gebhart/patrepeval huggingface dataset:
Canonical and non-canonical WNT signaling in cancer stem cells and their niches: Cellular heterogeneity, omics reprogramming, targeted therapy and tumor plasticity (Review) (2017)

Cancer stem cells (CSCs), which have the potential for self-renewal, differentiation and de-differentiation, undergo epigenetic, epithelial-mesenchymal, immunological and metabolic reprogramming to adapt to the tumor microenvironment and survive host defense or therapeutic insults. Intra-tumor heterogeneity and cancer-cell plasticity give rise to therapeutic resistance and recurrence through clonal replacement and reactivation of dormant CSCs, respectively. WNT signaling cascades cross-talk with the FGF, Notch, Hedgehog and TGFβ/BMP signaling cascades and regulate expression of functional CSC markers, such as CD44, CD133 (PROM1), EPCAM and LGR5 (GPR49). Aberrant canonical and non-canonical WNT signaling in human malignancies, including breast, colorectal, gastric, lung, ovary, pancreatic, prostate and uterine cancers, leukemia and melanoma, are involved in CSC survival, bulk-tumor expansion and invasion/metastasis. WNT signaling-targeted therapeutics, such as anti-FZD1/2/5/7/8 monoclonal antibody (mAb) (vantictumab), anti-LGR5 antibody-drug conjugate (ADC) (mAb-mc-vc-PAB-MMAE), anti-PTK7 ADC (PF-06647020), anti-ROR1 mAb (cirmtuzumab), anti-RSPO3 mAb (rosmantuzumab), small-molecule porcupine inhibitors (ETC-159, WNT-C59 and WNT974), tankyrase inhibitors (AZ1366, G007-LK, NVP-TNKS656 and XAV939) and β-catenin inhibitors (BC2059, CWP232228, ICG-001 and PRI-724), are in clinical trials or preclinical studies for the treatment of patients with WNT-driven cancers. WNT signaling-targeted therapeutics are applicable for combination therapy with BCR-ABL, EGFR, FLT3, KIT or RET inhibitors to treat a subset of tyrosine kinase-driven cancers because WNT and tyrosine kinase signaling cascades converge to β-catenin for the maintenance and expansion of CSCs. WNT signaling-targeted therapeutics might also be applicable for combination therapy with immune checkpoint blockers, such as atezolizumab, avelumab, durvalumab, ipilimumab, nivolumab and pembrolizumab, to treat cancers with immune evasion, although the context-dependent effects of WNT signaling on immunity should be carefully assessed. Omics monitoring, such as genome sequencing and transcriptome tests, immunohistochemical analyses on PD-L1 (CD274), PD-1 (PDCD1), ROR1 and nuclear β-catenin and organoid-based drug screening, is necessary to determine the appropriate WNT signaling-targeted therapeutics for cancer patients.
Colorization-based coding by focusing on characteristics of colorization bases (2010)

Colorization is a method that adds color components to a grayscale image using only a few representative pixels provided by the user. A novel approach to image compression called colorization-based coding has recently been proposed. It automatically extracts representative pixels from an original color image at an encoder and restores a full color image by using colorization at a decoder. However, previous studies on colorization-based coding extract redundant representative pixels and do not extract the pixels required for suppressing coding error. This paper focuses on the colorization basis that restricts the decoded color components. From this viewpoint, we propose a new colorization-based coding method. Experimental results revealed that our method can drastically suppress the information amount (number of representative pixels) compared conventional colorization based-coding while objective quality is maintained.
Development of a Chimeric Plasmodium berghei Strain Expressing the Repeat Region of the P. vivax Circumsporozoite Protein for<i>In Vivo</i>Evaluation of Vaccine Efficacy (2013)

The development of vaccine candidates against Plasmodium vivax-the most geographically widespread human malaria species-is challenged by technical difficulties, such as the lack of in vitro culture systems and availability of animal models. Chimeric rodent Plasmodium parasites are safe and useful tools for the preclinical evaluation of new vaccine formulations. We report the successful development and characterization of chimeric Plasmodium berghei parasites bearing the type I repeat region of P. vivax circumsporozoite protein (CSP). The P. berghei-P. vivax chimeric strain develops normally in mosquitoes and produces highly infectious sporozoites that produce patent infection in mice that are exposed to the bites of as few as 3 P. berghei-P. vivax-infected mosquitoes. Using this transgenic parasite, we demonstrate that monoclonal and polyclonal antibodies against P. vivax CSP strongly inhibit parasite infection and thus support the notion that these antibodies play an important role in protective immunity. The chimeric parasites we developed represent a robust model for evaluating protective immune responses against P. vivax vaccines based on CSP.
Automated coordination programs do not make correct results automatic (2002)

