gebhart/patrepeval huggingface dataset:
Inducible operation of the erythropoietin 3' enhancer in multiple cell lines: evidence for a widespread oxygen-sensing mechanism. (1993)

Adaptive responses to hypoxia occur in many biological systems. A well-characterized example is the hypoxic induction of the synthesis of erythropoietin, a hormone which regulates erythropoiesis and hence blood oxygen content. The restricted expression of the erythropoietin gene in subsets of cells within kidney and liver has suggested that this specific oxygen-sensing mechanism is restricted to specialized cells in those organs. Using transient transfection of reporter genes coupled to a transcriptional enhancer lying 3' to the erythropoietin gene, we show that an oxygen-sensing system similar, or identical, to that controlling erythropoietin expression is wide-spread in mammalian cells. The extensive distribution of this sensing mechanism contrasts with the restricted expression of erythropoietin, suggesting that it mediates other adaptive responses to hypoxia.
Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers fromArabidopsis thaliana (1990)

Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers from Arabidopsis thaliana Get access Inge Untried, Inge Untried Instit füur Botanik der Universitat Wien, Abteilung Cytologie und GenetikRennweg 14, A-1030 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Peter Gruendler Peter Gruendler Instit füur Botanik der Universitat Wien, Abteilung Cytologie und GenetikRennweg 14, A-1030 Vienna, Austria Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 13, 11 July 1990, Page 4011, https://doi.org/10.1093/nar/18.13.4011 Published: 11 July 1990
Metabolism of High Density Lipoproteins Reconstituted with [3H]Cholesteryl Ester and [14C]Cholesterol in the Rat, with Special Reference to the Ovary* (1985)

In order to study the metabolism of high density lipoprotein (HDL)-carried sterol in the rat, human HDL was reconstituted with [14C]cholesterol and [3H]cholesteryl ester. After iv injection into immature PMSG-human CG primed rats pretreated with 4-aminopyrazolopyrimidine and aminoglutethimide, there was time-dependent accumulation of 3H and 14C in various organs which reached a maximum by 15-90 min. On a milligram wet weight basis, uptake of 3H and 14C was greatest in the adrenals, next in ovaries, followed by the liver, with little uptake by kidneys and spleen. On an organ basis, accumulation was greatest by the liver. At 15-45 min post injection, 60% of the 3H in the ovary was in free sterol, indicating hydrolysis of the accumulated cholesteryl esters, whereas 95% of the 3H in serum remained in sterol esters associated with HDL. Coadministration of excess unlabeled HDL, but not human low density lipoprotein, reduced accumulation of radioactivity by the ovaries and adrenals by 60%, indicating a specific and saturable uptake process. Granulosa cells cultured in lipoprotein-deficient medium with reconstituted HDL formed 3H- and 14C-labeled 20 alpha-hydroxypregn-4-en-3-one. Over a 24-h period, utilization of both [14C]cholesterol and [3H]cholesteryl ester was linear, but rates of utilization of the two sterol moieties were not parallel. There was preferential uptake and utilization of free sterol. A dose-response study demonstrated a Michaelis-Menten constant (Km) of 40-60 micrograms sterol/ml for both free and esterified cholesterol. Lysosomotropic agents (chloroquine and NH4Cl) had no effect on utilization of either free or esterified cholesterol for steroidogenesis but reduced degradation of 125I-labeled low density lipoprotein apoprotein. These findings lend further support to the concept of a distinct HDL pathway in steroidogenic cells of the rat, which involves 1) preferential uptake and utilization of free cholesterol from HDL and 2) does not require lysosomal activity.
Proteomic analysis of renal calculi indicates an important role for inflammatory processes in calcium stone formation (2008)

