gebhart/patrepeval huggingface dataset:
Transgenic potato tubers accumulate high levels of 1‐kestose and nystose: functional identification of a sucrose sucrose 1‐fructosyltransferase of artichoke (Cynara scolymus) blossom discs (1997)

By screening a cDNA library of artichoke (Cynara scolymus) blossom discs for fructosyltransferases, we isolated a clone designated Cy21. The deduced amino acid sequence shows homology to acid beta-fructosyl hydrolases and to the sucrose-fructan 6-fructosyltransferase (6-SFT) of barley. Transiently expressed in Nicotiana tabacum protoplasts, the Cy21 gene-product synthesized 1-kestose, indicating that Cy21 codes for a sucrose sucrose 1-fructosyltransferase (1-SST). The enzyme worked at physiologically relevant sucrose concentrations (25 mM sucrose). In the protoplast system, 1-kestose seemed to be the only fructan product of the 1-SST. The enzyme activity was not affected by pyridoxal-HCl, an inhibitor of both the beta-fructosyl hydrolase and the fructosyltransferase activity of invertases. The fructosyltransferase activity of the Cy21 gene-product, however, could be inhibited by Zn2+, Ag+ and Cu2+ ions. In artichoke plants the Cy21 transcript was highly abundant in primary roots and blossom discs. Transgenic potato tubers expressing Cy21 contain high levels of 1-kestose along with nystose and traces of fructosyl-nystose, supporting the conclusion that the Cy21 clone encodes a sucrose sucrose 1-fructosyltransferase.
Vascular endothelial growth factor-B and vascular endothelial growth factor-C expression in renal cell carcinomas: regulation by the von Hippel-Lindau gene and hypoxia. (2001)

Angiogenesis is essential for tumor growth and metastasis. It is regulated by numerous angiogenic factors, one of the most important being vascular endothelial growth factor (VEGF). Recently VEGF-B and VEGF-C, two new VEGF family members, have been identified that bind to the tyrosine kinase receptors flt-1 (VEGFR1), KDR (VEGFR2), and flt-4 (VEGFR3). Although the importance of VEGF-A has been shown in renal carcinomas, the contribution of these new ligands in kidney tumors is not clear. We have, therefore, measured the mRNA level of VEGF-B and VEGF-C together with their receptors by RNase protection assay (RPA) in 26 normal kidney samples and 45 renal cell cancers. We observed a significant up-regulation of VEGF-B (P = 0.002) but not VEGF-C (P = 0.3) in neoplastic kidney compared with normal tissues. In addition, although VEGF receptors were higher in tumors than normal kidney, there was a significant up-regulation of only flt-1 (P = 0.003) but not KDR (P = 0.12) or flt-4 (P = 0.09). There was also a significant correlation between VEGF-C and both of its receptors flt-4 (P = 0.006) and KDR (P = 0.03) but no association between VEGF-B and its receptor flt-1 (P = 0.23). A significant increase was observed in flt-1 (P < 0.001), KDR (P = 0.02), and flt-4 (P = 0.01) but not VEGF-B (P = 0.82) or VEGF-C (P = 0.52) expression in clear cell compared with chromophil (papillary) carcinomas. No significant association was demonstrated between VEGF-B, VEGF-C, flt-1, KDR, and flt-4 with patient sex, patient age, or tumor size (P > 0.05). The effect of von Hippel-Lindau (VHL) gene and hypoxia on VEGF-B and VEGF-C expression in the renal carcinoma cell line 786-0 transfected with wild-type and mutant VHL was determined by growing cells under 21% O2- and 0.1% O2. In wild-type VHL cells, whereas VEGF-A was significantly up-regulated under hypoxic compared with normoxic conditions (P < 0.001), expression of VEGF-C was reduced (P < 0.002). Nevertheless, the repression of VEGF-C was lost in mutant VHL cell lines under hypoxia. In contrast VEGF-B was not regulated by VHL despite clear up-regulation in vivo. These findings strongly support an enhanced role for this pathway in clear cell carcinomas by regulating angiogenesis and/or lymphangiogenesis. The study shows that clear cell tumors are able to up-regulate angiogenic growth factor receptors more efficiently than chromophil (papillary), that clear cell tumors can use pathways independent of VHL to regulate angiogenesis, and that this combined regulation may account for their more aggressive phenotype, which suggests that targeting VEGFR1 (flt-l) may be particularly effective in these tumor types.
Preparation and Reactivity of 1,3,5,7‐Tetrakis[4‐(diacetoxyiodo)phenyl]adamantane, a Recyclable Hypervalent Iodine(III) Reagent (2004)

