gebhart/patrepeval huggingface dataset:
[Features of filamentous cytoskeletons in acquired multidrug-resistance of HL-60 human leukemia cell line]. (1994)

Acquired resistance to chemotherapeutic drugs by tumor cells is an important obstacle to effective therapy of human malignancy. These resistance cell lines originated from human or rodent have been characterized by increased expression of MDR (Multidrug-resistance) gene and P-glycoprotein which plays as efflux pump of drugs from cells. These multidrug-resistance sublines also have been reported increased activities of protein kinases and glutathione S-transferase-pi. Although there have been extensive biophysical and biochemical characterization of the differences between parental lines and MDR tumor cell sublines, morphologic observations have been limited. In this study, filamentous cytoskeletons which involve many biological phenomena such as maintenance of cell morphology, mitosis, cellular movement, transport, and adhesion, were observed by confocal laser microscopy. To compare the expression of each cytoskeletons, fluorescent intensities of cells stained for each cytoskeletons were measured by confocal laser microscopic system. Utilizing this methodology, higher microtubular expression was observed in HL-60/ADR and K562/ADR than in their parental lines, but no significant differences of actin and vimentin were observed. Phosphorylation by protein kinases has been established as a key factor in the regulation of cytoskeletal function. But little is known about the role of protein phosphorylation in cytoskeletal function. Since increased activities of PKC and PTK were detected in HL-60/ADR, the effect of PKC inhibitor, staurosporine (STR), or PTK inhibitor, genistein (GNS), on cell growth was detected. STR and GNS reduced the resistance to Adriamycin in HL-60/ADR. Furthermore, STR and GNS disrupted the filamentous structure of microtubules in HL-60/ADR, and suppressed the expression of microtubules to 37%, and 49%, respectively. In contrast, PKC activator, phorbol ester (TPA), caused stronger microtubular assembling in HL-60/ADR, and increased the expression of microtubules to 134%. Resulting from this study, it is likely that acquired MDR of HL-60 and K562 was associated with increased expression of microtubules, and microtubular assembling or disassembling was considered to be regulated in part by PKC and PTK.
Siderophores of bacteria and fungi. (1984)

Siderophore-mediated iron assimilation systems are widely distributed in bacteria and fungi. The systems are comprised of low molecular weight ferric-ion specific ligands (siderophores) and cognate cell-bound receptor and utilization components. Most siderophores are classed chemically as hydroxamic acids or catechols; expression of both types is regulated by iron. Of the various siderophore systems present in E. coli, the enterobactin and aerobactin genes, encoded on the chromosome and pColV respectively, have been the most intensively studied to date as regards their molecular genetics.
Aerosol Assisted Vapor Synthesis of Spherical Boron Nitride Powders (1999)

Spherical morphology BN powders have been produced in a two-step process. The first step involves drying and partial nitridation of a H3BO3/H2O aerosol at 1000 °C with an ammonia/nitrogen gas stream followed by final nitridation at 1700 °C with ammonia.
Deep Neural Networks for Acoustic Modeling in Speech Recognition (2012)

Most current speech recognition systems use hidden Markov models (HMMs) to deal with the temporal variability of speech and Gaussian mixture models to determine how well each state of each HMM fits a frame or a short window of frames of coefficients that represents the acoustic input. An alternative way to evaluate the fit is to use a feedforward neural network that takes several frames of coefficients as input and produces posterior probabilities over HMM states as output. Deep neural networks with many hidden layers, that are trained using new methods have been shown to outperform Gaussian mixture models on a variety of speech recognition benchmarks, sometimes by a large margin. This paper provides an overview of this progress and represents the shared views of four research groups who have had recent successes in using deep neural networks for acoustic modeling in speech recognition. I.
A New Allele of Interferon-αl7 Gene Encoding IFN-α17b Is the Major Variant in Human Population (1998)

