gebhart/patrepeval huggingface dataset:
Broadening the Heterologous Cross-Neutralizing Antibody Inducing Ability of Porcine Reproductive and Respiratory Syndrome Virus by Breeding the GP4 or M genes (2013)

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important swine pathogens, which causes reproductive failure in sows and respiratory disease in piglets. A major hurdle to control PRRSV is the ineffectiveness of the current vaccines to confer protection against heterologous strains. Since both GP4 and M genes of PRRSV induce neutralizing antibodies, in this study we molecularly bred PRRSV through DNA shuffling of the GP4 and M genes, separately, from six genetically different strains of PRRSV in an attempt to identify chimeras with improved heterologous cross-neutralizing capability. The shuffled GP4 and M genes libraries were each cloned into the backbone of PRRSV strain VR2385 infectious clone pIR-VR2385-CA. Three GP4-shuffled chimeras and five M-shuffled chimeras, each representing sequences from all six parental strains, were selected and further characterized in vitro and in pigs. These eight chimeric viruses showed similar levels of replication with their backbone strain VR2385 both in vitro and in vivo, indicating that the DNA shuffling of GP4 and M genes did not significantly impair the replication ability of these chimeras. Cross-neutralization test revealed that the GP4-shuffled chimera GP4TS14 induced significantly higher cross-neutralizing antibodies against heterologous strains FL-12 and NADC20, and similarly that the M-shuffled chimera MTS57 also induced significantly higher levels of cross-neutralizing antibodies against heterologous strains MN184B and NADC20, when compared with their backbone parental strain VR2385 in infected pigs. The results suggest that DNA shuffling of the GP4 or M genes from different parental viruses can broaden the cross-neutralizing antibody-inducing ability of the chimeric viruses against heterologous PRRSV strains. The study has important implications for future development of a broadly protective vaccine against PRRSV.
Carboetomidate (2010)

Carboetomidate is an etomidate analog that retains many beneficial properties of etomidate, but it is dramatically less potent as an inhibitor of adrenocortical steroid synthesis. Carboetomidate is a promising new sedative hypnotic for potential use in critically ill patients in whom adrenocortical suppression is undesirable.
‘Candidatus Liberibacter asiaticus’, Causal Agent of Citrus Huanglongbing, Is Reduced by Treatment with Brassinosteroids (2016)

Huanglongbing (HLB) constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, 'Candidatus Liberibacter asiaticus'. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with next generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. The results demonstrate that epibrassinolide may provide a useful tool for the management of HLB.
Laser action in strongly scattering rare-earth-metal-doped dielectric nanophosphors (2001)

We report continuous-wave laser action in two oxide nanopowders doped with ${\mathrm{Ce}}^{3+}$ and ${\mathrm{Pr}}^{3+}$ ions. To our knowledge, these are the first observations of stimulated emission from electrically pumped random media in which scattering and distributed feedback scale lengths are much shorter than a wavelength. The continuous nature of the laser emission in small volumes (on the order of a cubic wavelength) of these low gain systems, and the absence of coherent speckle, provide compelling evidence that these results are mediated by strong Anderson localization of light.
High‐strength fire‐ and heat‐resistant imide resins containing cyclotriphosphazene and hexafluoroisopropylidene groups (1984)

Abstract High‐strength fire‐ and heat‐resistant polymers were obtained by the thermally induced melt‐polymerization of maleimido‐phenoxy cyclotriphosphazenes linked by hexafluoroisopropyliden‐ediphthalimide groups. These polymers show good thermal stability and high char yields: 78–80% at 800°C in nitrogen and 60–68% in air at 700°C. Graphite‐fabric laminates did not burn in pure oxygen, even at 300°C (LOI = 100%), and were tested for shear, flexural, and tensile strengths. Two monomers were synthesized by reacting tris(4‐aminophenoxy)‐tris(phenoxy) cyclotriphosphazene with maleic anhydride and hexafluoroisopropylidenediphthalic anhydride. The triamine was synthesized by a stepwise reaction of hexachlorocyclotriphosphazene with phenol and 4‐nitrophenol to give tris(4‐nitrophenoxy)‐tris(phenoxy)cyclotriphosphazene and reducing the nitro groups. The structures of cyclic phosphazene‐trimeric precursors and the polymers were characterized by FT‐IR, 1 H‐NMR, 31 P‐NMR, and mass spectroscopy. The curing behaviors of polymer precursors were evaluated by differential scanning calorimetry and thermogravimetric analyses.
A universal CMOS voltage interface circuit (2003)

