gebhart/patrepeval huggingface dataset:
Development ofToxAandToxBpromoter-driven fluorescent protein expression vectors for use in filamentous ascomycetes (2005)

The green fluorescent protein (GFP) has been established as the premier in vivo reporter for investigations of gene expression, protein localization, and cell and organism dynamics. The fungal transformation vector pCT74, with sGFP under the control of the ToxA promoter from Pyrenophora tritici-repentis, effectively expresses GFP in a diverse group of filamentous ascomycetes. Due to the versatility of ToxA promoter-driven expression of GFP, we constructed an additional set of fluorescent protein expression vectors to expand the color palette of fluorescent markers for use in filamentous fungi. EYFP, ECFP and mRFP1 were successfully expressed from the ToxA promoter in its fungus of origin, P. tritici-repentis, and a distant relative, Verticillium dahliae. Additionally the ToxB promoter from P. tritici-repentis drove expression of sGFP in V. dahliae, suggesting a similar potential to the ToxA promoter for heterologous expression in ascomycetes. The suite of fungal transformation vectors presented here promise to be useful for a variety of fungal research applications.
FcεRI-Mediated Activation of Transcription Factors in Antigen-Presenting Cells (2001)

Professional antigen-presenting cells (APC) such as monocytes and dendritic cells (DC) bearing high-affinity IgE receptors (Fc epsilon RI) efficiently present IgE-bound antigens to T cells. Fc epsilon RI expression is upregulated on APC from atopic donors, especially in inflamed tissues. These data suggest a pathophysiological concept of an IgE-mediated delayed-type hypersensitivity reaction in atopic diseases. However, Fc epsilon RI ligation also leads to the synthesis of proinflammatory cytokines and other molecules involved in inflammatory reactions. The investigation of transcription factors mediating these effects has only recently commenced. In general, members of the NF-kappa B family are known to regulate APC function and differentiation, with the RelB subunit being especially important in DC generation. In addition, Ikaros and PU.1 have also been shown to be essential factors for DC differentiation, whereas Oct-2 is upregulated by differentiation towards macrophages. Recently, Fc epsilon RI has been demonstrated to induce NF-kappa B activation via I kappa B-alpha serine phosphorylation and degradation in monocytes and DC. Inhibitors of NF-kappa B activation such as N-acetylcysteine or N-tosyl-L-phenylalanine chloromethyl ketone can suppress Fc epsilon RI-induced TNF-alpha and MCP-1 release. Interestingly, in human epidermal Langerhans' cells (LC), NF-kappa B activation can only be observed when large amounts of Fc epsilon RI are present. In addition, the composition of NF-kappa B complexes differs between monocytes, monocyte-derived DC and LC, suggesting a cell type-specific regulation. Moreover, the transcription factor NFAT is induced upon Fc epsilon RI ligation in human APC. The elucidation of further transcription factors involved in Fc epsilon RI signaling in APC should contribute to the employment of new inhibition strategies for the treatment of atopic and other inflammatory diseases.
Homoharringtonine (2001)

HHT and its derivatives appear to have promising activity in hematologic malignancies, a finding that needs to be pursued.
Progress in Thermochemical Biomass Conversion (2001)

