gebhart/patrepeval huggingface dataset:
The production of hemagglutinin‐based virus‐like particles in plants: a rapid, efficient and safe response to pandemic influenza (2010)

During the last decade, the spectre of an influenza pandemic of avian origin has led to a revision of national and global pandemic preparedness plans and has stressed the need for more efficient influenza vaccines and manufacturing practices. The 2009 A/H1N1 (swine flu) outbreak has further emphasized the necessity to develop new solutions for pandemic influenza vaccines. Influenza virus-like particles (VLPs)-non-infectious particles resembling the influenza virus-represent a promising alternative to inactivated and split-influenza virions as antigens, and they have shown uniqueness by inducing a potent immune response through both humoral and cellular components of the immune system. Our group has developed a plant-based transient influenza VLP manufacturing platform capable of producing influenza VLPs with unprecedented speed. Influenza VLP expression and purification technologies were brought to large-scale production of GMP-grade material, and pre-clinical studies have demonstrated that low doses of purified, plant-produced influenza VLPs induce a strong and broad immune response in mice and ferrets. This review positions the recent developments towards the successful production of influenza VLPs in plants, including the production of VLPs from other human viruses and other forms of influenza antigens. The platform developed for large-scale production of VLPs is also presented along with an assessment of the speed of the platform to produce the first experimental vaccine lots from the identification of a new influenza strain.
Heterobimetallic Zeolite, InV-ZSM-5, Enables Efficient Conversion of Biomass Derived Ethanol to Renewable Hydrocarbons (2015)

Direct catalytic conversion of ethanol to hydrocarbon blend-stock can increase biofuels use in current vehicles beyond the ethanol blend-wall of 10-15%. Literature reports describe quantitative conversion of ethanol over zeolite catalysts but high C2 hydrocarbon formation renders this approach unsuitable for commercialization. Furthermore, the prior mechanistic studies suggested that ethanol conversion involves endothermic dehydration step. Here, we report the complete conversion of ethanol to hydrocarbons over InV-ZSM-5 without added hydrogen and which produces lower C2 (<13%) as compared to that over H-ZSM-5. Experiments with C2H5OD and in situ DRIFT suggest that most of the products come from the hydrocarbon pool type mechanism and dehydration step is not necessary. Thus, our method of direct conversion of ethanol offers a pathway to produce suitable hydrocarbon blend-stock that may be blended at a refinery to produce fuels such as gasoline, diesel, JP-8, and jet fuel, or produce commodity chemicals such as BTX.
An active power quality conditioner for reactive power and harmonics compensation (2002)

This paper presents a new three-phase active power quality conditioner (APQC) for compensating reactive power and harmonics in distribution systems. The scheme employs a multi-step inverter for reactive power compensation and PWM inverters for harmonic compensation. The inverters are decoupled in such a manner that the high-frequency harmonic compensation module uses inverters of low power rating, while the low-frequency reactive compensation module supports most of the stresses. This decoupled topology is expected to result in a significant reduction in cost and losses associated with active compensators for high-power applications. The principle of operation and the control strategy are described. Simulation results are presented to demonstrate the performance of the proposed system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Synthesis of Some Phthalocyanines and Napthalocyanines Derived from Sterically Hindered Phenols (1998)

A nucleophilic aromatic substitution reaction between a sterically hindered phenol and 4-nitrophthalonitrile, 3-nitrophthalonitrile or 6-fluoro-2,3-napthalonitrile has been used to prepare precursors for the synthesis of a number of phthalocyanines, such as 1, and naphthalocyanines bearing bulky substituents.
Cloning, mutagenesis, and characterization of the microalga <i>Parietochloris incisa</i> acetohydroxyacid synthase, and its possible use as an endogenous selection marker (2012)