Thirteen interferon (IFN)-alpha functional genes have been reported. Among these, a number of genes have allelic members (variants). In the case of IFN-alpha17, five variants, IFN-alpha17a, IFN-alpha17b, IFN-alpha17c, IFN-alpha17d, and IFN-alphaT, are known. The variants differ from each other by base changes in the coding region, leading to differences in amino acid sequences. We have developed oligonucleotide primers for amplification of IFN-alpha17 gene(s) using polymerase chain reaction (PCR). Genomic DNA, obtained from over 28,000 normal healthy individuals and from four cell lines, were used as templates in PCR to amplify the IFN-alpha17 gene sequences. The resulting PCR products were analyzed by restriction endonuclease digestion and DNA sequencing to identify the presence of variant sequences. The results show that a new variant of IFN-alpha17 is abundantly present (approximately 70%) along with another variant, possibly IFN-alpha17c (approximately 30%), in the genomic DNA of the population examined. This new variant, the protein product of which is identical to IFN-alpha17b, differs from the gene for IFN-alpha17b by a point mutation. We have named it IFN-alpha17b', which is the only variant found in U-937, KG-1, and EB-3 cell lines. Namalwa cells have IFN-alpha17b' and, possibly, IFN-alpha17c in equal proportions.
Borreliacidal OspC Antibodies Specific for a Highly Conserved Epitope Are Immunodominant in Human Lyme Disease and Do Not Occur in Mice or Hamsters (2005)

Humans produce highly specific borreliacidal antibodies against outer surface protein C (OspC) shortly after infection with Borrelia burgdorferi sensu stricto. We previously demonstrated the epitope recognized by immunoglobulin M (IgM) and IgG OspC borreliacidal antibodies was located within the 50 amino acids nearest the carboxy (C) terminus. In this study, we show the immunodominant epitope is located in the highly conserved region within the seven C-terminal amino acids. Six early Lyme disease sera that contained borreliacidal activity and IgM and/or IgG OspC antibodies were chosen randomly and adsorbed with truncated OspC containing the 16 or 7 amino acids nearest the C terminus. Adsorptions with each truncated protein abrogated the borreliacidal activity completely. In addition, only small concentrations of OspC antibodies remained detectable by enzyme-linked immunosorbent assay and Western blotting. Moreover, borreliacidal OspC antibodies were not induced in laboratory mice or hamsters despite heavy infections with B. burgdorferi spirochetes. These findings confirm that borreliacidal antibodies comprise the majority of the IgM and IgG OspC antibody response in human Lyme disease and that the epitope is located in the highly conserved C terminus. In addition, rodent animal models appear to be inappropriate subjects for assessing the effectiveness of the epitope for serodiagnosis or as a human Lyme disease vaccine.
Replication and neutralization of human immunodeficiency virus type 1 lacking the V1 and V2 variable loops of the gp120 envelope glycoprotein (1997)

A human immunodeficiency virus type 1 (HIV-1) mutant lacking the V1 and V2 variable loops in the gp120 exterior envelope glycoprotein replicated in Jurkat lymphocytes with only modest delays compared with the wild-type virus. Revertants that replicated with wild-type efficiency rapidly emerged and contained only a few amino acid changes in the envelope glycoproteins compared with the parent virus. Both the parent and revertant viruses exhibited increased sensitivity to neutralization by antibodies directed against the V3 loop or a CD4-induced epitope on gp120 but not by soluble CD4 or an antibody against the CD4 binding site. This result demonstrates the role of the gp120 V1 and V2 loops in protecting HIV-1 from some subsets of neutralizing antibodies.
A State-Machine Synthesizer -- SMS (1981)

Much of the work in implementing a state machine involves tedious calculations that require no creativity. This report describes the development of a digital-circuit synthesis program that helps reduce the tedium. SMS accepts a high-level description of a state machine and returns equations for implementation that assume a sum-of-products next-state and output functions and that also assume JK or D flip-flops for memory.
Hypercytokinemia in familial hemophagocytic lymphohistiocytosis (1991)

Familial hemophagocytic lymphohistiocytosis (FHL) is a frequently missed and almost uniformly fatal childhood disorder. It is characterized by fever, hepatosplenomegaly, cytopenia, coagulopathy, and hypertriglyceridemia. The pathogenesis of FHL is not known but the above clinical and laboratory findings are compatible with reported in vitro and in vivo effects of several inflammatory cytokines. We measured circulating interferon-gamma (IFN-gamma), tumor necrosis factor/cachectin (TNF), and interleukin-6 (IL-6) in nine children with FHL. During active disease, elevated IFN-gamma was detected in seven of seven children, TNF in six of six, and IL-6 in two of six children studied. Thus, important inflammatory cytokines are augmented in active FHL and may contribute to the pathogenesis of the disease. Soluble CD8 was also increased in seven of seven children, which suggests a pathophysiologic importance of cytotoxic T lymphocytes. Because FHL appears to be associated with a systemic hypercytokinemia, our results also indicate that studies of FHL may contribute to the understanding of cytokine effects in vivo. Moreover, FHL is a hereditary disorder, suggesting that the hypercytokinemia is caused by a genetic defect in cytokine regulation.
Sequence-dependent Primer Synthesis by the Herpes Simplex Virus Helicase-Primase Complex (1995)

