gebhart/patrepeval huggingface dataset:
Development of an fpga-based architecture enabling the hardware implementation of a three-dimensional finite-difference time-domain algorithm for the analysis of electromagnetic propagation (2004)

Although FDTD methods are accurate and well defined, current computer-system technology limits the speed at which these operations can be performed. Run times on the order of hours, weeks, months, or longer are common when solving problems of realistic size. Some problems are even too large to be effectively solved, due to practical time and memory constraints. The slow nature of the algorithm primarily results from the nested for-loops that are required to iterate over the three spatial dimensions and time. 
To shorten the computational time of this and other numerical techniques, people acquire faster computers, lease time on supercomputers, or build clusters of computers to gain a parallel processing speedup. These solutions can be prohibitively expensive and frequently impractical. As a result, an approach that increases the speed of the FDTD method in a relatively inexpensive and practical way is required. 
To this end, I have developed an FPGA-based acceleration architecture for the FDTD method. The acceleration hardware can accommodate larger problems than PCs and can solve them orders of magnitude faster. This system represents a new era in computational electromagnetic simulations, greatly increasing the speed at which current problems can be solved and permitting the analysis of new designs.
Ranking in Genealogy: Search Results Fusion at Ancestry (2019)

Genealogy research is the study of family history using available resources such as historical records. Ancestry provides its customers with one of the world's largest online genealogical index with billions of records from a wide range of sources, including vital records such as birth and death certificates, census records, court and probate records among many others. Search at Ancestry aims to return relevant records from various record types, allowing our subscribers to build their family trees, research their family history, and make meaningful discoveries about their ancestors from diverse perspectives. In a modern search engine designed for genealogical study, the appropriate ranking of search results to provide highly relevant information represents a daunting challenge. In particular, the disparity in historical records makes it inherently difficult to score records in an equitable fashion. Herein, we provide an overview of our solutions to overcome such record disparity problems in the Ancestry search engine. Specifically, we introduce customized coordinate ascent (customized CA) to speed up ranking within a specific record type. We then propose stochastic search (SS) that linearly combines ranked results federated across contents from various record types. Furthermore, we propose a novel information retrieval metric, normalized cumulative entropy (NCE), to measure the diversity of results. We demonstrate the effectiveness of these two algorithms in terms of relevance (by NDCG) and diversity (by NCE) if applicable in the offline experiments using real customer data at Ancestry.
Complementary reconstruction: Improving image quality in dynamic PET studies (2011)

One widely used method is the individual frame-by-frame reconstruction (IFR) method where the whole scan time duration is divided into multiple time frames, and the data in the each individual time frame is reconstructed separately. All the reconstructed images are used to obtain the temporal tracer uptake changes, and estimate kinetic parameters for quantitative studies. The method often has a drawback having low accuracy on the estimation process due to limited count rates when the frames are divided into very short time intervals to achieve enough temporal resolution. Forward model based iterative reconstruction methods have a potential to improve image quality, and a lot of research has shown their superior performance compared to analytical reconstruction methods, such as filtered-back projection (FBP). The (OS-)EM iterative reconstruction is now widely used in both pre-clinical and clinical imaging studies, and can be done very fast [2]. However, the non-negativity constraint imposed in such iterative reconstruction algorithms tends to produce asymmetric noise distribution (similar to Poisson distribution) in the reconstructed image. Here, we propose a novel reconstruction method which allows negative pixel values, and changes the noise distribution into a symmetric distribution (similar to Gaussian distribution) while still using iterative reconstruction methods.
Enediyne Natural Products: Biosynthesis and Prospect Towards Engineering Novel Antitumor Agents (2003)

This review gives a brief account on the current status of enediyne biosynthesis and the prospective of applying combinatorial biosynthesis methods to the enediyne system for novel analog production. Methods for cloning enediyne biosynthetic gene clusters are first reviewed. A unified paradigm for enediyne biosynthesis, characterized with (a) the enediyne PKS, (b) the enediyne PKS accessory enzymes, and (c) tailoring enzymes, is then presented. Strategies and tools for novel enediyne analog production by combinatorial biosynthesis are finally discussed. The results set the stage to decipher the molecular mechanism for enediyne biosynthesis and lay the foundation to engineer novel enediynes by combinatorial biosynthesis for future endeavors.
Doxorubicin Overproduction in <i>Streptomyces peucetius</i> : Cloning and Characterization of the <i>dnrU</i> Ketoreductase and <i>dnrV</i> Genes and the <i>doxA</i> Cytochrome P-450 Hydroxylase Gene (1999)

