gebhart/patrepeval huggingface dataset:
Fine mapping of antigenic site II of herpes simplex virus glycoprotein D (1989)

Glycoprotein D (gD) is a virion envelope component of herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) which plays an important role in viral infection and pathogenesis. Previously, anti-gD monoclonal antibodies (MAbs) were arranged into groups which recognize distinct type-common and type-specific sites on HSV-1 gD (gD-1) and HSV-2 gD (gD-2). Several groups recognize discontinuous epitopes which are dependent on tertiary structure. Three groups, VII, II, and V, recognize continuous epitopes present in both native and denatured gD. Previously, group II consisted of a single MAb, DL6, whose epitope was localized between amino acids 268 and 287. In the study reported here, we extended our analysis of the antigenic structure of gD, concentrating on continuous epitopes. The DL6 epitope was localized with greater precision to residues 272 to 279. Four additional MAbs including BD78 were identified, each of which recognizes an epitope within residues 264 to 275. BD78 and DL6 blocked each other in binding to gD. In addition, a mutant form of gD was constructed in which the proline at 273 was replaced by serine. This change removes a predicted beta turn in gD. Neither antibody reacted with this mutant, indicating that the BD78 and DL6 epitopes overlap and constitute an antigenic site (site II) within residues 264 to 279. A separate antigenic site (site XI) was recognized by MAb BD66 (residues 284 to 301). This site was only six amino acids downstream of site II, but was distinct as demonstrated by blocking studies. Synthetic peptides mimicking these and other regions of gD were screened with polyclonal antisera to native gD-1 or gD-2. The results indicate that sites II, V, VII, and XI, as well as the carboxy terminus, are the major continuous antigenic determinants on gD. In addition, the results show that the region from residues 264 through 369, except the transmembrane anchor, contains a series of continuous epitopes.
Assessment of Sample Contamination by Downhole NMR Fluid Analysis (2001)

Abstract A recently developed nuclear magnetic resonance (NMR) downhole fluid analyzer provides in-situ fluid characteristics at reservoir PVT conditions. The device is part of the Reservoir Description Tool (RDT*), a modular formation sampler and tester. This paper presents the theory and the experimental evidence that led to the use of NMR as a means to assess the amount of mud filtrate contained in the pumped formation fluid. In particular, the problem of differentiating oil base mud filtrate from connate hydrocarbons is difficult and has not been addressed by conventional measurements. NMR relaxometry uses the inherent differences in T1 time constant values and distributions to make these distinctions. The T1 data is available in real time and can be used to determine the optimum pump-out rates and durations while sampling reservoir fluids.
Agar barrier method for removal of yeast and other fungal contamination from<i>Leishmania</i>promastigotes culture (2012)

The present study explains a novel method of Leishmania promastigotes culture decontamination. The method is based on motility of Leishmania promastigotes across agar barrier which facilitates decontamination from yeast and other non motile contamination. This is inexpensive, easy, rapid and reliable physical method and is able to save valuable isolates in culture.
(109) Transdermally Powered, MRI Conditional Pump-in-Reservoir Implant Inflator System: Preclinical Studies (2023)

Abstract Introduction Inflatable medical implants have been used in the treatment of erectile dysfunction and both urinary and fecal incontinence. However, commercially available devices have required manual operation, which present difficulty in their use for patients lacking strength and dexterity to use such pumps. In women with urinary incontinence, anatomical constraints limit the use of manually operable inflatable devices. Objective The aim of this study was to conduct preclinical testing of a wirelessly powered inflatable medical implant system consisting of a medical provider software application, a patient external controller, and a magnetic resonance imaging (MRI)-conditional nonferrous pump-in-reservoir implant system. Methods An inflatable medical implant system was designed and tested. Serial prototypes designs included a nonferrous, reservoir-submerged package containing electronic motor and pump with piezoelectric valves, and an external controller resembling a TV remote. The implant system was evaluated after being connected to commercially available penile prosthetic cylinders. Power settings were tested at various thresholds; testing requirements considered to be clinically applicable were set as fluid transfer of 60 ml of normal saline at 25 psi within 45 seconds. The effectiveness of power transmission across the human abdominal wall was tested using an interface of a steak slab placed between the external controller and the implant system. Results Device testing at 24 and 36 volts determined that the latter was more efficient and afforded a smaller motor and pump package. Full penile cylinder inflation was recorded at 23 seconds. Effective power transmission was demonstrated across steak slabs. Conclusions A nonferrous pump-in-reservoir medical implant inflator system for penile prostheses is legitimate. It offers an improvement over manually operated inflatable devices, and because it eliminates a manual pump component there is feasibility of constructing a modified device for fluid transfer of urethral cuffs for treating urinary incontinence in men and women. The pump package within the reservoir is advantageous as a heatsinking feature that may limit implant overheating. Finally, the device design without ferrous components affords MRI compatibility. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: Boston Scientific, Novartis
Novel Antitumor 2-Cyanoaziridine-1-carboxamides (1999)

