gebhart/patrepeval huggingface dataset:
Killing of p53-deficient hepatoma cells by parvovirus H-1 and chemotherapeutics requires promyelocytic leukemia protein (2008)

pronounced in p53-negative than in p53-positive cells. Apoptosis rates in p53-negative cell lines treated by genotoxic drugs were further enhanced by a treatment with H-1 PV. In flow cytometric analyses, H-1 PV infection resulted in a reduction of the mitochondrial transmembrane potential. In addition, H-1 PV cells showed a significant increase in PML expression. Knocking down PML expression resulted in a striking reduction of the level of H-1 PV infected tumor cell death. CONCLUSION: H -1 P V i s a s u i t a b l e a g e n t t o circumvent the resistance of p53-negative HCC cells to genotoxic agents, and it enhances the apoptotic process which is dependent on functional PML. Thus, H-1 PV and its oncolytic vector derivatives may be considered as therapeutic options for HCC, particularly for p53-negative tumors.
Secure OCDM-Based PON (2009)

Different optical encryption schemes for secure PON and VPN systems are discussed and their confidentiality evaluated, within an accurate cryptanalysis framework. We consider both optical bit- and block-ciphering, and quantum-noise data protection.
The mode of pheromone evolution: evidence from bark beetles (2004)

Sex and aggregation pheromones consist of species-specific blends of chemicals. The way in which different species' blends have evolved has been the subject of some debate. Theoretical predictions suggest that differences between species have arisen not through the accruing of small changes, but through major shifts in chemical composition. Using data on the aggregation pheromones of 34 species of bark beetle from two genera, Dendroctonus and Ips, we investigated how the distributions of the chemical components of their pheromone blends mirror their phylogenetic relationships. We tested whether there were consistent patterns that could be used to help elucidate the mode of pheromone evolution. Although there were obvious differences in pheromone blends between the two genera, the differences between species within each genus followed a less clear phylogenetic pattern. In both genera, closely related species are just as different as more distantly related species. Within Dendroctonus, particularly, most chemical components were distributed randomly across the phylogeny. Indeed, for some chemicals, closely related species may actually be more different than would be expected from a random distribution of chemical components. This argues strongly against the idea of minor shifts in pheromone evolution. Instead, we suggest that, within certain phylogenetic constraints, pheromone evolution in bark beetles is characterized by large saltational shifts, resulting in sibling species being substantially phenotypically (i.e. pheromonally) different from one another, thus agreeing with theoretical predictions.
Conditional neuromodulation of neurogenic detrusor overactivity using transrectal stimulation in patients with spinal cord injury: A proof of principle study (2017)

It has been shown for the first time that conditional neuromodulation can be delivered and triggered via a single biocompatible device placed in the anal canal. The pudendal nerves lying in Alcock's canal were stimulated through the wall of the anal canal, and the dyssynergic activity of the EAS was used to detect NDO and trigger neuromodulation giving significant increases in bladder capacity and reduction in detrusor pressure in six male subjects with SCI.
Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca++ sensing (2016)

Optogenetic techniques allow intracellular manipulation of Ca<sup>++</sup> by illumination of light-absorbing probe molecules such as channelrhodopsins and melanopsins. The consequences of optogenetic stimulation would optimally be recorded by non-invasive optical methods. However, most current optical methods for monitoring Ca<sup>++</sup> levels are based on fluorescence excitation that can cause unwanted stimulation of the optogenetic probe and other undesirable effects such as tissue autofluorescence. Luminescence is an alternate optical technology that avoids the problems associated with fluorescence. Using a new bright luciferase, we here develop a genetically encoded Ca<sup>++</sup> sensor that is ratiometric by virtue of bioluminescence resonance energy transfer (BRET). This sensor has a large dynamic range and partners optimally with optogenetic probes. Ca<sup>++</sup> fluxes that are elicited by brief pulses of light to cultured cells expressing melanopsin and to neurons-expressing channelrhodopsin are quantified and imaged with the BRET Ca<sup>++</sup> sensor in darkness, thereby avoiding undesirable consequences of fluorescence irradiation.
Red pigment in Bacillus megaterium spores (1986)