Parietochloris incisa is an oleaginous fresh water green microalga that accumulates an unusually high content of the valuable long-chain polyunsaturated fatty acid (LC-PUFA) arachidonic acid within triacylglycerols in cytoplasmic lipid bodies. Here, we describe cloning and mutagenesis of the P. incisa acetohydroxyacid synthase (PiAHAS) gene for use as an herbicide resistance selection marker for transformation. Use of an endogenous gene circumvents the risks and regulatory difficulties of cultivating antibiotic-resistant organisms. AHAS is present in plants and microorganisms where it catalyzes the first essential step in the synthesis of branched-chain amino acids. It is the target enzyme of the herbicide sulfometuron methyl (SMM), which effectively inhibits growth of bacteria and plants. Several point mutations of AHAS are known to confer herbicide resistance. We cloned the cDNA that encodes PiAHAS and introduced a W605S point mutation (PimAHAS). Catalytic activity and herbicide resistance of the wild-type and mutant proteins were characterized in the AHAS-deficient E. coli, BUM1 strain. Cloned PiAHAS wild-type and mutant genes complemented AHAS-deficient bacterial growth. Furthermore, bacteria expressing the mutant PiAHAS exhibited high resistance to SMM. Purified PiAHAS wild-type and mutant proteins were assayed for enzymatic activity and herbicide resistance. The W605S mutation was shown to cause a twofold decrease in enzymatic activity and in affinity for the Pyruvate substrate. However, the mutant exhibited 7 orders of magnitude higher resistance to the SMM herbicide than that of the wild type.
Effects of calpastatin and μ-calpain markers in beef cattle on tenderness traits1,2 (2006)

The objective of this study was to assess the association of single nucleotide polymorphisms (SNP) developed at the calpastatin (CAST) and mu-calpain (CAPN1) genes with meat tenderness and palatability traits in populations with diverse genetic backgrounds. Three populations were used in the study. One population consisted of Bos taurus that included crossbred animals derived from Hereford, Angus, Red Angus, Limousin, Charolais, Gelbvieh, and Simmental (GPE7; n = 539). Another population consisted of Bos taurus with Bos indicus influence, including crossbred animals from Hereford, Angus, Brangus, Beefmaster, Bonsmara, and Romosinuano (GPE8; n = 580). The third population was Bos indicus and consisted of purebred Brahman (STARS; n = 444). Traits evaluated were meat tenderness measured as Warner-Bratzler shear force (WBSF; kg) at 14 d postmortem, and traits evaluated by trained sensory panels that included tenderness score, juiciness, and flavor intensity. A SNP at the CAST gene had a significant (P < 0.003) effect on WBSF and tenderness score in the GPE7 and GPE8 populations. Animals inheriting the TT genotype at CAST had meat that was more tender than those inheriting the CC genotype. The marker at the CAPN1 gene was significant (P < 0.03) for tenderness score in GPE7 and GPE8. Animals inheriting the CC genotype at CAPN1 had meat that was more tender than those inheriting the TT genotype. Markers at the CAST and CAPN1 genes were associated with flavor intensity in the GPE8 population. Animals inheriting the CC genotype at CAST and the TT genotype at CAPN1 produced steaks with an intense flavor when compared with the other genotypes. An interaction between CAST and CAPN1 was detected (P < 0.05) for WBSF on GPE8. The statistical significance of the interaction is questionable because of the limited number of observations in some cells. Markers developed at the CAST and CAPN1 genes are suitable for use in identifying animals with the genetic potential to produce meat that is more tender.
Novel methods for expression of foreign antigens in live vector vaccines (2013)

Bacterial live vector vaccines represent a vaccine development strategy that offers exceptional flexibility. In this approach, genes encoding protective antigens of unrelated bacterial, viral or parasitic pathogens are expressed in an attenuated bacterial vaccine strain that delivers these foreign antigens to the immune system, thereby eliciting relevant immune responses. Rather than expressing these antigens using low copy expression plasmids, here we pursue expression of foreign proteins from the live vector chromosome. Our strategy is designed to compensate for the inherent disadvantage of loss of gene dosage (vs. plasmid-based expression) by integrating antigen-encoding gene cassettes into multiple chromosomal sites already inactivated in an attenuated Salmonella enterica serovar Typhi vaccine candidate. We tested expression of a cassette encoding the green fluorescent protein (GFPuv) integrated separately into native guaBA, htrA or clyA chromosomal loci. Using single integrations, we show that expression levels of GFPuv are significantly affected by the site of integration, regardless of the inclusion of additional strong promoters within the incoming cassette. Using cassettes integrated into both guaBA and htrA, we observe cumulative synthesis levels from two integration sites superior to single integrations. Most importantly, we observe that GFPuv expression increases in a growth phase-dependent manner, suggesting that foreign antigen synthesis may be "tuned" to the physiology of the live vaccine. We expect this novel platform expression technology to prove invaluable in the development of a wide variety of multivalent live vector vaccines, capable of expressing multiple antigens from both chromosomal and plasmid-based expression systems within a single strain.
Place-pitch discrimination of single- versus dual-electrode stimuli by cochlear implant users (2005)