A wide range of oxidative reactions are mediated by novel, nonpolymeric, and recyclable hypervalent IIII reagents (e.g. 2). In all cases, tetraiodide 1 was recovered nearly quantitatively in pure form after a simple workup. Reoxidation of 1 to 2 with m-chloroperbenzoic acid also proceeded quantitatively, without loss of oxidative activity.
Camera calibration by vanishing lines for 3-D computer vision (1991)

A novel approach to camera calibration by vanishing lines is proposed. Calibrated parameters include the orientation, position, and focal length of a camera. A hexagon is used as the calibration target to generate a vanishing line of the ground plane from its projected image. It is shown that the vanishing line includes useful geometric hints about the camera orientation parameters and the focal length, from which the orientation parameters can be solved easily and analytically. And the camera position parameters can be calibrated by the use of related geometric projective relationships. The simplicity of the target eliminates the complexity of the environment setup and simplifies the feature extraction in relevant image processing. The calibration formulas are also simple to compute. Experimental results show the feasibility of the proposed approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Role Of Platelets In Acute Vascular Events (1981)

Platelets are postulated to have an important role in acute and chronic cardiovascular events. Clinical events may result during the sequence of platelet activation reactions of adhesion, aggregate formation, release of granular constituents, thromboxane A2 formation, microembolization and platelet vascular occlusion. For example, sudden death may occur in patients with increased platelet sensitivity to catecholamine stimulation, platelet aggregate formation and thromboxane A2 generation resulting in ischemic ventricular arrhythmia induced by small-vessel platelet microembolization and local thromboxane A2 vasoconstriction. Whereas angina might be manifest if the microemboli disaggregated and vasospasm were transient, myocardial infarction would follow extensive permanent occlusion of small vessels or localized narrowing by vasospasm and extension of platelet thrombus formation at the site of intimal thickening. Platelets may also have an important role in atherogenesis through the mediation of the platelet-derived growth factor in the proliferative smooth muscle cell intimal lesion. Direct experimental and indirect clinical studies support the concept that platelets are important in cardiovascular events, but the relationship to spasm and to other possibly even more important mechanisms is not clear. Acute myocardial infarction and mural thrombogenesis appear to have the greatest evidence of being platelet-related. Proof that platelets play a critical, primary role in coronary artery disease and its complications ultimately requires a successful clinical intervention with platelet modifying agents. Although there are positive aspects of several controlled studies with platelet inhibiting agents, the secondary intervention trials have so far been inconclusive.
A mouse Ckappa-specific T cell clone indicates that DC-SIGN is an efficient target for antibody-mediated delivery of T cell epitopes for MHC class II presentation (2002)

In vaccine development, a major objective is to induce strong, specific T cell responses. This might be obtained by targeting antigen to cell surface molecules that efficiently channel the antigen into endocytic compartments for loading of MHC molecules. Antibodies have been used to deliver antigen; however, it is important to define optimal targets on antigen-presenting cells (APC) for efficient delivery. For this purpose, we have established a T cell readout that can be used to screen large numbers of different mAb for their ability to load MHC class II molecules. The novel human CD4+ T cell clone is specific for mouse Ig C kappa (40-48) and restricted by HLA-DR4 (DRA1,B1*0401). DR4 apparently presents both mouse and human C kappa 40-48, but there is no cross-reaction at the T cell level. B cells from DR4 transgenic mice spontaneously process and present the mouse C kappa peptide. The mouse C kappa -specific T cell readout was used to demonstrate that mouse mAb specific for human dendritic cell (DC)-specific ICAM-grabbing non-integrin (DC-SIGN), a novel DC-specific molecule, were 10- to 1000-fold more potent at inducing kappa-specific human CD4+ T cell proliferation compared to control mAb. Consistent with this finding, DC-SIGN-specific mAb were rapidly internalized upon binding and found in intracellular vesicles. These results strongly argue that DC-SIGN-specific mAb are channeled into the MHC class II presentation pathway. Thus, DC-SIGN could be an efficient target for antibody-mediated delivery of T cell epitopes in vaccine development.
Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen (2012)

