gebhart/patrepeval huggingface dataset:
Menaquinone (vitamin K2) biosynthesis: overexpression, purification, and characterization of a new isochorismate synthase from Escherichia coli (1997)

The first committed step in the biosynthesis of menaquinone (vitamin K2) is the conversion of chorismate to isochorismate, which is mediated by an isochorismate synthase encoded by the menF gene. This isochorismate synthase (MenF) is distinct from the entC-encoded isochorismate synthase (EntC) involved in enterobactin biosynthesis. MenF has been overexpressed under the influence of the T7 promoter and purified to homogeneity. The purified protein was found to have a molecular mass of 98 kDa as determined by gel filtration column chromatography on Sephacryl S-200. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a molecular mass of 48 kDa. Thus, the enzyme is a homodimer. The purified enzyme showed a pH optimum of 7.5 to 8.0 and a temperature optimum of 37 degrees C. The enzyme carries out the irreversible conversion of chorismate to isochorismate in the presence of Mg2+. The enzyme was found to have a Km of 195 +/- 23 microM and a k(cat) of 80 min(-1). In the presence of 30 mM beta-mercaptoethanol (BME), the k(cat) increased to 176 min(-1). The reducing agents BME and dithiothreitol stimulated the enzymatic activity more than twofold. Treatment of the enzyme with the cysteine-specific modifying reagent N-ethylmaleimide (NEM) resulted in the complete loss of activity. Preincubation of the enzyme with the substrate, chorismate, before NEM treatment resulted in complete protection of the enzyme from inactivation.
Nitrogen-15 labeled deoxynucleosides. Synthesis of 15N6-and 15N1-deoxyadenosines from deoxyadenosine (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNitrogen-15 labeled deoxynucleosides. Synthesis of 15N6-and 15N1-deoxyadenosines from deoxyadenosineX. Gao and R. A. JonesCite this: J. Am. Chem. Soc. 1987, 109, 4, 1275–1278Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/ja00238a063https://doi.org/10.1021/ja00238a063research-articleACS PublicationsRequest reuse permissionsArticle Views609Altmetric-Citations44LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Relationship of ornithine decarboxylase activity and cAMP metabolism to proliferation of normal human bronchial epithelial cells (1985)

The mechanisms of action of extracellular mitogens for normal human bronchial epithelial cells (NHBE) were investigated by observing their effects on selected biochemical pathways when the cells were incubated in serum-free media. We find that (a) epidermal growth factor (EGF) stimulates ornithine decarboxylase (ODC) activity and the rate of cell division without stimulating cAMP; (b) alone, pituitary extract (PEX) does not stimulate ODC activity, cAMP levels, or cell division; (c) when PEX is added to medium containing EGF there is a further increase in both ODC activity and the rate of cell division, again with no increase in cAMP levels; (d) in contrast, alone, L-epinephrine (EPI) stimulates an increase in both ODC and cAMP but does not stimulate cell division; (e) when EPI is added to medium containing both EGF and PEX a further increase in the rate of cell division is noted; (f) the specific inhibitor of ODC, alpha-(difluoromethyl)-ornithine (DMFO), also inhibits NHBE cell proliferation; and (g) the beta-adrenergic receptor antagonist propranolol inhibits the mitogenic action and ODC induction by EPI observed under condition e. We conclude that an increase in ODC activity is necessary but not sufficient for an increase in proliferation of NHBE cells. In contrast, cAMP stimulation is not necessary for an increase in NHBE cell division. However, in the presence of undefined factors in PEX, increases in cAMP levels result in a synergistic increase in the rate of EGF-stimulated clonal growth. By correlating the biochemical pathways invoked by EGF, PEX, EPI, and combinations thereof with their mitogenic actions, we have better defined the role each of these different mitogens plays in stimulating epithelial cell division.
Electronics and sensors based on pyroelectric AlGaN/GaN heterostructures – Part B: Sensor applications (2003)

