gebhart/patrepeval huggingface dataset:
Light‐Powered Electrical Switch Based on Cargo‐Lifting Azobenzene Monolayers (2008)

We have liftoff! Tightly packed self-assembled monolayers (SAMs) of ultrarigid conjugated azobenzenes incorporated into a Hg-based junction undergo reversible photoisomerization (see picture). The current–voltage curves indicate that the junction operates as a current photoswitch as result of the forces expressed by the SAMs, which act as a light-powered cargo lifter. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z705339_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Compilation of the Dielectric Properties of Body Tissues at RF and Microwave Frequencies. (1996)

Abstract : Knowledge of the dielectric properties of biological materials is of importance in solving electromagnetic interaction problems. There is, as yet, no consensus on such data among scientists dealing with these issues. This project is geared towards producing a database of dielectric data based on measurements using recently developed techniques. This has been achieved through measurement over a wide frequency range. The new data were evaluated by comparison with corresponding data from the literature where available. To facilitate the incorporation of the dielectric data in numerical solutions, their frequency dependence was modelled to a spectrum characterised by 4 dispersion regions. The conductivity of tissues below 100 Hz was estimated from the recent measurements mitigated by data from the literature and used to estimate the body and of various body parts.
Increased Target Specificity of Anti-HER2 Genospheres by Modification of Surface Charge and Degree of PEGylation (2006)

Genospheres are cationic lipid-nucleic acid nanoparticles prepared by the assembly of the lipids and nucleic acids from an aqueous/organic liquid monophase that independently dissolves the components, where the resultant particles are homogeneously sized (70-110 nm), with efficiently incorporated and protected DNA. In the present study, we demonstrate pH-dependent modulation of the Genosphere surface charge using pH-titratable lipids. By incorporation of the lipids with titratable anionic or imidazole headgroups, Genospheres with neutral or anionic surface charge at neutral pH were produced and compared for cellular uptake and transfection of a reporter gene (luciferase) in culture of breast cancer cells. The extent of particle-cell association was also studied by fluorescent microscopy and quantified by cytofluorometery. The effects of Genosphere surface modification with poly(ethylene glycol) (molecular weight 2000) at low (0.5 mol %) and high (5 mol %) grafting densities, as well as the effects of HER2-receptor-directed targeting by an internalizable anti-HER2 scFv F5, linked via PEG spacer, were also studied. Inclusion in the Genosphere formulation of pH-titratable lipids CHEMS (cholesteryl hemisuccinate), CHIM (1-(3-(cholesteryloxycarbonylamino)propyl)imidazole), or DSGG (1,2-distearoyl-sn-glycero-3-hemiglutarate) rendered the particles surface-charge neutral or slightly anionic at neutral pH, and cationic at mildly acidic pH, as shown by zeta-potential measurements. In HER2-targeted systems, transfection activity and target specificity with HER2-overexpressing SKBR-3 breast cancer cells were dependent on Genosphere surface charge and PEGylation. The highest target specificity correlated with low cationic charge at neutral pH, while incorporation of 5 mol % PEG-lipid had only minor effects on Genosphere-cell association, internalization, and transfection activity. The implications of this work for potential in vivo applications are discussed.
Calcineurin Inhibitor–Free CD28 Blockade-Based Protocol Protects Allogeneic Islets in Nonhuman Primates (2002)

Recent success using a steroid-free immunosuppressive regimen has renewed enthusiasm for the use of islet transplantation to treat diabetes. Toxicities associated with the continued use of a calcineurin inhibitor may limit the wide-spread application of this therapy. Biological agents that block key T-cell costimulatory signals, in particular the CD28 pathway, have demonstrated extraordinary promise in animal models. LEA29Y (BMS-224818), a mutant CTLA4-Ig molecule with increased binding activity, was evaluated for its potential to replace tacrolimus and protect allogeneic islets in a preclinical primate model. Animals received either the base immunosuppression regimen (rapamycin and anti-IL-2R monoclonal antibody [mAb]) or the base immunosuppression and LEA29Y. Animals receiving the LEA29Y/rapamycin/anti-IL-2R regimen (n = 5) had significantly prolonged islet allograft survival (204, 190, 216, 56, and >220 days). In contrast, those animals receiving the base regimen alone (n = 2) quickly rejected the transplanted islets at 1 week (both at 7 days). The LEA29Y-based regimen prevented the priming of anti-donor T- and B-cell responses, as detected by interferon-gamma enzyme-linked immunospot and allo-antibody production, respectively. The results of this study suggest that LEA29Y is a potent immunosuppressant that can effectively prevent rejection in a steroid-free immunosuppressive protocol and produce marked prolongation of islet allograft survival in a preclinical model.
A digital library system for periodicals distribution (2002)

