gebhart/patrepeval huggingface dataset:
Efficient Infectious Cell Culture Systems of the Hepatitis C Virus (HCV) Prototype Strains HCV-1 and H77 (2014)

Hepatitis C virus (HCV) was discovered in 1989 with the cloning of the prototype strain HCV-1 genome. In 1997, two molecular clones of H77, the other HCV prototype strain, were shown to be infectious in chimpanzees, but not in vitro. HCV research was hampered by a lack of infectious cell culture systems, which became available only in 2005 with the discovery of JFH1 (genotype 2a), a genome that could establish infection in Huh7.5 cells. Recently, we developed in vitro infectious clones for genotype 1a (TN), 2a (J6), and 2b (J8, DH8, and DH10) strains by identifying key adaptive mutations. Globally, genotype 1 is the most prevalent. Studies using HCV-1 and H77 prototype sequences have generated important knowledge on HCV. Thus, the in vitro infectious clones developed here for these 1a strains will be of particular value in advancing HCV research. Moreover, our findings open new avenues for the culture adaptation of HCV isolates of different genotypes.
Association studies of serum prostate-specific antigen levels and the genetic polymorphisms at the androgen receptor and prostate-specific antigen genes. (2002)

Testing for serum prostate-specific antigen (PSA) levels has been widely used to screen for prostate cancer. However, PSA testing has low specificity and sensitivity because PSA is not prostate cancer-specific. PSA is encoded by the APS gene, and the expression of this gene is regulated by androgens. W. Xue et al. Cancer Res., 60: 839-841, 2000 reported recently that serum PSA levels are associated with a G/A polymorphism at androgen responsive element 1 (ARE1) of APS and/or the CAG repeats in exon 1 of the androgen receptor (AR) gene. This result, if confirmed, may significantly increase the specificity and sensitivity of PSA testing by incorporating genotype-specific thresholds. In this study, we tested for the association between serum PSA levels and these single nucleotide polymorphisms (SNPs) in a large sample of 518 men. For the AR gene, we observed slightly (but not statistically significant) higher mean serum PSA levels in men with shorter CAG repeats (<or=21) or shorter GGC repeats (<or=16). For the ARE1 of the APS, we found slightly (but not statistically significant) lower PSA levels in men with the AA genotype. It is worth noting that this observation is opposite to the findings of W. Xue et al. Cancer Res., 60: 839-841, 2000. We hypothesize that the effects of ARE1 and AR genotypes on mean PSA levels may reflect the effect of other causal polymorphisms in these genes, which are in linkage disequilibrium with these polymorphisms. A systematic approach is required to identify sequence variants in these genes and other related genes, and to test for an association between these variants and PSA levels in large samples.
Ungated radial quiescent‐inflow single‐shot (UnQISS) magnetic resonance angiography using optimized azimuthal equidistant projections (2014)

Using UnQISS, peripheral NEMRA can be performed without the need for cardiac gating. The use of fixed imaging parameters and body coil for signal reception further simplifies the scan procedure.
First-principles study of a hydrogen storage material CaSi (2005)

We report the results of the first-principles calculation on the hydrogen storage material CaSi. The stability and bonding nature of CaSi hydride have been investigated theoretically with the ultrasoft pseudopotential method based on the density functional theory before experimentation. Theoretical prediction has suggested that CaSi hydride is thermodynamically stable. In actual measurements [M. Aoki et al., Appl. Phys. Lett. 85 387 (2004)] it is confirmed that CaSi reversibly absorbs and desorbs hydrogen, and the maximum hydrogen content is $1.9\phantom{\rule{0.3em}{0ex}}\mathrm{wt}\phantom{\rule{0.2em}{0ex}}%$ which means CaSi forms $\mathrm{Ca}\mathrm{Si}{\mathrm{H}}_{1.3}$. The hydriding reaction enthalpy of $\mathrm{Ca}\mathrm{Si}{\mathrm{H}}_{1.3}$ is estimated as $\ensuremath{-}42\phantom{\rule{0.3em}{0ex}}\mathrm{kJ}∕\mathrm{mol}\phantom{\rule{0.2em}{0ex}}{\mathrm{H}}_{2}$ from the calculation based on the crystal structure symmetry determined by the Rietveld refinements of synchrotron x-ray diffraction data, which is in fairly good agreement with an experimental value of $\ensuremath{-}62\phantom{\rule{0.3em}{0ex}}\mathrm{kJ}∕\mathrm{mol}\phantom{\rule{0.2em}{0ex}}{\mathrm{H}}_{2}$. From the calculation results of density of states, $\mathrm{Ca}\mathrm{Si}{\mathrm{H}}_{1.3}$ has an energy gap of $0.013\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ and the electronic structure is nonmetallic. The charge-density distribution indicates that one Si atom and one H atom are bonding covalently. It is thought that these electronic structures cause the stability of $\mathrm{Ca}\mathrm{Si}{\mathrm{H}}_{1.3}$.
Compressive Sensing for streaming signals using the Streaming Greedy Pursuit (2010)

