gebhart/patrepeval huggingface dataset:
Inhibition of in Vitro Prostaglandin and Leukotriene Biosyntheses by Cinnamoyl-.BETA.-phenethylamine and N-Acyldopamine Derivatives. (1992)

N-trans- and N-cis-Feruloyltyramines were isolated as the inhibitors of in vitro prostaglandin (PG) synthesis from an Indonesian medicinal plant, Ipomoea aquatica (Convolvulaceae). In order to clarify structure activity relationships, cinnamoyl-beta-phenethylamines with possible combinations of naturally occurring cinnamic acids and beta-phenethylamines were synthesized and tested for their inhibitory activities against PG synthetase and arachidonate 5-lipoxygenase. The compounds containing catechol groups such as N-caffeoyl-beta-phenethylamine (CaP) showed higher inhibitory effects on PG synthetase. The catechol group was found to be essential for the inhibition of arachidonate 5-lipoxygenase. The investigation of concentration dependent effects on PG biosynthesis revealed that CaP enhanced PG biosynthesis at a lower concentration range, whereas it inhibited the reaction at a higher concentration. The effects of CaP on each reaction step were investigated with purified PG endoperoxide synthase and microsomal PG synthetase. CaP inhibited the cyclooxygenase reaction, while it enhanced the hydroperoxidase reaction. N-Acyldopamines which contain catechol and lipophylic group were synthesized from dopamine and fatty acids to test their inhibitory effects on arachidonate 5-lipoxygenase. N-Linoleoyldopamine was the most active compound and its IC50 value was 2.3 nM in our assay system, in which an IC50 value of AA 861, a specific inhibitor of 5-lipoxygenase, was 8 nM.
The IN service operations system based on the call processing history database (2002)

In existing INs, most effort has been concentrated on quickly developing service control functions, leaving the service management and operations functions insufficiently addressed. Existing operations systems (OpSs) are generally designed for specific networks or network elements, and, thus are not generic enough to suit the operations functions for services and customers. Since various network elements are related to IN services, it has been necessary for many OpSs to cooperate with each other to manage the services. We are developing an advanced intelligent network (IN) that can quickly and economically meet customer demands, and efficiently support IN services such as personal communication services. In particular, we are emphasizing service management and operations. For NTT's advanced IN, we are developing a service operations system called the IN Surveillance and Testing system (INSUT). This system is designed to make up for the lack of operation functions in existing OpSs, and thereby provide sufficient operations services for customers. This paper first explains NTT's service operations requirements for advanced INs such as customer traffic monitoring and customer-reported troubleshooting, it outlines the INSUT, and finally shows the INSUT applications.
Glucosylceramide and Glucosylsphingosine Modulate Calcium Mobilization from Brain Microsomes via Different Mechanisms (2003)

We recently demonstrated that elevation of intracellular glucosylceramide (GlcCer) levels results in increased functional Ca2+ stores in cultured neurons, and suggested that this may be due to modulation of ryanodine receptors (RyaRs) by GlcCer (Korkotian, E., Schwarz, A., Pelled, D., Schwarzmann, G., Segal, M. and Futerman, A. H. (1999) J. Biol. Chem. 274, 21673-21678). We now systematically examine the effects of exogenously added GlcCer, other glycosphingolipids (GSLs) and their lyso-derivatives on Ca2+ release from rat brain microsomes. GlcCer had no direct effect on Ca2+ release, but rather augmented agonist-stimulated Ca2+ release via RyaRs, through a mechanism that may involve the redox sensor of the RyaR, but had no effect on Ca2+ release via inositol 1,4,5-trisphosphate receptors. Other GSLs and sphingolipids, including galactosylceramide, lactosylceramide, ceramide, sphingomyelin, sphingosine 1-phosphate, sphinganine 1-phosphate, and sphingosylphosphorylcholine had no effect on Ca2+ mobilization from rat brain microsomes, but both galactosylsphingosine (psychosine) and glucosylsphingosine stimulated Ca2+ release, although only galactosylsphingosine mediated Ca2+ release via the RyaR. Finally, we demonstrated that GlcCer levels were approximately 10-fold higher in microsomes prepared from the temporal lobe of a type 2 Gaucher disease patient compared with a control, and Ca2+ release via the RyaR was significantly elevated, which may be of relevance for explaining the pathophysiology of neuronopathic forms of Gaucher disease.
A Mycobacterium tuberculosis operon encoding ESAT=6 and a novel low-molecular-mass culture filtrate protein (CFP-10) (1998)

