gebhart/patrepeval huggingface dataset:
Polyfluoroalkyl derivatives of nitrogen. Part XXVII. Some reactions of NN-bistrifluoromethylvinylamine (1968)

NN-Bistrifluoromethylvinylamine, prepared in high yield by the dehydrohalogenation of 2-iodo- or 2-bromo-NN-bistrifluoromethylethylamine, reacts with hydrogen bromide or with N-bromobistrifluoromethylamine in the dark to give 1-bromo-NN-bistrifluoromethylethylamine or 1,1-di(bistrifluoromethylamino)-2-bromoethane, respectively, which indicates that the olefin is polarised in the sense (CF3)2N·[graphic omitted]. The products from the same reactants under conditions conducive to the formation of free-radical intermediates are 2-bromo-NN-bistrifluoromethylethylamine and 1,2-di(bistrifluoromethylamino)-1-bromoethane, respectively. Dehydrobromination of the isomeric 1 : 1 adducts [(CF3)2N]2CH·CH2Br and (CF3)2N·CHBr·CH2·N(CF3)2 gives the corresponding olefins in good yield. Hydrogen bromide reacted with 1,1-di(bistrifluoromethylamino)ethylene when exposed to u.v. light, but not in the presence of aluminium bromide. N-Bromobistrifluoromethylamine reacts with cyclopropane to give bromocyclopropane and bistrifluoromethylamine, and not 3-bromo-NN-bistrifluoromethylpropylamine.
Advanced biofuel production in microbes (2010)

The cost-effective production of biofuels from renewable materials will begin to address energy security and climate change concerns. Ethanol, naturally produced by microorganisms, is currently the major biofuel in the transportation sector. However, its low energy content and incompatibility with existing fuel distribution and storage infrastructure limits its economic use in the future. Advanced biofuels, such as long chain alcohols and isoprenoid- and fatty acid-based biofuels, have physical properties that more closely resemble petroleum-derived fuels, and as such are an attractive alternative for the future supplementation or replacement of petroleum-derived fuels. Here, we review recent developments in the engineering of metabolic pathways for the production of known and potential advanced biofuels by microorganisms. We concentrate on the metabolic engineering of genetically tractable organisms such as Escherichia coli and Saccharomyces cerevisiae for the production of these advanced biofuels.
An octaethylene glycol monododecyl ether‐based mixed micellar assay for determining the lipid acyl hydrolase activity of patatin (2001)

Patatin was extracted from potato tubers (Solanum tuberosum L. cv. Spunta) and purified to homogeneity by ammonium sulfate salt fractionation and one sole chromatographic step. A spectrophotometric mixed micellar assay for patatin lipid acyl hydrolase (LAH) activity was designed with the detergent octaethylene glycol monododecyl ether (C12E8). Patatin LAH used p-nitrophenyl butyrate (PNP-butyrate) as substrate when solubilized in (C12E8) micelles. In the mixed micellar system, patatin LAH responds to the PNP-butyrate surface concentration expressed as mol% (= [PNP-butyratel x 100/([detergentl critical micellar concentration)) and not to the molarity of PNP-butyrate. The kinetic parameters were determined; Vmax was independent of the mixed micelle concentration, as was Km, when expressed as mol%. However, Km was dependent on C12E8 concentration when expressed in molar concentration. C12E8/PNP-butyrate proved to be a reliable system for assaying patatin LAH activity and is superior to the commonly used Triton X-100 and SDS methods. It permits investigation of the substrate requirements of patatin LAH activity because the concentration-independent Km can be determined both in mol% and as the absolute number of substrate molecules per micelle. In addition, the detergent did not affect the enzyme activity.
Programming pearls (1986)

article Free Access Share on Programming pearls: cutting the Gordian knot Author: Jon Bentley AT&T Bell Laboratories, Room 2C-317, 600 Mountain Ave., Murray Hill, NJ AT&T Bell Laboratories, Room 2C-317, 600 Mountain Ave., Murray Hill, NJView Profile Authors Info & Claims Communications of the ACMVolume 29Issue 2Feb. 1986 pp 92–96https://doi.org/10.1145/5657.315569Online:01 February 1986Publication History 4citation916DownloadsMetricsTotal Citations4Total Downloads916Last 12 Months27Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Stabilization of aβ-Hairpin Conformation in a Cyclic Peptide Using the Templating Effect of a Heterochiral Diproline Unit (1998)

