gebhart/patrepeval huggingface dataset:
Type-specific immunogenicity of a chemically synthesized peptide fragment of type 5 streptococcal M protein. (1983)

We determined the antigenic specificity and protective immunogenicity of two chemically synthesized peptides of type 5 streptococcal M protein. The synthetic peptides, designated S-M5(1-20) and S-M5(20-40), represent the amino-terminal amino acid sequence of the native pepsin-extracted M5 molecule, which is known to contain at least one heart cross-reactive epitope. Initial studies showed that neither of the synthetic peptides was able to bind purified heart-reactive M5 antibodies. In addition, S-M5(1-20), but not S-M5(20-40), contained type-specific antigenic determinants as measured by enzyme-linked immunosorbent inhibition assays. When covalently linked to tetanus toxoid, S-M5(1-20), but not S-M5(20-40), evoked significant levels of type-specific, opsonic (and presumably protective) antibodies in rabbits without evoking heart cross-reactive antibodies.
Stochastic Learning in Neuromorphic Hardware via Spike Timing Dependent Plasticity With RRAM Synapses (2017)

Hardware processors for neuromorphic computing are gaining significant interest as they offer the possibility of real in-memory computing, thus by-passing the limitations of speed and energy consumption of the von Neumann architecture. One of the major limitations of current neuromorphic technology is the lack of bio-realistic and scalable devices to improve the current design of artificial synapses and neurons. To overcome these limitations, the emerging technology of resistive switching memory has attracted wide interest as a nano-scaled synaptic element. This paper describes the implementation of a perceptron-like neuromorphic hardware capable of spike-timing dependent plasticity (STDP), and its operation under stochastic learning conditions. The learning algorithm of a single or multiple patterns, consisting of either static or dynamic visual input data, is described. The impact of noise is studied with respect to learning efficiency (false fire, true fire) and learning time. Finally, the impact of stochastic learning rule, such as the inversion of the time dependence of potentiation and depression in STDP, is considered. Overall, the work provides a proof of concept for unsupervised learning by STDP in memristive networks, providing insight into the dynamics of stochastic learning and supporting the understanding and design of neuromorphic networks with emerging memory devices.
Wide angle impedance matching metamaterials for waveguide-fed phased-array antennas (2010)

This work investigates the gains realisable through the use of artificially structured materials, otherwise known as metamaterials, in the wide angle impedance matching (WAIM) of waveguide-fed phased-array antennas. The authors propose that the anisotropic properties of a metamaterial layer, when designed appropriately, can be employed to achieve impedance matching at a wide contiguous range of phased-array antenna transmission angles. Simulation and numerical results show that an optimised impedance match over a broad angular range can be readily achieved using a doubly uniaxial (magnetic and electric) anisotropic layer, an outcome not found accomplishable when an optimised isotropic dielectric layer is used. The authors propose the possibility of using metamaterials to achieve anisotropic WAIM layer configurations, and the authors show, using two simple uniaxial designs, that a metamaterial layer over the phased-array gives performance characteristics similar to its homogeneous anisotropic effective medium counterpart.
Improvement of lecithin as an emulsifier for water‐in‐oil emulsions by thermalization (1994)

Abstract The various forms (granular, liquid, gum) of lecithin can be heated under certain conditions of time and temperature to greatly improve their properties as emulsifiers for water‐in‐oil emulsions. Viscosity, discontinuous phase‐holding capacity, stability and water retention were greatly enhanced in emulsions containing thermalized lecithins as the emulsifier compared to those prepared with corresponding amounts of nonthermalized lecithins. The improved emulsification properties of the thermalized lecithins appeared to be due, at least in part, to an increase in diglycerides and free fatty acids resulting from the thermal degradation of phosphatides.
A Complete Frontal Crash Sensor System - 1 (1993)

