gebhart/patrepeval huggingface dataset:
Lab-on-chip systems for integrated bioanalyses (2016)

Biomolecular detection systems based on microfluidics are often called lab-on-chip systems. To fully benefit from the miniaturization resulting from microfluidics, one aims to develop 'from sample-to-answer' analytical systems, in which the input is a raw or minimally processed biological, food/feed or environmental sample and the output is a quantitative or qualitative assessment of one or more analytes of interest. In general, such systems will require the integration of several steps or operations to perform their function. This review will discuss these stages of operation, including fluidic handling, which assures that the desired fluid arrives at a specific location at the right time and under the appropriate flow conditions; molecular recognition, which allows the capture of specific analytes at precise locations on the chip; transduction of the molecular recognition event into a measurable signal; sample preparation upstream from analyte capture; and signal amplification procedures to increase sensitivity. Seamless integration of the different stages is required to achieve a point-of-care/point-of-use lab-on-chip device that allows analyte detection at the relevant sensitivity ranges, with a competitive analysis time and cost.
Symbolic pruning of concurrent program executions (2009)

We propose a new algorithm for verifying concurrent programs, which uses concrete executions to partition the program into a set of lean partitions called concurrent trace programs (CTPs), and symbolically verifies each CTP using a satisfiability solver. A CTP, derived from a concrete execution trace, implicitly captures all permutations of the trace that also respect the control flow of the program. We show that a CTP, viewed as a coarser equivalence class than the popular (Mazurkiewicz) trace equivalence in partial order reduction (POR) literature, leads to more effective pruning of the search space during model checking. While classic POR can prune away redundant interleavings within each trace equivalence class, the pruning in POR is not property driven. We use symbolic methods to achieve property-driven pruning. The effort of exploration is distributed between a symbolic component (verification of a particular CTP) and an enumerative component (exploration of the space of CTPs). We show that the proposed method facilitates more powerful pruning of the search space during the enumerative exploration.
Anti-S100A4 Antibody Suppresses Metastasis Formation by Blocking Stroma Cell Invasion (2012)

The small Ca-binding protein, S100A4, has a well-established metastasis-promoting activity. Moreover, its expression is tightly correlated with poor prognosis in patients with numerous types of cancer. Mechanistically, the extracellular S100A4 drives metastasis by affecting the tumor microenvironment, making it an attractive target for anti-cancer therapy. In this study, we produced a function-blocking anti-S100A4 monoclonal antibody with metastasis-suppressing activity. Antibody treatment significantly reduced metastatic burden in the lungs of experimental animals by blocking the recruitment of T cells to the site of the primary tumor. In vitro studies demonstrated that this antibody efficiently reduced the invasion of T cells in a fibroblast monolayer. Moreover, it was capable of suppressing the invasive growth of human and mouse fibroblasts. We presume therefore that the antibody exerts its activity by suppressing stroma cell recruitment to the site of the growing tumor. Our epitope mapping studies suggested that the antibody recognition site overlaps with the target binding interface of human S100A4. We conclude here that this antibody could serve as a solid basis for development of an efficient anti-metastatic therapy.
Highly Ultramicroporous Single‐Walled Carbon Nanohorn Assemblies (2005)

Highly ultramicroporous single-walled carbon nanohorns (see Figure), porosity-designed by HNO3 treatment, show dramatically enhanced storage capacity of supercritical methane, which can be adsorbed into internal and interstitial spaces of the single-wall carbon nanohorns. This enhanced storage capacity of methane may result from the developed ultramicroporosity, which can promote the adsorptivity of methane.
A Biodegradable Surface Drifter for Ocean Sampling on a Massive Scale (2017)

