gebhart/patrepeval huggingface dataset:
Abstract 3554: The histone deacetylase inhibitor LBH589 augments anti-tumor immunity through direct effects on tumor and immune cells leading to impaired tumor progression in vivo (2012)

Abstract Overcoming immune tolerance is critical for the development of effective immunotherapy against cancer. Tumor cells induce tolerance through a variety of modalities including the secretion of IL-10 and TGF-β, the expression of inhibitory ligands, and the generation of cells with regulatory properties. Epigenetic modifiers have gained special attention due to their ability to modify immune regulatory pathways. In this context, a group of chemical compound collectively named histone deacetylase inhibitors (HDACi) have recently been shown to modulate tumor cell immunogenicity, adding a new property to their already well-documented cytotoxic effect against transformed cells. LBH589 is a potent, pan-HDACi that has been used in clinical trials for the treatment of several hematological malignancies. Here, we provide evidence of the anti-melanoma effect of LBH589 through its direct effects upon tumor cells as well as its modulatory effects upon immune cells. Indeed, treatment of human and murine melanoma cells in vitro with LBH589 resulted in inhibition of melanoma proliferation, characterized by cell cycle arrest in G1. Moreover, we found that LBH589 enhances the expression of MHC class I and II molecules on melanoma cells, which is critical for immune recognition. In addition, LBH589 treatment inhibits the production of IL-10, while enhancing the secretion of pro-inflammatory cytokines such as IL-12 and the expression of the costimulatory molecule B7.2 on antigen-presenting cells (APCs). LBH-treated APCs also displayed an enhanced capability to activate naïve antigen-specific T-cells as evidenced by their increased production of IL-2 and IFN-γ. More importantly, LBH589-treated APCs also restored the function of anergic T-cells isolated from tumor bearing mice. Finally, in vivo treatment of B16 melanoma bearing mice with LBH589 resulted in a substantial decrease in tumor growth when compared to vehicle-control treated mice (mean 602mm3 vs. 1316mm3, respectively). In conclusion, the dual ability of the pan-HDACi LBH589 to target both melanoma cells and to enhance anti-tumor immune responses provides the rationale for evaluating this compound either alone or in combination with immune enhancing therapeutic approaches (eg, CTLA4 blockade) for melanoma treatment. 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 3554. doi:1538-7445.AM2012-3554
SUBRETINAL HEMORRHAGES IN PROLIFERATIVE DIABETIC RETINOPATHY (1997)

Subretinal hemorrhages appear to be an uncommon feature associated with long-term, advanced proliferative diabetic retinopathy and portend a guarded visual prognosis. These hemorrhages may occur spontaneously in previously untreated eyes and are often unsuspected until observed at the time of vitreous surgery. In general, removal of subretinal hemorrhages was not necessary to achieve macular anatomic attachment, and most patients experienced improved visual function after surgery. Diabetic subretinal hemorrhages may indicate a retinal break, and, therefore, careful ophthalmic inspection should be performed in these patients.
Hepatic expression of CCL2 in alcoholic liver disease is associated with disease severity and neutrophil infiltrates (2012)

Serum levels and liver expression of CCL2 are increased in patients with alcoholic hepatitis (AH). In an experimental model of alcoholic liver disease (ALD), CCL2 was implicated in proinflammatory cytokines activation and hepatic lipid metabolism, but its role in human disease is currently unknown. In a large cohort of ALD patients, we analysed plasma levels and liver expression of CCL2 and their association with liver disease severity and histological lesions. We also studied the relationship between -2518 A > G CCL2 and CCR2 190 A/G polymorphisms and severity of ALD. We show that CCL2 plasma levels are increased in ALD patients compared with healthy subjects. AH patients had significantly higher plasma levels and hepatic expression of CCL2 than patients without AH. Plasma levels and hepatic expression of CCL2 were associated with disease severity. CCL2 liver expression was correlated with neutrophil infiltrate and interleukin (IL)-8 expression, but not with steatosis. Moreover, there were more G-allele carriers of -2518 A > G CCL2 polymorphism in severe AH patients than in other ALD patients. Our results demonstrate that CCL2 is increased in ALD, particularly in severe forms, and suggest a role for CCL2 in the pathogenesis of ALD via neutrophil recruitment.
Toward Functional Polyester Building Blocks from Renewable Glycolaldehyde with Sn Cascade Catalysis (2013)

