gebhart/patrepeval huggingface dataset:
Surface plasmon polaritons on thin-slab metal gratings (2003)

In a recently published paper [U. Schr\"oter and D. Heitmann, Phys. Rev. B 60, 4992 (1999)] an unexpected result occurred when light was incident upon a periodically corrugated thin metal film when the corrugations on the two interfaces were identical and in phase with each other. It was observed that it was not possible to excite the surface plasmon polariton on the metal surface facing away from the incoming light, and they ascribed this to the lack of a thickness variation within the metal. In this paper a somewhat different interpretation of their results is presented, which shows that the surface plasmon polariton (SSP) is in fact very weakly excited on the transmission side of such structures. It is explained why this coupling is so weak in terms of the cancellation of the evanescent diffracted orders from the two diffractive surfaces and how, by changing the phase between the grating on either surface, this coupling becomes much stronger. An explanation for the observation that SPP excitation on such structures may lead to either transmission maxima or minima is also presented.
Pt@UiO-66 Heterostructures for Highly Selective Detection of Hydrogen Peroxide with an Extended Linear Range (2015)

In this study, a good core-shell heterostructure of Pt NPs@UiO-66 was fabricated by encapsulating presynthesized platinum nanoparticles (Pt NPs) into the host matrix of UiO-66 which possesses the slender triangular windows with a diameter of 6 Å. The transmission electron microscopy images exhibited that the number of the encapsulated Pt NPs and the crystalline morphology of as-synthesized core-shell heterostructure samples had a series of changes with increasing the volume of the injected Pt NPs precursor solution. Among these samples, the Pt NPs@UiO-66-2 sample had a good crystalline morphology with several well-dispersed Pt NPs encapsulated in UiO-66 frameworks. But there were no obvious Pt NPs observed in the Pt NPs@UiO-66-1 sample, and for the Pt NPs@UiO-66-3 sample, the number of Pt NPs encapsulated in UiO-66 matrix notably reduced and the metal organic framework (MOF) crystals became small and aggregated. The electrochemical measurements showed that the Pt NPs@UiO-66-2 sample modified glass carbon electrode (GCE) presented a remarkable electrocatalytic activity toward hydrogen peroxide (H2O2) oxidation, including an excellent anti-interference performance even if the concentration of the interference species was the same as the H2O2, an extended linear range from 5 μM to 14.75 mM, a low detection limit, as well as good stability and reproducibility. The results indicate the superiority of MOFs in H2O2 detection. And more importantly, it will provide a new opportunity to promote the anti-interference performance of the nonenzyme electrochemical sensors.
Enzymatic depolymerization of heparin-related polysaccharides. Substrate specificities of mouse mastocytoma and human platelet endo-beta-D-glucuronidases. (1982)

Two endo-beta-D-glucuronidases acting on heparin-related polysaccharides were investigated: a mouse mastocytoma enzyme previously implicated in the postbiosynthetic modification of the heparin proteoglycan and a human platelet-derived enzyme, capable of degrading heparan sulfate as well as heparin (with elimination of anticoagulant activity). The mastocytoma enzyme was found to depolymerize a heparin precursor polysaccharide containing both N- and O-sulfate groups to fragments somewhat smaller in molecular size than commercially available heparin. In contrast, another heparin precursor species, containing N- but no O-sulfate groups was resistant to degradation. Furthermore, incubation of the mastocytoma endoglucuronidase with a heparin octasaccharide having high affinity for antithrombin failed to cleave the beta-glucuronidic linkage in the antithrombin-binding region. Previous studies established that the platelet endoglucuronidase can degrade the exclusively N-sulfated as well as the N- and O-sulfated heparin precursor polysaccharides (Oldberg, A., Heldin, C.-H., Wasteson, A., Busch, C., and Höök, M. (1980) Biochemistry 19, 5755-5762). This enzyme has now been found to attack also the beta-glucuronidic linkage in the antithrombin-binding region of the heparin molecule. The loss of bio-affinity resulting from cleavage of this linkage in the antithrombin-binding heparin octasaccharide was utilized to construct a sensitive, specific, and simple assay method for the platelet endoglucuronidase. It is concluded that the platelet endoglucuronidase has a lower degree of substrate specificity than has the mastocytoma enzyme, in reflection of the surmised functional roles of the two enzymes.
Mucosal adjuvant effect of cholera toxin in mice results from induction of T helper 2 (Th2) cells and IL-4 (1995)

