gebhart/patrepeval huggingface dataset:
The structure-function analysis of the Mpr1 metalloprotease determinants of activity during migration of fungal cells across the blood-brain barrier (2018)

Cryptococcal meningoencephalitis, the most common form of cryptococcosis, is caused by the opportunistic fungal pathogen, Cryptococcus neoformans. Molecular strategies used by C. neoformans to invade the central nervous system (CNS) have been the focus of several studies. Recently, the role of a novel secreted metalloprotease (Mpr1) in the pathogenicity of C. neoformans was confirmed by studies demonstrating that Mpr1 mediated the migration of fungal cells into the CNS. Given this central function, the aim here was to identify the molecular determinants of Mpr1 activity and resolve their role in the migration of cryptococci across the blood-brain barrier (BBB). The Mpr1 protein belongs to an understudied group of metalloproteases of the M36 class of fungalysins unique to fungi. They are generally synthesized as propeptides with fairly long prodomains and highly conserved regions within their catalytic core. Through structure-function analysis of Mpr1, our study identified the prodomain cleavage sites of Mpr1 and demonstrated that when mutated, the prodomain appears to remain attached to the catalytic C-terminus of Mpr1 rendering a nonfunctional Mpr1 protein and an inability for cryptococci to cross the BBB. We found that proteolytic activity of Mpr1 was dependent on the coordination of zinc with two histidine residues in the active site of Mpr1, since amino acid substitutions in the HExxH motif abolished Mpr1 proteolytic activity and prevented the migration of cryptococci across the BBB. A phylogenetic analysis of Mpr1 revealed a distinct pattern likely reflecting the neurotropic nature of C. neoformans and the specific function of Mpr1 in breaching the BBB. This study contributes to a deeper understanding of the molecular regulation of Mpr1 activity and may lead to the development of specific inhibitors that could be used to restrict fungal penetration of the CNS and thus prevent cryptococcal meningoencephalitis-related deaths.
Prolonged suppression of HBV in mice by a novel antibody that targets a unique epitope on hepatitis B surface antigen (2015)

These results provided new insight into understanding the therapeutic role and mechanism of antibody against persistent viral infection. The E6F6-like mAbs may provide a novel immunotherapeutic agent against human chronic HBV infection.
Rapid Silicon-to-Steel Bonding by Induction Heating for MEMS Strain Sensors (2012)

A rapid and manufacturable technique to bond silicon to steel for microelectromechanical system (MEMS) sensor applications is presented. Using an induction heating system, the process is simple, clean, inexpensive, and fast, with bonding occurring in 3-5 s. Heat generation is isolated to within several micrometers below the steel surface, allowing for a controllable thermal budget that does not damage the surface treatment of steel. The process requires minimal surface conditioning and may be used with a variety of different metal systems. Bonds formed with adhesion layers of gold, silver, and nickel showed excellent mechanical characteristics, surviving surface strains exceeding +/- 2000 με. The transferred strain was quantified by ANSYS simulation and measured experimentally for silicon substrates of varying thicknesses, with the 100 μm-thick substrates demonstrating the greatest strain sensitivity. A double-ended tuning fork MEMS resonant strain sensor, bonded to a steel parallel, demonstrated a repeatable 5.4-fold improvement in strain sensitivity compared to epoxy bonding. As such, this robust bonding process is well-suited for bonding MEMS sensors to monitor components in the automotive, manufacturing, and other harsh environment industries.
Effect of preservative removal from fixed-combination bimatoprost/timolol on intraocular pressure lowering: a potential timolol dose&ndash;response phenomenon (2016)

The evidence suggests that timolol may have an inverted U-shaped dose-response curve, and that its optimal IOP-lowering concentration is between 0.25% and 0.5%. Compared with bim/tim, removal of the permeability enhancer BAK in bim/tim PF could have resulted in a lower timolol concentration at the target site, bringing the effective concentration within the 0.25%-0.5% range and enhancing the efficacy of bim/tim PF.
Computational Reconstruction of Bole1a, a Representative Synthetic Hepatitis C Virus Subtype 1a Genome (2012)