Compressive Sensing (CS) has recently emerged as significant signal processing framework to acquire and reconstruct sparse signals at rates significantly below the Nyquist rate. However, most of the CS development to-date has focused on finite-length signals and representations. In this paper we present a new CS framework and a greedy reconstruction algorithm, the Streaming Greedy Pursuit (SGP), explicitly designed for streaming applications and signals of unknown length. Our sampling framework is designed to be causal and implementable using existing hardware architectures. Furthermore, our reconstruction algorithm provides explicit computational guarantees, which makes it appropriate for real-time system implementations. Our experimental results on very long signals demonstrate the good performance of the SGP and validate our approach.
Extended Global-Gradient Algorithm for Pressure-Dependent Water Distribution Analysis (2008)

Conventional water distribution models are formulated under the assumption that water consumptions or demands defined at nodes are known values, allowing nodal hydraulic heads and pipe flows to be determined by solving a set of quasi-linear equations. This formulation is well developed and is valid for the scenarios in which the hydraulic pressures throughout a system are adequate for delivering the required nodal demands. However, there are some scenarios where nodal pressure is not sufficient for supplying the required demand. These cases may include planned system maintenances, unplanned pipe outages, power failures at pump stations, and insufficient water supply from water sources. In addition, some water consumptions, such as leakages, are pressure dependent. This paper generalizes a robust and efficient approach for pressure-dependent water distribution analysis as a unified loop-node formulation. Nodal heads and flows are simultaneously solved by improving the global-gradient algorithm. The proposed approach has been applied to a pressure-deficient benchmark system, the criticality analysis of a small water system, and also to a large real water system. The paper demonstrates that good modeling performance has been achieved for simulating pressure-dependent demand conditions and evaluating the criticality of real water systems.
Head-related transfer function enhancement for improved vertical-polar localization. (2009)

Under ideal laboratory conditions, individualized head-related transfer functions (HRTFs) can produce virtual sound localization performance approaching the level achieved with real sound sources in the free field. However, in real-world applications of virtual audio, practical issues such as fit-refit variability in the headphone response and nonindividualized HRTFs generally lead to much worse localization performance, particularly in the up-down and front-back dimensions. Here we present a new technique that “enhances” the localizability of a virtual sound source by increasing the spectral contrast of the acoustic features that are relevant for spatial perception within a set of locations with nearly identical binaural cues (i.e., a “cone-of-confusion”). Validation experiments show that this enhancement technique can improve localization accuracy across a broad range of conditions, with as much as a 33% reduction in vertical-polar localization error for nonindividualized HRTFs measured on a KEMAR manikin; a 25% reduction in vertical-polar error for nonindividualized HRTFs measured on other human listeners; and a 33% reduction in vertical-polar error for individualized HRTFs presented under nonideal laboratory conditions (i.e., with headphone fit-refit variability). These results suggest that the proposed technique could provide benefits across a wide range of real-world virtual audio display applications. [Work sponsored by AFOSR.]
Reverse genetics approach towards understanding pathogenesis of H5N1 Hong Kong influenza A virus infection (2001)

