gebhart/patrepeval huggingface dataset:
Molecular‐Beacon‐Based Tricomponent Probe for SNP Analysis in Folded Nucleic Acids (2011)

Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.
Ultrasonic technique for dispersed-phase holdup measurements (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUltrasonic technique for dispersed-phase holdup measurementsJ. C. Bonnet and L. L. TavlaridesCite this: Ind. Eng. Chem. Res. 1987, 26, 4, 811–815Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://pubs.acs.org/doi/10.1021/ie00064a032https://doi.org/10.1021/ie00064a032research-articleACS PublicationsRequest reuse permissionsArticle Views246Altmetric-Citations50LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A novel four-quadrant analog multiplier using SOI four-gate transistors (g/sup 4-FETs) (2005)

A novel analog multiplier using SOI four-gate transistors (G/sup 4/-FETs) is presented. Thanks to the multiple inputs of the G/sup 4/-FET that may be biased independently, the number of transistors in the proposed circuit is dramatically reduced, compared to conventional single-gate MOSFET based multipliers. Only four G/sup 4/-FETs are needed to build the multiplier core. The circuit is feasible with a standard SOI CMOS process. Two different configurations, both based on the linear modulation of the front-gate threshold voltage by the junction-gates, are presented. This paper addresses the theoretical analysis as well as the preliminary measurement results.
<title>Phase-shifting and other challenges in optical mask technology</title> (1991)

Optical lithography has benefitted from progresses in wavelength reduction, lenses, resist systems, alignment, focussing, table accuracy, and insute metrology. As a result, the minimum feature size of integrated circuits has been reduced through many generations from 2 micrometers to 0.5 micrometers in manufacturing. There are many opportunities in improving the mask to help continue the progress. The image contrast can be restored by reducing stray light with mask anti-reflection coating at the absorber-air interface. Pre-distorting the mask against the distortion of the imaging lens can drastically improve the overlay performance. Adjusting the gray level or the feature size individually according to the pattern proximity environment can create a larger common exposure-defocus window for different feature shapes. Introducing phase shifts in the mask can simultaneously improve resolution and depth of focus, with the potential of a two-generation improvement with any given projection imaging equipment, provided the overlay capability is upgraded accordingly. In addition to describing and comparing these opportunities, the phase-shifting technology is given a special focus on the working principle, the different approaches to phase shifting, their imaging characteristics in terms of exposure-defocus diagrams, a systems view, and the scope of its development.
Compact snapshot real-time imaging spectrometer (2011)

The described spectral imaging system, referred to as a Snapshot Hyperspectral Imaging Fourier Transform (SHIFT) spectrometer, is capable of acquiring spectral image data of a scene in a single integration of a camera, is ultra-compact, inexpensive (commercial off-the-shelf), has no moving parts, and can produce datacubes (x, y, λ) in real time. Based on the multiple-image FTS originally developed by A. Hirai [1], the presented device offers significant advantages over his original implementation. Namely, its birefringent nature results in a common-path interferometer which makes the spectrometer insensitive to vibration. Furthermore, it enables the potential of making the instrument ultra-compact, thereby improving the portability of the sensor. By combining a birefringent interferometer with a lenslet array, the entire spectrometer consumes approximately 15×15×20 mm<sup>3</sup>, excluding the imaging camera. The theory of the birefringent FTS is provided, followed by details of its specific embodiment and a laboratory proof of concept of the sensor. Post-processing is currently accomplished in Matlab, but progress is underway in developing real-time reconstruction capabilities with software programmed on a graphics processing unit (GPU). It is anticipated that processing of >30 datacubes per second can be achieved with modest GPU hardware, with spatial/spectral data of or exceeding 256×256 spatial resolution elements and 60 spectral bands over the visible (400-800 nm) spectrum. Data were collected outdoors, demonstrating the sensor's ability to resolve spectral signatures in standard outdoor lighting and environmental conditions as well as retinal imaging.
An Unstructured Gridding Method for Densely-Spaced Complex Wells in Full-Field Reservoir Simulation (2013)