A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1-V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4-99.9% of OTUs represented by more than one read, using Good's coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.
Cell‐Surface labeling and internalization by a fluorescent inhibitor of prostate‐specific membrane antigen (2008)

Our results suggest that potent, small-molecule inhibitors of PSMA can be utilized as carriers for targeted delivery for prostate cancer for future imaging and therapeutic applications.
Methods of Detection of Vascular Reactive Species (2001)

The evanescent nature of reactive oxygen and nitrogen species, the multiple cellular mechanisms evolved to maintain these substances at low (submicromolar) concentrations within the vascular system, and the often multifaceted nature of their reactivities have made measurement of these compounds within the vasculature problematic. This review attempts to provide a critical description of some of the most common approaches to quantification of nitric oxide, superoxide, hydrogen peroxide, and peroxynitrite, with attention to key issues that may influence the utility of a particular assay when adapted for use in vascular cells and tissues.
Effect of ferric carboxymaltose on serum phosphate and C-terminal FGF23 levels in non-dialysis chronic kidney disease patients: post-hoc analysis of a prospective study (2013)

In non-dialysis CKD patients, FCM induces reduction in serum phosphate levels that persists for three months. FCM causes a significant decrease in FGF23 levels without changes to other bone metabolism parameters.
Acidic Extracellular pH Induces Matrix Metalloproteinase-9 Expression in Mouse Metastatic Melanoma Cells through the Phospholipase D-Mitogen-activated Protein Kinase Signaling (2005)

The extracellular pH (pHe) of tumor tissues is often acidic, which can induce the expression of several proteins. We previously showed that production of matrix metalloproteinase-9 (MMP-9) was induced by culturing cells at acidic pHe (5.4-6.5). Here we have investigated the signal transduction pathway by which acidic pHe induces MMP-9 expression. We found that acidic pHe (5.9) activated phospholipase D (PLD), and inhibition of PLD activity by 1-butanol and Myr-ARF6 suppressed the acidic pHe-induced MMP-9 expression. Exogenous PLD, but not phosphatidylinositol-specific PLC or PLA2, mimicked MMP-9 induction by acidic pHe. Western blot analysis revealed that acidic pHe increased the steady-state levels of phosphorylated extracellular signal-regulated kinases 1/2 and p38 and that the PLD inhibitors suppressed these increases. Using 5'-deletion mutant constructs of the MMP-9 promoter, we found that the acidic pHe-responsive region was located at nucleotide -670 to -531, a region containing the NF kappa B binding site. A mutation into the NF kappa B binding site reduced, but not completely, the acidic pHe-induced MMP-9 promoter activity, and NF kappa B activity was induced by acidic pHe. Pharmacological inhibitors specific for mitogen-activated protein kinase kinase 1/2 (PD098059) and p38 (SB203580) attenuated the acidic pHe-induced NF kappa B activity and MMP-9 expression. These data suggest that PLD, mitogen-activated protein kinases (extracellular signal-regulated kinases 1/2 and p38), and NF kappa B mediate the acidic pHe signaling to induce MMP-9 expression. A transcription factor(s) other than NF kappa B may also be involved in the MMP-9 expression.
Identification of an alternative polyadenylation site in the human C3b/C4b receptor (complement receptor type 1) transcriptional unit and prediction of a secreted form of complement receptor type 1. (1988)

