gebhart/patrepeval huggingface dataset:
Mechanism of an Amphipathic α-Helical Peptide’s Antiviral Activity Involves Size-Dependent Virus Particle Lysis (2009)

The N-terminal region of the hepatitis C virus (HCV) nonstructural protein NS5A contains an amphipathic alpha-helix that is necessary and sufficient for NS5A membrane association. A synthetic peptide (AH) comprising this amphipathic helix is able to lyse lipid vesicles that serve as a model system for virus particles. Based on quartz crystal microbalance-dissipation (QCM-D) experiments, the degree of vesicle rupturing was found to be inversely related to vesicle size, with maximal activity in the size range of several medically important viruses. In order to confirm and further study vesicle rupture, dynamic light scattering (DLS) and atomic force microscopy (AFM) experiments were also performed. The size dependence of vesicle rupturing helps explain the peptide's observed effect on the infectivity of a wide range of viruses. Further, in vitro studies demonstrated that AH peptide treatment significantly decreased the infectivity of HCV particles. Thus, the AH peptide might be used to rupture HCV particles extra-corporally (for HCV prevention) and within infected individuals (for HCV therapy).
Meta-data conditional language modeling (2004)

Automatic speech recognition (ASR) often occurs in circumstances in which knowledge external to the speech signal, or meta-data, is given. For example, a company receiving a call from a customer might have access to a database record of that customer. Conditioning the ASR models directly on this information to improve the transcription accuracy is hampered because, generally, the meta-data takes on many values and a training corpus has little data for each meta-data condition. The paper presents an algorithm to construct language models conditioned on such metadata. It uses tree-based clustering of the the training data to derive automatically meta-data projections, useful as language model conditioning contexts. The algorithm was tested on a multiple domain voice mail transcription task. We compare the performance of an adapted system aware of the domain shift to a system that only has meta-data to infer that fact. The meta-data used were the caller ID strings associated with the voice mail messages. The meta-data adapted system matched the performance of the system adapted using the domain knowledge explicitly.
A new class of analog of the bifunctional radiosensitizer .alpha.-(1-aziridinylmethyl)-2-nitro-1H-imidazole-1-ethanol (RSU 1069): the cycloalkylaziridines (1991)

A series of compounds related to alpha-(1-aziridinylmethyl)-2-nitro-1H-imidazole-1-ethanol (RSU 1069, 1) were synthesized and evaluated as selective hypoxic cell cytotoxic agents and as radiosensitizers. The aziridine moiety was replaced with a number of other potential alkylating groups including cycloalkylaziridines and azetidines. The data indicated that modification of the aziridine of 1 resulted in a substantial decrease in the ability of the compounds to selectively kill hypoxic cells. However, these modifications did not affect the compounds' in vitro radiosensitizing activity since many of the derivatives were as potent as 1. All of the compounds that were evaluated in vivo were less toxic than 1, and several members of this series had significant activity. The best compound was trans-alpha-[[(4-bromotetrahydro-2H-pyran-3-yl) amino]methyl]-2-nitro-1H-imidazole-1-ethanol (18), which, due to its activity and log P value, is a candidate for additional in vivo studies.
Imaging Contrast and Resolution in Multiply Scattered Low Coherence Interferometry (2011)

With recent results demonstrating imaging using low coherence interferometry to detect multiply scattered light, signal attenuation and imaging resolution remains to be an open question. To address this, we present detailed modeling results of light propagation in the multiply scattered low-coherence interferometry (ms/LCI) configuration. Analytical and Monte Carlo models are used to assess the theoretical resolution and contrast of the system, and to explore the effect of media anisotropy on imaging parameters. Imaging resolution and depth penetration are found to depend on the fraction of photons scattered into a narrow range of forward scattering angles rather than the overall media anisotropy.
Development of a novel method based on a photon counting technique with the aim of precise material identification in clinical x-ray diagnosis (2017)