A set of 20 2-cyanoaziridine-1-carboxamides was synthesized from 2-cyanoaziridine and appropriate isocyanates. These compounds were active against a variety of solid and hematological tumor cells in culture, including strains resistant to doxorubicin and mitoxantrone. Their potencies in these assays correlated with the lipophilicity of substituents. The N-phenyl derivative was more potent and equally effective to imexon, a cyclized 2-cyanoaziridine-1-carboxamide of clinical interest, against cloned fresh human tumors.
Method and apparatus for improving the efficiency of an acousto-optic deflector (1986)

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Biologically Based Fiber-Reinforced/Clay Aerogel Composites (2007)

Ultralow-density clay aerogels are formed via the freeze-drying of clay hydrogels. Although unmodified clay aerogels exhibit generally poor mechanical properties, the incorporation of short-cut natural fibers forms a woven-like structure, which significantly increases the mechanical properties of these materials. Incorporation of a matrix polymer into the aerogel/fiber composites further enhances compressive strengths and moduli. A woven-like structure composed of clay aerogel “warp” and fiber “weft” materials seems to be responsible for the enhancements in the material properties in each case examined.
Gamma-ray compton light source development at LLNL (2007)

A new class of tunable, monochromatic gamma-ray sources capable of operating at high peak and average brightness is currently being developed at LLNL for nuclear photo-science and applications. These novel systems are based on Compton scattering of laser photons by a high brightness relativistic electron beam produced by an rf photoinjector. Key technologies, basic scaling laws, and recent experimental results are presented, along with an overview of future research and development directions.
340mV&#x2013;1.1V, 289Gbps/W, 2090-gate NanoAES hardware accelerator with area-optimized encrypt/decrypt GF(2<sup>4</sup>)<sup>2</sup> polynomials in 22nm tri-gate CMOS (2014)

An on-die, lightweight nanoAES hardware accelerator is fabricated in 22nm tri-gate CMOS, targeted for ultra-low power mobile SOCs. Compared to conventional 128-bit AES implementations, this design uses an 8-bit Sbox datapath along with ShiftRow byte-order processing to compute all AES rounds in native GF(2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> ) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> composite-field. This approach along with a serial-accumulating MixColumns circuit, area-optimized encrypt and decrypt Galois-field polynomials and integrated on-the-fly key generation circuit results in a compact 2090-gate design, enabling peak energy-efficiency of 289Gbps/W and AES-128 encrypt/decrypt throughput of 432/671Mbps with total energy consumption of 4.7/3nJ measured at 0.9V, 25°C.
The Effects of a Botanical Blend on Post-Exercise Mucosal Antimicrobial Proteins (2018)

Exercise is a stressor that is known to in some cases suppress antimicrobial protein levels, particularly secretory immunoglobulin type A (IgA). Athletes in the midst of in-season training often demonstrate declining levels of sIgA as well as increased risk for ailments such as upper respiratory tract infections. Therefore, it is important to investigate natural supplements that may enhance post exercise mucosal immune function. Twenty healthy collegeaged males volunteered to participate in the present single blind, repeated measures study. Three treatments were administered (botanical spray, botanical drops, placebo) at the onset of 30 Min of 80% VO2 max cycle ergometer exercise. Secretory IgA and Human Alpha Defensin were quantified in saliva samples 30 Min and 90 Min post exercise. Analysis via repeated measures Anova revealed a significant treatment effect at 30 min (p=0.030) with post hoc testing revealing a difference between the botanical spray and placebo (p=0.027), but by 90 Min there was no differences by treatment (p=0.758). There was no difference by treatment observed at either 30 or 90 Min for human alpha defensin concentrations. Based upon these preliminary data, it appears that a single dose of the tested botanical blend delivered via mouth spray can increase sIgA, one of the primary anti-microbial proteins in the oral cavity, for a short time post exercise.
Self-supervised audio representation learning for mobile devices (2019)

We explore self-supervised models that can be potentially deployed on mobile devices to learn general purpose audio representations. Specifically, we propose methods that exploit the temporal context in the spectrogram domain. One method estimates the temporal gap between two short audio segments extracted at random from the same audio clip. The other methods are inspired by Word2Vec, a popular technique used to learn word embeddings, and aim at reconstructing a temporal spectrogram slice from past and future slices or, alternatively, at reconstructing the context of surrounding slices from the current slice. We focus our evaluation on small encoder architectures, which can be potentially run on mobile devices during both inference (re-using a common learned representation across multiple downstream tasks) and training (capturing the true data distribution without compromising users' privacy when combined with federated learning). We evaluate the quality of the embeddings produced by the self-supervised learning models, and show that they can be re-used for a variety of downstream tasks, and for some tasks even approach the performance of fully supervised models of similar size.
Implementing fair queueing in ATM switches: the discrete-rate approach (2002)