<div class="htmlview paragraph">This is the first paper in a new series to present a coherent theory of sensing frontal crashes, define the characteristics of future airbag sensor systems and to present examples of how this theory can be implemented. After summarizing the relevant conclusions from the authors' previous papers, this paper concludes that future systems should contain: crush zone sensors which sense relevant impacts to all portions of the vehicle front; an occupant position sensor as an input to the sensing system; and a mechanical safing/arming sensor having a long dwell. It is further concluded that cars should be designed so that only impacts involving the front of the vehicle need be sensed for the deployment of frontal protection airbags.</div> <div class="htmlview paragraph">This series of papers has the main goal of determining an overall theory of frontal crash sensing and the resulting desirable properties of sensor systems. A second goal is to give examples of how this theory can be realized in real sensor systems. There is a need for such an analysis as can be seen from the wide variety of sensor systems in use today - it is unlikely that they are all right. In addition several organizations are developing computer algorithms for “Single Point Sensors” based on a variety of different theories. This diversity of systems leads to the conclusion that there is no generally accepted theory of how to sense car crashes.</div> <div class="htmlview paragraph">This paper develops a general theory of crash sensing by combining conclusions from previous papers with new analysis and presents a system which conforms to this theory. In later papers in this series, careful analysis will be made of real world crashes to refine the theory and improve the system design.</div>
The isolation and characterization of rubradirin B. (1978)

Rubradirin B, C40H33N3O15, was separated from other components of the rubradirin complex by chromatographic and crystallization procedures. The spectrum of antibacterial activity is similar to that of rubradirin, but the antibiotic is less active.
Sketch-based Influence Maximization and Computation (2014)

Propagation of contagion through networks is a fundamental process. It is used to model the spread of information, influence, or a viral infection. Diffusion patterns can be specified by a probabilistic model, such as Independent Cascade (IC), or captured by a set of representative traces.
How Cells Activate ATR (2006)

ATR is a critical upstream regulator of checkpoint responses to incompletely replicated and damaged DNA. However, it had not been understood how the kinase activity of ATR is switched on during checkpoint responses. TopBP1 and its homologs are necessary for both DNA replication and checkpoint control. A recent report from this laboratory demonstrated that TopBP1 functions as an activator of ATR. It had been known that TopBP1 accumulates at sites of replicative stress and DNA damage. Thus, interaction of ATR with a critical protein at stalled replication forks and sites of DNA damage triggers its activation. This finding helps to explain how aberrant DNA structures in the genome induce ATR-dependent signaling processes.
Routerless Network-on-Chip (2018)

Traditional bus-based interconnects are simple and easy to implement, but the scalability is greatly limited. While router-based networks-on-chip (NoCs) offer superior scalability, they also incur significant power and area overhead due to complex router structures. In this paper, we explore a new class of on-chip networks, referred to as Routerless NoCs, where routers are completely eliminated. We propose a novel design that utilizes on-chip wiring resources smartly to achieve comparable hop count and scalability as router-based NoCs. Several effective techniques are also proposed that significantly reduce the resource requirement to avoid new network abnormalities in routerless NoC designs. Evaluation results show that, compared with a conventional mesh, the proposed routerless NoC achieves 9.5X reduction in power, 7.2X reduction in area, 2.5X reduction in zero-load packet latency, and 1.7X increase in throughput. Compared with a state-of-the-art low-cost NoC design, the proposed approach achieves 7.7X reduction in power, 3.3X reduction in area, 1.3X reduction in zero-load packet latency, and 1.6X increase in throughput.
Protograph-Based Design for QC Polar Codes (2021)

We propose a new family of polar codes to realize high coding gain, low complexity, and high throughput by introducing a protograph-based design. Our proposed technique, called quasi-cyclic (QC) polar codes, can be highly parallelized without sacrificing decoding complexity. We analyze short cycles in the protograph polar codes and develop a design method to increase the girth. Our approach can resolve the long-standing unsolved problem that belief propagation (BP) decoding does not work well for polar codes due to the inherently short cycles. We demonstrate that a high lifting factor of QC polar codes can improve the performance and that QC polar codes with BP decoding can outperform conventional polar codes with state-of-the-art list decoding. Moreover, we show that a greedy pruning method can improve the performance-complexity trade-off.
Flip-avoiding interpolating surface registration for skull reconstruction (2016)

