gebhart/patrepeval huggingface dataset:
TIMED Doppler Interferometer: Overview and recent results (2006)

The Thermosphere‐Ionosphere‐Mesosphere Energetics and Dynamics (TIMED) satellite carries a limb‐scanning Fabry‐Perot interferometer designed to perform remote‐sensing measurements of upper atmosphere winds and temperatures globally. This instrument is called the TIMED Doppler Interferometer, or TIDI. This paper provides an overview of the TIDI instrument design, on‐orbit performance, operational modes, data processing and inversion procedures, and a summary of wind results to date. Daytime and nighttime neutral winds in the mesosphere and lower thermosphere/ionosphere (MLTI) are measured on TIDI using four individual scanning telescopes that collect light from various upper atmosphere airglow layers on both the cold and warm sides of the high‐inclination TIMED spacecraft. The light is spectrally analyzed using an ultrastable plane etalon Fabry‐Perot system with sufficient spectral resolution to determine the Doppler line characteristics of atomic and molecular emissions emanating from the MLTI. The light from all four telescopes and from an internal calibration field passes through the etalon and is combined on a single image plane detector using a Circle‐to‐Line Interferometer Optic (CLIO). The four geophysical fields provide orthogonal line‐of‐sight measurements to either side of the satellite's path and these are analyzed to produce altitude profiles of vector winds in the MLTI. The TIDI wind measurements presented here are from the molecular oxygen (0‐0) band, covering the altitude region 85–105 km. The unique TIDI design allows for more extended local time coverage of wind structures than previous wind‐measuring instruments from high‐inclination satellites. The TIDI operational performance has been nominal except for two anomalies: (1) higher than expected background white light caused by a low‐level light leak and (2) ice deposition on cold optical surfaces. Both anomalies are well understood and the instrumental modes and data analysis techniques have been adjusted to mitigate their effects on data quality. The analysis techniques used to derive winds are described. The TIDI wind measurements from multiple yaw cycles of TIMED have been used to extract migrating diurnal and semidiurnal tides. The migrating tide results are compared with predictions from the Global Scale Wave Model (GSWM), and results from the Upper Atmospheric Research Satellite, High Resolution Doppler Imager (HRDI) instrument. TIDI wind measurements are also compared with ground‐based meteor radar observations, showing consistent results.
Classification and identification of geminiviruses using sequence comparisons (1995)

The genomes and ORFs of 36 geminiviruses were compared to obtain phylogenetic trees and frequency distributions of all possible pairwise comparisons with an objective to classify geminiviruses. Such comparisons show that geminiviruses form two distinct clusters of leafhopper-transmitted viruses that infect monocots (subgroup I) and whitefly-transmitted viruses that infect dicots (subgroup III), irrespective of the part of the genome considered. Of the two leafhopper-transmitted viruses that infect dicots, tobacco yellow dwarf virus has a sequence most similar to subgroup I viruses, and that of beet curly top virus differed depending upon the ORF considered. The distributions of identities within subgroups are significantly different suggesting that the taxonomic status of a particular isolate within a subgroup can be quantified. All the recognized strains of any one virus have greater than 90% sequence identity. It was observed that the 200 nucleotide intercistronic regions of geminiviruses are more variable than the remainder of the genome. The amino acid sequences of the coat protein (CP) of subgroup III viruses are more conserved than the remainder of the genome. However, a short N-terminal region (60-70 amino acids) of the CP is more variable than the rest of the CP sequence and is a close representation of the genome. PCR primers based on conserved sequences can be used to clone and sequence the N-terminal sequences of the CP of the geminiviruses; this sequence is sufficient to classify a virus isolate. A possible taxonomic structure for geminiviruses is proposed after considering the sequence comparisons and biological properties.
Transcellular Transport Is not Required for Transmucosal Bacterial Passage across the Intestinal Membrane <i>Ex Vivo</i> (2000)