Abstract Targeted observations of submesoscale currents are necessary to improve science’s understanding of oceanic mixing, but these dynamics occur at spatiotemporal scales that are currently challenging to detect. Prior studies have recently shown that the submesoscale surface velocity field can be measured by tracking hundreds of surface drifters released in tight arrays. This strategy requires drifter positioning to be accurate, frequent, and to last for several weeks. However, because of the large numbers involved, drifters must be low-cost, compact, easy to handle, and also made of materials harmless to the environment. Therefore, the novel Consortium for Advanced Research on Transport of Hydrocarbon in the Environment (CARTHE) drifter was designed following these criteria to facilitate massive sampling of near-surface currents during the Lagrangian Submesoscale Experiment (LASER). The drifting characteristics were determined under a wide range of currents, waves, and wind conditions in laboratory settings. Results showed that the drifter accurately follows the currents in the upper 0.60 m, that it presents minimal wave rectification issues, and that its wind-induced slip velocity is less than 0.5% of the neutral wind speed at 10 m. In experiments conducted in both coastal and deep ocean conditions under wind speeds up to 10 m s −1 , the trajectories of the traditional Coastal Ocean Dynamics Experiment (CODE) and the CARTHE drifters were nearly identical. Following these tests, 1100 units were produced and deployed during the LASER campaign, successfully tracking submesoscale and mesoscale features in the Gulf of Mexico. It is hoped that this drifter will enable high-density sampling near metropolitan areas subject to stress by the overpopulation, such as lakes, rivers, estuaries, and environmentally sensitive areas, such as the Arctic.
Cloning and Characterization of a Close Homologue of Human UDP-N-acetyl-α-d-galactosamine:Polypeptide N-Acetylgalactosaminyltransferase-T3, Designated GalNAc-T6 (1999)

The UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase, designated GalNAc-T3, exhibits unique functions. Specific acceptor substrates are used by GalNAc-T3 and not by other GalNAc-transferases. The expression pattern of GalNAc-T3 is restricted, and loss of expression is a characteristic feature of poorly differentiated pancreatic tumors. In the present study, a sixth human UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase, designated GalNAc-T6, with high similarity to GalNAc-T3, was characterized. GalNAc-T6 exhibited high sequence similarity to GalNAc-T3 throughout the coding region, in contrast to the limited similarity that exists between homologous glycosyltransferase genes, which is usually restricted to the putative catalytic domain. The genomic organizations of GALNT3 and GALNT6 are identical with the coding regions placed in 10 exons, but the genes are localized differently at 2q31 and 12q13, respectively. Acceptor substrate specificities of GalNAc-T3 and -T6 were similar and different from other GalNAc-transferases. Northern analysis revealed distinct expression patterns, which were confirmed by immunocytology using monoclonal antibodies. In contrast to GalNAc-T3, GalNAc-T6 was expressed in WI38 fibroblast cells, indicating that GalNAc-T6 represents a candidate for synthesis of oncofetal fibronectin. The results demonstrate the existence of genetic redundancy of a polypeptide GalNAc-transferase that does not provide full functional redundancy.
Capacitor voltage ripple reduction with state trajectory analysis for modular multilevel converter (2017)

The modular multi-level converter (MMC) is the most prominent interface converter used between the HVDC grid and the HVAC grid. One of the important design challenges in MMC is to reduce the capacitor size. In the current practice, a rather large capacitor bank is required to store line-frequency related circulating energy, even though a number of control strategies have been introduced to reduce the capacitor voltage ripples. In the present paper, a novel control strategy is proposed by the means of harmonic injections in the conjunction with gain control to eliminate completely both the line frequency and the second-order harmonic of the capacitor voltage ripple. Ideally, the proposed method works with the full bridge topology. However, the concept also works with half bridge topology with significant reduction of line frequency related ripple. To gain a better understanding of nature of circulating energy and means of reducing it, the method of state plane analysis is employed to offer visual support. In addition, the design trade-off between full bridge MMC and half bridge MMC is presented and a novel control strategy for hybrid MMC is proposed. Finally, the work is supported with a scale down hardware demonstration.
Deterministic Synthesis and Optical Properties of Glassy Chiral-Nematic Liquid Crystals (2003)

A new series of morphologically stable, glassy chiral-nematic liquid crystals were synthesized following three distinct deterministic approaches. A glass transition temperature from 67 to 82 °C and a clearing temperature from 175 to 225 °C were accomplished. A helical pitch length from 188 to 210 nm emerged with enantiomeric 1-phenylethylamine as the precursors, giving rise to selective reflection in the UV region. With (+)-estrone as the chiral moiety, a selective reflection in the near-infrared was observed. The concepts of high-performance circular polarizers and optical notch filters and reflectors were illustrated with a mixture of enantiomeric glassy chiral nematics. Selective reflection wavelength can be readily tuned by varying chemical composition in terms of the ratio of enantiomers or that of chiral-nematic to nematic components.
Intratumoral injection of interleukin-12 plasmid DNA, either naked or in complex with cationic lipid, results in similar tumor regression in a murine model. (2002)