Simultaneous or near-simultaneous activation of adjacent cochlear implant electrodes can produce pitch percepts intermediate to those produced by each electrode separately, thereby increasing the number of place-pitch steps available to cochlear implant listeners. To estimate how many distinct pitches could be generated with simultaneous dual-electrode stimulation, the present study measured place-pitch discrimination thresholds for single- versus dual-electrode stimuli in users of the Clarion CII device. Discrimination thresholds were expressed as the proportion of current directed to the secondary electrode of the dual-electrode pair. For 16 of 17 electrode pairs tested in six subjects, thresholds ranged from 0.11 to 0.64, suggesting that dual-electrode stimuli can produce 2-9 discriminable pitches between the pitches of single electrodes. Some subjects demonstrated a level effect, with better place-pitch discrimination at higher stimulus levels. Equal loudness was achieved with dual-electrode stimuli at net current levels that were similar to or slightly higher than those for single-electrode stimuli.
ARES: Adaptive, Reconfigurable, Erasure Coded, Atomic Storage (2019)

Emulating a shared atomic, read/write storage system is a fundamental problem in distributed computing. Replicating atomic objects among a set of data hosts was the norm for traditional implementations (e.g., [6]) in order to guarantee the availability and accessibility of the data despite host failures. As replication is highly storage demanding, recent approaches suggested the use of erasure-codes to offer the same fault-tolerance while optimizing storage usage at the hosts. Initial works focused on a fix set of data hosts. To guarantee longevity and scalability, a storage service should be able to dynamically mask hosts failures by allowing new hosts to join, and failed host to be removed without service interruptions. This work presents the first erasure-code based atomic algorithm, called ARES, which allows the set of hosts to be modified in the course of an execution. ARES is composed of three main components: (i) a reconfiguration protocol, (ii) a read/write protocol, and (iii) a set of data access primitives. The design of ARES is modular and is such to accommodate the usage of various erasure-code parameters on a per-configuration basis. We provide bounds on the latency of read/write operations and analyze the storage and communication costs of the ARES algorithm.
Permalloy Loaded Transmission Lines for High-Speed Interconnect Applications (2004)

The mutual inductance and self-inductance of global interconnects are important but difficult to extract and model in deep submicrometer very large scale integration (VLSI) designs. The absence of effective mutual magnetic field shielding limits the maximum unbuffered interconnect line length. In this paper, we propose and demonstrate that permalloy-loaded transmission lines can be used for high-speed interconnect applications to overcome these limitations. Permalloy films were incorporated into planar transmission lines using a CMOS-compatible process. The line characteristics show that eddy-current effects are the limiting factors for the high-frequency permalloy applications when ferromagnetic resonance are restrained through geometry design. Patterning permalloy films effectively extends their application to above 20 GHz. The line characteristic impedances are about /spl sim/90 /spl Omega/. Under 50 mA dc current biases, the line parameters did not change much. Moreover, the patterned permalloy reduces the magnetic field coupling between two adjacent transmission lines by about 10 dB in our design. The demonstrated operation frequency range, current carrying capability and magnetic field shielding properties indicate that the permalloy loaded lines are suitable for high-speed interconnect applications in CMOS technologies.
Synthesis and biological activity of flavipucine analogs (1980)

A series of analogues of flavipucine was prepared possessing side chain as well as nuclear variants. The analogue with an octyl side chain (5d) was found to exhibit enhanced activity against several bacteria and fungi as compared with the natural product itself. The separation and characterization of the individual diastereoisomeric pairs both spectroscopically and with respect to chromatographic mobility have been effected.
HIV-1 Envelope Proteins and V1/V2 Domain Scaffolds with Mannose-5 to Improve the Magnitude and Quality of Protective Antibody Responses to HIV-1 (2014)

