gebhart/patrepeval huggingface dataset:
New results with the opto-electronic oscillators (OEO) (2002)

A new class of oscillators based on photonic devices is presented. These opto-electronic oscillators (OEOs) generate microwave oscillation by converting continuous energy from a light source using a feedback circuit which includes a delay element, an electro-optic switch, and a photodetector. Different configurations of OEOs are presented, each of which may be applied to a particular application requiring ultra-high performance, or low cost and small size.
P47 * THE IDENTIFICATION OF NOVEL APTAMERS TO GLIOMA (2014)

INTRODUCTION: Glioma represent less than 2% of all cancer cases in the UK, however, 80% of these tumours are glioblastoma (GBM). GBM is a highly aggressive tumour with poor patient survival rates, despite treatment involving surgery and radiotherapy with adjuvant chemotherapy. Delivery systems that have the ability to distinguish neoplasms from non-cancerous tissues, such as aptamers, may improve patient outcome. Aptamers have previously been shown to selectively target glioma cell lines. Aptamers can also be raised to known biomarkers that are crucial for cell survival, and once bound may inhibit glioma growth. The aim of this study was to produce novel aptamers to known glioma targets and to optimise the systematic evolution of ligands by exponential enrichment (SELEX) procedure with a view to produce Aptamers against patient tissue biopsies which ultimately have low cell numbers. METHOD: Cell lines SVGp12 and U87MG were utilised to determine the lowest number of cells which returned detectable DNA aptamers. Each iterative round of SELEX was optimised by determining the optimal number of touchdown PCR cycles. Furthermore, aptamers were selected against biomarkers related to gliomagenesis via counter SELEX. RESULTS: Optimisation of cell SELEX showed 100 cells and 15-17 cycles of TD-PCR were sufficient for selection. After 6 rounds of counter SELEX, aptamers selected towards a biomarker indicative of glioma were sequenced. CONCLUSION: Aptamers were selected using minimal amounts of sample, and the optimised procedure will now be used to identify aptamers which target primary tissues. Speciﬁcity of sequenced aptamers to the known biomarker and potential inhibition of glioma growth will be confirmed in future studies.
Frequent subtree mining on the automata processor (2017)

Frequency counting of complex patterns such as subtrees is more challenging than for simple itemsets and sequences, as the number of possible candidate patterns in a tree is much higher than one-dimensional data structures, with dramatically higher processing times. In this paper, we propose a new and scalable solution for frequent subtree mining (FTM) on the Automata Processor (AP), a new and highly parallel accelerator architecture. We present a multi-stage pruning framework on the AP, called AP-FTM, to reduce the search space of FTM candidates. This achieves up to 353X speedup at the cost of a small reduction in accuracy, on four real-world and synthetic datasets, when compared with PatternMatcher, a practical and exact CPU solution. To provide a fully accurate and still scalable solution, we propose a hybrid method to combine AP-FTM with a CPU exact-matching approach, and achieve up to 262X speedup over PatternMatcher on a challenging database. We also develop a GPU algorithm for FTM, but show that the AP also outperforms this. The results on a synthetic database show the AP advantage grows further with larger datasets.
A 0.6V 45nm adaptive dual-rail SRAM compiler circuit design for lower VDD_min VLSIs (2008)

A 0.6 V 45 nm dual-rail SRAM design utilizing an adaptive voltage regulator targeting for an SRAM compiler application is proposed for the first time. The proposed work describes an adaptive mechanism to generate a cell-Vdd (CVDD), which tracks a certain voltage offset with respect to logic-Vdd (VDD), and provides a mean to lower the VDD down to 0.6 V. To relax IR-drop constraints of CVDD power routings in P&R flow, shifting bite-line (BL) pre-charge power supply from CVDD to VDD is adopted in this work. This also avoids the congestion of the VDD and CVDD power mesh. A 45 nm test chip has demonstrated that these concepts successfully can push the VDD_min down to 0.6 V, which is > 250 mV lower than the conventional single-rail SRAMpsilas.
Pulsed laser deposition of epitaxial Si/TiN/Si(100) heterostructures (1994)

