gebhart/patrepeval huggingface dataset:
Chromatin immunoprecipitation (ChIP) scanning identifies primary glucocorticoid receptor target genes (2004)

The global physiological effects of glucocorticoids are well established, and the framework of transcriptional regulation by the glucocorticoid receptor (GR) has been described. However, the genes directly under GR control that trigger these physiological effects are largely unknown. To address this issue in a single cell type, we identified glucocorticoid-responsive genes in A549 human lung adenocarcinoma cells by microarray analysis and quantitative real-time PCR. Reduction of GR expression by RNA interference diminished the effects of dexamethasone on all tested target genes, thus confirming the essential role of GR in glucocorticoid-regulated gene expression. To identify primary GR target genes, in which GR is a component of the transcriptional regulatory complex, we developed a strategy that uses chromatin immunoprecipitation to scan putative regulatory regions of target genes for sites occupied by specifically bound GR. We screened 11 glucocorticoid-regulated genes, and we identified GR-binding regions for eight of them (five induced and three repressed). Thus, our approach provides a means for rapid identification of primary GR target genes and glucocorticoid-response elements, which will facilitate analyses of transcriptional regulatory mechanisms and determination of hormone-regulated gene networks.
High-power visible GaAlAs lasers with self-aligned strip buried heterostructure (1984)

Transverse-mode-stabilized GaAlAs high-power visible lasers have been developed in such a way as to have a self-aligned strip buried heterostructure. Analysis of their waveguide properties shows that asymmetric AlAs composition in cladding layers, as well as a thin active layer, are important for increasing optical spot size and stabilizing the transverse mode. Lasers with such a waveguide structure operate in the fundamental transverse mode up to an output power as high as 30 mW, and at a lasing wavelength of around 780 nm under cw operation. In addition, fundamental transverse mode operation up to 75 mW under cw conditions has been achieved with optimization of facet reflectivities.
Interplay among Folding, Sequence, and Lipophilicity in the Antibacterial and Hemolytic Activities of α/β-Peptides (2006)

Host-defense peptides inhibit bacterial growth but manifest relatively little toxicity toward eukaryotic cells. Many host-defense peptides adopt alpha-helical conformations in which cationic side chains and lipophilic side chains are segregated to distinct regions of the molecular surface ("globally amphiphilic helices"). Several efforts have been made to develop unnatural oligomers that mimic the selective antibacterial activity of host-defense peptides; these efforts have focused on the creation of molecules that are globally amphiphilic in the preferred conformation. One such endeavor, from our laboratories, focused on helix-forming alpha/beta-peptides, i.e., oligomers containing a 1:1 pattern of alpha- and beta-amino acid residues in the backbone [Schmitt, M. A.; Weisblum, B.; Gellman, S. H. J. Am. Chem. Soc. 2004, 126, 6848-6849]. We found, unexpectedly, that the most favorable biological activity profile was displayed by a "scrambled" sequence, which was designed not to be able to form a globally amphiphilic helix. Here we report new data, involving an expanded set of alpha/beta-peptides, from experiments designed to elucidate the origins of this surprising result. In addition, we evaluate the susceptibility of alpha/beta-peptides to proteolytic degradation. Our results support the hypothesis that the ability to adopt a globally amphiphilic helical conformation is not a prerequisite for selective antibacterial activity. This conclusion represents a significant advance in our understanding of the relationship among molecular composition, conformation, and biological activity. Our results should therefore influence the design of other unnatural oligomers intended to function as antibacterial agents.
N-acetyl-aspartylglutamate (NAAG) elicits rapid increase in intraneuronal Ca2+ in vitro (1994)

N-acetyl-aspartylglutamate (NAAG) is an acidic dipeptide found at high concentrations almost exclusively in the brain and spinal cord. There is evidence that NAAG is an excitatory neurotransmitter/neuromodulator. On the other hand, the identification and characterization of an enzyme in the nervous system which hydrolyzes NAAG to liberate glutamic acid (Glu) has led to an alternative hypothesis that the dipeptide might serve as a precursor of the excitatory amino acid. Using an interactive laser cytometer to quantitate changes in intraneuronal Ca2+ in individual neurons, we demonstrate that NAAG, at the concentrations at which it is found in the brain, promotes a rapid increase in intraneuronal Ca2+. NAAG-induced effects are completely dependent on the presence of Ca2+ in the bathing medium and are inhibited by NMDA receptor and channel antagonists. Several factors have led us to conclude that it is NAAG itself, and not NAAG-derived Glu, which is responsible for the observed effects in this system.
Inhibition of Wnt/β-catenin signaling suppresses myofibroblast differentiation of lung resident mesenchymal stem cells and pulmonary fibrosis (2018)