Two lines of investigation have highlighted the importance of antibodies to the V1/V2 domain of gp120 in providing protection from HIV-1 infection. First, the recent RV144 HIV-1 vaccine trial documented a correlation between non-neutralizing antibodies to the V2 domain and protection. Second, multiple broadly neutralizing monoclonal antibodies to the V1/V2 domain (e.g. PG9) have been isolated from rare infected individuals, termed elite neutralizers. Interestingly, the binding of both types of antibodies appears to depend on the same cluster of amino acids (positions 167–171) adjacent to the junction of the B and C strands of the four-stranded V1/V2 domain β-sheet structure. However, the broadly neutralizing mAb, PG9, additionally depends on mannose-5 glycans at positions 156 and 160 for binding. Because the gp120 vaccine immunogens used in previous HIV-1 vaccine trials were enriched for complex sialic acid-containing glycans, and lacked the high mannose structures required for the binding of PG9-like mAbs, we wondered if these immunogens could be improved by limiting glycosylation to mannose-5 glycans. Here, we describe the PG9 binding activity of monomeric gp120s from multiple strains of HIV-1 produced with mannose-5 glycans. We also describe the properties of glycopeptide scaffolds from the V1/V2 domain also expressed with mannose-5 glycans. The V1/V2 scaffold from the A244 isolate was able to bind the PG9, CH01, and CH03 mAbs with high affinity provided that the proper glycans were present. We further show that immunization with A244 V1/V2 fragments alone, or in a prime/boost regimen with gp120, enhanced the antibody response to sequences in the V1/V2 domain associated with protection in the RV144 trial.
Tissue Engineering for the Replacement of Urologic Organs (2002)

Numerous urologic tissue substitutes have been attempted with both synthetic and organic materials (1). The first application of a free-tissue graft for bladder replacement was reported by Neuhoff in 1917, when fascia was used to augment bladders in dogs (2). Since that first report, multiple other free-graft materials have been used experimentally and clinically, including skin, bladder submucosa, omentum, dura, peritoneum, placenta, sero-muscular grafts, and small intestinal submucosa (3–8). Synthetic materials, which have been tried previously in experimental and clinical settings, include polyvinyl sponge, tetrafluoroethylene (Teflon), gelatin sponge, collagen matrices, vicryl matrices, resin-sprayed paper, and silicone (9–15). Some of the aforementioned attempts have not gained clinical acceptance owing to either mechanical, structural, functional, or biocompatibility problems. Permanent synthetic materials have been associated with mechanical failure and calculus formation. Natural materials usually resorb with time and have been associated with marked graft contracture.
Six Degrees Crankshaft Individual Air Fuel Ratio Estimation of Diesel Engines for Cylinder Balancing Purpose (2006)

<div class="htmlview paragraph">In the context of modern engine control, one important variable is the individual Air Fuel Ratio (AFR) which is a good representation of the produced torque. It results from various inputs such as injected quantities, boost pressure, and the exhaust gas recirculation (EGR) rate. Further, for forthcoming HCCI engines and regeneration filters (Particulate filters, DeNOx), even slight AFR unbalance between the cylinders can have dramatic consequences and induce important noise, possible stall and higher emissions. Classically, in Spark Ignition engine, overall AFR is directly controlled with the injection system. In this approach, all cylinders share the same closed-loop input signal based on the single λ-sensor (normalized Fuel-Air Ratio measurement, it can be rewritten with <img class="article-image inline" src="2006-01-0013_fig0001.jpg" alt=""/> AFR as they have the same injection set-point. Unfortunately, due to inherent flaws of the injection system (pressure waves, mechanical tolerances, …), the total mass of fuel injected in each cylinder is very difficult to predict with a relative precision better than 7%. Having a sensor in each cylinder would enable an accurate individual control. In practice, cost and reliability of multiple λ-sensors prevent them from reaching commercial products lines. In this context, individual cylinder AFR estimation can give crucial information to get the HCCI running better.</div> <div class="htmlview paragraph">The contribution of this paper is the design and experimental tests of a real-time observer for the individual cylinder AFR using the reliable and available λ-sensor placed downstream the turbine as only measurement. In previous works, the methods used to reconstruct the AFR of each cylinder from the UEGO (Universal Exhaust Gas Oxygen) λ-sensor measurement are based on the permutation dynamics at the TDC (Top-Dead Center) time-scale and a gain identification technique. Here, we propose a higher frequency approach (6 degree crankshaft angle modelling and update instead of 180(TDC)). We design an observer on the balance model of the exhaust and design a high frequency observer to solve the problem. We use a physics-based model underlying the role of periodic input flows (gas flows from the cylinders into the exhaust manifold). The observer is validated experimentally on a 4 cylinder HCCI engine. As a conclusion, we provide results of closed-loop control using the proposed technique to prove the relevance of this approach.</div>
Recycled Error Bits: Energy-Efficient Architectural Support for Floating Point Accuracy (2014)