Bacillus megaterium QM B1551 spores contained a unique red pigment in their membranes that was not found in other species. This red pigment, presumably a carotenoid, was synthesized about the time of dipicolinic acid synthesis during sporulation and was associated with the forespores. A yellow pigment was synthesized during sporulation in rich medium and was found in the mother cell compartment. Although the yellow pigment was also associated with spores, it could be removed by two different extraction procedures without impairing germination; it was absent when sporulation occurred in a minimal medium. Although the yellow pigment of the mother cell appeared to be dispensable, the red pigment may serve a more critical function, such as membrane stabilization.
Increased production of sonic hedgehog by ballooned hepatocytes (2011)

Ballooned hepatocytes distinguish non-alcoholic steatohepatitis (NASH) from steatosis. Such cells contain dilated endoplasmic reticulum and ubiquitin aggregates, characteristics of endoplasmic reticulum stress. Hepatocyte ballooning increases the risk for fibrosis in NASH, suggesting that ballooned hepatocytes release pro-fibrogenic factors. Hedgehog ligands function as pro-fibrogenic factors in liver diseases, but mechanisms for hedgehog ligand production remain poorly understood. We evaluated the hypothesis that endoplasmic reticulum stress induces hepatocyte production of hedgehog ligands that provide paracrine pro-fibrogenic signals to neighbouring cells. In livers from NASH patients, keratin 8/18 and ubiquitin staining demonstrated enlarged, keratin 8/18-negative/ubiquitin-positive hepatocytes (ballooned hepatocytes) that were positive for Sonic hedgehog. In order to model endoplasmic reticulum stress in vitro, primary mouse hepatocytes were treated with tunicamycin. Compared to vehicle, tunicamycin significantly increased Sonic hedgehog and Indian hedgehog expression. Furthermore, conditioned medium from tunicamycin-treated hepatocytes increased Gli-luciferase reporter activity 14-fold more than conditioned medium from vehicle-treated hepatocytes. Cyclopamine (hedgehog signalling inhibitor) abrogated the effect of conditioned medium from tunicamycin-treated hepatocytes, verifying that soluble hepatocyte-derived factors activate hedgehog signalling. Ballooned hepatocytes in NASH patients did not express the hedgehog target gene, Gli2, α-smooth muscle actin or vimentin, but were surrounded by Gli2-positive stromal cells expressing these myofibroblast markers. Trichrome staining demonstrated the accumulation of ballooned hepatocytes in areas of matrix deposition, and numbers of Sonic hedgehog-positive hepatocytes correlated with the degree of ballooning and fibrosis stage. Hepatocytes undergoing endoplasmic reticiulum stress generate hedgehog ligands which act as paracrine pro-fibrogenic factors for hedgehog-responsive stromal cells. These results help to explain why fibrosis stage correlates with hepatocyte ballooning in NASH.
Aminobenzoic acid diuretics. 7. 3-Substituted 4-phenyl-, 4-arylcarbonyl-, and 4-arylmethyl-5-sulfamoylbenzoic acids and related compounds (1975)

Various 4-substituted 3-alkylamino-, 3-alkoxy-, 3-alkylthio-, and 3-alkyl-5-sulfamoylbenzoic acids related to known aminobenzoic acid diuretics were synthesized and screened for their diuretic properties in dogs. The tabulated results from a 3-hr test period revealed that generally the diuretic profile and potency could be retained when 3-alkoxy, 3-alkylthio, and 3-phenethyl were substituted for the 3-alkylamino moiety. The high potency of several 3-alkoxy-, 3-alkylthio-, and 3-phenethyl-4-benzoyl-5-sulfamoylbenzoic acids confirmed previous suggestions that the apparent diuretic effect of 4- and 5-alkylamino-6-carboxy-3-phenyl-1,2-benzisothiazole 1,1-dioxides originates from the corresponding 4-benzoyl-5-sulfamoylbenzoic acid derivatives due to an existing equilibrium in plasma. 4-Benzoyl-5-sulfamoyl-3-(3-thenyloxy) benzoic acid (118) is among the most potent benzoic acid diuretics hitherto synthesized and shows significant diuretic activity in dogs at 1 mug/kg. The results obtained with different 3-substituted 4-phenyl-5-sulfamoylbenzoic acids supported the earlier concept regarding the steric influence of the 4-substituent on the diuretic potency of sulfamoylbenzoic acid diuretics.
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences (2012)