Reconstruction of skulls from defective models is a very important and challenging task in craniofacial surgery, forensics, and anthropology. Existing methods typically reconstruct approximating surfaces that regard corresponding points on the target skull as soft constraints, thus incurring non-zero error even for non-defective parts and high overall reconstruction error. This paper proposes a novel method that non-rigidly registers an interpolating surface that regards corresponding target points as hard constraints, thus achieving low reconstruction error. To overcome the shortcoming of interpolating surface, a flip-avoiding method is used to detect and exclude conflicting hard constraints that would otherwise cause surface patches to flip. Comprehensive test results show that our method is more accurate than existing methods and it is robust against severe outliers such as radiation artifacts in CT due to dental implants.
NARROW BAND OPTIMIZATION OF A COMPTON GAMMA-RAY SOURCE PRODUCED FROM AN X-BAND LINAC (2012)

Nuclear photonics is an emerging field of research that will require high precision gamma-ray (MeV) sources. In particular, nuclear resonance fluorescence applications [110] necessitate a low (< 1%) relative gamma-ray spectral width. Within this context, Compton scattering, where laser photons are scattered off relativistic electron beams to produce tunable, collimated gamma rays, will produce the desired gamma-ray output. This paper presents the spectral narrowband optimization of such a light source currently being built at LLNL. In this case, PARMELA and ELEGANT simulations of the high-gradient X-band linac provide the properties of the high brightness electron bunch. The electron beam simulations are then implemented into our newly developed weakly nonlinear Compton scattering code to produce theoretical gamma-ray spectra. The influence that the electron beam, laser beam and interaction geometry parameters have on the produced gamma-ray spectra will be shown with our simulations.
Compressive sampling in passive millimeter-wave imaging (2011)

We present a Hadamard transform based imaging technique and have implemented it on a single-pixel passive millimeter-wave imager in the 146-154 GHz range. The imaging arrangement uses a set of Hadamard transform masks of size p x q at the image plane of a lens and the transformed image signals are focused and collected by a horn antenna of the imager. The cyclic nature of Hadamard matrix allows the use of a single extended 2-D Hadamard mask of size (2p-1) x (2q-1) to expose a p x q submask for each acquisition by raster scanning the large mask one pixel at a time. A total of N = pq acquisitions can be made with a complete scan. The original p x q image may be reconstructed by a simple matrix operation. Instead of full N acquisitions, we can use a subset of the masks for compressive sensing. In this regard, we have developed a relaxation technique that recovers the full Hadamard measurement space from sub-sampled Hadamard acquisitions. We have reconstructed high fidelity images with 1/9 of the full Hadamard acquisitions, thus reducing the image acquisition time by a factor of 9.
Engineering an anti-CD52 antibody for enhanced deamidation stability (2019)

Deamidation evaluation and mitigation is an important aspect of therapeutic antibody developability assessment. We investigated the structure and function of the Asn-Gly deamidation in a human anti-CD52 IgG1 antibody light chain complementarity-determining region 1, and risk mitigation through protein engineering. Antigen binding affinity was found to decrease about 400-fold when Asn33 was replaced with an Asp residue to mimic the deamidation product, suggesting significant impacts on antibody function. Other variants made at Asn33 (N33H, N33Q, N33H, N33R) were also found to result in significant loss of antigen binding affinity. The co-crystal structure of the antigen-binding fragment bound to a CD52 peptide mimetic was solved at 2.2Å (PDB code 6OBD), which revealed that Asn33 directly interacts with the CD52 phosphate group via a hydrogen bond. Gly34, but sits away from the binding interface, rendering it more amendable to mutagenesis without affecting affinity. Saturation mutants at Gly34 were prepared and subjected to forced deamidation by incubation at elevated pH and temperature. Three mutants (G34R, G34K and G34Q) showed increased resistance to deamidation by LC-MS peptide mapping, while maintaining high binding affinity to CD52 antigen measured by Biacore. A complement -dependent cytotoxicity assay indicated that these mutants function by triggering antibody effector function. This study illustrates the importance of structure-based design and extensive mutagenesis to mitigate antibody developability issues.
Improved Prediction of Biochemical Recurrence After Radical Prostatectomy by Genetic Polymorphisms (2010)

