gebhart/patrepeval huggingface dataset:
Characterization of ICAM-2 and evidence for a third counter-receptor for LFA-1. (1991)

In an endeavor to further characterize human intercellular adhesion molecule-2 (ICAM-2), two murine monoclonal antibodies (mAb) were generated to ICAM-2 transfected COS cells, and designated CBR-IC2/1 and CBR-IC2/2. Immunoprecipitated, reduced ICAM-2 migrated as a broad band of Mr 60,000 in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Treatment with N-glycanase revealed a peptide backbone of Mr 31,000, consistent with the size predicted from the cDNA. ICAM-2 had a broad distribution on hematopoietic cell lines and little expression on other cell lines, the sole exception being cultured endothelial cells which possess high levels of ICAM-2. Resting lymphocytes and monocytes expressed ICAM-2, while neutrophils did not. Staining of tissue sections with anti-ICAM-2 mAb confirmed their strong reactivity to vascular endothelium, but demonstrated a lack of ICAM-2 expression on other tissues. Small clusters of ICAM-2 positive cells were, however, seen in germinal centers. In contrast to ICAM-1 there was little or no induction of ICAM-2 expression on lymphocytes or cultured endothelium upon stimulation with inflammatory mediators. One of the two mAb, CBR-IC2/2, was found to totally inhibit binding of ICAM-2+ COS cells to purified lymphocyte function-associated antigen-1 (LFA-1). Using this mAb, LFA-1-dependent binding to both stimulated and unstimulated endothelium was found to be totally accounted for by ICAM-1 and ICAM-2. Homotypic aggregation of an Epstein-Barr virus-transformed B cell line, JY, was found to be solely ICAM-1 and ICAM-2-dependent, while in the case of the T cell lymphoma cell line, SKW3, anti- ICAM-2 mAb in conjunction with anti-ICAM-1 mAb could not inhibit the LFA-1-dependent aggregation. This suggests an additional LFA-1 ligand exists. Using a cell binding assay to purified LFA-1 in conjunction with anti-ICAM-1 and anti-ICAM-2 mAb, we have demonstrated that this putative third ligand for LFA-1 exists on SKW3 and other cell lines.
Performance evaluation of code-spread OFDM (2008)

When spectral nulls are present in a channel, they can severely degrade or cancel out OFDM tones, resulting in an irreducible error rate. In Code Spread OFDM, each sinewave carries a weighted sum of all the information symbols being transmitted in an OFDM block interval. This creates a more robust modulation scheme which provides substantial performance improvement relative to standard OFDM. In this paper, the MMSE estimator is derived for each symbol for a number of cases, including when the number of carriers is greater than the number of symbols. The performance of both OFDM and CS-OFDM are evaluated with and without error control coding using the FEC techniques typically employed in OFDM standards.
Induction of apoptotic DNA fragmentation and cell death by natural ceramide (1995)

We have found that a solvent mixture of ethanol and dodecane was able to disperse natural ceramide (Cer) into aqueous solution. In U937 cells, addition of natural Cer to medium caused a characteristic pattern of DNA fragmentation, which is indistinguishable from that caused by TNF alpha. The effective concentration of Cer is as low as 25 nM. The present study provides direct evidence that natural Cer functions as a second messenger mediating TNF alpha-induced DNA fragmentation. The use of this solvent to deliver hydrophobic natural Cer to cells will contribute to the elucidation of the biological function of Cer.
Rod phototransduction in retinitis pigmentosa: estimation and interpretation of parameters derived from the rod a-wave. (1994)

The authors reached two conclusions. First, some forms of RP and CRD alter the activation stages of transduction. Transduction appears normal in other patients, despite extensive receptor damage as indicated by markedly reduced RmP3 values. Second, the cone contribution to a blue flash only affects the estimate of the key parameters in patients in whom the rod component is minimal. The cone contribution to a white flash contaminates the fit and the estimate of the parameters in all patients and normal subjects.
Efficient Synthesis of Vitamin E Amines (2009)