The mechanisms underlying the process of bacterial translocation are poorly defined. Possible routes for transmucosal passage of bacteria include transcellular and paracellular channels. Bacterial engulfment is a prerequisite for transcellular transport. To determine whether transcellular transport is required for transmucosal bacterial passage, we examined the effect of various inhibitors of endocytosis, such as colchicine, cytochalasin B, and sodium fluoride on transmucosal passage of bacteria across an ileal mucosal membrane mounted in the Ussing chamber. Colchicine and sodium fluoride increased the rate of decline of the potential difference across the membranes. However, neither colchicine, cytochalasin B, nor sodium fluoride affected the incidence of transmucosal bacterial passage. Sodium fluoride, which depletes intracellular ATP, significantly decreased the number of bacteria that passed per membrane. Our data suggest that transcellular transport may not be required for spontaneous transmucosal passage of bacteria, and furthermore bacterial passage may be, at least in part, an energy-dependent process.
Induction of Cancer Cell Death by Self-assembling Nanostructures Incorporating a Cytotoxic Peptide (2010)

Nanotechnology offers novel delivery vehicles for cancer therapeutics. Potential advantages of nanoscale platforms include improved pharmacokinetics, encapsulation of cytotoxic agents, enhanced accumulation of therapeutics in the tumor microenvironment, and improved therapeutic structures and bioactivity. Here, we report the design of a novel amphiphilic molecule that self-assembles into nanostructures for intracellular delivery of cytotoxic peptides. Specifically, a cationic alpha-helical (KLAKLAK)(2) peptide that is known to induce cancer cell death by membrane disruption was integrated into a peptide amphiphile (PA) that self-assembles into bioactive, cylindrical nanofibers. PAs are composed of a hydrophobic alkyl tail, a beta-sheet forming peptide, and a bioactive peptide that is displayed on the surface of the nanofiber after self-assembly. PA nanostructures that included (KLAKLAK)(2) were readily internalized by breast cancer cells, in contrast to the (KLAKLAK)(2) peptide that on its own was not cell permeable. (KLAKLAK)(2) nanostructures, but not the peptides alone, also induced breast cancer cell death by caspase-independent and Bax/Bak-independent mechanisms associated with membrane disruption. Significantly, (KLAKLAK)(2) nanostructures induced cell death more robustly in transformed breast epithelial cells than in untransformed cells, suggesting a degree of tumor selectivity. Our results provide proof-of-principle that self-assembling PAs can be rationally designed to generate nanostructures that can efficiently deliver cytotoxic peptides to cancer cells.
Efficiency of photoluminescence and excess carrier confinement in InGaAsP/GaAs structures prepared by metal-organic chemical-vapor deposition (1994)

Special double- and separate-confinement InGaAsP/GaAs heterostructures intended for photoluminescence measurements have been grown by low-pressure metal-organic chemical-vapor deposition. The band gap of the active region quaternary material was close to 1.5 eV, and the waveguide of the separate-confinement structures was near 1.8 eV. Measurement of the integrated luminescence efficiency at 300 K has shown that over a wide range of excitation level (10–103 W/cm2) radiative transitions are the dominant mechanism for excess carrier recombination in the active region of the structures studied. As determined by spectral measurements, the excess carrier concentration in the waveguide of the separate-confinement heterostructures and the intensity of the waveguide emission band correspond to a condition of thermal equilibrium of the excess carrier populations in the active region and the waveguide. The ratio of the intensity of the waveguide emission to the active region emission fits a model which assumes that the barrier height for minority carriers (holes) is equal to the difference in band gaps between the active region and the waveguide region.
Structure, Bonding, and Reactivity of Ti and Zr Amidate Complexes:  DFT and X-Ray Crystallographic Studies (2005)

Easily prepared and highly modular organic amide proligands have been used to synthesize a series of new bis(amidate)-bis(amido) Ti and Zr complexes via protonolysis. These complexes have been structurally characterized by NMR spectroscopy and X-ray crystallography. The solid-state molecular structures of these complexes indicate that the amidate ligands bind to the metal centers in an exclusively bidentate fashion, resulting in discrete monomeric species. Geometric isomerism in these species is highly dependent upon the steric characteristics of the proligands utilized in the synthesis. In solution, these complexes are observed to isomerize on the NMR time scale, with one isomer being predominant. Bonding in the bis(amidate)-bis(amido) complexes was investigated by DFT calculations. The geometric isomers predicted by theory matched the experimentally observed results, within experimental error. The orbitals associated with amidate-metal bonding are energetically well below the frontier orbitals. The HOMO in these complexes is a pi orbital associated with amido ligand-to-metal bonding character, while the LUMO in all cases is a vacant d orbital on the metal center.
Heme–Hemopexin Complex Attenuates Neuronal Cell Death and Stroke Damage (2009)

