gebhart/patrepeval huggingface dataset:
Aggregating semantic annotators (2013)

A growing number of resources are available for enriching documents with semantic annotations. While originally focused on a few standard classes of annotations, the ecosystem of annotators is now becoming increasingly diverse. Although annotators often have very different vocabularies, with both high-level and specialist concepts, they also have many semantic interconnections. We will show that both the overlap and the diversity in annotator vocabularies motivate the need for semantic annotation integration: middleware that produces a unified annotation on top of diverse semantic annotators. On the one hand, the diversity of vocabulary allows applications to benefit from the much richer vocabulary available in an integrated vocabulary. On the other hand, we present evidence that the most widely-used annotators on the web suffer from serious accuracy deficiencies: the overlap in vocabularies from individual annotators allows an integrated annotator to boost accuracy by exploiting inter-annotator agreement and disagreement. The integration of semantic annotations leads to new challenges, both compared to usual data integration scenarios and to standard aggregation of machine learning tools. We overview an approach to these challenges that performs ontology-aware aggregation. We introduce an approach that requires no training data, making use of ideas from database repair. We experimentally compare this with a supervised approach, which adapts maximal entropy Markov models to the setting of ontology-based annotations. We further experimentally compare both these approaches with respect to ontology-unaware supervised approaches, and to individual annotators.
Dynamic modelling and control of a vectored thrust aerial vehicle (2013)

This paper presents the modelling and control of a ducted fan UAV platform powered by three ducted fans. The primary aim is to develop a highly reliable navigation platform with spacious payload bay. The chosen configuration also provides forward flight with minimum pitch variation. A complete non-linear dynamic model is developed. Taking advantage of the redundancy of the control inputs, a novel control scheme is designed to control the position and attitude based on the structured H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> synthesis. A way-point navigation level is utilised to carry out “turn-and-cruise” flight in order to follow the given way-points. The performance of the overall control law tested with the nonlinear vehicle model is presented to show the operational capabilities of the vehicle.
Synergy between CpG- or non-CpG DNA and specific antigen for B cell activation (2003)

DNA or oligodeoxynucleotides (ODN) containing unmethylated CpG motifs (CpG DNA) activate antigen-presenting cells and switch on T(h)1 immunity to antigen. B cells are synergistically activated by CpG DNA in combination with non-physiologic B cell stimulators such as polyclonal mitogen and surface Ig cross-linkers. This study shows the unexpected finding that not only CpG ODN, but also non-CpG and methylated ODN synergize with specific antigen, hen egg lysozyme (HEL), in stimulating HEL-specific B cells to proliferate, to express the early activation marker CD69 and to activate the NF-kappaB pathway. In vivo, non-CpG and methylated CpG ODN also enhanced anti-HEL antibody production in HEL-immunized mice, with a bias towards the production of T(h)1-associated isotypes. The synergy with all ODN to enhance B cell immune function was epitope-specific since neither denatured HEL nor other antigens enhanced the ODN effect on HEL-specific B cells. Furthermore, the synergy was independent of whether the ODN backbone was phosphorothioate or phosphodiester, or whether natural vertebrate genomic DNA was used. In all functional analyses, non-CpG and methylated CpG ODN showed lower activity than CpG ODN. These studies demonstrate that the presence of specific physiologic antigen might broaden the spectrum of DNA/ODN that stimulate B cells, with potential implications for the initiation and regulation of normal and pathologic immune responses.
PI 3-kinase inhibition: a therapeutic target for respiratory disease (2004)

Asthma and COPD (chronic obstructive pulmonary disease) are a growing major health burden, which, despite improvements in disease management, still require new effective treatments. As our understanding of the cellular and molecular processes which govern respiratory diseases improves, the range of potential therapeutic targets increase. PI 3-kinases (phosphoinositide 3-kinases) are a family of closely related enzymes, which play pivotal roles in a diverse array of cellular mechanisms. In the present paper, we review the evidence for PI 3-kinase involvement in various cellular processes underlying asthma and COPD generated through inhibitor studies and gene-targeting approaches, and discuss the prospects for PI 3-kinase inhibition as a future therapeutic strategy for the treatment of respiratory disease.
Combinatorial Material Libraries on the Microgram Scale with an Example of Hydrothermal Synthesis (1998)

