gebhart/patrepeval huggingface dataset:
A simple method to enrich an Agrobacterium‐transformed population for plants containing only T‐DNA sequences (1999)

A simple modification to standard binary vector design has been utilized to enrich an Agrobacterium-transformed population for plants containing only T-DNA sequences. A lethal gene was incorporated into the non-T-DNA portion of a binary vector, along with a screenable marker. The resulting class of vectors is designated as NTL T-DNA vectors (non-T-DNA lethal gene-containing T-DNA vectors). The lethal gene used here is a CaMV 35S-barnase gene with an intron in the coding sequence (barnase-INT); the screenable marker is a pMAS-luciferase gene with an intron in the coding sequence (LUC-int). To evaluate the utility of this vector design, tobacco plants were transformed with either the NTL T-DNA vector or a control vector from which most of the barnase-INT gene was deleted. Populations of 50 transgenic plants were scored for LUC expression. The results indicated a dramatic reduction in the presence of non-T-DNA sequences in the transgenic population using the NTL T-DNA vector. Only one transgenic plant was found to be LUC+ using the NTL vector, compared with 42 of 50 plants using the control vector. Importantly, the efficiency with which transformed tobacco plants was obtained was reduced by no more than 30%. The reduction in LUC+ transgenics was partially reversed when a barstar-expressing tobacco line was transformed, indicating that barnase expression was responsible for the reduced frequency of incorporating non-T-DNA sequences. Similar transformation results were obtained with tomato and grape. The incorporation of a barnase-INT gene outside the left border appears to provide a generally applicable tool for enriching an Agrobacterium-transformed population for plants containing only T-DNA sequences.
Clinical and microbiologic characterization of hemorrhagic pneumonia due to extraintestinal pathogenic Escherichia coli in four young dogs. (2003)

Over a 21-month period, three Beagle dogs and one mixed-breed dog at our facility developed fatal pneumonia. The four dogs, all purpose bred, came from three vendors and had received the standard canine vaccines prior to shipment. In each instance, the affected dog had been shipped to our facility within the past 10 days. Three cases presented as a peracute clinical syndrome, and all had gross and microscopic findings consistent with hemorrhagic pneumonia. Escherichia coli was isolated from the lungs of all four dogs. Results of testing of lung tissue for canine parainfluenza virus and canine adenovirus were negative. Escherichia coli was also isolated from blood of three of the four dogs. Serotyping of the E. coli isolates indicated that two were serotype 06 and two were 04. Isolates from all four dogs were positive for the virulence factors alpha hemolysin and cytotoxic necrotizing factor 1 and for the adhesin factor class-III papG allele. These traits place the isolates in the class of extraintestinal pathogenic E. coli, which is being increasingly implicated as a cause of extraintestinal infections in animals and humans and may represent a zoonotic risk to humans working with research dogs.
Processes for engineering a system: an overview of the ANSI/EIA 632 standard and its heritage (2000)

The ANSI/EIA 632 standard was developed that describes the “processes for engineering a system.” This standard evolved from EIA/IS 632—the interim standard that describes a systems engineering process. This article gives an overview of the processes and describes key concepts for implementation. It also describes the heritage of this standard, reasons for this particular evolutionary step, and the approach in converting from the interim standard to the full standard. There are 13 processes defined, and each includes representative tasks that can be performed to implement each process. Expected outcomes are defined for each task such that these outcomes can be used as a checklist in performing the processes. Several key concepts are described such as the use of a building block and a hierarchy of building blocks. An important concept is the proper recognition of enabling products that are essential during the engineering of a system to assist in full consideration of the whole system life cycle. ©2000 John Wiley & Sons, Inc. Syst Eng 3: 1–26, 2000
Presence and origin of interface charges at atomic-layer deposited Al2O3/III-nitride heterojunctions (2011)

Unlike silicon and traditional III-V semiconductors, the III-nitrides exhibit high spontaneous and piezoelectric polarization charges at epitaxial polar heterojunctions. In the process of investigating scaling properties of gate-stacks consisting atomic-layer deposited Al2O3/III-Nitride heterojunctions, we find interface charges that appear closely linked to the polarization charges of the underlying nitride substrate. Through capacitance-voltage measurement on a series of samples of varying dielectric thicknesses, we find the presence and propose an origin of benign donor-type interface charges (Qit ∼6 × 1013 cm−2) at the AlN/Al2O3 junction. This interface charge is almost equal to the net polarization charge in AlN. The polarization-related dielectric/AlN interface charge and the role of oxygen in the dielectric as a possible modulation dopant potentially offer opportunities for various device applications.
Arteriolar oxygen reactivity: where is the sensor and what is the mechanism of action? (2016)

