gebhart/patrepeval huggingface dataset:
Rapid and Reliable DNA Assembly <i>via</i> Ligase Cycling Reaction (2014)

Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA assembly method is particularly important for high-throughput, automated DNA assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA assembly via ligase cycling reaction (LCR). LCR assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation–annealing–ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (<1 per 25 kb) and insertions/deletions (<1 per 50 kb). Experimental comparison of various sequence-independent DNA assembly methods showed that circular polymerase extension cloning (CPEC) and Gibson isothermal assembly did not enable assembly of more than four DNA parts with more than 50% of clones being correct. Yeast homologous recombination and LCR both enabled reliable assembly of up to 12 DNA parts with 60–100% of individual clones being correct, but LCR assembly provides a much faster and easier workflow than yeast homologous recombination. LCR combines reliable assembly of many DNA parts via a cheap, rapid, and convenient workflow and thereby outperforms existing DNA assembly methods. LCR assembly is expected to become the method of choice for both manual and automated high-throughput assembly of DNA parts into DNA constructs.
Plant sterol biosynthesis. Identification and characterization of two distinct microsomal oxidative enzymatic systems involved in sterol C4-demethylation (1993)

Membrane-bound enzymatic systems obtained from maize embryos that catalyze the oxidative C4-monodemethylation of 4,4-dimethyl- and 4 alpha-methylsterols have been investigated. Enzymatic assay conditions have been developed for the first time to detect the C4-monodemethylated products formed. The properties of the microsomal systems have been established for co-factor requirements and kinetics. The demethylation process has been interrupted to demonstrate the formation of stable, oxygenated intermediates. In addition to the 3-keto and 3 beta-hydroxy-4-monodemethylated products formed, three new sterols have been identified. 3 beta-Hydroxy-4 beta,14 alpha-dimethyl-5 alpha-ergosta-9 beta,19-cyclo-24(24(1))-en-4 alpha-hydroxy methyl was identified for the first time as the immediate metabolite of 24-methylenecycloartanol by 4 alpha-methyl oxidase in addition to 3 beta-hydroxy-4 beta,14 alpha-dimethyl-5 alpha-ergosta-9 beta,19-cyclo- 24(24(1))-en-4 alpha-carboxylic-acid and 3 beta-hydroxy-5 alpha-stigmasta-7,24(24(1))-dien-4 alpha-carboxylic-acid, intermediates involved respectively in the oxidative demethylation of 24-methylenecycloartanol and 24-ethylidenelophenol. Proton nuclear magnetic resonance studies of enzymatically produced 3 beta-hydroxy-4 beta,14 alpha-dimethyl-5 alpha-ergosta-9 beta,19-cyclo-24(24(1))en-4 alpha-carboxylic acid indicate that the 4 alpha-methyl group of 24-methylenecycloartanol is oxidized and subsequently removed during its enzymatic conversion to cycloeucalenol. From a series of incubations with 25 natural or synthetic 4,4-dimethyl and 4 alpha-methylsterols, a high degree of substrate specificity for the oxidation at C4 of 4,4-dimethyl- and 4 alpha-methylsterols was determined. Our results indicate that oxidation of the 4 alpha-methyl group of the 4,4-geminal dimethylsterols requires the more flexible and presumably bent conformation of 9 beta,19-cyclopropylsterols and the absence of a delta 24(25) unsaturation, whereas the rigid planar conformation of delta 7-unsaturated sterols favors oxidation of 4 alpha-methylsterols. Distinct strict structural requirements for the oxidation of 4,4-dimethyl- and 4 alpha-methylsterols and different sensitivity toward cyanide ions and 3 beta,5 alpha,6 alpha-stigmastatriol, a novel inhibitor of 4 alpha-methylsterol C4 oxidase activity, are consistent with the conclusion that two distinct oxidative systems are involved in the removal of the first and second C4-methyl group of phytosterol precursors. Moreover, the present study directly establishes that during the conversion of cycloartenol to phytosterol one C4 dealkylation occurs before the removal of the 14 alpha-methyl group.
Possible involvement of lysophosphatidic acid receptor‐5 gene in the acquisition of growth advantage of rat tumor cells (2011)

