gebhart/patrepeval huggingface dataset:
Tricarboxylic Acid Cycle Activity and Remodeling of Glycerophosphocholine Lipids Support Cytokine Induction in Response to Fungal Patterns (2019)

Increased glycolysis parallels immune cell activation, but the role of pyruvate remains largely unexplored. We found that stimulation of dendritic cells with the fungal surrogate zymosan causes decreases of pyruvate, citrate, itaconate, and α-ketoglutarate, while increasing oxaloacetate, succinate, lactate, oxygen consumption, and pyruvate dehydrogenase activity. Expression of IL10 and IL23A (the gene encoding the p19 chain of IL-23) depended on pyruvate dehydrogenase activity. Mechanistically, pyruvate reinforced histone H3 acetylation, and acetate rescued the effect of mitochondrial pyruvate carrier inhibition, most likely because it is a substrate of the acetyl-CoA producing enzyme ACSS2. Mice lacking the receptor of the lipid mediator platelet-activating factor (PAF; 1-O-hexadecyl-2-acetyl-sn-glycero-3-phosphocholine) showed reduced production of IL-10 and IL-23 that is explained by the requirement of acetyl-CoA for PAF biosynthesis and its ensuing autocrine function. Acetyl-CoA therefore intertwines fatty acid remodeling of glycerophospholipids and energetic metabolism during cytokine induction.
Microstructural evidence on electrical properties of Ta/Ti/Al and Ti/Ta/Al ohmic contacts to <i>n</i>-AlGaN/GaN (2001)

Electrical properties and microstructures of Ta/Ti/Al and Ti/Ta/Al contacts to n-AlGaN/GaN heterostructure field-effect transistor structures were investigated using the transmission line method and transmission electron microscopy. The specific resistivity (5.3×10−7 Ω cm2) of Ta/Ti/Al contacts is much lower than that (5.1×10−4 Ω cm2) of Ti/Ta/Al contacts, for the same heterostructure and similar metallization. The contact resistivity was found to depend on the thickness of the AlGaN layer, interfacial phase, and interface roughness. The formation of interfacial phases by solid-state reactions with the metal layer during annealing appears to be essential for ohmic behavior on n-III-nitrides suggesting a tunneling contact mechanism.
Engineering of solvent‐exposed loops in <i>Escherichia coli</i> β‐galactosidase (1998)

The Escherichia coli beta-galactosidase is a high molecular mass tetrameric enzyme extensively used as a molecular marker. Despite its proven utility as a partner in fusion proteins, previous attempts to generate insertional mutants rendered inactive or poorly active enzymes, hampering its further engineering for the construction of multifunctional enzymes. We have explored several solvent-exposed loops on the tetramer, namely those spanning residues 246-254, 271-287, 578-584, 770-773, and 793-806, as acceptor sites to accommodate functional protein segments on the surface of active beta-galactosidase enzymes. An RGD-containing antigenic peptide positioned in these sites interacts efficiently with specific monoclonal antibodies as well as target integrins on the surface of mammalian cells. The resulting chimeric enzymes are soluble, stable, produced in high yields and enzymatically active. Moreover, the identified insertion sites could be appropriated for the design of promising beta-galactosidase-based molecular sensors.
H/D‐exchange reactions with hydride‐activated catalysts (2007)

Abstract A safe, user friendly and efficient method to provide high deuterium incorporation into a variety of organic substrates was developed. Systematic screening of catalysts and activators revealed that the activation of the Pd‐ or Rh‐catalyst by NaBD 4 is essential for the H/D exchange. The feasibility has been demonstrated by the successful application of this method to bi‐ and tricyclic aromatic compounds as well as chiral natural products like dextrorphan or drugs like formoterol. Copyright © 2007 John Wiley & Sons, Ltd.
Inhibition of galactonolactone dehydrogenase activity by lycorine. (1996)