A straightforward and effective method of stabilizing a β-hairpin conformation in a cyclic protein loop mimetic is described, which exploits the templating effect of a heterochiral D-Pro-L-Pro dipeptide unit. A twelve-residue β-hairpin loop was grafted from the extracellular interferon γ receptor onto the heterochiral D-Pro-L-Pro dipeptide template to afford a fourteen-residue cyclic peptide. The residues directly attached to the D-Pro-L-Pro template are shown by NMR spectroscopy to structurally mimic corresponding residues in adjacent antiparallel β-strands in the receptor. MD Simulations with and without time-averaged distance restraints support this view and indicate that the tip of the loop is more flexible, as inferred also for the receptor protein from crystallographic data. The templating effect of the heterochiral diproline unit also promotes efficient backbone cyclization of the fourteen-residue linear peptide precursor, suggesting that a wide variety of related protein loop mimetics incorporating the D-Pro-L-Pro template might be readily accessible.
Volatile Surfactant-Assisted MOCVD: Application to LaAlO3 Thin-Film Growth (2000)

A new approach to the CVD of oxides with kinetically hindered diffusion, called volatile surfactant-assisted (VSA) metal–organic chemical vapor deposition (MOCVD), consisting of film deposition in the presence of a volatile low melting point oxide (Bi2O3) has been developed. The process was applied to the deposition of LaAlO3 films, and a model of the process was proposed. Epitaxial and textured LaAlO3 films on various substrates were obtained, both by thermal and VSA MOCVD. A marked improvement in crystalline quality and surface morphology was found for the films deposited by VSA MOCVD. LaAlO3 films obtained in the presence of Bi2O3 did not contain Bi. A significant increase (up to five times) of the deposition rate was observed for LaAlO3 films deposited by VSA MOCVD compared with that for the films grown by thermal MOCVD.
Evidence for a complex of three beta-oxidation enzymes in Escherichia coli: induction and localization (1977)

The enzymes for beta-oxidation of fatty acids in inducible and constitutive strains of Escherichia coli were assayed in soluble and membrane fractions of disrupted cells by using fatty acid and acyl-coenzyme A (CoA) substrates containing either 4 or 16 carbon atoms in the acyl moieties. Cell fractionation was monitored, using succinic dehydrogenase as a membrane marker and glucose 6-phosphate dehydrogenase as a soluble marker. Acyl-CoA synthetase activity was detected exclusively in the membrane fraction, whereas acyl-CoA dehydrogenase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase, and 3-ketoacyl-CoA thiolase activities that utilized both C4 and C16 acyl-CoA substrates were isolated from the soluble fraction. 3-Hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase, and 3-ketoacyl-CoA thiolase activities assayed with both C4 and C16 acyl-CoA substrates co-chromatographed on gel filtration and ion-exchange columns and cosedimented in glycerol gradients. The data show that these three enzyme activities of the fad regulon can be isolated as a multienzyme complex. This complex dissociates in very dilute preparations; however, in those preparations where the three activities are separated, the fractionated species retain activity with both C4 and C16 acyl-CoA substrates.
Fragment assembly with double-barreled data (2001)