The early secreted antigenic target 6 kDa protein (ESAT-6) is a potent T-cell protein antigen synthesized by Mycobacterium tuberculosis. Its corresponding gene (esat-6) is located in RD1, a 10 kb DNA region deleted in the attenuated tuberculosis vaccine strain Mycobacterium bovis BCG. The promoter region of M. tuberculosis esat-6 was cloned and characterized. A new gene, designated lhp and cotranscribed with esat-6, was identified. Moreover, computer searches in the M. tuberculosis genome identified 13 genes related to the lhp/esat-6 operon, defining a novel gene family. The transcription initiation sites of the lhp/esat-6 operon were mapped using M. tuberculosis RNA. The corresponding promoter signals were not recognized in Mycobacterium smegmatis, in which transcription of lhp/esat-6 is initiated at different locations. The M. tuberculosis lhp gene product was identified as CFP-10, a low-molecular-mass protein found in the short-term culture filtrate. These results show that the genes encoding CFP-10 and ESAT-6 are transcribed together in M. tuberculosis and that both code for small exported proteins.
Diversity Among Memory B Cells: Origin, Consequences, and Utility (2013)

Immunological memory is the residuum of a successful immune response that in the B cell lineage comprises long-lived plasma cells and long-lived memory B cells. It is apparent that distinct classes of memory B cells exist, distinguishable by, among other things, immunoglobulin isotype, location, and passage through the germinal center. Some of this variation is due to the nature of the antigen, and some appears to be inherent to the process of forming memory. Here, we consider the heterogeneity in development and phenotype of memory B cells and whether particular functions are partitioned into distinct subsets. We consider also how understanding the details of generating memory may provide opportunities to develop better, functionally targeted vaccines.
Nanoliter-Volume Discrete Drop Injection and Pumping In Microfabricaated Chemical Analysis Systems (1998)

This paper presents the combined use of selective hydrophobic patterns and on-chip pressure generation for injection, pumping, mixing, and positioning of discrete sample drops in a microfabricated chemical analysis device. The device consisting of a glass substrate bonded to a silicon/quartz substrate has been fabricated and tested. Specfic regions of the etched microchannel network are selectively patterned to be hydrophobic. These hydrophobic regions are used to control the location of liquid inside the microchannel network. Precise nanoliter-volume liquid samples are split-off and moved by heating air trapped in microfabricated chambers. Discrete sample drops of the order of 35 nl have been injected, moved, mixed and positioned in the device. This device demonstrates a simple valveless technique for performing microfluidic operations without the use of mechanical moving parts.
Aryl Hydrocarbon Receptor Activation by Dioxin Targets Phosphoenolpyruvate Carboxykinase (PEPCK) for ADP-ribosylation via 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-inducible Poly(ADP-ribose) Polymerase (TiPARP) (2013)

Effects of the environmental toxin and carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin) include a wasting syndrome associated with decreased gluconeogenesis. TCDD is a potent activator of the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor. The relationship between gene activation by the AHR and TCDD toxicities is not well understood. We recently identified a pathway by which the AHR target gene TiPARP (TCDD-inducible poly(ADP-ribose) polymerase) contributes to TCDD suppression of transcription of phosphoenolpyruvate carboxykinase (PEPCK), a key regulator of gluconeogenesis, by consuming NAD(+) and decreasing Sirtuin 1 activation of the peroxisome proliferator-activated receptor γ coactivator 1α (PGC1α), a transcriptional activator of PEPCK. We report here that TCDD-induced TiPARP also targets PEPCK for ADP-ribosylation. Both cytosolic and mitochondrial forms of PEPCK were found to undergo ADP-ribosylation. Unexpectedly, AHR suppression also enhanced ADP-ribosylation and did so by a poly(ADP-ribose) polymerase-independent mechanism. This report 1) identifies ADP-ribosylation as a new posttranslational modification for PEPCK, 2) describes a pathway by which transcriptional induction of TiPARP by the AHR can lead to a downstream posttranslational change in a TCDD target protein (PEPCK), and 3) reveals that the AHR exerts complex, previously unidentified modulatory effects on ADP-ribosylation.
Induction of Thioredoxin by Oxidative Stress and Overexpression of Thioredoxin in Lung Cancer Tissue (1999)