ABSTRACT Doxorubicin-overproducing strains of Streptomyces peucetius ATCC 29050 can be obtained through manipulation of the genes in the region of the doxorubicin (DXR) gene cluster that contains dpsH , the dpsG polyketide synthase gene, the putative dnrU ketoreductase gene, dnrV , and the doxA cytochrome P-450 gene. These five genes were characterized by sequence analysis, and the effects of replacing dnrU , dnrV , doxA , or dpsH with mutant alleles and of doxA overexpression on the production of the principal anthracycline metabolites of S. peucetius were studied. The exact roles of dpsH and dnrV could not be established, although dnrV is implicated in the enzymatic reactions catalyzed by DoxA, but dnrU appears to encode a ketoreductase specific for the C-13 carbonyl of daunorubicin (DNR) and DXR or their biosynthetic precursors. The highest DXR titers were obtained in a dnrX dnrU (N. Lomovskaya, Y. Doi-Katayama, S. Filippini, C. Nastro, L. Fonstein, M. Gallo, A. L. Colombo, and C. R. Hutchinson, J. Bacteriol. 180:2379–2386, 1998) double mutant and a dnrX dnrU dnrH (C. Scotti and C. R. Hutchinson, J. Bacteriol. 178:7316–7321, 1996) triple mutant. Overexpression of doxA in a doxA::aphII mutant resulted in the accumulation of DXR precursors instead of in a notable increase in DXR production. In contrast, overexpression of dnrV and doxA jointly in the dnrX dnrU double mutant or the dnrX dnrU dnrH triple mutant increased the DXR titer 36 to 86%.
DocHandles (2017)

In this paper, we describe DocHandles, a novel system that allows users to link to specific document parts in their chat applications. As users type a message, they can invoke the tool by referring to a specific part of a document, e.g., "@fig1 needs revision". By combining text parsing and document layout analysis, DocHandles can find and present all the figures "1" inside previously shared documents, allowing users to explicitly link to the relevant "document handle". In this way, Ddocuments become first-class citizens inside the conversation stream where users can seamlessly integrate documents in their text-centric messaging application.
Numerical Characterization of Shear Elasticity Values Estimated with the Time-of-Flight Approach (2019)

In clinical ultrasound applications, there is a need for accurate estimates of the shear elasticity, which is directly relevant to the characterization of liver fibrosis, cancer, and other pathologies. The time-of-flight (TOF) approach, which is widely used for estimating the shear elasticity, is effective in purely elastic media, but the TOF approach tends to overestimate the shear elasticity in viscoelastic shear wave phantoms and in soft tissues. To determine the range of shear viscosity values over which the TOF approach yields accurate estimates for the shear elasticity, multiple three-dimensional (3D) simulations of the acoustic radiation force and resulting shear wave particle displacement are assessed. The TOF method is evaluated for values of shear elasticity and shear viscosity within the range of values encountered in healthy liver tissue. A realistic 3D model of the acoustic radiation force is calculated using the fast nearfield method and the angular spectrum approach in FOCUS (https://www.egr.msu.edu/~fultras-web), and then the shear waves are simulated in 3D with Green's functions in viscoelastic media on a graphics processing unit (GPU). The TOF method is evaluated within a two-dimensional (2D) cross-section and is based on the Kelvin-Voigt model for a viscoelastic material. The results demonstrate that the accuracy of the TOF method is dependent on the shear elasticity and the shear viscosity, where the accuracy of the TOF method worsens as the shear viscosity increases within the ranges encountered in liver and also worsens as the elasticity increases for a fixed value of shear viscosity.
Chromosomal mapping of the genes GPRK5 and GPRK6 encoding G protein-coupled receptor kinases GRK5 and GRK6 (1995)