The herpes simplex virus helicase-primase complex, a heterotrimer of the UL5, UL8, and UL52 proteins, displays a single predominant site of primer synthesis on phi X174 virion DNA (Tenney, D. J., Hurlburt, W. W., Micheletti, P. M., Bifano, M., and Hamatake, R. K. (1994) J. Biol. Chem. 269, 5030-5035). This site was mapped and found to be deoxycytosine-rich, directing the synthesis of a primer initiating with several guanine residues. The size and sequence requirements for primer synthesis were determined using oligonucleotides containing variations of the predominant template. Although the efficiency of primer synthesis on oligonucleotides was influenced by template size, it was absolutely dependent on nucleotide sequence. Conversely, the ATPase activity on oligonucleotide templates was dependent on template size rather than nucleotide sequence. Furthermore, only oligonucleotides containing primase templates were inhibitory in a coupled primase-polymerase assay using phi X174 DNA as template, suggesting that primer synthesis or primase turnover is rate-limiting. Additionally, stimulation of helicase-primase by the UL8 component and that by the ICP8 protein were shown to differ mechanistically using different templates: the UL8 component stimulated the rate of primer synthesis on phi X174 virion DNA and oligonucleotide templates, while ICP8 stimulation occurred only on phi X174 virion DNA.
Mapping of the Tyrosine Kinase Receptors trkA (NTRK1), trkB (NTRK2) and trkC (NTRK3) to Human Chromosomes 1q22,9q22 and 15q25 by Fluorescence in situ Hybridization (1997)

trk (NTRK) genes encode tyrosine kinase transmembrane receptors that are stimulated by neurotrophins, and are responsible for the transduction of signals controlling neuropoiesis and neuron survival in the central and peripheral nervous system. trkA gene has earlier been assigned to three different loci on chromosome 1. To resolve these conflicting results, and confirm the localization of trkB and trkC, probes specific to each of these related genes were constructed and used in fluorescent in situ hybridization on human metaphase cells. Our results indicate that trkA, trkB and trkC are located in chromosome bands lq22, 9q22 and 15q25, respectively.
Thermal cataract formation in rabbits (1987)

Intraocularly circulating hot water was used to produce cataracts in nine eyes of seven rabbits by maintaining their retrolental temperatures between 43 degrees C and 45 degrees C. A rapid rate of heating (1.3 degrees C/min) plus a sharp temperature gradient across the eye may have been contributing factors in the consistent production of cataracts at these temperatures. Biomicroscopy and light microscopy showed lens changes similar to those associated with acute exposure to microwave radiation. These findings support the assumption that microwave cataractogenesis is due to the local production of elevated temperatures.
Identification of monoclonal antibodies against the trypomastigote stage ofTrypanosoma cruzi by use of iminobiotinylated surface polypeptides (1985)

The surface polypeptides of epimastigotes and tissue culture-derived trypomastigotes of Trypanosoma cruzi have been isolated free of most cytosolic components by use of the 2-iminobiotin-avidin interaction. Polypeptides of the trypomastigote stage obtained by this technique are recognized by serum antibodies from Chagasic patients and T. cruzi-infected mice. These polypeptides have been used as the detecting antigen for the identification of hybridoma cells producing monoclonal antibodies against the surface proteins of the trypomastigote stage of T. cruzi. These experiments document a practical approach for obtaining T. cruzi surface proteins in sufficient quantity and purity for use in immunological studies.
The Dll4/Notch pathway controls postangiogenic blood vessel remodeling and regression by modulating vasoconstriction and blood flow (2011)