We have successfully deposited multilayer Si/TiN/Si(100) epitaxial heterostructures using pulsed laser deposition technique. This silicon-on-conductor device configuration has potential applications in three-dimensional integrated circuits and radiation hardened devices. The Si and TiN films were deposited by pulsed laser (KrF: λ=248 nm, τ =25 ns) physical vapor deposition technique at a substrate temperature of 600 °C in a chamber maintained at a vacuum of ∼10−7 Torr. The epitaxial nature of the films was characterized using x-ray diffraction, Rutherford backscattering, and high resolution transmission electron microscopy techniques. The two interfaces (100)TiN/Si(100)substrate and (100)Si/(100)TiN layers were quite sharp without any indication of interfacial reaction between them. The epitaxial relationship was found to be 〈100〉Si∥〈100〉TiN∥〈100〉Si. In the plane, four unit cells of TiN matched with three unit cells of silicon with less than 4.0% misfit. This domain matching epitaxy provides a mechanism of epitaxial growth in systems with large lattice mismatch. Modeling of the domain matching epitaxial growth in the high lattice mismatch (100)Si/(100)TiN/(100)Si system and possible device implications are discussed.
Isomorphous substitution in zeolite frameworks. 1. Acidity of surface hydroxyls in [B]-, [Fe]-, [Ga]-, and [Al]-ZSM-5 (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsomorphous substitution in zeolite frameworks. 1. Acidity of surface hydroxyls in [B]-, [Fe]-, [Ga]-, and [Al]-ZSM-5Cynthia T. W. Chu and Clarence D. ChangCite this: J. Phys. Chem. 1985, 89, 9, 1569–1571Publication Date (Print):April 1, 1985Publication History Published online1 May 2002Published inissue 1 April 1985https://pubs.acs.org/doi/10.1021/j100255a005https://doi.org/10.1021/j100255a005research-articleACS PublicationsRequest reuse permissionsArticle Views2390Altmetric-Citations417LEARN 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 options Get e-Alerts
Tailoring liquid crystals to become fast and efficient terahertz devices (2012)

Liquid crystals have been employed for several decades in devices such as phase shifters, Fabry-Perot filters, polarizers, phase gratings, and Bragg switches at optical frequencies. However it is only recently that such devices have been demonstrated at terahertz frequencies. This is because of several fundamental frequency dependent relationships between device properties and frequency of operation. When designing liquid crystal devices, we need to find liquid crystals with high birefringence, low viscosity and low absorption at terahertz frequencies. In this paper we will present some measurements and simulations of potentially suitable liquid crystal mixtures.
The antiapoptotic DeltaNp73 is degraded in a c-Jun–dependent manner upon genotoxic stress through the antizyme-mediated pathway (2010)

p73, the structural and functional homologue of p53, exists as two major forms: the transactivation-proficient, proapoptotic TAp73 or the transactivation-deficient, antiapoptotic DNp73. Expectedly, expression of both these major forms has to be coordinated precisely to achieve the desired cellular outcome. Genotoxic insults resulting in cell death lead to the stabilization of TAp73, mainly through posttranslational modifications, and the concomitant degradation of DNp73, through poorly understood mechanisms. We have therefore investigated the possible mechanisms of stress-induced DNp73 degradation and show here that c-Jun, the AP-1 family member activated by stress signals and involved in stabilizing TAp73, promotes DNp73 degradation. Genotoxic stress-mediated DNp73 degradation was found to occur in a c-Jun-dependent manner through a ubiquitin-independent but proteasome-dependent mechanism. Absence or down-regulation of c-Jun expression abrogated the reduction of DNp73 levels upon stress insults, whereas overexpression of c-Jun led to its degradation. c-Jun controlled DNp73 degradation through the nonclassical, polyamine-induced antizyme (Az) pathway by regulating the latter's processing during stress response. Consistently, expression of c-Jun or Az, or addition of polyamines, promoted DNp73 degradation, whereas silencing Az expression or inhibiting Az activity in cells exposed to stress reduced c-Jun-dependent DNp73 degradation. Moreover, Az was able to bind to DNp73. These data together demonstrate the existence of a c-Jun-dependent mechanism regulating the abundance of the antiapoptotic DNp73 in response to genotoxic stress.
Extracting pressure and temperature from high speed fiber grating sensor data associated with energetic material tests (2019)