For the last twenty years fragment assembly was dominated by the "overlap - layout - consensus" algorithms that are used in all currently available assembly tools. However, the limits of these algorithms are being tested in the era of genomic sequencing and it is not clear whether they are the best choice for large-scale assemblies. Although the "overlap - layout - consensus" approach proved to be useful in assembling clones, it faces difficulties in genomic assemblies: the existing algorithms make assembly errors even in bacterial genomes. We abandoned the "overlap - layout - consensus" approach in favour of a new Eulerian Superpath approach that outperforms the existing algorithms for genomic fragment assembly (Pevzner et al. 2001 InProceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01), 256-26). In this paper we describe our new EULER-DB algorithm that, similarly to the Celera assembler takes advantage of clone-end sequencing by using the double-barreled data. However, in contrast to the Celera assembler, EULER-DB does not mask repeats but uses them instead as a powerful tool for contig ordering. We also describe a new approach for the Copy Number Problem: "How many times a given repeat is present in the genome?". For long nearly-perfect repeats this question is notoriously difficult and some copies of such repeats may be "lost" in genomic assemblies. We describe our EULER-CN algorithm for the Copy Number Problem that proved to be successful in difficult sequencing projects.
Common neuroectodermal antigens on human melanoma, neuroblastoma, retinoblastoma, glioblastoma and fetal brain revealed by hybridoma antibodies raised against melanoma cells (1981)

The hybridoma system has been utilized to produce antibodies to characterize the cell surface antigens on human melanoma cells. On initial screening, two antibodies derived by the fusion of mouse myeloma cell (SP2/0-Ag14) and splenocytes from a mouse immunized with a melanoma cell line (CaCL 78-1) showed cross-reactivity with 10 melanoma cell lines and did not react with any of 4 epithelial cancer lines, or 4 normal adult fibroblast lines. However, because of reactivity with 2 neuroblastoma cell lines, additional testing with other neuroectodermal derivatives was carried out and revealed a broad cross-reactivity among melanomas, neuroblastomas, retinoblastomas and glioblastomas and against antigens shared by fetal but not adult brain. Thus, these results indicate the existence of common neuroectodermal antigens on melanoma cells. Before melanoma specificity can be claimed for, an antibody reactivity with nonmelanoma cells bearing these neuroectodermal antigen should be excluded.
Cubic lipid-water phases: structures and biomembrane aspects (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCubic lipid-water phases: structures and biomembrane aspectsK. LarssonCite this: J. Phys. Chem. 1989, 93, 21, 7304–7314Publication Date (Print):October 1, 1989Publication History Published online1 May 2002Published inissue 1 October 1989https://pubs.acs.org/doi/10.1021/j100358a010https://doi.org/10.1021/j100358a010research-articleACS PublicationsRequest reuse permissionsArticle Views1684Altmetric-Citations500LEARN 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 options Get e-Alerts
Systemic Vesicular Stomatitis Virus Selectively Destroys Multifocal Glioma and Metastatic Carcinoma in Brain (2008)

Metastatic tumors and malignant gliomas make up the majority of cancers in the brain. They are invariably fatal and there is currently no cure. From in vitro comparisons of a number of viruses, we selected one that appeared the best in selectively killing glioblastoma cells. This replication-competent virus, the glioma-adapted vesicular stomatis virus strain VSVrp30a, was used for in vivo tests with the underlying view that infection of tumor cells will lead to an increase in the number of viruses subsequently released to kill additional tumor cells. Intravenous injection of VSVrp30a expressing a green fluorescent protein reporter, rapidly targeted and destroyed multiple types of human and mouse tumors implanted in the mouse brain, including glioblastoma and mammary tumors. When tumors were implanted both in the brain and peripherally, emulating systemic cancer metastasis, tumors inside and outside the brain were simultaneously infected. Intranasal inoculation, leading to olfactory nerve transport of the virus into the brain, selectively infected and killed olfactory bulb tumors. Neither control cortical wounds nor transplanted normal mouse or human cells were targeted, indicating viral tumor selectivity. Control viruses, including pseudorabies, adeno-associated, or replication-deficient VSV, did not infect the brain tumor. Confocal laser time-lapse imaging through a cranial window showed that intravenous VSV infects the tumor at multiple sites and kills migrating tumor cells. Disrupted tumor vasculature, suggested by dye leakage, may be the port of entry for intravenously delivered VSV. Quantitative PCR analysis of how VSVrp30a selectively infected tumor cells suggested multiple mechanisms, including cell surface binding and internalization.
Full‐color reflective display device using holographically fabricated polymer‐dispersed liquid crystal (HPDLC) (1999)

