gebhart/patrepeval huggingface dataset:
Immune Evasion of Porcine Reproductive and Respiratory Syndrome Virus through Glycan Shielding Involves both Glycoprotein 5 as Well as Glycoprotein 3 (2011)

Passive administration of porcine reproductive and respiratory syndrome virus (PRRSV) neutralizing antibodies (NAbs) can effectively protect pigs against PRRSV infection. However, after PRRSV infection, pigs typically develop a weak and deferred NAb response. One major reason for such a meager NAb response is the phenomenon of glycan shielding involving GP5, a major glycoprotein carrying one major neutralizing epitope. We describe here a type II PRRSV field isolate (PRRSV-01) that is highly susceptible to neutralization and induces an atypically rapid, robust NAb response in vivo. Sequence analysis shows that PRRSV-01 lacks two N-glycosylation sites, normally present in wild-type (wt) PRRSV strains, in two of its envelope glycoproteins, one in GP3 (position 131) and the other in GP5 (position 51). To determine the influence of these missing N-glycosylation sites on the distinct neutralization phenotype of PRRSV-01, a chimeric virus (FL01) was generated by replacing the structural genes of type II PRRSV strain FL12 cDNA infectious clone with those from PRRSV-01. N-glycosylation sites were reintroduced into GP3 and GP5 of FL01, separately or in combination, by site-directed mutagenesis. Reintroduction of the N-glycosylation site in either GP3 or GP5 allowed recovery of in vivo and in vitro glycan shielding capacity, with an additive effect when these sites were reintroduced into both glycoproteins simultaneously. Although the loss of these glycosylation sites has seemingly occurred naturally (presumably by passage through cell cultures), PRRSV-01 virus quickly regains these glycosylation sites through replication in vivo, suggesting that a strong selective pressure is exerted at these sites. Collectively, our data demonstrate the involvement of an N-glycan moiety located in GP3 in glycan shield interference.
The fed-batch principle for the molecular biology lab: controlled nutrient diets in ready-made media improve production of recombinant proteins in Escherichia coli (2016)

While the nutrient limited fed-batch technology is the standard of the cultivation of microorganisms and production of heterologous proteins in industry, despite its advantages in view of metabolic control and high cell density growth, shaken batch cultures are still the standard for protein production and expression screening in molecular biology and biochemistry laboratories. This is due to the difficulty and expenses to apply a controlled continuous glucose feed to shaken cultures. New ready-made growth media, e.g. by biocatalytic release of glucose from a polymer, offer a simple solution for the application of the fed-batch principle in shaken plate and flask cultures. Their wider use has shown that the controlled diet not only provides a solution to obtain significantly higher cell yields, but also in many cases folding of the target protein is improved by the applied lower growth rates; i.e. final volumetric yields for the active protein can be a multiple of what is obtained in complex medium cultures. The combination of the conventional optimization approaches with new and easy applicable growth systems has revolutionized recombinant protein production in Escherichia coli in view of product yield, culture robustness as well as significantly increased cell densities. This technical development establishes the basis for successful miniaturization and parallelization which is now an important tool for synthetic biology and protein engineering approaches. This review provides an overview of the recent developments, results and applications of advanced growth systems which use a controlled glucose release as substrate supply.
Net-shape diamond growth: applications in optics and electronics (2002)

A direct growth of CVD diamond components in order to avoid (or minimize) further surface treatment is considered. This transfer molding technique is based on diamond growth on a patterned substrate, the replica of those patterns being formed on the nucleation side of the diamond film. If the diamond nucleation density is high enough to provide the conformal coating of the microstructured substrate surface the exact replica of the original structure after removal of the substrate can be produced.
Identification and Characterization of Small Molecule Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase (2008)

