gebhart/patrepeval huggingface dataset:
Differential Activation of Cardiac c-Jun Amino-Terminal Kinase and Extracellular Signal-Regulated Kinase in Angiotensin II–Mediated Hypertension (1998)

Two subgroups of mitogen-activated protein kinases, c-jun NH2-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK), are thought to be involved in cultured cardiac myocyte hypertrophy and gene expression. To examine the in vivo activation of these kinases, we measured cardiac JNK and ERK activities in conscious rats subjected to acute or chronic angiotensin II (Ang II) infusion, by using in-gel kinase methods. About 50 mm Hg rise in blood pressure by Ang II (1000 ng . kg-1 . min-1) infusion caused larger activation of left ventricular JNK than ERK, via the AT1 receptor. In spite of short duration (about 30 minutes) of maximal blood pressure elevation by Ang II, JNK sustained the peak value (more than 5-fold increase) from 15 minutes up to at least 3 hours. Similar activation of JNK was seen in the right ventricle. Thus, cardiac JNK activation by Ang II seems to be in part mediated by its direct action via the AT1 receptor. The dose-response relationships for Ang II-induced rises in blood pressure and cardiac JNK and ERK activation indicated that cardiac JNK or ERK was not activated by a mild increase in blood pressure and that cardiac JNK was activated by Ang II-mediated hypertension in a more sensitive manner than ERK. Cardiac hypertrophy, induced by chronic Ang II infusion, was preceded by JNK activation without ERK activation. Furthermore, gel mobility shift analysis showed that cardiac JNK activation was followed by increased activator protein-1 DNA binding activity due to c-Fos and c-Jun. These results provided the first evidence for the preferential activation of cardiac JNK in Ang II-induced hypertension and suggested that JNK might play some role in Ang II-induced cardiac hypertrophic response in vivo. However, further study is needed to elucidate the role of JNK in cardiac hypertrophy in vivo.
Underwater image enhancement using guided trigonometric bilateral filter and fast automatic color correction (2013)

This paper describes a novel method to enhance underwater optical images by guided trigonometric bilateral filters and color correction. Scattering and color distortion are two major problems of distortion for underwater optical imaging. Scattering is caused by large suspended particles, like fog or turbid water which contains abundant particles. Color distortion corresponds to the varying degrees of attenuation encountered by light traveling in the water with different wavelengths, rendering ambient underwater environments dominated by a bluish tone. Our key contributions are proposed a new underwater model to compensate the attenuation discrepancy along the propagation path, and to propose a fast guided trigonometric bilateral filtering enhancing algorithm and a novel fast automatic color enhancement algorithm. The enhanced images are characterized by reduced noised level, better exposedness of the dark regions, improved global contrast while the finest details and edges are enhance significantly. In addition, our enhancement method is comparable to higher quality than the state-of-the-art methods by assuming in the latest image evaluation systems.
Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte (2013)

Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA), often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria) have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales), but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales). Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.
A General Method for meta and para Functionalization of Arenes Using TMP2Mg⋅2 LiCl (2008)

Getting directions: The (Me2N)2P(O)O substituent serves as an effective directing-metalation group in the magnesiation of substituted arenes with TMP2Mg⋅2 LiCl (see scheme). This reaction can be used to achieve difficult substitution patterens by meta,para or para,meta functionalization. TMP=2,2,6,6-tetramethylpiperamidyl, NEP=N-ethylpyrrolidone. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z703382_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Tumor Necrosis Factor-α Increases Circulating Osteoclast Precursor Numbers by Promoting Their Proliferation and Differentiation in the Bone Marrow through Up-regulation of c-Fms Expression (2006)

Osteoclasts are essential cells for bone erosion in inflammatory arthritis and are derived from cells in the myeloid lineage. Recently, we reported that tumor necrosis factor-alpha (TNFalpha) increases the blood osteoclast precursor (OCP) numbers in arthritic patients and animals, which are reduced by anti-TNF therapy, implying that circulating OCPs may have an important role in the pathogenesis of erosive arthritis. The aim of this study is to investigate the mechanism by which TNFalpha induces this increase in OCP frequency. We found that TNFalpha stimulated cell division and conversion of CD11b+/Gr-1-/lo/c-Fms- to CD11b+/Gr-1-/lo/c-Fms+ cells, which was not blocked by neutralizing macrophage colony-stimulating factor (M-CSF) antibody. Ex vivo analysis of monocytes demonstrated the following: (i) blood CD11b+/Gr-1-/lo but not CD11b-/Gr-1- cells give rise to osteoclasts when they were cultured with receptor activator NF-kappaB ligand and M-CSF; and (ii) TNF-transgenic mice have a significant increase in blood CD11b+/Gr-1-/lo cells and bone marrow proliferating CD11b+/Gr-1-/lo cells. Administration of TNFalpha to wild type mice induced bone marrow CD11b+/Gr-1-/lo cell proliferation, which was associated with an increase in CD11b+/Gr-1-/lo OCPs in the circulation. Thus, TNFalpha directly stimulates bone marrow OCP genesis by enhancing c-Fms expression. This results in progenitor cell proliferation and differentiation in response to M-CSF, leading to an enlargement of the marrow OCP pool. Increased marrow OCPs subsequently egress to the circulation, forming a basis for elevated OCP frequency. Therefore, the first step of TNF-induced osteoclastogenesis is at the level of OCP genesis in the bone marrow, which represents another layer of regulation to control erosive disease.
Transfer of glycerol by Endo-beta-N-acetylglucosaminidase F to oligosaccharides during chitobiose core cleavage. (1986)