Effective eradication of established tumors and generation of a lasting systemic immune response is an important goal for cancer gene immunotherapy. The method of gene delivery may also be critical for the generation of an effective antitumor response. We compared the level of transgene expression and antitumor activity of two different interleukin (IL)-12 DNA preparations (naked DNA versus DNA lipid complex). Established murine adenocarcinoma (CT26) and renal cell carcinoma (Renca) tumors in BALB/c mice were treated by direct intratumoral injection of a nonviral plasmid DNA vector encoding the murine IL-12 (mIL-12) gene, either alone (naked) or in complexes with cationic lipid. Both treatments resulted in the same percentage (87%) of mice undergoing a complete tumor regression of the CT26 tumor. For the Renca tumor model, complete tumor regression was observed in 67 and 75% of animals treated with naked mIL-12 DNA and mIL-12 DNA plus lipid, respectively. Mice that were rendered tumor free for > 50 days by mIL-12 gene therapy rejected a subsequent challenge of parental tumor cells but not of an unrelated, syngeneic tumor. The marked reduction of tumor growth in tumor-bearing mice treated with mIL-12 cDNA was associated with the augmentation of tumor-specific cytotoxic T cells, enhanced production of IFN-gamma in spleen and lymph node cells, and increased splenomegaly and lymphadenopathy. The CD8+: CD4+ ratio in tumor-infiltrating lymphocytes was significantly increased in the tumor-bearing mice treated with mIL-12 DNA alone and mIL-12 cDNA plus lipid as compared with a control vector-treated group. These results indicate that direct intratumoral gene transfer with naked nonviral IL-12 DNA provides an effective and simple method for the treatment of murine tumors, suggesting an approach for clinical application.
Current confinement in a GaAs/AlGaAs heterostructure by <i>i</i> <i>n</i> <i>s</i> <i>i</i> <i>t</i> <i>u</i> laser-patterned desorption of a current-blocking quantum well (1990)

Radiation from Ar+ and Nd:YAG lasers is used within a metalorganic chemical vapor deposition reactor to thermally desorb selected areas of GaAs quantum well (QW) layers during a pause in the epitaxial growth. The process, called laser-patterned desorption, is used to laterally pattern current confinement in an AlGaAs/GaAs diode laser structure. Current channels are produced by completely removing selected areas (∼3 mm wide) of an n+ GaAs QW blocking layer embedded in the AlGaAs p cladding of a separate confinement heterostructure laser. Scanning electron microscopy cross sections indicate the blocking layer is completely removed in regions illuminated with the focused laser beam. Current confinement is confirmed by observing the localized optical emission from a 1-cm-long bar containing a 1-mm-wide desorbed region. Broad-area diode lasers fabricated from the sample exhibit a forward voltage varying from a minimum (∼2 V) within the lase-desorbed region to a maximum (∼4 V) in the surrounding field. This work is the first demonstration of current confinement produced by epitaxial patterning in an optical device during growth.
3'-Spiro nucleosides, a new class of specific human immunodeficiency virus type 1 inhibitors: synthesis and antiviral activity of [2', 5'-bis-O-(tert-butyldimethylsilyl)-.beta.-D-xylo- and -ribofuranose]-3'-spiro-5''-[4''-amino-1'', 2''-oxathiole 2'', 2''-dioxide] (TSAO) pyrimidine nucleosides (1992)

