WorldWideScience

Sample records for genome fragmentation triggers

  1. Fractal Fragmentation triggered by meteor impact: The Ries Crater (Germany)

    Science.gov (United States)

    Paredes Marino, Joali; Perugini, Diego; Rossi, Stefano; Kueppers, Ulrich

    2015-04-01

    FRACTAL FRAGMENTATION TRIGGERED BY METEOR IMPACT: THE RIES CRATER (GERMANY) Joali Paredes (1), Stefano Rossi (1), Diego Perugini (1), Ulrich Kueppers (2) 1. Department of Physics and Geology, University of Perugia, Italy 2. Department of Earth and Environmental Sciences, University of Munich, Germany The Nördlinger Ries is a large circular depression in western Bavaria, Germany. The depression was caused by a meteor impact, which occurred about 14.3 million-14.5 million years ago. The original crater rim had an estimated diameter of 24 kilometers. Computer modeling of the impact event indicates that the impact or probably had diameters of about 1.5 kilometers and impacted the target area at an angle around 30 to 50 degrees from the surface in a west- southwest to east-northeast direction. The impact velocity is thought to have been about 20 km/s. The meteor impact generated extensive fragmentation of preexisting rocks. In addition, melting of these rocks also occurred. The impact melt was ejected at high speed provoking its extensive fragmentation. Quenched melt fragments are ubiquitous in the outcrops. Here we study melt fragment size distributions with the aim of understanding the style of melt fragmentation during ejection and to constrain the rheological properties of such melts. Digital images of suevite (i.e. the rock generated after deposition and diagenesis of ash and fragments produced by the meteor impact) were obtained using a high-resolution optical scanner. Successively, melt fragments were traced by image analysis and the images segmented in order to obtain binary images on which impact melt fragments are in black color, embedded on a white background. Hence, the size of fragments was determined by image analysis. Fractal fragmentation theory has been applied to fragment size distributions of melt fragments in the Ries crater. Results indicate that melt fragments follow fractal distributions indicating that fragmentation of melt generated by the

  2. Triggered fragmentation in gravitationally unstable discs: forming fragments at small radii

    Directory of Open Access Journals (Sweden)

    Meru Farzana

    2013-04-01

    Full Text Available We carry out three dimensional radiation hydrodynamical simulations of gravitationally unstable discs using to explore the movement of mass in a disc following its fragmentation. Compared to a more quiescent state before it fragments, the radial velocity of the gas increases by up to a factor of ≈ 2 – 3 after fragmentation. While the mass movement occurs both inwards and outwards, the inwards motion can cause the inner spirals to be suciently dense that they may become unstable and potentially fragment. Consequently, the dynamical behaviour of fragmented discs may cause subsequent fragmentation at smaller radii after an initial fragment has formed in the outer disc.

  3. Mind the gap; seven reasons to close fragmented genome assemblies.

    Science.gov (United States)

    Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

    2016-05-01

    Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.

  4. Golgi Fragmentation in Amyotrophic Lateral Sclerosis, an Overview of Possible Triggers and Consequences

    Directory of Open Access Journals (Sweden)

    Vinod eSundaramoorthy

    2015-10-01

    Full Text Available Amyotrophic Lateral Sclerosis (ALS is an invariably fatal neurodegenerative disorder, which specifically targets motor neurons in the brain, brain stem and spinal cord. Whilst the etiology of ALS remains unknown, fragmentation of the Golgi apparatus is detected in ALS patient motor neurons and in animal/cellular disease models. The Golgi is a highly dynamic organelle that acts as a dispatching station for the vesicular transport of secretory/transmembrane proteins. It also mediates autophagy and maintains endoplasmic reticulum (ER and axonal homeostasis. Both the trigger for Golgi fragmentation and the functional consequences of a fragmented Golgi apparatus in ALS remain unclear. However recent evidence has highlighted defects in vesicular trafficking as a pathogenic mechanism in ALS. This review summarises the evidence describing Golgi fragmentation in ALS, with possible links to other disease processes including cellular trafficking, ER stress, defective autophagy and axonal degeneration.

  5. Sequencing and Analysis of a Genomic Fragment Provide an Insight into the Dunaliella viridis Genomic Sequence

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ming SUN; Yuan-Ping TANG; Xiang-Zong MENG; Wen-Wen ZHANG; Shan LI; Zhi-Rui DENG; Zheng-Kai XU; Ren-Tao SONG

    2006-01-01

    Dunaliella is a genus of wall-less unicellular eukaryotic green alga. Its exceptional resistances to salt and various other stresses have made it an ideal model for stress tolerance study. However, very little is known about its genome and genomic sequences. In this study, we sequenced and analyzed a 29,268 bp genomic fragment from Dunaliella viridis. The fragment showed low sequence homology to the GenBank database. At the nucleotide level, only a segment with significant sequence homology to 18S rRNA was found. The fragment contained six putative genes, but only one gene showed significant homology at the protein level to GenBank database. The average GC content of this sequence was 51.1%, which was much lower than that of close related green algae Chlamydomonas (65.7%). Significant segmental duplications were found within this fragment. The duplicated sequences accounted for about 35.7% of the entire region. Large amounts of simple sequence repeats (microsatellites) were found, with strong bias towards (AC)n type (76%). Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749 bp) was in agreement with these findings. These sequence features made it difficult to sequence Dunaliella genomic sequences. Further investigation should be made to reveal the biological significance of these unique sequence features.

  6. Post-Fragmentation Whole Genome Amplification-Based Method

    Science.gov (United States)

    Benardini, James; LaDuc, Myron T.; Langmore, John

    2011-01-01

    This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at

  7. Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries.

    Science.gov (United States)

    Branscomb, E; Slezak, T; Pae, R; Galas, D; Carrano, A V; Waterman, M

    1990-10-01

    We present a statistical analysis of the problem of ordering large genomic cloned libraries through overlap detection based on restriction fingerprinting. Such ordering projects involve a large investment of effort involving many repetitious experiments. Our primary purpose here is to provide methods of maximizing the efficiency of such efforts. To this end, we adopt a statistical approach that uses the likelihood ratio as a statistic to detect overlap. The main advantages of this approach are that (1) it allows the relatively straightforward incorporation of the observed statistical properties of the data; (2) it permits the efficiency of a particular experimental method for detecting overlap to be quantitatively defined so that alternative experimental designs may be compared and optimized; and (3) it yields a direct estimate of the probability that any two library members overlap. This estimate is a critical tool for the accurate, automatic assembly of overlapping sets of fragments into islands called "contigs." These contigs must subsequently be connected by other methods to provide an ordered set of overlapping fragments covering the entire genome.

  8. Systematically fragmented genes in a multipartite mitochondrial genome

    Science.gov (United States)

    Vlcek, Cestmir; Marande, William; Teijeiro, Shona; Lukeš, Julius; Burger, Gertraud

    2011-01-01

    Arguably, the most bizarre mitochondrial DNA (mtDNA) is that of the euglenozoan eukaryote Diplonema papillatum. The genome consists of numerous small circular chromosomes none of which appears to encode a complete gene. For instance, the cox1 coding sequence is spread out over nine different chromosomes in non-overlapping pieces (modules), which are transcribed separately and joined to a contiguous mRNA by trans-splicing. Here, we examine how many genes are encoded by Diplonema mtDNA and whether all are fragmented and their transcripts trans-spliced. Module identification is challenging due to the sequence divergence of Diplonema mitochondrial genes. By employing most sensitive protein profile search algorithms and comparing genomic with cDNA sequence, we recognize a total of 11 typical mitochondrial genes. The 10 protein-coding genes are systematically chopped up into three to 12 modules of 60–350 bp length. The corresponding mRNAs are all trans-spliced. Identification of ribosomal RNAs is most difficult. So far, we only detect the 3′-module of the large subunit ribosomal RNA (rRNA); it does not trans-splice with other pieces. The small subunit rRNA gene remains elusive. Our results open new intriguing questions about the biochemistry and evolution of mitochondrial trans-splicing in Diplonema. PMID:20935050

  9. Size-selected genomic libraries: the distribution and size-fractionation of restricted genomic DNA fragments by gel electrophoresis.