Even though renal stones/calculi occur in approximately 10% of individuals, they are an enormous economic burden to the entire US health system. While the relative metabolic composition of renal calculi is generally known, there is no clear understanding of the genetics of renal stone formation, nor are there clear prognostic indicators of renal stone formation. The application of proteomics to the analysis of renal calculi axiomatically holds that insight into renal stone pathobiology can be gained by a more comprehensive understanding of renal calculus protein composition. We analyzed isolated renal stone matrix proteins with mass spectrometric and immunohistochemical methods identifying 158 proteins with high confidence, including 28 common proteins. The abundant proteins included those identified previously in stones and proteins identified here for the first time, such as myeloid lineage-specific, integral membrane and lipid regulatory proteins. Pathway analyses of all proteins identified suggested that a significant fraction of the most abundant matrix proteins participate in inflammatory processes. These proteomic results support the hypothesis that stone formation induces a cellular inflammatory response and the protein components of this response contribute to the abundant stone matrix proteome.
Human thymic epithelial cells express an endogenous lectin, galectin-1, which binds to core 2 O-glycans on thymocytes and T lymphoblastoid cells. (1995)

Thymic epithelial cells play a crucial role in the selection of developing thymocytes. Thymocyte-epithelial cell interactions involve a number of adhesion molecules, including members of the integrin and immunoglobulin superfamilies. We found that human thymic epithelial cells synthesize an endogenous lectin, galectin-1, which binds to oligosaccharide ligands on the surface of thymocytes and T lymphoblastoid cells. Binding of T lymphoblastoid cells to thymic epithelial cells was inhibited by antibody to galectin-1 on the epithelial cells, and by two antibodies, T305 and 2B11, that recognize carbohydrate epitopes on the T cell surface glycoproteins CD43 and CD45, respectively. T lymphoblastoid cells and thymocytes bound recombinant galectin-1, as demonstrated by flow cytometric analysis, and lectin binding was completely inhibited in the presence of lactose. The degree of galectin-1 binding to thymocytes correlated with the maturation stage of the cells, as immature thymocytes bound more galectin-1 than did mature thymocytes. Preferential binding of galectin-1 to immature thymocytes may result from regulated expression of preferred oligosaccharide ligands on those cells, since we found that the epitope recognized by the T305 antibody, the core 2 O-glycan structure on CD43, was expressed on cortical, but not medullary cells. The level of expression of the UDP-GlcNAc:Gal beta 1,3GalNAc-R beta 1, 6GlcNAc transferase (core 2 beta 1, 6 GlcNAc transferase, or C2GnT), which creates the core 2 O-glycan structure, correlated with the glycosylation change between cortical and medullary cells. Expression of mRNA encoding the C2GnT was high in subcapsular and cortical thymocytes and low in medullary thymocytes, as demonstrated by in situ hybridization. These results suggest that galectin-1 participates in thymocyte-thymic epithelial cell interactions, and that this interaction may be regulated by expression of relevant oligosaccharide ligands on the thymocyte cell surface.
Influence of kinetic parameters on the textural and chemical properties of silsesquioxane materials obtained by sol-gel process (1999)

The hydrolytic sol-gel polymerization of a ‘rigid’ molecular precursor 1,4-C 6 H 4 [Si(OMe) 3 ] 2 1 and a more ‘flexible’ one 1,4-C 6 H 4 [CH 2 CH 2 Si(OMe) 3 ] 2 2 was investigated varying the experimental conditions. Two solvents, MeOH and THF, were employed. The influence of the catalyst has been determined by using TBAF (tetrabutylammonium fluoride) or NH 4 F as nucleophilic catalysts, NH 4 OH and NaOH as basic catalysts and HCl as acid catalyst. The effect of concentration of the precursor was also studied. Molecular precursor 1 led always to hydrophilic solids with similar degrees of condensation (63-67%). In all cases high specific surface areas and poor chemical reactivity towards Cr(CO) 6 were observed and the solvent had an influence on the porosity. By contrast, the precursor 2 led to hydrophobic solids and the texture, the degree of condensation and the reactivity with Cr(CO) 6 were strongly dependent on the solvent, the catalyst and the concentration. In MeOH no significant specific surface areas were observed, whereas in THF a high specific surface area was observed with TBAF catalysis at both precursor concentrations studied. Degrees of condensation were higher in THF. All the kinetic parameters involved in the hydrolytic sol-gel polymerization of molecular organosilicon precursors were of importance on the properties of the resulting solids, the main factor being the geometry of the organic unit.
Biliverdin Reductase: PKC Interaction at the Cross-Talk of MAPK and PI3K Signaling Pathways (2007)