Abstract A short and efficient synthesis of all VE amines (‐, ‐, ‐, ‐tocopheramines and ‐tocotrienamines) in enantiopure form is described. These amino analogues of natural vitamin E compounds (‐, ‐, ‐, ‐tocopherols and ‐tocotrienols) can be prepared by Pd‐catalyzed N ‐arylation reactions on the corresponding triflates, synthesized under controlled conditions from the phenols. The benzophenone imine or benzylamine intermediates deliver the VE amines in high yield and purity after deprotection. The compounds prepared are key precursors of VE amides, which are of great interest in the search for new therapeutics with antitumoral activity.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Densely packed 1.1 μ m band vertical cavity surface emitting laser array for co-packaged optics (2022)

Abstract We demonstrated the 1.1 μ m band 16-channel vertical cavity surface emitting laser (VCSEL) array for multi-core fiber (MCF) transmission towards co-packaged optics. Single-mode 16-ch top and bottom emitting VCSEL arrays were fabricated by either 3 inch or 6 inch wafer foundry process. The thermal crosstalk is estimated by wavelength shift. When the distance between adjacent VCSELs is 40 μ m, the total thermal crosstalk is as low as 7 K. Bottom emitting metal-aperture VCSEL array were also fabricated via a full 3 inch wafer process. It shows low resistance and good single mode characteristic with an oxidation aperture of 7 μ m thanks to an intra-cavity metal aperture. A large mode field diameter of 6 μ m enables low coupling loss between bottom VCSEL array and MCF through a GaAs substrate for a flip-chip bonding process.
P04.33 Effects of Tumor Treating Fields (TTFields) on blood brain barrier (BBB) permeability (2018)

Brain tumors, especially glioblastoma multiforme (GBM), the most aggressive primary brain tumor in adults, are difficult to treat, because cerebral microvessels strictly regulate the transfer of substances between blood and brain tissue. Thereby they prevent clinical application of several promising drugs. This limitation in drug transport is due to the blood-brain barrier (BBB), mainly formed by intercellular tight junctions (TJ) between brain capillary endothelial cells. Recently, Tumor Treating Fields (TTFields), alternating electric fields with low intensity and intermediate frequency, have been introduced as a new adjuvant treatment modality for GBM. Here, the effect of TTFields on BBB permeability is investigated. Immortalized murine brain capillary endothelial cells (cerebEND) were grown on coverslips and transwell inserts. Cells were treated with TTFields at a frequency of 100–300 kHz for up to 72 h. Cell morphology was analyzed by immunofluorescence staining of the TJ proteins Claudin 5 and ZO-1. BBB integrity was determined by transendothelial resistance (TEER) and BBB permeability by flow cytometry analysis with fluoresceine isothiocyanate (FITC). TTFields application disturbs the BBB by delocalization of tight junction proteins from the cell boundaries to the cytoplasm with most dramatic effects at 100 kHz. The effects appear after 24 h and are most severe after 72 h TTFields treatment. The BBB integrity was significantly reduced by 65% and the BBB permeability for 4 kDa large molecules was significantly increased upon TTFields application. The cell morphology started to recover 48 h and was completed 96 h after end of TTFields treatment pointing to a reversibility of the TTFields-effect on the BBB. TTFields at a frequency of 100 kHz may potentially permeabilize the BBB. Thereby, TTFields could be utilized to deliver drugs usually unable to cross the BBB to the central nervous system. The presented in vitro data will be verified in an in vivo setting and hopefully may lead to a phase I clinical trial and clinical application in the future.
Trace Theory for Automatic Hierarchical Verification of Speed-Independent Circuits (1989)