A CMOS interface circuit to transfer a digital signal between two circuits of different supply voltages is described. The interface can be used, for example, between 3 volt and 5 volt or higher voltage families. The principal characteristics of the interface circuit are: no static power dissipation, high speed, and high speed buffering.
A partial-dithering strategy for edge-illumination x-ray phase-contrast tomography enabled by a joint reconstruction method (2020)

Edge-illumination x-ray phase-contrast tomography (EIXPCT) is a promising imaging technology where partially opaque masks are utilized with laboratory-based x-ray sources to estimate the distribution of the complex-valued refractive index. EIXPCT resolution is mainly determined by the period of a sample mask, but can be significantly improved by a dithering technique. Here, dithering means that multiple images per tomographic view angle are acquired as the object is moved over sub-pixel distances. Drawbacks of dithering include increased data-acquisition times and radiation doses. Motivated by the flexibility in data-acquisition designs enabled by a recently developed joint reconstruction method, a novel partial-dithering strategy for EIXPCT data-acquisition is proposed. In this strategy, dithering is implemented at only a subset of the tomographic view angles. The strategy can result in spatial resolution comparable to that of the conventional full-dithering strategy, where dithering is performed at every view angle, but the acquisition time is substantially decreased. Here, the effect of dithering parameters on image resolution is explored.
High-sensitivity cytometric detection using fluidic-photonic integrated circuits with array waveguides (2005)

We demonstrate a new detection scheme for a microfabricated flow cytometer. The fluidic-photonic integrated circuits (FPICs) that perform flow cytometric detection possess new functionality, such as on-chip excitation, time-of-flight measurement, and above all, greatly enhanced fluorescence detection sensitivity. Using the architecture of space-division waveguide demultiplexer and the technique of cross-correlation analysis, we obtained high detection sensitivity with a simple light source and a detector, without high-power laser excitation and lock-in amplifier (or photomultiplier tube) detection. Besides improving cytometric detection, the technology of integrating microfluidic circuits with photonic circuits into the FPIC presents a new platform for sophisticated biomedical-sensing devices with significant cost, size, and performance advantages.
Controlling Gene‐Silencing with Azobenzene‐Containing siRNAs (siRNAzos) (2020)

This article contains the detailed biophysical characterization, biological testing, and photo-switching protocols of azobenzene containing siRNAs (siRNAzos), which have photoswitchable properties that can be controlled with light. First, the siRNAzos are characterized by annealing the sense and anti-sense strands together and then measuring the circular dichroism (CD) profile, and the melting temperatures (T<sub>m</sub> ) of the duplexes. Second, the biological testing of the siRNAzos in cell culture is done to determine their gene silencing efficacy. Finally, their gene-silencing activities are measured after exposure to ultraviolet (UV) light in order to inactivate the siRNAzo, and then broadband visible light, which re-activates the siRNAzo. This inactivation/reactivation protocol can be done in real time, and is reversible and robust and can be performed multiple times on the same sample if desired. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Bio-physical characterization of siRNAzo duplexes Basic Protocol 2: Evaluation of azobenzene gene-silencing using Firefly Luciferase Basic Protocol 3: Evaluation of azobenzene gene-silencing using reverse transcriptase-polymerase chain reaction (RT-PCR).
<title>Text-dependent speaker verification using data fusion and channel detection</title> (1994)