Arterioles in the peripheral microcirculation are exquisitely sensitive to changes in PO2 in their environment: increases in PO2 cause vasoconstriction while decreases in PO2 result in vasodilatation. However, the cell type that senses O2 (the O2 sensor) and the signalling pathway that couples changes in PO2 to changes in arteriolar tone (the mechanism of action) remain unclear. Many (but not all) ex vivo studies of isolated cannulated resistance arteries and large, first-order arterioles support the hypothesis that these vessels are intrinsically sensitive to PO2 with the smooth muscle, endothelial cells, or red blood cells serving as the O2 sensor. However, in situ studies testing these hypotheses in downstream arterioles have failed to find evidence of intrinsic O2 sensitivity, and instead have supported the idea that extravascular cells sense O2 . Similarly, ex vivo studies of isolated, cannulated resistance arteries and large first-order arterioles support the hypotheses that O2 -dependent inhibition of production of vasodilator cyclooxygenase products or O2 -dependent destruction of nitric oxide mediates O2 reactivity of these upstream vessels. In contrast, most in vivo studies of downstream arterioles have disproved these hypotheses and instead have provided evidence supporting the idea that O2 -dependent production of vasoconstrictors mediates arteriolar O2 reactivity, with significant regional heterogeneity in the specific vasoconstrictor involved. Oxygen-induced vasoconstriction may serve as a protective mechanism to reduce the oxidative burden to which a tissue is exposed, a process that is superimposed on top of the local mechanisms which regulate tissue blood flow to meet a tissue's metabolic demand.
Strategies for Maritime Development: A case in Vietnam (2018)

Strategic assessors of the 21st century are "The Century of the Ocean," because, along with current economic and demographic growth, natural resources, especially non-renewable resources on land, will be exhausted after several decades. The world economy is increasingly dependent on the sea and the ocean. About 70% of the world's industrial potential is in the 500km wide area of ​​the coast. The mineral, biological and marine resources of the oceans and oceans have an important implication for the world economy. Marine ecosystems are the most important resource with hundreds of thousands of animals, plants, and microorganisms. Sea is a diversified and abundant source of seafood, chemicals, salt, oil and gas, clean energy from the sea and oceans, wind, seawater, ocean currents, and the tide is being exploited for transportation, energy and countless other human benefits. The sea and the continental shelf are waterways that can develop tourism, sightseeing and recreation activities. The role of marine economics, including maritime economics, has become increasingly important and has been identified as a key sector for investment. This paper analyzes the advantages, limitations, and causes in maritime economic development, and draws on experiences to develop the maritime economy.
Elucidation of O-Glycosylation Structures of the β-Amyloid Precursor Protein by Liquid Chromatography−Mass Spectrometry Using Electron Transfer Dissociation and Collision Induced Dissociation (2008)

Accumulation and deposition of beta-amyloid peptide, a major constituent in neuritic plaques are hallmarks of Alzheimer's disease (AD) and AD-related neurodegenerative diseases. beta-Amyloid (Abeta) is derived from the proteolytic cleavage of amyloid precursor protein (APP), a transmembrane protein present in three major isoforms in brain comprising 695, 751 and 770 amino acids, respectively. Among other post-translational modifications, APP is modified during maturation by N- and O-glycosylation, which are thought to be responsible for its expression and secretion. Unlike N-glycosylation, no sites of O-glycosylation of APP have previously been reported. We report here the identification of three specific O-glycosylation sites of the secreted APP695 (sAPP695) produced in CHO cells, using a combination of high-performance liquid chromatography and electrospray-tandem mass spectrometry. With the use of electron transfer dissociation and collision induced dissociation (ETD and CID), we identified type, composition and structures of the Core 1 type O-linked glycans attached at the residues Thr 291, Thr 292 and Thr 576 of the full-length APP695. The glycosylations comprise multiple short glycans, containing N-acetyl galactosamine (GalNAc), Gal-GalNAc and sialic acid terminated structures. The presence of the glycopeptides in the tryptic mixture was identified using the CID-generated sugar oxonium ions. ETD proved to be valuable for the unambiguous identification of the modified sites as ETD fragmentation occurred along the peptide backbone with little or no cleavage of the glycans. Thus, the combination of the CID and ETD techniques in LC-MS is shown here, as a powerful tool for de novo identification of O-glycosylations at unknown modification sites in proteins.
Very Fast Watermarking by Reversible Contrast Mapping (2007)