Despite pathophysiologic effects including diarrhea, cholera toxin (CT) is a potent mucosal immunogen and adjuvant. We investigated the influence of CT on T helper (Th)-type 1 (Th1) and Th2 cell-regulated Ag-specific B cell isotype and IgG subclass Ab responses elicited when the toxin was co-administered orally with different protein Ags. When mice were orally immunized with tetanus toxoid (TT) and CT as adjuvant, this regimen induced TT-specific secretory IgA responses in the gastrointestinal tract as well as serum IgG, including IgG1 and IgG2b subclasses, and IgA responses. This oral regimen also induced TT- and CT-B-specific IgE responses. In addition, CT also elicited adjuvant effects for Ag-specific IgG1, IgE, and IgA responses when two other protein Ags, OVA and hen egg white lysozyme, were given by the oral route. Quantitative reverse transcriptase-PCR was performed to assess levels of mRNA for Th1 (IFN-gamma) and Th2 (IL-4) cytokine expression in TT-stimulated CD4+ T cell cultures. Both Peyer's patches and splenic CD4+ T cells expressed markedly increased levels of IL-4-specific message, but did not result in changes in IFN-gamma mRNA expression. To determine whether the route of immunization influenced IgE responses, mice were immunized s.c. with TT and CT as adjuvant. Significant increases in total and TT-specific IgE Abs were induced when CT was co-administered. Taken together, these results show that CT acts as a mucosal adjuvant to enhance Th2-type responses and in particular, the IL-4 produced results in a characteristic Ab isotype pattern associated with this cytokine.
Core candidate neurochemical and imaging biomarkers of Alzheimer's disease (2007)

A number of neuroimaging candidate markers are promising, such as hippocampus and entorhinal cortex volumes, basal forebrain nuclei, cortical thickness, deformation-based and voxel-based morphometry, structural and effective connectivity by using diffusion tensor imaging, tractography, and functional magnetic resonance imaging. CSF Abeta42, BACE1, total tau, and p-tau are substantially altered in MCI and clinical AD. Other interesting novel marker candidates derived from blood are being currently proposed (phase I). Biomarker discovery through proteomic approaches requires further research. Large-scale international controlled multicenter trials (such as the U.S., European, Australian, and Japanese Alzheimer's Disease Neuroimaging Initiative and the German Dementia Network) are engaged in phase III development of the core feasible imaging and CSF biomarker candidates in AD. Biomarkers are in the process of implementation as primary outcome variables into regulatory guideline documents regarding study design and approval for compounds claiming disease modification.
Genetic characterization of the vaccinia virus DNA polymerase: cytosine arabinoside resistance requires a variable lesion conferring phosphonoacetate resistance in conjunction with an invariant mutation localized to the 3'-5' exonuclease domain (1993)

In this report, we describe the isolation, molecular genetic mapping, and phenotypic characterization of vaccinia virus mutants resistant to cytosine arabinoside (araC) and phosphonoacetic acid (PAA). At 37 degrees C, 8 microM araC was found to prevent macroscopic plaque formation by wild-type virus and to cause a 10(4)-fold reduction in viral yield. Mutants resistant to 8 microM araC were selected by serial passage of a chemically mutagenized viral stock in the presence of drug. Because recovery of mutants required that initial passages be performed under less stringent selective conditions, and because plaque-purified isolates were found to be cross-resistant to 200 micrograms of PAA per ml, it seemed likely that resistance to araC required more than one genetic lesion. This hypothesis was confirmed by genetic and physical mapping of the responsible mutations. PAAr was accorded by the acquisition of one of three G-A transitions in the DNA polymerase gene which individually alter cysteine 356 to tyrosine, glycine 372 to aspartic acid, or glycine 380 to serine. AraCr was found to require one of these substitutions plus an additional T-C transition within codon 171 of the DNA polymerase gene, a change which replaces the wild-type phenylalanine with serine. Congenic viral stocks carrying one of the three PAAr lesions, either alone or in conjunction with the upstream araCr lesion, in an otherwise wild-type background were generated. The PAAr mutations conferred nearly complete resistance to PAA, a slight degree of resistance to araC, hypersensitivity to aphidicolin, and decreased spontaneous mutation frequency. Addition of the mutation at codon 171 significantly augmented araC resistance and aphidicolin hypersensitivity but caused no further change in mutation frequency. Several lines of evidence suggest that the PAAr mutations primarily affect the deoxynucleoside triphosphate-binding site, whereas the codon 171 mutation, lying within a conserved motif associated with 3'-5' exonuclease function, is postulated to affect the proofreading exonuclease of the DNA polymerase.
Discovery of Small-Molecule Inhibitors of HCV NS3-4A Protease as Potential Therapeutic Agents against HCV Infection (2005)