    Science.gov (United States)

    Gondo, Y

    1995-02-01

    By using one-dimensional genome scanning, it is possible to directly identify the restricted genomic DNA fragment that reflects the site of genetic change. The subsequent strategies to obtain the molecular clones of the corresponding restriction fragment are usually as follows: (i) the restriction of a mass quantity of an appropriate genomic DNA, (ii) the size-fractionation of the restricted DNA on a preparative electrophoresis gel in order to enrich the corresponding restriction fragment, (iii) the construction of the size-selected libraries from the fractionated genomic DNA, and (iv) the screening of the library to obtain an objective clone which is identified on the analytical genome scanning gel. A knowledge of the size distribution pattern of restriction fragments of the genomic DNA makes it possible to calculate the heterogeneity or complexity of the restriction fragment in each size-fraction. This manuscript first describes the distribution of the restriction fragments with respect to their length. Some examples of the practical application of this theory to genome scanning is then discussed using presumptive genome scanning gels. The way to calculate such DNA complexities in the prepared size-fractionated samples is also demonstrated. Such information should greatly facilitate the design of experimental strategies for the cloning of a certain size of genomic DNA after digestion with restriction enzyme(s) as is the case with genome scanning.

  10. Excessive cytosolic DNA fragments as a potential trigger of Graves’ disease: an encrypted message sent by animal models

    Directory of Open Access Journals (Sweden)

    Yuqian Luo

    2016-11-01

    Full Text Available Graves’ hyperthyroidism is caused by autoantibodies directed against the thyroid stimulating hormone receptor (TSHR that mimic the action of TSH. The establishment of Graves’ hyperthyroidism in experimental animals has proven to be an important approach to dissect the mechanisms of self-tolerance breakdown that lead to the production of thyroid-stimulating TSHR autoantibodies (TSAbs. ‘Shimojo’s model was the first successful Graves’ animal model, wherein immunization with fibroblasts cells expressing TSHR and a major histocompatibility complex (MHC class II molecule, but not either alone, induced TSAb production in AKR/N (H-2k mice. This model highlights the importance of coincident MHC class II expression on TSHR-expressing cells in the development of Graves’ hyperthyroidism. These data are also in agreement with the observation that Graves’ thyrocytes often aberrantly express MHC class II antigens via mechanisms that remain unclear. Our group demonstrated that cytosolic self-genomic DNA fragments derived from sterile injured cells can induce aberrant MHC class II expression and production of multiple inflammatory cytokines and chemokines in thyrocytes in vitro, suggesting that severe cell injury may initiate immune responses in a way that is relevant to thyroid autoimmunity mediated by cytosolic DNA signaling. Furthermore, more recent successful Graves’ animal models were primarily established by immunizing mice with TSHR-expressing plasmids or adenovirus. In these models, double-stranded DNA vaccine contents presumably exert similar immune-activating effect in cells at inoculation sites and thus might pave the way toward successful Graves’ animal models. This review focuses on evidence suggesting that cell injury-derived self-DNA fragments could act as Graves’ disease triggers.

  11. Microfluidic DNA fragmentation for on-chip genomic analysis

    NARCIS (Netherlands)

    Shui, Lingling; Bomer, Johan G.; Jin, Mingliang; Carlen, Edwin T.; Berg, van den Albert

    2011-01-01

    We report a high-throughput clog-free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Salmon sperm DNA has been reproducibly fragmented down to ∼5k bp fragment lengths by applying low hydraulic pressures (≤1 bar) across micromachined constrictions

  12. Microfluidic DNA fragmentation for on-chip genomic analysis

    NARCIS (Netherlands)

    Shui, Lingling; Bomer, Johan G.; Jin, Mingliang; Carlen, Edwin; van den Berg, Albert

    2011-01-01

    We report a high-throughput clog-free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Salmon sperm DNA has been reproducibly fragmented down to ∼5k bp fragment lengths by applying low hydraulic pressures (≤1 bar) across micromachined constrictions

  13. TRIGGER

    CERN Multimedia

    Wesley Smith

    Level-1 Trigger Hardware and Software The hardware of the trigger components has been mostly finished. The ECAL Endcap Trigger Concentrator Cards (TCC) are in production while Barrel TCC firmware has been upgraded, and the Trigger Primitives can now be stored by the Data Concentrator Card for readout by the DAQ. The Regional Calorimeter Trigger (RCT) system is complete, and the timing is being finalized. All 502 HCAL trigger links to RCT run without error. The HCAL muon trigger timing has been equalized with DT, RPC, CSC and ECAL. The hardware and firmware for the Global Calorimeter Trigger (GCT) jet triggers are being commissioned and data from these triggers is available for readout. The GCT energy sums from rings of trigger towers around the beam pipe beam have been changed to include two rings from both sides. The firmware for Drift Tube Track Finder, Barrel Sorter and Wedge Sorter has been upgraded, and the synchronization of the DT trigger is satisfactory. The CSC local trigger has operated flawlessly u...

  14. Microfluidic DNA fragmentation for on-chip genomic analysis.

    Science.gov (United States)

    Shui, Lingling; Bomer, Johan G; Jin, Mingliang; Carlen, Edwin T; van den Berg, Albert

    2011-12-09

    We report a high-throughput clog-free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Salmon sperm DNA has been reproducibly fragmented down to ∼ 5k bp fragment lengths by applying low hydraulic pressures (≤1 bar) across micromachined constrictions positioned in larger microfluidic channels that create point-sink flow with large velocity gradients near the constriction entrance. Long constrictions (100 µm) produce shorter fragment lengths compared to shorter constrictions (10 µm), while increasing the hydrodynamic pressure requirement. Sample recirculation (10 ×) in short constrictions reduces the mean fragment length and fragment length variation, and improves yield compared to single-pass experiments without increasing the hydrodynamic pressure.

  15. TRIGGER

    CERN Multimedia

    Roberta Arcidiacono

    2013-01-01

    Trigger Studies Group (TSG) The Trigger Studies Group has just concluded its third 2013 workshop, where all POGs presented the improvements to the physics object reconstruction, and all PAGs have shown their plans for Trigger development aimed at the 2015 High Level Trigger (HLT) menu. The Strategy for Trigger Evolution And Monitoring (STEAM) group is responsible for Trigger menu development, path timing, Trigger performance studies coordination, HLT offline DQM as well as HLT release, menu and conditions validation – this last task in collaboration with PdmV (Physics Data and Monte Carlo Validation group). In the last months the group has delivered several HLT rate estimates and comparisons, using the available data and Monte Carlo samples. The studies were presented at the Trigger workshops in September and December, and STEAM has contacted POGs and PAGs to understand the origin of the discrepancies observed between 8 TeV data and Monte Carlo simulations. The most recent results show what the...

  16. Stathmin 1/2-triggered microtubule loss mediates Golgi fragmentation in mutant SOD1 motor neurons

    NARCIS (Netherlands)

    Bellouze, Sarah; Baillat, Gilbert; Buttigieg, Dorothée; de la Grange, Pierre; Rabouille, Catherine; Haase, Georg

    2016-01-01

    BACKGROUND: Pathological Golgi fragmentation represents a constant pre-clinical feature of many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) but its molecular mechanisms remain hitherto unclear. RESULTS: Here, we show that the severe Golgi fragmentation in transgenic muta

  17. Vapor film collapse triggered by external pressure pulse and the fragmentation of melt droplet in FCIs

    Institute of Scientific and Technical Information of China (English)

    LIN Qian; TONG Lili; CAO Xuewu; KRIVENTSEV Vladimir

    2008-01-01

    The fragmentation process of high-temperature molten drop is a key factor to determine the ratio heat transferred to power in FCIs,which estimates the possible damage degree during the hypothetical severe accident in the nuclear reactors.In this paper,the fragmentation process of melt droplet in FCIs is investigated by theoretic analysis.The fragmentation mechanism is studied when an external pressure pulse applied to a melt droplet,which is surrounded by vapor film.The vapor film collapse which induces fragmentation of melt droplet is analyzed and modeled.And then the generated pressure is calculated.The vapor film collapse model is introduced to fragmentation correlation,and the predicted fragment size is calculated and compared with experimental data.The result shows that the developed model can predict the diameter of fragments and can be used to calculate the fragmentation process appreciatively.