A series of 3'-spiro nucleosides have been synthesized and evaluated as anti-HIV-1 agents. Reaction of O-mesylcyanohydrins of furanos-3'-ulosyl nucleosides with base afforded [1-[2',5'-bis-O- (tert-butyldimethylsilyl)-beta-D-xylo- and -ribofuranosyl]]-3'-spiro-5"- [4"-amino-1",2"-oxathiole 2",2"-dioxide] derivatives of thymine, uracil and 4-N-acetylcytosine 11 and 12. Desilylation of 11 and 12 gave the full deprotected 3'-spiro xylo- and ribofuranosyl nucleosides 13 and 14 or the partially 5'-O-deprotected-3'-spiro beta-D-xylo- and -ribo-nucleosides 15 and 16, or 2'-O-deprotected-3'-spiro beta-D-ribo-nucleoside 17. 2'-Deoxygenation of 17 afforded 2'-deoxy-3'-spiro beta-D-erythro-pentofuranosyl derivative 18. These 3'-spiro derivatives were evaluated for their anti-HIV-1 activity. All 3'-spiro nucleosides having a xylo configuration did not show any anti-HIV-1 activity. 3'-Spiro ribo-nucleosides with none or only one silyl group at C-2' or C-5' or the 2'-deoxy derivative were also inactive at subtoxic concentrations. However, 3'-spiro ribo-nucleosides having two silyl groups at C-2' and C-5' were potent and selective inhibitors of HIV-1. None of the nucleoside analogues that showed anti-HIV-1 activity proved inhibitory to the replication of HIV-2 or SIV.
Clostridium perfringens enterotoxin carboxy-terminal fragment is a novel tumor-homing peptide for human ovarian cancer (2010)

Based on the high levels of claudin-3 and -4 expression in chemotherapy-resistant ovarian cancer and other highly aggressive human epithelial tumors including breast, prostate and pancreatic cancers, CPE peptide holds promise as a lead peptide for the development of new diagnostic tracers or alternative anticancer agents.
Development of a Weld Quality Monitor (1976)

Abstract : A weld monitoring system has been developed based on conditioning the primary signals from the welding machine and comparing them with preset limits. A light is activated when a welding parameter such as voltage, current, or heat input is outside the control limits. The circuitry has been tested with simulated primary signals. The voltage channel has also been tested using primary signals from an automatic gas metal-arc welding machine.
UV/Ozone Cleaning of Surfaces (1976)

The ultraviolet (UV)/ozone cleaning procedure is shown to be an effective method of rapidly removing a variety of contaminants from surfaces. It is a simple-to-use dry process which is inexpensive to set up and operate. It can produce · clean surfaces in air, at ambient temperatures. The experiments were performed on quartz and metal surfaces. The contaminants which were successfully removed include oils and greases (including silicones), fluxes, skin oils, and contamination adsorbed during prolonged exposure to air. The experiments were aimed at defining the variables and determining the optimum conditions for producing clean surfaces by UV irradiation. The important variables are: the contaminants initially present, the precleaning procedure, the wavelengths emitted by the UV source, the atmosphere between the source and sample, the distance between the source and' sample, and the time of exposure. For surfaces which are properly precleaned and placed within a few millimeters of an ozone-producing UV source, the process can consistently produce a clean surface in less than 1 rain. Experiments performed with two low-pressure mercury discharge UV sources, one which generates ozone and one which does not, indicate that the combination of short-wave UV light plus ozone produces a clean surface substantially faster than either short-wave UV light without ozone or ozone without UV light.
Multiple doughnut beams for trapping and dynamic manipulation of low-index microstructures (2004)

We demonstrate the use of independently controlled doughnut beams for trapping and manipulation of an array of low-index microstructures. These types of particles are generally difficult to handle using conventional optical traps due to the inverse effect of the gradient force, which repels the particles from the region of stronger light intensity. The configurable multiple doughnut beams are generated using a nearly loss-less phase-to-intensity conversion of a phase-encoded collimated coherent light source. The two-dimensional phase distribution corresponding to the optical trap pattern is encoded using a computer-programmable spatial light modulator enabling each trap to be moved arbitrarily along the transverse direction. Experiments show trapping and manipulation of hollow “air-filled” glass micro-spheres suspended in aqueous medium.
In Vivo Optical Spectroscopy Detects Radiation Damage in Brain Tissue (2005)

Optical spectroscopy detects radiation damage in brain tissues. The F500 spectral peak may allow accurate selection of tissues for biopsy in evaluating patients with new, contrast-enhancing lesions in the setting of previous irradiation.
Use of recycled glass for concrete masonry blocks. Final report (1997)

A two-year research project was conducted to study the technical and economic feasibility of using mixed-color crushed waste glass for concrete masonry. From a technical standpoint, two problems had to be confronted. First, it was known that the silica in glass is highly reactive in the alkaline environment of portland cement concrete. Second, there was the possibility of strength loss, as crushed glass particles with smooth surfaces were substituted for regular aggregate. Both problems were solved in the course of this research. It was found that waste glass ground to mesh size No. 30 or smaller does not exhibit any expansion due to alkali-silica reaction (ASR). Another significant research finding was that very finely ground glass exhibits pozzolanic properties and therefore is suitable as a partial replacement for portland cement. The economic feasibility of concrete block masonry with glass both as aggregate and cement substitution was evaluated and found to be encouraging.
The Kramers-Kronig Receiver: Opportunities and Challenges (2018)