Hemoproteins undergo degradation during hypoxic/ischemic conditions, but the pro-oxidant free heme that is released cannot be recycled and must be degraded. The extracellular heme associates with its high-affinity binding protein, hemopexin (HPX). Hemopexin is shown here to be expressed by cortical neurons and it is present in mouse cerebellum, cortex, hippocampus, and striatum. Using the transient ischemia model (90-min middle cerebral artery occlusion followed by 96-h survival), we provide evidence that HPX is protective in the brain, as neurologic deficits and infarct volumes were significantly greater in HPX(-/-) than in wild-type mice. Addressing the potential protective HPX cellular pathway, we observed that exogenous free heme decreased cell survival in primary mouse cortical neuron cultures, whereas the heme bound to HPX was not toxic. Heme-HPX complexes induce HO1 and, consequently, protect primary neurons against the toxicity of both heme and pro-oxidant tert-butyl hydroperoxide; such protection was decreased in HO1(-/-) neuronal cultures. Taken together, these data show that HPX protects against heme-induced toxicity and oxidative stress and that HO1 is required. We propose that the heme-HPX system protects against stroke-related damage by maintaining a tight balance between free and bound heme. Thus, regulating extracellular free heme levels, such as with HPX, could be neuroprotective.
An all digital implementation of a modified Hamming net for video compression with prediction and quantization circuits (1991)

The hardware and algorithms used to vector quantize (VQ) predicted pixel intensity differences for real-time video compression are described. The hardware is designed for rapid vector quantization performance, which entails the development of application-specific associative memory circuits. A modified DPCM algorithm is originally examined to determine how neural circuitry could enhance its operation. It was determined that quantization and encoding could be improved by consolidating these two functions into one, and by increasing the amount of information (i.e. number of pixels) quantized at a time. The result is a predictive scheme that vector quantizes differential values. Some of the disadvantages of VQ algorithms are solved using associative memories. The video compression algorithm and the associative memory design are described.
Construction and characterization of adriamycin‐loaded canine red blood cells as a potential slow delivery system (1990)

Adriamycin was internalized in canine red blood cells (RBC) by two procedures involving (a) simple diffusion of the drug into cells and (b) hypotonic dialysis followed by isotonic resealing. The two procedures yielded comparable amounts of encapsulated adriamycin, around 35 micrograms/10(9) RBC. Exposure of adriamycin-loaded RBC to 0.16% glutaraldehyde consistently slowed down the rate of efflux of the drug as compared with non-glutaraldehyde-treated cells: after 1 h of incubation at 37 degrees C, greater than 80% of adriamycin was still present inside the glutaraldehyde-treated RBC, while at 24 h it was 66%, compared to 10% and 1%, respectively, in the adriamycin-loaded, non-glutaraldehyde-treated cells. Canine RBC showed a higher rate of transformation of adriamycin than the human cells, the only intracellular metabolite being adriamycinol, which is apparently formed by the NADPH-dependent enzyme aldehyde reductase. Production of adriamycinol was remarkably lower in the glutaraldehyde-treated RBC, as a result of progressive and extensive inactivation of hexose monophosphate shunt activity responsible for NADPH formation. These results, coupled with the known selective targeting of glutaraldehyde-treated RBC to liver, hold promise as to in vivo applications of this drug delivery system in antineoplastic therapy.
On spin trapping hydroxyl and hydroperoxyl radicals (1978)

The assignments of the hydroxyl, hydroperoxyl, and alkylperoxyl radical spin adducts of α-phenyl N-tert-butyl nitrone (PBN) are discussed. Results of new experiments designed to test the assignments of the first two are described. It is concluded that the hydroxy adduct assignment is correct. The relationship between a β H and a N is[Formula: see text]This equation gives a good fit for the seven pairs of constants reported for the hydroxy adduct. The assignments for the hydroperoxy adduct may be correct but no proof is yet available for this assignment.
Assessment of the risk of transporting propane by truck and train (1980)