Plasmodium falciparum causes the most deadly form of malaria and accounts for over one million deaths annually. The malaria parasite is unable to salvage pyrimidines and relies on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHOD), a mitochondrially localized flavoenzyme, catalyzes the rate-limiting step of this pathway and is therefore an attractive antimalarial chemotherapeutic target. Using a target-based high throughput screen, we have identified a series of potent, species-specific inhibitors of P. falciparum DHOD (pfDHOD) that are also efficacious against three cultured strains (3D7, HB3, and Dd2) of P. falciparum. The primary antimalarial mechanism of action of these compounds was confirmed to be inhibition of pfDHOD through a secondary assay with transgenic malaria parasites, and the structural basis for enzyme inhibition was explored through in silico structure-based docking and site-directed mutagenesis. Compound-mediated cytotoxicity was not observed with human dermal fibroblasts or renal epithelial cells. These data validate pfDHOD as an antimalarial drug target and provide chemical scaffolds with which to begin medicinal chemistry efforts.
Fault-Tolerant Meshes with Small Degree (1997)

This paper presents constructions for fault-tolerant, two-dimensional mesh architectures. The constructions are designed to tolerate k faults while maintaining a healthy n by n mesh as a subgraph. They utilize several novel techniques for obtaining trade-offs between the number of spare nodes and the degree of the fault-tolerant network. We consider both worst-case and random fault distributions. In terms of worst-case faults, we give a construction that has constant degree and O(k3) spare nodes. This is the first construction known in which the degree is constant and the number of spare nodes is independent of n. In terms of random faults, we present several new degree-6 and degree-8 constructions and show (both analytically and through simulations) that these constructions can tolerate large numbers of randomly placed faults.
Consensus with Byzantine Failures and Little System Synchrony (2006)

We study consensus in a message-passing system where only some of the n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> links exhibit some synchrony. This problem was previously studied for systems with process crashes; we now consider Byzantine failures. We show that consensus can be solved in a system where there is at least one non-faulty process whose links are eventually timely; all other links can be arbitrarily slow. We also show that, in terms of problem solvability, such a system is strictly weaker than one where all links are eventually timely
Abstract 16908: Will Alternating Between Fast and Slow Chest Compressions Improve Resuscitation Outcomes? (2017)

Mechanical chest compression devices could be designed to deliver compression patterns impractical for manual CPR. Different compression patterns may increase or change the distribution of blood fl...
Antimonide-based barrier infrared detectors (2010)

The nearly lattice-matched InAs/GaSb/AlSb (antimonide) material system offers tremendous flexibility in realizing high-performance infrared detectors. Antimonide-based alloy and superlattice infrared absorbers can be customized to have cutoff wavelengths ranging from the short wave infrared (SWIR) to the very long wave infrared (VLWIR). They can be used in constructing sophisticated heterostructures to enable advanced infrared photodetector designs. In particular, they facilitate the construction of unipolar barriers, which can block one carrier type but allow the unimpeded flow of the other. Unipolar barriers are used to implement the barrier infra-red detector (BIRD) design for increasing the collection efficiency of photo-generated carriers, and reducing dark current generation without impeding photocurrent flow. We report our recent efforts in achieving state-of-the-art performance in antimonide alloy and superlattice based infrared photodetectors using the BIRD architecture. Specifically, we report a 10 μm cutoff superlattice device based on a complementary barrier infrared detector (CBIRD) design. The detector, without antireflection coating or passivation, exhibits a responsivity of 1.5 A/W and a dark current density of 1×10<sup>-5</sup> A/cm<sup>2</sup> at 77K under 0.2 V bias. It reaches 300 K background limited infrared photodetection (BLIP) operation at 87 K, with a blackbody BLIP D* value of 1.1×10<sup>11</sup> cm-Hz<sup>1/2</sup>/W for f/2 optics under 0.2 V bias.
SPC: Fast and Efficient Scalable Predictive Coding of Animated Meshes (2009)