As part of IBM's Digital Library Initiative, IBM's Almaden Research Center has teamed with the Institute for Scientific Information in a joint project to deliver on-line access to the bibliographic information and abstracts from the scientific journal articles indexed in Current Contents/Life Sciences as well as articles offered by the respective publishers. This requires both adaptation of existing technologies and development of new capabilities, especially regarding copyright protection. Since the Fall of 1995, a pilot system has been installed at four universities, two corporate libraries, and a major public research library, beginning a study that involves many publishers, libraries, and users to test the system and to experiment with new economic models. This article describes some requirements we identified for this system, and the solutions we have devised for these requirements.
Transmission of longitudinal optical phonons through a barrier in uniaxial crystals (2002)

Transmission of longitudinal optical (LO) phonons in double heterostructures with uniaxial anisotropy is investigated within a dielectric continuum model. When LO-like phonons are generated in the left semi-infinite layer, their transmission probability through a barrier to the right semi-infinite layer is calculated. ${\mathrm{In}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}\mathrm{N}/\mathrm{GaN}/{\mathrm{In}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}\mathrm{N}$ and $\mathrm{GaN}/{\mathrm{Al}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}\mathrm{N}/\mathrm{GaN}$ systems are considered for numerical calculations. In contrast to the isotropic case, where there is no transmission, it is shown that the propagation probability could be significant with only about 1% anisotropy. The propagation probability of phonons is found to increase with increasing wavelength of the LO-like phonon for a given barrier width.
Production of high levels of 8:0 and 10:0 fatty acids in transgenic canola by overexpression of Ch FatB2, a thioesterase cDNA from Cuphea hookeriana (1996)

The Mexican shrub Cuphea hookeriana accumulates up to 75% caprylate (8:0) and caprate (10:0) in its seed oil. An acyl-ACP thioesterase cDNA from C. hookeriana, designated Ch FatB2, has been identified, which, when expressed in Escherichia coli, provides thioesterase activity specific for 8:0- and 10:0-ACP substrates. Expression of this clone in seeds of transgenic canola, an oilseed crop that normally does not accumulate any 8:0 and 10:0, resulted in a dramatic increase in the levels of these two fatty acids accompanied by a preferential decrease in the levels of linoleate (18:2) and linolenate (18:3). The Ch FatB2 differs from Ch FatB1, another Cuphea hookeriana thioesterase reported recently, in both substrate specificity and expression pattern. The Ch FatB1 has a broad substrate specificity with strong preference for 16:0-ACP and is expressed throughout the plant; whereas Ch FatB2 is specific for 8:0/10:0-ACP and its expression is confined to the seed. It is proposed that the amplified expression of Ch FatB2 in the embryo provides the hydrolytic enzyme specificity determining the fatty acyl composition of Cuphea hookeriana seed oil.
Effect of physical activity on glutamine metabolism (2009)

After exercise, a reduced glutamine availability may be considered as a marker of overtraining. An increased glutamine availability may contribute to decreased inflammation and health benefits associated with optimal training. Thus, glutamine supplementation may enhance immunocompetence after strenuous exercise. The potential of glutamine supplementation during physical inactivity needs to be explored.
Deep Pyramidal Residual Networks (2016)