Biliverdin reductase (BVR) was characterized some 25 years ago as a unique dual-cofactor/pH-dependent enzyme that catalyzes the reduction of biliverdin-IXa. Our knowledge of functions of BVR has increased enormously in recent years. hBVR functions in the IR/IGF-1-controlled regulation of the MAPK and PI3K cascades that are linked by the PKC enzymes. The first of the two culminates in the activation of transcription factors for oxidative stress-responsive genes, including ho-1, where BVR functions as both a bZip (basic leucine zipper) transcription factor and a kinase. The second pathway amplifies the insulin/growth-factor signal for protein/DNA synthesis and glucose transport downstream of PI3K. hBVR is a transactivator of PKC-betaII, and thus an integral component of the "activation loop" linking MAPK, PKC-betaII, and PI3K to insulin/growth-factor signaling. The emergence of biliverdin and bilirubin as a newly defined category of modulators of cell signaling and kinase activity further underscores the critical input of hBVR in the response of intracellular pathways into the external environment. Structural features of BVR and recent findings relevant to its function in cell-signaling pathways are reviewed here and are intended to complement a recent commentary on the role of BVR in linking heme metabolism and cell signaling.
Sub-250 nm light emission and optical gain in AlGaN materials (2013)

We investigate the deep-UV optical emission and gain properties of AlxGa1−xN/AlyGa1−yN multiple quantum wells structures. These structures were grown by plasma-assisted molecular-beam epitaxy on 6H-SiC substrates, under a growth mode which promotes various degrees of band-structure potential fluctuations in the form of cluster-like features within the wells. The degree of inhomogeneities in these samples was determined by cathodoluminescence mapping. We measured the TE-polarized amplified spontaneous emission in the sample with cluster-like features and quantified the optical absorption/gain coefficients and gain spectra by the variable stripe length technique under ultrafast optical pumping. A maximum net modal gain of about 120 cm−1 is measured at 4.9 eV. On the other hand, we found that samples with homogeneous quantum wells lead to absorption. Numerical simulations are performed to support our experimental findings.
Pentosidine: A molecular marker for the cumulative damage to proteins in diabetes, aging, and uremia (1991)

Collagen undergoes progressive browning with age and diabetes characterized by yellowing, fluorescence, and cross-linking. The present research was undertaken in order to investigate the nature of the collagen-linked fluorescence. Human collagen was exhaustively cleaved into peptides by enzymatic digestion. Upon purification, a highly fluorescent chromophore was identified and purified from old human collagen. Structure elucidation revealed the presence of an imidazo [4,5-b] pyridinium-type structure acting as a cross-link between arginine, lysine, and a pentose. This advanced glycosylation end-product and protein cross-link results from the reaction of pentoses with proteins and was named pentosidine. Further work indicated that long-term glycosylation of proteins with hexoses also leads to pentosidine formation through sugar fragmentation. The proposed mechanism of pentosidine formation involves the dehydration of the pentose-derived Amadori compound to form an intermediate which is attacked under base catalysis by the guanido group of arginine. The strict requirement for the Amadori rearrangement is uncertain. However, oxidation is definitely involved since pentosidine is not formed in the absence of oxygen. Five-carbon sugars contributing to pentosidine formation could be formed from larger sugars by oxidative fragmentation or from trioses, tetroses, and ketoses by condensation and/or reverse aldol reactions. Pentosidine increases exponentially in human skin at autopsy. Mean age-adjusted skin levels were significantly increased in subjects with uremia and especially in type 1 diabetics with uremia vs. controls. In skin biopsy, levels were significantly elevated in all diabetic (type 1) vs. control subjects. The highest degree of association was with the cumulative grade of diabetic complication (retinopathy, nephropathy, arterial stiffness, and joint stiffness). Pentosidine also forms in various proteins other than collagen, although to a much lesser extent. In blood, pentosidine is mainly associated with plasma proteins and is highly elevated during uremia. In the lens, it is associated with both water-soluble and -insoluble protein fractions and is especially elevated during brunescent cataract formation. The origin of pentosidine in vivo is uncertain. Evidence suggests that the pentoses are the most reactive sugars in pentosidine formation in vitro; however, the origin and importance of free pentoses in vivo, especially during the diabetic state, are not certain. Possible origins include hemolysis and/or a defect in the primary pentose metabolism.(ABSTRACT TRUNCATED AT 400 WORDS)
Vision-Based State Estimation and Trajectory Control Towards High-Speed Flight with a Quadrotor (2013)