Speed-independent circuits offer a potential solution to the timing problems of VLSI. In this book David Dill develops and implements a theory for practical automatic verification of these control circuits. He describes a formal model of circuit operation, defines the proper relationship between an implementation and its specification, and constructs a computer program that can check this relationship. Asynchronous or speed-independent circuit design has gained renewed interest in the VLSI community because of the possibilities it provides for dealing with problems that arise with the increasing complexity of VLSI circuits. Speed-independent circuits offer a way around such phenomena as clock skew, which can be a serious obstacle in the design of large systems. They can expedite circuit design by reducing design time and simplifying the overall process. A major challenge to the successful utilization of speed-independent circuits is correctness. The verification method described here insures that a design is correct and because it can be automated it is a significant advantage over manual verification. Dill proposes two distinct theories - prefix-closed trace structures, which can model and specify safety properties, and complete trace structures, which can also deal with liveness and fairness properties. Trace Theory for Automatic Hierarchical Verification of Speed Independent Circuits is a 1988 ACM Distinguished Dissertation
1-(2,5-Dimethoxy-4-(trifluoromethyl)phenyl)-2-aminopropane: A Potent Serotonin 5-HT2A/2C Agonist (1994)

A method was found to synthesize 1-(2,5-dimethoxy-4-(trifluoromethyl) phenyl)-2-aminopropane, 5, and its des-alpha-methyl congener 2-(2,5-dimethoxy-4-(trifluoromethyl)phenyl)aminoethane, 6, the trifluoromethyl analogs of substituted hallucinogenic phenethylamine derivatives such as 1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane (3, DOI) that are potent 5-HT2A/2C agonists. In our hands, 5 and 6 have proven to have affinity for [3H]ketanserin or [125I]-3-labeled 5-HT2A/2C sites in rat cortex comparable to or higher than the analogous bromo or iodo analogs. Similarly, 5 and 6 had potency comparable to or slightly greater than that of their bromo or iodo congeners in the two-lever drug discrimination assay in rats trained to discriminate saline from LSD tartrate. The agonist properties of 5 and 6 were evaluated by measuring the accumulation of [3H]inositol monophosphate in cultured cells selectively expressing either 5-HT2A or 5-HT2C receptors. In comparison to serotonin (5-HT), compounds 3 (DOI), 5, and 6 were equally efficacious and full agonists at the 5-HT2C receptor. Similarly, 3 and 5 produced equivalent responses at the 5-HT2A receptor as compared to 5-HT. In contrast, 6, the alpha-desmethyl analog of 5, was only half as potent at stimulating inositol monophosphate accumulation at the 5-HT2A receptor. In conclusion, the title compound 5 and its alpha-desmethyl congener 6 appear to be the most potent of the so-called hallucinogenic amphetamine 5-HT agonists reported to date. Further, the reduced efficacy of 6 at the 5-HT2A receptor may offer at least a partial explanation for the observed higher in vivo potencies of alpha-methyl-substituted compounds in this series.
Integrated optics and new wave phenomena in optical waveguides (1977)

Research in integrated optics has two goals: One is to apply thin-film technology to the formation of optical devices and circuits. The other is the integration of a large number of optical devices on a small substrate, so forming an optical circuit reminiscent of the integrated circuit in microelectronics. The result is a new breed of optical devices in the form of miniature optical waveguides. They include lasers, modulators, switches, detectors, prisms, lenses, and polarizers, and many of them have efficiencies better than their bulk counterparts. Simple integrated optical circuits have also been constructed, and rapidly advancing semiconductor technology indicates that monolithic integrated optical circuits can readily be developed using GaAs-related compounds. In this paper, we review the state-of-the-art of integrated optics and explore new wave phenomena in optical circuits. The specific topics to be discussed are: light-wave couplers and $m$-line spectroscopy, refraction and reflection of light in thin films, normal modes of the uniform, the graded and the metal-clad waveguides, optics in tapered films, theory of corrugated waveguides, and more importantly, physics of various thin-film optical devices and the method of the circuit formation.
REDUCTION OF OXIMES WITH HYDROSILANE/H+ REAGENT (1986)

Abstract Hydrosilane/H+ reagent reduced oximes in good yields. Stereospecific reduction of (2-acetoxy-1-phenylpropylidene)benzyloxyazane (3) was observed: the (E)-isomer gave erythro-1-phenyl-1-benzyloxyamino-2-propanol (4) in 99% selectivity, whereas (Z)-3 afforded the threo isomer of 4 in 76% selectivity.
<title>Development of 1-3 ceramic-air composite transducers (Invited Paper)</title> (1992)

