gebhart/patrepeval huggingface dataset:
Conserved Surface Features Form the Double-stranded RNA Binding Site of Non-structural Protein 1 (NS1) from Influenza A and B Viruses (2007)

Influenza A viruses cause a highly contagious respiratory disease in humans and are responsible for periodic widespread epidemics with high mortality rates. The influenza A virus NS1 protein (NS1A) plays a key role in countering host antiviral defense and in virulence. The 73-residue N-terminal domain of NS1A (NS1A-(1-73)) forms a symmetric homodimer with a unique six-helical chain fold. It binds canonical A-form double-stranded RNA (dsRNA). Mutational inactivation of this dsRNA binding activity of NS1A highly attenuates virus replication. Here, we have characterized the unique structural features of the dsRNA binding surface of NS1A-(1-73) using NMR methods and describe the 2.1-A x-ray crystal structure of the corresponding dsRNA binding domain from human influenza B virus NS1B-(15-93). These results identify conserved dsRNA binding surfaces on both NS1A-(1-73) and NS1B-(15-93) that are very different from those indicated in earlier "working models" of the complex between dsRNA and NS1A-(1-73). The combined NMR and crystallographic data reveal highly conserved surface tracks of basic and hydrophilic residues that interact with dsRNA. These tracks are structurally complementary to the polyphosphate backbone conformation of A-form dsRNA and run at an approximately 45 degrees angle relative to the axes of helices alpha2/alpha2'. At the center of this dsRNA binding epitope, and common to NS1 proteins from influenza A and B viruses, is a deep pocket that includes both hydrophilic and hydrophobic amino acids. This pocket provides a target on the surface of the NS1 protein that is potentially suitable for the development of antiviral drugs targeting both influenza A and B viruses.
Effect of d-limonene on the Fermentation of Citrus Peel Waste (2006)

Approximately 10 million tons of oranges are processed in the US each year, producingapproximately 5 million tons of citrus peel waste consisting of peel, seeds and segment membranes.Conversion of citrus peel waste into more valuable products, such as fuel ethanol, would greatly benefitthe citrus industry. One of the problems in fermenting sugars in citrus processing waste is the presenceof peel oil, which predominantly consists of the antimicrobial terpene d-limonene. This study assessedthe tolerance of Saccharomyces cerevisiae to limonene during fermentation of hydrolyzed citrus peelwaste. Orange peel waste from a commercial facility was hydrolyzed by commercial pectinase, cellulase,and beta-glucosidae enzymes in 250 ml bottles. Peel oil containing 95% limonene was added back todeoiled citrus waste to give test citrus peel waste with limonene concentrations ranging from 0.08-0.43%(v/w). The peel was hydrolyzed, S. cerevisiae added to the bottles, and the bottles rotated at 10-12 rpmfor 24 h at 37 C under anaerobic conditions. Limonene concentration was measured before and afterfermentation and ethanol concentration was measured after fermentation. Ethanol production wasinhibited when initial limonene concentration was greater than 0.28% and when limonene concentrationafter fermentation was greater than 0.12%. Between 38% and 60% of the limonene present beforefermentation was removed during fermentation.
Generalized parity-check matrices for SEC-DED codes with fixed parity (2011)

Hsiao and extended Hamming parity-check matrices can be used to define systematic linear block codes for Single Error Correction-Double Error Detection (SEC-DED). Their fixed code word parity enables the construction of low density parity-check matrices and fast hardware implementations. Fixed code word parity is enabled by an all-one row in extended Hamming parity-check matrices or by the constraint that the modulo-2 sum of all rows is equal to the all-zero vector in Hsiao parity-check matrices. In this paper, we show that these two constraints are particular instantiations of a more general constraint which involves an arbitrary number of rows in the parity-check matrix. As a consequence, sparser parity-check matrices with faster hardware implementations can be found. Moreover, special instantiations of these matrices enable the detection of all triple-bit and quadruple-bit burst errors.
Packet-aware transport for metro networks (2004)