N-Linked oligosaccharides, when hydrolyzed by glycerol-containing preparations of endo-beta-N-acetylglucosaminidase (Endo) F from Flavobacterium meningosepticum were found to have glycerol attached to their reducing ends. The absence of a reducing end was confirmed by high-field 1H NMR spectroscopy, and the incorporated glycerol was verified through mass spectrometry and collisionally activated decomposition fast atom bombardment/mass spectrometry/mass spectrometry techniques. Periodate oxidation of [1(3)-14C]glycerol-labeled oligosaccharides indicated glycerol was glycosidically linked via its 1(3) carbon to the C1 of the reducing end N-acetylglucosamine. In a second, less favored reaction, the glycerol glycoside was hydrolyzed by Endo F using water as the terminal nucleophile, thus regenerating the N-acetylglucosamine reducing end. Glycerol could be removed from Endo F preparations without affecting enzyme stability, and chitobiosyl core hydrolysis in its absence provided intact oligosaccharides with normal N-acetylglucosamine reducing ends. The incorporation of labeled glycerol may provide a useful method for monitoring of Endo F release of oligosaccharides.
Molecular Interfacing of Enzymes on the Electrode Surface (1994)

Few redox enxymes undergo reversible electron transfer on the electrode surface primarily due to steric hindrance of the redox centers of these enzymes. Several molecular interfaces have been designed to promote electron transfer of electrode-bound redox enzymes. The authors have successfully interfaced fructose dehydrogenase and alcohol dehydrogenase on the electrode surface with conducting polymer of polypyrrole, which could cause these enzymes to make an electron transfer with retaining their enzymatic activity. The molecular-interfaced redox enzymes will find their application in fabricating biosensors that respond specifically to the corresponding substrates in current.
Ca3N2and Mg3N2: Unpredicted High-Pressure Behavior of Binary Nitrides (2011)

High-pressure synthesis allows both fundamental and materials science research to gain unprecedented insight into the inner nature of materials properties at extreme environment conditions. Here, we report on the high-pressure synthesis and characterization of γ-Ca(3)N(2) and the high-pressure behavior of Mg(3)N(2). Investigation of M(3)N(2) (M = Ca, Mg) at high-pressure has been quite challenging due to the high reactivity of these compounds. Ex situ experiments have been performed using a multianvil press at pressures from 8 to 18 GPa (1000-1200 °C). Additional in situ experiments from 0 to 6 GPa (at RT) at the multianvil press MAX 80 (HASYLAB, Beamline F.2.1, Hamburg) have been carried out. The new cubic high-pressure phase γ-Ca(3)N(2) with anti-Th(3)P(4) defect structure exhibits a significant increase in coordination numbers compared to α-Ca(3)N(2). Contrary, Mg(3)N(2) shows decomposition starting at surprisingly low pressures, thereby acting as a precursor for Mg nanoparticle formation with bcc structure. Soft X-ray spectroscopy in conjunction with first principles DFT calculations have been used to explore the electronic structure and show that γ-Ca(3)N(2) is a semiconductor with inherent nitrogen vacancies.
The Nonsignaling Extracellular Spacer Domain of Chimeric Antigen Receptors Is Decisive for In Vivo Antitumor Activity (2014)

The use of synthetic chimeric antigen receptors (CAR) to redirect T cells to recognize tumor provides a powerful new approach to cancer immunotherapy; however, the attributes of CARs that ensure optimal in vivo tumor recognition remain to be defined. Here, we analyze the influence of length and composition of IgG-derived extracellular spacer domains on the function of CARs. Our studies demonstrate that CD19-CARs with a long spacer from IgG4 hinge-CH2-CH3 are functional in vitro but lack antitumor activity in vivo due to interaction between the Fc domain within the spacer and the Fc receptor-bearing myeloid cells, leading to activation-induced T-cell death. We demonstrate that in vivo persistence and antitumor effects of CAR-T cells with a long spacer can be restored by modifying distinct regions in the CH2 domain that are essential for Fc receptor binding. Our studies demonstrate that modifications that abrogate binding to Fc receptors are crucial for CARs in which a long spacer is obligatory for tumor recognition as shown here for a ROR1-specific CAR. These results demonstrate that the length and composition of the extracellular spacer domain that lacks intrinsic signaling function can be decisive in the design of CARs for optimal in vivo activity.
Rational Design of DNA Nanoarchitectures (2006)