Blood vessel remodeling is crucial to the formation of the definitive vasculature, but little is known about the mechanisms controlling this process. We show that Delta-like ligand 4 (Dll4)/Notch pathway regulates vessel regression in normal pathologic conditions. Genetic and pharmacologic inhibition of Dll4/Notch prevented retinal capillary regression in the oxygen-induced retinopathy (OIR) model and during normal development. Deletion of the Notch-regulated ankyrin repeat protein, a negative regulator of the Notch pathway, produced an opposite phenotype. Inhibition of Dll4/Notch reduced vessel occlusion, maintaining blood flow that is essential for survival of microvessels. Dll4/Notch inhibition up-regulated the expression of vasodilators adrenomedullin and suppressed the expression of vasoconstrictor angiotensinogen. Angiotensin II induced rapid nonperfusion and regression of developing retinal capillaries, whereas Ace1 and AT1 inhibitors and adrenomedullin attenuated vasoobliteration in OIR, indicating that both pathways are involved in modulating vessel remodeling. In contrast, inhibition of vascular endothelial growth factor-A (VEGF-A) did not result in a pervasive loss of retinal capillaries, demonstrating that reduced expression of VEGF-A is not the proximate cause of capillary regression in OIR. Modulation of VEGF-A and Dll4/Notch signaling produced distinct changes in blood vessel morphology and gene expression, indicating that these pathways can have largely independent functions in vascular remodeling.
THE OXIDATIVE BURST IN PLANT DISEASE RESISTANCE (1997)

Rapid generation of superoxide and accumulation of H2O2 is a characteristic early feature of the hypersensitive response following perception of pathogen avirulence signals. Emerging data indicate that the oxidative burst reflects activation of a membrane-bound NADPH oxidase closely resembling that operating in activated neutrophils. The oxidants are not only direct protective agents, but H2O2 also functions as a substrate for oxidative cross-linking in the cell wall, as a threshold trigger for hypersensitive cell death, and as a diffusible signal for induction of cellular protectant genes in surrounding cells. Activation of the oxidative burst is a central component of a highly amplified and integrated signal system, also involving salicylic acid and perturbations of cytosolic Ca2+, which underlies the expression of disease-resistance mechanisms.
Ros-Based Sensor Fusion And Motion Planning For Autonomous Vehicles: Application To Automated Parkinig System (2019)

Research and development in autonomous vehicles are currently very active since these vehicles are expected to play an important role in future transportation. During the past decade, numerous Advanced Driver Assistance Systems (ADAS) features have been developed and implemented on production vehicles, such as Adaptive Cruise Control and Lane Keeping Assist. However, most ADAS features are aimed to assist driving on highways where the environments are usually more structured and decision making can be made more easily. Non-highway environments, such as in the case of self-parking, are unstructured and requires more complicated analysis of the image information, localization and path planning. Most camera-based auto-parking features are limited to partial autonomy, not intelligent enough to park a vehicle automatically without the participation of a driver. Camera-based auto-parking systems can detect parking spots but cannot accurately localize the vehicle as well as the parking spot. The objective of this thesis is to design advanced sensor fusion and motion planning algorithms, especially for Automated Parking Assist (APA) systems. These algorithms are specifically designed for ADAS under low velocity and require high precision vehicle maneuvering, by increasing the localization accuracy, in terms of vehicle and parking spot location. The APA system will help the driver to search for available parking spots and drive the vehicle into the parking spot safely. The strategic architecture of the auto-parking system includes environment perception, sensor data fusion, motion planning, and vehicle control. Perception algorithms such as line detection and object detection are discussed in this thesis. Sensor data fusion and data association using extended Kalman filter for parking spot and vehicle location tracking are developed in this thesis. Rapidly-exploring Random Tree (RRT) motion planning algorithm is used to generate a path, leading the vehicle to park into the parking spot. Simulations for sensor data processing, data association and motion planning are conducted in a Robot Operating System (ROS) environment. A versatile virtual environment with vehicle dynamics model and control algorithms are developed in the simulation environment. Parking spot detection, vehicle behavior decision making, and motion planning are tested based on virtual sensor signals modelled in ROS. Simulation results show that the vehicle can drive automatically into the parking spot without the participation of a driver. Vehicle localization field experiments based on GPS sensor fusion has been conducted in an open parking lot. Localization accuracy of ego vehicle is improved.
Incretin Mimetics and DPP-IV Inhibitors: New Paradigms for the Treatment of Type 2 Diabetes (2006)