Aberrant expressions of lysophosphatidic acid (LPA) receptor genes have been reported in tumor cells. Here, we measured the expression levels of the Lpa5 gene and its DNA methylation status in rat tumor cells, and investigated cell growth effects of LPA in Lpa5 expressed cells. Real-time reverse transcription (RT)-polymerase chain reaction (PCR) analysis revealed that increased expressions of the Lpa5 gene were detected in rat liver-derived hepatoma RH7777 and lung-derived adenocarcinoma RLCNR cells. For the analysis of methylation status, bisulfite sequencing was performed with RH7777 and RLCNR cells and compared with other tumor cells and liver epithelial cells. The Lpa5 gene in Lpa5 unexpressed cells and liver epithelial cells were highly methylated in the 5' upstream region. In contrast, the Lpa5 gene in RH7777 and RLCNR cells was unmethylated, correlating with increased expressions of Lpa5. In the assays for cell growth effects of LPA, LPA enhanced cell proliferation and motility in RH7777 and RLCNR cells. LPA also stimulated cell invasion in RLCNR, but not in RH7777 cells. In rat liver and lung tumors induced by nitroso-compounds, 4 out of 6 hepatocellular carcinomas and 5 out of 6 lung adenocarcinomas indicated increased expressions of Lpa5 with unmethylated status. These results suggest that increased Lpa5 expressions due to aberrant DNA methylation may be involved in the acquisition of growth advantage of rat tumor cells.
Comparative Analysis of Floyd Warshall and Dijkstras Algorithm using Opencl (2015)

Shortest path algorithms finds applications in large real world domains. All pair shortest path (APSP) and single source shortest path (SSSP) both have their special applications domains. All though every SSSP can be applied for all vertices to calculate APSP. But APSP cant. In this paper heterogeneous implementation of Floyd warshalls algorithm and Dijkstra's algorithm is compared on dense graphs have positive edge weights ranging from 1 to 10. It is found that Dijkstra's algorithm is better than Floyd warshall algorithm in sequencial implementation. But as there is less parallelism identified in dijkstra algorithm as compared to parallel to parallel FW gives less execution time as compared to Dijkstra's.
Vesicular Stomatitis Virus-Based Vaccines Protect Nonhuman Primates against Bundibugyo ebolavirus (2013)

Ebola virus (EBOV) causes severe and often fatal hemorrhagic fever in humans and nonhuman primates (NHPs). Currently, there are no licensed vaccines or therapeutics for human use. Recombinant vesicular stomatitis virus (rVSV)-based vaccine vectors, which encode an EBOV glycoprotein in place of the VSV glycoprotein, have shown 100% efficacy against homologous Sudan ebolavirus (SEBOV) or Zaire ebolavirus (ZEBOV) challenge in NHPs. In addition, a single injection of a blend of three rVSV vectors completely protected NHPs against challenge with SEBOV, ZEBOV, the former Côte d'Ivoire ebolavirus, and Marburg virus. However, recent studies suggest that complete protection against the newly discovered Bundibugyo ebolavirus (BEBOV) using several different heterologous filovirus vaccines is more difficult and presents a new challenge. As BEBOV caused nearly 50% mortality in a recent outbreak any filovirus vaccine advanced for human use must be able to protect against this new species. Here, we evaluated several different strategies against BEBOV using rVSV-based vaccines. Groups of cynomolgus macaques were vaccinated with a single injection of a homologous BEBOV vaccine, a single injection of a blended heterologous vaccine (SEBOV/ZEBOV), or a prime-boost using heterologous SEBOV and ZEBOV vectors. Animals were challenged with BEBOV 29-36 days after initial vaccination. Macaques vaccinated with the homologous BEBOV vaccine or the prime-boost showed no overt signs of illness and survived challenge. In contrast, animals vaccinated with the heterologous blended vaccine and unvaccinated control animals developed severe clinical symptoms consistent with BEBOV infection with 2 of 3 animals in each group succumbing. These data show that complete protection against BEBOV will likely require incorporation of BEBOV glycoprotein into the vaccine or employment of a prime-boost regimen. Fortunately, our results demonstrate that heterologous rVSV-based filovirus vaccine vectors employed in the prime-boost approach can provide protection against BEBOV using an abbreviated regimen, which may have utility in outbreak settings.
IBPP Research Associates - Sierra Leone/Ivory Coast (2003)

