gebhart/patrepeval huggingface dataset:
Identification of Amino Acids within Nonstructural Proteins 10 and 14 of the Avian Coronavirus Infectious Bronchitis Virus That Result in Attenuation <i>In Vivo</i> and <i>In Ovo</i> (2022)

The <i>Gammacoronavirus</i> infectious bronchitis virus (IBV) is a highly contagious global pathogen prevalent in all types of poultry flocks. IBV is responsible for economic losses and welfare issues in domestic poultry, resulting in a significant risk to food security. IBV vaccines are currently generated by serial passage of virulent IBV field isolates through embryonated hens' eggs. The different patterns of genomic variation accumulated during this process means that the exact mechanism of attenuation is unknown and presents a risk of reversion to virulence. Additionally, the passaging process adapts the virus to replicate in chicken embryos, increasing embryo lethality. Vaccines produced in this manner are therefore unsuitable for <i>in ovo</i> application. We have developed a reverse genetics system, based on the pathogenic IBV strain M41, to identify genes which can be targeted for rational attenuation. During the development of this reverse genetics system, we identified four amino acids, located in nonstructural proteins (nsps) 10, 14, 15, and 16, which resulted in attenuation both <i>in vivo</i> and <i>in ovo</i>. Further investigation highlighted a role of amino acid changes, Pro85Leu in nsp 10 and Val393Leu in nsp 14, in the attenuated <i>in vivo</i> phenotype observed. This study provides evidence that mutations in nsps offer a promising mechanism for the development of rationally attenuated live vaccines against IBV, which have the potential for <i>in ovo</i> application. <b>IMPORTANCE</b> The <i>Gammacoronavirus</i> infectious bronchitis virus (IBV) is the etiological agent of infectious bronchitis, an acute, highly contagious, economically important disease of poultry. Vaccination is achieved using a mixture of live attenuated vaccines for young chicks and inactivated vaccines as boosters for laying hens. Live attenuated vaccines are generated through serial passage in embryonated hens' eggs, an empirical process which achieves attenuation but retains immunogenicity. However, these vaccines have a risk of reversion to virulence, and they are lethal to the embryo. In this study, we identified amino acids in the replicase gene which attenuated IBV strain M41, both <i>in vivo</i> and in <i>ovo</i>. Stability assays indicate that the attenuating amino acids are stable and unlikely to revert. The data in this study provide evidence that specific modifications in the replicase gene offer a promising direction for IBV live attenuated vaccine development, with the potential for <i>in ovo</i> application.
Technique for Measuring the Spin Rate of Kinetic Energy Projectiles (1993)

Abstract : Kinetic energy projectiles were fitted with dihedral plugs in their tracer wells in an attempt to measure their spin histories via Doppler radar. Data from three projectiles were reduced and the approximate steady-state spin rates were obtained.... Doppler radar, Kinetic energy projectiles, Roll.
Optimized Driver Placement for Array-Driven Flat-Panel Loudspeakers (2017)

Abstract The recently demonstrated ‘modal crossover network’ method for flat panel loudspeaker tuning employs an array of force drivers to selectively excite one or more panel bending modes from a spectrum of panel bending modes. A regularly spaced grid of drivers is a logical configuration for a two-dimensional driver array, and although this can be effective for exciting multiple panel modes it will not necessarily exhibit strong coupling to all of the modes within a given band of frequencies. In this paper a method is described to find optimal force driver array layouts to enable control of all the panel bending modes within a given frequency band. The optimization is carried out both for dynamic force actuators, treated as point forces, and for piezoelectric patch actuators. The optimized array layouts achieve similar maximum mode coupling efficiencies in comparison with regularly spaced driver arrays; however, in the optimized arrays all of the modes within a specified frequency band may be independently addressed, which is important for achieving a desired loudspeaker frequency response. Experiments on flat panel loudspeakers with optimized force actuator array layouts show that each of the panel modes within a selected frequency band may be addressed independently and that the inter-modal crosstalk is typically −30 dB or less with non-ideal drivers.
Loss of ATRX, Genome Instability, and an Altered DNA Damage Response Are Hallmarks of the Alternative Lengthening of Telomeres Pathway (2012)