BACKGROUND: Reactive oxygen species are involved in multi -stage process of carcinogenesis. The most of cancer cell lines and cancer cells in tumor tissue produce reactive oxygen species and on the other hand, the activities of catalase, Mn - and CuZn-superoxide dismutase in tumor cells are usually low. These persistent oxidative stress in tumor tissue facilitates tumor invasion and metastasis. 12- kDa thioredoxin, which regulate the intracellular redox potential with glutathione and glutaredoxin is involved in cell activation, proliferation, differentiation and re dox- mediated apoptosis. It is also purified as 14 -kDa and 10- kDa eosinophilic cytotoxic enhancing factor(ECEF) from human histiocytic cell(U937) and 10 -kDa ECEF has more than 20 times eosinophilic stimulation activity than 14 - kDa ECEF. It has been reported that adult T-cell leukemia, squamous cell carcinoma of uterine cervix, and hepatocellular carcinoma show increased amounts of human thioredoxin and thioredoxin mRNA is increased in lung cancer. In this study, we investigated the expression of conventional antioxidant enzymes such as catalase, CuZn-SOD, and glutathione peroxidase and thioredoxin in lung cancer tissue compared to adjacent normal lung tissue and the induction of thioredoxin in macrophage cells after treatment of oxidative stress and endotoxin . METHODS: We measured the amount of conventional antioxidant enzymes such as catalase, CuZn-SOD, and glutathione peroxidase and thioredoxin in lung cancer tissue compared to adjacent normal lung tissue by immunoblot analysis and the induction of thioredo xin in mouse monocyte - macrophage cells(RAW 264.7) by treatment of 5 microM menadione and 1 microgram/ml endotoxin. RESULTS: On immunoblot analysis, the expression of 12 -kDa thioredoxin was increased in lung cancer tissue compared to paired normal lung tissue. but th e expression of catalase and CuZn-SOD were decreased in lung cancer tissue compared to paired normal tissue and the expression of glutathione peroxidase in lung cancer was variable. The expression of truncated thioredoxin was also increased in lung cancer. When mouse monocyte - macrophage cells were treated with 5 microM menadione and 1 microG/ml endotoxin, the expression of thioredoxin was peaked at 12 hrs and sustained to 48 hrs. CONCLUSION: In contrast with other conventional antioxidants, the expression of 12-kDa and truncated thioredoxin in lung cancer were increased and it is closely associated with persistent oxidative stress in tumor microenvironment. Considering especially the biological functions of truncated thioredoxin, the increased amount of truncated thioredoxin has significant role in tumor growth through cell proliferation.
Three-dimensional analysis of scattering losses due to sidewall roughness in microphotonic waveguides (2005)

We present a three-dimensional (3-D) analysis of scattering losses due to sidewall roughness in rectangular dielectric waveguides valid for any refractive-index contrast and field polarization. The analysis is based on the volume current method and uses array factors to introduce significant mathematical simplifications to better understand the influence of individual waveguide parameters on scattering losses. We show that the typical two-dimensional (2-D) analyses can substantially overestimate scattering losses in small waveguides and that scattering losses exhibit considerable polarization dependence. We produce scattering-loss estimates for a wide variety of waveguides and provide guidelines for design of waveguide cross sections that are less sensitive to sidewall roughness.
Cucurbit Grafting (2008)

Due to limited availability of arable land and high market demand for off-season vegetables, cucurbits (plants in the family Cucurbitaceae) are continuously cultivated under unfavorable conditions in some countries. These conditions include environments that are too cold, wet, or dry, or are cool low-light winter greenhouses. Successive cropping can increase salinity, the incidence of cucurbit pests, and soilborne diseases like fusarium wilt caused by Fusarium spp. These conditions cause various physiological and pathological disorders leading to severe crop loss. Chemical pest control is expensive, not always effective, and can harm the environment. Grafting can overcome many of these problems. In fact, in many parts of the world, grafting is a routine technique in continuous cropping systems. It was first commonly used in Japan during the late 1920s by grafting watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] onto pumpkin [Cucurbita moschata Duchesne ex. Poir] rootstocks. Soon after, watermelons were grafted onto bottle gourd [Lagenaria siceraria (Molina) Standl.] rootstocks. This practice helped control declining yield due to soilborne diseases. China produces more than half the world's watermelons and cucumbers (Cucumis sativus L.), and approximately 20% of these are grafted. Use of rootstocks can enhance plant vigor through vigorous attainment of soil nutrients, avoidance of soil pathogens and tolerance of low soil temperatures, salinity, and wet-soil conditions. The type of rootstock affects cucurbit plant growth, yield, and fruit quality. Cucurbit grafting is rare in the United States, but with continued loss of quality disease-free farmland along with the phase-out of methyl bromide, the U.S. cucurbit industry sees grafting as an attractive option. Some seed companies now offer watermelon transplants grafted onto squash or bottle gourd rootstocks, and some transplant facilities offer grafting services. There have been thorough analyses of cucurbit grafting in other countries, but the literature in English is limited. This review summarizes the state of the cucurbit grafting industry on a global level, translating work published in many languages.
RETRACTED: Identification of CD4 + T-Cell-Derived CD161 + CD39 + and CD39 + CD73 + Microparticles As New Biomarkers for Rheumatoid Arthritis (2017)