Abstract Accurate representation of near-well flow is an important subject matter in reservoir simulation. In today’s field-scale reservoir simulation, cell-centered structured grids remain the predominant practice. Typically, well inflow performance of the perforated cells is connected to the finite-volume solution via well indices which may not be well defined when the wellbore intersects the finite-volume cells in a complex trajectory. Fine gridding is required to resolve the flow dynamics in the near-well regions. Strong grid orientation sensitivities can also contribute to the numerical errors and may require significant local grid refinement to alleviate. There are on-going R&D efforts on applying unstructured grids to better represent the near-well flow in reservoir simulation, but their applications are mainly in single-well study or sector modeling with a few wells. Some of the reasons cited for this include: (1) the lack of an effective, easy-to-use full-field complex well gridding tool; (2) the lack of supporting unstructured workflow for full-cycle reservoir simulation; (3) the cost of unstructured grid simulation; (4) the availability of post analysis and visualization tools for unstructured grid simulation. The paper describes a method to generate unstructured grids which conform to complex well paths in field-scale simulation. The method uses a multi-level approach to place cells optimally within the solution domain based on the "regions of interests". The wellbore geometry is honored via the construction of a near-well grid that is complemented with multi-level quad-tree refinements to achieve the desired resolution in grid transition zones. The method includes an algorithm to remove small cells and pinching cells based on local grid quality measures and cell prioritization to honor well paths. The gridding process forms a component of a production level reservoir simulation workflow. The use of unstructured grid results in computational saving by placing cells where the resolution is needed. An in-house massively parallel simulator is used to run the unstructured grid models. Simulation examples for full-field applications with hundreds of complex wells using both structured grids and unstructured grids will be used to compare results, accuracy, and performance of the gridding method for reservoir simulation.
Orthogonal Time Frequency Space Modulation (2018)

This paper introduces a new two-dimensional modulation technique called Orthogonal Time Frequency Space (OTFS) modulation. OTFS has the novel and important feature of being designed in the delay-Doppler domain. When coupled with a suitable equalizer, OTFS modulation is able to exploit the full channel diversity over both time and frequency. Moreover, it converts the fading, time-varying wireless channel experienced by modulated signals such as OFDM into a time-independent channel with a complex channel gain that is essentially constant for all symbols. This design obviates the need for transmitter adaptation, and greatly simplifies system operation. The paper describes the basic operating principles of OTFS as well as a possible implementation as an overlay to current or anticipated standardized systems. OTFS is shown to provide significant performance improvement in systems with high Doppler, short packets, and/or large antenna array. In particular, simulation results indicate at least several dB of block error rate performance improvement for OTFS over OFDM in all of these settings.
Tone-dependent error diffusion (2004)

We present an enhanced error diffusion halftoning algorithm for which the filter weights and the quantizer thresholds vary depending on input pixel value. The weights and thresholds are optimized based on a human visual system model. Based on an analysis of the edge behavior, a tone dependent threshold is designed to reduce edge effects and start-up delay. We also propose an error diffusion system with parallel scan that uses variable weight locations to reduce worms.
Therapeutic Inhibition of Pro-Inflammatory Signaling and Toxicity to Staphylococcal Enterotoxin B by a Synthetic Dimeric BB-Loop Mimetic of MyD88 (2012)

Staphylococcal enterotoxin B (SEB) exposure triggers an exaggerated pro-inflammatory cytokine response that often leads to toxic shock syndrome (TSS) associated with organ failure and death. MyD88 mediates pro-inflammatory cytokine signaling induced by SEB exposure and MyD88(-/-) mice are resistant to SEB intoxication, suggesting that MyD88 may be a potential target for therapeutic intervention. We targeted the BB loop region of the Toll/IL-1 receptor (TIR) domain of MyD88 to develop small-molecule therapeutics. Here, we report that a synthetic compound (EM-163), mimic to dimeric form of BB-loop of MyD88 attenuated tumor necrosis factor (TNF)- α, interferon (IFN)-γ, interleukin (IL)-1β, IL-2 and IL-6 production in human primary cells, whether administered pre- or post-SEB exposure. Results from a direct binding assay, and from MyD88 co-transfection/co-immunoprecipitation experiments, suggest that EM-163 inhibits TIR-TIR domain interaction. Additional results indicate that EM-163 prevents MyD88 from mediating downstream signaling. In an NF-kB-driven reporter assay of lipopolysaccharide-stimulated MyD88 signaling, EM-163 demonstrated a dose-dependent inhibition of reporter activity as well as TNF-α and IL-1β production. Importantly, administration of EM-163 pre- or post exposure to a lethal dose of SEB abrogated pro-inflammatory cytokine responses and protected mice from toxic shock-induced death. Taken together, our results suggest that EM-163 exhibits a potential for therapeutic use against SEB intoxication.
Lock cohorting (2012)

Multicore machines are quickly shifting to NUMA and CC-NUMA architectures, making scalable NUMA-aware locking algorithms, ones that take into account the machines' non-uniform memory and caching hierarchy, ever more important. This paper presents lock cohorting, a general new technique for designing NUMA-aware locks that is as simple as it is powerful.
Tailoring nanoporous materials by atomic layer deposition (2011)