In the present article recent results concerning sensor applications of AlGaN layers and AlGaN/GaN heterostructures are summarized. The piezoresistive effect in piezoelectric AlGaN layers is investigated and the dependence of the piezoresistive gauge factor on the Al content is attributed to the influence of strain induced piezoelectric fields. An enhancement of this effect is observed in AlGaN/GaN heterostructures resulting in high longitudinal gauge factors. The response of gas sensitive Pt:GaN Schottky diodes to hydrogen and hydrogen containing gases is analyzed up to temperatures of 600 °C and employed to realize gas sensitive field effect transistors which are demonstrated to operate up to 400 °C. In addition, ion sensitive field effect transistors (ISFETs) have also been fabricated on the basis of AlGaN/GaN heterostructures. The GaN surface shows a high pH sensitivity which is attributed to the presence of a thin native metal oxide layer on the surface. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Targeting Medulloblastoma: Small-Molecule Inhibitors of the Sonic Hedgehog Pathway as Potential Cancer Therapeutics (2005)

Medulloblastoma is the most common malignant pediatric brain tumor for which no satisfactory treatments exist. The Sonic Hedgehog signaling pathway seems to play an important role in the pathology of this disease. Here we review our recent demonstration that a small-molecule inhibitor of this pathway can regress tumors that arise in a transgenic mouse model of medulloblastoma. These and other findings suggest that inhibitors of Sonic Hedgehog signaling may offer an effective way to target some malignancies.
Cholecystokinin receptors (1995)

The cholecystokinin (CCK) and gastrin families of peptides act as hormones and neuropeptides on central and peripheral CCK receptors to mediate secretion and motility in the gastrointestinal (GI) tract in the physiological response to a normal meal. CCK and its receptors are also widely distributed in the central nervous system (CNS) and contribute to the regulation of satiety, anxiety, analgesia, and dopamine-mediated behavior. Although the wide distribution, myriad number of functions, and reported pharmacological heterogeneity of CCK receptors would suggest a large number of receptor subtypes, the application of modern molecular biological techniques has identified two CCK receptors, CCK-A receptor (CCK-AR) and CCK-B receptor (CCK-BR), that mediate the actions of CCK and gastrin; gastrin receptors have been found to be identical to CCK-BR. CCK-AR, found predominantly in the GI system and select areas of the CNS, have high affinity for CCK and the nonpeptide antagonist L-364,718, whereas CCK-BR, found predominantly in the CNS and select areas of the GI system, have high affinity for CCK and gastrin and the nonpeptide antagonist L-365,260. Both CCK-AR and CCK-BR are highly conserved between species, although there is some tissue-specific variation in expression. Recombinant receptor expression faithfully reproduces the native receptor pharmacology and signal transduction pathways, allowing direct comparisons of receptor function between species as well as serving as a convenient source of receptor. Our present knowledge of the chromosomal localization, receptor gene structure, and primary sequence will allow further studies in disease association, receptor regulation, and structure-function analysis.
Silibinin Efficacy against Human Hepatocellular Carcinoma (2005)

Together, these results for the first time identify the biological efficacy of silibinin against HCC cells, suggesting the importance of conducting further investigations in preclinical HCC models, especially on in vivo efficacy, to support the clinical usefulness of silibinin against hepatocellular carcinoma in addition to its known clinical efficacy as an antihepatotoxic agent.
Trust management for the internet of things and its application to service composition (2012)

The Internet of Things (IoT) integrates a large amount of everyday life devices from heterogeneous network environments, bringing a great challenge into security and reliability management. Recognizing that the smart objects in IoT are most likely human-carried or human-operated devices, we propose a scalable trust management protocol for IoT, with the emphasis on social relationships. We consider multiple trust properties including honesty, cooperativeness, and community-interest to account for social interaction. Each node performs trust evaluation towards a limited set of devices of its interest only. The trust management protocol is event-driven upon the occurrence of a social encounter or interaction event, and trust is aggregated using both direct observations and indirect recommendations. We analyze the effect of trust parameters on trust assessment accuracy and trust convergence time. Our results show that there exists a trade-off between trust assessment accuracy vs. trust convergence time in the presence of false recommendations attacks performed by malicious nodes. We demonstrate the effectiveness of the proposed trust management protocol with a trust-based service composition application. Our results indicate that trust-based service composition significantly outperforms non-trust-based (random) service composition and its performance approaches the maximum achievable performance with global knowledge.
GFAP-Driven GFP Expression in Activated Mouse Müller Glial Cells Aligning Retinal Blood Vessels Following Intravitreal Injection of AAV2/6 Vectors (2010)