Today's metro networks have evolved from the need to support traditional voice and private line services. However, the tremendous growth in access to frame relay, ATM, IP, and Ethernet services, coupled with the desire of enterprise customers to interconnect via Ethernet interfaces, suggests the need for a new approach. This article proposes a new architecture for packet-aware transport networks (PATN) that supports both packet and traditional TDM services and leverages an assemblage of emerging technologies to provide efficient aggregation and switching of packet traffic in metro networks. The PATN has the potential to provide significant cost savings to carriers by reducing the number of network elements, reducing transport costs through statistical multiplexing, and eliminating the need for redundant multiplexing operations.
First results from the NSO/NJIT solar adaptive optics system (2004)

The National Solar Observatory and the New Jersey Institute of Technology have developed two 97 actuator solar adaptive optics (AO) systems based on a correlating Shack-Hartmann wavefront sensor approach. The first engineering run was successfully completed at the Dunn Solar Telescope (DST) at Sacramento Peak, New Mexico in December 2002. The first of two systems is now operational at Sacramento Peak. The second system will be deployed at the Big Bear Solar Observatory by the end of 2003. The correlating Shack-Hartmann wavefront sensor is able to measure wavefront aberrations for low-contrast, extended and time-varying objects, such as solar granulation. The 97-actuator solar AO system operates at a loop update rate of 2.5 kHz and achieves a closed loop bandwidth (0dB crossover error rejection) of about 130 Hz. The AO system is capable of correcting atmospheric seeing at visible wavelengths during median seeing conditions at both the NSO/Sacramento Peak site and the Big Bear Solar Observatory. We present an overview of the system design. The servo loop was successfully closed and first AO corrected images were recorded. We present first results from the new, high order AO system.
Detection of Hidden Insect Infestations by Feeding-Generated Ultrasonic Signals (1990)

Insects living hidden within seeds, wood, and certain other fibrous plant materials can be detected by the ultrasonic signals emitted when the insects feed on their organic substrate. Using cowpea weevil, Cal/osobruchus macuJatus (E), developing in cowpea seeds as our model, we have detected feeding activity by monitoring ultrasonic emissions at 40 KHz. The ultrasonic signals are produced when the insects strike the seed tissue during feeding, but not when they move in their tunnels. With cowpea weevil, feeding events can be detected from the early first ins tar through the last ins tar. The numbers of feeding events per unit time is directly proportional to the number of insects per seed. Many different species f hidden feeders can be detected by this technique, including other bruchids in a variety of legume seeds, SitophiJus spp. feeding in maize, lesser grain borer, Rhyzopertha dominica (E), feeding in rice, and termites feeding in wood. Ultrasonic monitoring should enable far greater insight into the life histories of insects feeding hidden within dry materials than has been possible by conventional techniques. Because the natural environment is relatively free of ultrasonic noise, monitoring insect activity is subject to little interference by extraneous signals. The "biomonitor," the electronic detector device developed to study the biology of feeding behavior, may have numerous practical applications, including early detection of hidden infestations, grain quality assessment, and rapid evaluation of efficacy of fumigation procedures.
Development of a thermal control coating optimized for cryogenic space applications (2022)

Abstract As NASA endeavors to extend the human presence in space beyond low Earth orbit, methods to efficiently store cryogenic propellants in space are required. Current state of the art rigid thermal control coatings absorb approximate 6% of the total solar irradiance, while state of the art thermal control paints absorb approximately 10% of the total solar irradiance. Consequently, radiative heat transfer a lone makes passive storage of cryogens in space impossible. A new rigid thermal control coating is in development and has achieved solar absorption values as low as -0.6 % (compared to a NIST standard) while maintaining high emissivity. This negative value for a rigid tile of pure yttria has required a new testing method be developed. Rigid tiles are very high performance but have more mass than paints and paper-th in coatings. Tiles must have a metallic substrate and create application challenges. While some use cases may necessarily address the challenges associated with rigid tiles in order to achieve required performance, a similar paint-like coating was also developed. The spray-on version of the new thermal control coating is easily applied to large complex surfaces and is very low mass. This version is also primarily yttria but includes a potassium bromide binder. Application to various substrates shows solar absorption values consistently below 5%, with a minimum of 2.8% achieved. Details of each version of this coating, along with test data is discussed.
Response: Stimulatory or tolerogenic role of CD40-activated B cells depends on the strength of the activation to T cells (2009)

