobramycin are two aminoglycosides commonly impregnated into polymethylmethacrylate for treatment and prevention of prosthetic joint infection. Susceptibilities of staphylococci to aminoglycosides are not reported routinely in the United States. The gentamicin and tobramycin minimum inhibitory value of 93 staphylococci from patients with PJI were determined. Forty-one and 66% of the isolates were resistant to gentamicin and tobramycin, respectively. Methicillin-resistant Staphylococcus aureus isolates were more likely to be resistant to gentamicin or tobramycin than were their methicillin susceptible counterparts. The findings suggest that consideration should be given to the further study of agents other than aminoglycosides for incorporation into polymethylmethacrylate for the treatment and prevention of prosthetic joint infection.
Reduction of multipath effects for FSK with frequency-discriminator detection (2002)

We analyze how multipath effects namely errors due to channel-induced intersymbol interference, can be reduced by frequency-discriminator detection for FSK. We first introduce a new mathematical technique that can be considered as generalization of FM noise-click theory, and thus allows insights into the error mechanisms. Building on those insights, we propose and verify that a nonlinear frequency discriminator can achieve zero error floor for pure binary FSK and drastically reduced the error floor for filtered FSK by clipping off the ISI-induced FM clicks. The stronger the filtering (before or after the frequency discriminator), the more the beneficial effect of the nonlinearity is reduced. Finally, we show that increasing the modulation index decreases the error floor, especially in the presence of frequency shifts. Our results suggest the design of improved receivers that are less sensitive to ISI.
Nitrogen and Hydrogen Induced Trap Passivation at the SiO<sub>2</sub>/4H-SiC Interface (2006)

Post-oxidation anneals that introduce nitrogen at the SiO2/4H-SiC interface have been most effective in reducing the large interface trap density near the 4H-SiC conduction band-edge for (0001) Si face 4H-SiC. Herein, we report the effect of nitridation on interfaces created on the (11 20) a-face and the (0001) C-face of 4H-SiC. Significant reductions in trap density (from &gt;1013 cm-2 eV-1 to ~ 1012 cm-2 eV-1 at EC-E ~0.1 eV) were observed for these different interfaces, indicating the presence of substantial nitrogen susceptible defects for all crystal faces. Annealing nitridated interfaces in hydrogen results in a further reduction of trap density (from ~1012 cm-2 eV-1 to ~5 x 1011 cm-2 eV-1 at EC-E ~0.1 eV). Using sequential anneals in NO and H2, maximum field effect mobilities of ~55 cm-2 V-1s-1 and ~100 cm-2 V-1s-1 have been obtained for lateral MOSFETs fabricated on the (0001) and (11 20) faces, respectively. These electronic measurements have been correlated to the interface chemical composition.
Abstract 3451: Lack of CD47 in the tumor microenvironment enhances anti-tumor adaptive immune responses when combined with ionizing radiation (2012)

Abstract Over half of the new cancer patients diagnosed this year in the United States will require ionizing radiation (IR) therapy as part of their course of treatment. Achieving a curative response, however, is limited by detrimental side effects and off-target toxicities of IR to normal cells. We previously demonstrated that CD47 null mice or blockade of CD47 confers radioprotection to normal tissues including radiosensitive hematopoietic progenitors. On the other hand, blockade of CD47 enhanced the radiation-induced tumor growth delay in two syngenic mouse models. One possible explanation for this observation is that, by protecting tumor-associated immune cells, CD47 suppression increases tumor immune surveillance. To examine the role of T cell immunity, we used the F15-12 RM mouse fibrosarcoma model in athymic mice. Blockade of CD47 in combination with IR did not alter tumor growth in these T-cell deficient mice versus IR alone. However, adoptive transfer of CD8+ T-cells in combination with CD47 blockade and IR significantly enhanced the reduction in tumor growth when compared to tumors of mice irradiated in combination with the T cell transfer alone (186 ± 50 vs. 370 ± 123 mm3 respectively, N=8). In vitro experiments showed that blockade of CD47 enhances antigen dependent CD8+ mediated cytotoxicity of tumor cells. Furthermore, in a syngeneic tumor model of B16 melanoma we observed over a 50% reduction in volume of irradiated tumors in a CD47-/- host versus a WT host. Immunohistochemical staining indicated an increase of intratumoral CD8+ cytotoxic T-cells. Further analysis indicated that lack or blockade of CD47 in combination with IR resulted in a significant increase in granzyme B expression, further indicating that the increased target cell death may be mediated by this pathway. CD47 suppression may also reduce tumor growth by altering the immunosuppressive factor VEGF. In both tumor models, either blockade of or lack of CD47 in combination with IR was associated with a reduction in VEGF. VEGF is a potent pro-angiogenic factor and a potent immunosuppressive factor that inhibits activation of cytotoxic T-cells. Our findings indicate that agents targeting CD47 enhance anti-tumor T cell immunity when combined with radiation. Combining CD47 suppression with IR and adoptive T cell transfer may increase the percentage of curative responses. 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 3451. doi:1538-7445.AM2012-3451
Basic Science and Dialysis: Nitric Oxide and Hemodialysis (2004)