This article - The Tragedy of Ivory Coast, by Lansana Gberie - was posted on the February 6, 2003 edition of Expo Times. Copyright permissions were not available for posting the article in Scholarly Commons for download. The author discusses the history of Ivory Coast and its independence from France in 1960 through the early 21st century, emphasizing the descent into political violence and regional instability.
Coherent optical eigenstate memory (1985)

A high capacity associative memory would find applications in computing and perhaps lend some insight into the understanding of collective neural networks and human memory. In this work an entirely optical associative memory device is proposed. The device operates on the principle that an optical resonator employing a holographic grating can have user prescribed eigenmodes. Information which is to be recalled is contained in the hologram. Each information entity (e.g., an image of a cat) defines an eigenmode of the resonator. The stored information is accessed by injecting partial information (e.g., an image of the cat’s ear) into the resonator. The appropriate eigenmode is selected through a competitive process in a gain medium placed inside the resonator. With a net gain greater than one, the gain amplifies the field belonging to the eigenmode which most resembles the injected field; the other eigenmodes are suppressed via the competition for the gain. The principles underlying the proposed device are outlined and the issues which must be addressed are delineated.
High Precision Surface Structuring with Ultra-Short Laser Pulses and Synchronized Mechanical Axes (2013)

For surface and 3D structuring in a 2.5D process, ultra-short pulsed laser systems are mostly used in combination with mechanical axes, whereas the mechanical axes can include electrical motor as well as beam deflecting systems like a galvo scanner. The motion of the axes is synchronized with the clock of the laser pulses, by a modification of the electronic axes control. This work shows the scalability of the ablation process up to MHz-regime in relation to surface quality and ablation efficiency, drilling of thin foils without any heat accumulation and deforming problems of the foil. Furthermore the transfer of the machining strategy from a synchronized galvo scanner to a rotating cylinder setup is shown.
Talbot self-image effect in digital holography and its application to spectrometry (2004)

For the first time to the authors' knowledge, the Talbot effect has been observed and investigated in digital holography. By numerical reconstruction of holograms, the Talbot self-imaging phenomenon is observed by reconstruction of the amplitude of the image at different distances and (or) wavelengths. A simple spectrometer based on Talbot self-imaging in digital holography is proposed and demonstrated.
Natural Convection Heat Transfer from the Upper Plate of a Colinear, Separated Pair of Vertical Plates (1980)

The effect of a buoyant boundary layer spawned by a heated vertical plate on the natural convection heat transfer from an upper colinear vertical plate has been determined analytically. The interplate spacing was varied parametrically, as were the relative temperatures and relative lengths of the two plates; the Prandtl number was equal to 0.7 for all cases. Heat transfer at the upper plate was found to be affected both by the preheating and by the finite velocity imparted to the fluid by the first plate, respectively tending to degrade and to enhance the heat transfer. The upper-plate heat transfer was compared to that of an otherwise identical vertical plate, but with the lower plate absent. When the temperatures of the upper and lower plates are the same, the overall upper-plate heat transfer is less than that of its single-plate counterpart for small interplate spacings, with the opposite relationship at larger spacings. If the temperature of the upper plate is substantially below that of the lower plate, the overall heat transfer is degraded. On the other hand, heat transfer enhancement generally occurs when the upper plate is relatively hot. In general, the heat transfer from relatively short upper plates is very sensitive to the presence of the lower plate, with a lessening sensitivity with increasing plate length. The computed temperature and velocity profiles demonstrated that near the leading edge of the upper plate, a new boundary layer develops within the already existing boundary layer spawned by the first plate.
The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA (2013)