The Alternative Lengthening of Telomeres (ALT) pathway is a telomerase-independent pathway for telomere maintenance that is active in a significant subset of human cancers and in vitro immortalized cell lines. ALT is thought to involve templated extension of telomeres through homologous recombination, but the genetic or epigenetic changes that unleash ALT are not known. Recently, mutations in the ATRX/DAXX chromatin remodeling complex and histone H3.3 were found to correlate with features of ALT in pancreatic neuroendocrine cancers, pediatric glioblastomas, and other tumors of the central nervous system, suggesting that these mutations might contribute to the activation of the ALT pathway in these cancers. We have taken a comprehensive approach to deciphering ALT by applying genomic, molecular biological, and cell biological approaches to a panel of 22 ALT cell lines, including cell lines derived in vitro. Here we show that loss of ATRX protein and mutations in the ATRX gene are hallmarks of ALT-immortalized cell lines. In addition, ALT is associated with extensive genome rearrangements, marked micronucleation, defects in the G2/M checkpoint, and altered double-strand break (DSB) repair. These attributes will facilitate the diagnosis and treatment of ALT positive human cancers.
A class of block-iterative equalizers for intersymbol interference channels (2002)

A new and efficient class of nonlinear equalizers is introduced for intersymbol interference (ISI) channels. These "iterated-decision equalizers" use an optimized multipass algorithm to successively cancel ISI from a block of received data and generate symbol decisions whose reliability increases monotonically with each iteration. Asymptotically they achieve the performance of maximum-likelihood sequence detection (MLSD), but only have a computational complexity on the order of a linear equalizer (LE). And because their structure allows cancellation of both pre- and post-cursor ISI, iterated-decision equalizers outperform the minimum mean-square error decision-feedback equalizer (DFE) by 2.5 dB on severe ISI channels even with uncoded systems. Even more importantly, unlike the DFE, iterated-decision equalizers can be readily used in conjunction with error-control coding, making them attractive for a wealth of applications.
Practical Distributed Turbo Coding Through Soft Information Relaying (2006)

In this paper, we propose a novel distributed turbo coding (DTC) scheme which can be used in a system where imperfect decoding occurs at a relay. For the proposed scheme, rather than making a decision on the transmitted information symbols at the relay as in the conventional DTC, we calculate and forward the corresponding soft information at the relay. For the proposed scheme, we derive the parity symbols soft estimates for the interleaved source information when only the a posteriori probabilities (APP) of the information symbols are known. Analytical results show that the performance of the proposed scheme, at high SNR, is limited by the ratio of the received SNR at the relay and that at the destination. In order to make the performance loss of the proposed scheme, compared to the perfect DTC as small as possible, the relay should be placed closer to the source than to the destination and/or make the transmit power from the source larger than that from the relay.
<title>Broadband phased array transducer design with frequency-controlled two-dimensional capability</title> (1998)

With the wide acceptance of ultrasound medical imaging as the non-invasive diagnostic modality of choice, sonography equipment must offer the tools to complete the diagnosis, including multi-frequency operation for difficult-to-image patients. The trade-off between greater depth of penetration at low frequency for large organs and the improved detail resolution at high frequency is an essential capability that necessitates wideband transducer design and matching system hardware. This paper presents a phased array transducer design with variable ceramic thickness in the elevation direction. The design offers tow major contributions: first, -6dB round trip fractional bandwidth is increased by as much as 120 percent. This is done by controlling the thickness of the crystal from the middle to the outer edge. Since each sampling point in the crystal resonates freely at half wavelength in its fundamental mode, extended bandwidth is achieved for the single element in the phased array. This method has considerable advantage over the usual methods, such as backing the transducer with a matched lossy material. The drawback to backing the transducer is that the acoustic power consumed by the backing represents a severe insertion loss, especially if optimum bandwidth is desired. The second contribution of this design is the use of software to control the elevation slice thickness with axial symmetry around the 2D imaging plane. This is done by controlling the excitation frequency on transmit, and filtering on receive, thereby controlling the transmit and receive apertures independently during imaging. Compared to the standard elevation sampled 1.5D or 2D arrays with an increased number of hardware system channels and extensive cable wires needed, the new design offers simplicity and cost effectiveness. This represents a key development, especially with the advent of second harmonic imaging, both from a point of view of bandwidth requirement and slice thickness on receive. This paper also discusses other advantages of the design, presents experimental and simulation results, and shows a Schlieren video segment of the performance versus standard uniform thickness.
Binding and Structural Properties of DNA Aptamers with VEGF-A-Mimic Activity (2020)