Abstract— A method of controlling the color of a holographic polymer‐dispersed liquid‐crystal (HPDLC) reflective display device has been achieved. By merely controlling the optical setup during fabrication, without changing the materials or laser light source, three primary‐color devices were fabricated. Since the color of the device can be controlled continuously, a large color‐reproducible area on the chromaticity diagram can be obtained. The resulting device was adequately transparent at other wavelengths to enable multiple devices to be stacked to obtain a mixture of colors. There was no significant change in color when applying an electric field. The three devices had similar reflectances and electro‐optical characteristics. Therefore, this device has good potential for full‐color display applications.
Application of ANN methods for instrument transformer correction in transmission line protection (2001)

The aim of this paper is to present ANN methods intended for dynamic compensation of current transformers (CTs) and capacitive voltage transformers (CVTs) used for measurements in high voltage power systems. The nonlinear multilayer recursive artificial neural networks (ANNs) have been used for modelling inverse transfer functions of the transformers. The problems as well as the results obtained for different network parameters are presented. The issue of correct application of these novel methods in real protective relays has been discussed.
Inhibition of signal transduction by the Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin results in cytostasis and apoptosis. (2001)

17-Allylamino-17-demethoxygeldanamycin (17AAG) is a first-in-class heat shock protein 90 (Hsp90) molecular chaperone inhibitor to enter clinical trials. The downstream molecular and cellular consequences of Hsp90 inhibition are not well defined. 17AAG has shown activity against human colon cancer in cell culture and xenograft models. In this study, we demonstrated that in addition to depleting c-Raf-1 and inhibiting ERK-1/2 phosphorylation in human colon adenocarcinoma cells, 17AAG also depleted N-ras, Ki-ras, and c-Akt and inhibited phosphorylation of c-AKT: A consequence of these events was the induction of cell line-dependent cytostasis and apoptosis, although the latter did not result from dephosphorylation of proapoptotic BAD: One cell line, KM12, did not exhibit apoptosis and in contrast to the other cell lines overexpressed Bag-1, but did not express BAX: Taken together with other determinants of 17AAG sensitivity, these results should contribute to a more complete understanding of the molecular pharmacology of 17AAG, which in turn should aid the future rational clinical development and use of the drug in colon and other tumor types.
Analysis of surface electrocardiograms in atrial fibrillation: techniques, research, and clinical applications (2006)

Atrial fibrillation (AF) is the most common arrhythmia encountered in clinical practice. Neither the natural history of AF nor its response to therapy is sufficiently predictable by clinical and echocardiographic parameters. The purpose of this article is to describe technical aspects of novel electrocardiogram (ECG) analysis techniques and to present research and clinical applications of these methods for characterization of both the fibrillatory process and the ventricular response during AF. Atrial fibrillatory frequency (or rate) can reliably be assessed from the surface ECG using digital signal processing (extraction of atrial signals and spectral analysis). This measurement shows large inter-individual variability and correlates well with intra-atrial cycle length, a parameter which appears to have primary importance in AF maintenance and response to therapy. AF with a low fibrillatory rate is more likely to terminate spontaneously and responds better to antiarrhythmic drugs or cardioversion, whereas high-rate AF is more often persistent and refractory to therapy. Ventricular responses during AF can be characterized by a variety of methods, which include analysis of heart rate variability, RR-interval histograms, Lorenz plots, and non-linear dynamics. These methods have all shown a certain degree of usefulness, either in scientific explorations of atrioventricular (AV) nodal function or in selected clinical questions such as predicting response to drugs, cardioversion, or AV nodal modification. The role of the autonomic nervous system for AF sustenance and termination, as well as for ventricular rate responses, can be explored by different ECG analysis methods. In conclusion, non-invasive characterization of atrial fibrillatory activity and ventricular response can be performed from the surface ECG in AF patients. Different signal processing techniques have been suggested for identification of underlying AF pathomechanisms and prediction of therapy efficacy.
Specific Association Of CD63 with the VLA-3 and VLA-6 Integrins (1995)