Galactonolactone dehydrogenase, a mitochondrial enzyme catalyzing the last step in ascorbate biosynthesis, is strongly inhibited by lycorine. A concentration of 10 microM of the alkaloid fully inhibits the activity of the enzyme. The high sensitivity of this enzyme to lycorine supports the hypothesis that the lycorine specifically inhibits ascorbate biosynthesis and that all the other metabolic responses to lycorine treatment depend on this primary inhibition of ascorbate biosynthesis.
Microstructural Development in Si<sub>3</sub>N<sub>4</sub>/Polysilazane Bodies During Heating (1988)

The development of microstructure during heating has been investigated for molded Si{sub 3}N{sub 4} bodies fabricated with commercial {alpha}-Si{sub 3}N{sub 4} powder and a preceramic polysilazane binder. After the N-methyl polysilazane binder is pyrolyzed at 800{degree}C under N{sub 2}, the bodies have a uniform microstructure composed of an intimate mixture of Si{sub 3}N{sub 4} particles and polysilazane-derived amorphous silicon nitride. After the particles undergo high-temperature treatment at 1,725{degree}C in an N{sub 2} overpressure of {approx} 700 kPa, significant grain growth occurs. SEM and microhardness data suggest local densification in the body and high reactivity for the polysilazane-derived silicon nitride.
Expression specificity of the mouse exonuclease 1 (mExo1) gene (1999)

Genetic recombination involves either the homo-logous exchange of nearly identical chromosome regions or the direct alignment, annealing and ligation of processed DNA ends. These mechanisms are involved in repairing potentially lethal or mutagenic DNA damage and generating genetic diversity within the meiotic cell population and antibody repertoire. We report here the identification of a mouse gene, termed mExo1 for mouse exonuclease 1, which encodes a approximately 92 kDa protein that shares homology to proteins of the RAD2 nuclease family, most notably human 5' to 3' exonuclease Hex1/hExo1, yeast exonuclease 1 (Exo1) proteins and Drosophila melanogaster Tosca. The mExo1 gene maps to distal chromosome 1, consistent with the recent mapping of the orthologous HEX1 / hEXO1 gene to chromosome 1q42-q43. mExo1 is expressed prominently in testis, an area of active homologous recombination, and spleen, a prominent lymphoid tissue. An increased level of mExo1 mRNA was observed during a stage of testis development where cells that are actively involved in meiotic recombination arise first and represent a significant proportion of the germ cell population. Comparative evaluation of the expression patterns of the human and mouse genes, combined with previous biochemical and yeast genetic studies, indicate that the Exo1-like proteins are important contributors to chromosome processing during mammalian DNA repair and recombination.
The eEF1A Proteins: At the Crossroads of Oncogenesis, Apoptosis, and Viral Infections (2015)

Eukaryotic translation elongation factors 1 alpha, eEF1A1 and eEF1A2, are not only translation factors but also pleiotropic proteins that are highly expressed in human tumors, including breast cancer, ovarian cancer, and lung cancer. eEF1A1 modulates cytoskeleton, exhibits chaperone-like activity and also controls cell proliferation and cell death. In contrast, eEF1A2 protein favors oncogenesis as shown by the fact that overexpression of eEF1A2 leads to cellular transformation and gives rise to tumors in nude mice. The eEF1A2 protein stimulates the phospholipid signaling and activates the Akt-dependent cell migration and actin remodeling that ultimately favors tumorigenesis. In contrast, inactivation of eEF1A proteins leads to immunodeficiency, neural and muscular defects, and favors apoptosis. Finally, eEF1A proteins interact with several viral proteins resulting in enhanced viral replication, decreased apoptosis, and increased cellular transformation. This review summarizes the recent findings on eEF1A proteins indicating that eEF1A proteins play a critical role in numerous human diseases through enhancement of oncogenesis, blockade of apoptosis, and increased viral pathogenesis.
Hybridization-sensitive fluorescence control in the near-infrared wavelength range (2011)