  18. Stathmin 1/2-triggered microtubule loss mediates Golgi fragmentation in mutant SOD1 motor neurons

    NARCIS (Netherlands)

    Bellouze, Sarah; Baillat, Gilbert; Buttigieg, Dorothée; de la Grange, Pierre; Rabouille, Catherine; Haase, Georg

    2016-01-01

    BACKGROUND: Pathological Golgi fragmentation represents a constant pre-clinical feature of many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) but its molecular mechanisms remain hitherto unclear. RESULTS: Here, we show that the severe Golgi fragmentation in transgenic

  19. TRIGGER

    CERN Multimedia

    Wesley Smith

    Level-1 Trigger Hardware and Software The trigger synchronization procedures for running with cosmic muons and operating with the LHC were reviewed during the May electronics week. Firmware maintenance issues were also reviewed. Link tests between the new ECAL endcap trigger concentrator cards (TCC48) and the Regional Calorimeter Trigger have been performed. Firmware for the energy sum triggers and an upgraded tau trigger of the Global Calorimeter Triggers has been developed and is under test. The optical fiber receiver boards for the Track-Finder trigger theta links of the DT chambers are now all installed. The RPC trigger is being made more robust by additional chamber and cable shielding and also by firmware upgrades. For the CSC’s the front-end and trigger motherboard firmware have been updated. New RPC patterns and DT/CSC lookup tables taking into account phi asymmetries in the magnetic field configuration are under study. The motherboard for the new pipeline synchronizer of the Global Trigg...

  20. TRIGGER

    CERN Multimedia

    W. Smith

    2012-01-01

      Level-1 Trigger The Level-1 Trigger group is ready to deploy improvements to the L1 Trigger algorithms for 2012. These include new high-PT patterns for the RPC endcap, an improved CSC PT assignment, a new PT-matching algorithm for the Global Muon Trigger, and new calibrations for ECAL, HCAL, and the Regional Calorimeter Trigger. These should improve the efficiency, rate, and stability of the L1 Trigger. The L1 Trigger group also is migrating the online systems to SLC5. To make the data transfer from the Global Calorimeter Trigger to the Global Trigger more reliable and also to allow checking the data integrity online, a new optical link system has been developed by the GCT and GT groups and successfully tested at the CMS electronics integration facility in building 904. This new system is now undergoing further tests at Point 5 before being deployed for data-taking this year. New L1 trigger menus have recently been studied and proposed by Emmanuelle Perez and the L1 Detector Performance Group...

  1. Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments

    Directory of Open Access Journals (Sweden)

    Arun S. Seetharam

    2013-12-01

    Full Text Available Type IIB restriction endonucleases are site-specific endonucleases that cut both strands of double-stranded DNA upstream and downstream of their recognition sequences. These restriction enzymes have recognition sequences that are generally interrupted and range from 5 to 7 bases long. They produce DNA fragments which are uniformly small, ranging from 21 to 33 base pairs in length (without cohesive ends. The fragments are generated from throughout the entire length of a genomic DNA providing an excellent fractional representation of the genome. In this study we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species using the predicted targets of 16 Type IIB restriction enzymes to effectively produce a large and arbitrary selection of loci from these genomes. The fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. Phylogenetic trees were then generated for each enzyme using this distance measure and the consensus was calculated. The consensus tree obtained agrees well with the currently accepted tree for the Drosophila species. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can accelerate studies of comparative genomics and the building of accurate phylogenetic trees.

  2. TRIGGER

    CERN Multimedia

    W. Smith

    At the March meeting, the CMS trigger group reported on progress in production, tests in the Electronics Integration Center (EIC) in Prevessin 904, progress on trigger installation in the underground counting room at point 5, USC55, the program of trigger pattern tests and vertical slice tests and planning for the Global Runs starting this summer. The trigger group is engaged in the final stages of production testing, systems integration, and software and firmware development. Most systems are delivering final tested electronics to CERN. The installation in USC55 is underway and integration testing is in full swing. A program of orderly connection and checkout with subsystems and central systems has been developed. This program includes a series of vertical subsystem slice tests providing validation of a portion of each subsystem from front-end electronics through the trigger and DAQ to data captured and stored. After full checkout, trigger subsystems will be then operated in the CMS Global Runs. Continuous...

  3. TRIGGER

    CERN Multimedia

    Wesley Smith

    Level-1 Trigger Hardware and Software The production of the trigger hardware is now basically finished, and in time for the turn-on of the LHC. The last boards produced are the Trigger Concentrator Cards for the ECAL Endcaps (TCC-EE). After the recent installation of the four EE Dees, the TCC-EE prototypes were used for their commissioning. Production boards are arriving and are being tested continuously, with the last ones expected in November. The Regional Calorimeter Trigger hardware is fully integrated after installation of the last EE cables. Pattern tests from the HCAL up to the GCT have been performed successfully. The HCAL triggers are fully operational, including the connection of the HCAL-outer and forward-HCAL (HO/HF) technical triggers to the Global Trigger. The HCAL Trigger and Readout (HTR) board firmware has been updated to permit recording of the tower “feature bit” in the data. The Global Calorimeter Trigger hardware is installed, but some firmware developments are still n...

  4. TRIGGER

    CERN Multimedia

    by Wesley Smith

    2010-01-01

    Level-1 Trigger Hardware and Software The overall status of the L1 trigger has been excellent and the running efficiency has been high during physics fills. The timing is good to about 1%. The fine-tuning of the time synchronization of muon triggers is ongoing and will be completed after more than 10 nb-1 of data have been recorded. The CSC trigger primitive and RPC trigger timing have been refined. A new configuration for the CSC Track Finder featured modified beam halo cuts and improved ghost cancellation logic. More direct control was provided for the DT opto-receivers. New RPC Cosmic Trigger (RBC/TTU) trigger algorithms were enabled for collision runs. There is further work planned during the next technical stop to investigate a few of the links from the ECAL to the Regional Calorimeter Trigger (RCT). New firmware and a new configuration to handle trigger rate spikes in the ECAL barrel are also being tested. A board newly developed by the tracker group (ReTRI) has been installed and activated to block re...

  5. Sequence Determination from Overlapping Fragments: A Simple Model of Whole-Genome Shotgun Sequencing

    Science.gov (United States)

    Derrida, Bernard; Fink, Thomas M.

    2002-02-01

    Assembling fragments randomly sampled from along a sequence is the basis of whole-genome shotgun sequencing, a technique used to map the DNA of the human and other genomes. We calculate the probability that a random sequence can be recovered from a collection of overlapping fragments. We provide an exact solution for an infinite alphabet and in the case of constant overlaps. For the general problem we apply two assembly strategies and give the probability that the assembly puzzle can be solved in the limit of infinitely many fragments.

  6. TRIGGER

    CERN Multimedia

    W. Smith

    2010-01-01

    Level-1 Trigger Hardware and Software The Level-1 Trigger hardware has performed well during both the recent proton-proton and heavy ion running. Efforts were made to improve the visibility and handling of alarms and warnings. The tracker ReTRI boards that prevent fixed frequencies of Level-1 Triggers are now configured through the Trigger Supervisor. The Global Calorimeter Trigger (GCT) team has introduced a buffer cleanup procedure at stops and a reset of the QPLL during configuring to ensure recalibration in case of a switch from the LHC clock to the local clock. A device to test the cables between the Regional Calorimeter Trigger and the GCT has been manufactured. A wrong charge bit was fixed in the CSC Trigger. The ECAL group is improving crystal masking and spike suppression in the trigger primitives. New firmware for the Drift Tube Track Finder (DTTF) sorters was developed to improve fake track tagging and sorting. Zero suppression was implemented in the DT Sector Collector readout. The track finder b...

