gebhart/patrepeval huggingface dataset:
DNA-intercalators Causing Rapid Re-expression of Methylated and Silenced Genes in Cancer Cells (2013)

// M. Zulfiquer Hossain 1 , Megan A. Healey 1 , Calvin Lee 1 , Weijie Poh 1 , Sashidhar R. Yerram 1 , Kalpesh Patel 1 , Nilofer S. Azad 1 , James G. Herman 1 , and Scott E. Kern 1 1 Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland Correspondence: Scott E. Kern, email: // Keywords : cancer, gene methylation, demethylation, DNA-intercalator, quinacrine, DNMT inhibitor, epigenetics, silencing and re-activation of gene expression, small molecule-DNA interactions Received : February 8, 2013 Accepted : February 25, 2013 Published : February 26, 2013 Abstract Epigenetic inactivation of tumor-suppressor and other regulatory genes plays a critical role in carcinogenesis. Transcriptional silencing is often maintained by DNA methyl transferase (DNMT)-mediated hypermethylation of CpG islands in promoter DNA. Nucleoside analogs including azacytidine and decitabine have been used to inhibit DNMT and re-activate genes, and are clinically used. Their shortcomings include a short half-life and a slow onset of action due to required nucleotide incorporation during DNA replication, which may limit clinical utility. It might be useful to begin to identify lead compounds having novel properties, specifically distinct and fast-acting gene desilencing. We previously identified chemicals augmenting gene expression in multiple reporter systems. We now report that a subset of these compounds that includes quinacrine re-expresses epigenetically silenced genes implicated in carcinogenesis. p16, TFPI2, the cadherins E-cadherin and CDH13, and the secreted frizzle-related proteins (SFRPs) SFRP1 and SFRP5 were desilenced in cancer cell lines. These lead compounds were fast-acting: re-expression occurred by 12-24 hours. Re-activation of silenced genes was accompanied by depletion of DNMT1 at the promoters of activated genes and demethylation of DNA. A model compound, 5175328, induced changes more rapidly than decitabine. These gene desilencing agents belonged to a class of acridine compounds, intercalated into DNA, and inhibited DNMT1 activity in vitro. Although to define the mechanism would be outside the scope of this initial report, this class may re-activate silenced genes in part by intercalating into DNA and subsequently inhibiting full DNMT1 activity. Rapid mechanisms for chemical desilencing of methylated genes therefore exist.
Elevation of transforming growth factor alpha in cat aqueous humor after corneal endothelial injury. (1994)

Wounding of cat endothelium causes a rapid increase in mitogenic proteins in aqueous humor including TGF alpha, which may act by an autocrine mechanism to stimulate endothelial wound healing.
Cover Picture: Benzene Ring Trimer Interactions Modulate Supramolecular Structures (Angew. Chem. Int. Ed. 20/2007) (2007)

The benzene trimer is difficult to observe and isolate as such. However, by adopting a supramolecular platform with three phenyl substituents, as shown in the cover picture and as H. Furuta and co-workers describe in their Communication on page 3672 ff., the strength of the interaction between the three benzene rings in a “trimer” can be evaluated. The presence of such aromatic–aromatic interactions in higher-order aromatic clusters in biopolymers may contribute to some extent to stabilization of their tertiary structures.
Oral 5-ASA Therapy in Ulcerative Colitis (2008)

5-aminosalicylic acid (5-ASA) is the standard first-line treatment for mild-to-moderate ulcerative colitis. A variety of 5-ASA delivery systems are available and in development, including both oral and rectal formulations; all of which aim to deliver the active drug to the colon while minimizing systemic absorption. Because the efficacy of most oral 5-ASA therapies is broadly similar, the appropriate selection of a given formulation often relies on other factors. This article explores the differences between oral 5-ASA formulations in terms of their delivery system, reviews the available data on oral 5-ASA treatment efficacy and tolerability, and examines the rationale for changing from one 5-ASA formulation to another if a patient does not respond to, or worsens on, their existing agent.
Modulators and Demodulators (2011)