Microbial community profiling using 16S rRNA gene sequences requires accurate taxonomy assignments. 'Universal' primers target conserved sequences and amplify sequences from many taxa, but they provide variable coverage of different environments, and regions of the rRNA gene differ in taxonomic informativeness--especially when high-throughput short-read sequencing technologies (for example, 454 and Illumina) are used. We introduce a new evaluation procedure that provides an improved measure of expected taxonomic precision when classifying environmental sequence reads from a given primer. Applying this measure to thousands of combinations of primers and read lengths, simulating single-ended and paired-end sequencing, reveals that these choices greatly affect taxonomic informativeness. The most informative sequence region may differ by environment, partly due to variable coverage of different environments in reference databases. Using our Rtax method of classifying paired-end reads, we found that paired-end sequencing provides substantial benefit in some environments including human gut, but not in others. Optimal primer choice for short reads totaling 96 nt provides 82-100% of the confident genus classifications available from longer reads.
Screening of 3, 4-Disubstituted Phenyl-L-alanine-producible Microorganisms (1973)

Microbial transaminase which catalyzes the reaction between 3, 4-disubstituted phenyl pyruvate and certain amino acids to produce 3, 4-disubstituted phenyl-L-alanine was investigated. Wide distribution of this enzyme among the various kinds of microorganisms was confirmed. 3, 4-Dihydroxyphenyl-L-alanine (L-Dopa) or 3, 4-dimethoxyphenyl-L-alanine was isolated from corresponding keto acids using three strains of selected microorganisms.
Anilides of (<i>R</i>)-Trifluoro-2-hydroxy-2-methylpropionic Acid as Inhibitors of Pyruvate Dehydrogenase Kinase (2000)

The optimization of a series of anilide derivatives of (R)-3,3, 3-trifluoro-2-hydroxy-2-methylpropionic acid as inhibitors of pyruvate dehydrogenase kinase (PDHK) is described that started from N-phenyl-3,3,3-trifluoro-2-hydroxy-2-methylpropanamide 1 (IC(50) = 35 +/- 1.4 microM). It was found that small electron-withdrawing groups on the ortho position of the anilide, i.e., chloro, acetyl, or bromo, increased potency 20-40-fold. The oral bioavailability of the compounds in this series is optimal (as measured by AUC) when the anilide is substituted at the 4-position with an electron-withdrawing group (i.e., carboxyl, carboxyamide, and sulfoxyamide). N-(2-Chloro-4-isobutylsulfamoylphenyl)-(R)-3,3, 3-trifluoro-2-hydroxy-2-methylpropionamide (10a) inhibits PDHK in the primary enzymatic assay with an IC(50) of 13 +/- 1.5 nM, enhances the oxidation of [(14)C]lactate into (14)CO(2) in human fibroblasts, lowers blood lactate levels significantly 2.5 and 5 h after oral doses as low as 30 micromol/kg, and increases the ex vivo activity of PDH in muscle, kidney, liver, and heart tissues. However, in contrast to sodium dichloroacetate (DCA), these PDHK inhibitors did not lower blood glucose levels. Nevertheless, they are effective at increasing the utilization and disposal of lactate and could be of utility to ameliorate conditions of inappropriate blood lactate elevation.
Biomarker discovery: tissues versus fluids versus both (2007)

Proteins are principal regulators and effectors of physiologic and pathophysiologic processes within solitary cells, cell lines and highly complex organisms. For these reasons, proteomics is expect...
A Mid-Level Description of Video, with Application to Non-photorealistic Animation (2004)

The contribution of this paper is a novel spatiotemporal description of real video sequences. Our description comprises a set of surfaces that separate objects in the video, and an accompanying database which describes objects in the video. We explain how to automatically process video into our description, and use it to solve a long-standing problem in Computer Graphics; that of automatically producing non-photorealistic (NPR) animations from video sequences. We show empirically that our description is highly compact relative to alternative coding schemes, and that our NPR animation technique out performs the current state-of-the-art in automatic video painting by about an order of magnitude, in terms of temporal coherence.
Testing or Formal Verification: DO-178C Alternatives and Industrial Experience (2013)