Our experiments indicate that AAV2 vectors carrying the GFAP promoter are a promising tool for specific expression of transgenes in activated glial cells.
Molecular-Scale Characterization of the Reaction of Ozone with Decanethiol Monolayers on Au(111) (1999)

The chemical reaction of ozone with decanethiol monolayers on Au(111) was characterized using X-ray photoelectron spectroscopy and scanning tunneling microscopy. Our results show that exposure to ozone results in oxidation of the thiol terminus. The reaction initiates at the domain boundary network of the alkanethiol monolayer and propagates into the domains. Above a threshold surface oxygen content, the monolayer converts to a two-dimensional fluid that can subsequently recrystallize to a commensurate monolayer of partially oxidized thiol. Further exposure to ozone results in conversion of the monolayer to a fluid phase and a 10% to 30% expansion of the Au lattice at the Au−thiol interface with concomitant formation of Au islands. Our results demonstrate that crystallographic defects in monolayer films can play an important role in their chemical reactions.
Interaction between the min locus and ftsZ (1990)

In Escherichia coli, distinct but similar minicell phenotypes resulting from mutation at the minB locus and increased expression of ftsZ suggested a possible interaction between these genes. A four- to fivefold increase in FtsZ resulting from increased gene dosage was found to suppress the lethality of minCD expressed from the lac promoter. Since increased MinCD did not affect the level of FtsZ, this suggested that MinCD may antagonize FtsZ to inhibit its cell division activity. This possibility was supported by the finding that alleles of ftsZ isolated as resistant to the cell division inhibitor SulA were also resistant to MinCD. Among the ftsZ(Rsa) alleles, two appeared to be completely resistant to MinCD as demonstrated by the lack of an effect of MinCD on cell length and a minicell phenotype observed in the absence of a significant increase in FtsZ. It was shown that SulA inhibits cell division independently of MinCD.
Cutaneous manifestations of internal malignant disease. (1987)

The skin can provide clues to the well-being of our patients. Some skin changes, such as hypertrichosis lanuginosa acquisita or erythema gyratum repens, are so specific that there is a virtual certainty of internal malignancy. Other changes, such as severe pruritus, are significant management problems in late-stage lymphoma and leukemia. Still others, such as herpes zoster in a cancer patient in remission, may be a marker for recurrent malignant disease. This review will discuss many of the skin changes associated with systemic cancer.
Compact broadband circularly polarized square microstrip antenna (1999)

A new design for achieving compact broadband circular polarization (CP) radiation of a square microstrip antenna is presented. The compactness of the microstrip antenna is easily obtained by inserting four slits of equal lengths at the patch edges, and broadband CP radiation is achieved simply by loading a chip resistor at a proper position in the patch. The present proposed CP design has been implemented with an increase of about 50% in CP bandwidth as compared to the compact CP design using inserted slits of unequal lengths. Details of the antenna design and experimental results are presented and discussed. ©1999 John Wiley & Sons, Inc. Microwave Opt Technol Lett 21: 423–425, 1999.
Bioinformatic tools and guideline for PCR primer design (2003)

&nbsp; Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no product due to non-specific amplification and/or primer-dimer formation, which can become competitive enough to suppress product formation. There are several online tools devoted to serving molecular biologist design effective PCR primers. This review intends to provide a guide to choosing the most efficient way to design a new specific-primer by applying current publicly available links and Web services. Also, the purpose here is to provide general recommendations for the design and use of PCR primers. &nbsp; Key words:&nbsp;Bio-computing,&nbsp;primer design,&nbsp;web-based resources.
Acute Intraoperative Arterial Lengthening for Closure of Large Vascular Gaps (1992)