Over the past eight years, 1 - 3 ceramic-polymer composites have come into widespread use as the piezoelectric material in many ultrasonic transducer arrays used for medical imaging. The success of these materials for this application is a result of three major advantages which the composites enjoy over piezoelectric ceramics alone. These are, increased thickness mode coupling, reduced acoustic impedance, and reduced lateral coupling. These three parameters can not all be optimized simultaneously. The engineering trade-offs in the composite design can be avoided if the polymer material is replaced with air. This paper discusses the nature of the trade-offs in the ceramic-polymer material and shows how the use of ceramic-air (air kerf) avoids these limitations. Requirements for good performance in ceramic-air composites are presented and experimental results for a transducer made from a ceramic-air composite are shown. The potential for improvements and the probable limitations for transducers made from air-ceramic composites are discussed.
Magnetic self-bias in the barber pole MR structure (1977)

The Barber Pole structure is shown to have a magnetic bias field produced by the sense current in the shorting bars. This introduces an asymmetry in the magnetic response and aligns the domains in the magnetoresistive sensor.
The return of private property: rural life after agrarian reform in the Republic of Azerbaijan (2012)

The return of private property: rural life after agrarian reform in the Republic of Azerbaijan, by Lale Yalcin-Heckmann, Berlin, Lit Verlag, 2010, £29.95, ISBN 978-3-643-10629-2 In this book the au...
Stability of Peptide-Condensed Plasmid DNA Formulations (1998)

Low molecular weight homogeneous peptides were used to form peptide/DNA condensates. A peptide possessing 18 lysines was found to protect plasmid DNA from serum endonuclease and sonicative-induced degradation whereas a shorter peptide possessing 8 lysines dissociated in 0.1 M sodium chloride and failed to protect DNA from enzymatic degradation. Peptide-condensed DNA showed no change in the ratio of supercoiled to circular DNA following 100 W sonication for up to 60 s and was able to transfect HepG2 cells with equivalent efficiency as untreated condensed plasmid DNA. Alternatively, uncondensed plasmid DNA was rapidly fragmented by sonication and serum endonucleases and resulted in negligible gene expression following condensation with peptide. Cationic lipid/DNA complexes were only partially effective at stabilizing DNA in serum compared to the complete stabilization afforded by peptide/DNA condensation. These results indicate that the stabilization afforded by condensation with a peptide protects DNA during formulation and preserves its structure in serum. These functions are important to achieve optimal gene expression from a nonviral gene delivery system.
A chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with recruitment of actin (2004)

The obligate intracellular bacterium Chlamydia trachomatis rapidly induces its own entry into host cells. Initial attachment is mediated by electrostatic interactions to heparan sulfate moieties on the host cell, followed by irreversible binding to an unknown secondary receptor. This secondary binding leads to the recruitment of actin to the site of attachment, formation of an actin-rich, pedestal-like structure, and finally internalization of the bacteria. How chlamydiae induce this process is unknown. We have identified a high-molecular-mass tyrosine-phosphorylated protein that is rapidly phosphorylated on attachment to the host cell. Immunoelectron microscopy studies revealed that this tyrosine-phosphorylated protein is localized to the cytoplasmic face of the plasma membrane at the site of attachment of surface-associated chlamydiae. The phosphoprotein was isolated by immunoprecipitation with the antiphosphotyrosine antibody 4G10 and identified as the chlamydial protein CT456, a hypothetical protein with unknown function. The chlamydial protein (Tarp) appears to be translocated into the host cell by type III secretion because it is exported in a Yersinia heterologous expression assay. Phosphotyrosine signaling across the plasma membrane preceded the recruitment of actin to the site of chlamydial attachment and may represent the initial signal transduced from pathogen to the host cell. These results suggest that C. trachomatis internalization is mediated by a chlamydial type III-secreted effector protein.
Reactor Design Issues for Synthesis‐Gas Fermentations (1999)

