gebhart/patrepeval huggingface dataset:
Increased Exposure of Phosphatidylethanolamine on the Surface of Tumor Vascular Endothelium (2011)

We have previously shown that oxidative stress within the tumor microenvironment causes phosphatidylserine (PS) to redistribute from the inner to the outer membrane leaflet of the endothelial cells (EC) creating a highly specific marker for the tumor vasculature. Because the distribution of phosphatidylethanolamine (PE) and PS within the membrane is coregulated, we reasoned that PE would also be localized in the outer membrane leaflet of tumor EC. To demonstrate this, the PE-binding peptide duramycin was biotinylated and used to determine the distribution of PE on EC in vitro and in vivo. Exposure of cultured EC to hypoxia, acidity, reactive oxygen species, or irradiation resulted in the formation of membrane blebs that were intensely PE-positive. When biotinylated duramycin was intravenously injected into tumor-bearing mice, it preferentially localized to the luminal surface of the vascular endothelium. Depending on tumor type, 13% to 56% of the tumor vessels stained positive for PE. PE-positive vessels were observed in and around hypoxic regions of the tumor. With the exception of intertubular vessels of the kidney, normal vessels remained unstained. To test the potential of PE as a biomarker for imaging, duramycin was conjugated to the near-infrared fluorophore 800CW and used for optical imaging of RM-9 prostate carcinomas. The near-infrared probe was easily detected within tumors in live animals. These results show that PE, like PS, becomes exposed on tumor vascular endothelium of multiple types of tumors and holds promise as a biomarker for noninvasive imaging and drug targeting.
A Phosphatidylinositol 3-Kinase/Akt Pathway, Activated by Tumor Necrosis Factor or Interleukin-1, Inhibits Apoptosis but Does Not Activate NFκB in Human Endothelial Cells (2000)

Tumor necrosis factor (TNF) and interleukin-1 (IL-1) activate the transcription of both anti-apoptotic and pro-inflammatory gene products in human endothelial cells (EC) via NFkappaB. Here we report that both TNF and IL-1 activate the anti-apoptotic protein kinase Akt in growth factor and serum-deprived EC, assessed by Western blotting for phospho-Akt. Phosphorylation of Akt is blocked by LY294002 or wortmannin, inhibitors of phosphatidylinositol 3-kinase (PI 3-kinase). Consistent with these biochemical observations, TNF and IL-1 reduce apoptosis caused by growth factor and serum deprivation, and this action is also blocked by LY294002. Although Akt has been reported to activate NFkappaB, LY294002 does not prevent TNF- or IL-1-induced degradation of IkappaBalpha, beta, or epsilon, transcription of NFkappaB-dependent E-selectin or ICAM-1 promoter-reporter genes, or surface expression of E-selectin or ICAM-1 in human EC. LY294002 potentiates the activation of mitogen-activated protein kinases and stress-activated protein kinases by TNF and IL-1, suggesting Akt inhibits these responses. We conclude that TNF and IL-1 activate a PI 3-kinase/Akt anti-apoptotic pathway and that the anti-apoptotic effects of Akt are independent of NFkappaB. Moreover, the PI 3-kinase/Akt pathway does not play a major role in the pro-inflammatory responses of EC to TNF or IL-1.
The emerging science of epigenomics (2006)

One of the most exciting frontiers in both epigenetics and genome sciences is the new field of epigenomics. This new discipline promises novel insights into the genome because of its potential to detect quantitative alterations, multiplex modifications and regulatory sequences outside of genes. A number of new epigenomic strategies are emerging to exploit microarray formats with varying substrate choice, pre-processing and data analysis. These approaches are designed to detect large numbers of variations in DNA methylation and chromatin modification. Many groups are joining forces toward developing an organized Human Epigenome Project to exploit these new technologies to better understand the basis of normal development and human disease.
Design Strategies for Water-Soluble Small Molecular Chromogenic and Fluorogenic Probes (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTDesign Strategies for Water-Soluble Small Molecular Chromogenic and Fluorogenic ProbesXiaohua Li*, Xinghui Gao, Wen Shi, and Huimin Ma*View Author Information Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China*E-mail: [email protected] (H.M.M.).*E-mail: [email protected] (X.H.L.).Cite this: Chem. Rev. 2014, 114, 1, 590–659Publication Date (Web):September 11, 2013Publication History Received19 December 2012Published online11 September 2013Published inissue 8 January 2014https://pubs.acs.org/doi/10.1021/cr300508phttps://doi.org/10.1021/cr300508preview-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views28076Altmetric-Citations1558LEARN 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:Analytical apparatus,Fluorescence,Fluorescence detection,Mercury,Probes Get e-Alerts
Gastric emptying rate and hormonal response in type II diabetics. (1991)