Having been inspired by formose-based hypotheses surrounding the origin of life, we report on a novel catalytic route toward a series of recently discovered four-carbon α-hydroxy acids (AHA) and their esters from accessible and renewable glycolaldehyde (GA) in various solvents. The synthesis route follows a cascade type reaction network, and its mechanism with identification of the rate-determining step was investigated with in situ 13C NMR. The mechanistic understanding led to optimized reaction conditions with higher overall rates of AHA formation by balancing Brønsted and Lewis acid activity, both originating from the tin halide catalyst. An optimal H+/Sn ratio of 3 was identified, and this number was surprisingly irrespective of the Sn oxidation state. Further rate enhancement was accomplished by adding small amounts of water to the reaction mixture, boosting the rate by a factor of 4.5 compared with pure methanol solvent. The cascade reaction selectively yields near 60% methyl-4-methoxy-2-hydroxybutanoate (MMHB). In the optimized rate regime in methanol, an initial TOF of 7.4 molGA molSn–1 h–1 was found. In sterically hindered alcohols (isopropyl alcohol), the rate of AHA formation was even higher, and the corresponding vinyl glycolate esters arose as the main product. Vinyl glycolic acid, 2,4-dihydroxybutanoic acid, and its lactone were formed significantly in nonprotic solvent. The corresponding AHAs have serious potential as building blocks in novel biobased polymers with tunable functionality. The incorporation of vinyl glycolic acid in polylactic acid-based polyesters is illustrated, and postmodification at the vinyl side groups indeed allows access to a range of properties, such as tunable hydrophilicity, which is otherwise difficult to attain for pure poly(l-lactic acid).
Structure-Function Study of the Extracellular Domain of the Human IFN-α Receptor (hIFNAR1) Using Blocking Monoclonal Antibodies: The Role of Domains 1 and 2 (1998)

Abstract We have performed a structure-function analysis of extracellular domain regions of the human IFN-α receptor (hIFNAR1) using mAbs generated by immunizing mice with a soluble hIFNAR1-IgG. Five mAbs described in this study recognize different epitopes as determined by a competitive binding ELISA and by alanine substitution mutant analyses of the hIFNAR1-IgG. Two mAbs, 2E1 and 4A7, are able to block IFN-stimulated gene factor 3 (ISGF3) formation and inhibit the antiviral cytopathic effect induced by several IFN-α (IFN-α2/1, -α1, -α2, -α5, and -α8). None of these anti-IFNAR1 mAbs were able to block activity of IFN-β. mAb 4A7 binds to a domain 1-hIFNAR1-IgG but not to a domain 2-hIFNAR1-IgG, which suggests that its binding region is located in domain 1. The binding of the most potent blocking mAb, 2E1, requires the presence of domain 1 and domain 2. The most critical residue for 2E1 binding is a lysine residue at position 249, which is in domain 2. These findings suggest that both domain 1 and domain 2 are necessary to form a functional receptor and that a region in domain 2 is important. IFN-β recognizes regions of the hIFNAR complex that are distinct from those important for the IFN-α.
Heat-removal wavelength-conversion module by air-bubble reduction (2015)

We report improved thermal performance in the heat-removal module for stable wavelength conversion, fabricated by a new method, air-bubble reduction. The quantitative relation between focusing position, normalized conversion efficiency and effective heat capacity is investigated.
Flying Objects Detection from a Single Moving Camera (2016)

We propose an approach to detect flying objects such as UAVs and aircrafts when they occupy a small portion of the field of view, possibly moving against complex backgrounds, and are filmed by a camera that itself moves. Solving such a difficult problem requires combining both appearance and motion cues. To this end we propose a regression-based approach to motion stabilization of local image patches that allows us to achieve effective classifica-tion on spatio-temporal image cubes and outperform state-of-the-art techniques. As the problem is relatively new, we collected two chal-lenging datasets for UAVs and Aircrafts, which can be used as benchmarks for flying objects detection and vision-guided collision avoidance. 1.
Kinetic Studies and Biochemical Pathway Analysis of Anaerobic Poly-( R )-3-Hydroxybutyric Acid Synthesis in Escherichia coli (2005)