This study demonstrates the feasibility of acute extraluminal expansion to elongate arteries intraoperatively in order to overcome defects too large to be repaired primarily. Twenty Sprague-Dawley rats were divided into two groups: an expander-elongation group and a nonexpanded control group of 10 rats each. Arterial resections were performed ranging from 6 to 22 mm. A miniaturized tissue expander was used to stretch vessels in three consecutive cycles over a 15- to 20-minute period (expander-elongation group). Defects twice as long as those which could be overcome by mobilization alone (nonexpanded control group) could be closed following the application of this technique without thrombosis. Initial laboratory findings and the application of this method in a clinical case are presented.
Long non-coding RNA HOTTIP promotes tumor growth and inhibits cell apoptosis in lung cancer. (2015)

Lung cancer is one of the leading causes of cancer-related deaths worldwide. Early diagnosis is the best defense against this threat and is therefore of vital importance. In this study, we investigated the role of long non-coding RNA HOTTIP in the tumor growth of lung cancer. Initially, we found that expression of HOTTIP was significantly elevated in 20 cases of lung cancer. HOTTIP was also differentially expressed in a consecutive of lung cancer cell lines. Furthermore, specific shRNA against HOTTIP was employed to deplete expression of HOTTIP in A549 cells and NCI-H446 cells. After successfully depletion of HOTTIP, cell proliferation and colony formation were significantly inhibited in vitro. Tumor growth in vivo was also suppressed after depletion of HOTTIP in a mouse model of lung cancer. Moreover, depletion of HOTTIP caused cell cycle arrest in G0/G1 phase and induced significant cell apoptosis. Cell cycle regulators Cdc25C, Cyclin B1 and Cyclin D1 were decreased upon depletion of HOTTIP. Pro-apoptotic factor Bad was up-regulated, whereas anti-apoptotic factors Bcl-2 and Bcl-xL were down-regulated after HOTTIP ablation. These data suggest that lncRNA HOTTIP contributes to tumor growth in vivo and in vitro and inhibits cell apoptosis in lung cancer.
Decline of exhaled isoprene in lung cancer patients correlates with immune activation (2012)

Isoprene (2-methylbuta-1,3-diene) represents a precursor molecule of isoprenoids (steroids, terpens), and available data suggest that isoprene is related to cholesterol biosynthesis. Breath concentrations of isoprene have been reported to be altered in a number of clinical conditions. However, the physiological meaning of isoprene changes has not yet been established. Utilizing proton-transfer-mass spectroscopy, we analyzed isoprene concentrations (m/z 69, tentatively identified as isoprene) in breath samples in Tedlar bags collected from 79 lung cancer patients (23 females, 56 males). Results were compared to the concentrations of immune activation marker neopterin (ELISA, BRAHMS, Hennigsdorf, Germany), lipid parameters (routine enzymology) and C-reactive protein (CRP). Isoprene concentrations were median 92.5 ppb (25th-75th percentile: 79-131 ppb). There was no relationship with staging, grading or age, but isoprene concentrations correlated significantly with total cholesterol (rs = 0.281, p < 0.01) and LDL cholesterol (rs = 0.236, p < 0.05). There was no significant relationship between exhaled isoprene concentrations and HDL cholesterol (rs = 0.048), triglycerides (rs = 0.164) and CRP (rs = -0.115; all not significant). A significant inverse correlation existed between isoprene and neopterin concentrations (rs = -0.215, p < 0.05); the latter also correlated with total cholesterol (rs = -0.343, p = 0.001), HDL cholesterol (rs = -0.273, p = 0.01), LDL cholesterol (rs = -0.236, p < 0.05) and CRP (rs = 0.230, p < 0.05) but not with triglycerides (rs = 0.035, not significant). Results suggest that immune activation might play a role in the decline of isoprene which is probably related to lipid metabolic changes. Interestingly, similar relationships between elevated neopterin and decreased lipid concentrations have been reported earlier in other clinical conditions, e.g. in patients with HIV-1 infection.
Studies on the Synthesis of Pyrimidine Deoxynucleosides. I. Synthesis of 2', 3'-Dideoxyuridine and 1-(3-Ethylthio-3-deoxy-β-D-xylofuranosyl) uracil (1970)