A new system is presented for text-dependent speaker verification. The system uses data fusion concepts to combine the results of distortion-based and discriminant-based classifiers. Hence, both intraspeaker and interspeaker information are utilized in the final decision. The distortion and discriminant-based classifiers used are dynamic time warping and the neural tree network, respectively. The system is evaluated with several hundred one word utterances collected over a telephone channel. All handsets considered in this experiment use electret microphones. The new system is found to perform exceptionally well for this task. A second experiment uses handsets having both electret and carbon button microphones. Here, a channel detection scheme is proposed that improves performance under these conditions.
Self-Frequency Doubled Nd:YCOB laser (1998)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text B. H. T. Chai, J. M. Eichenholz, Q. Ye, D. A. Hammons, W. K. Jang, L. Shah, G. M. Luntz, and M. Richardson, "Self-Frequency Doubled Nd:YCOB laser," in Advanced Solid State Lasers, W. Bosenberg and M. Fejer, eds., Vol. 19 of OSA Trends in Optics and Photonics Series (Optica Publishing Group, 1998), paper VL5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Word Characters and Phone Pronunciation Embedding for ASR Confidence Classifier (2019)

Confidence classifier is an integral component of an automatic speech recognition (ASR) system. These classifiers predict the accuracy of an ASR hypothesis by associating a confidence score in [0,1] range, where larger score implies higher probability of the hypothesis being correct. Confidence scores have significant applications in ASR system design, training data selection, model adaptation, and other ASR applications. In this work we focus on word embedding features to improve confidence classifier, and introduce character and phone embeddings as confidence features. We motivate these features in the context of representing and factorizing acoustic scores along the proposed features. We evaluate our work on large scale ASR tasks, and demonstrate significant improvement in the confidence performance with the proposed features. At our typical operating point, we report 8% relative reduction in false alarm (FA) for limited vocabulary enUS Xbox task, and 9.9% relative reduction in FA for large vocabulary enUS server task. We also conducted server experiments for our proposed features in combination with natural language Glove embeddings, and improved the overall relative reduction in FA to 16%.
Deep Learning in Label-free Cell Classification (2016)

Abstract Label-free cell analysis is essential to personalized genomics, cancer diagnostics, and drug development as it avoids adverse effects of staining reagents on cellular viability and cell signaling. However, currently available label-free cell assays mostly rely only on a single feature and lack sufficient differentiation. Also, the sample size analyzed by these assays is limited due to their low throughput. Here, we integrate feature extraction and deep learning with high-throughput quantitative imaging enabled by photonic time stretch, achieving record high accuracy in label-free cell classification. Our system captures quantitative optical phase and intensity images and extracts multiple biophysical features of individual cells. These biophysical measurements form a hyperdimensional feature space in which supervised learning is performed for cell classification. We compare various learning algorithms including artificial neural network, support vector machine, logistic regression, and a novel deep learning pipeline, which adopts global optimization of receiver operating characteristics. As a validation of the enhanced sensitivity and specificity of our system, we show classification of white blood T-cells against colon cancer cells, as well as lipid accumulating algal strains for biofuel production. This system opens up a new path to data-driven phenotypic diagnosis and better understanding of the heterogeneous gene expressions in cells.
A Hidden Environment Model for Constructing Indoor Radio Maps (2005)

Constructing indoor radio maps plays an important role in many services and applications, such as wireless base station planning. We propose a hybrid approach to constructing indoor radio maps by developing a novel indoor signal propagation model, called the hidden environment model (HEM). The model is hybrid because it combines on-site measurements with a number of different types of calculations. As part of this model, we introduce the idea of an environment factor matrix (EFM). The EFM represents a model of the environmental features that affect radio attenuation. We also develop a lazy sampling algorithm to help generate the EFM. The goal of the lazy sampling algorithm is to balance the number of measurements that need to be taken with our model's accuracy. The goal is to minimize the measurement workload while maintaining satisfactory accuracy. We evaluate our model by comparing the radio maps calculated from the model to a radio map obtained by exhaustive measurements. The results show that our hidden environment model achieves good accuracy.
Cloning, expression, and genetic mapping of Sema W, a member of the semaphorin family (1999)

