gebhart/patrepeval huggingface dataset:
Development of High-Frequency Delivery System for Transposon Tn <i>919</i> in Lactic Streptococci: Random Insertion in <i>Streptococcus lactis</i> subsp. <i>diacetylactis</i> 18-16 (1987)

The conjugative transposon Tn919, originally isolated in Streptococcus sanguis FC1, is capable of low-frequency transfer (10 and 10 per recipient) on membrane filters to a wide number of streptococcal recipients including the industrially important lactic streptococci. The introduction of pMG600 (Lac Lax; a lactose plasmid capable of conjugative transfer at high frequencies and which, in certain hosts, confers an unusual clumping phenotype) into a Streptococcus lactis CH919 donor, generating S. lactis CH001, resulted in a significant improvement in the transfer frequency of Tn919 to S. lactis CK50 (1.25 x 10 per recipient). In addition, these matings could be performed on agar surfaces, allowing the recovery of a greater number of recipients than with filter matings. Tn919 also transferred at high frequency to S. lactis subsp. diacetylactis 18-16S but not to Streptococcus cremoris strains. Insertion in 18-16S transconjugants generated from filter matings with an S. lactis CH919 donor was random, occurring at different sites on the chromosome and also in plasmid DNA. Thus, the conditions necessary for the practical exploitation of Tn919 in the targeting and cloning of genes from a member of the lactic streptococci, namely, high-frequency delivery and random insertion in host DNA, were achieved.
N-Acetylglucosaminyltransferase III Antagonizes the Effect of N-Acetylglucosaminyltransferase V on α3β1 Integrin-mediated Cell Migration (2006)

N-acetylglucosaminyltransferase V (GnT-V) catalyzes the addition of beta1,6-GlcNAc branching of N-glycans, which contributes to metastasis. N-acetylglucosaminyltransferase III (GnT-III) catalyzes the formation of a bisecting GlcNAc structure in N-glycans, resulting in the suppression of metastasis. It has long been hypothesized that the suppression of GnT-V product formation by the action of GnT-III would also exist in vivo, which will consequently lead to the inhibition of biological functions of GnT-V. To test this, we draw a comparison among MKN45 cells, which were transfected with GnT-III, GnT-V, or both, respectively. We found that alpha3beta1 integrin-mediated cell migration on laminin 5 was greatly enhanced in the case of GnT-V transfectant. This enhanced cell migration was significantly blocked after the introduction of GnT-III. Consistently, an increase in bisected GlcNAc but a decrease in beta1,6-GlcNAc-branched N-glycans on integrin alpha3 subunit was observed in the double transfectants of GnT-III and GnT-V. Conversely, GnT-III knockdown resulted in increased migration on laminin 5, concomitant with an increase in beta1,6-GlcNAc-branched N-glycans on the alpha3 subunit in CHP134 cells, a human neuroblastoma cell line. Therefore, in this study, the priority of GnT-III for the modification of the alpha3 subunit may be an explanation for why GnT-III inhibits GnT-V-induced cell migration. Taken together, our results demonstrate for the first time that GnT-III and GnT-V can competitively modify the same target glycoprotein and furthermore positively or negatively regulate its biological functions.
Black start capability assessment in power system restoration (2011)

Black start (BS) capability assessment is important for system planners to prepare the power system restoration (PSR) plan. To achieve a faster restoration process, installing new BS generators can be beneficial in accelerating system restoration. While additional BS capability does not automatically benefit the restoration process, power systems have to update the PSR plan and quantify the benefit based on appropriate criteria. In this paper, a decision support tool, developed in an EPRI project, using Generic Restoration Milestones (GRMs)-based strategy is utilized to provide a quantitative way for assessing the optimal installation location and amount of BS capability. Based on the proposed criteria, the benefit from additional BS capability is quantified in terms of system restoration time. The IEEE Reliability Test System (RTS) 24-bus test system is used for validation of the proposed strategy, using the System Restoration Navigator (SRN) restoration tool. It is shown that power systems can benefit from new BS generators to reduce the restoration time. However, there is a threshold beyond which system restoration time cannot be further reduced from additional BS capability. Economic considerations should be taken into account when assessing additional BS capabilities.
Dual coenzyme specificity of <i>Archaeoglobus fulgidus</i> HMG‐CoA reductase (2000)