A series of near-infrared fluorescent probes were designed based on the concept of emission control caused by interdye excitonic interaction. The fluorescent probes showed very weak emission in the unhybridized state, whereas they emitted near-infrared fluorescence after hybridization with the complementary nucleic acid. The hybridization-dependent switching of fluorescence emission made it possible to monitor mRNA in human cells in the range of near-infrared wavelengths.
NO more muscle fatigue (2009)

NOS is a key enzyme in the production of NO, a molecule that directly regulates vasorelaxation and blood supply. Diverse forms of muscle disease have been clinically associated with unusual fatigue after exercise. The localization of neuronal NOS (nNOS) at the plasma membrane of muscle has recently been shown to prevent muscle fatigue after exercise. In this issue of the JCI, Lai et al. show that dystrophin--the structural protein missing in individuals with Duchenne muscular dystrophy--anchors nNOS to the sarcolemma through a direct interaction with dystrophin spectrin-like repeats 16 and 17 (see the related article, doi:10.1172/JCI36612). Furthermore, in another recently reported study of mouse models of muscular dystrophy, phosphodiesterase 5A inhibitors were used to treat the downstream ischemia that is associated with nNOS mislocalization. Collectively, these findings significantly advance our understanding of exercise-induced muscle fatigue and its role in muscle disease.
Dinuclear (Pt,Pt) and heteronuclear (Pt,Pd) complexes of uracil nucleobases with identical and mixed amine (NH3, en, bpy) ligands on the two metals. Effects of the heterometal and amine on the oxidizability (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDinuclear (Pt,Pt) and heteronuclear (Pt,Pd) complexes of uracil nucleobases with identical and mixed amine (NH3, en, bpy) ligands on the two metals. Effects of the heterometal and amine on the oxidizabilityWolfgang Micklitz, Juergen Riede, Brigitte Huber, Gerhard Mueller, and Bernhard LippertCite this: Inorg. Chem. 1988, 27, 11, 1979–1986Publication Date (Print):June 1, 1988Publication History Published online1 May 2002Published inissue 1 June 1988https://pubs.acs.org/doi/10.1021/ic00284a029https://doi.org/10.1021/ic00284a029research-articleACS PublicationsRequest reuse permissionsArticle Views262Altmetric-Citations37LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
RAMPAGE: Promoter Activity Profiling by Paired‐End Sequencing of 5′‐Complete cDNAs (2013)

RNA annotation and mapping of promoters for analysis of gene expression (RAMPAGE) is a method that harnesses highly specific sequencing of 5'-complete complementary DNAs to identify transcription start sites (TSSs) genome-wide. Although TSS mapping has historically relied on detection of 5'-complete cDNAs, current genome-wide approaches typically have limited specificity and provide only scarce information regarding transcript structure. RAMPAGE allows for highly stringent selection of 5'-complete molecules, thus allowing base-resolution TSS identification with a high signal-to-noise ratio. Paired-end sequencing of medium-length cDNAs yields transcript structure information that is essential to interpreting the relationship of TSSs to annotated genes and transcripts. As opposed to standard RNA-seq, RAMPAGE explicitly yields accurate and highly reproducible expression level estimates for individual promoters. Moreover, this approach offers a streamlined 2- to 3-day protocol that is optimized for extensive sample multiplexing, and is therefore adapted for large-scale projects. This method has been applied successfully to human and Drosophila samples, and in principle should be applicable to any eukaryotic system.
Fingerprint image quality assessment based on BP neural network with hierarchical clustering (2019)

Fingerprint image quality assessment is important because the good performance of the minutiae‐based matching algorithm is heavily dependent on fingerprint images with high quality. Many efforts have been made in existing methods, but most methods either use full fingerprint images or use local areas and involve subjective judgments. Unlike previous methods, the proposed method considers both local and global assessments. Local feature vectors are extracted from the fingerprint image block for hierarchical clustering, and the results are used as target outputs of the back‐propagation (BP) neural network without any subjective judgments. Global feature vectors based on the local quality assessment results are used for hierarchical clustering and fed into the BP neural network that calculates the overall error rate of genuine and imposter errors to achieve global quality assessment. Furthermore, the minutiae quality assessment method is also proposed and incorporated into the minutiae‐based matching algorithm. The experimental results based on the FVC2002 and FVC2004 databases show that the proposed methods can effectively assess the quality of fingerprint images and ensure the overall improvement of matching performance.
Amino acid permeases in developing seeds of<i>Vicia faba</i>L.: expression precedes storage protein synthesis and is regulated by amino acid supply (2001)