Hepatitis C virus (HCV) research is hampered by the use of arbitrary representative isolates in cell culture and immunology. The most replicative isolate in vitro is a subtype 2a virus (JFH-1); however, genotype 1 is more prevalent worldwide and represents about 70% of infections in the United States, and genotypes differ from one another by 31% to 33% at the nucleotide level. For phylogenetic and immunologic analyses, viruses H77 and HCV-1 (both subtype 1a) are commonly used based on their historic importance. In an effort to rationally design a representative subtype 1a virus (Bole1a), we used Bayesian phylogenetics, ancestral sequence reconstruction, and covariance analysis on a curated set of 390 full-length human HCV 1a sequences from GenBank. By design, Bole1a contains variations present in widely circulating strains and matches more epitope-sized peptides in a full-genome comparison to subtype 1a isolates than any other sequence studied. Parallel analyses confirm that selected epitopes from the Bole1a genome were able to elicit a robust T cell response. In a proof of concept for infectivity, the envelope genes (E1 and E2) of Bole1a were expressed in an HIV pseudoparticle system containing HCV envelope genes and HIV nonenvelope genes with luciferase expression. The resulting Bole1a pseudoparticle robustly infected Hep3B cells. In this study, we demonstrate that a rationally designed, fully synthetic HCV genome contains representative epitopes and envelope genes that assemble properly and mediate entry into target cells.
Amino Acid Substitutions That Convert the Protein Substrate Specificity of Farnesyltransferase to That of Geranylgeranyltransferase Type I (1997)

Protein farnesyltransferase (FTase), a heterodimer enzyme consisting of alpha and beta subunits, catalyzes the addition of farnesyl groups to the C termini of proteins such as Ras. In this paper, we report that the protein substrate specificity of yeast FTase can be switched to that of a closely related enzyme, geranylgeranyltransferase type I (GGTase I) by a single amino acid change at one of the three residues: Ser-159, Tyr-362, or Tyr-366 of its beta-subunit, Dpr1. All three Dpr1 mutants can function as either FTase or GGTase I beta subunit in vivo, although some differences in efficiency were observed. These results point to the importance of two distinct regions (one at 159 and the other at 362 and 366) of Dpr1 for the recognition of the protein substrate. Analysis of the protein, after site directed mutagenesis was used to change Ser-159 to all possible amino acids, showed that either asparagine or aspartic acid at this position allowed FTase beta to function as GGTase I beta. A similar site-directed mutagenesis study on Tyr-362 showed that leucine, methionine, or isoleucine at this position also resulted in the ability of mutant FTase beta to function as GGTase I beta. Interestingly, in both position 159 and 362 substitutions, amino acids that could change the protein substrate specificity had similar van der Waals volumes. Biochemical characterization of the S159N and Y362L mutant proteins showed that their kcat/Km values for GGTase I substrate are increased about 20-fold compared with that of the wild type protein. These results demonstrate that the conversion of the protein substrate specificity of FTase to that of GGTase I can be accomplished by introducing a distinct size amino acid at either of the two residues, 159 and 362.
Anti-β2 glycoprotein I (β2GPI) autoantibodies recognize an epitope on the first domain of β2GPI (1998)

Anticardiolipin (aCL) autoantibodies are associated with thrombosis, recurrent fetal loss, and thrombocytopenia. Only aCL found in autoimmune disease require the participation of the phospholipid binding plasma protein beta2 glycoprotein I (beta2GPI) for antibody binding and now are called anti-beta2GPI. The antigenic specificity of aCL affinity purified from 11 patients with high titers was evaluated in an effort to better understand the pathophysiology associated with aCL. Seven different recombinant domain-deleted mutants of human beta2GPI, and full length human beta2GPI (wild-type), were used in competition assays to inhibit the autoantibodies from binding to immobilized wild-type beta2GPI. Only those domain-deleted mutants that contained domain 1 inhibited the binding to immobilized wild-type beta2GPI from all of the patients. The domain-deleted mutants that contained domain 1 inhibited all aCL in a similar but not identical pattern, suggesting that these aCL recognize a similar, but distinguishable, epitope(s) present on domain 1.
Ce:LiSrAlF6 Laser Performance with Antisolarant Pump Beam (1996)