Comparison of the inferred amino acid sequence of orf AF1736 of Archaeoglobus fulgidus to that of Pseudomonas mevalonii HMG-CoA reductase suggested that AF1736 might encode a Class II HMG-CoA reductase. Following polymerase chain reaction-based cloning of AF1736 from A. fulgidus genomic DNA and expression in Escherichia coli, the encoded enzyme was purified to apparent homogeneity and its enzymic properties were determined. Activity was optimal at 85 degrees C, deltaHa was 54 kJ/mol, and the statin drug mevinolin inhibited competitively with HMG-CoA (Ki 180 microM). Protonated forms of His390 and Lys277, the apparent cognates of the active site histidine and lysine of the P. mevalonii enzyme, appear essential for activity. The mechanism proposed for catalysis of P. mevalonii HMG-CoA reductase thus appears valid for A. fulgidus HMG-CoA reductase. Unlike any other HMG-CoA reductase, the A. fulgidus enzyme exhibits dual coenzyme specificity. pH-activity profiles for all four reactions revealed that optimal activity using NADP(H) occurred at a pH from 1 to 3 units more acidic than that observed using NAD(H). Kinetic parameters were therefore determined for all substrates for all four catalyzed reactions using either NAD(H) or NADP(H). NADPH and NADH compete for occupancy of a common site. k(cat)[NAD(H)]/k(cat)[NADP(H)] varied from unity to under 70 for the four reactions, indicative of slight preference for NAD(H). The results indicate the importance of the protonated status of active site residues His390 and Lys277, shown by altered K(M) and k(cat) values, and indicate that NAD(H) and NADP(H) have comparable affinity for the same site.
Carfilzomib, Rituximab and Dexamethasone (CaRD) Is Highly Active and Offers a Neuropathy Sparing Approach For Proteasome-Inhibitor Based Therapy In Waldenstrom’s Macroglobulinemia (2013)

Abstract Bortezomib is active in Waldenstrom’s macroglobulinemia (WM) but associated with considerable peripheral neuropathy (PN). The proteasome inhibitor carfilzomib (CFZ) is approved in the USA for relapsed/refractory myeloma. Herein, we examined the efficacy and safety of carfilzomib, rituximab, and dexamethasone (CaRD) in 31 proteasome inhibitor and rituximab naive WM patients with symptomatic disease. Median baseline characteristics: age 61, prior therapies 0 (range 0-1), hematocrit 32.3%, hemoglobin 10.7 g/dL, serum IgM 3375 mg/dL, serum M-protein 2.185 g/dL, B2M 3.6 mg/L, and bone marrow disease involvement 60%. Therapy consisted of IV CFZ 20 mg/m2 (cycle 1) then 36 mg/m2 (cycles 2 and beyond) with IV dexamethasone (dex) 20 mg given on days 1,2,8,9 and rituximab 375 mg/m2 on days 2,9 of each 21-day cycle. Treatment consisted of six induction cycles, then maintenance beginning 8 weeks after induction (given every 8 weeks for eight cycles; consisted of CFZ 36 mg/m2, and IV dex 20 mg on days 1,2 and rituximab 375 mg/m2 on day 2). Patients with IgM level >4000 mg/dL underwent plasmapheresis and/or had rituximab held until IgM <4000 mg/dL to prevent symptomatic IgM flare. Patients received oral acyclovir (400 mg twice daily) and famotidine (20 mg twice daily) as concomitant medications. For all 31 patients, median serum IgM levels and M-protein declined to 749 mg/dL and 0.7 g/dL, respectively (p<0.00001). Median hematocrit and hemoglobin rose to 40.9% and 13.7 g/dL, respectively (p<0.00001). A total of 30 patients concluded induction therapy with bone marrow tumor involvement reduced to a median of 7.5% (p=0.0003). The best overall response rate using criteria adapted from the 3rd International Workshop on WM was 81% (1 CR, 8 VGPR, 12 PR, 4 Minor Responses). With a median follow-up of 8 cycles, 22 patients remain on study, including 20 currently on maintenance therapy. Median time to response (for minor responders or better) was 2.1 months. Grade >2 treatment related toxicities included asymptomatic elevation in lipase (12.9%), dex-related hyperglycemia (6.45%), reversible neutropenia (9.67%), and cardiomyopathy (3.22%). There were no grade 2 or greater PN events. Treatment discontinuation occurred for non-response (n=8), cardiomyopathy in a patient with multiple cardiac risk factors (n=1), and progressive disease (n=1). CaRD is highly active and offers a neuropathy sparing approach for proteasome-inhibitor based therapy in WM. Disclosures: Off Label Use: Carfilzomib is a novel proteasome inhibitor, which offers a neuropathic sparing approach on waldenstrom macroglobulinemia disease when used in a combination therapy with rituximab and dexamethasome.
Rhinoviral stimuli, epithelial factors and ATP signalling contribute to bronchial smooth muscle production of IL-33 (2015)