In order to characterize energetic materials, it is highly desirable to be able to measure velocity, position, pressure, and temperature throughout the event. This paper looks at approaches associated with extracting these parameters from data obtained using high speed fiber grating sensor systems. Prior work has demonstrated that velocity, position, and local pressure data may be obtained using chirped fiber grating sensors (CFBGs). Uniform fiber grating sensors have been used to quantify local pressures beyond the range associated with CFBGs. A main challenge faced today is the separate of these parameters from temperature. A novel approach that may be used to isolate temperature and pressure measurements using a high-speed fiber grating sensor system is presented in this paper.
Seizure detection using wearable sensors and machine learning: Setting a benchmark (2021)

Automatic seizure detection using ML from multimodal wearable sensor data is feasible across a broad spectrum of epileptic seizures. Preliminary results show better than chance seizure detection. The next steps include validation of our results in larger datasets, evaluation of the detection utility tool for additional clinical seizure types, and integration of additional clinical information.
Properties of a meq-Deleted rMd5 Marek's Disease Vaccine: Protection Against Virulent MDV Challenge and Induction of Lymphoid Organ Atrophy Are Simultaneously Attenuated by Serial Passage In Vitro (2013)

We have previously shown that deletion of the meq gene from the genome of Cosmid-cloned rMd5 strain of Marek's disease virus (MDV-1) resulted in loss of transformation and oncogenic capacity of the virus. The rMd5deltaMeq (Meq null) virus has been shown to be an excellent vaccine in maternal antibody positive (MAb+) chickens challenged with a very virulent plus (vv+) strain of MDV, 648A. The only drawback was that it retained its ability to induce bursa and thymus atrophy (BTA) like that of the parental rMd5 in maternal antibody negative (MAb-) chickens. We recently reported that the attenuated Meq null virus did not induce BTA at the 40th cell culture passage onward. Its protective ability against challenge with vv+ MDV, strain 686 was similar to the original virus at the 19th passage in MAb- chickens. In this study, we compared the same series of attenuated meq null viruses in commercial chickens. In commercial chickens with MAb, the attenuated viruses quickly lost protection with increasing cell culture attenuation. These data suggest that although attenuation of these meq null viruses eliminated BTA, it had no influence on their protective efficacy in MAb- chickens. However, in commercial chickens (MAb+), the best protection was provided by the original 19th passage; the attenuated 40th passage was as good as one of the currently commercial CVI988/Rispens vaccine, and it did not induce BTA. Therefore, protection against virulent MDV challenge and induction of lymphoid organ atrophy are simultaneously attenuated by serial passage in vitro.
Fully automatic segmentation of the open mitral leaflets in 3D transesophageal echocardiographic images using multi-atlas label fusion and deformable medial modeling (2012)

The goal of this work is to develop a fully automatic method for segmentation of the mitral leaflets in 3D transesophageal echocardiographic (3D TEE) images. The method combines complementary probabilistic segmentation and geometric modeling techniques to generate 3D patient-specific reconstructions of the mitral leaflets and annulus from 3D TEE image data with no user interaction. In the model-based segmentation framework, mitral leaflet geometry is described with 3D continuous medial representation (cm-rep). To capture leaflet geometry in a target 3D TEE image, a pre-defined cm-rep template of the mitral leaflets is deformed such that the negative log of a Bayesian posterior probability is minimized. The likelihood of the objective function is given by a probabilistic segmentation of the mitral leaflets generated by multi-atlas joint label fusion, while the validity constraints and regularization terms imposed by cm-rep act as shape priors that preserve leaflet topology and constrain model fitting. The method is tested on ten 3D TEE images of human mitral leaflets at mid-diastole, using manual segmentation as the gold standard.
Unsupervised color image segmentation using a dynamic color gradient thresholding algorithm (2008)