Atomic layer deposition (ALD) is a cyclic process which relies on sequential self-terminating reactions between gas phase precursor molecules and a solid surface. The self-limiting nature of the chemical reactions ensures precise film thickness control and excellent step coverage, even on 3D structures with large aspect ratios. At present, ALD is mainly used in the microelectronics industry, e.g. for growing gate oxides. The excellent conformality that can be achieved with ALD also renders it a promising candidate for coating porous structures, e.g. for functionalization of large surface area substrates for catalysis, fuel cells, batteries, supercapacitors, filtration devices, sensors, membranes etc. This tutorial review focuses on the application of ALD for catalyst design. Examples are discussed where ALD of TiO(2) is used for tailoring the interior surface of nanoporous films with pore sizes of 4-6 nm, resulting in photocatalytic activity. In still narrower pores, the ability to deposit chemical elements can be exploited to generate catalytic sites. In zeolites, ALD of aluminium species enables the generation of acid catalytic activity.
An infant formula with large, milk phospholipid–coated lipid droplets containing a mixture of dairy and vegetable lipids supports adequate growth and is well tolerated in healthy, term infants (2018)

An infant formula with large, milk phospholipid-coated lipid droplets containing dairy lipids is safe, well tolerated, and supports an adequate growth in healthy infants. This trial was registered in the Dutch Trial Register (www.trialregister.nl) as NTR3683.
Near-infrared Optical-resolution Photoacoustic Microscopy with 1046 nm Illumination (2014)

Due to weaker scattering, near-infrared light can penetrate deep in biological tissue. We demonstrate near-infrared optical-resolution photoacoustic microscopy (NIR-OR-PAM) with 1046 nm illumination and validate its deep imaging capability both in phantoms and in vivo.
Video Classification Based On Hmm Using Text And Faces (2000)

Publication in the conference proceedings of EUSIPCO, Tampere, Finland, 2000
Recombinant Adeno-Vaccine Expressing Enterovirus 71-Like Particles against Hand, Foot, and Mouth Disease (2015)

Enterovirus 71 (EV71) and coxsackieviruses (CV) are the major causative agents of hand, foot and mouth disease (HFMD). There is not currently a vaccine available against HFMD, even though a newly developed formalin-inactivated EV71 (FI-EV71) vaccine has been tested in clinical trial and has shown efficacy against EV71. We have designed and genetically engineered a recombinant adenovirus Ad-EVVLP with the EV71 P1 and 3CD genes inserted into the E1/E3-deleted adenoviral genome. Ad-EVVLP were produced in HEK-293A cells. In addition to Ad-EVVLP particles, virus-like particles (VLPs) formed from the physical association of EV71 capsid proteins, VP0, VP1, and VP3 expressed from P1 gene products. They were digested by 3CD protease and confirmed to be produced by Ad-EVVLP-producing cells, as determined using transmission electron microscopy and western blotting. Mouse immunogenicity studies showed that Ad-EVVLP-immunized antisera neutralized the EV71 B4 and C2 genotypes. Activation of VLP-specific CD4+ and CD8+/IFN-γ T cells associated with Th1/Th2-balanced IFN-ɣ, IL-17, IL-4, and IL-13 was induced; in contrast, FI-EV71 induced only Th2-mediated neutralizing antibody against EV71 and low VLP-specific CD4+ and CD8+ T cell responses. The antiviral immunity against EV71 was clearly demonstrated in mice vaccinated with Ad-EVVLP in a hSCARB2 transgenic (hSCARB2-Tg) mouse challenge model. Ad-EVVLP-vaccinated mice were 100% protected and demonstrated reduced viral load in both the CNS and muscle tissues. Ad-EVVLP successfully induced anti-CVA16 immunities. Although antisera had no neutralizing activity against CVA16, the 3C-specific CD4+ and CD8+/IFN-γ T cells were identified, which could mediate protection against CVA16 challenge. FI-EV71 did not induce 3C-mediated immunity and had no efficacy against the CVA16 challenge. These results suggest that Ad-EVVLP can enhance neutralizing antibody and protective cellular immune responses to prevent EV71 infection and cellular immune responses against CV infection.
The Critical Role of Asphaltene Gradients and Data Integration in Reservoir Fluid Geodynamics Analysis (2017)