  7. TRIGGER

    CERN Multimedia

    Wesley Smith

    Trigger Hardware The status of the trigger components was presented during the September CMS Week and Annual Review and at the monthly trigger meetings in October and November. Procedures for cold and warm starts (e.g. refreshing of trigger parameters stored in registers) of the trigger subsystems have been studied. Reviews of parts of the Global Calorimeter Trigger (GCT) and the Global Trigger (GT) have taken place in October and November. The CERN group summarized the status of the Trigger Timing and Control (TTC) system. All TTC crates and boards are installed in the underground counting room, USC55. The central clock system will be upgraded in December (after the Global Run at the end of November GREN) to the new RF2TTC LHC machine interface timing module. Migration of subsystem's TTC PCs to SLC4/ XDAQ 3.12 is being prepared. Work is on going to unify the access to Local Timing Control (LTC) and TTC CMS interface module (TTCci) via SOAP (Simple Object Access Protocol, a lightweight XML-based messaging ...

  8. Mind the gap; seven reasons to close fragmented genome assemblies

    Science.gov (United States)

    Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including tho...

  9. TRIGGER

    CERN Multimedia

    W. Smith from contributions of C. Leonidopoulos

    2010-01-01

    Level-1 Trigger Hardware and Software Since nearly all of the Level-1 (L1) Trigger hardware at Point 5 has been commissioned, activities during the past months focused on the fine-tuning of synchronization, particularly for the ECAL and the CSC systems, on firmware upgrades and on improving trigger operation and monitoring. Periodic resynchronizations or hard resets and a shortened luminosity section interval of 23 seconds were implemented. For the DT sector collectors, an automatic power-off was installed in case of high temperatures, and the monitoring capabilities of the opto-receivers and the mini-crates were enhanced. The DTTF and the CSCTF now have improved memory lookup tables. The HCAL trigger primitive logic implemented a new algorithm providing better stability of the energy measurement in the presence of any phase misalignment. For the Global Calorimeter Trigger, additional Source Cards have been manufactured and tested. Testing of the new tau, missing ET and missing HT algorithms is underw...

  10. TRIGGER

    CERN Multimedia

    R. Carlin with contributions from D. Acosta

    2012-01-01

    Level-1 Trigger Data-taking continues at cruising speed, with high availability of all components of the Level-1 trigger. We have operated the trigger up to a luminosity of 7.6E33, where we approached 100 kHz using the 7E33 prescale column.  Recently, the pause without triggers in case of an automatic "RESYNC" signal (the "settle" and "recover" time) was reduced in order to minimise the overall dead-time. This may become very important when the LHC comes back with higher energy and luminosity after LS1. We are also preparing for data-taking in the proton-lead run in early 2013. The CASTOR detector will make its comeback into CMS and triggering capabilities are being prepared for this. Steps to be taken include improved cooperation with the TOTEM trigger system and using the LHC clock during the injection and ramp phases of LHC. Studies are being finalised that will have a bearing on the Trigger Technical Design Report (TDR), which is to be rea...

  11. TRIGGER

    CERN Multimedia

    Wesley Smith

    Level-1 Trigger Hardware and Software The final parts of the Level-1 trigger hardware are now being put in place. For the ECAL endcaps, more than half of the Trigger Concentrator Cards for the ECAL Endcap (TCC-EE) are now available at CERN, such that one complete endcap can be covered. The Global Trigger now correctly handles ECAL calibration sequences, without being influenced by backpressure. The Regional Calorimeter Trigger (RCT) hardware is complete and working in USC55. Intra-crate tests of all 18 RCT crates and the Global Calorimeter Trigger (GCT) are regularly taking place. Pattern tests have successfully captured data from HCAL through RCT to the GCT Source Cards. HB/HE trigger data are being compared with emulator results to track down the very few remaining hardware problems. The treatment of hot and dead cells, including their recording in the database, has been defined. For the GCT, excellent agreement between the emulator and data has been achieved for jets and HF ET sums. There is still som...

  12. TRIGGER

    CERN Multimedia

    W. Smith

    Level-1 Trigger Hardware and Software The trigger system has been constantly in use in cosmic and commissioning data taking periods. During CRAFT running it delivered 300 million muon and calorimeter triggers to CMS. It has performed stably and reliably. During the abort gaps it has also provided laser and other calibration triggers. Timing issues, namely synchronization and latency issues, have been solved. About half of the Trigger Concentrator Cards for the ECAL Endcap (TCC-EE) are installed, and the firmware is being worked on. The production of the other half has started. The HCAL Trigger and Readout (HTR) card firmware has been updated, and new features such as fast parallel zero-suppression have been included. Repairs of drift tube (DT) trigger mini-crates, optical links and receivers of sector collectors are under way and have been completed on YB0. New firmware for the optical receivers of the theta links to the drift tube track finder is being installed. In parallel, tests with new eta track finde...

  13. TRIGGER

    CERN Multimedia

    W. Smith

    At the December meeting, the CMS trigger group reported on progress in production, tests in the Electronics Integration Center (EIC) in Prevessin 904, progress on trigger installation in the underground counting room at point 5, USC55, and results from the Magnet Test and Cosmic Challenge (MTCC) phase II. The trigger group is engaged in the final stages of production testing, systems integration, and software and firmware development. Most systems are delivering final tested electronics to CERN. The installation in USC55 is underway and moving towards integration testing. A program of orderly connection and checkout with subsystems and central systems has been developed. This program includes a series of vertical subsystem slice tests providing validation of a portion of each subsystem from front-end electronics through the trigger and DAQ to data captured and stored. This is combined with operations and testing without beam that will continue until startup. The plans for start-up, pilot and early running tri...

  14. TRIGGER

    CERN Multimedia

    W. Smith from contributions of C. Leonidopoulos, I. Mikulec, J. Varela and C. Wulz.

    Level-1 Trigger Hardware and Software Over the past few months, the Level-1 trigger has successfully recorded data with cosmic rays over long continuous stretches as well as LHC splash events, beam halo, and collision events. The L1 trigger hardware, firmware, synchronization, performance and readiness for beam operation were reviewed in October. All L1 trigger hardware is now installed at Point 5, and most of it is completely commissioned. While the barrel ECAL Trigger Concentrator Cards are fully operational, the recently delivered endcap ECAL TCC system is still being commissioned. For most systems there is a sufficient number of spares available, but for a few systems additional reserve modules are needed. It was decided to increase the overall L1 latency by three bunch crossings to increase the safety margin for trigger timing adjustments. In order for CMS to continue data taking during LHC frequency ramps, the clock distribution tree needs to be reset. The procedures for this have been tested. A repl...

  15. TRIGGER

    CERN Multimedia

    R. Arcidiacono

    2013-01-01

      In 2013 the Trigger Studies Group (TSG) has been restructured in three sub-groups: STEAM, for the development of new HLT menus and monitoring their performance; STORM, for the development of HLT tools, code and actual configurations; and FOG, responsible for the online operations of the High Level Trigger. The Strategy for Trigger Evolution And Monitoring (STEAM) group is responsible for Trigger Menu development, path timing, trigger performance studies coordination, HLT offline DQM as well as HLT release, menu and conditions validation – in collaboration and with the technical support of the PdmV group. Since the end of proton-proton data taking, the group has started preparing for 2015 data taking, with collisions at 13 TeV and 25 ns bunch spacing. The reliability of the extrapolation to higher energy is being evaluated comparing the trigger rates on 7 and 8 TeV Monte Carlo samples with the data taken in the past two years. The effect of 25 ns bunch spacing is being studied on the d...