Combustion: Co-combustion of coal and biomass wastes in fluidised bed Development of catalytic wood fired boiler The mathematical modelling of biomass pyrolysis in a fixed bed and experimental verification Operating parameters for the circulating fluidised bed (CFB) processing of biomass Combustion properties of a fuel bed - Experimental and modelling study Summary of recent parametric studies of small-scale domestic biomass combustion Combustion processes in a biomass fuel bed - Experimental results of the influence of airflow and of particle size and density Influence of the ash composition in slagging and defluidisation in a biomass fired commercial CFB boiler A new type of a boiler plant for dry and wet biofuel Gasification: Modern technologies of biomass conversion Redox process for the production of clean hydrogen from biomass Dynamic Modelling of Char Gasification in a Fixed-Bed A two stage pyrolysis/gasification process for herbaceous waste biomass from agriculture Fundamental fluid-dynamic investigations in a scaled cold model for biomass-steam gasification Biomass Power Generation: Sugar Cane Bagasse and Trash Biomass and waste to energy conversion in the Netherlands by means of (in) direct co-combustion: Status, projects and future applications in the Dutch utility sector Gasification study of biomass mixed with plastic wastes The development of methanol synthesis with biomass gasification Final report: Varnamo demonstration programme Design of a moving bed granular filter for biomass gasification Pyrolysis: Bagasse pyrolysis in a wire mesh reactor BCO/Diesel oil emulsification: Main achievements of the emulsification process and preliminary results of tests on diesel engine Overview of fast pyrolysis Production of hydrogen from biomass-derived liquids Levoglucosenone - A product of catalytic fast pyrolysis of cellulose Pyrolysis and gasification of black liquors from alkaline pulping of straw in a fixed bed reactor Thermal efficiency of the HTU process for biomass liquefaction Low-temperature pyrolysis as a possible technique for the disposal of CCA treated wood waste Mathematical modelling of the flash-pyrolysis process for wood particles Flash pyrolysis of biomass in a conical spouted bed. Kinetic study in the 400-500C range Scale up effect on plastics waste pyrolysis Research on the rotating cone reactor for sawdust flash pyrolysis Thermal desorption technology: Low temperature carbonisation of the biomass for manufacturing of activated carbon Scaling-up and operation of a flash-pyrolysis system for bio-oil production and applications on basis of the rotating cone technology Systems: Utilisation of bagasse residues in power production Barriers for the introduction of biomass in the Netherlands Assessment of the techno-economic viability of a bioelectricity demonstration plant in Spain Innovative components for decentralised combined heat and power generation from biomass gasification A role of bioenergy utilization technologies considering bioenergy supply potential and energy systems using a global energy and land use model
A Major Lineage of Enteroendocrine Cells Coexpress CCK, Secretin, GIP, GLP-1, PYY, and Neurotensin but Not Somatostatin (2012)

Enteroendocrine cells such as duodenal cholecystokinin (CCK cells) are generally thought to be confined to certain segments of the gastrointestinal (GI) tract and to store and release peptides derived from only a single peptide precursor. In the current study, however, transgenic mice expressing enhanced green fluorescent protein (eGFP) under the control of the CCK promoter demonstrated a distribution pattern of CCK-eGFP positive cells that extended throughout the intestine. Quantitative PCR and liquid chromatography-mass spectrometry proteomic analyses of isolated, FACS-purified CCK-eGFP-positive cells demonstrated expression of not only CCK but also glucagon-like peptide 1 (GLP-1), gastric inhibitory peptide (GIP), peptide YY (PYY), neurotensin, and secretin, but not somatostatin. Immunohistochemistry confirmed this expression pattern. The broad coexpression phenomenon was observed both in crypts and villi as demonstrated by immunohistochemistry and FACS analysis of separated cell populations. Single-cell quantitative PCR indicated that approximately half of the duodenal CCK-eGFP cells express one peptide precursor in addition to CCK, whereas an additional smaller fraction expresses two peptide precursors in addition to CCK. The coexpression pattern was further confirmed through a cell ablation study based on expression of the human diphtheria toxin receptor under the control of the proglucagon promoter, in which activation of the receptor resulted in a marked reduction not only in GLP-1 cells, but also PYY, neurotensin, GIP, CCK, and secretin cells, whereas somatostatin cells were spared. Key elements of the coexpression pattern were confirmed by immunohistochemical double staining in human small intestine. It is concluded that a lineage of mature enteroendocrine cells have the ability to coexpress members of a group of functionally related peptides: CCK, secretin, GIP, GLP-1, PYY, and neurotensin, suggesting a potential therapeutic target for the treatment and prevention of diabetes and obesity.
Half-Strength Citrate CPD Combined with a New Additive Solution for Improved Storage of Red Blood Cells Suitable for Clinical Use (1993)