Deep convolutional neural networks (DCNNs) have shown remarkable performance in image classification tasks in recent years. Generally, deep neural network architectures are stacks consisting of a large number of convolutional layers, and they perform downsampling along the spatial dimension via pooling to reduce memory usage. Concurrently, the feature map dimension (i.e., the number of channels) is sharply increased at downsampling locations, which is essential to ensure effective performance because it increases the diversity of high-level attributes. This also applies to residual networks and is very closely related to their performance. In this research, instead of sharply increasing the feature map dimension at units that perform downsampling, we gradually increase the feature map dimension at all units to involve as many locations as possible. This design, which is discussed in depth together with our new insights, has proven to be an effective means of improving generalization ability. Furthermore, we propose a novel residual unit capable of further improving the classification accuracy with our new network architecture. Experiments on benchmark CIFAR-10, CIFAR-100, and ImageNet datasets have shown that our network architecture has superior generalization ability compared to the original residual networks. Code is available at https://github.com/jhkim89/PyramidNet}
Molecular Wiring of Insulators:  Charging and Discharging Electrode Materials for High-Energy Lithium-Ion Batteries by Molecular Charge Transport Layers (2007)

Self-assembled monolayers (SAMs) of redox-active molecules on mesoscopic substrates exhibit two-dimensional conductivity if their surface coverage exceeds the percolation threshold. Here, we show for the first time that such molecular charge transport layers can be employed to electrochemically address insulating battery materials. The widely used olivine-structured LiFePO4 was derivatized with a monolayer of 4-[bis(4-methoxyphenyl)amino]benzylphosphonic acid (BMABP) in this study. Fast cross-surface hole percolation was coupled to interfacial charge injection, affording charging and discharging of the cathode material. These findings offer the prospect to greatly reduce the amount of conductive carbon additives necessary to electrochemically address present metal phosphate cathode materials, opening up the possibility for a much improved energy storage density. When compared at equal loading, the rate capability is also enhanced with respect to conventional carbon-based conductive additives.
Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. (2002)

We have identified two synthetic oligonucleotides (aptamers) that bind to prostate cancer cells,with low nanomolar affinity, via the extracellular portion of the prostate-specificmembrane antigen (PSMA). These two specific aptamers were selected from an initial 40mer library of approximately 6 x 10(14) random-sequence RNA molecules for their ability to bind to a recombinant protein representing the extracellular 706 amino acids of PSMA, termed xPSM. Six rounds of in vitro selection were performed, enriching for xPSM binding as monitored by aptamer inhibition of xPSM N-acetyl-alpha-linked acid dipeptidase (NAALADase) enzymatic activity. By round six, 95% of the aptamer pool consisted of just two sequences. These two aptamers, termed xPSM-A9 and xPSM-A10, were cloned and found to be unique, sharing no consensus sequences. The affinity of each aptamer for PSMA was quantitated by its ability to inhibit NAALADase activity. Aptamer xPSM-A9 inhibits PSMA noncompetitively with an average K(i) of 2.1 nM, whereas aptamer xPSM-A10 inhibits competitively with an average K(i) of 11.9 nM. Distinct modes of inhibition suggest that each aptamer identifies a unique extracellular epitope of xPSM. One aptamer was truncated from 23.4 kDa to 18.5 kDa and specifically binds LNCaP human prostate cancer cells expressing PSMA but not PSMA-devoid PC-3 human prostate cancer cells. These are the first reported RNA aptamers selected to bind a tumor-associated membrane antigen and the first application of RNA aptamers to a prostate specific cell marker. These aptamers may be used clinically as NAALADase inhibitors or be modified to carry imaging agents and therapeutic agents directed to prostate cancer cells.
AMP-Activated Protein Kinase Activation by Adrenoceptors in L6 Skeletal Muscle Cells (2006)

AMP-activated protein kinase (AMPK), which functions as a sensor of cellular energy homeostasis, was phosphorylated after norepinephrine stimulation in L6 skeletal muscle cells. This effect was mediated by alpha1-adrenoceptors, with no stimulatory effects due to interactions at alpha2- or beta-adrenoceptors. Alpha1-adrenoceptors are Gq-coupled receptors, and calcium but not phorbol esters could mimic the effect of alpha1-adrenergic stimulation; and we show that protein kinase C is not involved as an upstream signal to AMPK by alpha1-adrenergic stimulation and that the AMP-to-ATP ratio is unaltered after alpha1-adrenergic stimulation. We further show that glucose uptake mediated by alpha1- but not by beta-adrenoceptors can be inhibited by AMPK inhibition. Acetyl-CoA carboxylase (ACC) is phosphorylated at Ser218 by AMPK, and alpha1- but not beta-adrenoceptor stimulation results in phosphorylation of ACC at this residue. These results suggest a novel pathway where alpha1-adrenoceptor activation, independent of protein kinase C, leads to activation of AMPK in skeletal muscle, which contributes to alpha1-adrenoceptor-mediated increases in glucose uptake.
Microfluidic Platforms for Single-Cell Analysis (2010)