G protein-coupled receptor kinases (GRKs) play an important role in phosphorylating and regulating the activity of a variety of G protein-coupled receptors. Chromosomal mapping of the human genes for the two most recently identified members of the GRK family, GRK5 (GPRK5) and GRK6 (GPRK6), was accomplished by correlation of the presence of the GPRK5 and GPRK6 loci with specific chromosome regions in a rodent-human hybrid panel. These analyses revealed that GPRK5 maps to chromosome region 10q24-->qter while GPRK6 maps to 5q35. A GPRK6 related locus maps to 13pter-->q21.
Prediction of the Reflection Spectra of Three Ink Colour Prints (2001)

We have developed a colour prediction model and an ink-spreading model. The present study aims at confirming the validity of both models for the case of ink-jet prints using cyan, magenta and yellow inks.Our colour prediction model, augmented by the ink-jet spreading model, predicts accurately the reflection spectra of halftoned samples printed on an HP printer and on an Epson printer. For each printer, the reflection spectra of 125 samples uniformly distributed in the CMY colour cube were computed. The average prediction error between measured and predicted spectra is about ΔE = 2.5 in CIELAB. The model requires the estimation of a set of parameters which are deduced from a small set of measured samples. Such a model simplifies the calibration of ink-jet printers, as well as their recalibrations when ink or paper is changed.
Mechanisms of the Formation of Silica Particles from Precursors with Different Volatilities by Flame Spray Pyrolysis (2009)

The flame spray pyrolysis (FSP) synthesis of silica particles from two different precursors, tetraethylorthosilicate (TEOS) and silicic acid which have significantly different volatilities, was investigated. The size and morphology of the particles produced using various concentrations of precursors and flame temperatures were examined. Significantly different volatilities of the precursors affected the particle formation mechanism. Two different particle formation mechanisms, vapor phase reaction (VPR) and intradroplet reaction (IDR), are proposed based on the relative time scale for the evaporation of sprayed precursor droplets and for particle formation at the same process conditions. VPR resulted in silica agglomerates with small primary particles of around 10 nm sizes. IDR resulted in isolated and spherical silica particles with the sizes of around 650 nm from silicic acid.
High-sensitivity photoacoustic detection of chemical warfare agents (2004)

We report sensitive and selective detection of Diisopropyl methylphosphonate (DIMP) - a decomposition product of Sarin and a common surrogate for the nerve gases - in presence of several gases expected to be interferences in an urban setting. By employing photoacosutic spectroscopy with broadly tunable CO<sub>2</sub> laser as a radiation source we demonstrate detection sensitivity for DIMP in the presence of these interferences of better than 0.5 ppb in 60 second long measurement time, which satisfies most current homeland and military security requirements and validates the photoacoustic spectroscopy as a powerful technology for nerve gas sensing instrumentation.
Soliton Compression to Few-cycle Pulses by Cascaded Quadratic Nonlinearities (2007)

Theoretical and numerical investigation of pulse-compression in a nonlinear crystal is presented. SHG soliton number is introduced and show that compression only takes place when it is larger than the "usual" Kerr soliton number. Pulse compression with cascaded quadratic nonlinearities requires that the ratio of the SHG and Kerr soliton numbers N>1.
CO<sub>2</sub> enabled process integration for the production of cellulosic ethanol using bionic liquids (2016)

An integrated one-pot ionic liquid based biomass processing technology is developed that overcomes pH mismatch of the unit operations and enables ionic liquid reuse resulting in a 50% cost reduction compared with previously studied methods.
Macro-micro frequency tuning antenna for reconfigurable wireless communication systems (2007)

A small-sized (radiator ≃10×8 mm) microstrip monopole antenna for reconfigurable macro-micro frequency tuning is presented. The proposed antenna operates in WiBro (2.3–2.4 GHz) and WLAN 802.11a/b (2.4–2.48 GHz/5.15–5.35 GHz) service bands with a constant antenna gain. Two frequency tuning diodes, a pin diode and a varactor, are incorporated into a meander type radiator. The pin diode is used for frequency switching (macro-tuning) between 2 GHz band and 5 GHz band. In addition, the varactor is used for frequency tuning (micro-tuning) within wireless service bands (2.3–2.48 GHz and 5.15–5.35 GHz) to produce constant antenna gain.
An interpretive analysis of magnetotelluric data (1984)