We have explored the impact of 266 nm pump-induced solarization on the 290 nm laser performance of Ce:LiSrAlF6 crystals. Among the issues considered are the incorporation of codopants (e.g. Na+, Mg2+, Zn2+), and the use of an additional 532 nm beam to rapidly destroy the interfering color centers. The solarization mechanism has been unraveled and found to involve two-photon creation of color centers (via the 4f → 5d → conduction band pathway of Ce3+), followed by the one-photon bleaching of the color centers. Ce:LiSrAlF6 (Ce:LiSAF) laser slope efficiencies as high as 47% can be achieved with the simultaneous introduction of the 266 nm pump and 532 nm bleaching beams; 33% with the 266 nm beam only.
Remarkable Enhancement of Chemiluminescent Signal by Dioxetane–Fluorophore Conjugates: Turn-ON Chemiluminescence Probes with Color Modulation for Sensing and Imaging (2016)

Chemiluminescence is among the most sensitive methods for achieving a high signal-to-noise ratio in various chemical and biological applications. We have developed a modular practical synthetic route for preparation of turn-ON fluorophore-tethered dioxetane chemiluminescent probes. The chemiluminescent emission of the probes was significantly amplified through an energy-transfer mechanism under physiological conditions. Two probes were composed with green and near-infrared (NIR) fluorescent dyes tethered to Schaap's dioxetane. While both probes were able to provide chemiluminescence in vivo images following subcutaneous injection, only the NIR probe could provide a chemiluminescence image following intraperitoneal injection. These are the first in vivo images produced by Schaap's dioxetane chemiluminescence probes with no need of an enhancer. Previously, chemiluminescence cell images could only be obtained with a luciferin-based probe. Our NIR probe was able to image cells transfected with β-galactosidase gene by chemiluminescence microscopy. We also report, for the first time, the instability of dioxetane-fluorophore conjugates to ambient light. Our synthetic route effectively overcomes this limitation through a late-stage functionalization of the dioxetane intermediate. We anticipate that our practical synthetic methodology will be useful for preparation of various chemiluminescent probes for numerous applications.
Antineoplastic Agents. 607. Emetine Auristatins (2020)

The remarkable biological activity of the dolastatin 10 structural modifications quinstatins and isoquinstatins prompted further investigation into drug hybrids containing biologically active isoquinoline moieties. In this study, the isoquinoline alkaloid emetine was selected as one of the structural domains of a hybrid molecule. That was accomplished by covalently bonding the Dov-Val-Dil-Dap peptide sequence of dolastatin 10 peptide at the N-2' secondary amine of emetine. Three new hybrids were synthesized, <b>5</b>, <b>9</b>, and <b>10</b>. Comparison of the biological activity of these new peptide-emetine analogues with emetine showed complete retention of activity for <b>5</b> and a 10-fold decrease for hybrids <b>9</b> and <b>10</b>. The result was surprising, as the activity of emetine is usually lost or greatly reduced when substituted at the N-2' position.
Pinning-Based Distributed Cooperative Control for Autonomous Microgrids Under Uncertain Communication Topologies (2015)

In this study, a new pinning-based distributed cooperative control scheme is proposed for multi-agent system (MAS)-based autonomous microgrids. By pinning parts of selected agents, only a small fraction of the pinned agents are controlled by simple feedback controllers, while the other DGAs in the MAS synchronize through the communication coupling among the pinned agents in a distributed manner. The main contributions of this study are as follows: 1) the proposal of a fully distributed control for autonomous microgrids where each agent shares its operation information only with its neighbors, which obviates the requirement for a central controller and complex communication topology; 2) the proposal of a pinning-based control scheme, which reduces the number of controllers, for a predefined consensus can be reached if a small fraction of the pinned agents is controlled; and 3) the proposal of the pinning consensus under uncertain communication topologies that can meet the requirements of line switches and plug-and-play operation. Simulation results are demonstrated to verify the effectiveness and adaptability of the proposed scheme.
At-speed scan test with low switching activity (2010)

This paper presents a novel method to generate test vectors that mimic functional operation from switching activity point of view. The method uses states obtained by applying a number of functional clock cycles starting from the scan-in state of a test vector to fill the unspecified scan cell values in test cubes. Experimental results presented for industrial circuits demonstrate the effectiveness of the proposed method.
Seismo-acoustic characterization of a seismic vibrator (2014)