Gastric emptying time was measured by ultrasonography in 18 NIDDM patients with and without autonomic neuropathy, evaluated by cardiovascular autonomic tests and in 10 controls before and after a physiologic test meal. Six neuropathic subjects showed gastrointestinal symptoms such as fullness and early satiety. Blood glucose, gastrin and pancreatic polypeptide were evaluated before and up to 200 min after the test meal. The gastric emptying rate was similar in controls (275 +/- 45 min) and in diabetic patients without (260 +/- 49 min) and with autonomic neuropathy (257 +/- 48 min) (p = ns), while diabetic symptomatics showed a significant reduction of gastric emptying rate (420 +/- 19.7 min) (p less than 0.001). Basal serum glucose concentration was similar in all diabetic patients (132 +/- 18 mg/dl, 166 +/- 52 mg/dl, 161 +/- 61 mg/dl, p = ns). A basal value of serum gastrin was similar in all groups while the test meal produced a rise with a peak at 40' significantly higher only in symptomatics (195 +/- 58 pg/ml vs control 107 +/- 88 pg/ml, diabetics without and with autonomic neuropathy: 98 +/- 12 pg/ml and 88 +/- 22 pg/ml respectively; p less than 0.01). Basal and stimulated PP values were similar in all groups. In conclusion ultrasonography is a simple, reliable method to evaluate gastric emptying rate without any interference in the mechanism of digestion and absorption of nutrients. The presence of non specific symptoms, such as nausea and gastric fullness, may indicate an early gastric involvement as supported by sonographic evidence of impaired emptying.
Protection against experimental pseudomembranous colitis in gnotobiotic mice by use of monoclonal antibodies against Clostridium difficile toxin A (1991)

The pathogenicity of Clostridium difficile is due to the production of two toxins (toxins A and B). We prepared monoclonal antibodies against toxin A and determined whether axenic mice passively immunized with the monoclonal antibodies were protected against C. difficile disease. The mice were kept in an isolator and were given ascites fluid intravenously prior to challenge with a toxinogenic strain of C. difficile. Control mice and mice receiving ascites fluid devoid of toxin antibody died within 2 days and had high levels of toxins A and B in their feces. Mice that received ascites fluid containing high amounts of toxin A monoclonal antibodies directed against the repeating units of the toxin survived. In protected mice, toxin B levels were similar to those in dying mice, but toxin A levels were greatly reduced. These data show that passive immunity induced by monoclonal antibodies against toxin A was effective against pseudomembranous cecitis.
Chromobacterium violaceum: A Review of Pharmacological and Industiral Perspectives (2001)

Violet-pigmented bacteria, which have been described since the end of the 19th century, are occasionally the causative agent of septicemia and sometimes cause fatal infection in human and animals. Bacteria, producing violet colonies due to the production of a nondiffusible pigment violacein, were classified as a redefined genus Chromobacterium. Chromobacterium violaceum is gram-negative, and saprophyte from soil and water is normally considered nonpathogenic to human, but is an opportunistic pathogen of extreme virulence for human and animals. The biosynthesis and biological activities of violacein and the diverse effects of this pigment have been studied. Besides violacein, C. violaceum produces other antibiotics, such as aerocyanidin and aerocavin, which exhibit in vitro activity against both gram-negative and gram-positive bacteria. 3,6-Dihydroxyindoxazene and Y-TO678h exhibit a selective activity against gram-negative bacteria. Arphamenine A and B, and FR901228, that enhanced immunoresponse, and potentiators of beta-lactam antibiotics and chelators such as ferrioxamine exhibit important clinical potential applications. Lipopolysaccharides and polyhydroxyesters together with several enzymes appear as important metabolites with biotechnological applications. Many of these metabolites were already studied at the genome level.
The Control of Ribonucleic Acid Synthesis in Escherichia coli (1969)

Stringent strains of Escherichia coli are shown to produce one, and usually two, 32P-labeled compounds specifically in response to amino acid starvation. This pattern of labeling is not observed in three derived relaxed strains. Comparison of properties of the system regulating the synthesis of these compounds with those of the amino acid control of RNA biosynthesis suggests that the unusual compounds participate in an early step in the mechanism which leads to the slowing of RNA biosynthesis during amino acid starvation of stringent strains.
Deiodination of Thyroid Hormones by Iodothyronine Deiodinase Mimics: Does an Increase in the Reactivity Alter the Regioselectivity? (2011)

Organoselenium compounds as functional mimics of iodothyronine deiodinase are described. The naphthyl-based compounds having two selenol groups are remarkably efficient in the inner-ring deiodination of thyroxine. The introduction of a basic amino group in close proximity to one of the selenol moieties enhances the deiodination. This study suggests that an increase in the nucleophilic reactivity of the conserved Cys residue at the active site of deiodinases is very important for effective deiodination.
Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II (1991)