An emerging paradigm proposes a crucial role for lung resident mesenchymal stem cells (LR-MSCs) via a fibroblastic transdifferentiation event in the pathogenesis of idiopathic pulmonary fibrosis (IPF). Aberrant activation of Wnt/β-catenin signaling occurs in virtually all fibrotic lung diseases and is relevant to the differentiation of mesenchymal stem cells (MSCs). In vitro, by measuring the protein levels of several key components involved in Wnt/β-catenin signaling, we confirmed that this signaling pathway was activated in the myofibroblast differentiation of LR-MSCs. Targeted inhibition of Wnt/β-catenin signaling by a small molecule, ICG-001, dose-dependently impeded the proliferation and transforming growth factor-β1 (TGF-β1)-mediated fibrogenic actions of LR-MSCs. In vivo, ICG-001 exerted its lung protective effects after bleomycin treatment through blocking mesenchymal-myofibroblast transition, repressing matrix gene expression, and reducing cell apoptosis. Moreover, delayed administration of ICG-001 attenuated bleomycin-induced lung fibrosis, which may present a promising therapeutic strategy for intervention of IPF. Interestingly, these antifibrotic actions of ICG-001 are operated by a mechanism independent of any disruption of Smad activation. In conclusion, our study demonstrated that Wnt/β-catenin signaling may be an essential mechanism underlying the regulation of myofibroblast differentiation of LR-MSCs and their further participation in the development of pulmonary fibrosis.
Too many shots? Parent, nurse, and physician attitudes toward multiple simultaneous childhood vaccinations (1994)

Most parents, nurses, and physicians are uncomfortable with three simultaneous injections for children. This discomfort may be a significant barrier to the adoption of the new immunization recommendations. The development of effective combination vaccines should be a research priority.
SUPERCOMPUTER INVESTIGATIONS OF A CHAOTIC ENCRYPTION ALGORITHM (1991)

A non-linear pseudo-random number generator based on chaos theory [3] was criticized for producing cycling keys if used with low-precision arithmetic [4]. We present here the results of a numerical investigation of the algorithm's properties using a Cray Y-MP machine. This suggests that the cycling problem can be combatted to any desired degree. We conclude that the generator is still of cryptographic interest.
Small-Molecule NSC59984 Restores p53 Pathway Signaling and Antitumor Effects against Colorectal Cancer via p73 Activation and Degradation of Mutant p53 (2015)

The tumor-suppressor p53 prevents cancer development via initiating cell-cycle arrest, cell death, repair, or antiangiogenesis processes. Over 50% of human cancers harbor cancer-causing mutant p53. p53 mutations not only abrogate its tumor-suppressor function, but also endow mutant p53 with a gain of function (GOF), creating a proto-oncogene that contributes to tumorigenesis, tumor progression, and chemo- or radiotherapy resistance. Thus, targeting mutant p53 to restore a wild-type p53 signaling pathway provides an attractive strategy for cancer therapy. We demonstrate that small-molecule NSC59984 not only restores wild-type p53 signaling, but also depletes mutant p53 GOF. NSC59984 induces mutant p53 protein degradation via MDM2 and the ubiquitin-proteasome pathway. NSC59984 restores wild-type p53 signaling via p73 activation, specifically in mutant p53-expressing colorectal cancer cells. At therapeutic doses, NSC59984 induces p73-dependent cell death in cancer cells with minimal genotoxicity and without evident toxicity toward normal cells. NSC59984 synergizes with CPT11 to induce cell death in mutant p53-expressing colorectal cancer cells and inhibits mutant p53-associated colon tumor xenograft growth in a p73-dependent manner in vivo. We hypothesize that specific targeting of mutant p53 may be essential for anticancer strategies that involve the stimulation of p73 in order to efficiently restore tumor suppression. Taken together, our data identify NSC59984 as a promising lead compound for anticancer therapy that acts by targeting GOF-mutant p53 and stimulates p73 to restore the p53 pathway signaling.
Information theoretical probe selection for hybridisation experiments (2000)