Abstract Reservoir fluid geodynamics (RFG) has recently been launched as a formal technical arena that accounts for fluid redistributions and tar formation in reservoirs largely after trap filling. Elements of RFG, such as analysis of biodegradation, have long been in place; nevertheless, RFG is now strongly enabled by recent developments: 1) downhole fluid analysis (DFA) allows routine elucidation of reservoir fluid gradients, 2) the development of the first equation of state for asphaltene gradients allows identification of equilibrium vs. geodynamic processes of reservoir fluids and 3) RFG analyses of 35 oilfields systematize a multitude of RFG processes and show their direct impact on wide-ranging production concerns. Thermodynamic analyses identifying reservoir fluid geodynamic processes rely heavily on measurement of fluid gradients to avoid ambiguous interpretations. The unique role of asphaltene gradients and their integration with other data streams are the focus herein. RFG oilfield studies have repeatedly shown that analyses of asphaltene gradients are critical to proper evaluation of RFG processes. Naturally, any reservoir concern that directly involves asphaltenes such as heavy oil, viscosity gradients, asphaltene onset pressure, bitumen deposition, tar mat formation, and indirectly, GOR gradients are strongly dependent on asphaltene gradients. Moreover, as shown in numerous case studies herein, asphaltene gradients can be measured with accuracy and the corresponding thermodynamic analyses allow explicit identification of RFG processes not traditionally associated with asphaltenes, such as analysis of connectivity, fault block migration, baffling, spill-fill mechanisms and many others discussed below. In turn, these processes imply other corroborative reservoir and fluid properties that can then be confirmed. Crude oil chemical compositional data, such as ultrahigh resolution two-dimensional gas chromatography, combined with geochemical interpretation, is highly desirable for understanding RFG processes. Nevertheless, biomarkers and other fluid properties often exhibit small gradients relative to standard deviations (except with biodegradation) but often can still corroborate specific RFG processes. In general, integration of fluid gradient analysis with other data streams including petrophysics, core analysis, stratigraphy, geology and geophysics is critical; nevertheless, which integration is most needed depends on particular reservoir attributes and RFG processes that are in question. Examples of data integration are shown for ten reservoirs undergoing various fluid geodynamic processes. Asphaltene gradient analysis is relatively new, yet it is essential for characterization of RFG processes.
4'-Methylangelicins: new potential agents for the photochemotherapy of psoriasis (1983)

Three derivatives of angelicin (1) [4'-methyl-, 4,4'-dimethyl-, and 4',5-dimethylangelicin (2a-c)] have been prepared with the aim of obtaining new agents for the photochemotherapy of psoriasis. These compounds form a complex in the dark with DNA that shows an affinity for the macromolecule higher than that of the parent angelicin (1). A correlation between their octanol/water partition coefficients and the association constants of the complexes has been observed. Compounds 2a-c photobind to DNA to a much higher extent than 1 and also more effectively than 8-methoxypsoralen (8-MOP), taken as reference compound. When activated with UV-A, the three compounds strongly inactivate T2 phage and inhibit epidermal DNA synthesis in mice. Moreover, they show a mutagenic activity markedly lower than that of 8-methoxypsoralen on Escherichia coli wild-type strain. Due to its lack of skin phototoxicity, its low mutagenic activity, and its antiproliferative activity, 2c was chosen for clinical evaluation. It proved to be effective in clearing psoriasis in two patients.
Conversion of Glucose to 2-Keto- <scp>l</scp> -Gulonate, an Intermediate in <scp>l</scp> -Ascorbate Synthesis, by a Recombinant Strain of <i>Erwinia citreus</i> (1988)

A gene for 2,5-diketo-d-gluconate (25DKG) reductase, which encodes an enzyme composed of 277 amino acid residues catalyzing the reduction of 25DKG to 2-keto-l-gulonate (2KLG), was cloned from Corynebacterium sp. strain SHS752001 and expressed in Erwinia citreus SHS2003, a strain which oxidizes glucose to 25DKG. The recombinant microorganism converted glucose to 2KLG, a compound which can be readily converted to l-ascorbate (vitamin C). Improvements in the yield of 2KLG were obtained by changing fermentation conditions, using the p(l) promoter of bacteriophage lambda to express the reductase, and selecting a mutant of E. citreus which could use neither 25DKG nor 2KLG as a sole carbon source for growth. When a culture of the recombinant strain was fed with glucose to a total of 40 g/liter, 49.4% of the glucose was converted to 2KLG during a 72-h fermentation.
Speaker clustering and transformation for speaker adaptation in speech recognition systems (1998)

A speaker adaptation strategy is described that is based on finding a subset of speakers, from the training set, who are acoustically close to the test speaker, and using only the data from these speakers (rather than the complete training corpus) to reestimate the system parameters. Further, a linear transformation is computed for every one of the selected training speakers to better map the training speaker's data to the test speaker's acoustic space. Finally, the system parameters (Gaussian means) are reestimated specifically for the test speaker using the transformed data from the selected training speakers. Experiments showed that this scheme is capable of providing an 18% relative improvement in the error rate on a large-vocabulary task with the use of as little as three sentences of adaptation data.