We propose a novel algorithm for unsupervised segmentation of color images. The proposed approach utilizes a dynamic color gradient thresholding scheme that guides the region growing process. Given a color image, a weighted vectorbased color gradient map is generated. Seeds are identified and a dynamic threshold is then used to perform reliable growing of regions on the weighted gradient map. Over-segmentation, if any, is addressed by a Similarity Measurebased region merging stage to produce the final segmented image. Comparative results demonstrate the effectiveness of this algorithm for color image segmentation.
Characterization of Bacillus thuringiensis <scp>l</scp> -Isoleucine Dioxygenase for Production of Useful Amino Acids (2011)

We determined the enzymatic characteristics of an industrially important biocatalyst, α-ketoglutarate-dependent l-isoleucine dioxygenase (IDO), which was found to be the enzyme responsible for the generation of (2S,3R,4S)-4-hydroxyisoleucine in Bacillus thuringiensis 2e2. Depending on the amino acid used as the substrate, IDO catalyzed three different types of oxidation reactions: hydroxylation, dehydrogenation, and sulfoxidation. IDO stereoselectively hydroxylated several hydrophobic aliphatic l-amino acids, as well as l-isoleucine, and produced (S)-3-hydroxy-l-allo-isoleucine, 4-hydroxy-l-leucine, (S)-4-hydroxy-l-norvaline, 4-hydroxy-l-norleucine, and 5-hydroxy-l-norleucine. The IDO reaction product of l-isoleucine, (2S,3R,4S)-4-hydroxyisoleucine, was again reacted with IDO and dehydrogenated into (2S,3R)-2-amino-3-methyl-4-ketopentanoate, which is also a metabolite found in B. thuringiensis 2e2. Interestingly, IDO catalyzed the sulfoxidation of some sulfur-containing l-amino acids and generated l-methionine sulfoxide and l-ethionine sulfoxide. Consequently, the effective production of various modified amino acids would be possible using IDO as the biocatalyst.
Microseismic Calibration of a Geomechanical Simulation of a Horn River Basic Hydraulic Fracture Treatment (2016)

Summary A coupled hydraulic-geomechanical simulation is used to model hydraulic fracture growth and predict the corresponding microseismicity. Using a case study from the Horn River Basin, a quantitative match between the modeled and observed microseismic deformation is used to calibrate a reconstruction of the hydraulic fracture network that reconciles the geological and geomechanical earth model with the fracture engineering. The calibrated fracture model includes an estimate of the propped portion of the fracture network and can then be used to investigate alternate designs to optimize the well, completion and injection to maximize the conductive fracture and thereby reservoir drainage.
Parallel processing for combined intra prediction in high efficiency video coding (2011)

Advanced intra prediction is one of the key components in highly efficient video coding since it reduces the bit-rate of the most costly intra frames. Combined Intra Prediction (CIP) is a novel tool that takes into account well established directional prediction from neighboring blocks, as well as local mean prediction from current block. In this way, it reduces bit-rate by further exploiting spatial redundancy. This paper proposes an implementation that will overcome its potential limitation limited parallelization capabilities. In order to make it more computationally parallelizable, adaptive open-loop prediction templates have been designed. Experiments have been performed which show that the proposed design preserves coding gains introduced by CIP, while providing a solution for more parallelizable, and therefore faster, implementations.
Cavity enhanced few-cycle THz generation and coherent spectroscopy (2003)

Photoconductive Terahertz emitters with integrated Bragg mirrors are presented which show increased THz emission efficiency due to cavity enhanced absorption. These emitters also allow intracavity THz generation in mode-locked Ti:sapphire lasers.
Ultraviolet LED based compact and fast cortisol detector with ultra high sensitivity (2016)