Nitric oxide (NO), previously thought of as a noxious gas, is now recognized as an important mediator of vascular responsiveness. Soon after its discovery, it was realized that the actions of NO are similar to the previously described endothelium-derived relaxing factor (EDRF). It is synthesized in the vascular endothelium utilizing the enzyme nitric oxide synthase (NOS) and diffuses in the adjacent vascular media, where it has a vasodilatory action. Opposing actions of NO and vasoconstrictor agents (such as endothelin-1, angiotensin IotaIota, and others) maintain the vascular tone of the renal arteries. The same balance at the level of the macula densa maintains glomerular filtration rate (GFR) during varying levels of salt excretion. Lack of NO can result in disruption of this fine balance, with resultant vasoconstriction and disease progression, hypertension, and accelerated atherosclerosis. In addition, hypertension may result from positive salt balance that occurs when macula densa NOS is inhibited. While most investigators report low levels of NO in uremic subjects, the levels in hemodialysis (HD) patients have not been characterized adequately. This is primarily because HD patients are exposed to both stimulatory and inhibitory factors for NO synthesis. Retention of inhibitors of NOS tends to decrease NO levels, whereas production of NO will be increased by cytokines generated during blood-dialyzer interaction. There is less disagreement, however, over the finding of elevated levels in those with dialyzer reactions and dialysis-induced hypotension. Recent developments in the isolation of inducible and constitutive forms of NOS makes understanding of its pathophysiologic effects more complete. Newer treatment directed at inhibiting only the inducible forms of NOS (sparing the constitutive forms) may soon be found useful for the treatment and prevention of hypotension and dialyzer reactions in HD patients.
The protein tyrosine kinase Tec regulates mast cell function (2009)

Mast cells play crucial roles in a variety of normal and pathophysiological processes and their activation has to be tightly controlled. Here, we demonstrate that the protein tyrosine kinase Tec is a crucial regulator of murine mast cell function. Tec was activated upon Fc epsilon RI stimulation of BM-derived mast cells (BMMC). The release of histamine in the absence of Tec was normal in vitro and in vivo; however, leukotriene C(4) levels were reduced in Tec(-) (/) (-) BMMC. Furthermore, the production of IL-4 was severely impaired, and GM-CSF, TNF-alpha and IL-13 levels were also diminished. Finally, a comparison of WT, Tec(-) (/) (-), Btk(-) (/) (-) and Tec(-) (/) (-)Btk(-) (/) (-) BMMC revealed a negative role for Btk in the regulation of IL-4 production, while for the efficient production of TNF-alpha, IL-13 and GM-CSF, both Tec and Btk were required. Our results demonstrate a crucial role for Tec in mast cells, which is partially different to the function of the well-characterized family member Btk.
Pulse-actuated micromechanical resonator using digital Kalman observer (2006)