Reversible contrast mapping (RCM) is a simple integer transform that applies to pairs of pixels. For some pairs of pixels, RCM is invertible, even if the least significant bits (LSBs) of the transformed pixels are lost. The data space occupied by the LSBs is suitable for data hiding. The embedded information bit-rates of the proposed spatial domain reversible watermarking scheme are close to the highest bit-rates reported so far. The scheme does not need additional data compression, and, in terms of mathematical complexity, it appears to be the lowest complexity one proposed up to now. A very fast lookup table implementation is proposed. Robustness against cropping can be ensured as well
Evidence for localized calcium mobilization and influx in single rat gonadotropes. (1991)

Dynamic video-imaging microscopy was used to investigate the spatial and temporal nature of Ca2+ mobilization and Ca2+ influx in acutely dissociated, fura-2-loaded, rat gonadotropes. Addition of luteinizing hormone-releasing hormone (LHRH) to an isolated gonadotrope stimulated a wave of Ca2+ originating from a specific locus of the cell. This probably reflects Ca2+ mobilization from an intracellular store, since this response was unaffected by the removal of extracellular Ca2+. Application of the dihydropyridine-sensitive Ca2+ channel agonist Bay K 8644 (Bay K) stimulated a rise in cytosolic free Ca2+ concentration in the rat gonadotrope. This response was blocked by the removal of extracellular Ca2+ and probably reflects the influx of Ca2+ across the cell membrane. High speed (30 frames.s-1) imaging of the Bay K-induced Ca2+ influx revealed a wave of Ca2+ originating from a localized part of the cell membrane, which, in general, was spatially distinct from the LHRH-induced Ca2+ wave produced in the same cell. This suggests that Ca2+ channels in the cell membrane may be clustered in a specific area of the cell membrane. The velocity of the LHRH-induced Ca2+ mobilization wave was faster (mean = 79 +/- 5 microns.s-1, n = 9) than the Bay K-induced Ca2+ influx wave (39 +/- 7 microns.s-1, n = 9) (p less than or equal to 0.01, Wilcoxon signed rank test) measured in the same cells. Thus, both Ca2+ mobilization from intracellular stores and Ca2+ influx through the cell membrane appear to be spatially localized in the rat gonadotrope. These findings may have important implications in the intracellular regulation of Ca(2+)-dependent cell functions such as hormone biosynthesis and secretion.
WHIM syndrome: congenital immune deficiency disease (2008)

Subjects reviewed include clinical presentation, diagnosis, and treatment of WHIM and advances in understanding the genetic basis of WHIM.
Immunolocalization of vacuolar‐type H<sup>+</sup>‐ATPase, cathepsin K, matrix metalloproteinase‐9, and receptor activator of NFkB ligand in odontoclasts during physiological root resorption of human deciduous teeth (2001)

To investigate the cellular mechanisms of physiological root resorption in human deciduous teeth, the authors examined the immunocytochemical localization of vacuolar-type H+-ATPase, a lysosomal cysteine proteinase, cathepsin K, matrix metalloproteinase-9 (MMP-9), and receptor activator of NFKB ligand (RANKL) in odontoclasts. H+-ATPase, cathepsin K, and MMP-9 are the most important enzymes for decalcification of apatite crystals and degradation of type-I collagen. In addition, RANKL is one of the key regulatory molecules in osteoclast formation and functions. Odontoclasts developed extensive ruffled borders and clear zones apposed to the resorbing root dentine surfaces. On immunoelectron microscopy, the expression of vacuolar-type H+-ATPase was detected along the limiting membranes of pale vacuoles and the ruffled border membranes of odontoclasts. Cathepsin K in odontoclasts was localized within pale vacuoles, lysosomes, the extracellular canals of ruffled borders, and the underlying resorbing dentine surfaces. MMP-9 localization in odontoclasts was similar to those of cathepsin K. RANKL was detected in both mononuclear stromal cells and odontoclasts located on resorbing dentine surfaces. These results suggest that (1) odontoclasts are directly involved in decalcification of apatite crystals by active extrusion of proton ions mediated by H+-ATPase and (2) extracellular degradation of dentine type-I collagen by both cathepsin K and MMP-9, and (3) odontoclast differentiation and activity are regulated, at least in part, by RANKL, possibly produced by mononuclear stromal cells and odontoclasts themselves in the resorbing tissues. Thus, the cellular mechanisms of physiological root resorption appear to be quite similar to those of osteoclastic bone resorption.
Indoor Location Using Trilateration Characteristics (2005)