The GIY-YIG nuclease domain is found within protein scaffolds that participate in diverse cellular pathways and contains a single active site that hydrolyzes DNA by a one-metal ion mechanism. GIY-YIG homing endonucleases (GIY-HEs) are two-domain proteins with N-terminal GIY-YIG nuclease domains connected to C-terminal DNA-binding and they are thought to function as monomers. Using I-BmoI as a model GIY-HE, we test mechanisms by which the single active site is used to generate a double-strand break. We show that I-BmoI is partially disordered in the absence of substrate, and that the GIY-YIG domain alone has weak affinity for DNA. Significantly, we show that I-BmoI functions as a monomer at all steps of the reaction pathway and does not transiently dimerize or use sequential transesterification reactions to cleave substrate. Our results are consistent with the I-BmoI DNA-binding domain acting as a molecular anchor to tether the GIY-YIG domain to substrate, permitting rotation of the GIY-YIG domain to sequentially nick each DNA strand. These data highlight the mechanistic differences between monomeric GIY-HEs and dimeric or tetrameric GIY-YIG restriction enzymes, and they have implications for the use of the GIY-YIG domain in genome-editing applications.
Increased Activity of L-Type Ca <sup>2+</sup> Channels Exposed to Serum from Patients with Type I Diabetes (1993)

Type I diabetes [insulin-dependent diabetes mellitus (IDDM)] is an autoimmune disease associated with the destruction of pancreatic beta cells. Serum from patients with IDDM increased L-type calcium channel activity of insulin-producing cells and of GH3 cells derived from a pituitary tumor. The subsequent increase in the concentration of free cytoplasmic Ca2+ ([Ca2+]i) was associated with DNA fragmentation typical of programmed cell death or apoptosis. These effects of the serum were prevented by adding a blocker of voltage-activated L-type Ca2+ channels. When the serum was depleted of immunoglobulin M (IgM), it no longer affected [Ca2+]i. An IgM-mediated increase in Ca2+ influx may thus be part of the autoimmune reaction associated with IDDM and contribute to the destruction of beta cells in vivo.
Ready syntheses of benzoporphyrins via Diels–Alder reactions with protoporphyrin IX (1984)

Reaction of protoporphyrin IX dimethyl ester with strongly activated dienophiles causes a Diels–Alder reaction to occur with the porphyrin periphery; elimination of the angular methyl group from these adducts gives monobenzoporphyrins.
Thermal Deligation of Mo6S8L6 Cluster Complexes. EXAFS and Other Spectroscopic Techniques Support Retention of the Mo6S8 Cluster Unit up to 500 .degree.C (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal Deligation of Mo6S8L6 Cluster Complexes. EXAFS and Other Spectroscopic Techniques Support Retention of the Mo6S8 Cluster Unit up to 500 .degree.CShane J. Hilsenbeck, Robert E. McCarley, and Alan I. GoldmanCite this: Chem. Mater. 1995, 7, 3, 499–506Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/cm00051a010https://doi.org/10.1021/cm00051a010research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations22LEARN 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-Alertsclose Get e-Alerts
Development of neutralization antibodies against highly pathogenic H5N1 avian influenza virus using ostrich (Struthio camelus) yolk (2008)