A novel label free, compact, fast and noninvasive absorbance based optical sensing technique was devised for the first time to detect cortisol, a physical and psychological stress biomarker, using ultraviolet (UV) LEDs. LEDs at three different UV wavelengths were employed to demonstrate cortisol sensing with different cortisol concentration. From the differential photoresponse versus concentration curves, we calculated the sensitivity of the sensors to be 1 mV/μM, 0.15 mV/μM and 0.08 mV/μM at 240 nm, 250 nm and 260 nm wavelength respectively. The developed sensing technique can be easily incorporated with microfluidic system for point-of-care cortisol detection and such developed protocol can be used in personalized health monitoring.
Designs for a Microfabricated Magnetic Sifter (2009)

A microfabricated magnetic sifter has been designed and fabricated for applications in biological sample preparation. The device enables high-throughput, high-gradient magnetic separation of magnetic nanoparticles by utilizing parallel fluid flow through a dense array (~500 /mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) of micropatterned slots in a magnetically soft membrane. Finite element models have been carried out to map the magnetic field and magnetic field gradients of two variations of slot geometry resulting in two distinct capture behaviors. Experimental separations have been conducted using 20 nm diameter iron oxide nanoparticles with streptavidin functionalized surfaces. Inspection of the sifter with a scanning electron microscope revealed dense aggregates of nanoparticles captured at the regions of high magnetic field gradients calculated by the finite element models. Capture efficiencies ranging from 88.8%-100% were measured for a single <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pass</i> through the sifter, and elution efficiencies ranging from 50%-70.5% were measured for a single elution step.
A Genetically Encoded Direct Sensor of Antibody–Antigen Interactions (2009)

Fluorescent FABS: We have genetically encoded a 7-hydroxycoumarin moiety in an antibody combining site. The fluorescent Fab fragment reports change in fluorescence intensity upon binding of its antigen. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Rapid Three-Dimensional Thermal Characterization of Large-Scale Computing Facilities (2008)

We demonstrate a mobile measurement technology which allows for fast and systematic 3-D temperature mapping of data centers. This technology yields the first experimental 3-D temperature images of an actual data center. The experimental temperature distributions reveal strong hot spots in the data center suggesting that current cooling schemes can be readily improved.
Photonic crystal fibres and effective index approaches (2002)

Photonic crystal fibres are investigated with an effective index approach. The effective index of both core and cladding is found to be wavelength dependent. Accurate modelling must respect the rich topology of these fibres.
Precision micro drilling with copper vapor lasers (1994)

We have developed a copper vapor laser based micro machining system using advanced beam quality control and precision wavefront tilting technologies. Micro drilling has been demonstrated through percussion drilling and trepanning using this system. With a 30 W copper vapor laser running at multi-kHz pulse repetition frequency, straight parallel holes with size varying from 500 microns to less than 25 microns and with aspect ratio up to 1:40 have been consistently drilled on a variety of metals with good quality. For precision trepanned holes, the hole-to-hole size variation is typically within 1 % of its diameter. Hole entrance and exit are both well defined with dimension error less than a few microns. Materialography of sectioned holes shows little (sub-micron scale) recast layer and heat affected zone with surface roughness within 1-2 microns.
Immunization with the Truncated Adhesin<i>Moraxella catarrhalis</i>Immunoglobulin D–Binding Protein (MID<sup>764–913</sup>) Is Protective against<i>M. catarrhalis</i>in a Mouse Model of Pulmonary Clearance (2004)

Most Moraxella catarrhalis isolates express the outer membrane protein MID. In addition to its specific affinity for immunoglobulin D, MID functions as an adhesin and binds to human epithelium. The adhesive part is localized within MID(764-913). Two mid-deficient M. catarrhalis isolates were constructed and examined in a mouse model of pulmonary clearance. M. catarrhalis devoid of MID was cleared more efficiently, compared with the wild-type counterparts. Furthermore, mice immunized with MID(764-913) cleared M. catarrhalis much more efficiently, compared with mice immunized with bovine serum albumin. MID(764-913) is suggested as a promising candidate in a future M. catarrhalis vaccine.