The availability of computer programs which aide in protective device coordination studies has led to the assignment of coordination problems to those who are computer literate rather than protection literate. For those put in this unfortunate situation, some of the finer points of time current coordination are presented which are often not learned until after the news of that first false trip. This paper is intended as an addendum to, rather than a replacement for a typical time current coordination seminar. It covers: delta-wye transformers, instantaneous relays, protective device tap ranges, transformer damage curves, and combination starters.
Organic-to-inorganic structural chirality transfer in a 2D hybrid perovskite and impact on Rashba-Dresselhaus spin-orbit coupling (2020)

Translation of chirality and asymmetry across structural motifs and length scales plays a fundamental role in nature, enabling unique functionalities in contexts ranging from biological systems to synthetic materials. Here, we introduce a structural chirality transfer across the organic-inorganic interface in two-dimensional hybrid perovskites using appropriate chiral organic cations. The preferred molecular configuration of the chiral spacer cations, R-(+)- or S-(-)-1-(1-naphthyl)ethylammonium and their asymmetric hydrogen-bonding interactions with lead bromide-based layers cause symmetry-breaking helical distortions in the inorganic layers, otherwise absent when employing a racemic mixture of organic spacers. First-principles modeling predicts a substantial bulk Rashba-Dresselhaus spin-splitting in the inorganic-derived conduction band with opposite spin textures between R- and S-hybrids due to the broken inversion symmetry and strong spin-orbit coupling. The ability to break symmetry using chirality transfer from one structural unit to another provides a synthetic design paradigm for emergent properties, including Rashba-Dresselhaus spin-polarization for hybrid perovskite spintronics and related applications.
Practical conflict graphs for dynamic spectrum distribution (2013)

Most spectrum distribution proposals today develop their allocation algorithms that use conflict graphs to capture interference relationships. The use of conflict graphs, however, is often questioned by the wireless community because of two issues. First, building conflict graphs requires significant overhead and hence generally does not scale to outdoor networks, and second, the resulting conflict graphs do not capture accumulative interference. In this paper, we use large-scale measurement data as ground truth to understand just how severe these issues are in practice, and whether they can be overcome. We build "practical" conflict graphs using measurement-calibrated propagation models, which remove the need for exhaustive signal measurements by interpolating signal strengths using calibrated models. These propagation models are imperfect, and we study the impact of their errors by tracing the impact on multiple steps in the process, from calibrating propagation models to predicting signal strength and building conflict graphs. At each step, we analyze the introduction, propagation and final impact of errors, by comparing each intermediate result to its ground truth counterpart generated from measurements. Our work produces several findings. Calibrated propagation models generate location-dependent prediction errors, ultimately producing conservative conflict graphs. While these "estimated conflict graphs" lose some spectrum utilization, their conservative nature improves reliability by reducing the impact of accumulative interference. Finally, we propose a graph augmentation technique that addresses any remaining accumulative interference, the last missing piece in a practical spectrum distribution system using measurement-calibrated conflict graphs.
Toner Adhesion: Effects of Electrostatic and van der Waals Interactions (2002)

The force needed to detach spherical toner particles having a number average radius of 7.1 μm from an organic photoconductor was determined by ultracentrifugation. In the absence of any release agents applied to the photoconductor, it was found that only a small fraction of the toner particles could be removed from the photoconductor, even at the highest centrifugal accelerations (354,000 g). However, when the photoconductor was coated with a thin layer of zinc stearate, the release force was reduced substantially and detachment was readily achieved, the remaining release force varying with the square of the toner charge-to-mass ratio. Hence, the residual detachment force varied as the square of the particle charge. These results suggest that electrostatic forces become dominant when van der Waals forces are greatly reduced. Conversely, the large increase in toner adhesion to a photoconductor observed in the absence of a good release agent suggests that van der Waals forces may often dominate toner adhesion for this size particle.
Determination of the absolute configuration of the active amlodipine enantiomer as (-)-S: a correction (1992)