Incretin mimetics are a new class of pharmacological agents with multiple antihyperglycemic actions that mimic several of the actions of incretin hormones originating in the gut, such as glucagon-like peptide (GLP)-1. Dipeptidyl peptidase-IV (DPP-IV) inhibitors suppress the degradation of many peptides, including GLP-1, thereby extending their bioactivity. These agents seem to have multiple mechanisms of action for the treatment of type 2 diabetes mellitus (T2DM), including some or all the following: enhancement of glucose-dependent insulin secretion, suppression of inappropriately elevated glucagon secretion, slowing of gastric emptying, and decreased food intake. Exenatide (BYETTA) is the first incretin mimetic approved for clinical use by the US Food and Drug Administration. In phase 3 clinical trials, exenatide reduced HbA(1c) by approximately 1% and body weight by approximately 2 kg in T2DM patients failing to achieve glycemic control with metformin and/or a sulfonylurea, with mild-to-moderate nausea the most common side effect. Several GLP-1 analogues and DPP-IV inhibitors are in late-stage clinical testing and may soon become available for treating T2DM patients. The use of these agents may provide an opportunity to bring about new improvements in diabetes care.
In-scene-based atmospheric correction of uncalibrated VISible-SWIR (VIS-SWIR) hyper- and multi-spectral imagery (2008)

The QUAC (Quick Atmospheric Correction) algorithm for in-scene-based atmospheric correction of VIS-SWIR (VISible-Short Wave InfraRed) Multi- and Hyperspectral Imagery (MSI and HSI) is reviewed and applied to radiometrically uncalibrated data. Quite good agreement was previously demonstrated for the retrieved pixel spectral reflectances between QUAC and the physics-based atmospheric correction code FLAASH (Fast Line-of-sight Atmospheric Analysis of Spectral Hypercubes) for a variety of HSI and MSI data cubes. In these code-to-code comparisons, all the data cubes were obtained with well-calibrated sensors. However, many sensors operate in an uncalibrated manner, precluding the use of physics-based codes to retrieve surface reflectance. The ability to retrieve absolute spectral reflectances from such sensors would significantly increase the utility of their data. We apply QUAC to calibrated and uncalibrated versions of the same Landsat MSI data cube, and demonstrate nearly identical retrieved spectral reflectances for the two data sets.
Desulfovibrio desulfuricans PglB homolog possesses oligosaccharyltransferase activity with relaxed glycan specificity and distinct protein acceptor sequence requirements† (2010)

Oligosaccharyltransferases (OTases) are responsible for the transfer of carbohydrates from lipid carriers to acceptor proteins and are present in all domains of life. In bacteria, the most studied member of this family is PglB from Campylobacter jejuni (PglB(Cj)). This enzyme is functional in Escherichia coli and, contrary to its eukaryotic counterparts, has the ability to transfer a variety of oligo- and polysaccharides to protein carriers in vivo. Phylogenetic analysis revealed that in the delta proteobacteria Desulfovibrio sp., the PglB homolog is more closely related to eukaryotic and archaeal OTases than to its Campylobacter counterparts. Genetic analysis revealed the presence of a putative operon that might encode all enzymes required for N-glycosylation in Desulfovibrio desulfuricans. D. desulfuricans PglB (PglB(Dd)) was cloned and successfully expressed in E. coli, and its activity was confirmed by transferring the C. jejuni heptasaccharide onto the model protein acceptor AcrA. In contrast to PglB(Cj), which adds two glycan chains to AcrA, a single oligosaccharide was attached to the protein by PglB(Dd). Site-directed mutagenesis of the five putative N-X-S/T glycosylation sites in AcrA and mass spectrometry analysis showed that PglB(Dd) does not recognize the "conventional bacterial glycosylation sequon" consisting of the sequence D/E-X(1)-N-X(2)-S/T (where X(1) and X(2) are any amino acid except proline), and instead used a different site for the attachment of the oligosaccharide than PglB(Cj.). Furthermore, PglB(Dd) exhibited relaxed glycan specificity, being able to transfer mono- and polysaccharides to AcrA. Our analysis constitutes the first characterization of an OTase from delta-proteobacteria involved in N-linked protein glycosylation.