The semaphorins comprise a large family of membrane-bound and secreted proteins, some of which have been shown to function in axon guidance. We have cloned a transmembrane semaphorin, Sema W, that belongs to the class IV subgroup of the semaphorin family. The mouse and rat forms of Sema W show 97% amino acid sequence identity with each other, and each shows about 91% identity with the human form. The gene for Sema W is divided into 15 exons, up to 4 of which are absent in the human cDNAs that we sequenced. Unlike many other semaphorins, Sema W is expressed at low levels in the developing embryo but was found to be expressed at high levels in the adult central nervous system and lung. Functional studies with purified membrane fractions from COS7 cells transfected with a Sema W expression plasmid showed that Sema W has growth-cone collapse activity against retinal ganglion-cell axons, indicating that vertebrate transmembrane semaphorins, like secreted semaphorins, can collapse growth cones. Genetic mapping of human SEMAW with human/hamster radiation hybrids localized the gene to chromosome 2p13. Genetic mapping of mouse Semaw with mouse/hamster radiation hybrids localized the gene to chromosome 6, and physical mapping placed the gene on bacteria artificial chromosomes carrying microsatellite markers D6Mit70 and D6Mit189. This localization places Semaw within the locus for motor neuron degeneration 2, making it an attractive candidate gene for this disease.
Cross-sectional structural analysis for 3D printing optimization (2013)

We propose a novel cross-sectional structural analysis technique that efficiently detects critical stress inside a 3D object. We slice the object into cross-sections and compute stress based on bending momentum equilibrium. Unlike traditional approaches based on finite element methods, our method does not require a volumetric mesh or solution of linear systems, enabling interactive analysis speed. Based on the stress analysis, the orientation of an object is optimized to increase mechanical strength when manufactured with 3D printing.
Unlimited Sampling of Sparse Signals (2018)

In a recent paper [1], we introduced the concept of “Unlimited Sampling”. This unique approach circumvents the clipping or saturation problem in conventional analog-to-digital converters (ADCs) by considering a radically different ADC architecture which resets the input voltage before saturation. Such ADCs, also known as Self-Reset ADCs (SR-ADCs), allow for sensing modulo samples. In analogy to Shannon's sampling theorem, the unlimited sampling theorem proves that a bandlimited signal can be recovered from modulo samples provided that a certain sampling density criterion, that is independent of the ADC threshold, is satisfied. In this way, our result allows for perfect recovery of a bandlimited function whose amplitude exceeds the ADC threshold by orders of magnitude. By capitalizing on this result, in this paper, we consider the inverse problem of recovering a sparse signal from its low-pass filtered version. This problem frequently arises in several areas of science and engineering and in context of signal processing, it is studied in several flavors, namely, sparse or FRI sampling, super-resolution and sparse deconvolution. By considering the SR-ADC architecture, we develop a sampling theory for modulo sampling of lowpass filtered spikes. Our main result consists of a new sparse sampling theorem and an algorithm which stably recovers a K -sparse signal from low-pass, modulo samples. We validate our results using numerical experiments.
Application of photoluminescence characterization to the development and manufacturing of high-efficiency silicon solar cells (2006)

Characterization techniques based on quasi-steady-state photoluminescence have recently emerged as accurate, fast, and powerful tools for developing high-efficiency silicon solar cells. These techniques are contactless and provide complementary spatial and injection level dependent information about recombination. In this paper, we demonstrate the application of different photoluminescence techniques to several important aspects of high-efficiency solar cell fabrication: wafer handling, furnace contamination, process-induced defects, cell design, and cell process monitoring. The experimental results demonstrate that photoluminescence characterization techniques are excellent tools for laboratory experiments and also potentially for industrial process monitoring.
Development of Alumina-Forming Austenitic Stainless Steels (2008)