Abstract Animated meshes are often represented by a sequence of static meshes with constant connectivity. Due to their frame‐based representation they usually occupy a vast amount of bandwidth or disk space. We present a fast and efficient scalable predictive coding (SPC) scheme for frame‐based representations of animated meshes. SPC decomposes animated meshes in spatial and temporal layers which are efficiently encoded in one pass through the animation. Coding is performed in a streamable and scalable fashion. Dependencies between neighbouring spatial and temporal layers are predictively exploited using the already encoded spatio‐temporal neighbourhood. Prediction is performed in the space of rotation‐invariant coordinates compensating local rigid motion. SPC supports spatial and temporal scalability, and it enables efficient compression as well as fast encoding and decoding. Parts of SPC were adopted in the MPEG‐4 FAMC standard. However, SPC significantly outperforms the streaming mode of FAMC with coding gains of over 33%, while in comparison to the scalable FAMC, SPC achieves coding gains of up to 15%. SPC has the additional advantage over FAMC of achieving real‐time encoding and decoding rates while having only low memory requirements. Compared to some other non‐scalable state‐of‐the‐art approaches, SPC shows superior compression performance with gains of over 16% in bit‐rate.
Guided modes in photonic crystal slabs (1999)

We analyze the properties of two-dimensionally periodic dielectric structures that have a band gap for propagation in a plane and that use index guiding to confine light in the third dimension. Such structures are more amenable to fabrication than photonic crystals with full three-dimensional band gaps, but retain or approximate many of the latter's desirable properties. We show how traditional band-structure analysis can be adapted to slab systems in the context of several representative structures, and describe the unique features that arise in this framework compared to ordinary photonic crystals.
Reliability of metal–oxide–semiconductor capacitors on nitrogen implanted 4H-silicon carbide (1998)

4H- SiC epitaxial layers were implanted with nitrogen up to doses of 1×1015 cm−2 and annealed at different temperatures. Atomic force microscopy revealed that the roughness of the SiC surface increased with the annealing temperature. It was shown that the oxide grows thicker on substrates with doping levels exceeding 1×1018 cm−3. The barrier height at the SiC/SiO2 interface, determined by voltage ramping on metal–oxide–semiconductor capacitors, decreased with increasing implantation dose. This decrease was attributed to residual implantation damage. Constant current injection experiments revealed an opposite charge buildup at the SiC/SiO2 interface for the highest implantation dose compared to samples with no implantation. It was shown that the breakdown behavior can be improved by annealing at 1700 °C compared to 1450 °C despite a higher surface roughness.
Image Coding with Parameter-Assistant Inpainting (2007)

This paper carves out an image compression approach that integrates our parameter-assistant inpainting (PAI) technique to exploit the visual redundancy inherent in color-gradation image regions. In our scheme, an input image is first classified at block level according to the degree of edge content as well as chromatic variation in each block. An exemplar selection approach is then adopted to skip a majority of the gradation blocks during encoding. Only their positions and certain parameters extracted for condensed description are encoded along with the reserved blocks. At the decoder side, the skipped regions are recovered through image inpainting, relying on both the delivered parameters and reserved regions. Experimental results show that our proposed method outperforms baseline JPEG at color-gradation regions by nearly 80% bits-saving, at similar visual quality levels.
Experimental Evaluation of an ATM Host Interface (1993)

We have previously reported a design for a host interface board intended to connect workstations to ATM networks, and an implementation that was underway. Since then, we have made some modifications to the hardware implementation, and implemented software support. Our prototype connects an IBM RS/6000 to a SONET-based ATM network carrying data at the OC-3c rate of 155Mbps. In this paper, we discuss an experimental evaluation of the interface and supporting software. Our experiments uncovered an unexpected bottleneck in providing high bandwidth to application processes, and we suggest a number of possible improvements to workstation architectures to address this bottleneck.
Synthesis of submicron titanium diboride powders (1985)

New methods for the synthesis of submicron TiB/sub 2/ powders have been found and experimentally demonstrated. Three reactions schemes are proposed that all can give submicron TiB/sub 2/ powders as end product. The reactions take place as either 900 or 1500 K. Some properties of these powders are discussed.
Vertical waveguides integrated with silicon photodetectors: Towards high efficiency and low cross-talk image sensors (2012)