Microfluidics, the study and control of the fluidic behavior in microstructures, has emerged as an important enabling tool for single-cell chemical analysis. The complex procedures for chemical cytometry experiments can be integrated into a single microfabricated device. The capability of handling a volume of liquid as small as picoliters can be utilized to manipulate cells, perform controlled cell lysis and chemical reactions, and efficiently minimize sample dilution after lysis. The separation modalities such as chromatography and electrophoresis within microchannels are incorporated to analyze various types of intracellular components quantitatively. The microfluidic approach offers a rapid, accurate, and cost-effective tool for single-cell biology. We present an overview of the recent developments in microfluidic technology for chemical-content analysis of individual cells.
Strategies for enhancing bioluminescent bacterial sensor performance by promoter region manipulation (2010)

Genetically engineered microbial reporter strains are based upon the fusion of an inducible sensing element upstream of a reporting element, so that the construct emits a dose-dependent signal when exposed to the inducing compound(s) or stress factor(s). In this communication we described several general approaches undertaken in order to enhance the sensing performance of such promoter::reporter fusions. Significant improvements in detection sensitivity, response kinetics and signal intensity were achieved by modification of the length of the promoter-containing DNA fragment, by random or site-directed mutagenesis and by promoter duplication. The general nature of these genetics manipulations makes them applicable to other types of promoter::reporter fusions.
Safety and efficacy of delayed intraarterial urokinase therapy with mechanical clot disruption for thromboembolic stroke. (1994)

Intraarterial cerebral thrombolysis with mechanical disruption of clot seems to be a useful therapy in selected stroke cases even after 6 hours.
Hypoxia Increases Heparanase-Dependent Tumor Cell Invasion, Which Can Be Inhibited by Antiheparanase Antibodies (2004)

The beta-endoglucuronidase heparanase plays an important role in tumor invasion, a process that is significantly enhanced by hypoxia. We have used a strategy of stable transfection with antisense to derive ovarian carcinoma cell lines that express different levels of heparanase and used these to demonstrate that invasion correlates with heparanase activity. Secreted heparanase activity was increased by reduction, hypoxia, and growth of cells under reduced oxygen (1%) augmented heparanase activity and invasion, both of which are inhibited by treatment with antiheparanase antibodies. This is the first demonstration that heparanase activity may be regulated by microenvironmental redox conditions, which influence invasion, and that invasion can be blocked with specific heparanase-neutralizing antibodies.
Feature-based retrieval of similar shapes (2002)

A shape similarity-based retrieval method for image databases that supports a variety of queries is proposed. It is flexible with respect to the choice of feature and definition of similarity and is implementable using existing multidimensional point access methods. A prototype system that handles the problems of distortion and occlusion is described. Experiments with one specific point access method (PAM) are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Anti‐inflammatory effect of synthetic somatostatin analogues in the rat (2001)