In a 8-μL multichambered microreactor (the photo shows the components) material libraries can be produced in a simple manner through combinatorial hydrothermal synthesis. In a model experiment the synthesis of the zeolite TS-1 has been varied combinatorially. The resulting library is characterized directly by automated microdiffraction.
p34Cdc2 Kinase Activity Is Excluded from the Nucleus during the Radiation-induced G2 Arrest in HeLa Cells (1999)

The progression of cells from G(2) into mitosis is blocked by exposure to DNA-damaging agents such as ionizing radiation. This G(2) delay is associated with reduced cyclin B1-specific associated histone H1 kinase activity, increased inhibitory phosphorylation of p34(Cdc2), and depressed cyclin B1 levels in HeLa cells. Induction of cyclin B1 or expression of Cdc2AF, a mutant p34(Cdc2) that lacks the sites of inhibitory phosphorylation, only partially reverses the radiation-associated G(2) delay, although both maneuvers rapidly result in increased histone H1 kinase activity. To account for the persistent G(2) delay in the face of active p34(Cdc2) kinase, we determined the location of the kinase activity. Although p34(Cdc2) was active in the cytoplasm, the nuclear p34(Cdc2) was inactive. Irradiation led to nuclear accumulation of the inactive tyrosine-phosphorylated form of p34(Cdc2), whereas the active form was seen in the cytoplasm. At later times when cells had resumed cell cycle progression, nuclear kinase activity was detectable. These results give evidence of segregation of cytoplasmic and nuclear kinase activity after DNA damage that has the effect of enhancing checkpoint control. Shielding the nucleus from the potentially deleterious effects of kinase activity after DNA damage may help irradiated human cancer cells respond to irradiation.
Improved Synthesis of Unsymmetrical, Heteroaromatic 1,2-Diketones and the Synthesis of Carbazole Ring Substituted Tetraaryl Cyclopentadieneones (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTImproved Synthesis of Unsymmetrical, Heteroaromatic 1,2-Diketones and the Synthesis of Carbazole Ring Substituted Tetraaryl CyclopentadieneonesChristopher J. Walsh and Braja K. MandalView Author Information Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, 3255 South Dearborn, Chicago, Illinois 60616 Cite this: J. Org. Chem. 1999, 64, 16, 6102–6105Publication Date (Web):July 14, 1999Publication History Received9 March 1999Published online14 July 1999Published inissue 1 August 1999https://pubs.acs.org/doi/10.1021/jo9904213https://doi.org/10.1021/jo9904213brief-reportACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views2026Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aromatic compounds,Electronic absorption,Hydrocarbons,Oxidation,Oxidation reactions Get e-Alerts
Investigation of living pancreas tumor cells by digital holographic microscopy (2006)

Digital holographic microscopy provides new facilities for contactless and marker-free quantitative phase contrast imaging. In this work, a digital holographic microscopy method for the integral refractive index determination of living single cells in cell culture medium is presented. Further, the obtained refractive index information is applied to full field thickness and shape determination of adherent pancreas tumor cells, as well as for analysis of drug-induced dynamic changes of a single cell's cytoskeleton. The results demonstrate that digital holographic microscopy is a quantitative phase contrast technique for living cells under conventional laboratory conditions.
Dirigent (2016)

Latency-critical applications suffer from both average performance degradation and reduced completion time predictability when collocated with batch tasks. Such variation forces the system to overprovision resources to ensure Quality of Service (QoS) for latency-critical tasks, degrading overall system throughput. We explore the causes of this variation and exploit the opportunities of mitigating variation directly to simultaneously improve both QoS and utilization. We develop, implement, and evaluate Dirigent, a lightweight performance-management runtime system that accurately controls the QoS of latency-critical applications at fine time scales, leveraging existing architecture mechanisms. We evaluate Dirigent on a real machine and show that it is significantly more effective than configurations representative of prior schemes.
A method of camera calibration based on image processing (2007)