A description of the oligonucleotide fingerprinting pipeline is published on our web-page http://www.molgen.mpg.de/ approximately ag_onf/met.htm. An executable of the algorithm and probe lists designed for human and rodents can be downloaded from the ftp-site ftp://ftp.molgen.mpg.de/pub/mpimg/probe_design/.
Imaging polymers with supercritical carbon dioxide (1997)

In lithographic techniques for forming nanostructures in surface and polymer thin films, the selectivity of the solvent becomes increasingly important as the target dimensions decrease. Polymer‐based developers. The Figure shows the SC CO 2 –developed image of a copolymer of pentafluoroproyl methacrylate and tert ‐butyl methacrylate. magnified image
Primary Prevention of Cardiovascular Disease and Type 2 Diabetes in Patients at Metabolic Risk: An Endocrine Society Clinical Practice Guideline (2008)

Healthcare providers should incorporate into their practice concrete measures to reduce the risk of developing CVD and T2DM. These include the regular screening and identification of patients at metabolic risk (at higher risk for both CVD and T2DM) with measurement of blood pressure, waist circumference, fasting lipid profile, and fasting glucose. All patients identified as having metabolic risk should undergo 10-yr global risk assessment for either CVD or coronary heart disease. This scoring will determine the targets of therapy for reduction of apolipoprotein B-containing lipoproteins. Careful attention should be given to the treatment of elevated blood pressure to the targets outlined in this guideline. The prothrombotic state associated with metabolic risk should be treated with lifestyle modification measures and in appropriate individuals with low-dose aspirin prophylaxis. Patients with prediabetes (impaired glucose tolerance or impaired fasting glucose) should be screened at 1- to 2-yr intervals for the development of diabetes with either measurement of fasting plasma glucose or a 2-h oral glucose tolerance test. For the prevention of CVD and T2DM, we recommend that priority be given to lifestyle management. This includes antiatherogenic dietary modification, a program of increased physical activity, and weight reduction. Efforts to promote lifestyle modification should be considered an important component of the medical management of patients to reduce the risk of both CVD and T2DM.
Baculovirus-mediated expression of bacterial genes in dipteran and mammalian cells (1985)

A recombinant baculovirus containing the Escherichia coli chloramphenicol acetyltransferase (CAT) gene under the control of the Rous sarcoma virus long terminal repeat promoter and the E. coli beta-galactosidase gene under the control of the very late baculoviral polyhedrin promoter was used to determine if Autographa californica nuclear polyhedrosis virus, a baculovirus of Lepidoptera, can enter and express viral DNA in dipteran (Drosophila sp.) and mammalian (Mus sp.) cells that are considered refractory to baculovirus replication. Following infection, CAT gene expression was observed in both dipteran and mammalian cells, but expression in the mammalian cell line was less than 0.05% of that observed in either dipteran or lepidopteran cells. Although the level of CAT gene expression was similar in permissive lepidopteran and nonpermissive dipteran cells, expression of beta-galactosidase activity from the late polyhedrin promoter in dipteran or mammalian cells was less than 0.3% of the levels observed in lepidopteran cells. These results indicate that foreign gene expression in nonpermissive cells is promoter dependent and that late viral gene expression is restricted in these cells. The Rous sarcoma virus long terminal repeat allows substantial CAT gene expression in both a D. melanogaster cell line and Aedes aegypti midgut cells. Baculovirus DNA undergoes a limited number of replications in Drosophila cells. The results are relevant to baculovirus host range, the safety of baculoviruses as pesticides, and the development of baculovirus pesticides with expanded host ranges.
Evidence for involvement of tumor necrosis factor‐α in apoptotic death of bone marrow cells in myelodysplastic syndromes (1999)