The active (-) enantiomer of amlodipine was originally reported to have R configuration. This does not concur with other 1,4-dihydropyridines with known absolute configuration. This configuration has now been determined by X-ray structural analysis using (1S)-camphanic acid and (S)-2-methoxy-2-phenylethanol as chiral probes. Both determinations gave the S configuration for the amlodipine (-) enantiomer with the greater Ca-antagonistic activity.
(-)-Epigallocatechin-3-gallate Reduces Cigarette Smoke-Induced Airway Neutrophilic Inflammation and Mucin Hypersecretion in Rats (2017)

<b>Background:</b> Cigarette smoking is the leading cause of chronic obstructive pulmonary disease. (-)-Epigallocatechin-3-gallate (EGCG), the major catechins in Chinese green tea, has been studied for its anti-oxidative and anti-inflammatory properties in cell and animal models. In this study, we aimed to analyze the effects of EGCG on cigarette smoke (CS)-induced airway inflammation and mucus secretion in the CS-exposed rat model. <b>Methods:</b> Male Sprague-Dawley rats were randomly divided into either sham air (SA) or CS exposure. EGCG (50 mg/kg b.wt.) was given by oral gavage every other day in both SA and CS-exposed animals. Oxidative stress and inflammatory markers were determined in serum and/or bronchoalveolar lavage fluid by biochemical assays or ELISA. Lung morphological changes were examined by Periodic Acid-Schiff, Masson's Trichrome staining and immunohistochemical analysis. Western blot analysis was performed to explore the effects of EGCG on epidermal growth factor receptor (EGFR)-mediated signaling pathway. <b>Results:</b> (-)-Epigallocatechin-3-gallate treatment attenuated CS-induced oxidative stress, lung cytokine-induced neutrophil chemoattractant-1 release and neutrophil recruitment. CS exposure caused an increase in the number of goblet cells in line with MUC5AC upregulation, and increased lung collagen deposition, which were alleviated in the presence of EGCG. In addition, CS-induced phosphorylation of EGFR in rat lung was abrogated by EGCG treatment. <b>Conclusion:</b> (-)-Epigallocatechin-3-gallate treatment ameliorated CS-induced oxidative stress and neutrophilic inflammation, as well as airway mucus production and collagen deposition in rats. The present findings suggest that EGCG has a therapeutic effect on chronic airway inflammation and abnormal airway mucus production probably via inhibition of EGFR signaling pathway.
Phosphorylation of Ribosomal Protein S3 and Antiapoptotic TRAF2 Protein Mediates Radioresistance in Non-small Cell Lung Cancer Cells (2012)

Radioresistance is considered as a main factor restricting efficacy of radiotherapy. However, the exact molecular mechanism of radioresistance has not been explained yet. In this study, to elucidate radioresistance mechanism in lung cancer, we compared radiation responses in two types of non-small cell lung cancer (NSCLC) cells with different radiosensitivity and identified key molecules conferring radioresistance. In radioresistant NSCLC cells, ionizing radiation (IR) led to casein kinase 2α (CK2α)- and PKC-mediated phosphorylation of rpS3 and TRAF2, respectively, which induced dissociation of rpS3-TRAF2 complex and NF-κB activation, resulting in significant up-regulation of prosurvival genes (cIAP1, cIAP2, and survivin). Also, dissociated phospho-rpS3 translocated into nucleus and bound with NF-κB complex (p65 and p50), contributing to p65 DNA binding property and specificity. However, in radiosensitive NSCLC cells, IR-mediated rpS3 phosphorylation was not detected due to the absence of CK2α overexpression. Consequently, IR-induced rpS3-TRAF2 complex dissociation, NF-κB activation, and prosurvival gene expression were not presented. Taken together, our findings revealed a novel radioresistance mechanism through functional orchestration of rpS3, TRAF2, and NF-κB in NSCLC cells. Moreover, we provided the first evidence for the function of rpS3 as a new TRAF2-binding protein and demonstrated that phosphorylation of both rpS3 and TRAF2 is a key control point of radioresistance in NSCLC cells. These results suggest that regulation of rpS3 and TRAF2 in combination with radiotherapy could have high pharmacological therapeutic potency for radioresistance of NSCLC.
A Survey on Network Coordinates Systems, Design, and Security (2010)