This chapter contains sections titled: Introduction Modulators Demodulators Applications Conclusion Sound and music References
Structural Changes in the Retinal Microvasculature and Renal Function (2013)

Quantitative changes of the retinal vascular geometry and qualitative changes in the vessel architecture are associated with markers of renal dysfunction and damage.
Improved Contactless Heartbeat Estimation in FMCW Radar via Kalman Filter Tracking (2020)

Radar systems enable a contactless, noninvasive method to simultaneously monitor the respiration and heart rate of a human target. To enhance the stability and accuracy of the detected heart rate, this letter introduces a Kalman filter-based tracking of the heartbeat signal. After providing a first rough estimation, the bandwidth of the applied band-pass filter is successively narrowed down, and the filter limits are steadily updated with respect to the current heart rate of the target. Measurement segments with random body movements are automatically identified and consequentially ignored for the Kalman filter update. The functionality of the proposed algorithm is proven by various verification measurements using a 60-GHz frequency-modulated continuous-wave radar system. The determined heart rates are compared to the output of a commercial chest belt. Measurement data with common breathing, as well as during breath-holding, were recorded for 14 different subjects.
A high random-access-data-rate 4 Mb DRAM with pipeline operation (1990)

A novel circuit technology which introduces a pipeline scheme in a read operation and improves the random-access data rate by roughly 30% is described. This technology has been applied to a 4M DRAM, and the RAM showed a short cycle time of less than 100 ns, i.e. a more than 10-MHz data rate, under the worst operating condition. In addition, a very fast virtual RAD access time of 20 ns has been obtained. Since the pipeline DRAM does not require any new process and/or assembly technologies, it can be added to the standard DRAM family
Estimation of the Toxicity of Silver Nanoparticles by Using Planarian Flatworms (2014)

The regeneration of planarian flatworms - specifically, changes to the area of the regeneration bud (blastema) after surgical dissection - was proposed for use as a robust tool for estimating the toxicity of silver nanoparticles. The use of Planaria species, due to their unique regenerative capacity, could result in a reduction in the use of more-traditional laboratory animals for toxicity testing. With our novel approach, silver nanoparticles were found to be moderately toxic to the planarian, Girardia tigrina.
Effect of terminal sterilization by irradiation on amber Type I and Type III glass containers containing veterinary oxytetracycline suspension. (2004)

The purpose of this study is to determine the effect of terminal sterilization by gamma irradiation on 500-mL amber Type I and Type III glass containers (bottles) containing oxytetracycline (OTC) (25% W/V) suspension formulated using 20% (W/V) phospholipids syrup. The formulation was developed for veterinary parenteral administration. The results of terminal sterilization were used to assess the acceptability for this suspension product. OTC is light-sensitive and needs to be stored in amber glass containers. Amber Type I and Type III glass containers were considered for this formulation during development. Type I is a highly resistant, borosilicate glass (oxidized glass). Type III, which is soda-lime glass (reduced glass, see Materials and Methods), may also be used for parenteral products. The amber Type I and Type III glass containers, containing the suspension, were irradiated at 20-40 kGy for 150 min. In order to determine the sterility of the suspension, ampoules of the biological indicator, Bacillus pumilus, were placed in a number of bottles of the suspension. The bottles with the biological indicators were then positioned among the rest of the production bottles as per a radiation dose-mapping study conducted at the sterilization facility. Potency determination and stability evaluations for OTC were performed using high pressure liquid chromatography (HPLC). The results indicate that the gamma irradiation dose of 20-40 kGy for 150 min was able to inactivate 10(6) Bacillus pumilus spores in ampoules. After gamma sterilization, OTC concentration, pH, particle size, endotoxins, and sterility were evaluated. The assay results were comparable for the suspension in amber Type I and Type III glass containers. Sterility and pyrogenicity were measured by the USP Membrane Filtration Method and USP Bacterial Endotoxins Test, respectively. The suspension in the amber Type III glass container was also chemically (HPLC) and physically (suspension mean particle size, viscosity, density, and syringeability) stable for at least 12 months at room temperature. However, amber Type I glass darkened following irradiation, leading to a substantial reduction in glass transparency. The appearance of amber Type III glass was acceptable. Thus, the "reduced" glass, such as soda-lime, was found to be much less susceptible to darkening than the highly oxidized borosilicate amber. Due to the potential aesthetic concerns with Type I glass, the amber Type III glass container was selected for this suspension formulation.
Hair follicle stem cell replication stress drives IFI16/STING-dependent inflammation in hidradenitis suppurativa (2020)