Response

We thank Shimabukuro-Vornhagen et al for their comments on our recent study where we developed a simple and low-cost protocol using allogeneic CD40-activated B cells to induce and expand highly efficient human alloantigen-specific CD4highCD25+Foxp3+ regulatory T cells (Tregs) from naive
Applying Nonlinear Signal Analysis Technologies to Flame Scanner Signals to Improve Staging of Cyclone Boilers for NOx control (2006)

Cyclone{trademark} boiler owners continue to drive down NO{sub x} emissions by increasingly sophisticated staging and air distribution schemes. For example, Alliant Energy has employed RMT's SmartBurn{reg_sign} technology, and Ameren UE has pioneered neural nets to reduce emissions. Over the last 11 years under sponsorship of EPRI, the team of ORNL and B&W has developed pulverized coal burner diagnostic technology by applying nonlinear signal analysis techniques to flame scanner signals. The team has extended the technology to cyclones to facilitate deeper staging of the cyclones to reduce NO{sub x} emissions. Development projects were conducted at the Alliant Energy Edgewater Units 3 and 4, and Ameren UE Sioux Unit 1. Nonlinear analysis statistics were correlated to upsets in cyclone operation resulting from poor air distribution in the burner and barrel. The team demonstrated that the lighter and main flame scanners can be used to independently guide adjustments to the burner and barrel.
Motion having a Flight Phase: Experiments Involving a One-legged Robot (2007)

In the present paper, we introduce a new method by which to generate motions having flight phases such as jumping or running. Such motions are expected to expand the speed and stability of legged robots. Motions with flight phases are examined with respect to jumping, stability and implementation. A novel method of determining the Center of Mass (COM) and foot locations is proposed that is independent of the target robot actuators or assignments of joints. Moreover, the proposed method allows an on-line system to be built easily and is useful for actual robots. A one-legged jumping robot having a toe joint is built in order to demonstrate the feasibility of this method. Using the toe joint of the robot, the proposed method can reduce the angular velocities of the joints remarkably. Experiments are conducted to investigate the control of the direction, velocity and turning of the robot.
The Super Anti-apoptotic Factor Bcl-xFNK Constructed by Disturbing Intramolecular Polar Interactions in Rat Bcl-xL (2000)

A powerful artificial anti-apoptotic factor will be useful for medical applications of the future therapies for many diseases by prolonging survival of sick cells. For constructing it, we designed the super anti-apoptotic factor by disturbing three intramolecular polar interactions among alpha-helix structures of Bcl-x(L). The resultant mutant Bcl-x(L), named Bcl-xFNK, was expected to make the pore-forming domain more mobile and flexible than the wild-type. When overexpressed in Jurkat cells, Bcl-xFNK was markedly more potent in prolonging survival following apoptosis-inducing treatment with a kind of cell death cytokines (anti-Fas), a protein kinase inhibitor (staurosporine), cell cycle inhibitors (TN-16, camptothecin, hydroxyurea, and trichostatin A), or oxidative stress (hydrogen peroxide and paraquat) than wild-type Bcl-x(L). Furthermore, the transfectants of bcl-xFNK became more resistant against a calcium ionophore and even a heat treatment than wild-type Bcl-x(L). In addition, Bcl-xFNK showed marked anti-apoptotic activity in Chinese hamster ovary and Jurkat cells deprived of serum. Thus, Bcl-xFNK may be the first mutant generated by site-directed mutagenesis of Bcl-x(L) with a gain-of-function phenotype. Interestingly, Bcl-xFNK was found to allow interleukin-3-dependent FDC-P1 to grow without interleukin-3, but not BaF/3. In Bcl-xFNK transfectants of FDC-P1 and Jurkat, the p42/p44 mitogen-activated protein kinase was activated by 2 to 5 times, but not in those of BaF/3 and Chinese hamster ovary. Bcl-xFNK might gain a new function to activate the mitogen-activated protein kinase in a cell-type specific manner. The findings of this study suggest that the central alpha5-alpha6 pore-forming region of anti-apoptotic factor Bcl-x(L) has a pivotal role in suppressing apoptosis.
THE RECOVERY OF USED FRYING OILS WITH VARIOUS ADSORBENTS (1998)