  16. TRIGGER

    CERN Multimedia

    W. Smith, from contributions of D. Acosta

    2012-01-01

      The L1 Trigger group deployed several major improvements this year. Compared to 2011, the single-muon trigger rate has been reduced by a factor of 2 and the η coverage has been restored to 2.4, with high efficiency. During the current technical stop, a higher jet seed threshold will be applied in the Global Calorimeter Trigger in order to significantly reduce the strong pile-up dependence of the HT and multi-jet triggers. The currently deployed L1 menu, with the “6E33” prescales, has a total rate of less than 100 kHz and operates with detector readout dead time of less than 3% for luminosities up to 6.5 × 1033 cm–2s–1. Further prescale sets have been created for 7 and 8 × 1033 cm–2s–1 luminosities. The L1 DPG is evaluating the performance of the Trigger for upcoming conferences and publication. Progress on the Trigger upgrade was reviewed during the May Upgrade Week. We are investigating scenarios for stagin...

  17. TRIGGER

    CERN Multimedia

    Wesley Smith

    2011-01-01

    Level-1 Trigger Hardware and Software New Forward Scintillating Counters (FSC) for rapidity gap measurements have been installed and integrated into the Trigger recently. For the Global Muon Trigger, tuning of quality criteria has led to improvements in muon trigger efficiencies. Several subsystems have started campaigns to increase spares by recovering boards or producing new ones. The barrel muon sector collector test system has been reactivated, new η track finder boards are in production, and φ track finder boards are under revision. In the CSC track finder, an η asymmetry problem has been corrected. New pT look-up tables have also improved efficiency. RPC patterns were changed from four out of six coincident layers to three out of six in the barrel, which led to a significant increase in efficiency. A new PAC firmware to trigger on heavy stable charged particles allows looking for chamber hit coincidences in two consecutive bunch-crossings. The redesign of the L1 Trigger Emulator...

  18. TRIGGER

    CERN Multimedia

    W. Smith

    Level-1 Trigger Hardware and Software The road map for the final commissioning of the level-1 trigger system has been set. The software for the trigger subsystems is being upgraded to run under CERN Scientific Linux 4 (SLC4). There is also a new release for the Trigger Supervisor (TS 1.4), which implies upgrade work by the subsystems. As reported by the CERN group, a campaign to tidy the Trigger Timing and Control (TTC) racks has begun. The machine interface was upgraded by installing the new RF2TTC module, which receives RF signals from LHC Point 4. Two Beam Synchronous Timing (BST) signals, one for each beam, can now be received in CMS. The machine group will define the exact format of the information content shortly. The margin on the locking range of the CMS QPLL is planned for study for different subsystems in the next Global Runs, using a function generator. The TTC software has been successfully tested on SLC4. Some TTC subsystems have already been upgraded to SLC4. The TTCci Trigger Supervisor ...

  19. An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function

    Directory of Open Access Journals (Sweden)

    Satoko Kikuchi

    2012-01-01

    Full Text Available To decode a long genome sequence, shotgun sequencing is the state-of-the-art technique. It needs to properly sequence a very large number, sometimes as large as millions, of short partially readable strings (fragments. Arranging those fragments in correct sequence is known as fragment assembling, which is an NP-problem. Presently used methods require enormous computational cost. In this work, we have shown how our modified genetic algorithm (GA could solve this problem efficiently. In the proposed GA, the length of the chromosome, which represents the volume of the search space, is reduced with advancing generations, and thereby improves search efficiency. We also introduced a greedy mutation, by swapping nearby fragments using some heuristics, to improve the fitness of chromosomes. We compared results with Parsons’ algorithm which is based on GA too. We used fragments with partial reads on both sides, mimicking fragments in real genome assembling process. In Parsons’ work base-pair array of the whole fragment is known. Even then, we could obtain much better results, and we succeeded in restructuring contigs covering 100% of the genome sequences.

  20. TRIGGER

    CERN Multimedia

    W. Smith

    2011-01-01

    Level-1 Trigger Hardware and Software Overall the L1 trigger hardware has been running very smoothly during the last months of proton running. Modifications for the heavy-ion run have been made where necessary. The maximal design rate of 100 kHz can be sustained without problems. All L1 latencies have been rechecked. The recently installed Forward Scintillating Counters (FSC) are being used in the heavy ion run. The ZDC scintillators have been dismantled, but the calorimeter itself remains. We now send the L1 accept signal and other control signals to TOTEM. Trigger cables from TOTEM to CMS will be installed during the Christmas shutdown, so that the TOTEM data can be fully integrated within the CMS readout. New beam gas triggers have been developed, since the BSC-based trigger is no longer usable at high luminosities. In particular, a special BPTX signal is used after a quiet period with no collisions. There is an ongoing campaign to provide enough spare modules for the different subsystems. For example...

  1. TRIGGER

    CERN Multimedia

    J. Alimena

    2013-01-01

    Trigger Strategy Group The Strategy for Trigger Evolution And Monitoring (STEAM) group is responsible for the development of future High-Level Trigger menus, as well as of its DQM and validation, in collaboration and with the technical support of the PdmV group. Taking into account the beam energy and luminosity expected in 2015, a rough estimate of the trigger rates indicates a factor four increase with respect to 2012 conditions. Assuming that a factor two can be tolerated thanks to the increase in offline storage and processing capabilities, a toy menu has been developed using the new OpenHLT workflow to estimate the transverse energy/momentum thresholds that would halve the current trigger rates. The CPU time needed to run the HLT has been compared between data taken with 25 ns and 50 ns bunch spacing, for equivalent pile-up: no significant difference was observed on the global time per event distribution at the only available data point, corresponding to a pile-up of about 10 interactions. Using th...

  2. TRIGGER

    CERN Multimedia

    by Wesley Smith

    2011-01-01

    Level-1 Trigger Hardware and Software After the winter shutdown minor hardware problems in several subsystems appeared and were corrected. A reassessment of the overall latency has been made. In the TTC system shorter cables between TTCci and TTCex have been installed, which saved one bunch crossing, but which may have required an adjustment of the RPC timing. In order to tackle Pixel out-of-syncs without influencing other subsystems, a special hardware/firmware re-sync protocol has been introduced in the Global Trigger. The link between the Global Calorimeter Trigger and the Global Trigger with the new optical Global Trigger Interface and optical receiver daughterboards has been successfully tested in the Electronics Integration Centre in building 904. New firmware in the GCT now allows a setting to remove the HF towers from energy sums. The HF sleeves have been replaced, which should lead to reduced rates of anomalous signals, which may allow their inclusion after this is validated. For ECAL, improvements i...

  3. Human tyrosine hydroxylase (TH) genomic fragment (pHGTH4) identifies a PstI polymorphism

    Energy Technology Data Exchange (ETDEWEB)

    Kelsoe, J.R.; Stubblefield, B.K.; Ginns, E.I. (National Institute of Mental Health, Bethesda, MD (USA))

    1988-08-11

    pHGTH4 is a 2.3 kb Bam HI genomic fragment of tyrosine hydroxylase isolated from a lambda EMBL3 Sau3A partial digest human genomic library prepared from lymphoblasts. The fragment was subcloned into the Bam HI site of pBLUESCRIPT. The absence of a polymorphic Pst I site results in the 1.3 kb fragment, A1; whereas its presence results in a 0.7 kb and a 0.6 kb fragment, A2, as shown in the figure. It was located at 11p15 by in situ hybridization. Mendelian inheritance was demonstrated in a 23 member family with 12 children. Pst I was not polymorphic (all homoallelic for A2) in a panel of 6 subjects from Amish pedigree 110 (IMR 884), in which two other chromosome 11 RFLP's have been reported to be linked to manic-depressive illness.