Summary A seismic vibrator generates seismic and acoustic noise as soon as it is pressured up and located in the proximity of a recording spread. The noise in the seismic bandwidth is more critical in vibroseis surveys where a large number of vibrators are used as in the case of simultaneous acquisitions. The noise in the acoustic bandwidth is particularly important when the survey takes place in populated areas. We carried out a seismo-acoustic experiment to characterize these noises. We present the results obtained while the vibrator is pressured up but not sweeping, with the baseplate in contact or not with the ground. We demonstrate that several monochromatic noise components can be related to the cooling and exhaust systems. We also show the effects in the seismic and acoustic bandwidths of modifications to the cooling and exhaust systems.
Vanadium dioxide current limiters for incandescent lamps (1976)

A VO2 resistor, which switches from high to low resistance as it passes through a phase transition at 68 °C, can eliminate the initial current surge when an incandescent lamp is first turned on; this inrush current, which is often harmful, occurs because the cold resistance of the lamp is low. We here analyze the progress of (and the instabilities in) the electrically driven thermal switching of VO2, and determine the size and properties that a current-limiting resistor must have. Current limiters were made from a ceramic with a VO2 base and various additives; such limiters work well, and the steady-state power loss in them is 0.5% for 100-W lamps.
Ormen Lange Subsea Condition and Leakage Monitoring (2007)

Abstract With the Ormen Lange development, Norsk Hydros subsea solutions are taking technological developments on the Norwegian continental shelf a significant step ahead. Nothing will be visible on the surface when the enormous gas field comes onstream in 2007. High pressure, large water depth and distant location called for a new way of thinking in many ways. This paper will present the leakage and condition monitoring system developed to ensure safe and pollution free operation of the two templates at 850 meters of water depth. Hydro and Naxys Naval Technology started already back in 2000 the development of a new type of subsea monitoring system based on technology originally developed for naval warefare and surveillance. After successful testing on the subsea processing plant, Troll Pilot in 2001, the system was further developed and qualified. On the Ormen Lange Templates one centrally positioned module containing an array of acoustic sensors monitors the complete 44 × 33-m template. The system provides location and magnitude of any leak, structural vibration or valve malfunction on the template.
Marginalizing Out Future Passengers in Group Elevator Control (2012)

Group elevator scheduling is an NP-hard sequential decision-making problem with unbounded state spaces and substantial uncertainty. Decision-theoretic reasoning plays a surprisingly limited role in fielded systems. A new opportunity for probabilistic methods has opened with the recent discovery of a tractable solution for the expected waiting times of all passengers in the building, marginalized over all possible passenger itineraries. Though commercially competitive, this solution does not contemplate future passengers. Yet in up-peak traffic, the effects of future passengers arriving at the lobby and entering elevator cars can dominate all waiting times. We develop a probabilistic model of how these arrivals affect the behavior of elevator cars at the lobby, and demonstrate how this model can be used to very significantly reduce the average waiting time of all passengers.
Reservoir Geomechanical Modeling and Ground Uplift During CO2 Injection Into Khuff Reservoir (2019)

Abstract In this investigation, coupled-geomechanical modeling is performed using the COMSOL Multiphysics software, during carbon dioxide injection into the deep Khuff carbonate reservoir. Khuff reservoir is a carbonate reservoir that is capped by the low permeability Sudair shale geological layer. The main objective of the study was to evaluate safe values of the carbon dioxide injection parameters for the Khuff reservoir that will act as a benchmark for the similar reservoirs and injection scenarios around the globe. Carbon dioxide was injected for a period of 10 years into the reservoir and the corresponding variations in the reservoir pore-pressure and ground uplift was evaluated. The Mohr-Coulomb failure criterion was utilized to perform the stability analysis for the Khuff reservoir during carbon dioxide injection.
Optical Filters, Reflectors and Polarizers Fashioned with Periodic Leaky-Mode Resonant Layers (2007)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text R. Magnusson, M. Shokooh-Saremi, and Y. Ding, "Optical Filters, Reflectors, and Polarizers Fashioned with Periodic Leaky-Mode Resonant Layers," in Optical Interference Coatings, OSA Technical Digest (CD) (Optica Publishing Group, 2007), paper TuC2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Purification and Characterization of an Acetoin Dehydrogenase from<i>Lactobacillus Kefir</i>Suitable for the Production of (+)-Acetoin (1989)