A photon counting system has the ability of energy discrimination, therefore obtaining new information using X-rays for material identification is an expected goal to achieve precise diagnosis. The aim of our study is to propose a novel method for material identification based on a photon counting technique. First, X-ray spectra at 40-60 kV were constructed using a published database. Second, X-ray spectra penetrating different materials having atomic numbers from 5-13 were calculated. These spectra were divided into two energy regions, then linear attenuation factors concerning these regions were obtained. In addition, in order to accomplish highly accurate material identification, correction of beam hardening effects based on soft-tissue was applied to each linear attenuation factor. Then, using the linear attenuation factors, a normalized linear attenuation coefficient was derived. Finally, an effective atomic number was determined using the theoretical relationship between the normalized linear attenuation coefficient and atomic number. In order to demonstrate our method, four different phantoms (acrylic, soft-tissue equivalent, bone equivalent, and aluminum) were measured using a single-probe-type CdTe detector under the assumption that the response of the single-probe-type CdTe detector is equal to the response of one pixel of a multi-pixel-type photon counting detector. Each of these phantoms can be completely separated using our method. Furthermore, we evaluated an adoptive limit of beam hardening correction. We found that the adoptive limit depends on the mass thickness and atomic number. Our vision is to realize highly accurate identification for material with narrow range in atomic number.
Technology Lookup Table based Default Timing Assertions for Hierarchical Timing Closure (2021)

This paper presents an approach to dynamically generating representative external driving cell and external wire parasitic assertions for the ports of sub-blocks of a hierarchical design. The assertions are based on a technology lookup table and use attributes of the port and the hierarchical wire connected to the port as keys. A concept of reverse timing calculation at the input of the driving cell is described that facilitates the approach to drive efficient timing optimization of boundary paths of design sub-blocks. Experimental results in an industrial timing environment demonstrate significantly improved timing optimization accuracy when compared to prior work.
Light-weight titanium magnesium alloys by vapor deposition (1995)

A novel range of Ti-Mg alloys were produced by a high rate evaporation and vapor quenching route. Magnesium is virtually insoluble in titanium under equilibrium conditions, and this alloy combination is not possible by conventional ingot metallurgy due to the high vapor pressure of magnesium, which boils at atmospheric pressure below the melting point of titanium. X-ray diffraction data showed that at least 27 wt% magnesium was retained in solid solution. Each 1 wt% addition of magnesium reduced the alloy density by approximately 1%. For the more dilute alloys (< 10 wt%) heat treatment in air or in vacuum up to 700 C was accompanied by a very substantial increase in hardness, which could not be explained in terms of oxygen absorption by the titanium lattice. A Ti-9Mg alloy has been studied by transmission electron microscopy using electron energy loss (PEELS) and energy dispersive X-ray techniques. After hot-pressing, particles in the 2--20 nm range, and others at about 100 nm diameter were found within the grains and in the grain boundaries respectively. These particles were identified as magnesium. Controlled oxidation led to the formation of MgO particles, and an increase in hardness by a factor of 2.3.
Induction of host signal transduction pathways by <i>Helicobacter pylori</i> (1997)

Adherence of Helicobacter pylori to cultured gastric epithelial cells is associated with several cellular events, including the tyrosine phosphorylation of a 145-kDa host protein; the reorganization of the host cell actin and associated cellular proteins, like vasodilator-stimulated phosphoprotein, adjacent to the attached bacterial cell; and the subsequent release of the cytokine, interleukin 8 (IL-8). H. pylori isolated from patients with ulcer disease and gastric cancer contain a DNA insertion, the cag pathogenicity island (PAI), that is not present in bacteria isolated from individuals with asymptomatic infection. Mutations in a number of PAI genes abolish tyrosine phosphorylation and IL-8 synthesis but not the cytoskeletal rearrangements. Kinase inhibition studies suggest there are two distinct pathways operative in stimulating IL-8 release from host cells and one of these H. pylori pathways is independent of the tyrosine phosphorylation step.
Recombinant <i>Fasciola hepatica</i> fatty acid binding protein (Fh15) as a novel anti-inflammatory biotherapeutic in an acute gram-negative non-human primate sepsis model (2021)