We previously reported excessive apoptosis and high levels of tumor necrosis factor-alpha (TNF-alpha) in the bone marrows of patients with myelodysplastic syndromes (MDS), using histochemical techniques. The present studies provide further circumstantial evidence for the involvement of TNF-alpha in apoptotic death of the marrow cells in MDS. Using our newly developed in situ double-labeling technique that sequentially employs DNA polymerase (DNA Pol) followed by terminal deoxynucleotidyl transferase (TdT) to label cells undergoing apoptosis, we have characterized DNA fragmentation patterns during spontaneous apoptosis in MDS bone marrow and in HL60 cells treated with TNF-alpha or etoposide (VP16). Clear DNA laddering detected by gel electrophoresis in MDS samples confirmed the unique length of apoptotic DNA fragments (180-200 bp). Surprisingly, however, phenotypically heterogeneous population of MDS cells as well as the homogenous population of HL60 cells showed three distinct labeling patterns after double labeling--only DNA-Pol reaction, only TdT reaction, and a combined DNA Pol + TdT reaction, albeit in different cohorts of cells. Each labeling pattern was found at all morphological stages of apoptosis. MDS mononuclear cells, during spontaneous apoptosis in 4 hr cultures, showed highest increase in double-labeled cells (DNA Pol + TdT reaction). Interestingly, this was paralleled by TNF-alpha-induced apoptosis in HL60 cells. In contrast, VP16 treatment of HL60 cells led to increased apoptosis in cells showing only TdT reaction. The double-labeling technique was applied to normal bone marrow and peripheral blood mononuclear cells after treatment with known endonucleases that specifically cause 3' recessed (BamHI), 5' recessed (PstI), or blunt ended (DraI) double-stranded DNA breaks. It was found that the DNA-Pol reaction in MDS and HL60 cells corresponds to 3' recessed DNA fragments, the TdT reaction to 5' recessed and/or blunt ended fragments, and a combined "DNA Pol + TdT reaction" corresponds to a copresence of 3' recessed with 5' recessed and/or blunt ended fragments. Clearly, therefore, apoptotic DNA fragments, in spite of a unique length, may have differently staggered ends that could be cell (or tissue) specific and be selectively triggered by different inducers of apoptosis. The presence of TNF-alpha-inducible apoptotic DNA fragmentation pattern in MDS supports its involvement in these disorders and suggests that anti-TNF-alpha (or anticytokine) therapy may be of special benefit to MDS patients, where no definitive treatment is yet available.
Role of bradykinin in cardiac functional protection after global ischemia-reperfusion in rat heart (1995)

We have reported that cardiac preconditioning against ischemia-reperfusion (IR) can be induced by transient ischemia (TI) and alpha 1-adrenoreceptor stimulation, both mediated by protein kinase C (PKC) (Mitchell, M., X. Meng, C. Parker, E. Brew, A. Harken, and A. Banerjee. Circ. Res. 76: 73-81, 1995). Our study objective was to explore the mechanism of endogenous preconditioning and address the role of PKC activation in bradykinin-mediated cardiac functional protection. Isolated rat heart was used to assess the effects of exogenous bradykinin, TI, selective B2-receptor blocker, and PKC antagonism on cardiac functional recovery after a global IR injury. Final recovery of developed pressure was improved in hearts treated with bradykinin and TI compared with controls. Bradykinin- and TI-mediated preconditioning was eliminated with coinfusion of the B2-receptor antagonist. Further evaluation of bradykinin-mediated preconditioning revealed that PKC blockade also eliminated functional protection. Immunofluorescent stains of bradykinin-treated hearts demonstrated translocation and activation of specific PKC isoforms in the preconditioned heart. We conclude that TI-mediated preconditioning involves intrinsic cardiac bradykinin receptor stimulation. Bradykinin, through the B2 receptor, initiates a series of intracellular events culminating in the activation of PKC.
The influence of spacers on forces exerted on the abutment teeth of complete mandibular overdentures (1990)

The avoidance of lateral forces on overdenture retainers is essential to prevent pathological change in the supporting tissues of the root abutment. In this study, the influence of spacer thickness on the vertical and lateral forces exerted on overdenture abutments was examined clinically. Two subjects with an edentulous maxilla, two canines and a left first premolar remaining in the mandible were selected for the experiment. The anchor type attachment was embedded in the left canine portion of the denture base. The transducer used for the previous study (Ogata et al., 1990), was embedded in this left canine portion. The transducer could detect the magnitude and direction of lateral forces exerted on an abutment tooth parallel to the Camper's plane. The other transducer was embedded in the left first mandibular premolar area, and could detect vertical forces exerted on the abutment tooth perpendicular to the Camper's plane. Furthermore, the transducer could change the space between a denture base and an abutment tooth to 1.5 mm, 0.6 mm or 0.3 mm. Therefore measurements could be made in the same way as if three experimental dentures had been used with a different thickness spacer. Recordings of forces were taken during food chewing, using each spacer on the day of denture insertion and twice at intervals of 1-2 weeks thereafter. The results demonstrated that as spacer thickness decreased, the magnitude of the lateral forces decreased, while the magnitude of the vertical forces increased. These findings suggest that a large part of the lateral component of forces exerted on an abutment tooth could be converted into a vertical component by using a thinner spacer.
Application of an ultrathin LiF/Al bilayer in organic surface-emitting diodes (2001)