Treatment of 2, 2'-anhydro-1-(3, 5-di-O-acetyl-β-D-arabinofuranosyl) uracil (II) with sodium ethanethiol afforded 1-(3-ethylthio-3-deoxy-β-D-xylofuranosyl) uracil (IV) in 90% yield. Hydrogenation of 2, 2'-anhydro-1-(5-O-benzoyl-3-O-mesyl-β-D-arabinofuranosyl)-uracil (III) with Raney nickel resulted in formation of the 5, 6-dihydro derivative (VI). 5'-O-Benzoyl-2'-bromo-2'-deoxy-3'-O-mesyluridine (VII) was hydrogenated in the presence of Pd·BaSO4 or Raney nickel to yield 5'-O-benzoyl-2', 3'-dideoxyruidine (VIII). VIII was treated with alkali to give 2', 3'-dideoxyuridine (IX) in 50% overall yield from uridine. The mechanism of the reductive elimination of the cis-bromohydrin mesylate (VII) was presented. The treatment of VII with sodium methoxide in methanol gave 1-(2-bromo-2, 3-dideoxy-2-ene-β-D-glyceropentofuranosyl) uracil (XII) which was converted to IX by the catalytic hydrogenation. Bromination of IX afforded 5-bromo-2', 3'-dideoxyuridine (XIV).
Continuous-wave mode-locked and dispersion-compensated femtosecond optical parametric oscillator (1990)

We describe dispersion compensation of a cw mode-locked optical parametric oscillator based on a thin crystal of KTiOPO4 pumped intracavity by a standard colliding-pulse mode-locked dye laser, The device provides potential cw tunability from 0.72 to 4.5 μm with milliwatt outputs. Transform-limited pulses should be possible throughout the tuning range;here we report pulse widths of 105 fsec at 840 nm and 108 Hz. Active stabilization of the oscillator cavity is also discussed.
Connectionism in Perspective (1989)

Knowledge Representation and Memory. Perception and Action. Learning. Problem Solving and Reasoning. Trends, Research Programs. Abstracts, Work in Progress.
Early onset familial Alzheimer’s disease (2003)

Sequence variants in APP and PSEN1 accounted for the majority of neuropathologically confirmed autosomal dominant early onset AD; no mutations in PSEN2 were detected. There may be a further genetic factor involved in the etiology of autosomal dominant early onset AD.
Formation and intracellular localization of hepatitis C virus envelope glycoprotein complexes expressed by recombinant vaccinia and Sindbis viruses (1994)

Hepatitis C virus (HCV) encodes two putative virion glycoproteins (E1 and E2) which are released from the polyprotein by signal peptidase cleavage. In this report, we have characterized the complexes formed between E1 and E2 (called E1E2) for two different HCV strains (H and BK) and studied their intracellular localization. Vaccinia virus and Sindbis virus vectors were used to express the HCV structural proteins in three different cell lines (HepG2, BHK-21, and PK-15). The kinetics of association between E1 and E2, as studied by pulse-chase analysis and coprecipitation of E2 with an anti-E1 monoclonal antibody, indicated that formation of stable E1E2 complexes is slow. The times required for half-maximal association between E1 and E2 were 60 to 85 min for the H strain and more than 165 min for the BK strain. In the presence of nonionic detergents, two forms of E1E2 complexes were detected. The predominant form was a heterodimer of E1 and E2 stabilized by noncovalent interactions. A minor fraction consisted of heterogeneous disulfide-linked aggregates, which most likely represent misfolded complexes. Posttranslational processing and localization of the HCV glycoproteins were examined by acquisition of endoglycosidase H resistance, subcellular fractionation, immunofluorescence, cell surface immunostaining, and immunoelectron microscopy. HCV glycoproteins containing complex N-linked glycans were not observed, and the proteins were not detected at the cell surface. Rather, the proteins localized predominantly to the endoplasmic reticular network, suggesting that some mechanism exists for their retention in this compartment.
GridLAB-D Technical Support Document: Tape Modules Version 1.0 (2008)

GridLAB-D Technical Support Document describing tape modules, version 1.0.