Chronic infection with hepatitis C virus (HCV) is associated with liver cirrhosis that often leads to hepatic failure and hepatocellular carcinoma (HCC). HCV infection has become a global health threat and the main cause of adult liver transplants in developed nations. Current approved anti-HCV therapies (interferon and pegylated interferon alone or in combination with ribavirin) are not effective in eliminating the viral infection in a significant population of patients (e.g., those infected with HCV genotype 1). Furthermore, these therapies are plagued with many undesirable side effects. Therefore, the HCV epidemic represents a huge unmet medical need that has triggered intensive research efforts towards the development of more effective drugs. Given its essential role in the process of HCV replication, the viral NS3/4A serine protease is arguably the most thoroughly characterized HCV enzyme and the most intensively pursued anti-HCV target for drug development. This is further fueled by the successful use of small-molecule inhibitors of the human immunodeficiency virus (HIV) viral protease, which have had an impressive effect on HIV-related morbidity and mortality, offering hope that analogous drugs might also have a similar impact against HCV. Here, we review the recent progress and development of small-molecule inhibitors of the HCV NS3/4A protease. In particular, we focus on the discovery of VX-950, the latest HCV NS3-4A protease inhibitor to be advanced to clinical studies. While the challenges of designing potent inhibitors of the viral protease have been solved, as highlighted by BILN 2061 and VX-950, it is still too early to determine whether these efforts will eventually yield promising drug candidates. For the emerging small-molecule HCV inhibitors, viral resistance will likely be a big problem. Thus, combination therapy of different drugs with different targets/mechanisms will be necessary to effectively inhibit HCV replication. It is also hoped that a detail characterization of how the resistance mutations that affect NS3 inhibitor binding may provide useful information for the design of inhibitors with the potential to treat resistant viruses that may arise during chronic HCV infection.
Range queries in OLAP data cubes (1997)

A range query applies an aggregation operation over all selected cells of an OLAP data cube where the selection is specified by providing ranges of values for numeric dimensions. We present fast algorithms for range queries for two types of aggregation operations: SUM and MAX. These two operations cover techniques required for most popular aggregation operations, such as those supported by SQL.
Optimal Waveform-Based Clutter Suppression for SAR Imaging (2014)

Radar performance improvement through waveform optimization has been an ongoing topic of research recent years. In this paper, we use the optimal waveform design method based on Neyman-Pearson (NP) detector criterion to meet the application of SAR system and aim at enhancing SAR image quality. The optimal waveform is designed theoretically corresponding to the target response and clutter power spectrum density (PSD) and an amplitude limiter is set to suppress the clutter response while maintain most of the target response. Simulated results are presented based on our method and improvement in image is approached. Finally, the conclusions are drawn based on our analysis and simulations.
Development of an optical waveguide cantilever scanner (2003)