Abstract: This paper proposes a method for indoor location that uses the results of trilateration of Wi-Fi signal strength to learn what is expected at specific locations. It discusses why indoor location is needed, and the reasons for using Wi-Fi networks as the basis of the location process. It also describes the problems with trilateration using radio signals, and introduces some proposals to improve the precision of the trilateration algorithm. 1.
Namur Modul Type Package – Definition (2016)

Die Modularisierung von Prozessanlagen wird als erfolgversprechende Möglichkeit angesehen, die künftigen Anforderungen an die Prozessindustrie zu bewältigen. Mit dem Projekt Dezentrale Intelligenz für modulare Anlagen (Dima) hat Wago auf der Namur-Hauptsitzung 2014 einen Weg gezeigt, wie sich die Anforderungen, die in der NE148 formuliert worden sind, erfüllen lassen. Bisherige Arbeiten ergaben, dass die Verwendung von Module Type Packages (MTP) zur Beschreibung von Prozessmodulen eine vielversprechende Lösung darstellt. Der Namur-Arbeitskreis AK 1.12 arbeitet derzeit, in Zusammenarbeit mit verschiedenen Ad-Hoc-Arbeitskreisen der Namur und dem ZVEI, an der Standardisierung des Namur-MTP. Dieser Beitrag gibt eine Übersicht über die Arbeiten der Arbeitsgruppen. Die Fragestellungen und Anforderungen der Arbeitskreise für Zustandsbasierte Prozessführung, Bedienbilder und Diagnose und Wartung modularer Anlagen werden skizziert. Ferner wird eine mögliche Architektur des Namur-MTP vorgestellt.
History of the Film (General) (1970)

Robert M. Honderson's D. W. Griffith: The Years at Biograph (Farrar, Straus & Giroux, $7.50) Martin Levin's edited collection, Hollywood and the Great Fan Magazines (Arbor House/ World, $10.00) Kalton C. Lahue and Sam Gill's Clown Princes and Court Jesters (A.S. Barnes, $8.50) Collecting Classic Films (Hastings House, $6.95) Sheilah Graham's The Garden of Allah (Crown, $5.95) Hugo Munsterberg's The Film: A Psychological Study (sub-titled The Silent Photoplay in 1916) (Dover Paperbacks, $2.00) Sergei Eisenstein's Notes of a Film Director (Dover Paperbacks, $3.00) Jay Leyda's Film Essays and a Lecture (Praeger Paperbacks, $2.95) George P. Garrett, O.B. Hardison Jr., and Jane R. Gelfman, Film Scripts One (Appleton-Century-Crofts, price to be set) Peter Noble's The Negro in Films (Port Washington, NY: Konnihat Press, $10.00) Eileen Bowser's edited collection, Film Notes (Museum of Modern Art, $5.00)
<scp>l</scp>-Tryptophan Reacts with Naturally Occurring and Food-Occurring Phenolic Aldehydes To Give Phenolic Tetrahydro-β-carboline Alkaloids:  Activity as Antioxidants and Free Radical Scavengers (2003)