Currently used systems for red blood cell (RBC) collection and storage for transfusion have the disadvantage that the RBC 2,3-bisphosphoglycerate (BPG) concentration is depleted within two weeks of storage, resulting in a left-shift of the oxygen dissociation curve and a temporarily impaired capacity to deliver oxygen. We have studied the effects on red cell metabolism, morphology and in vivo recovery of 49-day storage of RBC, with collection in half-strength citrate CPD (0.5CPD) and storage in an additive solution containing citrate, adenine, mannitol, phosphate and glucose (RAS2). Traditional CPD-SAGM was used for comparison. Component preparation was performed after an initial holding period of the whole blood at ambient temperature for 8h. The BPG concentration in 0.5CPD-RAS2 RBC was 0.633±0.120 mol (mol Hb)^-1 as compared to 0.454±0.138 mol (mol Hb)^-1 in CPD-SAGM RBC which implied a decrease to 67 and 48% of normal concentration, respectively. The mean RBC BPG concentration was maintained at the initial level for 28 days in the new system but decreased to very low levels within 14 days in the controls. The total adenine nucleotides were well maintained in both systems, adenosine triphosphate slightly better in the new system. Hemolysis after 49 days was 0.35±0.21% in the new system and 0.72±0.25% in the controls (p<0.001). The morphology was better maintained in the new system (p<0.001). The 24-hour posttransfusion survival of 49-day stored RBC was 78.9±7.1%. The membrane leakage of sodium and potassium was not significantly different in the two systems. The concentration of inorganic phosphate (Pi) in the extracellular fluid of 0.5 CPD-RAS2 RBC was initially 7.1±0.8 mmol l^-1. It decreased to approximately 5.5 mmol l^-1 during the first 2 weeks of storage and then slowly increased to 9.4±0.9 mmol l^-1 on day 49. Pi in the CPD-SAGM controls was low initially but rose to 6.2±0.4 mmol l^-1 at the end of storage. The new system offers clearcut advantages as compared to traditional systems and does not seem to raise any serious clinical objections against its use even in massive transfusions.
The Measurement of Craving (2001)

This article presents an overview of the definition and measurement of "craving" as it is applied to drug and alcohol abuse research. Examples of craving measures are described and organized in terms of whether they structure craving as a single factor or as a multifactorial construct. The application of craving scales in cue-conditioning studies, in medication treatment trials, and as outcome measures in other treatment studies is considered. It is concluded that no single craving scale, or type of scale, has unequivocal support, because few studies have administered more than one scale to the same population. It is suggested that our understanding of craving will be advanced by designing studies that compare and contrast several craving scales within the same study. Likewise, craving is only one possible cause of relapse. Future studies should compare several alternate relapse mechanisms within the same study.
The Mouse Clock Locus: Sequence and Comparative Analysis of 204 Kb from Mouse Chromosome 5 (2000)

The Clock gene encodes a basic helix-loop-helix (bHLH)-PAS transcription factor that regulates circadian rhythms in mice. We previously cloned Clock in mouse and human using a battery of behavioral and molecular techniques, including shotgun sequencing of two bacterial artificial chromosome (BAC) clones. Here we report the finished sequence of a 204-kb region from mouse chromosome 5. This region contains the complete loci for the Clock and Tpardl (pFT27) genes, as well as the 3' partial locus of the Neuromedin U gene; sequence analysis also suggests the presence of two previously unidentified genes. In addition, we provide a comparative genomic sequence analysis with the syntenic region from human chromosome 4. Finally, a new BAC transgenic line indicates that the genomic region that is sufficient for rescue of the Clock mutant phenotype is no greater than 120 kb and tightly flanks the 3' end of the Clock gene.
Secretion of heterologous gene products to the culture medium ofEscherichia coli (1986)

Different constructs containing fragments of the Staphylococcal protein A gene have been introduced in Escherichia coli and the effect on expression and translocation of the various heterologous gene products have been studied. By reversing the orientation of the different protein A gene constructions in the plasmid vector, a dramatic 20-fold difference in expression was obtained, accompanied with secretion of the gene product to the culture medium. Similar results were obtained by "heat-shock" treatment of the E.coli host cells. These results suggest the presence in the protein A gene of a stress induced promoter, functional in E.coli. The system was used to efficiently secrete a fusion protein consisting of a protein A fragment and human insulin-like growth factor I (IGF-I) to the culture medium of E.coli HB101. The fusion protein was purified from the culture medium by IgG affinity chromatography in a one-step procedure giving more than 95% yield.
Application of Self-Organizing Maps in Conformational Analysis of Lipids (2001)