In 1990, Palese and colleagues established a method (reverse genetics) that allowed one to generate influenza virus containing a gene segment derived from cloned cDNA. Although this method contributed tremendously to our understanding of influenza pathogenesis, the requirement of helper viruses limited its use in many experimental settings. Recently, we and others established systems for the generation of influenza viruses entirely from cloned cDNAs. These systems require only DNA cloning and transfection techniques, and can therefore be easily implemented by laboratories working in the fields of molecular biology and virology. Thus, for the first time, a system is now available that allows highly efficient generation of influenza virus without technical limitations. Using this technology, we generated the same strain of H5N1 influenza viruses that caused an outbreak in Hong Kong in 1997, killing six people.
Development of a Chemoenzymatic Process for Dehydroepiandrosterone Acetate Synthesis (2016)

Dehydroepiandrosterone (DHEA, 2) is an important endogenous steroid hormone in mammals used in the treatment of a variety of dysfunctions in female and male health,1 as well as an intermediate in the synthesis of steroidal drugs, such as abiraterone acetate which is used for the treatment of prostate cancer.2−4 In this manuscript we describe a novel, concise, and cost-efficient route toward DHEA (2) and DHEA acetate (3) from 4-androstene-3,17-dione (4-AD, 1). Crucial to success was the identification of a ketoreductase from Sphingomonas wittichii for the highly regio- and stereoselective reduction of the C3-carbonyl group of 5-androstene-3,17-dione (5) to the required 3β-alcohol (2, >99% de). The enzyme displayed excellent robustness and solvent stability under high substrate concentrations (up to 150 g/L).
Pistachio vicilin, Pis v 3, is immunoglobulin E‐reactive and cross‐reacts with the homologous cashew allergen, Ana o 1 (2008)

Of the 37% of pistachio/cashew-allergic patients' sera that recognized the pistachio allergen, rPis v 3, all showed complete cross-reactivity with rAna o 1. The data does not identify the primary sensitizing agent but suggests that IgE reactivity to rPis v 3 and rAna o 1 is focused on the most conserved regions of the proteins. Clinical histories suggest that in some cases, cashew was the sensitizing agent. rPis v 3 is a likely contributor to the observed co-sensitivity to pistachio and cashew in some patients.
Plant-Derived Chimeric Virus Particles for the Diagnosis of Primary Sjögren Syndrome (2015)

Plants are ideal for the production of protein-based nanomaterials because they synthesize and assemble complex multimeric proteins that cannot be expressed efficiently using other platforms. Plant viruses can be thought of as self-replicating proteinaceous nanomaterials generally stable and easily produced in high titers. We used Potato virus X (PVX), chimeric virus particles, and Cowpea mosaic virus, empty virus-like particles to display a linear peptide (lipo) derived from human lipocalin, which is immunodominant in Sjögren's syndrome (SjS) and is thus recognized by autoantibodies in SjS patient serum. These virus-derived nanoparticles were thus used to develop a diagnostic assay for SjS based on a direct enzyme linked immunosorbent assay format. We found that PVX-lipo formulations were more sensitive than the chemically synthesized immunodominant peptide and equally specific when used to distinguish between healthy individuals and SjS patients. Our novel assay therefore allows the diagnosis of SjS using a simple, low-invasive serum test, contrasting with the invasive labial biopsy required for current tests. Our results demonstrate that nanomaterials based on plant viruses can be used as diagnostic reagents for SjS, and could also be developed for the diagnosis of other diseases.
Synthesis and Use of Colloidal Silica for Reinforcement in Silicone Elastomers (2001)

Abstract Aqueous suspensions of colloidal silicas are readily silylated with either chlorosilanes or disiloxanes in the presence of acid and isopropyl alcohol without aggregation of the silica particle. By using a mixture of chlorosilanes or disiloxanes, spherical nanoparticles with controlled functionality can be made and transferred to an organic phase to provide stable, water free suspensions. The hydrophobic silica particles readily disperse into silicone polymers. At sufficient loading levels, they provide mechanical reinforcement comparable to traditional fillers but with improved clarity and lower viscosities. Modulus and durometer control in the cured elastomer is possible by varying the ratio of the vinyl concentration on the filler particle to the vinyl concentration in the polymer phase.
High-Throughput Detection of Glutathione <b> <i>S</i> </b>-Transferase Polymorphic Alleles in a Pediatric Cancer Population (2004)