RV infection of BSMCs and activation of TLR3 and RIG-I-like receptors cause expression and production of IL-33. Epithelial-released factor(s) increase BSMC expression of IL-33 and exhibit positive interaction with dsRNA. Increased BSMC IL-33 associates with ATP release and is antagonised by suramin. We suggest that epithelial-derived factors contribute to baseline BSMC IL-33 production, which is further augmented by RV infection of BSMCs and stimulation of their pathogen-recognising receptors.
Urinary loss of glucose, phosphate, and protein by diffusion into proximal straight tubules injured by D-serine and maleic acid. (1985)

In several models of acute renal failure leakage of glomerular filtrate out of the tubule is an important pathogenetic mechanism; however, bidirectional diffusion of solute to account for certain pathophysiologic features of acute renal failure has received meager attention. Using micropuncture and clearance methods, we assessed sequentially leakage of solutes and inulin across proximal straight tubules (PST) injured by two nephrotoxins. In d-serine-treated rats with extensive necrosis of PST, the basis for glucosuria and tubular leakage of inulin was studied. Glucose absorption by the proximal convoluted tubule and glucose delivery to the PST were normal, but glucose delivery to the distal tubule was increased nearly 8-fold, indicating diffusion of glucose from interstitial to tubular luminal fluid across the necrotic PST. Total kidney inulin clearance was greatly reduced, but single nephron glomerular filtration rate, based on proximal convoluted tubule samples, was normal, indicating tubular loss of inulin. Urinary recovery of [14C]inulin infused into tubular lumina revealed that proximal convoluted tubule and distal tubule were impermeable to inulin and that inulin diffused out of the necrotic PST. The progressive return over 6 days of tubular impermeability for inulin correlated with relining of PST with new cells. In maleic acid-treated rats the site and extent of tubular necrosis and the nature of urinary loss of solutes were studied. Microdissection revealed that maleic acid caused limited necrosis of PST which averaged 7.4% of total proximal tubular length. Increased urinary excretion of protein, phosphate, and glucose and increased tubular permeability to microinfused [14C]inulin occurred with the onset of PST necrosis, and return of these abnormalities to normal correlated with the degree of cellular repair of the PST. Together these data indicate that with severe cellular injury there is bidirectional, concentration-dependent diffusion of solutes between the interstitial and tubular fluids. Thus, experimental or human toxic nephropathies should not be classified as acquired Fanconi's syndrome unless specific tubular transport defects are present.
Mechanisms Involved in the Pathogenesis of Sepsis Are Not Necessarily Reflected by In Vitro Cell Activation Studies (1998)

It is thought that lipopolysaccharide (LPS) from gram-negative bacteria contributes significantly to the pathogenesis of septic shock. In vitro studies to address the mechanisms involved in this process have often investigated human monocytes or mouse macrophages, since these cells produce many of the mediators found in septic patients. Targeting of these mediators, especially tumor necrosis factor alpha (TNF-alpha), has been pursued as a means of reducing mortality in sepsis. Two experimental approaches were designed to test the assumption that in vitro studies with macrophages accurately predict in vivo mechanisms of LPS pathogenesis. In the first approach, advantage was taken of the fact that on consecutive days after injection of thioglycolate into mice, increased numbers of macrophages could be harvested from the peritoneum. These cells manifested markedly enhanced levels of in vitro TNF-alpha, interleukin 6 (IL-6), and nitric oxide production in response to LPS. In D-galactosamine-sensitized mice, however, thioglycolate treatment significantly decreased mortality due to LPS, as well as levels of circulating TNF-alpha and IL-6. Anti-TNF-alpha treatment confirmed this cytokine's role in the observed lethality. In a second experimental approach, we compared the mouse macrophage-stimulating potencies of different LPS preparations with their lethalities to mice. In these studies, the in vitro macrophage-stimulating profiles presented by rough-LPS and smooth-LPS preparations were the reverse of their relative lethal potencies in vivo. In conclusion, peritoneal macrophages appear not to be the major cells responsible for the overall host response during endotoxic shock. These findings underscore the importance of verifying the correlation of in vivo systems with in vitro systems when attributing specific functions to a cell type.
FOCUS ON PLASMA MEDICINE (2009)