  4. TRIGGER

    CERN Multimedia

    W. Smith

    Level-1 Trigger Hardware The CERN group is working on the TTC system. Seven out of nine sub-detector TTC VME crates with all fibers cabled are installed in USC55. 17 Local Trigger Controller (LTC) boards have been received from production and are in the process of being tested. The RF2TTC module replacing the TTCmi machine interface has been delivered and will replace the TTCci module used to mimic the LHC clock. 11 out of 12 crates housing the barrel ECAL off-detector electronics have been installed in USC55 after commissioning at the Electronics Integration Centre in building 904. The cabling to the Regional Calorimeter Trigger (RCT) is terminated. The Lisbon group has completed the Synchronization and Link mezzanine board (SLB) production. The Palaiseau group has fully tested and installed 33 out of 40 Trigger Concentrator Cards (TCC). The seven remaining boards are being remade. The barrel TCC boards have been tested at the H4 test beam, and good agreement with emulator predictions were found. The cons...

  5. Phorbol ester-modulation of estrogenic genomic effects triggered by the environmental contaminant benzanthracene.

    Science.gov (United States)

    Kolasa, Elise; Balaguer, Patrick; Houlbert, Noémie; Fardel, Olivier

    2012-09-01

    Aryl hydrocarbon receptor-dependent genomic effects of environmental polycyclic aromatic hydrocarbons (PAHs) have been shown to be modulated by non-genomic protein kinase C (PKC)-related pathways. The present study was designed to determine whether PKC activation may also impair estrogenic genomic response triggered by PAHs. Treatment by the PKC activator phorbol 12-myristate 13-acetate (PMA) was found to markedly and differentially impair the up-regulation of estrogenic markers triggered by the estrogenic PAH benzanthracene (BZA) in cultured human mammary cells; BZA-mediated mRNA up-regulation of pS2 and amphiregulin was thus increased, whereas that of progesterone receptor and CXCL12 was repressed. BZA/PMA cotreatment however failed to alter BZA-mediated increase of activity of a luciferase gene reporter construct driven by an estrogen response element, thus discarding any global effect of PMA toward BZA-triggered estrogen receptor activation. Various chemicals inhibiting PKCs or extracellular signal-regulated kinase (ERK) as well as the knock-down of PKCδ expression counteracted the PMA-mediated increase of pS2 mRNA up-regulation triggered by BZA, demonstrating that it was dependent on PKCs, including PKCδ isoform, and ERKs. This non-genomic modulation of estrogenic effects of PAHs by PKC activation may have to be considered when considering the deleterious effects of these environmental contaminants towards the endocrine system.

  6. Isolation of recombinant field strains of Marek's disease virus integrated with reticuloendotheliosis virus genome fragments

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Zhi; CUI; Zhizhong

    2005-01-01

    Two Marek's disease virus (MDV) field strains were isolated from chickens with tumors independently from Guangdong and Guangxi provinces, and it was confirmed that there were no co-infections with reticuloendotheliosis viruses (REV) in chicken embryo fibroblast cells (CEF) in indirect fluorescence antibody test (IFA) with REV-specific monoclonal antibodies. By dot blot hybridization and PCR of genomic DNA of MDV-infected CEF, it was indicated that LTR fragments of REV genome were integrated into genome of these two MDV field strains. To amplify and clone the integrated REV LTR with MDV sequence at the junction, 4 primers from REV LTR and 7 primers from MDV genome fragment with REV LTR insertion hot points were synthesized and 28 (4x7) pairs of primers (one from REV and another from MDV for each pair) were used in PCR while using the genomic DNA of both strains as the templates. The sequence data demonstrated that both recombinant field strains contained the same REV LTR inserted into MDV at the identical sites in US fragment of the genomes. From the above, it was speculated that both recombinant field MDVs were originated from a same recombinant virus and spread among chicken flocks in two provinces.

  7. Fragment-based cocktail crystallography by the Medical Structural Genomics of Pathogenic Protozoa Consortium

    Science.gov (United States)

    Verlinde, Christophe L.M.J.; Fan, Erkang; Shibata, Sayaka; Zhang, Zongsheng; Sun, Zhihua; Deng, Wei; Ross, Jennifer; Kim, Jessica; Xiao, Liren; Arakaki, Tracy L.; Bosch, Jürgen; Caruthers, Jonathan M.; Larson, Eric T.; LeTrong, Isolde; Napuli, Alberto; Kelly, Angela; Mueller, Natasha; Zucker, Frank; Van Voorhis, Wesley C.; Buckner, Frederick S.; Merritt, Ethan A.; Hol, Wim G.J.

    2010-01-01

    The history of fragment-based drug discovery, with an emphasis on crystallographic methods, is sketched, illuminating various contributions, including our own, which preceded the industrial development of the method. Subsequently, the creation of the BMSC fragment cocktails library is described. The BMSC collection currently comprises 68 cocktails of 10 compounds that are shape-wise diverse. The utility of these cocktails for initiating lead discovery in structure-based drug design has been explored by soaking numerous protein crystals obtained by our MSGPP (Medical Structural Genomics of Pathogenic Protozoa) consortium. Details of the fragment selection and cocktail design procedures, as well as examples of the successes obtained are given. The BMSC Fragment Cocktail recipes are available free of charge and are in use in over 20 academic labs. PMID:19929835

  8. Cloning of open reading frames and promoters from the Saccharomyces cerevisiae genome: construction of genomic libraries of random small fragments.

    Science.gov (United States)

    Santangelo, G M; Tornow, J; Moldave, K

    1986-01-01

    We have developed a novel efficient method, carrier-facilitated insertion, to insert small (150-600 bp) DNA fragments into plasmid vectors. This method employs a carrier segment of vector DNA to circumvent the difficulties in ligating two fragments together to generate a recombinant circle efficiently. We have used carrier-facilitated insertion to construct three genomic libraries of random (DNase I-generated) fragments from the Saccharomyces cerevisiae genome. One of these was an expression library, and the other two were promoter-cloning libraries. 87-90% of the Escherichia coli colonies in each library contained recombinant plasmids, and less than 3% of the recombinants contained more than one insert. Detection of open reading frames among the inserts in the expression library was accomplished by testing for beta-galactosidase activity. This methodology, unencumbered by the intrinsic disproportionality of cDNA libraries, can be used to identify and clone DNA that codes for a specific antigenic determinant. When used in combination with a method to detect and isolate random constitutive, repressible and inducible yeast promoters, these libraries should permit a comprehensive analysis of the yeast genome and its expression.

  9. A Peptidoglycan Fragment Triggers β-lactam Resistance in Bacillus licheniformis

    Science.gov (United States)

    Amoroso, Ana; Boudet, Julien; Berzigotti, Stéphanie; Duval, Valérie; Teller, Nathalie; Mengin-Lecreulx, Dominique; Luxen, André; Simorre, Jean-Pierre; Joris, Bernard

    2012-01-01

    To resist to β-lactam antibiotics Eubacteria either constitutively synthesize a β-lactamase or a low affinity penicillin-binding protein target, or induce its synthesis in response to the presence of antibiotic outside the cell. In Bacillus licheniformis and Staphylococcus aureus, a membrane-bound penicillin receptor (BlaR/MecR) detects the presence of β-lactam and launches a cytoplasmic signal leading to the inactivation of BlaI/MecI repressor, and the synthesis of a β-lactamase or a low affinity target. We identified a dipeptide, resulting from the peptidoglycan turnover and present in bacterial cytoplasm, which is able to directly bind to the BlaI/MecI repressor and to destabilize the BlaI/MecI-DNA complex. We propose a general model, in which the acylation of BlaR/MecR receptor and the cellular stress induced by the antibiotic, are both necessary to generate a cell wall-derived coactivator responsible for the expression of an inducible β-lactam-resistance factor. The new model proposed confirms and emphasizes the role of peptidoglycan degradation fragments in bacterial cell regulation. PMID:22438804

  10. Genome fragmentation is not confined to the peridinin plastid in dinoflagellates.

    Science.gov (United States)