We screened monoclonal antibodies to cell-surface proteins and selected an antibody, called 6H1, that recognizes a putative integrin-associated protein. The 6H1 monoclonal antibody (mAb) indirectly coprecipitated alpha 3 beta 1 and/or alpha 6 beta 1, but not alpha 2 beta 1, or alpha 5 beta 1 from Brij 96 detergent lysates of multiple cell lines. Large scale purification using the 6H1 mAb yielded a single protein of 45-60 kDa with an amino-terminal sequence that exactly matched CD63. Confirming that the 6H1 mAb recognized the CD63 protein, 6H1 and a known anti-CD63 mAb yielded identical coprecipitation results and identical colocalization into lysosomal granules containing cathepsin D. Furthermore, we used an established anti-CD63 mAb to detect this protein in an alpha 3 beta 1 immunoprecipitate, and also we observed VLA-3 and CD63 colocalization in cellular "footprints." Notably, the cytoplasmic domain of alpha 3 was neither required nor sufficient for CD63 association, suggesting that it occurred elsewhere within the alpha 3 beta 1 complex. Knowledge of these specific CD63-alpha 3 beta 1 and CD63-alpha 6 beta 1 biochemical associations should lead to critical insights into the specialized functions of alpha 3 beta 1, alpha 6 beta 1, and CD63.
Enhanced Isoamyl Acetate Production upon Manipulation of the Acetyl-CoA Node in Escherichia coli (2004)

Coenzyme A (CoA) and its thioester derivative acetyl-Coenzyme A (acetyl-CoA) participate in over 100 different reactions in intermediary metabolism of microorganisms. Earlier results indicated that overexpression of upstream rate-limiting enzyme pantothenate kinase with simultaneous supplementation of precursor pantothenic acid to the culture media increased intracellular CoA levels significantly ( approximately 10-fold). The acetyl-CoA levels also increased ( approximately 5-fold) but not as much as that of CoA, showing that the carbon flux from the pyruvate node is rate-limiting upon an increase in CoA levels. In this study, pyruvate dehydrogenase was overexpressed under elevated CoA levels to increase carbon flux from pyruvate to acetyl-CoA. This coexpression did not increase intracellular acetyl-CoA levels but increased the accumulation of extracellular acetate. The production of isoamyl acetate, an industrially useful compound derived from acetyl-CoA, was used as a model reporter system to signify the beneficial effects of this metabolic engineering strategy. In addition, a strain was created in which the acetate production pathway was inactivated to relieve competition at the acetyl-CoA node and to efficiently channel the enhanced carbon flux to the ester production pathway. The synergistic effect of cofactor CoA manipulation and pyruvate dehydrogenase overexpression in the acetate pathway deletion mutant led to a 5-fold increase in isoamyl acetate production. Under normal growth conditions the acetate pathway deletion mutant strains accumulate intracellular pyruvate, leading to excretion of pyruvate. However, upon enhancing the carbon flux from pyruvate to acetyl-CoA, the excretion of pyruvate was significantly reduced.
Fluorescence-activated droplet sorting of lipolytic microorganisms using a compact optical system (2017)

Lipases are ubiquitous enzymes of great physiological significance that have been used extensively in multiple industries. Environmental microorganisms are a major source for the discovery of novel lipases with high catalytic efficiency and selectivity. However, current plate-based screening of lipase-producing strains is time consuming, labour intensive and inefficient. In this study, we developed an ultra-high throughput screening pipeline for lipase-producing strains based on fluorescence-activated droplet sorting (FADS) using a compact optical system that could be easily set up in an alignment-free manner. The pipeline includes droplet generation, droplet incubation, picoinjection of the fluorescence probe, and sorting of droplets with a throughput of 2 × 10<sup>6</sup> drops per h. We applied the pipeline to screen samples collected from different locations, including sediments from a hot spring in Tibet, soils from the Zoige wetland, contaminated soils from an abandoned oilfield, and a Chinese Daqu starter. In total, we obtained 47 lipase-producing bacterial strains belonging to seven genera, including Staphylococcus, Bacillus, Enterobacter, Serratia, Prolinoborus, Acinetobacter, and Leclercia. We believe that this FADS-based pipeline could be extended to screen various enzymes from the environment, and may find wide applications in breeding of industrial microorganisms.