The human C3b/C4b receptor or complement receptor type one (CR1) is an approximately 200-kD single chain membrane glycoprotein of human peripheral blood cells that mediates the binding, processing, and transport of C3b-bearing immune complexes and regulates the activity of the complement cascade. Analysis of partial cDNA clones has shown that the COOH terminus is composed predominantly of three tandemly repeated regions of 450 amino acids each (15). In this report, we present a cDNA sequence that encodes the NH2 terminus of CR1. It appears to have been derived from an alternatively processed transcript, caused by polyadenylation occurring at a site within an intron in the CR1 transcriptional unit. The resulting truncated messenger carries an open reading frame that would produce a short, secreted CR1 form. We present genomic sequences and Northern blots which support this hypothesis and we propose that the NH2-terminal end of CR1 is a likely location for active sites. In addition, we report evidence for a CR1-like sequence in the human genome and we present a model for the organization of CR1.
Activation of the β2-Adrenergic Receptor Involves Disruption of an Ionic Lock between the Cytoplasmic Ends of Transmembrane Segments 3 and 6 (2001)

The movements of transmembrane segments (TMs) 3 and 6 at the cytoplasmic side of the membrane play an important role in the activation of G-protein-coupled receptors. Here we provide evidence for the existence of an ionic lock that constrains the relative mobility of the cytoplasmic ends of TM3 and TM6 in the inactive state of the beta(2)-adrenergic receptor. We propose that the highly conserved Arg-131(3.50) at the cytoplasmic end of TM3 interacts both with the adjacent Asp-130(3.49) and with Glu-268(6.30) at the cytoplasmic end of TM6. Such a network of ionic interactions has now been directly supported by the high-resolution structure of the inactive state of rhodopsin. We hypothesized that the network of interactions would serve to constrain the receptor in the inactive state, and the release of this ionic lock could be a key step in receptor activation. To test this hypothesis, we made charge-neutralizing mutations of Glu-268(6.30) and of Asp-130(3.49) in the beta(2)-adrenergic receptor. Alone and in combination, we observed a significant increase in basal and pindolol-stimulated cAMP accumulation in COS-7 cells transiently transfected with the mutant receptors. Moreover, based on the increased accessibility of Cys-285(6.47) in TM6, we provide evidence for a conformational rearrangement of TM6 that is highly correlated with the extent of constitutive activity of the different mutants. The present experimental data together with the recent high-resolution structure of rhodopsin suggest that ionic interactions between Asp/Glu(3.49), Arg(3.50), and Glu(6.30) may constitute a common switch governing the activation of many rhodopsin-like G-protein-coupled receptors.
Silicon microcavities fabricated with a new technique (1986)

A new fabrication technique for silicon microcavities is described. The technique makes use of lithographic patterning and etching techniques, high-temperature bonding between hydrated surfaces and selective etching. Cavities with dimensions 100 × 250 × 12 μm and with a confining membrane consisting of a 1 μm-thick SiO2, film are demonstrated. The technique is potentially totally IC-compatible and can be used to realise a variety of sensor and actuator structures.
Cell surface receptor‐antibody association constants and enumeration of receptor sites for monoclonal antibodies (2000)

Background Fluorescent markers (labeled antibodies) and flow cytometry are used to enumerate the average number of receptors (antigens) on formed bodies (cells) in whole blood by using a new method that avoids the extra steps of separating bound from unbound fluorescent markers or the use of external standards. Methods Mean channel fluorescence intensities of equilibrated marker-cell suspension mixtures, total concentrations of marker, and targeted cell counts obtained by standard cytometry procedures are used to complete the analyses for receptors per cell. Also, flow cytometric assays using competitive binding between fluorescent marker (CD4-RD1, CD8-FITC, CD3-FITC, CD3-RD1) and unlabeled antibody (CD4, CD8, CD3, CD3-dextran) for receptors on white blood cells in whole blood are described for determination of relative and specific binding constants of unlabeled/labeled antibody for targeted receptors. Results Ranges that were obtained for receptors per cell (lymphocytes) in normal blood donors were as follows: CD4, 4.9 × 104–1.5 × 105; CD8, 5.0 × 105–2.1 × 106; CD3, 6.6–7.8 × 105. Binding constants were highest for unlabeled CD4 antibody, 2.7 × 1010–2.1 × 1012 M-1, and then unlabeled CD3 antibody, 1.1 × 1010–1.9 × 1011 M-1. FITC- and RD1-labeled antibodies typically had binding constants that were 10-to 100-fold lower than the native antibodies. Conclusions Values of receptors per cell and binding constants obtained by the new method from flow cytometric analyses of mixtures of whole blood with FITC- or RD1-labeled CD4, CD8, and CD3 antibodies compare well with literature values determined by other methods. Cytometry 40:316–326, 2000 © 2000 Wiley-Liss, Inc.
VAMP4 Is an Essential Cargo Molecule for Activity-Dependent Bulk Endocytosis (2015)