Hidradenitis suppurativa (HS) is a chronic, relapsing, inflammatory skin disease. HS appears to be a primary abnormality in the pilosebaceous-apocrine unit. In this work, we characterized hair follicle stem cells (HFSCs) isolated from HS patients and more precisely the outer root sheath cells (ORSCs). We showed that hair follicle cells from HS patients had an increased number of proliferating progenitor cells and lost quiescent stem cells. Remarkably, we also showed that the progression of replication forks was altered in ORSCs from hair follicles of HS patients, leading to activation of the ATR/CHK1 pathway. These alterations were associated with an increased number of micronuclei and with the presence of cytoplasmic ssDNA, leading to the activation of the IFI16/STING pathway and the production of type I IFNs. This mechanistic analysis of the etiology of HS in the HFSC compartment establishes a formal link between genetic predisposition and skin inflammation observed in HS.
Solvent Degradation and Reduced Fracture Toughness in Aged Composites (1992)

Qartz- and barium-glass-filled composites aged for more than one year in ethanol experienced a significant reduction in fracture toughness (K1c), essentially identical to that experienced after two months of aging. This reduction is mainly attributed to a softening of the resin matrix, but cracking within the resin and at the filler/matrix interface, as revealed by SEM microscopy, may also have contributed. No significant cracking could be seen in the composites aged in water. Composites post-cured at temperatures approaching their glass-transition temperature also experienced a reduction in K1c after alcohol storage. Storage in water for one year had little effect on the K1c of composites cured at oral temperatures, but a significant increase was observed for those post-cured at elevated temperatures. This increase is difficult to explain, but appears to involve a filler/matrix interfacial phenomenon, because it was not observed in the unfilled resin. The results of this study demonstrate that an alteration in the fracture resistance and some degradation of the filler/matrix interface, as has been observed clinically, occur after long-term exposure of dental composites to certain solvents used as food-simulating liquids.
Multiple scattering from submerged bodies with dissimilar acoustical properties. Part I. Local impedance models (1995)

A numerical solution for a two-body acoustical multiple scattering problem based on the analytical infinite series solution of the wave equation was developed. FORTRAN 77 codes implementing this solution were written which are capable of simulating the case of two spheres of arbitrary radius and distinct material properties subject to an acoustic plane wave of arbitrary incidence. Far-field solutions involving permutations of the two ‘‘degenerate’’ boundary conditions (pressure release and rigid) were compared to solutions obtained with the combined Helmholtz integral equation formulation problem (CHIEF) program. Surface pressures and velocities were also calculated. [Work supported by ONR.]
Influence of Membrane Ion Exchange Capacity on the Catalyst Layer Performance in an Operating PEM Fuel Cell (2005)

The effect of ion exchange capacity (IEC) of polymer electrolyte membranes (PEMs) on cathode catalyst layer operation is investigated using a hydrogen/oxygen proton exchange membrane fuel cell (PEMFC) and a series of tetrafluoroethylene--polystyrene sulfonic acid (ETFE--PSSA) membranes. The electrochemically active surface area (ESA) of the catalyst layer reveals a slight dependence on IEC. The steady-state beginning-of-life polarization curves show an increase in fuel cell performance with increased IEC. The membrane's IEC and molecular structure controls the water content within, and regulates the water balance in the complete MEA. Comparing half-fuel-cell and fuel cell systems reveals that the ESA in the latter is lower as a result of reduced wetting of the catalyst layer but this is offset by an order of magnitude improvement of the effective diffusion. Consequently oxygen reduction reaction (ORR) performance is higher in the fuel cell system. The balance between electro-osmotic flux and hydraulic counterflux in the membrane is employed to explain the distinct effects of IEC in the half fuel cell and fuel cell systems. The two types of measurements thus provide a convenient tool for studying the interplay of different mechanisms of water flux in the membrane.
Current status of high-index immersion lithography development (2007)