Zymomonas mobilis genes for pyruvate decarboxylase (pdc) and alcohol dehydrogenase II (adhB) were integrated into the Escherichia coli chromosome within or near the pyruvate formate-lyase gene (pfl). Integration improved the stability of the Z. mobilis genes in E. coli, but further selection was required to increase expression. Spontaneous mutants were selected for resistance to high level of chloramphenicol that also expressed high levels of the Z. mobilis genes. Analogous mutants were selected for increased expression of alcohol dehydrogenase on aldehyde indicator plates. These mutants were functionally equivalent to the previous plasmid-based strains for the fermentation of xylose and glucose to ethanol. Ethanol concentrations of 54.4 and 41.6 g/liter were obtained from 10% glucose and 8% xylose, respectively. The efficiency of conversion exceeded theoretical limits (0.51 g of ethanol/g of sugar) on the basis of added sugars because of the additional production of ethanol from the catabolism of complex nutrients. Further mutations were introduced to inactivate succinate production (frd) and to block homologous recombination (recA).
Stable Carbanions by Quantitative Metalation of Cationically Obtained Diphenylvinyl and Diphenylmethoxy Compounds:  New Initiators for Living Anionic Polymerizations (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTStable Carbanions by Quantitative Metalation of Cationically Obtained Diphenylvinyl and Diphenylmethoxy Compounds: New Initiators for Living Anionic PolymerizationsJesper Feldthusen, Béla Iván, and Axel H. E. MüllerView Author Information Institut für Physikalische Chemie, Universität Mainz, Welderweg 15, D-55099 Mainz, Germany Cite this: Macromolecules 1997, 30, 22, 6989–6993Publication Date (Web):November 3, 1997Publication History Received26 March 1997Revised30 July 1997Published online3 November 1997Published inissue 1 November 1997https://pubs.acs.org/doi/10.1021/ma9704166https://doi.org/10.1021/ma9704166brief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views211Altmetric-Citations28LEARN 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:Absorption,Alloys,Anionic polymerization,Anions,Metalation Get e-Alerts
Nucleotide sequence of cDNA encoding the group II allergen of cocksfoot/orchard grass (Dactylis glomerata), Dac g II (1993)

Cocksfoot/orchard grass (Dactylis glomerata) anther cDNA clones encoding the group II allergen Dac g II were previously isolated on the basis of immunoreactivity of human, rabbit, and murine antibodies with a 24-kDa protein expressed as a fusion protein with beta-galactosidase. Nucleotide sequencing reveals an open reading frame predicting expression of a 98-amino-acid (11-kDa) polypeptide exhibiting > 90% homology with the group II allergen of Lolium perenne, Lol p II. In vitro translation of different sized clone fragments generated by polymerase chain amplification confirms eukaryotic expression of a 10-12-kDa polypeptide by SDS-PAGE and the position of a translational stop apparently unrecognized during expression of lambda gt11 in E. coli. The unusual characteristics of the prokaryote-expressed fusion proteins may be exerting conformational alterations in Dac g II, as reflected by previous demonstrations of differences in human IgE immunoreactivity. Northern blot analysis using PCR-generated partial and full-length probes suggests that group II allergens may be encoded by a different family or families of temporally expressed genes from those encoding group I major allergens, although a group I gene may have been the progenitor.
Pressure-assisted melt-filling and optical characterization of Au nano-wires in microstructured fibers (2011)

We report a novel splicing-based pressure-assisted melt-filling technique for creating metallic nanowires in hollow channels in microstructured silica fibers. Wires with diameters as small as 120 nm (typical aspect ration 50:1) could be realized at a filling pressure of 300 bar. As an example we investigate a conventional single-mode step-index fiber with a parallel gold nanowire (wire diameter 510 nm) running next to the core. Optical transmission spectra show dips at wavelengths where guided surface plasmon modes on the nanowire phase match to the glass core mode. By monitoring the side-scattered light at narrow breaks in the nanowire, the loss could be estimated. Values as low as 0.7 dB/mm were measured at resonance, corresponding to those of an ultra-long-range eigenmode of the glass-core/nanowire system. By thermal treatment the hollow channel could be collapsed controllably, permitting creation of a conical gold nanowire, the optical properties of which could be monitored by side-scattering. The reproducibility of the technique and the high optical quality of the wires suggest applications in fields such as nonlinear plasmonics, near-field scanning optical microscope tips, cylindrical polarizers, optical sensing and telecommunications.
Gene trap strategies in ES cells (1999)