A bstract Due to their phylogenetic proximity to human, non-human primates (NHP) are considered an adequate choice for basic and pre-clinical model of sepsis. Gram-negative bacteria are the primary causative of sepsis. During infection bacteria continuously release the potent toxin lipopolysaccharide (LPS) into the bloodstream, which triggers an uncontrolled systemic inflammatory response leading to death. Our previous research has demonstrated in vitro and in vivo using a mouse model of septic shock that Fh15, a recombinant variant of the Fasciola hepatica fatty acid binding protein, acts as an antagonist of TLR4 suppressing the LPS-induced pro-inflammatory cytokine storm. The present study aimed to demonstrate that Fh15 suppress the cytokine storm and other inflammatory markers during the early phase of an endotoxemia induced in rhesus macaques by i.v. infusion with lethal doses of live E. coli . Fh15 was administrated as isotonic infusion 30 min prior to the bacterial infusion. Among the novel findings reported in this communication, I) Fh15 significantly prevented bacteremia, suppressed LPS levels in plasma and the production of C-reactive protein and procalcitonin, which are key signature of inflammation and bacterial infection, respectively, II) notably reduced the production of pro-inflammatory cytokines, and III) increased innate immune cell populations in blood, which suggest a role in promoting a prolonged steady state in rhesus macaques even in the presence of inflammatory stimuli. This is the first report demonstrating that a F. hepatica -derived molecule possesses potential as anti-inflammatory drug against endotoxemia in an NHP-model. T weet This is the first communication demonstrating that a F. hepatica -derived molecule possesses potential as anti-inflammatory drug against endotoxemia in an NHP-model. I mportance Sepsis caused by Gram-negative bacteria affect 1.7 million adults annually in the United States and is one of the most important causes of death at intensive care units. Although the effective use of antibiotics has resulted in improved prognosis of sepsis, the pathological and deathly effects has been attributed to the persistent inflammatory cascade. There is a present need to develop anti-inflammatory agents that can suppress or neutralize the inflammatory responses and prevent the lethal consequences of sepsis. We demonstrated herein that a small molecule of 14.5kDa can suppress the bacteremia, endotoxemia and many other inflammatory markers in a rhesus macaque model. These results reinforce the notion that Fh15 constitute an excellent candidate for drug development against sepsis.
Surface Coatings that Promote Rapid Release of Peptide‐Based AgrC Inhibitors for Attenuation of Quorum Sensing in <i>Staphylococcus aureus</i> (2013)

Staphylococcus aureus is a major human pathogen responsible for a variety of life-threatening infections. The pathogenicity of this organism is attributed to its ability to produce a range of virulence factors and toxins, including the superantigen toxic shock syndrome toxin-1 (TSST-1). While many S. aureus infections can be treated using conventional antibiotics, strains resistant to these bactericidal agents have emerged. Approaches that suppress pathogenicity through mechanisms that are nonbactericidal (i.e., antivirulence approaches) could provide new options for treating infections, including those caused by resistant strains. Here, we report a nonbactericidal approach to suppressing pathogenicity based on the release of macrocyclic peptides (1 and 2) that inhibit the agr quorum sensing (QS) circuit in group-III S. aureus. It is demonstrated that these peptides can be immobilized on planar and complex objects (on glass slides, nonwoven meshes, or within absorbent tampons) using the rapidly dissolving polymer carboxymethylcellulose (CMC). Peptide-loaded CMC films released peptide rapidly (<5 min) and promoted strong (>95%) inhibition of the agr QS circuit without inducing cell death when incubated in the presence of a group-III S. aureus gfp-reporter strain. Peptide 1 is among the most potent inhibitors of QS in S. aureus reported to date, and the group-III QS circuit regulates production of TSST-1, the primary cause of toxic shock syndrome (TSS). These results thus suggest approaches to treat the outer covers of tampons, wound dressings, or other objects to suppress toxin production and reduce the severity of TSS in clinical and personal care contexts. Because peptide 1 also inhibits QS in S. aureus groups-I, -II, and -IV, this approach could also provide a pathway for attenuation of QS and associated virulence phenotypes in a broader range of contexts.
Adeno‐Associated Viral Vectors (1999)