We describe the experimental realization of vertical silicon nitride waveguides integrated with silicon photodetectors. The waveguides are embedded in a silicon dioxide layer. Scanning photocurrent microscopy is performed on a device containing a waveguide, and on a device containing the silicon dioxide layer, but without the waveguide. The results confirm the waveguide’s ability to guide light onto the photodetector with high efficiency. We anticipate that the use of these structures in image sensors, with one waveguide per pixel, would greatly improve efficiency and significantly reduce inter-pixel crosstalk.
Unconstrained motion compensated temporal filtering (UMCTF) framework for wavelet video coding (2003)

The paper presents a new framework for adaptive temporal filtering in wavelet interframe codecs, called unconstrained motion compensated temporal filtering (UMCTF). This framework allows flexible and efficient temporal filtering by combining the best features of motion compensation, used in predictive coding, with the advantages of interframe scalable wavelet video coding schemes. UMCTF provides higher coding efficiency, improved visual quality and flexibility of temporal and spatial scalability, higher coding efficiency and lower decoding delay than conventional MCTF schemes. Furthermore, UMCTF can also be employed in alternative open-loop scalable coding frameworks using DCT for the texture coding.
Dendritic cells differentiated in the presence of IFN-β and IL-3 are potent inducers of an antigen-specific CD8+ T cell response (2005)

Dendritic cells (DC) are professional antigen-presenting cells that are used in vaccine approaches to cancer. Classically, mature monocyte-derived DC are generated in vitro in the presence of interleukin (IL)-4, granulocyte macrophage-colony stimulating factor, and inflammatory cytokines (G4-DC). Recently, it has been described that DC can also be generated in the presence of IL-3 and interferon (IFN)-beta and that these DC are efficiently matured using polyriboinosinic polyribocytidylic acid (I3-DC). In this study, a series of in vitro experiments was performed to compare side-by-side I3-DC and G4-DC as vaccine adjuvants. Phenotypic characterization of the DC revealed differences in the expression of the monocyte marker CD14 and the maturation marker CD83. Low expression of CD14 and high expression of CD83 characterized G4-DC, whereas I3-DC displayed intermediate expression of CD14 and CD83. Both types of DC were as potent in the induction of allogeneic T cell proliferation. Upon CD40 ligation, G4-DC produced lower amounts of IFN-alpha and pulmonary and activation-regulated chemokine, similar amounts of IL-6, macrophage-inflammatory protein (MIP)-1alpha, and MIP-1beta, and higher amounts of IL-12 p70, tumor necrosis factor alpha, and MIP-3beta than I3-DC. We further evaluated whether the DC could be frozen/thawed without loss of cell number, viability, phenotype, and function. After freezing/thawing, 56.0% +/- 9.0% of I3-DC and 77.0% +/- 3.0% of G4-DC (n=9) were recovered as viable cells, displaying the same phenotype as their fresh counterparts. Finally, in vitro stimulations showed that fresh and frozen peptide-loaded I3-DC are more potent inducers of Melan-A-specific CD8(+) T cell responses than G4-DC. The antigen-specific T cells were functional as shown in cytotoxicity and IFN-gamma secretion assay.
On the fundamentals of optical scanning holography (2008)

Optical scanning holography is a real-time holographic recording technique in which holographic information about a three-dimensional (3D) object is acquired using a single two-dimensional active optical scan. Applications of the technique include optical scanning microscopy, pattern recognition, 3D holographic display, and optical remote sensing. This paper introduces the basics of optical scanning holography.
Deployed ARMOR protection: the application of a game theoretic model for security at the Los Angeles International Airport (2008)