According to the principle of optical measurement, an effective and simple method to measure the distortion of CCD camera and lens is presented in this paper. The method is based on computer active vision and digital image processing technology. The radial distortion of camera lens is considered in the method, while the camera parameters such as the pixel interval and focus of camera are calibrated. The optoelectronic theodolite is used in our experiment system. The light spot can imaging in CCD camera from the theodolite. The position of the light spot should be changed without the camera's rotation, while the optoelectronic theodolite rotates an angle. All view reference points in the image are worked out by computing the angle between actual point and the optical center where the distortion can be ignored. The error correction parameters are computed, and then the camera parameters are calibrated. The sub-pixel subdivision method is used to improve the point detection precision in our method. The experiment result shows that our method is effective, simple and practical.
Transgenic Remodeling of the Contractile Apparatus in the Mammalian Heart (1996)

The structure-function relationships of the sarcomeric proteins in the mammalian cardiac compartment remain ill-defined because of the lack of a suitable model in which they can be readily manipulated or exchanged in vivo. To establish the validity of the transgenic paradigm for remodeling the mammalian heart, the murine alpha -cardiac myosin heavy chain gene promoter was used to express a ventricular myosin light chain-2 transgene (MLC2v) in both the atria and ventricles of the adult animal. Expression resulted in high levels of the transgene's transcript in both compartments. In the ventricle, the transgene was expressed against the background expression of the normal isoform. In the atrium, the transgene's expression would be ectopic, in that normally, MLC2v expression is restricted to the ventricle. Ectopic expression of the transgene in the atria resulted in a complete replacement of the atrial myosin light chain-2 protein isoform, although the endogenous isoform's steady state transcript levels were unchanged. In contrast, ventricular expression of the transgene had no effect at the protein level, despite an eightfold increase in MLC2v transcript levels. The data show that sarcomeric protein stoichiometry is maintained rigorously via posttransciptional regulation and that protein replacement can be achieved through a single transgenic manipulation.
Depression and memory impairment: A meta-analysis of the association, its pattern, and specificity. (1995)

The existing evidence paints an unclear picture of whether an association exists between depression and memory impairment. The purpose of this investigation was to determine whether depression is associated with memory impairment, whether moderator variables determine the extent of this association, and whether any obtained association is unique to depression. Meta-analytic techniques were used to synthesize data from 99 studies on recall and 48 studies on recognition in clinically depressed and nondepressed samples. Associations between memory impairment and other psychiatric disorders (e.g., schizophrenia, dementia) were also examined. A significant, stable association between depression and memory impairment was revealed. Further analyses indicated, however, that it is likely that depression is linked to particular aspects of memory, the linkage is found in particular subsets of depressed individuals, and memory impairment is not unique to depression.
Antisense Oligonucleotide Inhibition of PDGFR-β Receptor Subunit Expression Directs Suppression of Intimal Thickening (1997)

Thus, myointimal proliferation depends on both PDGFR-beta overexpression and its activation by PDGF-BB. Removal of either of these two elements can suppress neointimal formation.
De novo likelihood-based measures for comparing genome assemblies (2013)

Likelihood-based measures, such as ours proposed here, will become the new standard for de novo assembly evaluation.
Characterization of the 4C8 Antigen Involved in Transendothelial Migration of CD26hi T Cells after Tight Adhesion to Human Umbilical Vein Endothelial Cell Monolayers (1999)