Organic surface-emitting diodes have been constructed with a multilayer stacked cathode consisting of (1) an ultrathin LiF/Al bilayer acting as an effective electron injector, (2) an optically low-loss and electrically conducting silver intermediate layer for sheet resistance reduction, and (3) a transparent and nonconducting capping layer for refractive index matching to optimize optical transmission. The entire cathode structure is prepared by conventional thermal evaporation without incurring radiation damage, and the resulting organic surface-emitting diodes exhibit superior electrical and optical characteristics.
Macrophage-specific expression of group IIA sPLA2 results in accelerated atherogenesis by increasing oxidative stress (2005)

Group IIA secretory phospholipase A2 (sPLA2) is an acute-phase protein mediating decreased plasma HDL cholesterol and increased atherosclerosis. This study investigated the impact of macrophage-specific sPLA2 overexpression on lipoprotein metabolism and atherogenesis. Macrophages from sPLA2 transgenic mice have 2.5 times increased rates of LDL oxidation (thiobarbituric acid-reactive substances formation) in vitro (59 +/- 5 vs. 24 +/- 4 nmol malondialdehyde/mg protein; P < 0.001) dependent on functional 12/15-lipoxygenase (12/15-LO). Low density lipoprotein receptor-deficient (LDLR-/-) mice were transplanted with bone marrow from either sPLA2 transgenic mice (sPLA2--> LDLR-/-; n = 19) or wild-type C57BL/6 littermates (C57 BL/6-->LDLR-/-; n = 19) and maintained for 8 weeks on chow and then for 9 weeks on a Western-type diet. Plasma sPLA2 activity and plasma lipoprotein profiles were not significantly different between sPLA2-->LDLR-/- and C57BL/6-->LDLR-/- mice. Aortic root atherosclerosis was increased by 57% in sPLA2-->LDLR-/- mice compared with C57BL/6-->LDLR-/- controls (P < 0.05). Foam cell formation in vitro and in vivo was increased significantly. Urinary, plasma, and aortic levels of the isoprostane 8,12-iso-iPF2alpha-VI and aortic levels of 12/15-LO reaction products were each significantly higher (P < 0.001) in sPLA2-->LDLR-/- compared with C57BL/6-->LDLR-/- mice, indicating significantly increased in vivo oxidative stress in sPLA2--> LDLR-/-. These data demonstrate that macrophage-specific overexpression of human sPLA2 increases atherogenesis by directly modulating foam cell formation and in vivo oxidative stress without any effect on systemic sPLA2 activity and lipoprotein metabolism.
Molecular Mechanism of Human CD38 Gene Expression by Retinoic Acid (1998)

CD38 is a nonlineage-restricted type II transmembrane glycoprotein possessing ecto-NAD+ glycohydrolase activity. Because of its unique expression pattern in lymphocyte differentiation, it appears to function as an immunoregulatory molecule. We previously reported that CD38 was specifically induced by all-trans-retinoic acid (RA) in human promyelocytic leukemia HL-60 cells. Here we studied the molecular mechanism of the RA-dependent induction of human CD38. The expression of CD38 mRNA by RA appeared to be caused by the transcriptional stimulation of the gene, since it was blocked by an RNA synthesis inhibitor, but not by a protein synthesis inhibitor. In search of the RA response element (RARE) possibly present in human CD38 gene promoter, we isolated and sequenced the genomic DNA covering the 5'-flanking region, exon 1, and partial intron 1. Transient transfection experiments revealed that the responsiveness to RA was conferred through an RARE consisting of two direct repeat TGACCT-like hexamer motifs with a 5-nucleotide spacer, which was located in the first intron rather than the 5'-flanking region of the CD38 gene. This RARE interacted with heterodimer composed of RA receptor and retinoid X receptor in vitro. Thus, the RA-induced expression of the human CD38 gene was demonstrated to be mediated through the RARE located in the first intron.