Poly-(R)-3-hydroxybutyric acid (PHB) was synthesized anaerobically in recombinant Escherichia coli. The host anaerobically accumulated PHB to more than 50% of its cell dry weight during cultivation in either growth or nongrowth medium. The maximum specific PHB production rate during growth-associated synthesis was approximately 2.3 +/- 0.2 mmol of PHB/g of residual cell dry weight/h. The by-product secretion profiles differed significantly between the PHB-synthesizing strain and the control strain. PHB production decreased acetate accumulation for both growth and nongrowth-associated PHB synthesis. For instance under nongrowth cultivation, the PHB-synthesizing culture produced approximately 66% less acetate on a glucose yield basis as compared to a control culture. A theoretical biochemical network model was used to provide a rational basis to interpret the experimental results like the fermentation product secretion profiles and to study E. coli network capabilities under anaerobic conditions. For example, the maximum theoretical carbon yield for anaerobic PHB synthesis in E. coli is 0.8. The presented study is expected to be generally useful for analyzing, interpreting, and engineering cellular metabolisms.
Halftone postprocessing for improved rendition of highlights and shadows (2000)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Sn doping of [beta]-Ga2O3 grown by plasma-assisted molecular beam epitaxy (2021)

Sn doping of β-Ga2O3 grown by conventional plasma-assisted molecular beam epitaxy (PAMBE) and via metal oxide catalyzed epitaxy (MOCATAXY) using a supplied indium flux during MBE growth was investigated. Sn doping of (010) β-Ga2O3 via MOCATAXY allowed for sharper doping profiles as well as a wider range of donor concentrations from 4 x 10^16 cm-3 to 2 x 10^19 cm-3 with a maximum Hall mobility of 136 cm2/Vs and a Sn donor level of 77 meV below the conduction band. Expansion of MOCATAXY to (001) β-Ga2O3 also showed improved Hall mobility, growth rates, and smoother films in this orientation.
High-speed GaAs metal gate semiconductor field effect transistor structure grown on a composite Ge∕GexSi1−x∕Si substrate (2007)

In this study we used a low-pressure metal organic vapor phase epitaxy method to investigate the growth of GaAs metal gate semiconductor field effect transistor (MESFET) structures on a Si substrate. The buffer layer between the Si substrate and the grown GaAs epitaxial layers was a composite Ge∕Si0.05Ge0.95∕Si0.1Ge0.9 metamorphic layer. We used transmission electron microscopy to observe the microstructures formed in the grown GaAs∕Ge∕SixGe1−x∕Si material and atomic force microscopy to analyze the surface morphology and the formation of antiphase domains in the GaAs epitaxial layers. The measured Hall electron mobility in the channel layer of a MESFET structure grown on a 6° misoriented Si substrate was 2015 cm2 V−1 s−1 with a carrier concentration of 5.0×1017 cm−3. The MESFET device fabricated on this sample exhibited good current-voltage characteristics.
Skin color reproduction algorithm for portrait images shown on the mobile display (2006)

The preferred skin color reproduction algorithm is developed for the mobile display especially for a portrait image with one person as a main object occupying most of the screen. According to the developed technique, the skin area in an image is detected using color value of each pixel in YCbCr color space. The skin color boundary is defined as a quadrangle in Cb-Cr plane. The colors of pixels belonging to skin area are shifted toward the preferred colors while there is no color change for the other pixels. The psychophysical experiments are conducted to investigate the optimal model parameters providing the most pleasant image to the users. Then, the performance of developed algorithm is tested using the optimal parameters. The result shows that for more than 95% cases, the observers prefer the images treated with the developed algorithm compared to the original image. It is believed that the developed algorithm can be applied to the mobile application to improve the image quality regardless the input sources.
From grape to grape: novel stereoselective syntheses of chiral pyrethroids - synthesis of the most potent commercially available insecticides (1990)

Abstract
Characterization of bovine patellar cartilage by NMR (2007)