A dehydrogenase catalyzing the NADH-dependent reduction of diacetyl to (+)-acetoin was found in Lactobacillus kefir. The enzyme could be purified by heat treatment, ion exchange chroraatography and gel filtration (130 U/mg). Further purification resulted in two isoenzymes, E1 (1061 U/mg) with a molecular weight of 66 kD and E2 (366 U/mg) of 74 kD. Important biochemical data concerning the application of the enzyme are: pH-optimum at 4.3 (E1,) and 5.0 (E2), temperature optimum at 70d`C, stable at 57d`C for 10 min. Besides diacetyl several other diketones were reduced. For diacetyl, a KM-value of 310 mM for E1 and 67 mM for E2 was measured. The reverse reaction of acetoin oxidation in the presence of NAD could not be observed, whereas D(—)-lactate was oxidized by the enzyme. In exploratory experiments conversions of 200 mM diacetyl in batch reactions with coenzyme regeneration resulted in 170 mM product concentration. The formation of (+)-acetoin was confirmed by determination of its molar optical rotation and by chiral gas chromatography. Another diacetyl-reducing enzyme enriched from Candida boidinii (23-fold purified) yielded a nearly racemic mixture of acetoin.
Light-Induced Assembly and Reconfiguration of Chiral Nanostructures (2019)

Summary form only given. Matured syntheses of inorganic nanocolloids today have allowed production of diverse asymmertic nanoparticles (NP) and even more complex assemblies, introducing a variety of nanomaterials with unique properties. Chirality is one of most intriguing symmetry groups in field of material science due to the optical rotatory power of chiral substances. Strong optical activity of inorganic nanoparticles (NPs) afford photosynthetic routes to chiral superstructures using circularly polarized photons (1). Although plasmonic NPs are promising candidates for such synthetic routes due to the strong rotatory power of highly delocalized plasmonic states (2), realization of light- driven synthesis of chiral nanostructures has been more challenging for plasmonic NPs than for the semiconductor due to the short lifetime of the plasmonic states. The process also can be difficult to recognize, and therefore requires unconventional approaches for the quantification of chiral products. Here, we demonstrate that illumination of Au precursors in the presence of citric acid with right- (left-) handed circularly polarized light (CPL) induces the formation of chiral Au nanostructures. Despite seemingly irregular shape of the particles, the resulted colloids showed distinctive mirror-imaged opposite circular dichroism (CD) bands according to the handedness of illuminated CPL. Circular dichroic response and geometric chirality from these seemingly achiral structures were successfully demonstrated and quantified by implementing three-dimensional (3D) electron tomography (e-tomo) into computational model. The mechanism of the light-driven assembly of chiral nanostructures is based on the asymmetric displacement of NPs in dynamic assemblies by plasmonic fields fol-lowed by particle-to-particle attachment. The ability of Au nanostructures to retain the polarization information of incident photons can be applicable to light absorbing materials, thus to create a variety of chiral nanomaterials. Similar examination of seemingly irregular NP through suggested chirality measure can also elucidate previously puzzling optical response from unclear geometric asymmetry of nanomaterials.
<title>Laser-Plasma Source For Pulsed X-Ray Lithography</title> (1978)

The exposure of an x-ray resist by radiation from laser-heated plasmas was recently demonstrated. Single-shot submicrosecond exposures with a very favorable x-ray spectrum are possible. In order to reduce the cost of a laser-plasma x-ray lithography system, it is desirable to maximize the intensity in the soft (1 to about 3 keV) range. The x-ray output of laser-plasmas depends on laser pulse parameters (wavelength, pulse shape and energy), the focal conditions, and the target composition and geometry. Laser-plasma x-ray characteristics and their sensitivity to experimental parameters are reviewed in this paper. Presently available information indicates that a Nd:glass laser having pulse width in or near the 1-10 nsec range with at least 500 J of energy should be adequate for practical single-shot x-ray lithography.