The total implementation cost of schedulers which approximate the generalized processor sharing (GPS) policy is dominated by the complexity of maintaining and sorting the time-stamps for all connections. Several approaches have been proposed which reduce the cost of the sorting operation and only introduce a small degradation in the delay bounds of the scheduler; they include logarithmic calendar queues and schedulers supporting a discrete set of guaranteed rates. All these techniques still require computing and storing one time-stamp per connection, thus maintaining the cost of GPS-related algorithms clearly higher than that of less sophisticated schedulers. Furthermore, in the case of the discrete-rate approach, the complexity increases linearly with the number of supported rates, thus making it attractive only for relatively small numbers of rates. In this paper, we introduce a discrete-rate GPS-related scheduler which does not require the computation and storage of one time-stamp per connection, and only maintains a single time-stamp per rate. The elimination of the per-connection time-stamps has no negative effect on the delay bounds. Then, we present a generalized discrete-rate approach, which uses a given number of FIFO queues to support a larger number of guaranteed rates, and only introduces a modest degradation in delay bounds for certain rates. The technique can be applied to our no-per-connection-time-stamp scheduler, as well as to any discrete-rate scheduler.
Effects of Intergrinding Fly Ash on the Sulfate Resistance of Fly Ash Concrete (1992)

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Deadlock-free routing based on ordered links (2003)

This paper describes a new class of deadlock-free routing algorithms for irregular networks based on ordered links. In this case, the links are ordered by partitioning them into a set of layers, each layer containing a spanning tree (when possible). Deadlock free routes can then be derived by using links with non-decreasing order. The deadlock-freedom property is proved. Two different implementations of the routing algorithm are studied. The resultant performance of these algorithms is then compared to other known algorithms: the shortest-path algorithm (which may result in deadlocks) and the up*/down* algorithm. Various performance metrics are considered, including path-length, network capacity, fault tolerance and time of computation. We argue that network capacity is the most important metric to optimize. It is shown that the proposed algorithms are promising since they usually achieve higher network capacity than up*/down*, while they perform only slightly worse than up*/down* in other metrics.
Dielectric and Other Properties of Polyimide Aerogels Containing Fluorinated Blocks (2014)

The dielectric and other properties of a series of low-density polyimide block copolymer aerogels have been characterized. Two different anhydride-capped polyimide oligomers were synthesized: one from 2,2-bis(3,4-dicarboxyphenyl)hexafluoropropane dianhydride (6FDA) and 4,4'-oxidianiline (ODA) and the other from biphenyl-3,3',4,4'-tetracarboxylic dianhydride and ODA. The oligomers were combined with 1,3,5-triaminophenoxybenzene to form a block copolymer networked structure that gelled in under 1 h. The polyimide gels were supercritically dried to give aerogels with relative dielectric constants as low as 1.08. Increasing the amount of 6FDA blocks by up to 50% of the total dianhydride decreased the density of the aerogels, presumably by increasing the free volume and also by decreasing the amount of shrinkage seen upon processing, resulting in a concomitant decrease in the dielectric properties. In this study, we have also altered the density independent of fluorine substitution by changing the polymer concentration in the gelation reactions and showed that the change in dielectric due to density is the same with and without fluorine substitution. The aerogels with the lowest dielectric properties and lowest densities still had compressive moduli of 4-8 MPa (40 times higher than silica aerogels at the same density), making them suitable as low dielectric substrates for lightweight antennas for aeronautic and space applications.
An x-space magnetic particle imaging scanner (2012)

Magnetic particle imaging (MPI) is an imaging modality with great promise for high-contrast, high-sensitivity imaging of iron oxide tracers in animals and humans. In this paper, we present the first x-space MPI hardware and reconstruction software; show experimentally measured signals; detail our reconstruction technique; and present images of resolution and "angiography" phantoms.
Heuristic recurrent algorithms for photonic Ising machines (2020)

The inability of conventional electronic architectures to efficiently solve large combinatorial problems motivates the development of novel computational hardware. There has been much effort toward developing application-specific hardware across many different fields of engineering, such as integrated circuits, memristors, and photonics. However, unleashing the potential of such architectures requires the development of algorithms which optimally exploit their fundamental properties. Here, we present the Photonic Recurrent Ising Sampler (PRIS), a heuristic method tailored for parallel architectures allowing fast and efficient sampling from distributions of arbitrary Ising problems. Since the PRIS relies on vector-to-fixed matrix multiplications, we suggest the implementation of the PRIS in photonic parallel networks, which realize these operations at an unprecedented speed. The PRIS provides sample solutions to the ground state of Ising models, by converging in probability to their associated Gibbs distribution. The PRIS also relies on intrinsic dynamic noise and eigenvalue dropout to find ground states more efficiently. Our work suggests speedups in heuristic methods via photonic implementations of the PRIS.
Improving a nonenumerative method to estimate path delay fault coverage (1997)