CD4<sup>+</sup> T-cell-derived CD161<sup>+</sup>CD39<sup>+</sup> and CD39<sup>+</sup>CD73<sup>+</sup> MPs could serve as new reciprocal biomarkers for RA evaluation.
Interleukin-4 (IL-4) and IL-13 Signaling Pathways Do Not RegulateBorrelia burgdorferi-Induced Arthritis in Mice: IgG1 Is Not Required for Host Control of Tissue Spirochetes (2000)

Previous studies have suggested that interleukin-4 (IL-4) has a protective effect in host defense to Borrelia burgdorferi infection, both in limiting the severity of arthritis and in controlling spirochete numbers in tissues, and a mapping study revealed suggestive linkage to a cluster of genes on mouse chromosome 11, including the genes for IL-4 and IL-13. In contrast, other studies have questioned the importance of IL-4. In this study the involvement of IL-4 in murine Lyme disease was examined in C57BL/6J and BALB/cJ mice with targeted disruptions in the IL-4 gene, the IL-4Ralpha chain gene, or both. A spectrum of arthritis severity was seen in BALB/cJ mice, and ablation of IL-4, IL-4Ralpha, or both had no effect on the overall severity of arthritis as determined by joint swelling and histopathology. Wild-type C57BL/6J mice exhibited mild to moderate arthritis, and ablation of IL-4 again had no effect on arthritis severity. IL-4- and IL-4Ralpha-deficient mice produced extremely low levels of immunoglobulin G1 (IgG1) and showed increased production of IgG2b. This shift in immunoglobulin isotype had no effect on the host's ability to control spirochete growth in either strain of mouse, as determined by PCR detection of B. burgdorferi DNA from heart and ankle tissues. In summary, the IL-4-IL-4Ralpha pathway, including IL-13 signaling, neither limits arthritis severity nor is required for control of spirochete growth during B. burgdorferi infection of mice. Furthermore, the IgG1 isotype is not required to control B. burgdorferi cell numbers in tissues. These findings suggest the host defense against B. burgdorferi infection is not dependent on the Th1-Th2 paradigm of T-cell responses.
Interactively deformable models for surgery simulation (1993)

A methodology that addresses important issues concerned with the underlying graphical models designed for surgical simulation, as well as issues related to the real-time interactivity with, and manipulation of, these models is presented. The specific application of interest is laparoscopic surgery, which is performed using endoscopes that present a video image of the organs to the clinicians. The surgeon then performs the surgery while looking at the video monitor. The particular focus is gall bladder surgery, which involves various gastrointestinal organs. The overall objective is to simulate this environment by creating realistic, manipulable models of these organs. The models are interactively manipulable and exhibit behavior both visually acceptable and physically accurate. The approach is based on the notion of active surfaces. The rationale, mathematical formalism, and visualization techniques encompassed by the methodology are described. Recent results obtained from applying these methods to the problem of endoscopic gall bladder surgery simulation are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Functional stoichiometry of the unitary calcium-release-activated calcium channel (2008)