High index immersion lithography (HIL) is one candidate for the next generation lithography technology following water immersion lithography. This technology may require only moderate changes of chip making processes and result in lower cost of ownership (CoO) compared with other technologies such as double processing, extreme ultra violet lithography (EUVL), and nano-imprinting, and other technologies. In this paper, the current status of high index lens material and immersion fluid development compared with our requirements is discussed considering microlithographic lens design feasibility and attainable NA.
Reliability and Failure Impact Analysis of Distributed Storage Systems with Dynamic Refuging (2016)

In recent data centers, large-scale storage systems storing big data comprise thousands of large-capacity drives. Our goal is to establish a method for building highly reliable storage systems using more than a thousand low-cost large-capacity drives. Some large-scale storage systems protect data by erasure coding to prevent data loss. As the redundancy level of erasure coding is increased, the probability of data loss will decrease, but the increase in normal data write operation and additional storage for coding will be incurred. We therefore need to achieve high reliability at the lowest possible redundancy level. There are two concerns regarding reliability in large-scale storage systems: (i) as the number of drives increases, systems are more subject to multiple drive failures and (ii) distributing stripes among many drives can speed up the rebuild time but increase the risk of data loss due to multiple drive failures. If data loss occurs by multiple drive failure, it affects many users using a storage system. These concerns were not addressed in prior quantitative reliability studies based on realistic settings. In this work, we analyze the reliability of large-scale storage systems with distributed stripes, focusing on an effective rebuild method which we call Dynamic Refuging. Dynamic Refuging rebuilds failed blocks from those with the lowest redundancy and strategically selects blocks to read for repairing lost data. We modeled the dynamic change of amount of storage at each redundancy level caused by multiple drive failures, and performed reliability analysis with Monte Carlo simulation using realistic drive failure characteristics. We showed a failure impact model and a method for localizing the failure. When stripes with redundancy level 3 were sufficiently distributed and rebuilt by Dynamic Refuging, the proposed technique turned out to scale well, and the probability of data loss decreased by two orders of magnitude for systems with a thousand drives compared to normal RAID. The appropriate setting of a stripe distribution level could localize the failure.
Probabilistic Shaping for High-Speed Unamplified IM/DD Systems With an O-Band EML (2023)

Probabilistic constellation shaping has been used in long-haul optically amplified coherent systems for its capability to approach the Shannon limit and realize fine rate granularity. The availability of high-bandwidth optical-electronic components and the previously mentioned advantages have invigorated researchers to explore probabilistic shaping (PS) in intensity-modulation and direct-detection (IM/DD) systems. This article presents an extensive comparison of uniform 8-ary pulse amplitude modulation (PAM) with PS PAM-8 using cap and cup Maxwell-Boltzmann (MB) distributions as well as MB distributions of different Gaussian orders. We report that in the presence of linear equalization, PS-PAM-8 outperforms uniform PAM-8 in terms of bit error ratio, achievable information rate and operational net bit rate indicating that cap-shaped PS-PAM-8 shows high tolerance against nonlinearities. In this paper, we have focused our investigations on O-band electro-absorption modulated laser unamplified IM/DD systems, which are operated close to the zero dispersion wavelength.
Supplementary Figure S12 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer (2023)

&lt;p&gt;Analyses of Tregs and macrophage scores in clinical datasets with respect to SHP2 phosphorylation.&lt;/p&gt;
Understanding the vibrational mode-specific polarization effects in femtosecond Raman-induced Kerr-effect spectroscopy (2016)

Optically heterodyne-detected femtosecond Raman-induced Kerr-effect spectroscopy (OHD-FRIKES) was observed in neat cyclohexane. In this Letter, an examination of the effect of the Raman pump ellipticity on the multiplex OHD-FRIKES spectra is discussed. The Raman pump ellipticity scanned OHD-FRIKES results reproduce anomalous observables from previous OHD-FRIKES experiments and suggest new methods of tracking transient vibrational mode polarization in complex systems.
A Generative Word Embedding Model and its Low Rank Positive Semidefinite Solution (2015)