Polymorphisms of glutathione S-transferase (GST) enzymes have been correlated with altered risk of several cancers, as well as altered response and toxicity from cancer chemotherapy. We report a low cost, highly reproducible and specific PCR-based high-throughput assay for genotyping different GSTs designed for use in large clinical trials. In comparison to an alternative genotyping method (single nucleotide extension), the sensitivity and specificity of the high throughput assay was shown to be 92 and 97%, respectively, depending on the source of genomic DNA. Using the high-throughput assay, we demonstrate by multivariate analysis an increased risk of acute lymphoblastic leukemia, glial brain tumors, and osteosarcoma for patients carrying nonnull alleles of GSTM1 and/or GSTT1.
New Serotype 2 and Attenuated Serotype 1 Marek's Disease Vaccine Viruses: Comparative Efficacy (1987)

Attempts were made, through selection of optimum viral strains, to develop improved vaccines against Marek's disease (MD). Seven attenuated serotype 1 strains and 22 avirulent serotype 2 strains, both alone and in combination with the FC126 strain of serotype 3, were screened for protective efficacy against challenge with virulent and very virulent MD viral strains. The three viruses selected as most promising were evaluated alone and in various combinations and compared with commercially available vaccines, including FC126, bivalent (FC126 + SB-1), and CV1988/C, in 12 separate assays. Two of these new viruses--301B/1 (serotype 2) and Md11/75C/R2 (serotype 1)--were exceptionally protective compared with prototype vaccine strains. Four new monovalent and polyvalent vaccines based on these two isolates protected chickens better than FC126 alone or CV1988/C alone. Three of these new vaccines provided better protection than the bivalent (FC126 + SB-1) vaccine. Protective synergism was noted commonly between viruses of serotypes 2 and 3 but only sporadically between serotypes 1 and 2 or between serotypes 1 and 3. Strain CVI988/C was protective but was no better than FC126 alone, and it was less effective than bivalent (FC126 + SB-1) vaccine, even when used as a bivalent vaccine with FC126 or SB-1.
Serial-Link Bus: A Low-Power On-Chip Bus Architecture (2008)

As technology scales, the shrinking wire width increases the interconnect resistivity, while the decreasing interconnect spacing significantly increases the coupling capacitance. This paper proposes reducing the number of bus lines of the conventional parallel-line bus (PLB) architecture by multiplexing each m-bits onto a single line. This bus architecture, the serial-link bus (SLB), transforms an <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> -bit conventional PLB into an <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</i> -line (serial link) bus. The advantage of SLBs is that they have fewer lines, and if the bus width is kept the same, SLBs will have a larger line pitch. Increasing the line width has a twofold reduction effect on the line resistance; as the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">resistivity</i> of sub-100 nm wires drops significantly, the line width increases. Also, increasing the line width and spacing reduces the coupling capacitance between adjacent lines, but increases the line-to-ground capacitance. Thus, an optimum degree of multiplexing <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">opt</sub> and an optimum width to pitch ratio eta <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">opt</sub> exist, which minimizes the bus energy dissipation and maximizes the bus throughput per unit area. The optimum degree of multiplexing and optimum width-to-pitch ratio for maximum throughput per unit area and minimum energy dissipation for the 25-130-nm technologies was determined in this paper. Also, an encoding technique was proposed and implemented to reduce the switch activity penalty due to serialization. HSPICE simulations show that for the same throughput per unit area as conventional parallel-line data buses, the SLB architecture reduces the energy dissipation by up to 31% for a 64-bit bus implemented in an intermediate metal layer of a 50-nm technology, and a reduction of 53% is projected for a 25-nm technology.
Rapid, Efficient, and Modular Generation of Adenoviral Vectors via Isothermal Assembly (2016)

Adenoviral vectors have yielded promising results as carriers for gene transfer and vaccines in basic research and clinical applications. However, most common procedures to construct adenoviral vectors and manipulate adenovirus (Ad) genomes are complex and labor-intensive. An easy and detailed protocol for the rapid, efficient, and modular generation of chimpanzee Ad serotype 68 (AdC68) as a molecular clone via isothermal assembly, which directionally assembles multiple DNA fragments in a single isothermal reaction without restriction enzymes or ligases, is presented. Any serotype of adenovirus with the sequence of genome known can be constructed as a molecular clone by this method. Recombinant adenoviral vectors can be created via one-step isothermal assembly in <3 days, and recombinant Ads can be rescued within 8 days. This protocol is practical for manipulations of Ad genomes, because an entire Ad genome can be divided into specific fragments within modular plasmids. © 2016 by John Wiley & Sons, Inc.
Engineering industrial Saccharomyces cerevisiae strains for xylose fermentation and comparison for switchgrass conversion (2010)