This paper addresses the development of a lightweight autonomous quadrotor that uses cameras and an inexpensive IMU as its only sensors and onboard processors for estimation and control. We describe a fully-functional, integrated system with a focus on robust visual-inertial state estimation, and demonstrate the quadrotor's ability to autonomously travel at speeds up to 4 m/s and roll and pitch angles exceeding 20 . The performance of the proposed system is demonstrated via challenging experiments in three dimensional indoor environments.
‘Psy’ research beyond late modernity: towards praxis-congruent research (2010)

Lees and Freshwater's Practitioner-based Research is a significant intervention into the struggle for the ‘research soul’ of the psychological therapies. Positivistic notions beloved of the managerialist ‘audit culture’, centred on the totem of ‘evidence-based practice’, are increasingly colonizing psy research, creating a new ‘regime of truth’ that privileges ‘standards’, ‘competencies’ and ‘quality assurance’, and presages a shift in the locus of power away from practitioners' professional autonomy and towards managerialist bureaucracy. In arguing that no one (‘scientific’) paradigm should necessarily be assumed to be more ‘valid’ than a multiplicity of possible others, they advocate the practitioner's voice having at least equal validity to that of academics and bureaucrats, aiming to establish an ‘epistemology of practice’ that redresses a balance that has become too skewed towards uncritical, and in many ways anti-human, ‘technical rationality’. This review article explores the rationale for this shift, and finds it compelling and convincing. It is also argued here that great benefit can be gained for the future flourishing of psy research from building bridges to other radical-critical research traditions and innovations in late-modern culture. Copyright © 2010 John Wiley & Sons, Ltd.
Efficacy, safety, and tolerability of quetiapine in patients with schizophrenia. (2002)

Schizophrenia is a serious and disabling psychiatric disorder affecting approximately 1% of the world's population, with its economic cost in the United States alone estimated to exceed that of all cancers combined. The new generation of atypical antipsychotics introduced over the past decade have comparable or greater efficacy than traditional antipsychotics in treating the psychotic symptoms of schizophrenia and a much improved neurologic side effect profile. Quetiapine, the fourth atypical antipsychotic marketed in the United States, was approved by the U.S. Food and Drug Administration in September 1997 and is also currently approved in over 70 countries worldwide for the treatment of psychosis associated with schizophrenia. This article will review the clinical trials examining the efficacy, safety, and tolerability of quetiapine in the treatment of patients with schizophrenia.
Lambda Int Protein Bridges Between Higher Order Complexes at Two Distant Chromosomal Loci att L and att R (1992)

The excisive recombination reaction of bacteriophage lambda involves a specific and efficient juxtaposition of two distant higher order protein-DNA complexes on the chromosome of Escherichia coli. These complexes, which mediate synapsis and strand exchange, consist of two DNA sequences, attL and attR, the bivalent DNA binding protein Int, and the sequence-specific DNA bending proteins, IHF, Xis, and Fis. The protein-protein and protein-DNA interactions within, and between, these complexes were studied by various biochemical techniques and the patterns of synergism among pairs of mutants with marginally impaired recombination function were analyzed. The DNA bending proteins facilitated long-range tethering of high- and low-affinity DNA sites by the bivalent Int protein, and a specific map is proposed for the resulting Int bridges. These structural motifs provide a basis for postulating the mechanism of site-specific recombination and may also be relevant to other pathways in which two distant chromosomal sites become associated.
ADAM8 as a drug target in pancreatic cancer (2015)