    Espelund, Mari; Minge, Marianne A; Gabrielsen, Tove M; Nederbragt, Alexander J; Shalchian-Tabrizi, Kamran; Otis, Christian; Turmel, Monique; Lemieux, Claude; Jakobsen, Kjetill S

    2012-01-01

    When plastids are transferred between eukaryote lineages through series of endosymbiosis, their environment changes dramatically. Comparison of dinoflagellate plastids that originated from different algal groups has revealed convergent evolution, suggesting that the host environment mainly influences the evolution of the newly acquired organelle. Recently the genome from the anomalously pigmented dinoflagellate Karlodinium veneficum plastid was uncovered as a conventional chromosome. To determine if this haptophyte-derived plastid contains additional chromosomal fragments that resemble the mini-circles of the peridin-containing plastids, we have investigated its genome by in-depth sequencing using 454 pyrosequencing technology, PCR and clone library analysis. Sequence analyses show several genes with significantly higher copy numbers than present in the chromosome. These genes are most likely extrachromosomal fragments, and the ones with highest copy numbers include genes encoding the chaperone DnaK(Hsp70), the rubisco large subunit (rbcL), and two tRNAs (trnE and trnM). In addition, some photosystem genes such as psaB, psaA, psbB and psbD are overrepresented. Most of the dnaK and rbcL sequences are found as shortened or fragmented gene sequences, typically missing the 3'-terminal portion. Both dnaK and rbcL are associated with a common sequence element consisting of about 120 bp of highly conserved AT-rich sequence followed by a trnE gene, possibly serving as a control region. Decatenation assays and Southern blot analysis indicate that the extrachromosomal plastid sequences do not have the same organization or lengths as the minicircles of the peridinin dinoflagellates. The fragmentation of the haptophyte-derived plastid genome K. veneficum suggests that it is likely a sign of a host-driven process shaping the plastid genomes of dinoflagellates.

  11. A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata

    Directory of Open Access Journals (Sweden)

    Wörheide Gert

    2008-07-01

    Full Text Available Abstract Background Animal mitochondrial (mt genomes are characteristically circular molecules of ~16–20 kb. Medusozoa (Cnidaria excluding Anthozoa are exceptional in that their mt genomes are linear and sometimes subdivided into two to presumably four different molecules. In the genus Hydra, the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2. Results The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns. Strong correlations between the AT content of rRNA genes (rns and rnl and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR occur on both chromosomes; these ITR contain a partial copy or part of the 3' end of cox1 (54 bp. Additionally, both mt chromosomes possess identical oriented sequences (IOS at the 5' and 3' ends (5' and 3' IOS adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp, whereas the 3' IOS comprises a larger part (mt2 with a larger partial copy of cox1 (243 bp. Conclusion ITR are also documented in the two other available medusozoan mt genomes (Aurelia aurita and Hydra oligactis. In H. magnipapillata, the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of

  12. Unraveling the sperm proteome and post-genomic pathways associated with sperm nuclear DNA fragmentation.

    Science.gov (United States)

    Intasqui, Paula; Camargo, Mariana; Del Giudice, Paula T; Spaine, Deborah M; Carvalho, Valdemir M; Cardozo, Karina H M; Cedenho, Agnaldo P; Bertolla, Ricardo P

    2013-09-01

    Sperm DNA fragmentation has been suggested as a marker for infertility diagnosis and prognosis. Hence, understanding its impact on male physiology and post-genomic pathways would be clinically important. We performed the proteomics and functional enrichment analyses of viable spermatozoa from ejaculates with low and high sperm DNA fragmentation to identify protein expression and pathways altered in association with sperm DNA fragmentation. Sperm DNA fragmentation using the Comet assay and the Komet 6.0.1 software was assessed in raw samples from 89 subjects from a human reproduction service. The Low and High sperm DNA fragmentation groups were formed according to the Olive Tail Moment variable. Spermatozoa proteins from these groups were pooled and analyzed by a shotgun proteomic approach (2D nanoUPLC-ESI-MS(E)). Differentially expressed proteins were used for a functional enrichment study. Two hundred and fifty-seven proteins were identified or quantified in sperm from the Low and High sperm DNA fragmentation groups. Of these, seventy-one proteins were exclusively or overexpressed in the Low group, whereas twenty-three proteins were exclusively or overexpressed in the High group. One hundred and sixty-three proteins were conserved between these groups. We also functionally related the differentially expressed proteins in viable spermatozoa from the groups. Processes such as triacylglycerol metabolism, energy production, protein folding, response to unfolded proteins, and cellular detoxification were found to be altered in these cells. Sperm DNA fragmentation is associated with differential protein expression in viable spermatozoa. These proteins may potentially be used as biomarkers for sperm DNA integrity.

  13. High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

    DEFF Research Database (Denmark)

    Kokotovic, Branko; On, Stephen L.W.

    1999-01-01

    A method for high-resolution genomic fingerprinting of the enteric pathogens Campylobacter jejuni and Campylobacter coli, based on the determination of amplified fragment length polymorphism, is described. The potential of this method for molecular epidemiological studies of these species...

  14. Fenton fragmentation for faster electrophoretic on chip purification of amplifiable genomic DNA.

    Science.gov (United States)

    Hakenberg, S; Hügle, M; Meyer, P; Behrmann, O; Dame, G; Urban, G A

    2015-05-15

    With a rapid and simple actuation protocol electrophoretic nucleic acid extraction is easy automatable, requires no moving parts, is easy to miniaturize and furthermore possesses a size dependent cut-off filter adjustable by the pore size of the hydrogel. However electrophoretic nucleic acid extraction from bacteria has so far been applied mainly for short RNA targets. One of the reasons is that electrophoretic processing of unfragmented genomic DNA strands is time-consuming, because of the length. Here DNA fragmentation would accelerate extraction and isolation. We introduce on-chip lysis and non-enzymatic DNA cleavage directly followed by a purifying step for receiving amplifiable DNA fragments from bacteria in less than 25 min. In contrast to restriction enzymes the Fenton reaction is known to cleave DNA without nucleotide specificity. The reaction mix contains iron(II) EDTA, sodium ascorbate, hydrogen peroxide and lysozyme. The degree of fragmentation can be adjusted by the concentration of reagents. The results enable electrophoretic extraction methods to unspecifically process long genomic DNA in a short time frame, e.g. for pathogen detection in a lab-on-a-chip format. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Multi-antigenic DNA immunization using herpes simplex virus type 2 genomic fragments.

    Science.gov (United States)

    Braun, Ralph P; Dong, Lichun; Jerome, Sarah; Herber, Renee; Roberts, Lee K; Payne, Lendon G

    2008-01-01

    A novel DNA vaccine was generated using genomic fragments of a pathogen as the source of both the antigen coding and regulatory regions. The constructs, termed subgenomic vaccines (SGVs), incorporated genomic DNA sequences up to 45 kbp that encompass 15-20 different genes. The SGVs were developed to generate vaccines capable of expressing multiple genes from a single construct, which could be of great benefit for commercialization. The unique feature of the SGVs is that genes are expressed from their native promoters rather than heterologous promoters typical of DNA vaccines. SGVs composed of genomic fragments from the DS-DNA virus Herpes Simplex Virus Type 2 (HSV-2) induced HSV-2 specific immune responses following particle-mediated epidermal delivery (PMED) in mice and these responses protected animals from lethal infectious challenge. A second generation SGV (SGV-H2), intended as an HSV-2 therapeutic vaccine, was generated that had five HSV-2 genes and was capable of generating multi-antigenic responses in naïve mice, and enhancing responses in infected animals. When compared with standard single plasmid vaccines, immunization with the SGV-H2 was found to be at least as effective as single plasmids or plasmid mixtures. The activity of the SGV-H2 could be greatly enhanced by co-delivering plasmids expressing E. coli heat labile toxin (LT) or cholera toxin CT as adjuvants as has been found previously for standard single-gene DNA vaccines.