Security at major locations of economic or political importance is a key concern around the world, particularly given the threat of terrorism. Limited security resources prevent full security coverage at all times, which allows adversaries to observe and exploit patterns in selective patrolling or monitoring, e.g. they can plan an attack avoiding existing patrols. Hence, randomized patrolling or monitoring is important, but randomization must provide distinct weights to different actions based on their complex costs and benefits. To this end, this paper describes a promising transition of the latest in multi-agent algorithms -- in fact, an algorithm that represents a culmination of research presented at AAMAS - into a deployed application. In particular, it describes a software assistant agent called ARMOR (Assistant for Randomized Monitoring over Routes) that casts this patrolling/monitoring problem as a Bayesian Stackelberg game, allowing the agent to appropriately weigh the different actions in randomization, as well as uncertainty over adversary types. ARMOR combines three key features: (i) It uses the fastest known solver for Bayesian Stackelberg games called DOBSS, where the dominant mixed strategies enable randomization; (ii) Its mixed-initiative based interface allows users to occasionally adjust or override the automated schedule based on their local constraints; (iii) It alerts the users if mixed-initiative overrides appear to degrade the overall desired randomization. ARMOR has been successfully deployed since August 2007 at the Los Angeles International Airport (LAX) to randomize checkpoints on the roadways entering the airport and canine patrol routes within the airport terminals. This paper examines the information, design choices, challenges, and evaluation that went into designing ARMOR.
Joint-reconstruction-enabled partial-dithering strategy for edge-illumination x-ray phase-contrast tomography (2019)

Edge illumination X-ray phase-contrast tomography (EIXPCT) is a emerging imaging technology in which partially opaque gratings are utilized with laboratory-based X-ray sources to estimate the distribution of the complex-valued refractive index. Spatial resolution in EIXPCT is mainly determined by the grating period of a sample mask, but can be significantly improved by a dithering technique in which multiple projection images are required per tomographic view angle 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 (JR) method, a novel partial-dithering strategy for data acquisition is proposed. In this strategy, dithering is implemented at only a subset of the tomographic view angles. This results in spatial resolution that is comparable to that of the conventional full-dithering strategy where dithering is performed at every view angle, but the acquisition time is substantially decreased. The effect of dithering parameters on image resolution is explored.
Is Climate Change Controversial? Modeling Controversy as Contention Within Populations (2017)

A growing body of research focuses on computationally detecting controversial topics and understanding the stances people hold on them. Yet gaps remain in our theoretical and practical understanding of how to define controversy, how it manifests, and how to measure it. In this paper, we introduce a novel measure we call "contention", defined with respect to a topic and a population. We model contention from a mathematical standpoint. We validate our model by examining a diverse set of sources: real-world polling data sets, actual voter data, and Twitter coverage on several topics. In our publicly-released Twitter data set of nearly 100M tweets, we examine several topics such as Brexit, the 2016 U.S. Elections, and "The Dress", and cross-reference them with other sources. We demonstrate that the contention measure holds explanatory power for a wide variety of observed phenomena, such as controversies over climate change and other topics that are well within scientific consensus. Finally, we re-examine the notion of controversy, and present a theoretical framework that defines it in terms of population. We present preliminary evidence suggesting that contention is one dimension of controversy, along with others, such as "importance". Our new contention measure, along with the hypothesized model of controversy, suggest several avenues for future work in this emerging interdisciplinary research area.
Exploiting Nonlinearity to Design Robust Wireless Power Transfer and Wideband RF Energy Harvesting (2018)

In this paper, the design of position-insensitive wireless power transfer (WPT) circuits and wideband RF wireless energy harvesting (WEH) circuits are presented. The unique properties of a specific class of nonlinear resonant circuits described by a 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> order nonlinear differential equation with cubic or higher order nonlinear terms are exploited to design such circuits.The position-insensitive WPT circuit maintains a high power transmission efficiency (PTE) over large transmission distance and misalignment variations without tuning the source's operating frequency or employing tunable matching networks and active feedback/control circuitry. The wideband WEH circuit utilizes a nonlinear resonant circuit to significantly enhance its bandwidth. Both a WPT and a WEH circuit have been designed and tested. The WPT circuit achieves a constant power transfer and PTE of 20 W and 85%, respectively, over a varying transmission distance of 250 mm. On the other hand, the WEH circuit using a nonlinear resonator achieves 2.7 times bandwidth enhancement as compared to a similar circuit employing a linear resonator having the same quality factor,Q.