Predicting biochemical recurrence after radical prostatectomy based on clinicopathological data can be significantly improved by including patient genetic information.
Noribogaine reduces nicotine self-administration in rats (2015)

Noribogaine, a polypharmacological drug with activities at opioid receptors, ionotropic nicotinic receptors, and serotonin reuptake transporters, has been investigated for treatment of substance abuse-related disorders. Smoking cessation has major benefits for both individuals and society, therefore the aim of this study was to evaluate the potential of noribogaine for use as a treatment for nicotine dependence. Adult male Sprague-Dawley rats were trained to self-administer nicotine intravenous. After initial food pellet training, followed by 26 sessions of nicotine self-administration training, the rats were administered noribogaine (12.5, 25 or 50 mg/kg orally), noribogaine vehicle, varenicline or saline using a within-subject design with a Latin square test schedule. Noribogaine dose-dependently decreased nicotine self-administration by up to 64% of saline-treated rats' levels and was equi-effective to 1.7 mg/kg intraperitoneal varenicline. Noribogaine was less efficient at reducing food pellets self-administration than at nicotine self-administration, inhibiting the nondrug reinforcing effects of palatable pellets by 23% at the highest dose. These results suggest that noribogaine dose-dependently attenuates drug-taking behavior for nicotine, attenuates the reinforcing effects of nicotine and is comparable to varenicline power in that regard. The findings from the present study hold promise for a new therapy to aid smoking cessation.
Binaural jitter improves interaural time-difference sensitivity of cochlear implantees at high pulse rates (2008)

Interaural time difference (ITD) arises whenever a sound outside of the median plane arrives at the two ears. There is evidence that ITD in the rapidly varying fine structure of a sound is most important for sound localization and for understanding speech in noise. Cochlear implants (CIs), neural prosthetic devices that restore hearing in the profoundly deaf, are increasingly implanted to both ears to provide implantees with the advantages of binaural hearing. CI listeners have been shown to be sensitive to fine structure ITD at low pulse rates, but their sensitivity declines at higher pulse rates that are required for speech coding. We hypothesize that this limitation in electric stimulation is at least partially due to binaural adaptation associated with periodic stimulation. Here, we show that introducing binaurally synchronized jitter in the stimulation timing causes large improvements in ITD sensitivity at higher pulse rates. Our experimental results demonstrate that a purely temporal trigger can cause recovery from binaural adaptation. Thus, binaurally jittered stimulation may improve several aspects of binaural hearing in bilateral recipients of neural auditory prostheses.
The Active Core in a Triazole Peptide Dual‐Site Antagonist of HIV‐1 gp120 (2010)

In an effort to identify broadly active inhibitors of HIV-1 entry into host cells, we previously reported a family of dodecamer triazole-peptide conjugates with nanomolar affinity for the viral surface protein gp120. This peptide class exhibits potent antiviral activity and the capacity to simultaneously inhibit interaction of the viral envelope protein with both CD4 and co-receptor. In this investigation, we minimized the structural complexity of the lead triazole inhibitor HNG-156 (peptide 1) to explore the limits of the pharmacophore that enables dual antagonism and to improve opportunities for peptidomimetic design. Truncations of both carboxy- and amino-terminal residues from the parent 12-residue peptide 1 were found to have minimal effects on both affinity and antiviral activity. In contrast, the central triazole(Pro)-Trp cluster at residues 6 and 7 with ferrocenyl-triazole(Pro) (Ftp) was found to be critical for bioactivity. Amino-terminal residues distal to the central triazole(Pro)-Trp sequence tolerated decreasing degrees of side chain variation upon approaching the central cluster. A peptide fragment containing residues 3-7 (Asn-Asn-Ile-Ftp-Trp) exhibited substantial direct binding affinity, antiviral potency, dual receptor site antagonism, and induction of gp120 structuring, all properties that define the functional signature of the parent compound 1. This active core contains a stereochemically specific hydrophobic triazole(Pro)-Trp cluster, with a short N-terminal peptide extension providing groups for potential main chain and side chain hydrogen bonding. The results of this work argue that the pharmacophore for dual antagonism is structurally limited, thereby enhancing the potential to develop minimized peptidomimetic HIV-1 entry inhibitors that simultaneously suppress binding of envelope protein to both of its host cell receptors. The results also argue that the target epitope on gp120 is relatively small, pointing to a localized allosteric inhibition site in the HIV-1 envelope that could be targeted for small-molecule inhibitor discovery.
Experiences and observations on the industrial implementation of a system to search over outsourced encrypted data. (2014)