ABSTRACT The recovery of used frying oils is of commercial and economic importance. One additional reuse of recovered oil could provide considerable savings to the food processors. Seven commonly used filter aids: Silasorb, Britesorb, HB 600, Purifry, Frypowder, Activated Carbon, and Magnesol, as well as two commercially unavailable adsorbents, Sorbead AF and Calsilite were studied. A number of AOCS official methods were used to evaluate their adsorptiveness, free fatty acids (FFA), conjugated diene value (CDV), total polar components (TPC), oxidative stability index (OSI), color and viscosity (V). High performance size exclusion chromatography was employed to determine the amount of polymers and low molecular weight compounds. When heated to 150C prior to filtration, HB 600 was found to reduce FFA content by 84.5%. Frypowder improved oil stability by 38.3%, and Magnesol lightened oil color by 46.3%. After statistical analysis of the data, five of them were selected, two or three of which were blended to obtain the most effective combination. The blending of HB 600 and Magnesol reduced FFA and TPC by 90.8–93.7% and 6.0–17.8%, respectively, and improved oil stability by 23.4–24.7%. The adsorbent combinations have potential for use in practical frying operation to improve the functional and healthy aspects of used frying oils.
Improved specificity and sensitivity when using pronase-digested lymphocytes to perform flow-cytometric crossmatch prior to renal transplantation (2002)

Several laboratories have resorted to flow-cytometric crossmatch (FCXM) in an effort to prevent hyperacute and accelerated renal allograft rejections. The currently employed FCXM has problems with both false-positive and -negative reactions, largely as a result of irrelevant IgG binding to Fc IgG receptors. In 1980, we circumvented this problem by digesting Fc IgG receptors with pronase, and demonstrated that, with immunofluorescence microscopy (IF), detection of IgG anti-HLA antibodies was highly sensitive and specific. In 1995, we introduced the pronase technique to FCXM and showed that this enzyme did not decrease HLA expression. We present herein a prospective study at our institution to determine whether FCXM using pronase-digested (PD) lymphocytes is as sensitive and more specific than FCXM with undigested (UD) lymphocytes when compared with the highly sensitive and specific IF assay. In analyzing the 186 donor-specific pre-renal-transplant crossmatches, we found that PD FCXM was as sensitive and specific as IF and was able to detect weak IgG anti-HLA antibodies that bound to B cells. Fourteen of these patients would have been denied transplants if one were to have relied on UD FCXM. The data clearly indicate that PD FCXM can reliably be used to detect weak IgG anti-HLA antibodies before renal transplantation.
Lyotropic mesophase of cellulose in ammonia/ammonium thiocyanate solution (1986)

Abstract Solutions of cellulose in a mixture of 27:73 (w/w) of liquid ammonia and ammonium thiocyanate become liquid crystalline at room temperature above a certain critical concentration which depends on the degree of polymerization of the dissolved cellulose. The high optical rotations of the solution suggest that the cellulose mesophase is cholesteric in nature. In the two‐phase region, the cellulose solutions exhibit negatively birefringent spherulites that possess both ringed and nonringed internal structures. The anisotropic solutions can be oriented by shear, indicating high potential for spinning them into useful fibers.
Measurements of device parameters on large arrays of Josephson interferometers (1980)