This article was published in the journal, New Journal of Physics, [© IOP Publishing Ltd and Deutsche Physikalische Gesellschaft] and is also available:- http://dx.doi.org/10.1088/1367-2630/11/11/115011
Fabrication of MgAl2O4 tunnel barrier by radio frequency-sputtering method and magnetoresistance effect through it with Fe or Fe4N ferromagnetic electrode (2015)

Spinel MgAl2O4 thin films were deposited on MgO single-crystal substrates and epitaxial Fe (or Fe4N) thin films by RF-sputtering from a ceramic target. Epitaxial relationship was confirmed by X-ray diffraction analysis between the crystalline spinel MgAl2O4 films and the respective substrate and underlayers, while no diffraction peak was observed from the films deposited on amorphous substrates. Spin-valve type magnetic tunnel junctions (MTJs) with a stacking structure of Fe [Fe4N]/MgAl2O4/CoFeB/Ru/Fe/MnIr exhibited normal [inverse] tunnel magnetoresistance (TMR) effect, reflecting the sign of spin polarization of Fe [Fe4N]. The maximum magnitude of the TMR ratio obtained for the Fe-based and Fe4N-based MTJs was 67% and 18%, respectively. The resistance area product values of the MTJs were significantly larger than the reported values for the MTJs with a post-oxidized spinel MgAl2O4 barrier.
Special Issue on “Nanocarbon Electrochemistry and Electroanalysis” (2016)

This Special Issue contains a collection of papers from the 2015 E-MRS Fall Meeting (European Materials Research Society), Symposium R entitled “Nanocarbon Electrochemistry and Interfaces”. The meeting was held September 15–18 in Warsaw, Poland. Approximately 60 scientists and students from 11 countries participated in the symposium. There were 9 invited talks, 22 oral presentations and 27 posters presented during the 2.5 day symposium. This symposium focused on the material properties, electrochemical behavior and electrochemical application of novel carbon materials including diamond, carbon nanotubes (CNTs), graphene, graphene oxide, carbon fiber, carbon onions, porous carbon, carbon black, carbon/diamond nanoparticles, carbon nitride, silicon carbide and their nanocomposites. Applications of these nanocarbons in electroanalysis, biosensing, electrocatalysis, electrosynthesis, environmental degradation, energy conversion and storage were covered.1 This Special Issue contains 5 reviews and 27 original research papers. The reviews include (i) recent progress with nanocarbon electrodes and electroanalytical applications, (ii) electrochemical grafting and surface functionalization of carbon electrodes for electroanalytical applications, (iii) the use of graphene for immunosensors, (iv) bioelectroanalytical applications of carbon nanoparticles, and (v) diamond-based scanning probe microscopic tips. Among 27 original research papers, 5 papers focus on the electrochemical properties of carbon materials, 18 papers are about the sensor development using nanocarbons, and 4 papers are devoted to electrochemical applications of nanocarbons. We believe this Special Issue will bring the readership up to dateabout progress with preparation and characterization of nanocarbons and their emerging applications in electrochemistry. The content will hopefully stimulate new ideas for nanocarbon-based materials in electroanalytical chemistry and facilitate interactions between material scientists, chemists, biochemists, physics, and engineers working in the field. 1 1
Optimising trade-offs among stakeholders in ad auctions (2014)

We examine trade-offs among stakeholders in ad auctions. Our metrics are the revenue for the utility of the auctioneer, the number of clicks for the utility of the users and the welfare for the utility of the advertisers. We show how to optimize linear combinations of the stakeholder utilities, showing that these can be tackled through a GSP auction with a per-click reserve price. We then examine constrained optimization of stakeholder utilities.
Faraday rotation in highly birefringent optical fibers (1980)

Faraday rotation is obtained in highly birefringent single-mode fibers by using alternating or periodically spaced regions of magnetic field. This approach has potential applications in isolators, circulators, combination tuning and unidirectional elements, and for studying fiber birefringence.
Aggregate Constraints for Virtual Manipulation with Soft Fingers (2015)