Synthesis gas is readily obtained by gasifying coal, oil, biomass, or waste organics and represents an abundant, potentially inexpensive, feedstock for bioprocessing. The primary components of synthesis gas, carbon monoxide and hydrogen, can be converted into methane, organic acids, and alcohols via anaerobic fermentations. Bioconversion of synthesis gas is an attractive alternative to catalytic processing because the biological catalysts are highly specific and often more tolerant of sulfur contaminants than inorganic catalysts. However, because the aqueous solubilities of carbon monoxide and hydrogen are low, synthesis-gas fermentations are typically limited by the rate of gas-to-liquid mass transfer. Consequently, a major engineering challenge in commercial development of synthesis-gas fermentations is to provide sufficient gas mass transfer in an energy-efficient manner. This paper reviews recent progress in the development of synthesis-gas fermentations, with emphasis on efforts to increase the efficiency of gas mass transfer. Metabolic properties of several microbes able to ferment synthesis gas are described. Results of synthesis-gas fermentations conducted in various bioreactor configurations are summarized. Recent results showing enhancement of synthesis-gas fermentations using microbubble dispersions are presented, and studies of the mass-transfer and coalescence properties of microbubbles are described.
Improving Calibration in Mixup-trained Deep Neural Networks through Confidence-Based Loss Functions. (2020)

Deep Neural Networks (DNN) represent the state of the art in many tasks. However, due to their overparameterization, their generalization capabilities are in doubt and are still under study. Consequently, DNN can overfit and assign overconfident predictions, as they tend to learn highly oscillating decision thresholds. This has been shown to affect the calibration of the confidences assigned to unseen data. Data Augmentation (DA) strategies have been proposed to overcome some of these limitations. One of the most popular is Mixup, which has shown a great ability to improve the accuracy of these models. Recent work has provided evidence that Mixup also improves the uncertainty quantification and calibration of DNN. In this work, we argue and provide empirical evidence that, due to its fundamentals, Mixup does not necessarily improve calibration. Based on our observations we propose a new loss function that improves the calibration, and also sometimes the accuracy. Our loss is inspired by Bayes decision theory and introduces a new training framework for designing losses for probabilistic modelling. We provide state-of-the-art accuracy with consistent improvements in calibration performance.
In vivo measurement of fatty acids and cholesterol synthesis using D2O and mass isotopomer analysis (1994)

The synthesis of palmitate, stearate, and cholesterol in liver and nervous tissues (brain, cord, and nerve) of Sprague-Dawley rats was determined using deuterated water (D2O) and mass isotopomer analysis. Rats were given 4% deuterium in their drinking water after each receiving an intraperitoneal priming dose. Animals were killed at 1, 2, 4, and 8 wk for deuterium enrichment in body water and determination of mass isotopomer distribution in lipids from various tissues. In 1 wk, the enrichment in the body water reached a plateau of 2.6%, which is 65% of that in the drinking water. We observed the maximum incorporation number (N) in all lipids to be higher than those previously observed, being 22, 24, and 30 for liver palmitate, stearate, and cholesterol, respectively, and N may vary among tissues. Using a single exponential model, we found the half-time (t1/2) and the plateau levels of the newly synthesized lipids of the nervous tissues (t1/2 values ranging from 5 to 28 days) to be different from those of the liver (t1/2 values < or = 4 days) in this relatively long-term study. Mass isotopomer distribution analysis and D2O can be used not only to quantitate the replacement rate of many lipids in various compartments but may also be used to elucidate the tissue-specific synthetic pathways from N.
Deconvolution methods for 3-D fluorescence microscopy images (2006)

This paper presents an overview of various deconvolution techniques of 3D fluorescence microscopy images. It describes the subject of image deconvolution for 3D fluorescence microscopy images and provides an overview of the distortion issues in different areas. The paper presents a brief schematic description of fluorescence microscope systems and provides a summary of the microscope point-spread function (PSF), which often creates the most severe distortion in the acquired 3D image. Finally, it discusses the ongoing research work in the area and provides a brief review of performance measures of 3D deconvolution microscopy techniques. It also provides a summary of the numerical results using simulated data and presents the results obtained from the real data.