Adeno-associated virus (AAV) is a non-pathogenic human virus that also has tumour suppressor properties. Its life cycle has two phases – replicative and latent. In the productive phase it co-infects the host cell with a helper virus. In the absence of a helper virus, AAV usually enters the latent phase, integrating into the human genome, commonly within a specific region of chromosome 19. Its principal advantage for gene therapy is the poor inflammatory response to infected cells. Recombinant AAV is efficient at cell entry and tends to persist in cells for long times, although expression of the transgene may be limited in both amount and duration. AAV vectors have been used in a range of cell lines and in in vitro models of specific disease applications, e.g. haemoglobinopathies and cystic fibrosis. Initial in vivo applications focused on the brain and lung as target organs.
Unresolved questions, changing definitions, and novel paradigms for defining endothelial progenitor cells (2005)

The field of vascular biology has been stimulated by the concept that circulating endothelial progenitor cells (EPCs) may play a role in neoangiogenesis (postnatal vasculogenesis). One problem for the field has been the difficulty in accurately defining an EPC. Likewise, circulating endothelial cells (CECs) are not well defined. The lack of a detailed understanding of the proliferative potential of EPCs and CECs has contributed to the controversy in identifying these cells and understanding their biology in vitro or in vivo. A novel paradigm using proliferative potential as one defining aspect of EPC biology suggests that a hierarchy of EPCs exists in human blood and blood vessels. The potential implications of this view in relation to current EPC definitions are discussed.
Oscillation burst generation in transferred-electron devices with picosecond optical pulses (1981)

Bursts of oscillations have been triggered in GaAs transferred-electron devices by picosecond optical pulses focused onto the region between the gate and anode. The oscillation frequency was varied between 6.7 and 10.5 GHz by changing the position of the optical spot. The burst duration depended logarithmically upon the optical input power, indicating a decay of the optically excited electron-hole plasma with a measured lifetime of 430 psec, and could be varied between 1.5 and 5.0 nsec.
Synthesis of 1,4-anhydro-<scp>D</scp>-xylitol heteroanalogues of the naturally occurring glycosidase inhibitor salacinol and their evaluation as glycosidase inhibitors (2002)

The syntheses of two 1,4-anhydro-D-xylitol heteroanalogues (8 and 9) of the naturally occurring sulfonium ion, salacinol (3), containing a sulfur or nitrogen atom in the ring are described. Salacinol (3) is one of the active principles in the aqueous extracts of Salacia reticulata that are traditionally used in Sri Lanka and India for the treatment of Type 2 diabetes. The synthetic strategy relies on the nucleophilic attack of sulfur or nitrogen analogues of 1,4-anhydro-D-xylitol at the least-hindered carbon of 2,4-O-benzylidene-L-erythritol-1,3-cyclic sulfate. The sulfonium ion 8 inhibited barley-α-amylase (AMY1) and porcine pancreatic-α-amylase (PPA), with K i values of 109 ± 11 and 55 ± 5 µM, respectively. In contrast, the ammonium ion 9 showed no significant inhibition of either AMY1 or PPA. Compounds 8 and 9 also showed no significant inhibition of glucoamylase.Key Words: glycosidase inhibitors, salacinol analogues, anhydro-D-xylitol heteroanalogues, enzyme inhibition.
Generative predecessor models for sample-efficient imitation learning (2019)