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.
Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene. (1991)

Inactivation of the retinoblastoma gene appears to have a fundamental role in the genesis of retinoblastoma, osteosarcoma, and other malignant tumors. The gene is generally inactivated because of loss-of-function mutations, although epigenetic phenomena, such as hypermethylation of the promoter region, could possibly have the same effect. We investigated the methylation pattern at the 5' end of the retinoblastoma gene, including its promoter region and exon 1, in DNA purified from 56 primary retinoblastomas. We found five tumors with evidence for hypermethylation, all from unilateral, simplex patients. No methylation abnormalities were detected in DNA purified from the leukocytes from these patients. It is interesting that in one of these tumors the hypermethylation was confined to one allele. There were no mutations in a 1,306-bp sequence including the hypermethylated region that might account for the allele-specific hypermethylation. We believe that the hypermethylation of the retinoblastoma gene that we found in these tumors corresponds to the allelic inactivation of the gene, and we speculate that erroneous hypermethylation without alteration of nucleotide sequence occasionally plays a role in the genesis of this cancer. If this is true, then retinoblastomas with hypermethylation might be treatable with chemotherapeutic agents that interfere with methylation of DNA.
Techniques for data hiding (1995)

Data hiding is the process of embedding data into image and audio signals. The process is constrained by the quantity of data, the need for invariance of the data under conditions where the `host' signal is subject to distortions, e.g., compression, and the degree to which the data must be immune to interception, modification, or removal. We explore both traditional and novel techniques for addressing the data hiding process and evaluate these techniques in light of three applications: copyright protecting, tamper-proofing, and augmentation data embedding.
Amplification of Antioxidant Activity and Xanthine Oxidase Inhibition of Catechin by Enzymatic Polymerization (2003)

To amplify the antioxidant activity, we synthesized poly(catechin) by the enzyme-catalyzed oxidative coupling using horseradish peroxidase as a catalyst. The poly(catechin) showed great improvement in antioxidant activity such as radical scavenging activity against the superoxide anion and inhibition effects against free radical induced-oxidation of low-density lipoprotein, compared with a catechin monomer. In addition, poly(catechin) showed very high inhibition effects on xanthine oxidase activity, whereas the catechin monomer showed very less inhibition effects. The amplified activities might offer a high potential as a therapeutic agent for prevention of various free radicals and/or enzyme-related diseases.
Lipidheme-Microsphere (LH-M) A New Type of Totally Synthetic Oxygen Carrier and its Oxygen Carrying Ability (1994)

We have succeeded in synthesizing a new type of totally artificial oxygen carrier which was produced by covering oil droplets (microsphere) with synthetic hemes (LH-M). We studied its oxygen-transporting ability in hemorrhagic dogs. Four beagles weighing about 8 kg were studied. Under controlled ventilation, exchange-transfusion of 30 ml/kg was carried out. Cardiac output, hemoglobin and LH-M concentration in the blood, and blood gas were measured to 5 hours after intravenous injection of LH-M solution. LH-M delivered 15.7 to 22.3 ml/min (11 to 16%) of oxygen to the tissue and 5.5 to 8.2 ml/min (11 to 17%) of oxygen was consumed from LH-M to 5 hours after intravenous injection. Its half-life time in the blood stream was about 12 hours. It was confirmed that LH-M transported oxygen and released it to the tissue in vivo.
Laminin‐5 (laminin‐332): Unique biological activity and role in tumor growth and invasion (2006)

The development and progression of tumor cells is controlled by their interactions with neighboring host cells and a variety of microenvironmental factors including extracellular matrix (ECM) molecules, growth factors and proteinases. Cell-adhesive ECM proteins are a prerequisite for growth and migration of many types of cells. Their interactions with integrins and other cell surface receptors induce intracellular signaling that regulates the actin cytoskeleton and gene expression. The basement membrane protein laminin-5 is a notable cell adhesion molecule, which promotes cellular adhesion and migration much more efficiently than other ECM proteins. There is accumulating evidence that laminin-5 is involved in tumor growth and progression. With special reference to laminin-5, this article reviews the regulatory mechanisms of cellular adhesion and migration by ECM molecules and their significance in tumor progression.
The Chemistry of Vitamin A and Vision (1990)