Vascular endothelial growth factors (VEGFs) are hypoxia-inducible secreted proteins to promote angiogenesis, in which VEGF-A is an important molecule that binds and activates VEGF receptor-1 (VEGFR-1) and VEGFR-2. In this study, two DNA aptamers, Apt01 and Apt02, were successfully isolated by alternating consecutive systematic evolution of ligands by exponential enrichment (SELEX) against VEGFR-1 and -2 using deep sequencing analysis in an early selection round. Their binding affinities for VEGFR-2 were lower than that of VEGFR-1, which is similar to that of VEGF-A. Structural analyses with the measurements of circular dichroism spectra and ultraviolet melting curve showed that Apt01 possessed the stem-loop structure in the molecule, whereas Apt02 formed G-quadruplex structures. In addition, Apt02 accelerated a tube formation of human umbilical vein endothelial cells faster than Apt01, which was affected by difference of binding affinity and nuclease resistance due to G-quadruplex structures. These results demonstrated that Apt02 might have a potential to function as an alternative to VEGF-A.
A topology based dynamic traffic scheduling in time-domain wavelength interleaved networks (2005)

This study investigates the problem of scheduling data bursts in a wavelength division multiplexing (WDM) optical network called time-domain wavelength interleaved network (TWIN) I. Widjaja et al. (2003). Due to the innovative architecture of the TWIN, four issues are essential in the design of the traffic scheduling: there are no transmitting/receiving conflicts; propagation delays are observed; throughput is maximized and latency is kept as small as possible. In this paper, we introduce a novel topology-based dynamic scheduling (TBDS) framework, in which we deal with not only the transmitting/receiving conflicts, but also the network topology and link propagation delays. The consideration of network topology will take advantage of the interleaving opportunity in the TWIN to improve efficiency. We formulate the problem into an integer linear programming (ILP). We present the framework and simulation-based analysis of the system performance. We show that the TBDS algorithm achieves the same maximum throughput as the algorithm of K. Ross et al., (2003), but has relatively lower complexity and significantly less queuing delays.
ZVS Control strategy of dual active bridge DC/DC converter with triple‐phase‐shift modulation considering RMS current optimization (2019)

Dual active bridge (DAB) DC/DC converter is an ideal high‐power bidirectional DC/DC converter with multiple control methods. In this paper, the working characteristics of the DAB converters are analysed by the example of medium power mode, in which the voltage transfer ratio is less than 1. For the situation that the DAB converter is difficult to achieve soft switching at light load, a triple phase shift (TPS) control method is used. Combining with RMS current optimisation, a control method to achieve soft switching for full‐power range is proposed. The control strategy enables the converter to realise zero voltage switching (ZVS) of all the switching device, which not only improves the operating conditions of the switching device, but also improves the converter efficiency. Finally, a prototype of DAB was built. Compared with the traditional control method, the experimental results verify the effectiveness of the proposed control strategy.
Initial Development of Composite Repair Resins With Low Hazardous Air Pollutant Contents (2008)