Interactive dexterous manipulation of virtual objects remains a complex challenge that requires both appropriate hand models and accurate physically-based simulation of interactions. In this paper, we propose an approach based on novel aggregate constraints for simulating dexterous grasping using soft fingers. Our approach aims at improving the computation of contact mechanics when many contact points are involved, by aggregating the multiple contact constraints into a minimal set of constraints. We also introduce a method for non-uniform pressure distribution over the contact surface, to adapt the response when touching sharp edges. We use the Coulomb-Contensou friction model to efficiently simulate tangential and torsional friction. We show through different use cases that our aggregate constraint formulation is well-suited for simulating interactively dexterous manipulation of virtual objects through soft fingers, and efficiently reduces the computation time of constraint solving.
Uncritical positive regard? Issues in the efficacy and safety of psychotherapy (2007)

The recent review of the selective serotonin reuptake inhibitors (SSRIs) by the Committee on Safety of Medicines (CSM) and the Food and Drug Administration was occasioned by media concerns about the safety of this class of antidepressant. In much of the prior and subsequent reporting of this issue, two assumptions have consistently been aired. The first is that psychotherapy is equally effective as drugs and the second is that since psychotherapy is not a drug, it is necessarily safer than drug treatments. From these two assumptions emerges a common presumption that psychotherapy should be the preferred approach for many if not most cases of depressive and anxiety disorders. But is this true? And if not, what implications does it have for the management of the new therapists that will soon be employed following the UK government’s award of £150 m for psychotherapy services in depression and anxiety? (http://www.rcpsych.ac.uk/pressparliament/pressreleases2006/ pr955.aspx)
Genetic Analysis of Organ Fusion in Arabidopsis thaliana (1998)

Postgenital organ fusion occurs most commonly during reproductive development and is important in many angiosperms during genesis of the carpel. Although a number of mutants have been described that manifest ectopic organ fusion, little is known about the genes involved in regulating this process. In this article we describe the characterization of a collection of 29 Arabidopsis mutants showing an organ fusion phenotype. Mapping and complementation analyses revealed that the mutant alleles define nine different loci distributed throughout the Arabidopsis genome. Multiple alleles were isolated for the four complementation groups showing the strongest organ fusion phenotype while the remaining five complementation groups, all of which show only weak floral organ fusion, have a single representative allele. In addition to fusion events between aerial parts of the shoot, some mutants also show abnormal ovule morphology with adjacent ovules joined together at maturity. Many of the fusion mutants isolated have detectable differences in the rate at which chlorophyll can be extracted; however, in one case no difference could be detected between mutant and wild-type plants. In three mutant lines pollen remained unresponsive to contact with the mutant epidermis, demonstrating that organ fusion and pollen growth responses can be genetically separated from one another.
ChemInform Abstract: SYNTHESIS AND BIOLOGICAL CHARACTERIZATION OF 2‐(TETRAHYDROPYRAN‐4‐YL)THIAZOLES (1983)

Abstract Das Säurechlorid (I) wird im Ammoniakstrom in das Amid (II) und weiter mit Phosphorsulfid in das Thioamid (III) übergeführt.
Membrane antigen in small cell carcinoma of the lung defined by monoclonal antibody SM1. (1984)

Mouse myeloma cells were fused with spleen cells from BALB/c mice immunized with a cell line derived from human small cell carcinoma (SCC) of the lung. The cloned hybridoma SM1 produced antibody that was reactive with the surface membrane of SCC cell lines and SCC tumors but not with the membrane of several non-SCC cell lines and tumors. SM1 ascites fluid was used to screen for reactivity of the antibody with other human cancer cell lines, tumor tissues, and normal tissues. SM1 antibody was found to be unreactive with neuroblastoma, adrenal carcinoma, melanoma, and bronchial carcinoid. Reactivity was detected with some breast carcinoma cell lines but not with breast cancer tissue specimens. In the same individual, the antibody was reactive with SCC lung tumor and SCC metastatic to the liver but not with normal tissues, including bronchus, lung parenchyma, liver, kidney, and brain. Human erythrocytes and marrow cells were also unreactive. Since SM1 detects an antigen that is present in greatest amounts on the surface membrane of SCC of the lung, this antibody may be useful in tracing the lineage patterns of human lung cancers.