A recently proposed method obtains path delay fault coverages by estimating the count of the number of tested faults instead of actually enumerating them. The estimate becomes pessimistic when several paths share a set of lines. In this communication, we present a continuum of improved approximations for the counting method, approaching exact fault simulation, to allow tradeoffs between accuracy and complexity. Higher accuracy is obtained at the expense of CPU time. We propose the use of flags corresponding to fixed-length path segments. A flag indicates whether or not the segment has been included in a previously detected path fault. A path fault, detected by a pair of vectors, is counted as a new detection only if it includes at least one segment not included in any previously tested path fault. The results show that as the length of segments is increased, the accuracy becomes close to that of the exact fault simulation, even with small segment lengths.
Ceramide Remodeling and Risk of Cardiovascular Events and Mortality (2018)

The ratio of C24:0/C16:0 ceramides in blood may be a valuable new biomarker of CHD risk, HF risk, and all-cause mortality in the community.
Formation Mechanism and Suppression of Hot Cracking in Full Penetration Welding of Thick Steel Plate Using High Power CO2 Laser (2004)

Full penetration laser welding has been carried out on 11, 15 and 20 mm thick steel plates. Dynamic keyhole behaviour has been observed using a micro-focused x-ray transmission imaging system to elucidate the formation mechanism of the hot cracking. Back shielding by inert gas is effective to prevent the porosity caused by supersaturation of nitrogen in the molten pool. However, the indissoluble inert gas entered from the back surface significantly perturbs the keyhole, and then forms the hot cracking susceptible convex shaped weld section. Increase in the plate thickness raises the hot cracking susceptibility due to promoting the keyhole perturbation. A small amount of aluminium addition is effective in preventing the porosity caused by nitrogen even if the back surface is not shielded by the inert gas. Hot cracking is also prevented by stabilizing the keyhole.
Synthesis and Characterization of Ultrafine Tungsten and Tungsten Oxide Nanoparticles by a Reverse Microemulsion-Mediated Method (2006)

Ultrafine tungsten and tungsten oxide powders with controllable particle size and structure have been synthesized by a reverse microemulsion-mediated synthesis method. The nanoparticles were characterized by transmission electron microcopy, X-ray diffraction, and thermal analysis. Synthesis conditions, including water-to-surfactant ratio, annealing temperature, water-to-alkoxide ratio, and drying method, have been shown to be critical in controlling the size and structure of tungsten nanoparticles. Using the same synthesis technique, carbon-supported metallic tungsten and tungsten oxide nanoparticles with controllable size and dispersion can also be prepared. The ultrafine nanoparticles prepared by this synthesis method may find interesting applications in various fields such as catalysis, electronics, illumination, gas sensors, and so forth.
Charge-magnetic interference resonant scattering studies of ferromagnetic crystals and thin films (2012)

The element- and site-specificity of X-ray resonant magnetic scattering (XRMS) makes it an ideal tool for furthering our understanding of complex magnetic systems. In the hard X-rays, XRMS is readily applied to most antiferromagnets where the relatively weak resonant magnetic scattering (10−2–10−6 I c ) is separated in reciprocal space from the stronger, Bragg charge scattered intensity, I c . In ferro(ferri)magnetic materials, however, such separation does not occur and measurements of resonant magnetic scattering in the presence of strong charge scattering are quite challenging. We discuss the use of charge-magnetic interference resonant scattering for studies of ferromagnetic (FM) crystals and layered films. We review the challenges and opportunities afforded by this approach, particularly when using circularly polarized X-rays. We illustrate current capabilities at the Advanced Photon Source with studies aimed at probing site-specific magnetism in ferromagnetic crystals, and interfacial magnetism in films.
Corner guided curve matching and its application to scene reconstruction (2002)

Corners and curves are important image features in many vision-based applications. Corners are usually more stable and easier to match than curves, while curves contain richer information of scene structure. In previously work, corners are often used to recover the epipolar geometry between two views, which is then used in curve matching to reduce the search space. However, information of the scene structure contained in this set of matched corners is ignored. In this paper we present a curve matching algorithm that is guided by a set of matched corners. Within a probabilistic framework, the role of the corner guidance is explicitly defined by a set of similarity-invariant unary measurements and by a similarity function. The similarity function provides stronger capability of resolving matching ambiguity than the epipolar constraint, and is integrated into a relaxation scheme to reduce computational complexity and improve accuracy of curve matching. Experimental results clearly demonstrate the benefit of integrating corner matches into the curve matching procedure.