The characteristics of lipid assemblies are important for the functions of biological membranes. This has led to an increasing utilization of molecular dynamics simulations for the elucidation of the structural features of biomembranes. We have applied the self-organizing map (SOM) to the analysis of the complex conformational data from a 1-ns molecular dynamics simulation of PLPC phospholipids in a membrane assembly. Mapping of 1.44 million molecular conformations to a two-dimensional array of neurons revealed, without human intervention, the main conformational features in hours. Both the whole molecule and the characteristics of the unsaturated fatty acid chains were analyzed. All major structural features were easily distinguished, such as the orientational variability of the headgroup, the mainly trans state dihedral angles of the sn-1 chain, and both straight and bent conformations of the unsaturated sn-2 chain. Furthermore, presentation of the trajectory of an individual lipid molecule on the map provides information on conformational dynamics. The present results suggest that the SOM method provides a powerful tool for routinely gaining rapid insight to the main molecular conformations as well as to the conformational dynamics of any simulated molecular assembly without the requirement of a priori knowledge.
Three-Dimensional Electronic Delocalization in Chiral Conjugated Polymers (2002)

Chiral network: Poly(phenylacetylene) chains were derivatized with chiral side chains and bulky pentiptycene groups to give interlocking optically active aggregates (see figure; A forms initially and the aggregate then tightens to form B) in both solution and solid state. The resultant grid is a stable organization with high optical activity, high quantum yields, and superior detection limits for trinitrotoluene.
Multiple mechanisms involved in the large-spectrum therapeutic potential of cannabidiol in psychiatric disorders (2012)

Cannabidiol (CBD) is a major phytocannabinoid present in the Cannabis sativa plant. It lacks the psychotomimetic and other psychotropic effects that the main plant compound Δ(9)-tetrahydrocannabinol (THC) being able, on the contrary, to antagonize these effects. This property, together with its safety profile, was an initial stimulus for the investigation of CBD pharmacological properties. It is now clear that CBD has therapeutic potential over a wide range of non-psychiatric and psychiatric disorders such as anxiety, depression and psychosis. Although the pharmacological effects of CBD in different biological systems have been extensively investigated by in vitro studies, the mechanisms responsible for its therapeutic potential are still not clear. Here, we review recent in vivo studies indicating that these mechanisms are not unitary but rather depend on the behavioural response being measured. Acute anxiolytic and antidepressant-like effects seem to rely mainly on facilitation of 5-HT1A-mediated neurotransmission in key brain areas related to defensive responses, including the dorsal periaqueductal grey, bed nucleus of the stria terminalis and medial prefrontal cortex. Other effects, such as anti-compulsive, increased extinction and impaired reconsolidation of aversive memories, and facilitation of adult hippocampal neurogenesis could depend on potentiation of anandamide-mediated neurotransmission. Finally, activation of TRPV1 channels may help us to explain the antipsychotic effect and the bell-shaped dose-response curves commonly observed with CBD. Considering its safety profile and wide range of therapeutic potential, however, further studies are needed to investigate the involvement of other possible mechanisms (e.g. inhibition of adenosine uptake, inverse agonism at CB2 receptor, CB1 receptor antagonism, GPR55 antagonism, PPARγ receptors agonism, intracellular (Ca(2+)) increase, etc.), on CBD behavioural effects.
Kinetics of rod outer segment phagocytosis by cultured retinal pigment epithelial cells. Relationship to cell morphology. (1996)

Kinetics of ROS binding and ingestion differ markedly among phenotypic variants of RPE cells typically found in primary cultures at confluence. Thus, accurate quantitation requires comparison of equivalent microscopic fields or like RPE subtypes, and the heterogeneous responses of various RPE subtypes should be considered when interpreting phagocytic data obtained from entire cultures at a particular time.
Generally Applicable Self-Masked Dry Etching Technique for Nanotip Array Fabrication (2004)

Well-aligned nanotip arrays were fabricated by electron cyclotron resonance (ECR) plasma process using gas mixtures of silane, methane, argon, and hydrogen. The resultant tips have nanoscale apexes (∼1 nm) with high aspect ratios (∼50), which were achieved by simultaneous SiC nanomask formation and dry etching during ECR plasma process. This technique was applied to a variety of substrates such as silicon, polycrystalline silicon, gallium nitride, gallium phosphide, sapphire, and aluminum, indicating its general applicability. High-resolution transmission electron microscopy and Auger depth profile analyses revealed that the SiC cap, with Si:C ratio of 1:1, exhibited 3C−SiC and 2H−SiC structure on Si and GaP, respectively, with heteroepitaxial relationship. This one-step self-masked dry etching technique enables the fabrication of uniform nanotip arrays on various substrates over large area at low process temperatures, thereby demonstrating a high potential for practical industrial application.
Large-Size KCa0.8Sr0.2I3:Eu2+ Crystals: Growth and Characterization of Scintillation Properties (2016)