Software for commercial aircraft is subject to the stringent certification processes described in the DO-178B standard, "Software Considerations in Airborne Systems and Equipment Certification." Issued in 1992, this document focuses strongly on the verification process, with a major emphasis on testing. In 2005, the avionics industry initiated an effort to update DO-178B, in large part to accommodate development practices (including formal verification techniques) that had matured since its publication. A revised standard, DO-178C, was issued in late 2011, incorporating new guidance that allows formal verification to replace certain forms of testing. In this article, the authors describe some of the new objectives and activities in the area of formal methods, explain how these methods may be used instead of testing in a DO-178C context, and summarize the practical experience of Dassault-Aviation and Airbus in successfully applying the new DO-178C approach. The first Web extra at http://youtu.be/tRtK4xOK-8o is part 1 of a video talk by Hervé Delseny, describing Airbus's use of formal methods to verify avionics software and summarizing the integration of formal methods in the upcoming ED-12/DO-178 issue C. The second Web extra at http://youtu.be/BVI5J1GAQ30 is part 2 of a video talk by Hervé Delseny, describing Airbus's use of formal methods to verify avionics software and summarizing the integration of formal methods in the upcoming ED-12/DO-178 issue C. The third Web extra at http://youtu.be/U3G1ZOoqg78 is part 3 of a video talk by Hervé Delseny, describing Airbus's use of formal methods to verify avionics software and summarizing the integration of formal methods in the upcoming ED-12/DO-178 issue C. The fourth Web extra at http://youtu.be/WtlqS-JOHrA is part 4 of a video talk by Hervé Delseny, describing Airbus's use of formal methods to verify avionics software and summarizing the integration of formal methods in the upcoming ED-12/DO-178 issue C.
Chip-Based Bioassay Using Bacterial Sensor Strains Immobilized in Three-Dimensional Microfluidic Network (2004)

A whole-cell bioassay has been performed using Escherichia coli sensor strains immobilized in a chip assembly, in which a silicon substrate is placed between two poly(dimethylsiloxane) (PDMS) substrates. Microchannels fabricated on the two separate PDMS layers are connected via perforated microwells on the silicon chip, and thus, a three-dimensional microfluidic network is constructed in the assembly. Bioluminescent sensor strains mixed with agarose are injected into the channels on one of the two PDMS layers and are immobilized in the microwells by gelation. Induction of the firefly luciferase gene expression in the sensor strains can be easily carried out by filling the channels on the other layer with sample solutions containing mutagen. Bioluminescence emissions from each well are detected after injection of luciferin/ATP mixtures into the channels. In this assay format using two multichannel layers and one microwell array chip, the interactions between various types of samples and strains can be monitored at each well on one assembly in a combinatorial fashion. Using several genotypes of the sensor strains or concentrations of mitomycin C in this format, the dependence of bioluminescence on these factors was obtained simultaneously in the single screening procedure. The present method could be a promising on-chip format for high-throughput whole-cell bioassays.
Lyn tyrosine kinase signals cell cycle arrest but not apoptosis in B-lineage lymphoma cells. (1994)

Signal transduction initiated by binding of antibodies to cell surface molecules can have an important impact on the growth of tumor cells. The malignant behavior of the murine lymphoma BCL1 can be suppressed and the neoplastic cells can be induced to enter a dormant state by in vivo ligation of membrane immunoglobulin. Anti-CD19 antibodies can prolong the survival of SCID mice challenged with the human Burkitt lymphoma cell line, Daudi. Here, we show that cross-linking of membrane immunoglobulin on both murine BCL1 and human Daudi cells initiates a cascade of signals leading to the induction of both apoptosis and cell cycle arrest in vitro. Using antisense oligonucleotides, we demonstrate that the immunoglobulin-associated Lyn tyrosine kinase is required for anti-immunoglobulin-mediated cell cycle arrest but is not required for the signal leading to apoptosis. These results define a branch point in the cytosolic signaling pathways mediating cell cycle arrest and apoptosis. In Daudi cells, Lyn is also critical for cell cycle arrest induced by anti-CD19 signaling. Thus, the Lyn tyrosine kinase may be an important mediator of cell cycle arrest in neoplastic B lymphocytes and, perhaps, other cell types.
Helical Antennas with Truncated Spherical Geometry (2000)