Unsaturated polyester-based repair resins, such a Bondo, are widely used for automotive repair, marine repair, sporting equipment repair, and household repair of metal, composites, plastics, and wood. Commercial repair resins usually contain 10 to 40 weight-percent styrene, which is a hazardous air pollutant (HAP). Reducing HAPs in Army materials has become a high priority because of Environmental Protection Agency regulations, including the Defense Land Systems for Miscellaneous Equipment National Emissions Standard for Hazardous Air Pollutants (NESHAP) and the Reinforced Plastic Composites NESHAP. Fortunately, nonvolatile fatty acid monomers can be used to replace the styrene in these repair resins. Fatty acid monomers were formulated with vinyl ester or unsaturated polyester monomers to match the glass transition temperature of commercial repair resins. Various inorganic fillers were incorporated to match the rheological and mechanical properties of commercial repair resins. These resins have zero to low HAP contents and therefore are well within emissions regulations and reduce toxicity effects on workers.
<title>Internet roaming: a WLAN/3G integration system for enterprises</title> (2002)

This paper proposes an enterprise-oriented WLAN/3G network integration solution, called the Internet Roaming system. Differing from other operator-oriented WLAN/3G network integration solutions, the Internet Roaming system is a practical IP-based corporate network architecture that provides seamless internetworking across office WLAN, home WLAN, public WLAN, and 2.5G/3G cellular network for corporate wireless data users. An Internet Roaming system may have four building blocks. They are IRC (Internet Roaming Client), SMG (secure mobility gateway), SIA (Secure IP Access) gateway, and VSA (virtual single account) server. The IRC is a special client tool (software or hardware) installed on a wireless data device. It provides a secure mobile IP connection from the wireless data device to the corporate network transparent to the operating system of the wireless data devices. The SMG is a mobile IPsec gateway installed on the corporate core network facing the Internet. It works with the IRC to maintain a secure mobile IP connection when the wireless data device is connected on the Internet through a home WLAN, a public WLAN, or a cellular network. The SIA server is a special IPsec gateway installed on the corporate intranet where office WLAN is installed. It works with the IRC to assure the security of office WLAN while improving the routing efficiency for users computers. The VSA server manages the IRC, SMG, and SIA servers.
Effect of operating variables on the separation of DNA molecules by capillary polyacrylamide gel electrophoresis. (1992)

The influence of operating conditions on the separation of double stranded DNA molecules in capillary polyacrylamide gel electrophoresis is presented in continuation of previous work. In this study, an equation was derived that relates the effects of electrophoresis variables such as gel concentration, field strength, molecular weight and temperature to the migration velocity. As a model system, phage phi X174 DNA restriction fragments obtained by digestion with HaeIII have been examined. As an illustration of optimized conditions, DNA molecules up to the 10(3) base pair range were separated at high temperature (50 degrees C) in less than 6 min and with efficiencies as high as 5000 plates m-1 s-1.
Wavelength-coded multifocal microscopy (2010)

A wavelength-coded multifocal microscope incorporating multiplexed and wavelength-coded holographic gratings to generate wavelength-selective multifocal planes is presented. The focal planes are longitudinally spaced on the object plane, and each focal plane is probed by a designated wavelength. The recording of the multiplexed gratings takes place at a single wavelength by utilizing the Bragg degeneracy property; thus the maximum sensitive wavelength of blue 488 nm is used for recording, but the device is operated at a broad wavelength band of interest, all the way to red 633 nm. We present the design, implementation, and experimental image data demonstrating this microscope's ability to obtain biological tissue structures simultaneously at different focal planes using broadband illumination by LEDs.
Optomechanical ultrasound sensors in silicon photonics (2021)

Future applications of ultrasound and photoacoustic imaging require a matrix of small and sensitive ultrasound sensors with read-out through a flexible cable. Silicon photonic ultrasound sensors have good prospects: small and sensitive sensors, wafer-scale fabrication, and matrix read-out via single optical fiber using photonic multiplexing. Here, we discuss different types of silicon photonic ultrasound sensors and their applications. This includes our optomechanical ultrasound sensor with extreme sensitivity that is achieved with an innovative optomechanical silicon photonic waveguide in an acoustical membrane. We discuss limitations of state-of-the-art piezoelectric sensors, how silicon photonic sensors overcome these, and applications in medical imaging.
Quantifying undesired parallel components in Thévenin-equivalent acoustic source parameters (2018)