In this work, we provide energy-efficient architectural support for floating point accuracy. For each floating point addition performed, we "recycle" that operation's rounding error. We make this error architecturally visible such that it can be used, whenever desired, by software. We also design a compiler pass that allows software to automatically use this feature. Experimental results on physical hardware show that software that exploits architecturally recycled error bits can (a) achieve accuracy comparable to a 64-bit FPU with performance and energy that are comparable to a 32-bit FPU, and (b) achieve accuracy comparable to an all-software scheme for 128-bit accuracy with far better performance and energy usage.
Use of modified live feline panleukopenia virus vaccine to immunize dogs against canine parvovirus (1983)

Modified live feline panleukopenia virus (FPLV) vaccine protected dogs against canine parvovirus (CPV) infection. However, unlike the long-lived (greater than or equal to 20-month) immunity engendered by CPV infection, the response of dogs to living FPLV was variable. Doses of FPLV (snow leopard strain) in excess of 10(5.7) TCID50 were necessary for uniform immunization; smaller inocula resulted in decreased success rates. The duration of immunity, as measured by the persistence of hemagglutination-inhibiting antibody, was related to the magnitude of the initial response to vaccination; dogs with vigorous initial responses resisted oronasal CPV challenge exposure 6 months after vaccination, and hemagglutination-inhibiting antibodies persisted in such dogs for greater than 1 year. Limited replication of FPLV in dogs was demonstrated, but unlike CPV, the feline virus did not spread to contact dogs or cats. Adverse reactions were not associated with living FPLV vaccination, and FPLV did not interfere with simultaneous response to attenuated canine distemper virus.
Method and apparatus for dynamic reproduction of transient and steady state voices in an electronic musical instrument (1985)

First Page
Therapeutic Potential of Targeting the Oncogenic SHP2 Phosphatase (2014)

The Src homology 2 domain containing protein tyrosine phosphatase-2 (SHP2) is an oncogenic phosphatase associated with various kinds of leukemia and solid tumors. Thus, there is substantial interest in developing SHP2 inhibitors as potential anticancer and antileukemia agents. Using a structure-guided and fragment-based library approach, we identified a novel hydroxyindole carboxylic acid-based SHP2 inhibitor 11a-1, with an IC50 value of 200 nM and greater than 5-fold selectivity against 20 mammalian PTPs. Structural and modeling studies reveal that the hydroxyindole carboxylic acid anchors the inhibitor to the SHP2 active site, while interactions of the oxalamide linker and the phenylthiophene tail with residues in the β5-β6 loop contribute to 11a-1's binding potency and selectivity. Evidence suggests that 11a-1 specifically attenuates the SHP2-dependent signaling inside the cell. Moreover, 11a-1 blocks growth factor mediated Erk1/2 and Akt activation and exhibits excellent antiproliferative activity in lung cancer and breast cancer as well as leukemia cell lines.
<title>In-vivo local determination of tissue optical properties</title> (1998)

Local and superficial optical characterization of biological tissues can be achieved by measuring the spatially resolved diffuse reflectance at small source-detector separations. The sensitivity of the signal to the phase function, absorption and scattering coefficients were studied using Monte Carlo simulations. Measurements of spatially resolved reflectance were performed in vivo on human brain with source-detector separations from 0.3 to 1.5 mm. Distinct optical properties were found between normal cortex, astrocytoma of optic nerve and normal optic nerve.