Saccharomyces' physiology and fermentation-related properties vary broadly among industrial strains used to ferment glucose. How genetic background affects xylose metabolism in recombinant Saccharomyces strains has not been adequately explored. In this study, six industrial strains of varied genetic background were engineered to ferment xylose by stable integration of the xylose reductase, xylitol dehydrogenase, and xylulokinase genes. Aerobic growth rates on xylose were 0.04-0.17 h(-1). Fermentation of xylose and glucose/xylose mixtures also showed a wide range of performance between strains. During xylose fermentation, xylose consumption rates were 0.17-0.31 g/l/h, with ethanol yields 0.18-0.27 g/g. Yields of ethanol and the metabolite xylitol were positively correlated, indicating that all of the strains had downstream limitations to xylose metabolism. The better-performing engineered and parental strains were compared for conversion of alkaline pretreated switchgrass to ethanol. The engineered strains produced 13-17% more ethanol than the parental control strains because of their ability to ferment xylose.
Phase control through Huygens' metasurfaces (2017)

We describe a dielectric Huygens' metasurface, operating in the visible spectrum, that can manipulate the phase of the transmitted light over a full 2π with high transmission efficiency. The metasurface is comprised of dielectric cylindrical nanoparticles embedded in a glass-like medium. The size of the nanoparticles and their separation are much smaller than the wavelength of visible light. From the metasurface, we construct a lens that focuses light to a diffraction limited spot size with high efficiency.
Nonsilica glasses for holey fibers (2005)

The authors of this paper investigated the thermal properties and optical properties of typical nonsilica glasses, including viscosity, surface tension, thermal conductivity, transmission, linear and nonlinear refractive index, and fiber attenuation in order to judge the feasibility of using nonsilica glasses as the background material of holey fibers (HFs). Novel techniques were presented to fabricate the nonsilica glass microstructured fiber preforms. Examples of fabricated nonsilica glass HFs with various promising optical applications were finally exhibited.
A Reconfigurable 28-/37-GHz MMSE-Adaptive Hybrid-Beamforming Receiver for Carrier Aggregation and Multi-Standard MIMO Communication (2019)

This paper presents a multi-standard fully connected hybrid beamforming (FC-HBF) receiver that can be reconfigured between two fully connected two-stream multi-input-multi-output (MIMO) modes at 28- or 37-GHz band, and an inter-band carrier-aggregation (CA) mode enabling concurrent single-stream operation at 28 and 37 GHz. A new image-reject (IR) heterodyne beamforming architecture is introduced that facilitates easy reconfiguration. Concurrent dual-band operation of the beamformer front end is achieved by using an inherently wideband Cartesian-combining-based RF-domain complex-weighting architecture, which is implemented using coupled-resonator-based dual-band gain stages, and current-mode dual-band active combiners. The downconversion stage comprises a cascade of complex-quadrature mixing stages that combines Cartesian complex-weighting operation with image rejection. A new quadrature error detection and calibration scheme is also introduced to improve the image rejection of the proposed architecture. A minimum mean-square error (MMSE) beam adaptation technique, introduced for the first time in an RF or hybrid beamformer, breaks the need for individual access to the beamformer inputs needed in a traditional least-mean-square (LMS) scheme and allows both main lobe and null adaptation. A 28-/37-GHz hybrid beamforming receiver with four antenna inputs and two baseband output streams is designed in 65-nm CMOS that demonstrates the above features. In each antenna path, the receiver achieves 33-dB (26.5 dB) peak conversion gain, 2.75-GHz (3.75 GHz) RF bandwidth, and 5.7-dB (8.5 dB) NF at 28 GHz (37 GHz). The entire receiver consumes 310 mW and occupies 2.2 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> core area. Extensive characterization results for single-element and several multi-element scenarios are presented including concurrent dual-band receiving (>35-dB image rejection), null-steering (>25-dB peak to null for two elements), and multi-element CA (~50-dB inter-carrier interference rejection).