Full length cDNAs encoding three amino acid permeases were isolated from seed-specific libraries of Vicia faba. The predicted proteins VfAAP1, VfAAP3 and VfAAP4 share up to 66% identity among themselves. Functional characterization of VfAAP1 and VfAAP3 in a yeast mutant showed that these permeases transport a broad range of amino acids. However, VfAAP1 had a preference for cysteine and VfAAP3 for lysine and arginine. VfAAP1 was highly expressed in cotyledons at early developmental stages and moderately in other sink tissues. Its peak of expression in cotyledons corresponded to the appearance of storage protein transcripts, suggesting that this transporter fulfills an important role in providing amino acids for storage protein biosynthesis. VfAAP3 was expressed most abundantly in maternal tissues, that is in roots, stems, gynoecia, pods and seed coats at different developmental stages. VfAAP4 transcripts could not be detected by northern hybridization. In situ hybridization showed that VfAAP1 mRNA is distributed throughout cotyledon storage parenchyma cells, but could not be detected in the abaxial epidermal cell layer. It also accumulate in the chlorenchyma and thin-walled parenchyma cells of seed coats. VfAAP1 mRNA levels were lower in cotyledons cultured in the presence of glutamine, whereas expression of a vicilin storage protein gene was up-regulated under similar conditions. Cysteine repressed the expression of the GUS reporter gene under control of the VfAAP1 promoter, suggesting that this transporter is modulated at the transcriptional level. Regulation of amino acid transport in relation to storage protein accumulation is discussed.
Tumor suppressor genes encoding proteins required for cell interactions and signal transduction in <i>Drosophila</i> (1993)

Tumor suppressor genes, whose products are required for the control of cell proliferation, have been identified by their mutant phenotype of tissue overgrowth. Here we describe recent work on the molecular identification of tumor suppressor genes that function in two different cell types of the Drosophila larva: the blood cells, and the undifferentiated epithelial cells of developing imaginal discs. Mutations in the aberrant immune response8 (air8) gene lead to overproduction and precocious differentiation of blood cells. This gene encodes the Drosophila homolog of human ribosomal protein S6. The mutant phenotype is consistent with a role for S6 in the control of cell proliferation, and is compatible with findings from mammalian cells where alterations in S6 expression and phosphorylation are associated with changes in cell proliferation. Mutations in the discs large (dlg) gene cause neoplastic overgrowth of imaginal discs in the larva. The mutant discs show loss of septate junctions and of apical-basal cell polarity, and they also lose the ability to differentiate cuticular structures. The dlg protein product (DlgA) is localized at septate junctions between epithelial cells, and cDNA sequencing indicates that the gene product includes a domain with homology to guanylate kinase (GUK). Two mammalian homologs of this gene have been identified, and one of them (PSD-95/SAP90) encodes a component of synaptic densities in the brain; this protein therefore resembles the DlgA protein in being located in a specialized cell junction that functions in information transfer between cells. Mutations in the fat gene cause hyperplastic imaginal disc overgrowth, in which the overgrowing disc tissue retains its epithelial structure and its ability to differentiate. Some of the excess disc tissue is shed as vesicles suggesting a loss of cell adhesion. In support of this hypothesis, the predicted gene product shows homology to cadherins in its extracellular domain. However, the fat protein is much larger than known cadherins. As in human cancer, somatic loss of the normal alleles of tumor suppressor genes can lead to tumor formation in Drosophila; an example of this is provided by the warts (wts) locus. The wts gene was identified by the dramatic overgrowth of mitotic recombination clones that are homozygous for a wts deletion. In these clones the cuticle intrudes between epithelial cells, suggesting an alteration in cell adhesion. The study of these and other tumor suppressor genes in Drosophila is providing new evidence supporting the critical role of cell interactions and specialized apical junctions in controlling epithelial cell proliferation.
Prenatal diagnosis of partial trisomy 4q26-qter and monosomy for the Wolf-Hirschhorn critical region in a fetus with split hand malformation (2000)