We propose Generative Predecessor Models for Imitation Learning (GPRIL), a novel imitation learning algorithm that matches the state-action distribution to the distribution observed in expert demonstrations, using generative models to reason probabilistically about alternative histories of demonstrated states. We show that this approach allows an agent to learn robust policies using only a small number of expert demonstrations and self-supervised interactions with the environment. We derive this approach from first principles and compare it empirically to a state-of-the-art imitation learning method, showing that it outperforms or matches its performance on two simulated robot manipulation tasks and demonstrate significantly higher sample efficiency by applying the algorithm on a real robot.
Co/sup 2+/:ZnSe Q-switching of diode-pumped 1.53 μm Er:Yb:glass mini-laser (2002)

The present work demonstrates the passive Q-switching of a diode-pumped Er:Yb:glass mini-laser by a new crystal saturable absorber: (/spl sim/001%)Co/sup 2+/:ZnSe, without intracavity focusing. The primary advantage of Co:ZnSe Over U-doped materials is its much higher absorption cross-section.
Robotic manifold tracking of coherent structures in flows (2012)

Tracking Lagrangian coherent structures in dynamical systems is important for many applications such as oceanography and weather prediction. In this paper, we present a collaborative robotic control strategy designed to track stable and unstable manifolds. The technique does not require global information about the fluid dynamics, and is based on local sensing, prediction, and correction. The collaborative control strategy is implemented on a team of three robots to track coherent structures and manifolds on static flows as well as a noisy time-dependent model of a wind-driven double-gyre often seen in the ocean. We present simulation and experimental results and discuss theoretical guarantees of the collaborative tracking strategy.
Self-interference digital holography with a geometric-phase hologram lens (2017)

Self-interference digital holography (SIDH) is actively studied because the hologram acquisition under the incoherent illumination condition is available. The key component in this system is wavefront modulating optics, which modulates an incoming object wave into two different wavefront curvatures. In this Letter, the geometric-phase hologram lens is introduced in the SIDH system to perform as a polarization-sensitive wavefront modulator and a single-path beam splitter. This special optics has several features, such as high transparency, a modulation efficiency up to 99%, a thinness of a few millimeters, and a flat structure. The demonstration system is devised, and the numerical reconstruction results from an acquired complex hologram are presented.
11.2: A New Process for Manufacture of Low Voltage, Polymer‐Stabilized Blue Phase LCDs (2011)

Abstract We realized a blue‐phase liquid crystal display with low driving voltage and high contrast by using a liquid crystal material which is easily twisted and a protrusion electrode structure. Further, we made a prototype of a 3.4‐inch panel by a novel manufacturing process suitable for a large‐sized panel.
Superhard self-lubricating AlMgB14 films for microelectromechanical devices (2003)

Performance and reliability of microelectromechanical system (MEMS) components can be enhanced dramatically through the incorporation of protective thin-film coatings. Current-generation MEMS devices prepared by the lithographie-galvanoformung-abformung (LIGA) technique employ transition metals such as Ni, Cu, Fe, or alloys thereof, and hence lack stability in oxidizing, corrosive, and/or high-temperature environments. Fabrication of a superhard self-lubricating coating based on a ternary boride compound AlMgB14 described in this letter has great potential in protective coating technology for LIGA microdevices. Nanoindentation tests show that the hardness of AlMgB14 films prepared by pulsed laser deposition ranges from 45 GPa to 51 GPa, when deposited at room temperature and 573 K, respectively. Extremely low friction coefficients of 0.04–0.05, which are thought to result from a self-lubricating effect, have also been confirmed by nanoscratch tests on the AlMgB14 films. Transmission electron microscopy studies show that the as-deposited films are amorphous, regardless of substrate temperature; however, analysis of Fourier transform infrared spectra suggests that the higher substrate temperature facilitates the formation of the B12 icosahedral framework, therefore leading to the higher hardness.
Neutron Probe of Building-Wall Composition (1984)

Walls of historic buildings charted by neutron radiography. Neutron source and Gamma-Ray Detector alined with each other yield map of composition of wall. Points spaced for minimal overlap based on mean free path of gamma rays emitted from wall materials. Map indicates nature and extent of changes in building materials so proper treatment is applied.