Most existing word embedding methods can be categorized into Neural Embedding Models and Matrix Factorization (MF)-based methods. However some models are opaque to probabilistic interpretation, and MF-based methods, typically solved using Singular Value Decomposition (SVD), may incur loss of corpus information. In addition, it is desirable to incorporate global latent factors, such as topics, sentiments or writing styles, into the word embedding model. Since generative models provide a principled way to incorporate latent factors, we propose a generative word embedding model, which is easy to interpret, and can serve as a basis of more sophisticated latent factor models. The model inference reduces to a low rank weighted positive semidefinite approximation problem. Its optimization is approached by eigendecomposition on a submatrix, followed by online blockwise regression, which is scalable and avoids the information loss in SVD. In experiments on 7 common benchmark datasets, our vectors are competitive to word2vec, and better than other MF-based methods.
Wavelets for a vision (1996)

Early on, computer vision researchers have realized that multiscale transforms are important to analyze the information content of images. The wavelet theory gives a stable mathematical foundation to understand the properties of such multiscale algorithms. This tutorial describes major applications to multiresolution search, multiscale edge detection, and texture discrimination.
AFM Force−Distance Curve Methods for Measuring the Kinetics of Silicon Chemical Etching and Reactions between Silylating Agents and a Silicon Surface (1999)

Atomic force microscopy (AFM) was used to probe the kinetics of several chemical reactions on different silicon surfaces via the force−distance curve technique in air. The reactions included formation and subsequent oxidative aging of porous luminescent silicon. The kinetics of the reactions of silylating agents with various silicon surfaces can also be followed. The use of functionalized AFM tips for such measurements is discussed. This simple method can be used to monitor certain reactions on surfaces that cannot be readily analyzed by traditional spectroscopic techniques.
Antithrombotic Activity of a Lumbrokinase Immobilized Polyurethane Surface (1993)

Six fractions of strong and novel fibrinolytic enzymes (lumbrokinase, LK) were extracted from the earthworm Lumbri-cus rubellus. The enzymes in these fractions appeared to be very stable and showed greater antithrombotic activity than other currently used antithrombotics. The authors immobilized an LK fraction that shows the most potent fibrinolytic activity on a polyurethane (PU) surface to investigate its enzymatic and antithrombotic activity. The methanol extracted PU surface was treated with a 3% (wt/vol) maleic anhydride methylvinyl ether copolymer (MAMEC) solution and finally incubated in an LK solution in PBS (pH 7.4). The immobilized LK activity was estimated by the fibrin plate method and caseinolytic activity assay. The antithrombotic activity was evaluated by in vitro 125l-fibrinogen adsorption in fresh whole blood and 99mTc platelet adhesion tests. In addition, the occlusion time was determined through ex vivo rabbit A-A shunt experiments. The content and unit activity of immobilized LK were found to be 24 jig/cm2 and 18 IU/cm2' respectively. The relative activity ratio of immobilized LK to soluble LK was found to be approximately 34%. Immobilized LK was stable within a various pH range and resistant to inhibitors and thermal inactivation. Less fi-brinogen was adsorbed and fewer platelets adhered on an LK-immobilized surface than on PU and PU-MAMEC controls. The ex vivo occlusion time of untreated PU and PU-MAMEC surfaces were only 32 and 42 minutes, respectively. But that of LK-immobilized PU was extended to 140 minutes. These results suggest that the immobilized LK on PU surface decreases fibrinogen adsorption by digesting the adsorbed fibrinogen, and inhibits platelet adhesion/aggregation to the artificial surface as well, indicating that an LK-immobilized surface is highly antithrombogenic.
ChemInform Abstract: General Approach for the Synthesis of Sarpagine/Macroline Indole Alkaloids. Enantiospecific Total Synthesis of the Indole Alkaloid Trinervine. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.