The rapid outbreak of the highly pathogenic H5N1 avian influenza virus and its transmission to humans have induced world-wide fears of a new influenza pandemic. The most effective method for the reduction of the impact of such a pandemic would be prophylaxis with a safe and effective vaccine, as well as anti-viral materials. In this study, we generated the specific antibodies 'immunoglobulin yolk (IgY)' from ostrich eggs immunized with a full-length glycosylated recombinant H5 protein of the strain H5N1/Vietnam/1203/2004. Using this simple method, abundant specific antibody (about 200 g) against H5 was successfully produced by one female ostrich in a year. The IgY from the immunized ostrich eggs had strong reactivity to the H5N1 virus as well as to H5 proteins. Furthermore, the antibodies strongly inhibited cytopathic effects in MDCK cells and prevented the death of an embryonated chick after a viral inoculation, indicating strong neutralization activity against H5N1 infections. These findings suggest that the neutralization antibody produced by the H5-immunized ostrich is suitable for industrial purposes, such as the development of antibody-binding filters, which can be applied to a mask or to air-conditioners to prevent the influenza pandemic through antigen-antibody reactions. Of note, the mortality rate of chicks inoculated with the H5N1 virus was dramatically decreased with antibody injection. This indicates that ostrich IgY is a potentially effective therapeutic modality for H5N1 infection.
Two Secondary Effects in Bending of Slit Thin-Walled Tubes (1966)

During bending of a slit, thin-walled circular tube two secondary effects are observed to occur simultaneously. One, the so-called Brazier effect, occurs in thin-walled tubes generally when they are subjected to bending, and consists of an ovaling of the cross section. The second effect is a peculiarity of slit tubes only and manifests itself as an overlap of the free edges. The severity of both effects depends upon the location of the slit. The bending moment and the radial and tangential displacements have been determined as function of the curvature for four different slit locations with respect to the neutral axis. The value of the curvature at instability has also been derived. Subsequently an approximate equation has been obtained for the cantilever. The results of experiments on a cantilever are compared with the theoretical predictions.
Genetic Risk Assessment and <i>BRCA</i> Mutation Testing for Breast and Ovarian Cancer Susceptibility: Systematic Evidence Review for the U.S. Preventive Services Task Force (2005)

A primary care approach to screening for inherited breast and ovarian cancer susceptibility has not been evaluated, and evidence is lacking to determine benefits and harms for the general population.
Electrical conduction behavior of LiNixCo1-xO2 thin films (2012)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation M. C. Rao, Sk. Muntaz Begum, E. Sivanagi Reddy, O. M. Hussain; Electrical conduction behavior of LiNixCo1-xO2 thin films. AIP Conf. Proc. 9 June 2012; 1447 (1): 613–614. https://doi.org/10.1063/1.4710152 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
An echocardiographic assessment of atrial mechanical behaviour. (1991)

Relations between movement of the atrioventricular ring and changes in left atrial and ventricular dimensions were studied by echocardiography and compared with apexcardiography and Doppler mitral flow velocity traces in 20 healthy controls and in patients with left ventricular hypertrophy (n = 28) or dilatation (n = 16). During left ventricular systole the atrioventricular ring, a structure common to ventricle and atrium, moved towards the ventricular apex, thus increasing left atrial volume. This action matched pulmonary venous return because it was in phase with the transverse left atrial dimension measured from aortic root to posterior left atrial wall. During early diastole, the mitral ring moved rapidly towards the atrium as transmitral flow accelerated. This requires a force directed from ventricle to atrium, likely to be the result of elastic recoil arising from compression of the ventricular myocardium or stretching of the atrial myocardium during ventricular systole. Two additional mechanisms of ventricular filling with atrial systole were recognised: (a) an increase in ventricular volume as the atrioventricular ring moved upwards and (b) transverse left ventricular expansion by pressure driven transmitral flow. The former is undetectable by Doppler from the apex; it accounted for 10% of ventricular filling in the healthy controls, but for significantly less in those with ventricular dilatation. In left ventricular hypertrophy, left ventricular filling was maintained by both mechanisms compensating for the reduced increase in volume early in diastole. Interactions between the atrium and ventricle are functionally important during ventricular systole, early diastole, and in atrial systole. They are not included in the traditional separation of atrial function into reservoir, conduit, and pump functions.