1. Somatostatin (6.11 nmol kg(-1) i.p.) inhibited neurogenic plasma extravasation evoked by 1% mustard oil and non-neurogenic oedema induced by 5% dextran in the rat skin. 2. Cyclic synthetic octapeptide (TT-248 and TT-250) and heptapeptide (TT-232) somatostatin analogues proved to be more effective in reducing neurogenic and non-neurogenic inflammatory reactions but octreotide had no influence on either neurogenic or non-neurogenic inflammation. 3. TT-232 administered i.p. or i.v. (1.06 - 42.40 nmol kg(-1)) inhibited in a dose-dependent manner the plasma extravasation evoked by mustard oil in the rat's paw. Neither diclofenac (15.78 - 315.60 micromol kg(-1)) nor the selective COX-2 inhibitor meloxicam (2.95 - 569.38 micromol kg(-1)) attenuated the mustard oil-induced neurogenic plasma extravasation. 4. TT-232, diclofenac and meloxicam dose-dependently diminished non-neurogenic dextran-oedema of the paw the ED(35) values were 1.73 nmol kg(-1) for TT-232 and 34.37 micromol kg(-1) for diclofenac. 5. TT-232 inhibited in the dose range of 1.06 - 21.21 nmol kg(-1) the bradykinin-induced plasma extravasation in the skin of the chronically denervated paw. 6. Mustard oil-induced cutaneous plasma extravasation was dose-dependently diminished by s.c. TT-232 1, 2, 4, 6 or 16 h after the treatment. TT-232 (2 x 106, 2 x 212 and 2 x 530 nmol kg(-1) per day s.c. for 18 days) caused dose-dependent inhibition of chronic Freund adjuvant-induced arthritis during the experimental period. 7. TT-232 (200 and 500 nM) inhibited the release of SP, CGRP and somatostatin from the rat isolated trachea induced by electrical field stimulation (40 V, 0.1 ms, 10 Hz, 120 s) or by capsaicin (10(-7) M), but did not influence the basal, non-stimulated peptide release. 8. It is concluded that somatostatin analogues without endocrine functions as TT-232 are promising compounds with a novel site of action for inhibition of non-neurogenic and neurogenic inflammatory processes.
Restriction Enzyme-Mediated Integration Used to Produce Pathogenicity Mutants of Colletotrichum graminicola (2000)

We have developed a restriction enzyme-mediated insertional mutagenesis (REMI) system for the maize pathogen Colletotrichum graminicola. In this report, we demonstrate the utility of a REMI-based mutagenesis approach to identify novel pathogenicity genes. Use of REMI increased transformation efficiency by as much as 27-fold over transformations with linearized plasmid alone. Ninety-nine transformants were examined by Southern analysis, and 51% contained simple integrations consisting of one copy of the vector integrated at a single site in the genome. All appeared to have a plasmid integration at a unique site. Sequencing across the integration sites of six transformants demonstrated that in all cases the plasmid integration occurred at the corresponding restriction enzyme-recognition site. We used an in vitro bioassay to identify two pathogenicity mutants among 660 transformants. Genomic DNA flanking the plasmid integration sites was used to identify corresponding cosmids in a wild-type genomic library. The pathogenicity of one of the mutants was restored when it was transformed with the cosmids.
Ultrasensitive Label-Free Nanosensing and High-Speed Tracking of Single Proteins (2017)

Label-free detection, analysis, and rapid tracking of nanoparticles is crucial for future ultrasensitive sensing applications, ranging from understanding of biological interactions to the study of size-dependent classical-quantum transitions. Yet optical techniques to distinguish nanoparticles directly among their background remain challenging. Here we present amplified interferometric scattering microscopy (a-iSCAT) as a new all-optical method capable of detecting individual nanoparticles as small as 15 kDa proteins that is equivalent to half a GFP. By balancing scattering and reflection amplitudes the interference contrast of the nanoparticle signal is amplified 1 to 2 orders of magnitude. Beyond high sensitivity, a-iSCAT allows high-speed image acquisition exceeding several hundreds of frames-per-second. We showcase the performance of our approach by detecting single Streptavidin binding events and by tracking single Ferritin proteins at 400 frames-per-second with 12 nm localization precision over seconds. Moreover, due to its extremely simple experimental realization, this advancement finally enables a cheap and routine implementation of label-free all-optical single nanoparticle detection platforms with sensitivity operating at the single protein level.
An Integrated Approach for Improving Cache Behavior (2003)

The widening gap between processor and memory speeds renders data locality optimization a very important issue in data-intensive embedded applications. Throughout the years hardware designers and compiler writers focused on optimizing data cache locality using intelligent cache management mechanisms and program-level transformations, respectively. Until now, there has not been significant research investigating the interaction between these optimizations. In this work, we investigate this interaction and propose a selective hardware/compiler strategy to optimize cache locality for integer, numerical (array-intensive), and mixed codes. In our framework, the role of the compiler is to identify program regions that can be optimized at compile time using loop and data transformations and to mark (at compile-time) the unoptimizable regions with special instructions that activate/deactivate a hardware optimization mechanism selectively at run-time. Our results show that our technique can improve program performance by as much as 60% with respect to the base configuration and 17% with respect to a non-selective hardware/compiler approach.