In extravasation of T cells, little is known about the mechanisms of transendothelial migration subsequent to the T cells' tight adhesion to endothelium. To investigate these mechanisms, we developed a monoclonal antibody (mAb), termed anti-4C8, that blocks transmigration but not adhesion in a culture system in which high CD26-expressing (CD26(hi)) T cells preferentially migrate through human umbilical vein endothelial cell (HUVEC) monolayers cultured on collagen gels. Anti-4C8 reacted with all CD3(+) T cells and monocytes but not neutrophils or HUVECs. The structure defined by this antibody was an 80-kD molecule. The mAb at 1 mug/ml inhibited 80-90% of migration of CD3(+) T cells through unstimulated and interferon gamma-stimulated HUVEC monolayers without interfering with adhesion and cell motility. When added to the cultures after the adhesion, anti-4C8 completely blocked subsequent transmigration of adherent T cells. Phase-contrast and electron microscopy revealed that T cells are arrested at the intercellular junctions of HUVECs in the presence of anti-4C8. Anti-4C8 exhibited agonistic effects on resting T cells without other stimuli under culture conditions in which anti-4C8 can stimulate T cells. First, in the checkerboard assay using collagen gels, the antibody promoted chemokinetic migration of the cells in a dose-dependent manner from 0.1 to 10 mug/ml. The predominant population of T cells that migrated into collagen gels with impregnated anti-4C8 were CD26(hi). Second, solid-phase-immobilized anti-4C8 induced adhesion of T cells to the substrate, often with polarizations in cell shape and large pseudopods rich in filamentous (F-) actin. Third, soluble anti-4C8 augmented F-actin content preferentially in CD26(hi) T cells when added to T cells at a high dose of 10 mug/ml. Finally, both anti-4C8-induced chemokinetic migration and transendothelial migration were inhibited by pretreatment of T cells with pertussis toxin. These findings suggest that stimulation via the 4C8 antigen increases cell motility of CD26(hi) cells with profound cytoskeletal changes through signaling pathways including G proteins. The 4C8 antigen may be involved in preferential transmigration of CD26(hi) cells adherent to HUVECs.
Development of a fast solid-state high-resolution density profile reflectometer system on the DIII-D tokamak (1997)

A new fast-sweep, broadband frequency-modulated reflectometer on the DIII-D tokamak has produced routine, reliable density profiles with high spatial (⩽1 cm) and temporal resolution (∼100 μs). The system utilizes a solid-state microwave source and an active quadrupler, covering the full Q-band (33–50 GHz) and providing high output power (20–60 mW). The rf source frequency is linearized using an arbitrary function generator and the temperature of the source is actively controlled to reduce rf frequency drifts. The system hardware allows the rf frequency to be swept fullband in 10 μs, but, due to digitization limits, the sweep time used currently is 75–100 μs. The reliability of the reconstructed profiles was improved by a combination of fast frequency sweep, which reduces density fluctuation effects on the measurements, and advanced signal analysis based on digital complex demodulation, which improves phase accuracy. The fast-sweep system has resolved fast-changing edge density profiles during edge localized modes with unprecedented resolution.
Studies of oligonucleotide interactions by hybridisation to arrays: the influence of dangling ends on duplex yield (1994)

Effects of dangling ends on duplex yield have been assessed by hybridisation of oligonucleotides to an array of oligonucleotides synthesised on the surface of a solid support. The array consists of decanucleotides and shorter sequences. One of the decanucleotides in the array was fully complementary to the decanucleotide used as solution target. Others were complementary over seven to nine bases, with overhangs of one to three bases. Duplexes involving different decanucleotides had different overhangs at the 3' and 5' ends. Some duplexes involving shorter oligonucleotides had the same regions of complementarity as these decanucleotides, but with fewer overhanging bases. This analysis allows simultaneous assessment of the effects of differing bases at both 5' and 3' ends of the oligonucleotide in duplexes formed under identical reaction conditions. The results indicate that a 5' overhang is more stabilising than a 3' overhang, which is consistent with previous results obtained with DNA overhangs. However, it is not clear whether this is due to the orientation of the overhang or to the effect of specific bases.
Linkage of G Protein-Coupled Receptors to the MAPK Signaling Pathway Through PI 3-Kinase γ (1997)