The Kramers–Kronig (KK) receiver allows the reconstruction of complex-valued optical fields from the detection of their intensity. This presentation reviews the operation principles and various implementations of the KK scheme, after almost two years since its proposal. Advantages and limitations of this new scheme will be discussed.
Dynamic compressive magnetic resonance imaging using a Gaussian scale mixtures model (2011)

Dynamic magnetic resonance imaging (MRI) is commonly used to observe dynamic physiological changes in tissue or to study organs with mobile structures such as the heart. In order to accurately capture spatiotemporal changes, it is desirable to have dynamic images with high temporal resolution in addition to high spatial resolution. Due to the nature of data acquisition in current MRI systems, there exists a trade-off between temporal and spatial resolution. In this work, we present two methods for improving the spatiotemporal resolution in dynamic MRI using compressive sampling (CS). Experimental results illustrate that the proposed Bayes least squares-Gaussian scale mixtures (BLS-GSM) model-based CS algorithm compares favorably with other state-of-the-art compressive dynamic MRI techniques.
A 3D mixed-mode ESD protection circuit simulation-design methodology (2004)

Electrostatic discharge (ESD) is a serious IC reliability problem. On-chip ESD protection is used to protect ICs against ESD damage. This paper presents a real 3D mixed-mode ESD protection circuit simulation-design methodology for ESD design prediction. Practical ESD protection design examples in 0.35 /spl mu/m BiCMOS are given.
Isolation of High-Affinity Single-Chain Antibodies against <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> Surface Proteins from Sheep with Johne's Disease (2006)

Johne's disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, causes significant economic losses to the livestock farming industry. Improved investigative and diagnostic tools-necessary to understand disease processes and to identify subclinical infection-are much sought after. Here, we describe the production of single-chain antibodies with defined specificity for M. avium subsp. paratuberculosis surface proteins. Single-chain antibodies (scFv) were generated from sheep with Johne's disease by cloning heavy-chain and lambda light-chain variable regions and expressing these in fusion with gene III of filamentous phages. Two scFv clones (designated SurfS1.2 and SurfS2.2) were shown to be immunoreactive against M. avium subsp. paratuberculosis surface targets by flow cytometry, and immunoblotting identified specificity for a 34-kDa proteinase-susceptible determinant. Both antibodies were cross-reactive against Mycobacterium avium subsp. avium but nonreactive against Mycobacterium bovis or Mycobacterium phlei cells and were shown to be capable of enriching M. avium subsp. paratuberculosis cells by a factor of approximately 10(6)-fold when employed in magnetic bead separation of mixed Mycobacterium sp. cultures. Further, magnetic bead separation using SurfS1.2 and SurfS2.2 was capable of isolating as few as 10(3) M. avium subsp. paratuberculosis cells from ovine fecal samples, indicating the diagnostic potential of these reagents. Finally, inclusion of SurfS1.2 or SurfS2.2 in in vitro broth culture with M. avium subsp. paratuberculosis indicated that surface binding activity did not impede bacterial growth, although colony clumping was prevented. These results are discussed in terms of the potential use of single-chain phage display monoclonal antibodies as novel diagnostic reagents.
Synergism of CAY-1 with Amphotericin B and Itraconazole (2006)

CAY-1 had predominantly additive-synergistic interaction with AB or IT against the Aspergillus NG and G conidia. Excellent synergy between CAY-1 and AB occurred at 24 and 48 h against C. albicans. Results suggest CAY-1 enhances AB and IT efficacy.
Optical Time-Domain Measurement of Brillouin Dynamic Grating Spectrum in a Polarization Maintaining Fiber (2009)

We demonstrate the distributed measurement of Brillouin dynamic grating spectrum in a polarization maintaining fiber based on time-domain analysis. By synchronized propagation of the pump and the probe pulses, the local spectrum of Brillouin dynamic grating is acquired together with the local Brillouin gain spectrum in a single experimental setup. The temperature sensitivity as high as −370 MHz/°C is observed with a spatial resolution of 1.5 m.