The accurate formation of synaptic vesicles (SVs) and incorporation of their protein cargo during endocytosis is critical for the maintenance of neurotransmission. During intense neuronal activity, a transient and acute accumulation of SV cargo occurs at the plasma membrane. Activity-dependent bulk endocytosis (ADBE) is the dominant SV endocytosis mode under these conditions; however, it is currently unknown how ADBE mediates cargo retrieval. We examined the retrieval of different SV cargo molecules during intense stimulation using a series of genetically encoded pH-sensitive reporters in neuronal cultures. The retrieval of only one reporter, VAMP4-pHluorin, was perturbed by inhibiting ADBE. This selective recovery was confirmed by the enrichment of endogenous VAMP4 in purified bulk endosomes formed by ADBE. VAMP4 was also essential for ADBE, with a cytoplasmic di-leucine motif being critical for this role. Therefore, VAMP4 is the first identified ADBE cargo and is essential for this endocytosis mode to proceed.
AlGaInN laser diodes grown on an ELO-GaN substrate vs. on a sapphire substrate (2002)

The lifetime of AlGaInN-based violet laser diodes is restricted by the high dislocation densities caused by the large difference between the lattice constants and thermal expansion coefficients of GaN and sapphire. In order to reduce the dislocation density, epitaxial lateral overgrowth (ELO) techniques have been proposed, leading to the higher performance of AlGaInN lasers. In this work, we compared the lasing characteristics of AlGaInN lasers grown on ELO-GaN with those grown on sapphire substrates.
Impact of Morphological Orientation in Determining Mechanical Properties in Triblock Copolymer Systems (1996)

In contrast to other types of segmented multiblock thermoplastic elastomers, simple ABA block copolymers represent a class of well-defined nanostructured materials. Due to the inherent block lengths built in during the polymerization, the microdomain structure of block copolymers exhibits a size scale of typically 10−100 nm. The ability to control the individual chemistry of each block as well as the size and the shape of the domains in a block copolymer affords enormous advantages to tailor physical properties. By globally orienting the microdomains, a well-defined initial morphological state aids greatly in the interpretation and modeling of mechanical deformation and allows for exploitation of the inherent anisotropy of the cylindrical and lamellar structures. Several types of orientation techniques are reviewed. Experiments investigating structure−mechanical properties in styrene−diene triblock copolymers with spherical, cylindrical, and lamellar morphologies are discussed, with emphasis on the clarifying role of global morphological orientation in data interpretation. Composite theory which treats each microphase as a continuum describes small strain behavior of cylinders and lamellae quite well. Molecular variables such as the number of effective bridge vs loop conformations in the rubber midblock become more important at large strains. With controlled chemistry and morphology as well as with improved dynamic probes, further understanding between the interplay of molecular and morphological structure in influencing the deformation process is expected.
New Bioluminogenic Substrates for Monoamine Oxidase Assays (2006)

Novel bioluminogenic substrates were designed for probing monoamine oxidase (MAO) activity based on a simple and effective beta-elimination strategy. By modifying the amino group and the central core of luciferin derivatives, we have developed a series of substrates useful for assays of MAO A or B, or both. One of these substrates, exhibiting low Km values and high signal-to-background ratios with both isozymes, was shown to accurately measure the Ki values of known MAO inhibitors. This substrate is a key component in the development of a highly sensitive homogeneous MAO assay for high-throughput screening (HTS) of compounds in drug discovery and for monitoring MAO activity in complex biological systems. This design strategy should be applicable to fluorogenic MAO substrates and could broaden the structural requirements of substrates for other enzyme assays.