The risk of shipping propane is discussed and the risk assessment methodology is summarized. The risk assessment model has been constructed as a series of separate analysis steps to allow the risk to be readily reevaluated as additional data becomes available or as postulated system characteristics change. The transportation system and accident environment, the responses of the shipping system to forces in transportation accidents, and release sequences are evaluated to determine both the likelihood and possible consequences of a release. Supportive data and analyses are given in the appendices. The risk assessment results are related to the year 1985 to allow a comparison with other reports in this series. Based on the information presented, accidents involving tank truck shipments of propane will be expected to occur at a rate of 320 every year; accidents involving bobtails would be expected at a rate of 250 every year. Train accidents involving propane shipments would be expected to occur at a rate of about 60 every year. A release of any amount of material from propane trucks, under both normal transportation and transport accident conditions, is to be expected at a rate of about 110 per year. Releases from propane rail tank cars would occur about 40 times a year. However, only those releases that occur during a transportation accident or involve a major tank defect will include sufficient propane to present the potential for danger to the public. These significant releases can be expected at the lower rate of about fourteen events per year for truck transport and about one event every two years for rail tank car transport. The estimated number of public fatalities resulting from these significant releases in 1985 is fifteen. About eleven fatalities per year result from tank truck operation, and approximately half a death per year stems from the movement of propane in rail tank cars.
Introduction to the Language of Three-dimensional Imaging with Multidetector CT (2005)

The recent proliferation of multi-detector row computed tomography (CT) has led to an increase in the creation and interpretation of images in planes other than the traditional axial plane. Powerful three-dimensional (3D) applications improve the utility of detailed CT data but also create confusion among radiologists, technologists, and referring clinicians when trying to describe a particular method or type of image. Designing examination protocols that optimize data quality and radiation dose to the patient requires familiarity with the concepts of beam collimation and section collimation as they apply to multi-detector row CT. A basic understanding of the time-limited nature of projection data and the need for thin-section axial reconstruction for 3D applications is necessary to use the available data effectively in clinical practice. The axial reconstruction data can be used to create nonaxial two-dimensional images by means of multiplanar reformation. Multiplanar images can be thickened into slabs with projectional techniques such as average, maximum, and minimum intensity projection; ray sum; and volume rendering. By assigning a full spectrum of opacity values and applying color to the tissue classification system, volume rendering provides a robust and versatile data set for advanced imaging applications.
Quantum Circuit Identities (2003)

There are quantum circuit identities that simplify quantum circuits, reducing the effort needed physically to implement them. This paper constructs all identities made from 3 or fewer operations taken from a common set of one qubit operations, and explains how they may be used to simplify the cost of constructing quantum circuit identities.
Atomic-scale structure of the fivefold surface of an AlPdMn quasicrystal: A quantitative x-ray photoelectron diffraction analysis (2004)

The atomic-scale structure of the fivefold symmetric surface of an AlPdMn quasicrystal is investigated quantitatively by comparing x-ray photoelectron diffraction simulations to experiment. The observed fivefold symmetry of the diffraction patterns indicates that the surface is quasicrystalline with no hint of a reconstruction from the bulk structure. In analyzing the experimental data, many possible bulk terminations have been tested. Those few that fit best to the data have in common that they contain an Al-rich surface layer followed by a dense mixed Al/Pd/Mn layer. These best terminations, while not identical to each other, are suggested to form terraces coexisting on a real surface. Structural relaxations of the quasicrystal surface are also analyzed: mixing several best-fit terminations gives average best-fit interlayer spacing changes of $\ensuremath{\Delta}{d}_{12}=\ensuremath{-}0.057\AA{}$ and $\ensuremath{\Delta}{d}_{24}=+0.159\AA{}.$ These results are in good agreement with a prior structure determination by low-energy electron diffraction on a sample that was prepared in a different manner.
Extracorporeal Shock Wave Lithotripsy of Distal-Ureteral Calculi: Is It Worthwhile? (1987)