This paper presents an industrial report on the implementation of a system that supports execution of queries over encrypted data. While this idea is not new, e.g. [HILM02, AKRX04, PRZB11], the implementation in a real world large scale in-memory database is still challenging. We will provide an overview of our architecture and detail two use cases to give the reader an insight into how we technically realized the implementation. We then provide three main contributions, reporting that: a) We significantly improve functionality by intelligently splitting query execution, i.e. which parts of a query can be performed in the cloud and which on the client. b) We share some initial performance measurements with the community on basis of the TPCH benchmark. c) We present a domain-specific analysis of three data sets that shows the effects of executing queries over encrypted data and what adjustments are required with respect to the encryption of individual columns. The three made observations on query execution, execution time measurements and domain-specific query analysis will lead us to the conclusion that although searching over outsourced encrypted data is always a trade off between functionality, performance and security, it is realistic to assume that working solutions can be provided in the not too distant future to the market.
High thermoelectric conversion efficiency of MgAgSb-based material with hot-pressed contacts (2015)

High conversion efficiency is demonstrated at a relatively small temperature difference for a MgAgSb-based single thermoelectric leg with hot-pressed contacts.
Manipulation of thermal phonons: a phononic crystal route to High-ZT thermoelectrics (2011)

Phononic crystals (PnCs) are acoustic devices composed of a periodic arrangement of scattering centers embedded in a homogeneous background matrix with a lattice spacing on the order of the acoustic wavelength. When properly designed, a superposition of Bragg and Mie resonant scattering in the crystal results in the opening of a frequency gap over which there can be no propagation of elastic waves in the crystal, regardless of direction. In a fashion reminiscent of photonic lattices, PnC patterning results in a controllable redistribution of the phononic density of states. This property makes PnCs a particularly attractive platform for manipulating phonon propagation. In this communication, we discuss the profound physical implications this has on the creation of novel thermal phenomena, including the alteration of the heat capacity and thermal conductivity of materials, resulting in high-ZT materials and highly-efficient thermoelectric cooling and energy harvesting.
Grating interferometer with extremely high stability, suitable for measuring small refractive index changes (1991)

We describe here a grating interferometer with extremely high stability and which can be used as a differential refractometer. The instrument uses heterodyne techniques to achieve high sensitivity. We present an analysis of the operation of the system and results which show that it has a long term stability of the order of 1/1500 wavelength over 2 h.
High-Performance 13.56-MHz Large Air-Gap Capacitive Wireless Power Transfer System for Electric Vehicle Charging (2018)

This paper introduces a high-performance large airgap capacitive wireless power transfer (WPT) system for electric vehicle charging. This system operates at 13.56 MHz, and utilizes coupled-inductor based L-section matching networks that provide gain and reactive compensation. The high operating frequency and coupled-inductor matching network design are shown to significantly enhance the system's efficiency and reduce its size. Efficiency is further enhanced by realizing the matching network capacitors entirely using parasitic capacitances, thus eliminating the losses associated with on-board capacitors. A 13.56-MHz 12-cm air-gap prototype capacitive WPT system is designed, built and tested. This system transfers 884 W at an efficiency of 91.3%, achieving a power transfer density of 29.5 kW/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Additionally, the prototype system achieves a peak efficiency of 95% when transferring 348 W. Compared to a prototype 6.78-MHz capacitive WPT system, the 13.56-MHz system exhibits up to 53% reduced losses and 69% reduced inductor volume.