Metabolic and structural changes in cartilage tissue are thought to be at the root of degenerative joint disease. We identify here the NMR resonances in bovine patellar cartilage tissue by static and high-resolution magic angle spinning (HRMAS) NMR spectroscopy, (1)H-(13)C heteronuclear single-quantum correlation (HSQC) spectroscopy, total correlation spectroscopy (TOCSY), and saturation transfer experiments. Some differences between the patellar cartilage samples studied here and earlier nasal cartilage and intervertebrate disc studies were found. In addition, we show assignments downfield of the water signal, which also includes the assignment of amide and hydroxy protons on the basis of their exchangeability with water. These results will allow an identification of spectroscopic markers of cartilage degradation using techniques such as chemical exchange saturation transfer imaging.
π-Extension of heterocycles via a Pd-catalyzed heterocyclic aryne annulation: π-extended donors for TADF emitters (2022)

We report the annulation of heterocyclic building blocks to access π-extended polycyclic aromatic hydrocarbons (PAHs). The method involves the trapping of short-lived hetarynes with catalytically-generated biaryl palladium intermediates and allows for the concise appendage of three or more fused aromatic rings about a central heterocyclic building block. Our studies focus on annulating the indole and carbazole heterocycles through the use of indolyne and carbazolyne chemistry, respectively, the latter of which required the synthesis of a new carbazolyne precursor. Notably, these represent rare examples of transition metal-catalyzed reactions of N-containing hetarynes. We demonstrate the utility of our methodology in the synthesis of heterocyclic π-extended PAHs, which were then applied as ligands in two-coordinate metal complexes. As a result of these studies, we identified a new thermally-activated delayed fluorescence (TADF) emitter that displays up to 81% photoluminescence efficiency, along with insight into structure-property relationships. These studies underscore the utility of heterocyclic strained intermediates in the synthesis and study of organic materials.
Persistent Spinal Pain Syndrome: A Proposal for Failed Back Surgery Syndrome and ICD-11 (2021)

This project is important to those in the fields of pain management, spine surgery, and neuromodulation, as well as patients labeled with FBSS. Through a shift in perspective, it could facilitate the application of the new ICD-11 classification and allow clearer discussion among medical professionals, industry, funding organizations, academia, and the legal profession.
FuelCalc: A Method for Estimating Fuel Characteristics (2006)

This paper describes the FuelCalc computer program. FuelCalc is a tool to compute surface and canopy fuel loads and characteristics from inventory data, to support fuel treatment decisions by simulating effects of a wide range of silvicultural treatments on surface fuels and canopy fuels, and to provide linkages to stand visualization, fire behavior and fire effects programs that rely on estimates of fuel loads and qualities. Canopy fuel characteristics, including available fuel, canopy bulk density, canopy base height and canopy cover are estimated from a list of trees.
OptEEmAL: Decision-Support Tool for the Design of Energy Retrofitting Projects at District Level (2019)

Abstract Designing energy retrofitting actions poses an elevated number of problems, as the definition of the baseline, selection of indicators to measure performance, modelling, setting objectives, etc. This is time-consuming and it can result in a number of inaccuracies, leading to inadequate decisions. While these problems are present at building level, they are multiplied at district level, where there are complex interactions to analyse, simulate and improve. OptEEmAL proposes a solution as a decision-support tool for the design of energy retrofitting projects at district level. Based on specific input data (IFC(s), CityGML, etc.), the platform will automatically simulate the baseline scenario and launch an optimisation process where a series of Energy Conservation Measures (ECMs) will be applied to this scenario. Its performance will be evaluated through a holistic set of indicators to obtain the best combination of ECMs that complies with user’s objectives. A great reduction in time and higher accuracy in the models are experienced, since they are automatically created and checked. A subjective problem is transformed into a mathematical problem; it simplifies it and ensures a more robust decision-making. This paper will present a case where the platform has been tested.
Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer (2021)