Pancreatic ductal adenocarcinoma (PDAC) has a grim prognosis with <5% survivors after 5 years. High expression levels of ADAM8, a metalloprotease disintegrin, are correlated with poor clinical outcome. We show that ADAM8 expression is associated with increased migration and invasiveness of PDAC cells caused by activation of ERK1/2 and higher MMP activities. For biological function, ADAM8 requires multimerization and associates with β1 integrin on the cell surface. A peptidomimetic ADAM8 inhibitor, BK-1361, designed by structural modelling of the disintegrin domain, prevents ADAM8 multimerization. In PDAC cells, BK-1361 affects ADAM8 function leading to reduced invasiveness, and less ERK1/2 and MMP activation. BK-1361 application in mice decreased tumour burden and metastasis of implanted pancreatic tumour cells and provides improved metrics of clinical symptoms and survival in a Kras(G12D)-driven mouse model of PDAC. Thus, our data integrate ADAM8 in pancreatic cancer signalling and validate ADAM8 as a target for PDAC therapy.
Genetic Analysis and Gene Fine Mapping of Yellow-Green Leaf Mutant ygl80 in Rice (2014)

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Photovoltaic Technologies Beyond the Horizon: Optical Rectenna Solar Cell, Final Report, 1 August 2001-30 September 2002 (2003)

ITN Energy Systems is developing next-generation solar cells based on the concepts of an optical rectenna. ITN's optical rectenna consists of two key elements: (1) an optical antenna to efficiently absorb the incident solar radiation, and (2) a high-frequency metal-insulator-metal (MIM) tunneling diode that rectifies the AC field across the antenna, providing DC power to an external load. The combination of a rectifying diode at the feedpoints of a receiving antenna is often referred to as a rectenna. Rectennas were originally proposed in the 1960s for power transmission by radio waves for remote powering of aircraft for surveillance or communications platforms. Conversion efficiencies greater than 85% have been demonstrated at radio frequencies (efficiency defined as DC power generated divided by RF power incident on the device). Later, concepts were proposed to extend the rectennas into the IR and optical region of the electromagnetic spectrum for use as energy collection devices (optical rectennas).
HLA-Ig Based Artificial Antigen Presenting Cells for Efficient <em>ex vivo</em> Expansion of Human CTL (2011)

CTL with optimal effector function play critical roles in mediating protection against various intracellular infections and cancer. However, individuals may exhibit suppressive immune microenvironment and, in contrast to activating CTL, their autologous antigen presenting cells may tend to tolerize or anergize antigen specific CTL. As a result, although still in the experimental phase, CTL-based adoptive immunotherapy has evolved to become a promising treatment for various diseases such as cancer and virus infections. In initial experiments ex vivo expanded CMV (cytomegalovirus) specific CTL have been used for treatment of CMV infection in immunocompromised allogeneic bone marrow transplant patients. While it is common to have life-threatening CMV viremia in these patients, none of the patients receiving expanded CTL develop CMV related illness, implying the anti-CMV immunity is established by the adoptively transferred CTL. Promising results have also been observed for melanoma and may be extended to other types of cancer. While there are many ways to ex vivo stimulate and expand human CTL, current approaches are restricted by the cost and technical limitations. For example, the current gold standard is based on the use of autologous DC. This requires each patient to donate a significant number of leukocytes and is also very expensive and laborious. Moreover, detailed in vitro characterization of DC expanded CTL has revealed that these have only suboptimal effector function. Here we present a highly efficient aAPC based system for ex vivo expansion of human CMV specific CTL for adoptive immunotherapy (Figure 1). The aAPC were made by coupling cell sized magnetic beads with human HLA-A2-Ig dimer and anti-CD28mAb. Once aAPC are made, they can be loaded with various peptides of interest, and remain functional for months. In this report, aAPC were loaded with a dominant peptide from CMV, pp65 (NLVPMVATV). After culturing purified human CD8(+) CTL from a healthy donor with aAPC for one week, CMV specific CTL can be increased dramatically in specificity up to 98% (Figure 2) and amplified more than 10,000 fold. If more CMV-specific CTL are required, further expansion can be easily achieved by repetitive stimulation with aAPC. Phenotypic and functional characterization shows these expanded cells have an effector-memory phenotype and make significant amounts of both TNFα and IFNγ (Figure 3).