Measurements on large arrays of Josephson interferometers were carried out to obtain individual device parameters and their spread. Each array contained 784 identical interferometers with junction diameters of 5 and 7 μm and was deposited on a 6.35×6.35-mm Si chip. Threshold currents Im(0), subgap resistances Rj, and Vm —the product of Rj and Im(0) —were investigated. Statistical analysis indicated that the standard deviation σ of Im(0) and Rj ranged between 6 and 18% and that of Vm ranged between 5 and 7%. A systematic spatial dependence of Im(0) and Rj on the chips was obtained which is attributed as being due to nonuniformities in the rf oxygen discharge used to form the tunnel barrier. With improvements in the process, namely, eliminating these nonuniformities, the standard deviation in Im(0) (and Rj) can be reduced to about 5%. From the observed variations in the junction areas it is estimated that the random variation in the Josephson current density is about 4%. Large scale applications of these interferometers in the design of computer memory and logic thus seem feasible.
Optimization of Salting-Out Taste-Masking System for Micro-Beads Containing Drugs with High Solubility (2008)

The salting-out taste-masking system is a multiparticulate system consisting of a drug core, a salting-out layer containing salts and water-soluble polymers, and a water-penetration control layer containing water-insoluble materials. The system generates a long lag time (time when released drug is less than 1%) for numbness masking, and a subsequent immediate drug release for high bioavailability. Aiming to contain the system and drugs that cause numbness in oral disintegrating tablets, the system was optimized to reduce the particle size and contain drugs with high water solubility in this study. The amount of coating on the layers, the coating solvent, and the positioning of the components were also optimized. The findings in this study will lead to the provision of numbness-masked oral disintegrating tablets to patients.
Optical approaches to incorporation of displays within eyeglasses (1998)

Abstract— We report the development of a new approach to design and fabrication of eyeglass‐based displays. The principal feature of this technique is the incorporation of an optical relay between the display and the eye within the eyeglass lens, and the incorporation of a display within the eyeglass temple. Color eyeglass‐based displays are described.
Developments in magnetic bubble memories (1978)

Two new developments for magnetic bubble memories, a bubble propagation circuit and a bubble detector, are presented. The propagation circuit uses a channel with periodic traps coupled with asymmetrically placed bars of soft magnetic material to propagate bubbles nondirectionally with an alternating transverse magnetic field. This structure lends itself to very compact corners and transfer gates used in bubble memories with operating margins virtually identical to those of the straight line propagation circuit. A major-minor loop memory structure based on the channel-bar propagator is discussed. The structure yields independent propagation in the assembly and the storage loops using two mutually perpendicular transverse magnetic fields. The active bubble detector designed to match the excellent properties of the above circuit and to provide a means of nondestructive read-out is also discussed. The detector is based on a magneto-elastic phenomenon and does not require any electric current to operate.
Overcoming EGFR T790M-based Tyrosine Kinase Inhibitor Resistance with an Allele-specific DNAzyme (2014)

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are the main therapeutic agents used to treat non-small-cell lung cancer patients harboring EGFR-activating mutations. However, most of these patients will eventually develop resistance, 50% of which are due to a secondary mutation at T790M in the EGFR. In this paper, we describe the development of an allele-specific DNAzyme, DzT, that can specifically silence EGFR T790M mutant messenger RNA while leaving wild-type EGFR intact. Allele-specific silencing of EGFR T790M expression and downstream signaling by DzT triggered apoptosis in non-small-cell lung cancer cells harboring this mutant. Adding a cholesterol-triethylene glycol group on the 3'-end of DzT (cDzT) improved drug efficacy, increasing inhibitory effect on cell viability from 46 to 79% in T790M/L858R-harboring H1975(TM/LR) non-small-cell lung cancer cells, without loss of allele specificity. Combined treatment with cDzT and BIBW-2992, a second-generation EGFR-tyrosine kinase inhibitor, synergistically inhibited EGFR downstream signaling and suppressed the growth of xenograft tumors derived from H1975(TM/LR) cells. Collectively, these results indicate that the allele-specific DNAzyme, DzT, may provide an alternative treatment for non-small-cell lung cancer that is capable of overcoming EGFR T790M mutant-based tyrosine kinase inhibitor resistance.Molecular Therapy-Nucleic Acids (2014) 3, e150; doi:10.1038/mtna.2014.3; published online 4 March 2014.