A new variation of the spherical helical antenna made of a wire wound over a hemispherical surface and backed by a conducting ground plane is introduced. A constant spacing is maintained between the turns of winding. The geometry of this antenna is fully described by the number of turns and the radius of hemispherical surface. In addition to the hemispherical geometry, truncated double spherical helices are also examined. Radiation properties of the proposed antennas are studied both theoretically and experimentally. The wire antenna code ESP (electromagnetic surface patch), which is based on the method of moments, is used to obtain simulation results. The results for far-field patterns, gain, axial ratio, bandwidth, and input impedance are presented. Several prototypes of this antenna were constructed and tested using an outdoor antenna range. Far-field patterns were measured over a wide range of frequencies. The measured and calculated radiation patterns are in good agreement. A unique property of the hemispherical helix is its broad half-power beamwidth. Furthermore, this antenna provides circular polarization and relatively high gain over a narrow frequency range. The results of this research show that, for example, a 4.5-turn hemispherical helix with a radius of 0.02 meter designed for operation around 2.8 GHz provides a half-power beamwidth of about 90 degrees, more than 9 dB gain, and less than 3 dB axial ratio over a 300 MHz bandwidth. The input impedance of the antenna is largely resistive and is about 150 ohms in the above frequency range. Compared with a full spherical helix, the hemispherical helix provides comparable radiation characteristics, but occupies only half the volume. The compact size of this antenna makes it attractive to mobile communication applications
Reinforcement Learning for Dynamic Bidding in Truckload Markets: an Application to Large-Scale Fleet Management with Advance Commitments (2018)

Truckload brokerages, a $100 billion/year industry in the U.S., plays the critical role of matching shippers with carriers, often to move loads several days into the future. Brokerages not only have to find companies that will agree to move a load, the brokerage often has to find a price that both the shipper and carrier will agree to. The price not only varies by shipper and carrier, but also by the traffic lanes and other variables such as commodity type. Brokerages have to learn about shipper and carrier response functions by offering a price and observing whether each accepts the quote. We propose a knowledge gradient policy with bootstrap aggregation for high-dimensional contextual settings to guide price experimentation by maximizing the value of information. The learning policy is tested using a carefully calibrated fleet simulator that includes a stochastic lookahead policy that simulates fleet movements, as well as the stochastic modeling of driver assignments and the carrier's load commitment policies with advance booking.
Intelligent Use of CFAR Algorithms (1993)

Abstract : The objective of this program is to demonstrate CFAR detection improvement by applying artificial intelligence techniques. The basic concept is one in which a system that dynamically selects the most appropriate CFAR algorithms based upon the characteristics of the interference, out-perform a single, fixed CFAR algorithm. This report describes one prototype Expert System CFAR Processor, its current status, implementation details and capabilities. Also discussed are CFAR algorithm testing and evaluation, and rulebase development.... Radar signal processing, CFAR Detection, Expert systems.
Hypoxia‐inducible factor as a physiological regulator (2005)

Hypoxia-inducible factor (HIF) is a transcription complex which responds to changes in oxygen, providing cells with a master regulator that coordinates changes in gene transcription. HIF operates in all mammalian cell types and is ancient in evolutionary terms, being conserved in C. elegans and D. melanogaster. This review summarizes recent insights into the molecular events that link reduced oxygenation to HIF activation and emerging insights into the extensive role of HIF in a broad range of physiological processes.
The performance of double-grid O-18 water target for FDG production (2006)

The main stream of our study about the target is increasing the lifetime of the target windows. Mainly we conduct our study to increase the cooling performance and secondly about the structural design of the targets and target window foils. We already had developed and had published the results of our research about O-18 double-grid water target, which had installed on our 13 MeV cyclotron KIRAMS-13. The beam size of the accelerated proton was 9×18 (0.35 in×0.7 in). The double-grid target shows relatively low pressure during irradiation and good yield of F-18. The average yield of F-18 after irradiation was more than 1 Ci at 12.5 MeV, around 26 µA. Additionally, we are conducting new research for new techniques to increase the performance of low energy double-grid target and a new state-of-the-art pleated double foil target.