Abstract A simple analysis to determine the dimensionality of magnetotelluric resistivity variations, to separate the near-surface resistivity variation from the variations at depth, and to find the relative resistivity variations with depth is described. Parameters derived from the magnetotelluric impedance tensor are mapped in pseudosection and planar view for two-dimensional (2-D) model data and for survey data from Montana. These data illustrate procedures that can qualitatively map complex resistivity structures in the lateral distance-frequency domain or, equivalently, the lateral distance-scaled vertical distance domain. Phase-dependent parameters have better vertical resolution than parameters related to scalar apparent resistivity, but the latter allow estimates of the resistivities encountered. Phase parameters for the Montana data provide a semiquantitatively accurate cross-section of a geologically known anticlinal structure. This suggests a means of subsurface structural mapping with magnetotelluric data. The use of these parameters with sufficiently dense and accurate data provides a first-order indication of structure for subsequent quantitative modeling.
Monoclonal Antibodies to Human Prostate and Bladder Tumor-Associated Antigens (1983)

No AccessJournal of Urology1 Dec 1983Monoclonal Antibodies to Human Prostate and Bladder Tumor-Associated Antigens J.J. Starling, S.M. Sieg, M.L. Beckett, P.F. Schellhammer, L.E. Ladaga, and G.L. Wright J.J. StarlingJ.J. Starling More articles by this author , S.M. SiegS.M. Sieg More articles by this author , M.L. BeckettM.L. Beckett More articles by this author , P.F. SchellhammerP.F. Schellhammer More articles by this author , L.E. LadagaL.E. Ladaga More articles by this author , and G.L. WrightG.L. Wright More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)51779-6AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Monoclonal Antibodies to Human Prostate and Bladder Tumor-Associated Antigens." The Journal of Urology, 130(6), p. 1250 © 1983 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 130Issue 6December 1983Page: 1250 Advertisement Copyright & Permissions© 1983 by The American Urological Association Education and Research, Inc.MetricsAuthor Information J.J. Starling More articles by this author S.M. Sieg More articles by this author M.L. Beckett More articles by this author P.F. Schellhammer More articles by this author L.E. Ladaga More articles by this author G.L. Wright More articles by this author Expand All Advertisement PDF downloadLoading ...
Mining bilingual data from the web with adaptively learnt patterns (2009)

Mining bilingual data (including bilingual sentences and terms) from the Web can benefit many NLP applications, such as machine translation and cross language information retrieval. In this paper, based on the observation that bilingual data in many web pages appear collectively following similar patterns, an adaptive pattern-based bilingual data mining method is proposed. Specifically, given a web page, the method contains four steps: 1) preprocessing: parse the web page into a DOM tree and segment the inner text of each node into snippets; 2) seed mining: identify potential translation pairs (seeds) using a word based alignment model which takes both translation and transliteration into consideration; 3) pattern learning: learn generalized patterns with the identified seeds; 4) pattern based mining: extract all bilingual data in the page using the learned patterns. Our experiments on Chinese web pages produced more than 7.5 million pairs of bilingual sentences and more than 5 million pairs of bilingual terms, both with over 80% accuracy.
Bulk Lifetimes up to 20 ms Measured on Unpassivated Silicon Discs Using Photoluminescence Imaging (2017)

With high-efficiency silicon solar cells approaching 25% efficiency in mass production, the requirements on the bulk lifetime and its uniformity across the wafer and the ingot increase dramatically. Since some cell architectures require these high lifetimes on starting material, the need arises for characterization methods to measure very high bulk lifetimes that are spatially resolved at an early stage before cell processing. A method based on the spectral ratio of two photoluminescence images is applied here on two unpassivated silicon discs from different positions within a Czochralski-grown phosphorous-doped n-type silicon ingot. The method allows the determination of spatially resolved bulk lifetime images on samples with adequate thickness and can be done within seconds and without the need to passivate surfaces. As-grown bulk lifetimes up to 20 ms are measured on the ingot's central disc, indicating recent improvements in crystallization technology, but are strongly reduced closer to the crown. Evidence suggesting the impact of thermal donors on the lifetime and effective doping concentration near the crown is found from combining spectral photoluminescence and infrared spectroscopy analyses. The technique could find applications in research and development activities, particularly in the optimization of Czochralski silicon crystal growth conditions.
Computer-aided detection system for clustered microcalcifications in digital breast tomosynthesis using joint information from volumetric and planar projection images (2015)