The calibration of an ear probe to determine its Thévenin-equivalent acoustic source parameters facilitates the measurement of ear-canal impedance and reflectance. Existing calibration error metrics, used to evaluate the quality of a calibration, are unable to reveal undesired parallel components in the source parameters. Such parallel components can result from, e.g., a leak in the ear tip or improperly accounting for evanescent modes, and introduce errors into subsequent measurements of impedance and reflectance. This paper proposes a set of additional error metrics that are capable of detecting such parallel components by examining the causality of the source admittance in the frequency domain and estimating the source pressure in the time domain. The proposed and existing error metrics are applied to four different calibrations using two existing calibration methods, representing typical use cases and introducing deliberate parallel components. The results demonstrate the capability of the proposed error metrics in identifying various undesired components in the source parameters that might otherwise go undetected.
ECT: Improved detection performance using a multi-frequency method of eddy current testing for outside circumferential cracks near an expansion of heat exchanger tubes (2010)

In eddy current testing (ECT), the vicinity of an expansion of heat exchanger tubes is a difficult area to inspect. This is because there are two noise sources near the tube expansion. One is a ferromagnetic tube sheet around the outside surface of the tube and the other is a circumferential step deformation on the inside surface. To detect outside circumferential cracks near the tube expansion, noise from both sources should be eliminated. To solve this problem, we devised an eddy current probe with an original coil arrangement and applied it using a multi-frequency method. In the coil arrangement, two exciting coils induced an eddy current flow in the axial direction of the tube and the pick-up coil detected only a circumferential component, while the axial components from both noise sources were not detected. Consequently, noise from both sources was appreciably suppressed and the noise amplitude due to the tube sheet was smaller than the signal amplitude from an outside circumferential notch with a depth of 20% of the tube thickness (20%t). The noise due to the circumferential step deformation was eliminated by a simple subtraction of the waveforms measured at two freguencies.
Phosphoric acid activation of nutshells for metals and organic remediation: process optimization (1998)

Almond, pecan, English walnut, black walnut and macadamia nut shells were chosen as hard, lignocellulosic precursors for the production of granular activated carbons (GACs). They were activated with H3PO4 under a variety of conditions. Following activation, a portion of each GACs was oxidized in air at 300°C for 4 h in order to create a carbon surface presumably with more oxygen functional groups for the adsorption of metal cations. Also investigated was a streamlining of the production techniques used. Several of the samples were subjected to a ‘Continuous’ process in which the carbon was activated and upon cooling to 300°C was oxidized with air. Beyond this activation, methods were developed wherein the activation process took place under air and without a discrete, separate oxidation step. These processes were designed to determine if any of the carbon's capabilities would be lost or enhanced in comparison to the more standard activate–cool–wash–oxidize method. The carbons produced from these various activation/oxidation methods consistently, and without regard to precursor composition, sequestered over 90% of available copper from a 3 mM copper chloride test solution and often adsorbed organic contaminants as effectively as some commercial carbons. © 1998 SCI
A 10-GHz Code-Modulated Interferometric Imager Using Commercial-Off-The-Shelf Phased Arrays (2019)

Code-modulated interferometric imaging is a lens-less approach to imaging in which existing analog phased-arrays are repurposed as an interferometer using code modulation. A 33-pixel, eight-element prototype is created using two commercially-available ADAR1000 phased-array receivers from Analog Devices Inc. The chips are connected at board level to a patch antenna array. The serial interface is used to apply codes whereas the on-chip power detector and data converter are used for direct read out of the composite code-multiplexed imaging data. These are then processed off-line in Matlab to reconstruct the image. The 33-pixel camera is demonstrated in hardware for point-source detection.