We describe the results of prenatal analyses and postnatal findings in a male fetus with a partial trisomy for the long arm and a small terminal monosomy for the short arm of chromosome 4 with the following karyotype: 46,XY,add(4)(p16.3).ish dup(4)(q26qter)(wcp4+, D4S2336x3,AFMb280xa5x2,4ptel-,WHCR-). G-banding did not identify the origin of the additional chromosomal segment, but this was achieved prenatally by application of RxFISH and whole chromosome painting probes. Subsequent FISH analysis with region-specific YAC clones was used to relate the phenotypic findings such as bilateral split hand formation, specific cardiac and kidney anomalies, microtia, and hypoplastic thorax more exactly to the partial trisomy of the segment 4q26-qter.
Metabolic availability of medium-chain triglycerides coingested with carbohydrates during prolonged exercise (1995)

The present study examined the metabolic response to medium-chain triglycerides (MCTs) ingestion with or without carbohydrates (CHOs). Eight well-trained athletes cycled 4 x 180 min at 50% maximal work rate (57% maximal O2 consumption). Subjects drank a bolus of 4 ml/kg at the start and 2 ml/kg every 20 min during exercise of either a 15% (214 g) CHO solution (CHO trial), an equicaloric 149 g CHO-29 g MCT suspension (CHO+MCT trial), 214 g CHO [high CHO (HCHO)]-29 g MCT suspension (HCHO+MCT trial) or 29 g MCT solution (MCT trial). Exogenous MCT oxidation was measured by adding a [1,1,1-13C]trioctanoate tracer to the MCT oil. 13CO2 enrichment of breath samples were measured every 15 min. During the second hour (60- to 120-min period), the amount of MCT oxidized was 72% of the amount ingested during the CHO+MCT trial, whereas during the MCT trial only 33% was oxidized. The rate of MCT oxidation increased more rapidly during the HCHO+MCT and CHO+MCT trials compared with the MCT trial, yet in all three cases the oxidation rate stabilized at 0.12 g/min during 120-180 min of exercise. It is concluded that more MCTs are oxidized when ingested in combination with CHOs. Data do confirm the hypothesis that oral MCTs might serve as an energy source in addition to glucose during exercise because the metabolic availability of MCTs was high during the last hour of exercise, with oxidation rates being approximately 70% of the ingestion rate.(ABSTRACT TRUNCATED AT 250 WORDS)
Fast reactive control for illumination through rain and snow (2012)

During low-light conditions, drivers rely mainly on headlights to improve visibility. But in the presence of rain and snow, headlights can paradoxically reduce visibility due to light reflected off of precipitation back towards the driver. Precipitation also scatters light across a wide range of angles that disrupts the vision of drivers in oncoming vehicles. In contrast to recent computer vision methods that digitally remove rain and snow streaks from captured images, we present a system that will directly improve driver visibility by controlling illumination in response to detected precipitation. The motion of precipitation is tracked and only the space around particles is illuminated using fast dynamic control. Using a physics-based simulator, we show how such a system would perform under a variety of weather conditions. We build and evaluate a proof-of-concept system that can avoid water drops generated in the laboratory.
Automated detection of vessel lumen and stent struts in intravascular optical coherence tomography to evaluate stent apposition and neointimal coverage (2016)

The presented automatic algorithm enables robust and fast detection of lumen contours and stent struts and provides quantitative measurements of PD and NT. In addition, the algorithm was validated using various clinical cases to demonstrate its reliability. Therefore, this technique can be effectively utilized for clinical trials on stent-related side effects, including in-stent thrombosis and in-stent restenosis.