Among 44 patients with distal-ureteral stones, 32 had no contraindications to extracorporeal shock wave lithotripsy (ESWL); i.e., they were not women of childbearing age and did not have ipsilateral renal stones. All these patients underwent simulation for ESWL. In 18 patients, it proved possible to localize the stone, and in 16 of these ESWL was successful. In the other two, localization was not possible at the start of ESWL, and ureteroscopy was used to remove the stones. In the 15 patients in whom simulation failed, the stone was moved up the ureter for ESWL in eight and was removed ureteroscopically in seven. In the eight women of childbearing age, the stone was moved out of the pelvis for ESWL in five and removed ureteroscopically in three. All three of the patients with ipsilateral renal stones underwent ESWL after manipulation of the stone. Thus stones were ultimately removed by ESWL in 32 of the 44 patients. ESWL can be used for distal-ureteral stones, although it is less straightforward than for stones else-where in the urinary tract.
Scalable manufacturing of boron nitride nanotubes and their assemblies: a review (2016)

Boron nitride nanotubes (BNNTs) are wide bandgap semiconducting materials with a quasiparticle energy gap larger than 6.0 eV. Since their first synthesis in 1995, there have been considerable attempts to develop novel BNNT-based applications in semiconductor science and technology. Inspired by carbon nanotube synthesis methods, many BNNT synthesis methods have been developed so far; however, it has been very challenging to produce BNNTs at a large scale with the structural quality high enough for exploring practical applications. Very recently there has been significant progress in the scalable manufacturing of high-quality BNNTs. In this article, we will review those particular breakthroughs and discuss their impact on semiconductor industries. Freestanding BNNT assemblies such as transparent thin films, yarns or buckypapers are highly advantageous in the development of novel BNNT-based semiconductor devices. The latest achievements in their manufacturing processes will be also presented along with their potential applications.
Casein Kinase 2 Is Activated and Essential for Wnt/β-Catenin Signaling (2006)

Wnt/beta-catenin signaling is essential to early development. Activation of Frizzled-1 by Wnts induces nuclear accumulation of beta-catenin and activation of Lef/Tcf-dependent gene expression. Casein kinase 2 has been shown to affect Wnt/beta-catenin signaling. How casein kinase 2 exerts an influence in Wnt signaling is not clear; casein kinase 2 has been reported to be constitutively active (i.e. not regulated). Herein we show to the contrary that casein kinase 2 activity is rapidly and transiently increased in response to Wnt3a stimulation and is essential for Wnt/beta-catenin signaling. Chemical inhibition of casein kinase 2 or suppression of its expression blocks Frizzled-1 activation of Lef/Tcf-sensitive gene expression. Treatment with pertussis toxin or knock down of Galpha(q) or Galpha(o) blocks Wnt stimulation of casein kinase 2 activation, as does suppression of the phosphoprotein Dishevelled, demonstrating that casein kinase 2 is downstream of heterotrimeric G proteins and Dishevelled. Expression of a constitutively active mutant of either Galpha(q) or Galpha(o) stimulates casein kinase 2 activation and Lef/Tcf-sensitive gene expression. Thus, casein kinase 2 is shown to be regulated by Wnt3a and essential to stimulation of the Frizzled-1/beta-catenin/Lef-Tcf pathway.
Identification of a Novel Rhabdovirus in Spodoptera frugiperda Cell Lines (2014)

The Spodoptera frugiperda Sf9 cell line is used as a cell substrate for the development and manufacture of biological products. Extensive testing has not previously identified any viruses in this cell line. This paper reports on the identification and characterization of a novel rhabdovirus in Sf9 cells. This was accomplished through the use of next-generation sequencing platforms, de novo assembly tools, and extensive bioinformatics analysis. Rhabdovirus identification was further confirmed by transmission electron microscopy. Infectivity studies showed the lack of replication of Sf-rhabdovirus in human cell lines. The overall study highlights the use of a combinatorial testing approach including conventional methods and new technologies for evaluation of cell lines for unexpected viruses and use of comprehensive bioinformatics strategies for obtaining confident next-generation sequencing results.