During the last decade, a new class of large-scale globally-distributed network services and applications have emerged. Those systems are flexible in the sense that they can select their communication path among a set of available ones. However, ceaselessly gathering network information such as latency to select a path is infeasible due to the large amount of measurement traffic it would generate. To overcome this issue, Network Coordinates Systems (NCS) have been proposed. An NCS allows hosts to predict latencies without performing direct measurements and, consequently, reduce the network resources consumption. During these last years, NCS opened new research fields in which the networking community has produced an impressive amount of work. We believe it is now time to stop and take stock of what has been achieved so far. In this paper, we survey the various NCS proposed as well as their intrinsic limits. In particular, we focus on security issues and solutions proposed to fix them. We also discuss potential future NCS developments, in particular how to use NCS for predicting bandwidth.
Effects of anti-intercellular adhesion molecule-1 and anti-lymphocyte-function-associated antigen-1 monoclonal antibodies on the metastasis of murine tumors. (1996)

Anti-intercellular adhesion molecule-1 (anti-ICAM-1) and anti-lymphocyte-function-associated antigen-1 (anti-LFA-1) monoclonal antibodies (mAbs) were injected into mice and their effects on tumor metastasis were investigated using two murine models. Depending on the dose, the anti-ICAM-1 mAb (KAT-1) expressed both inhibitory and promoting effects on liver metastases of ICAM-1 + LFA-1 + P815 mastocytoma cells, whereas it enhanced lung metastases of the ICAM-1-LFA-1-Meth-A fibrosarcoma cells at any doses. In contrast, anti-LFA-1 mAb (KBA) showed promoting effects only on the metastases of both tumor lines. Treatment of mice with either mAb enhanced metastases of P815 mastocytoma cells in the spleen.
Antimicrobial Gentamicin Activity in the Presence of Exogenous Protease Inhibitor (Bowman-Birk Inhibitor) in Gentamicin-lnduced Nephrotoxicity in Rats (1992)

In our previous studies, we found increased levels of urinary trypsin inhibitory activity in gentamicin-induced nephrotoxicity in rats. Following administration of the Bowman-Birk trypsin and chymotrypsin inhibitor (BBI), no proteinuria was detected in gentamicin-treated rats, and a decrease in creatinine clearance was noted in only 50% of the injected rats. In the present study, we examined the antimicrobial activity of gentamicin against Escherichia coli in the presence of BBI in gentamicin-induced nephrotoxicity in rats. We found that 50% of rats with E. coli-positive blood cultures died of septicemia. All the rats injected with E. coli plus gentamicin or E. coli plus gentamicin plus BBI survived, the latter showing no proteinuria or deterioration in creatinine clearance. In conclusion, BBI, which is an effective inhibitor of gentamicin-induced nephrotoxicity, does not affect the antimicrobial activity of gentamicin sulfate.
Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non–Small Cell Lung Cancer (2017)

Effective therapies for non-small cell lung cancer (NSCLC) remain challenging despite an increasingly comprehensive understanding of somatically altered oncogenic pathways. It is now clear that therapeutic agents with potential to impact the tumor immune microenvironment potentiate immune-orchestrated therapeutic benefit. Herein, we evaluated the immunoregulatory properties of histone deacetylase (HDAC) and bromodomain inhibitors, two classes of drugs that modulate the epigenome, with a focus on key cell subsets that are engaged in an immune response. By evaluating human peripheral blood and NSCLC tumors, we show that the selective HDAC6 inhibitor ricolinostat promotes phenotypic changes that support enhanced T-cell activation and improved function of antigen-presenting cells. The bromodomain inhibitor JQ1 attenuated CD4<sup>+</sup>FOXP3<sup>+</sup> T regulatory cell suppressive function and synergized with ricolinostat to facilitate immune-mediated tumor growth arrest, leading to prolonged survival of mice with lung adenocarcinomas. Collectively, our findings highlight the immunomodulatory effects of two epigenetic modifiers that, together, promote T cell-mediated antitumor immunity and demonstrate their therapeutic potential for treatment of NSCLC.<b>Significance:</b> Selective inhibition of HDACs and bromodomain proteins modulates tumor-associated immune cells in a manner that favors improved T-cell function and reduced inhibitory cellular mechanisms. These effects facilitated robust antitumor responses in tumor-bearing mice, demonstrating the therapeutic potential of combining these epigenetic modulators for the treatment of NSCLC. <i>Cancer Discov; 7(8); 852-67. ©2017 AACR.</i><i>This article is highlighted in the In This Issue feature, p. 783</i>.
Repression of Jasmonate-Dependent Defenses by Shade Involves Differential Regulation of Protein Stability of MYC Transcription Factors and Their JAZ Repressors in <i>Arabidopsis</i> (2014)