Work in fiscal year 2008 focused on the development of creep-resistant, alumina-forming austenitic (AFA) stainless steel alloys, which exhibit a unique combination of excellent oxidation resistance via protective alumina (Al2O3) scale formation and high-temperature creep strength through the formation of stable nano-scale MC-type carbides [1-8]. Levels of Nb additions(&gt; 1 wt. % Nb and/or Ni additions in the range of ∼25-30 wt. % and Al levels of 2.5-4 wt.%, were found to correlate with an increase in the upper-temperature limit for Al2O3 scale formation in air (∼900°C) and air with 10 % water vapor (∼800°C). Creep resistance also showed a strong dependence on the level of Nb additions, and was correlated with volume fraction of MC-type carbides using thermodynamic computational tools. A ∼50 lb trial heat of a AFA alloy ingot was made using conventional single-melt vacuum techniques, and that alloy was successfully hot-rolled without any cracking [2]. This heat showed good weldability using matching filler material of the same alloy.
Dependence of ultra-low timing jitter on intra-cavity loss for modelocked semiconductor light sources (2001)

Summary form only given. The use of stable optical pulse-trains as sampling pulses may allow for accurate analog-to-digital conversion of wide-band RF signals. Specifically, 10 Gbps pulse trains with 10 fs of timing jitter could provide for 12-bit A/D conversion of 10 GHz signals. Modelocked semiconductor lasers may provide the needed sampling pulses for such an application. In determining timing jitter, the phase noise is typically integrated at offset frequencies below 10 MHz. To be useful for such systems, however, characterization of the phase noise up to the roundtrip frequency may be needed. In the paper, comparative measurements of timing jitter (10 Hz to 10 MHz) of a modelocked semiconductor laser under gain and loss modulation is shown. Further, a numerical model incorporating spontaneous emission is developed which points toward low-frequency noise as the main source of jitter. Indications of total timing jitter (10 Hz-5 GHz) of the order of 40 fs is given.
Phase noise and spur performance limits for fractional-N frequency synthesizers (2015)

The output phase noise of a fractional-N frequency synthesizer comprises two components: intrinsic noise in the controlled oscillator itself, and extrinsic noise caused by unwanted modulation at its control input. The extrinsic noise contains both stochastic and deterministic components. This paper considers strategies to minimize the extrinsic noise component by addressing deterministic nonlinear dynamical mechanisms.
Synthesis and stability of iron nanoparticles for lunar environment studies (2010)

Abstract– Simulants of lunar dust are needed when researching the lunar environment. However, unlike the true lunar dust, today’s simulants do not contain nanophase iron. Two different processes have been developed to fabricate nanophase iron to be used as part of a lunar dust simulant. (1) The first is to sequentially treat a mixture of ferric chloride, fluorinated carbon, and soda lime glass beads at about 300 °C in nitrogen, at room temperature in air, and then at 1050 °C in nitrogen. The product includes glass beads that are gray in color, can be attracted by a magnet, and contains α-iron nanoparticles (which seem to slowly lose their lattice structure in ambient air during a period of 12 months). This product may have some similarity to the lunar glassy agglutinate, which contains FeO. (2) The second is to heat a mixture of carbon black and a lunar simulant (a mixed metal oxide that includes iron oxide) at 1050 °C in nitrogen. This process simulates lunar dust reactions with the carbon in a micrometeorite at the time of impact. The product contains a chemically modified simulant that can be attracted by a magnet and has a surface layer whose iron concentration increased during the reaction. The iron was found to be α-iron and Fe3O4 nanoparticles, which appear to grow after the fabrication process. This growth became undetectable after 6 months of ambient air storage, but may last for several years or longer.