Gene trap (GT) strategies in mouse embryonic stem (ES) cells are increasingly being used for detecting patterns of gene expression (1-4, isolating and mutating endogenous genes (5-7), and identifying targets of signalling molecules and transcription factors (3, 8-10). The general term gene trap refers to the random integration of a reporter gene construct (called entrapment vector) (11, 12) into the genome such that ‘productive’ integration events bring the reporter gene under the transcriptional regulation of an endogenous gene. In some cases this also simultaneously generates an insertional mutation. Entrapment vectors were originally developed in bacteria (13), and applied in Drosophila to identify novel developmental genes and/or regulatory sequences (14-17). Subsequently, a modified strategy was developed for mouse in which the reporter gene mRNA becomes fused to an endogenous transcript. Such ‘gene trap’ vectors were initially used primarily as a tool to discover genes involved in development (1, 2,18). In the last five years there has been a significant shift of GT approaches in mouse to much broader, large scale applications in the context of the analysis of mammalian genomes and ‘functional genomics’. Sequencing and physical mapping of both the human and mouse genomes is expected to be completed within the next five years. Already, a large number of mouse and human genes have been identified as expressed sequence tags (ESTs), and very likely the majority of genes will be discovered as ESTs shortly. This vast sequence information contrasts with a rather limited understanding of the in vivo functions of these genes. Whereas DNA sequence can provide some indication of the potential functions of these genes and their products, their physiological roles in the organism have to be determined by mutational analysis. Thus, the sequencing effort of the human genome project has to be complemented by efficient functional analyses of the identified genes. One potentially powerful complementation to the efforts of the human genome project would be a strategy whereby large scale random mutagenesis in mouse is combined with the rapid identification of the mutated genes (6,7,19, and German gene trap consortium, W. W. unpublished data).
Decentralized Demand-Side Contribution to Primary Frequency Control (2010)

Frequency in large power systems is usually controlled by adjusting the production of generating units in response to changes in the load. As the amount of intermittent renewable generation increases and the proportion of flexible conventional generating units decreases, a contribution from the demand side to primary frequency control becomes technically and economically desirable. One of the reasons why this has not been done was the perceived difficulties in dealing with many small loads rather than a limited number of generating units. In particular, the cost and complexity associated with two-way communications between many loads and the control center appeared to be insurmountable obstacles. This paper argues that this two-way communication is not essential and that the demand can respond to the frequency error in a manner similar to the generators. Simulation results show that, using this approach, the demand side can make a significant and reliable contribution to primary frequency response while preserving the benefits that consumers derive from their supply of electric energy.
Calculation of critical layer thickness considering thermal strain in Si1−xGex/Si strained-layer heterostructures (1998)

In this article, interactions of thermal strain in growth of Si1−xGex strained-layers on Si are analyzed. A formula of critical layer thickness (hc) is obtained based on energy balance considering thermal strain under the assumption that the screw dislocation energy density equals to the sum of the areal strain energy density and thermal strain energy density. The relationship between the thermal expansion coefficient associated with thermal strain and Ge content x is linear. Our calculated values for hc of Si1−xGex strained layers on Si substrates versus mismatch, considering thermal strain, are better agreement with measurements of hc by People and Bean.
Clinical features of a Japanese case with Bothnia dystrophy (2011)

The clinical characteristics of a Japanese patient with a homozygous R234W mutation in RLBP1 are very similar to that of Swedish patients with Bothnia dystrophy. The origin of the Japanese R234W mutation is probably not the same as that of the Swedish patients, but more likely due to the high incidence of C to T transitions.
Aspects of Total Variation RegularizedL1Function Approximation (2005)

Abstract. The total variation based image denoising model of Rudin, Osher, and Fatemi has been generalized and modified in many ways in the literature; one of these modifications is to use the L 1 norm as the fidelity term. We study the interesting consequences of this modification, especially from the point of view of geometric properties of its solutions. It turns out to have interesting new implications for data driven scale selection and multiscale image decomposition.
Real-time view-dependent rendering of parametric surfaces (2009)

We propose a view-dependent adaptive subdivision algorithm for rendering parametric surfaces on parallel hardware. Our framework allows us to bound the screen space error of a piecewise linear approximation. We naturally assign more primitives to curved areas while keeping quads large for flatter parts of the model and avoid cracks resulting from the polygonal approximation of non-uniform patch subdivision. The overall algorithm is simple, fits current GPUs extremely well, and is surprisingly fast while producing little to no artifacts.
High-throughput optical image crossbar switch that uses a point light source array (1993)

A high-throughput optical image crossbar switch (OPIX) that uses a point light source array as the switching device is constructed. A prototype OPIX is used to create various switching patterns for two-dimensional images. The newly constructed OPIX is suitable for high-speed operation because it uses point light sources instead of an optical shutter array as the switching device. Since it is based on an imaging system, the OPIX has a large space-bandwidth product. The introduction of OPIX to optical image data buses of parallel optical processing systems is particularly significant.