Abstract Vision is initiated in the retina by the photochemical isomerization of an 11‐ cis ‐retinal Schiff base to its all‐ trans counterpart in the photosensitive protein rhodopsin. All‐ trans ‐retinal is released, reduced to form all‐ trans ‐retinol (vitamin A), and finally esterified. In order for vision to proceed an 11‐ cis ‐retinoid must be regenerated in the eye. Kühne observed in the 1870s that the pigment epithelium must be in place behind the retina in order for rhodopsin to form. And indeed it was in the pigment epithelium that an isomerase system was recently discovered that can produce 11‐ cis ‐retinol from added vitamin A. Pauling predicted in the 1930s that certain cis double bonds in carotenoids and retinoids, including 11‐ cis ‐retinoids, should be quite unstable with respect to their all‐ trans congeners. This prediction is borne out by experiment, but leaves open the crucial question as to where the energy comes from to drive the isomerization process in the eye. This question was answered by the demonstration that the energy is found in the membrane phospholipids. The fact that membranes may serve as an energy source reveals a previously unsuspected biological function of membranes. The chemistry of the novel energy‐linked isomerization process is explored in this review.
Randomized placebo‐controlled trial assessing the effect of bifidobacteria‐fermented milk on active ulcerative colitis (2004)

Supplementation with this bifidobacteria-fermented milk product is safe and more effective than conventional treatment alone, suggesting possible beneficial effects in managing active ulcerative colitis. This is a pilot study and further larger studies are required to confirm the result these preliminary results.
Imaging of Freeze-Fractured Cells with in Situ Fluorescence and Time-of-Flight Secondary Ion Mass Spectrometry (2002)

Bioanalytical imaging techniques have been employed to investigate cellular composition at the single-cell and subcellular regimes. Four imaging modes have been performed sequentially in situ to demonstrate the utility of a more integrated approach to imaging cells. The combination of bright-field, scanning ion, and fluorescence microscopy complements TOF-SIMS imaging of native biomolecules. Bright-field microscopy provides a blurred visualization of cells in frozen-hydrated samples, while scanning ion imaging provides a morphological view of freeze-fractured cells after TOF-SIMS analysis is completed. With the use of selective fluorescent labels, fluorescence microscopy allows single mammalian cells to be located in the complex ice matrix of freeze-fractured samples, a task that has not been routine with either bright-field or TOF-SIMS. A fluorescent label, DiI (m/z 834), that does not interfere with the mass spectra of membrane phosphatidylcholine, has been chosen for fluorescence and TOF-SIMS imaging of membrane phospholipids. In this paper, in situ fluorescence microscopy allows the distinction of single cells from ice and other sample debris, previously not possible with bright-field or scanning ion imaging. Once cells are located, TOF-SIMS imaging reveals the localization of membrane lipids, even in the membrane of a single 15-microm rat pheochromocytoma cell. The utility of mapping lipids in the membranes of single cells using this integrated approach will provide more understanding of the functional role of specific lipids in functions of cellular membranes.
TBBT: scalable and accurate trace replay for file server evaluation (2005)

This paper describes the design, implementation, and evaluation of TBBT, the first comprehensive NFS trace replay tool. Given an NFS trace, TBBT automatically detects and repairs missing operations in the trace, derives a file system image required to successfully replay the trace, ages the file system image appropriately, initializes the file server under test with that image, and finally drives the file server with a workload that is derived from replaying the trace according to user-specified parameters. TBBT can scale a trace temporally or spatially to meet the need of a simulation run without violating dependencies among file system operations in the trace.
ChemInform Abstract: Regioselective Nucleophilic Attack on N‐BOC‐Pyroglutamate Ethyl Ester. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Nitrosation and oxidation in the regulation of gene expression (2000)

A growing body of evidence suggests that the cellular response to oxidative and nitrosative stress is primarily regulated at the level of transcription. Posttranslational modification of transcription factors may provide a mechanism by which cells sense these redox changes. In bacteria, for example, OxyR senses redox-related changes via oxidation or nitrosylation of a free thiol in the DNA binding region. This mode of regulation may serve as a paradigm for redox-sensing by eukaryotic transcription factors as most-including NF-kappaB, AP-1, and p53-contain reactive thiols in their DNA binding regions, the modification of which alters binding in vitro. Several of these transcription factors have been found to be sensitive to both reactive oxygen species and nitric oxide-related species in vivo. It remains entirely unclear, however, if oxidation or nitrosylation of eukaryotic transcription factors is an important mode of regulation, or whether transcriptional activating pathways are principally controlled at other redox-sensitive levels.-Marshall, H. E., Merchant, K., Stamler, J. S. Nitrosation and oxidation in the regulation of gene expression.