Design, fabrication, and testing of a micromachined cantilever beam that is optically transmissive and mechanically resonant is presented with application as a micro-optical scanner. An optical waveguide is formed from a 2.2&mu;m thick SiO<sub>2</sub> layer deposited on a single crystal silicon wafer and etched to yield a SiO<sub>2</sub>/Si composite slab cantilever. Using a novel capacitively-coupled reactive ion etching technique, a cavity is back-etched in the silicon to release the 30-40&mu;m thick and 0.5-1.5 mm long cantilevers from the wafer. An etch rate of 2.0-2.2&mu;m/min in Si, an anisotropy of 0.5 and selectivity to thermal oxide (Si: SiO<sub>2</sub> = 10:1) and to photoresist (Si: +PR = 8.6:1) are reported. Evaporated aluminum film is used as a passivation material. Optical and mechanical tests are performed on these microfabricated structures. The first mode resonances are found between 16-52 kHz with response amplitudes ranging from 80 to 420 mm. Optical throughput is visible, but greatly diminished due to scattering losses, primarily at the edges of the waveguide. Since cantilever waveguides with resonant frequencies above 20 kHz are potentially suitable for video rate scanning, these devices may be used for image acquisition and display.
Spin-transfer-torque-driven domin-wall dynamics in Permalloy nanowires (2007)

Pulse-current-driven domain-wall (DW) dynamics in Permalloy nanowires are studied using high-temporal-resolution magneto-optical techniques. The time-resolved measurements reveal prompt displacements proportional to current density above a well-defined threshold and yield values of DW velocity and spin-flip efficiency that are a factor of 10 higher than those determined in prior experiments. A stochastic variation in the wall displacements associated with termination of the current pulse is observed. The experimental results suggest the presence of both adiabatic and nonadiabatic spin-transfer-torque mechanisms, but do not appear to be fully explained by existing theoretical models.
Angelica Sinensis Polysaccharides Stimulated UDP-Sugar Synthase Genes through Promoting Gene Expression of IGF-1 and IGF1R in Chondrocytes: Promoting Anti-Osteoarthritic Activity (2014)

We demonstrated for the first time that APS-3c presented anti-OA activity through stimulating IGF-1 and IGF1R gene expression, but not directly activating the IGF1R signaling pathway, which consequently promoted UDP-sugars and GAG synthesis due to up-regulating gene expression of USSs. Our findings presented a better understanding of APS-3c's anti-OA activity and suggested that APS-3c could potentially be a novel therapeutic agent for OA.
Fabrication of Patterned Sensor Arrays with Aryl Azides on a Polymer-Coated Imaging Optical Fiber Bundle (1994)

Arrays of sensing regions are photodeposited on the distal tip of a single imaging optical fiber. First, the distal surface of the fiber is spin-coated with a thin film of poly(hydroxyethyl methacrylate). The fluorophor is then derivatized with a photoreactive group and subsequently immobilized in a finite area of the film by discrete illumination. Dye incorporation occurs only in the illuminated areas, creating distinct regions of analyte-sensitive fluorescent dye at the fiber's distal end. This paper describes both the chemistry and the manipulations required to make an optical microarray and demonstrates the technique with pH sensors. The fabrication of a four-sensor array is described along with performance data.
Determination of the Substrate Specificity of Tripeptidyl-peptidase I Using Combinatorial Peptide Libraries and Development of Improved Fluorogenic Substrates (2005)

Classical late-infantile neuronal ceroid lipofuscinosis is a fatal neurodegenerative disease caused by mutations in CLN2, the gene encoding the lysosomal protease tripeptidyl-peptidase I (TPP I). The natural substrates for TPP I and the pathophysiological processes associated with lysosomal storage and disease progression are not well understood. Detailed characterization of TPP I substrate specificity should provide insights into these issues and also aid in the development of improved clinical and biochemical assays. To this end, we constructed fluorogenic and standard combinatorial peptide libraries and analyzed them using fluorescence and mass spectrometry-based activity assays. The fluorogenic group 7-amino-4-carbamoylmethylcoumarin was incorporated into a series of 7-amino-4-carbamoylmethylcoumarin tripeptide libraries using a design strategy that allowed systematic evaluation of the P1, P2, and P3 positions. TPP I digestion of these substrates liberates the fluorescence group and results in a large increase in fluorescence that can be used to calculate kinetic parameters and to derive the substrate specificity constant kcat/KM. In addition, we implemented a mass spectrometry-based assay to measure the hydrolysis of individual peptides in peptide pools and thus expand the scope of the analysis. Nonfluorogenic tetrapeptide and pentapeptide libraries were synthesized and analyzed to evaluate P1' and P2' residues. Together, this analysis allowed us to predict the relative specificity of TPP I toward a wide range of potential biological substrates. In addition, we evaluated a variety of new fluorogenic peptides with a P3 Arg residue, and we demonstrated their superiority compared with the widely used substrate Ala-Ala-Phe-AMC for selectively measuring TPP I activity in biological specimens.
Analysis of autopilot disengagements occurring during autonomous vehicle testing (2017)