The reaction between the essential amino acid l-tryptophan and flavoring or naturally occurring phenyl and phenolic aldehydes was studied, and the alkaloidal reaction products were characterized by NMR and HPLC-MS. Benzaldehyde, vanillin, syringaldehyde, salicylaldehyde, and anisaldehyde condensed with l-tryptophan in aqueous-acidic media affording the corresponding phenolic tetrahydro-beta-carboline-3-carboxylic acid as two diastereoisomers, 1S,3S-cis and 1R,3S-trans. With the exception of benzaldehyde, the rest of the aldehydes needed heating conditions (70 degrees C) to significantly form tetrahydro-beta-carbolines over time with the cyclization highly favored at low pH. This suggests a likely formation of these compounds under conditions that may occur in foods, food processing, or cooking. The new phenolic tetrahydro-beta-carboline alkaloids were assayed, for the first time, for their activity as free radical scavengers and antioxidants and showed good antioxidant properties with Trolox equivalent antioxidant capacity (TEAC) values much higher than those of ascorbic acid and the water soluble vitamin E analogue, Trolox, in the 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) assay.
<title>Reconstruction of bilevel images from a low-quality JPEG</title> (2000)

Using concepts from projection onto convex sets (POCS), we develop algorithms for reconstructing bilevel images from a low quality JPEG. The constraint that the image is bilevel is not convex, so simple iteration does not suffice, but we develop techniques for enforcing the constraints gradually (soft-thresholding) and for using randomness to improve convergence (random thresholding). Our final algorithm succeeded in finding a bilevel image satisfying our constraints in every tested case.
Attenuation of Dysfunction in the Ischemia-Reperfused Liver by Glycyrrhizin (1992)

The present study evaluated the effect of glycyrrhizin (GR) on an injury of the liver caused by ischemia-reperfusion in rats. In the liver ischemia-reperfusion model, levels of serum GOT, GPT and LDH activities and lipid peroxides in the liver tissue were significantly increased. On the contrary, total glutathione content in the liver tissue and NADPH cytochrome P-450 reductase activity of liver microsomes were decreased. Pretreatment with GR 20 mg/kg. i.v. 10 min before induction of ischemia resulted in significant decreases in serum GOT, GPT, LDH activities and the lipid peroxide level and a higher tissue glutathione content during the period of reperfusion. Electron microscopic studies revealed various hepatocellular damages with an almost intact sinusoidal endothelium in ischemia-reperfused livers. However, the degree of damage was less severe in the livers from the rats pretreated with 20 mg/kg GR. The results indicate that GR is able to provide partial protection against ischemia-reperfused damage.
Eliciting Renal Failure in Mosquitoes with a Small-Molecule Inhibitor of Inward-Rectifying Potassium Channels (2013)

Mosquito-borne diseases such as malaria and dengue fever take a large toll on global health. The primary chemical agents used for controlling mosquitoes are insecticides that target the nervous system. However, the emergence of resistance in mosquito populations is reducing the efficacy of available insecticides. The development of new insecticides is therefore urgent. Here we show that VU573, a small-molecule inhibitor of mammalian inward-rectifying potassium (Kir) channels, inhibits a Kir channel cloned from the renal (Malpighian) tubules of Aedes aegypti (AeKir1). Injection of VU573 into the hemolymph of adult female mosquitoes (Ae. aegypti) disrupts the production and excretion of urine in a manner consistent with channel block of AeKir1 and renders the mosquitoes incapacitated (flightless or dead) within 24 hours. Moreover, the toxicity of VU573 in mosquitoes (Ae. aegypti) is exacerbated when hemolymph potassium levels are elevated, suggesting that Kir channels are essential for maintenance of whole-animal potassium homeostasis. Our study demonstrates that renal failure is a promising mechanism of action for killing mosquitoes, and motivates the discovery of selective small-molecule inhibitors of mosquito Kir channels for use as insecticides.
MoFvAb: Modeling the Fv region of antibodies (2015)

Knowledge of the 3-dimensional structure of the antigen-binding region of antibodies enables numerous useful applications regarding the design and development of antibody-based drugs. We present a knowledge-based antibody structure prediction methodology that incorporates concepts that have arisen from an applied antibody engineering environment. The protocol exploits the rich and continuously growing supply of experimentally derived antibody structures available to predict CDR loop conformations and the packing of heavy and light chain quickly and without user intervention. The homology models are refined by a novel antibody-specific approach to adapt and rearrange sidechains based on their chemical environment. The method achieves very competitive all-atom root mean square deviation values in the order of 1.5 Å on different evaluation datasets consisting of both known and previously unpublished antibody crystal structures.