We propose a novel approach for the detection of microcalcification clusters (MCs) using joint information from digital breast tomosynthesis (DBT) volume and planar projection (PPJ) image. A data set of 307 DBT views was collected with IRB approval using a prototype DBT system. The system acquires 21 projection views (PVs) from a wide tomographic angle of 60° (60°-21PV) at about twice the dose of a digital mammography (DM) system, which allows us the flexibility of simulating other DBT acquisition geometries using a subset of the PVs. In this study, we simulated a 30° DBT geometry using the central 11 PVs (30°-11PV). The narrower tomographic angle is closer to DBT geometries commercially available or under development and the dose is matched approximately to that of a DM. We developed a new joint-CAD system for detection of clustered microcalcifications. The DBT volume was reconstructed with a multiscale bilateral filtering regularized method and a PPJ image was generated from the reconstructed volume. Task-specific detection strategies were designed to combine information from the DBT volume and the PPJ image. The data set was divided into a training set (127 views with MCs) and an independent test set (104 views with MCs and 76 views without MCs). The joint-CAD system outperformed the individual CAD systems for DBT volume or PPJ image alone; the differences in the test performances were statistically significant (p < 0.05) using JAFROC analysis.
A single-atom sharp iridium tip as an emitter of gas field ion sources (2009)

We report a reliable method for preparing a pure Ir single-atom tip by thermal treatment in oxygen. The atomic structure of the tip apex and its ion emission characteristics are investigated with field ion microscopy. We have shown that the Ir single-atom tip can be a good field ion emitter, capable of emitting a variety of gas ion beams, such as He+, H2+, N2+, and O2+, with high brightness and stability. In addition, this tip can easily be maintained and regenerated in vacuum, ensuring it has sufficient lifetime for practical applications.
Porcine circoviruses: a minuscule yet mammoth paradox (2008)

Porcine circovirus type 2 (PCV2) is the primary causative agent for porcine circovirus-associated disease (PCVAD). PCVAD has been the cause of considerable economic losses to the pork industry worldwide. The disease is primarily characterized by wasting, enlarged lymph nodes, jaundice and weight loss in affected weanling pigs. Several other complex syndromes involving reproductive failure, enteritis, pneumonia and necrotizing dermatitis have also been associated with PCV2 infection. Lymphoid depletion, which is the hallmark lesion of PCVAD, predisposes the host to immunosuppression. Disease progression is further complicated by co-infections with other bacterial and viral pathogens. Despite the availability of effective vaccines for the last 2 years, newly emerging strains of the virus have been reported to cause more severe outbreaks in parts of the USA and Canada. While knowledge of the biology and pathogenesis of PCV2 has progressed considerably over the last 12 years since the disease was recognized, many questions still remain to be answered.
Revival of Silenced Echo for Optical Quantum Memories: Efficiency and Noise Level (2012)

We present a novel quantum memory protocol inspired by the two photon echo that overcomes the main drawbacks of the latter, namely, contamination of the retrieval pulse by spontaneous emission and free induction decay. It makes use of two rephasing pulses instead of one, the second is intended to send the atoms back to the fundamental state so that the echo is emitted in a non-inverted medium. The emission of the echo after the first pulse is prevented by unfulfillment of the spatial phase matching condition. Experimental maximum efficiency is found to be limited to 30% for 0:5 at. % Tm3+:YAG, mainly because of finite coherence lifetime. We have performed a preliminary analysis of noise, finding a significant reduction of spontaneous emission noise in the retrieval mode. However, further improvements are to be done since the signal to noise ratio is still close to one.