The tyrosine kinase class of receptors induces mitogen-activated protein kinase (MAPK) activation through the sequential interaction of the signaling proteins Grb2, Sos, Ras, Raf, and MEK. Receptors coupled to heterotrimeric guanine triphosphate-binding protein (G protein) stimulate MAPK through Gbetagamma subunits, but the subsequent intervening molecules are still poorly defined. Overexpression of phosphoinositide 3-kinase gamma (PI3Kgamma) in COS-7 cells activated MAPK in a Gbetagamma-dependent fashion, and expression of a catalytically inactive mutant of PI3Kgamma abolished the stimulation of MAPK by Gbetagamma or in response to stimulation of muscarinic (m2) G protein-coupled receptors. Signaling from PI3Kgamma to MAPK appears to require a tyrosine kinase, Shc, Grb2, Sos, Ras, and Raf. These findings indicate that PI3Kgamma mediates Gbetagamma-dependent regulation of the MAPK signaling pathway.
Expression of the RelB transcription factor correlates with the activation of human dendritic cells (1999)

The RelB gene product is a member of the nuclear factor (NF)-kappaB family of transcription factors. It has been identified recently within mouse antigen-presenting cells and human monocyte-derived dendritic cells (DC). Disruption of the mouse RelB gene is accompanied, amongst other phenotypes, by abnormalities in the antigen-presenting cell lineages. In order to define RelB expression during human DC differentiation, we have analysed RelB mRNA by reverse transcriptase-polymerase chain reaction and RelB protein by intracellular staining in CD34+ precursors and different types of DC preparations. RelB mRNA was not detected in CD34+ precursor populations. Fresh blood DC (lineage-human leucocyte antigen-DR+ (lin-HLA-DR+)) lacked RelB mRNA and cytoplasmic RelB protein but a period of in vitro culture induced RelB expression in blood DC. Purified Langerhans' cells (LC) (CD1a+ HLA-DR+) failed to express RelB mRNA. Immunocytochemical staining identified RelB protein in human skin epithelium. RelB protein was expressed in a very few CD1a+, CD83+ or CMRF-44+ dermal DC but was not present in CD1a+ LC. Tonsil DC (lin-HLA-DR+ CMRF-44+) were positive for RelB mRNA and RelB protein. Intestinal DC (HLA-DR+) also lacked immunoreactive RelB protein. The majority of interdigitating CD83+, CMRF-44+, CMRF-56+ or p55+ DC located in paracortical T-lymphocyte areas of lymph node and tonsil contained RelB protein. The expression of RelB mRNA and RelB protein correlates with the activated phase of blood DC and the postmigration cell (activated) stage of tissue DC development.
Alternative Lengthening of Telomeres in Human Cells (2001)

Activation of a telomere maintenance mechanism appears to be essential for immortalization. In most human tumors and tumor cell lines, the telomere maintenance mechanism involves the activity of telomerase, a reverse transcriptase holoenzyme that synthesizes telomeric repeat DNA. In some cases, telomere maintenance occurs in the absence of telomerase activity by a mechanism referred to as alternative lengthening of telomeres (ALT). The development of telomere-targeted anticancer therapies will be facilitated by an understanding of the molecular mechanisms of ALT and of the means whereby ALT is repressed in normal cells.
Evaluation of herbicidal potential of depsides from Cladosporium uredinicola, an endophytic fungus found in Guava fruit (2012)

Two natural products produced by Cladosporium uredinicola, an endophytic fungus isolated from guava fruit, were evaluated for their effects on photosynthesis. Both of them inhibited electron flow (basal, phosphorylating, and uncoupled) from water to methylviologen (MV), acting as Hill reaction inhibitors in freshly lysed spinach thylakoids. These polyketides, belonging to depsides class, inhibited partial reactions of photosystem II (PS II) electron flow from water to 2,5-dichloro-1,4-benzoquinone (DCBQ), from water to sodium silicomolybdate (SiMo Na+), and partially inhibited electron flow from 1,5-diphenylcarbazide (DPC) to 2,6-dichloroindophenol (DCPIP). These results established that the depsides sites of inhibition are located on the donor and acceptor sides of PS II, between P680 and Q A. Chlorophyll a fluorescence measurements corroborated this mechanism of action. None of the tested compounds inhibited photosystem I (PS I) electron transport.