In present-day highly-automated vehicles, there are occasions when the driving system disengages and the human driver is required to take-over. This is of great importance to a vehicle's safety and ride comfort. In the U.S state of California, the Autonomous Vehicle Testing Regulations require every manufacturer testing autonomous vehicles on public roads to submit an annual report summarizing the disengagements of the technology experienced during testing. On 1 January 2016, seven manufacturers submitted their first disengagement reports: Bosch, Delphi, Google, Nissan, Mercedes-Benz, Volkswagen, and Tesla Motors. This work analyses the data from these disengagement reports with the aim of gaining abetter understanding of the situations in which a driver is required to takeover, as this is potentially useful in improving the Society of Automotive Engineers (SAE) Level 2 and Level 3 automation technologies. Disengagement events from testing are classified into different groups based on attributes and the causes of disengagement are investigated and compared in detail. The mechanisms and time taken for take-over transition occurred in disengagements are studied. Finally, recommendations for OEMs, manufacturers, and government organizations are also discussed.
Analysis of Ultra Wide Band (UWB) Technology for an Indoor Geolocation and Physiological Monitoring System (2002)

The goal of this research is to analyze the utility of UWB for indoor geolocation and to evaluate a prototype system, which will send information detailing a persons position and physiological status to a command center. In a real world environment, geolocation and physiological status information needs to be sent to a command and control center that may be located several miles away from the operational environment. This research analyzes and characterizes the UWB signal in the various operational environments associated with indoor geolocation. Additionally, "typical usage scenarios" for the interaction between UWB and other devices are also tested and evaluated.
Tales of regeneration in zebrafish (2003)

Complex tissue regeneration involves exquisitely coordinated proliferation and patterning of adult cells after severe injury or amputation. Certain lower vertebrates such as urodele amphibians and teleost fish have a greater capacity for regeneration than mammals. However, little is known about molecular mechanisms of regeneration, and cellular mechanisms are incompletely defined. To address this deficiency, we and others have focused on the zebrafish model system. Several helpful tools and reagents are available for use with zebrafish, including the potential for genetic approaches to regeneration. Recent studies have shed light on the remarkable ability of zebrafish to regenerate fins.
Electroporation-mediated transfer of cytokine genes into human esophageal tumors produces anti-tumor effects in mice. (2001)

Electroporation facilitates transfer of chemicals or plasmid DNA from extracellular milieu into cells by increasing the permeability of the cell membrane. Delivery of electric pulses to established tumors thereby can improve the susceptibility of tumors to an anti-cancer agent administered. We examined whether electroporation-mediated transfer of cytokine genes into solid tumors could produce anti-tumor effects in the tumor-bearing mice. Plasmid DNA containing cytokine genes were injected into human esophageal T.Tn tumors developed in nude mice and electric pulses were then delivered. Administration of murine GM-CSF or human IL-2 gene followed by electroporation significantly suppressed the subsequent growth of T.Tn tumors and prolonged the survival of the inoculated mice. In contrast, electroporation-mediated introduction of a control gene, human GM-CSF gene, whose products do not bind to murine GM-CSF receptors, did not achieve any anti-tumor effects. In vivo transfection of cytokine genes with electroporation could be a possible therapeutic strategy for established solid tumors.
mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues (2018)

Using the poly(A) protocol for FFPE exhibited, unexpectedly, similar efficiency to the ribosomal-depletion protocol, with the latter requiring much higher (2-3 fold) sequencing depth to compensate for the relative low fraction of reads mapped to the transcriptome. The results indicate that standard poly(A)-based RNA sequencing of archived FFPE samples is a reliable and cost-effective alternative for measuring mRNA-seq on FF samples. Expression profiling of FFPE samples by mRNA-seq can facilitate much needed extensive retrospective clinical genomic studies.