The newly developed KCa0.8Sr0.2I3:Eu2+ scintillator with 2.5% energy resolution at 662 keV shows great potential for use in gamma-ray spectroscopy applications, but progress toward large-size crystal growth has been hindered by cracking and inclusion problems. In this paper, we report a detailed study on the role of process variables of Bridgman growth, including grain selector designs, ampule surface treatments, and temperature gradients. It was found that crystal cracking can be effectively prevented by using a carbon-coated quartz ampule with a bent capillary. A high temperature gradient of 45 °C/cm at the solid–liquid interface can positively contribute to the suppression of the formation of visible inclusions caused by constitutional supercooling. By using optimized growth parameters, high quality 22 mm diameter KCa0.8Sr0.2I3 single crystals doped with 0.5, 1, and 3 mol % Eu2+ and 38 mm diameter KCa0.8Sr0.2I3 single crystals doped with 0.5 mol % Eu2+ were grown by the Bridgman method. The scintillation properties, including radioluminescence, light yield, energy resolution, and scintillation decay, of ϕ22 mm × 22 mm and ϕ38 mm × 35 mm samples were also investigated.
Voriconazole against fluconazole-susceptible and resistant candida isolates: in-vitro efficacy compared with that of itraconazole and ketoconazole (1998)

We compared the in-vitro activity of fluconazole, itraconazole, ketoconazole and voriconazole against 67 blood isolates of Candida spp. exhibiting a wide range of fluconazole MICs (0.125 to >64 mg/L). Voriconazole was the most potent in vitro, followed by itraconazole, ketoconazole and fluconazole. Itraconazole and voriconazole had in-vitro activity against fluconazole-susceptible and -resistant candida isolates. Higher itraconazole and voriconazole MICs were observed in isolates exhibiting higher fluconazole MICs, suggesting cross-resistance. Itraconazole and voriconazole MICs of > or =16 mg/L were observed only in Candida albicans and Candida tropicalis. Candida krusei and Candida glabrata exhibited itraconazole MICs of 0.5-1 mg/L and voriconazole MICs of 0.25-0.5 mg/L.
Hyperfractionated Radiation Therapy With or Without Concurrent Low-Dose Daily Cisplatin in Locally Advanced Squamous Cell Carcinoma of the Head and Neck: A Prospective Randomized Trial (2000)

As compared with Hfx RT alone, Hfx RT and concurrent low-dose daily CDDP offered a survival advantage, as well as improved LRPFS and DMFS.
Neisseria meningitidis produces iron-regulated proteins related to the RTX family of exoproteins (1993)

A monoclonal antibody (A4.85) which reacted with Fe-regulated proteins of Neisseria meningitidis, was used to isolate a lambda gt11 clone from N. meningitidis FAM20. Chromosomal fragments flanking the fragment expressing the A4.85 epitope were cloned, and their DNA sequences revealed a 3,345-bp open reading frame predicting a 122-kDa protein. This gene was named frpA (Fe-regulated protein). A computer similarity search of GenBank revealed high levels of similarity to members of the RTX family of cytotoxins, especially in a region of tandem 9-amino-acid repeats. These repeats are found in all members of the RTX family; similar repeats were present 13 times in the predicted FrpA protein. Antigenic relatedness between the meningococcal proteins and the RTX proteins was demonstrated by the reactivity of A4.85 with Escherichia coli hemolysin (HlyA) and Bordetella pertussis adenylate cyclase-hemolysin (CyaA). Similarly, FrpA was recognized by 9D4, a monoclonal antibody directed against B. pertussis CyaA. In addition to the frpA gene, a second gene (frpC) produced a larger RTX-related protein. The frpA and frpC loci were mutagenized in strain FAM20, resulting in the loss of RTX-related proteins. A 120-kDa protein was expressed from the reconstructed frpA gene in E. coli. The biological function of FrpA is unknown, but its similarity to other RTX toxins suggests that it may play an important role in the pathogenesis of meningococcal infection.