The paper presents a digital oscillating loop for a MEMS resonator in which the instantaneous resonator position is estimated on-line with a Kalman observer. The approach is applied to an oscillating loop with a pulse-actuated /spl mu/mechanical resonator, where the predicted resonator position can be used for oscillation amplitude control or resonator parameters measurement. We demonstrate the very good immunity of the method toward internal system and measurement noises.
Recent Progress on the Electrochemical Biosensing of Escherichia coli O157:H7: Material and Methods Overview (2020)

<i>Escherichia coli</i> O157:H7 (<i>E. coli</i> O157:H7) is a pathogenic strain of <i>Escherichia coli</i> which has issued as a public health threat because of fatal contamination of food and water. Therefore, accurate detection of pathogenic <i>E. coli</i> is important in environmental and food quality monitoring. In spite of their advantages and high acceptance, culture-based methods, enzyme-linked immunosorbent assays (ELISAs), polymerase chain reaction (PCR), flow cytometry, ATP bioluminescence, and solid-phase cytometry have various drawbacks, including being time-consuming, requiring trained technicians and/or specific equipment, and producing biological waste. Therefore, there is necessity for affordable, rapid, and simple approaches. Electrochemical biosensors have shown great promise for rapid food- and water-borne pathogen detection. Over the last decade, various attempts have been made to develop techniques for the rapid quantification of <i>E. coli</i> O157:H7. This review covers the importance of <i>E. coli</i> O157:H7 and recent progress (from 2015 to 2020) in the development of the sensitivity and selectivity of electrochemical sensors developed for <i>E. coli</i> O157:H7 using different nanomaterials, labels, and electrochemical transducers.
Correction to Discovery of ((S)-5-(Methoxymethyl)-7-(1-methyl-1H-indol-2-yl)-2-(trifluoromethyl)-4,7-dihydropyrazolo[1,5-a]pyrimidin-6-yl)((S)-2-(3-methylisoxazol-5-yl)pyrrolidin-1-yl)methanone As a Potent and Selective IKur Inhibitor (2013)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Discovery of ((S)-5-(Methoxymethyl)-7-(1-methyl-1H-indol-2-yl)-2-(trifluoromethyl)-4,7-dihydropyrazolo[1,5-a]pyrimidin-6-yl)((S)-2-(3-methylisoxazol-5-yl)pyrrolidin-1-yl)methanone As a Potent and Selective IKur InhibitorHeather J. Finlay*, John Lloyd*, Wayne Vaccaro, Alexander Kover, Lin Yan, Gauri Bhave, Joseph Prol, Tram Huynh, Rao Bhandaru, Yolanda Caringal, John DiMarco, Jinping Gan, Tim Harper, Christine Huang, Mary Lee Conder, Huabin Sun, Paul Levesque, Michael Blanar, Karnail Atwal, and Ruth WexlerCite this: J. Med. Chem. 2013, 56, 17, 7133Publication Date (Web):August 22, 2013Publication History Published online22 August 2013Published inissue 12 September 2013https://pubs.acs.org/doi/10.1021/jm4010576https://doi.org/10.1021/jm4010576correctionACS PublicationsCopyright © 2013 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views446Altmetric-Citations-LEARN 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 PDF (110 KB) Get e-Alertsclose Get e-Alerts
A paradigm for endogenous causation of mass extinctions (1990)

This chapter reviews the data pertaining to the Cretaceous/Tertiary (K/T) and other extinction events in light of a developing model of coupled core-mantle thermal release (via periodically accelerated plume activity). In this model the D″ layer becomes unstable, causing an increased frequency of geomagnetic reversals and sending plumes of lower mantle material upward toward the lithosphere. The arrival of this material at the Earth's surface causes increased tectonism and associated climatic and sea-level changes, and thus causes accelerated preboundary extinctions. Massive flood basalt volcanism, which correlates one-to-one with every mass extinction in the Mesozoic and Cenozoic, produces progressive climatic deterioration and a carbonate crisis in the oceans. We propose that the plume model can better account for much of the evidence associated with mass extinctions. Although an endogenous mechanism for the production and distribution of shocked quartz at the K/T boundary remains problematic, it is further proposed that the iridium and other chemical signatures across the K/T boundary are equally well explained by terrestrial mechanisms.