The switch/sucrose non-fermentable (SWI/SNF) complex has a crucial role in chromatin remodelling<sup>1</sup> and is altered in over 20% of cancers<sup>2,3</sup>. Here we developed a proteolysis-targeting chimera (PROTAC) degrader of the SWI/SNF ATPase subunits, SMARCA2 and SMARCA4, called AU-15330. Androgen receptor (AR)<sup>+</sup> forkhead box A1 (FOXA1)<sup>+</sup> prostate cancer cells are exquisitely sensitive to dual SMARCA2 and SMARCA4 degradation relative to normal and other cancer cell lines. SWI/SNF ATPase degradation rapidly compacts cis-regulatory elements bound by transcription factors that drive prostate cancer cell proliferation, namely AR, FOXA1, ERG and MYC, which dislodges them from chromatin, disables their core enhancer circuitry, and abolishes the downstream oncogenic gene programs. SWI/SNF ATPase degradation also disrupts super-enhancer and promoter looping interactions that wire supra-physiologic expression of the AR, FOXA1 and MYC oncogenes themselves. AU-15330 induces potent inhibition of tumour growth in xenograft models of prostate cancer and synergizes with the AR antagonist enzalutamide, even inducing disease remission in castration-resistant prostate cancer (CRPC) models without toxicity. Thus, impeding SWI/SNF-mediated enhancer accessibility represents a promising therapeutic approach for enhancer-addicted cancers.
Islet Cell Associated Autoantibodies and C-Peptide Levels in Patients with Diabetes and Symptoms of Gastroparesis (2018)

NCT01696747.
In-depth qualitative and quantitative analysis of composite glycosylation profiles and other micro-heterogeneity on intact monoclonal antibodies by high-resolution native mass spectrometry using a modified Orbitrap (2013)

Here, we describe a fast, easy-to-use, and sensitive method to profile in-depth structural micro-heterogeneity, including intricate N-glycosylation profiles, of monoclonal antibodies at the native intact protein level by means of mass spectrometry using a recently introduced modified Orbitrap Exactive Plus mass spectrometer. We demonstrate the versatility of our method to probe structural micro-heterogeneity by describing the analysis of three types of molecules: (1) a non-covalently bound IgG4 hinge deleted full-antibody in equilibrium with its half-antibody, (2) IgG4 mutants exhibiting highly complex glycosylation profiles, and (3) antibody-drug conjugates. Using the modified instrument, we obtain baseline separation and accurate mass determination of all different proteoforms that may be induced, for example, by glycosylation, drug loading and partial peptide backbone-truncation. We show that our method can handle highly complex glycosylation profiles, identifying more than 20 different glycoforms per monoclonal antibody preparation and more than 30 proteoforms on a single highly purified antibody. In analyzing antibody-drug conjugates, our method also easily identifies and quantifies more than 15 structurally different proteoforms that may result from the collective differences in drug loading and glycosylation. The method presented here will aid in the comprehensive analytical and functional characterization of protein micro-heterogeneity, which is crucial for successful development and manufacturing of therapeutic antibodies.
Phase-sensitive parametric motion transducer (1984)

We have built a parametric motion transducer that is a prototype for a "back-action-evasion" measuring device. Our tests demonstrate that it has the expected phase sensitivity in its fundamental mechanical-to-electrical coupling when appropriately pumped. Another test verifies the anticipated frequency and loss dependence of the coupling. A third test verifies that the absolute magnitude of coupling is reasonably close to model predictions.
On-Off Quantization of an MPC Policy for Coupled Station Keeping, Attitude Control, and Momentum Management of GEO Satellites (2018)

This paper introduces a novel on-off quantization scheme used with a control architecture based on model predictive control (MPC) to simultaneously perform station keeping, attitude control, and momentum management of a nadir-pointing geostationary satellite equipped with three reaction wheels and four on-off electric thrusters. The MPC policy includes an inner-loop SO(3)-based attitude control law to maintain a nadir-pointing attitude, and an outer loop for station keeping and momentum management. The continuous thrust command generated by the MPC policy is quantized as a single on-off pulse every feedback period in such a way that the predicted error in the states induced by quantization is minimized. This quantization scheme introduces very limited change in behavior and performance compared to results with the non-quantized MPC policy, and uses significantly less on-off pulses compared to other approaches in the literature, such as pulse-width modulation. The tuning parameters of the proposed quantization scheme are discussed in detail and their effects on closed-loop performance are analyzed numerically.