Two proteins, STIM1 in the endoplasmic reticulum and Orai1 in the plasma membrane, are required for the activation of Ca(2+) release-activated Ca(2+) (CRAC) channels at the cell surface. How these proteins interact to assemble functional CRAC channels has remained uncertain. Here, we determine how many Orai1 and STIM1 molecules are required to form a functional CRAC channel. We engineered several genetically expressed fluorescent Orai1 tandem multimers and a fluorescent, constitutively active STIM1 mutant. The tandem multimers assembled into CRAC channels, as seen by rectifying inward currents and by cytoplasmic calcium elevations. CRAC channels were visualized as fluorescent puncta in total internal reflection microscopy. With single-molecule imaging techniques, it was possible to observe photo-bleaching of individual fluorophores and to count the steps of bleaching as a measure of the stoichiometry of each CRAC channel complex. We conclude that the subunit stoichiometry in an active CRAC channel is four Orai1 molecules and two STIM1 molecules. Fluorescence resonance energy transfer experiments also showed that four Orai1 subunits form the assembled channel. From the fluorescence intensity of single fluorophores, we could estimate that our transfected HEK293 cells had almost 400,000 CRAC channels and that, when intracellular Ca(2+) stores were depleted, the channels clustered in aggregates containing approximately 1,300 channels, amplifying the local Ca(2+) entry.
Protein Folding (1981)

After some general remarks on protein structure, there follows a discussion on primary, secondary, and tertiary organization. The account of primary structure includes a discussion of the conformation of disulfide bonds. Types of helices, sheets, and turns are described in the section on secondary structure, followed by a discussion of super-secondary structure and the effects of metals and prosthetic groups of protein fold. The crux of the review lies in an examination of tertiary structure, or specifically of domains that are defined, in part, as functional units within a polypeptide chain. An assembly of domains can in turn result in a protein whose function is quite sophisticated. Some consideration of domain recognition is given in the section on taxonomy and in the appendix. The key part of the tertiary structure section concentrates on a taxonomic protein classification dependent not only on structure but also on function. A discussion of the requirements by quaternary structure on a fold are omitted in this review. Finally, no review of this kind can escape a discussion of evolutionary convergence and divergence.
Prevalence and Prognostic Significance of Acinar Cell Differentiation in Pancreatic Endocrine Tumors (2002)

We have noted that many histologically and immunohistochemically confirmed pancreatic endocrine tumors show immunophenotypic evidence of acinar cell differentiation, but the clinical relevance of this finding is unknown. We performed this study to evaluate the prevalence and prognostic significance of exocrine differentiation by immunohistochemistry in pancreatic endocrine tumors that do not show morphologic features of acinar cell differentiation. Routinely processed tissue sections from 87 pancreatic endocrine tumors were immunohistochemically stained with monoclonal antibodies against acinar (lipase, chymotrypsin, trypsin) and endocrine cell markers (chromogranin A, neuron-specific enolase, synaptophysin, Leu-7) and for the proliferation-associated peptide Ki67. The degree of staining with each marker was graded on a three-tier scale for acinar markers (grade 0, <5%; grade 1, 5-10%; grade 2, 11-25%; and grade 3, >25%) and on a four-tier scale for endocrine markers (grade 0, <5%; grade 1, 5-25%; grade 2, 26-50%; grade 3, 51-75%; and grade 4, >75%), and the results were correlated with clinical outcome (mean follow-up 53 months). Greater than 75% of the tumor cells stained for chromogranin A, neuron-specific enolase, synaptophysin, and Leu-7 in 100%, 96%, 93%, and 27% of cases, respectively. Overall, 66% of tumors stained positively for at least one acinar cell marker, 31% stained for at least two acinar cell markers, and 13% stained for all three acinar cell markers. Forty-seven percent stained for lipase (23 grade 1, 11 grade 2, seven grade 3), 37% for trypsin (22 grade 1, three grade 2, seven grade 3), and 25% stained for chymotrypsin (13 grade 1, five grade 2, four grade 3). No correlation was noted between the presence or extent of expression of any single or combination of acinar cell markers and clinical outcome. However, higher tumor stage correlated with a poor clinical outcome (p = 0.002), and location in the tail of the pancreas was associated with a longer interval to tumor recurrence (p = 0.03). The presence of synaptophysin (p = 0.03) and Leu-7 expression (p = 0.03) correlated significantly with less aggressive clinical behavior. An association was observed between increased Ki67 labeling and poorer clinical outcome, but this was not statistically significant (p >0.05). In conclusion, immunophenotypic evidence of acinar cell differentiation is common in pancreatic endocrine tumors, but this feature does not have any relevance to clinical prognosis. However, in addition to tumor stage, location in the pancreatic tail and the immunohistochemical expression of synaptophysin and/or Leu-7 may be useful prognostic indicators in patients with these lesions.