Reduction of the red/far-red (R/FR) light ratio that occurs in dense canopies promotes plant growth to outcompete neighbors but has a repressive effect on jasmonate (JA)-dependent defenses. The molecular mechanism underlying this trade-off is not well understood. We found that the JA-related transcription factors MYC2, MYC3, and MYC4 are short-lived proteins degraded by the proteasome, and stabilized by JA and light, in Arabidopsis thaliana. Dark and CONSTITUTIVE PHOTOMORPHOGENIC1 destabilize MYC2, MYC3, and MYC4, whereas R and blue (B) lights stabilize them through the activation of the corresponding photoreceptors. Consistently, phytochrome B inactivation by monochromatic FR light or shade (FR-enriched light) destabilizes these three proteins and reduces their stabilization by JA. In contrast to MYCs, simulated shade conditions stabilize seven of their 10 JAZ repressors tested and reduce their degradation by JA. MYC2, MYC3, and MYC4 are required for JA-mediated defenses against the necrotrophic pathogen Botrytis cinerea and for the shade-triggered increased susceptibility, indicating that this negative effect of shade on defense is likely mediated by shade-triggered inactivation of MYC2, MYC3, and MYC4. The opposite regulation of protein stability of MYCs and JAZs by FR-enriched light help explain (on the molecular level) the long-standing observation that canopy shade represses JA-mediated defenses, facilitating reallocation of resources from defense to growth.
Bayesian-Game-Based Fuzzy Reinforcement Learning Control for Decentralized POMDPs (2012)

This paper proposes a Bayesian-game-based fuzzy reinforcement learning (RL) controller for decentralized partially observable Markov decision processes (Dec-POMDPs). Dec-POMDPs have recently emerged as a powerful platform for optimizing multiagent sequential decision making in partially observable stochastic environments. However, finding exact optimal solutions to a Dec-POMDP is provably intractable (NEXP-complete), necessitating the use of approximate/suboptimal solution approaches. This approach proposes an approximate solution by employing fuzzy inference systems (FISs) in a game-based RL setting. It uses the powerful universal approximation capability of fuzzy systems to compactly represent a Dec-POMDP as a fuzzy Dec-POMDP, allowing the controller to progressively learn and update an approximate solution to the underlying Dec-POMDP. The proposed controller envisages an FIS-based RL controller for Dec-POMDPs modeled as a sequence of Bayesian games (BGs). We implement the proposed controller for two scenarios: 1) Dec-POMDPs with free communication between agents; and 2) Dec-POMDPs without communication. We empirically evaluate the proposed approach on three standard benchmark problems: 1) multiagent tiger; 2) multiaccess broadcast channel; and 3) recycling robot. Simulation results and comparative evaluation against other Dec-POMDP solution approaches elucidate the effectiveness and feasibility of employing FIS-based game-theoretic RL for designing Dec-POMDP controllers.
Temperature- and Magnetic-Field-Dependent Longitudinal Spin Relaxation in Nitrogen-Vacancy Ensembles in Diamond (2012)

We present an experimental study of the longitudinal electron-spin relaxation time (T1) of negatively charged nitrogen-vacancy (NV) ensembles in diamond. T1 was studied as a function of temperature from 5 to 475 K and magnetic field from 0 to 630 G for several samples with various NV and nitrogen concentrations. Our studies reveal three processes responsible for T1 relaxation. Above room temperature, a two-phonon Raman process dominates; below room temperature, we observe an Orbach-type process with an activation energy of 73(4) meV, which closely matches the local vibrational modes of the NV center. At yet lower temperatures, sample dependent cross-relaxation processes dominate, resulting in temperature independent values of T1 from milliseconds to minutes. The value of T1 in this limit depends sensitively on the magnetic field and can be tuned by more than 1 order of magnitude.