  16. Isolation of restriction fragments containing origins of replication from complex genomes.

    Science.gov (United States)

    Mesner, Larry D; Hamlin, Joyce L

    2015-01-01

    The identification and isolation of origins of replication from mammalian genomes has been a demanding task owing to the great complexity of these genomes. However, two methods have been refined in recent years each of which allows significant enrichment of recently activated origins of replication from asynchronous cell cultures. In one of these, nascent strands are melted from the long template DNA, and the small, origin-centered strands are isolated on sucrose gradients. The second method involves the selective entrapment of bubble-containing fragments in gelling agarose and their subsequent recovery and isolation by molecular cloning. Libraries prepared by this method from Chinese hamster and human cells have been shown to be extremely pure, and provide a renewable resource of origins that can be used as probes on microarrays or sequenced by high-throughput techniques to localize them within the genomic source. The bubble-trapping method is described here for asynchronous mammalian cells that grow with reasonable doubling times and from which nuclear matrices can be reliably prepared. The method for nuclear matrix preparation and enrichment of replication intermediates is described in an accompanying chapter entitled "Purification of restriction fragments containing replication intermediates from mammalian cells for 2-D gel analysis" (Chapter 16 ).

  17. Small-fragment genomic libraries for the display of putative epitopes from clinically significant pathogens.

    Science.gov (United States)

    Henics, T; Winkler, B; Pfeifer, U; Gill, S R; Buschle, M; von Gabain, A; Meinke, A L

    2003-07-01

    Taking advantage of whole genome sequences of bacterial pathogens in many thriving diseases with global impact, we developed a comprehensive screening procedure for the identification of putative vaccine candidate antigens. Importantly, this procedure relies on highly representative small-fragment genomic libraries that are expressed to display frame-selected epitope-size peptides on a bacterial cell surface and to interact directly with carefully selected disease-relevant high-titer sera. Here we describe the generation of small-fragment genomic libraries of Gram-positive and Gram-negative clinically significant pathogens, including Staphylococcus aureus and Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus pneumoniae, Enterococcus faecalis, Helicobacter pylori, Chlamydia pneumoniae, the enterotoxigenic Escherichia coli, and Campylobacter jejuni. Large-scale sequencing revealed that the libraries, which provide an average of 20-fold coverage, were random and, as demonstrated with two S. aureus libraries, highly representative. Consistent with the comprehensive nature of this approach is the identification of epitopes that reside in both annotated and putatively novel open reading frames. The use of these libraries therefore allows for the rapid and direct identification of immunogenic epitopes with no apparent bias or difficulty that often associate with conventional expression methods.

  18. Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences

    Institute of Scientific and Technical Information of China (English)

    Axel Mosig; Katrin Sameith; Peter Stadler

    2006-01-01

    Many classes of non-coding RNAs (ncRNAs; including Y RNAs, vault RNAs,RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but wellconserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment,the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.

  19. Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA

    Directory of Open Access Journals (Sweden)

    Metsis Madis

    2008-06-01

    Full Text Available Abstract Background In a traditional electrophoresis mobility shift assay (EMSA a 32P-labeled double-stranded DNA oligonucleotide or a restriction fragment bound to a protein is separated from the unbound DNA by polyacrylamide gel electrophoresis (PAGE in nondenaturing conditions. An extension of this method uses the large population of fragments derived from long genomic regions (approximately 600 kb for the identification of fragments containing protein binding regions. With this method, genomic DNA is fragmented by restriction enzymes, fragments are amplified by PCR, radiolabeled, incubated with nuclear proteins and the resulting DNA-protein complexes are separated by two-dimensional PAGE. Shifted DNA fragments containing protein binding sites are identified by using additional procedures, i. e. gel elution, PCR amplification, cloning and sequencing. Although the method allows simultaneous analysis of a large population of fragments, it is relatively laborious and can be used to detect only high affinity protein binding sites. Here we propose an alternative and straightforward strategy which is based on a combination of native and denaturing PAGE. This strategy allows the identification of DNA fragments containing low as well as high affinity protein binding regions, derived from genomic DNA ( Results We have combined an EMSA-based selection step with subsequent denaturing PAGE for the localization of protein binding regions in long (up to10 kb fragments of genomic DNA. Our strategy consists of the following steps: digestion of genomic DNA with a 4-cutter restriction enzyme (AluI, BsuRI, TruI, etc, separation of low and high molecular weight fractions of resultant DNA fragments, 32P-labeling with Klenow polymerase, traditional EMSA, gel elution and identification of the shifted bands (or smear by denaturing PAGE. The identification of DNA fragments containing protein binding sites is carried out by running the gel-eluted fragments alongside

  20. Selective binding of specific mouse genomic DNA fragments by mouse vimentin filaments in vitro.

    Science.gov (United States)

    Wang, X; Tolstonog, G; Shoeman, R L; Traub, P

    1996-03-01

    Mouse vimentin intermediate filaments (IFs) reconstituted in vitro were analyzed for their capacity to select certain DNA sequences from a mixture of about 500-bp-long fragments of total mouse genomic DNA. The fragments preferentially bound by the IFs and enriched by several cycles of affinity binding and polymerase chain reaction (PCR) amplification were cloned and sequenced. In general, they were G-rich and highly repetitive in that they often contained Gn, (GT)n, and (GA)n repeat elements. Other, more complex repeat sequences were identified as well. Apart from the capacity to adopt a Z-DNA and triple helix configuration under superhelical tension, many fragments were potentially able to form cruciform structures and contained consensus binding sites for various transcription factors. All of these sequence elements are known to occur in introns and 5'/3'-flanking regions of genes and to play roles in DNA transcription, recombination and replication. A FASTA search of the EMBL data bank indeed revealed that sequences homologous to the mouse repetitive DNA fragments are commonly associated with gene-regulatory elements. Unexpectedly, vimentin IFs also bound a large number of apparently overlapping, AT-rich DNA fragments that could be aligned into a composite sequence highly homologous to the 234-bp consensus centromere repeat sequence of gamma-satellite DNA. Previous experiments have shown a high affinity of vimentin for G-rich, repetitive telomere DNA sequences, superhelical DNA, and core histones. Taken together, these data support the hypothesis that, after penetration of the double nuclear membrane via an as yet unidentified mechanism, vimentin IFs cooperatively fix repetitive DNA sequence elements in a differentiation-specific manner in the nuclear periphery subjacent to the nuclear lamina and thus participate in the organization of chromatin and in the control of transcription, replication, and recombination processes. This includes aspects of global

  1. Heterogeneity in the methylation status of genomic DNA fragments demonstrating similar elution profiles in methyl-CpG binding domain column chromatography

    National Research Council Canada - National Science Library

    SHIRAISHI, Masahiko; SEKIGUCHI, Azumi; OATES, Adam; TERRY, Michael; MIYAMOTO, Yuji; SEKIYA, Takao

    2001-01-01

    .... However, the exact elution profile of a specific DNA fragment is unpredictable. In order to address this problem, we have investigated the methylation status of genomic DNA fragments having similar elution profiles...

  2. Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism.

    Science.gov (United States)

    Thompson, F L; Hoste, B; Vandemeulebroecke, K; Swings, J

    2001-12-01

    The genomic diversity among 506 strains of the family Vibrionaceae was analysed using Fluorescent Amplified Fragments Length Polymorphisms (FAFLP). Isolates were from different sources (e.g. fish, mollusc, shrimp, rotifers, artemia, and their culture water) in different countries, mainly from the aquacultural environment. Clustering of the FAFLP band patterns resulted in 69 clusters. A majority of the actually known species of the family Vibrionaceae formed separate clusters. Certain species e.g. V. alginolyticus, V. cholerae, V. cincinnatiensis, V. diabolicus, V. diazotrophicus, V. harveyi, V. logei, V. natriegens, V. nereis, V. splendidus and V. tubiashii were found to be ubiquitous, whereas V. halioticoli, V. ichthyoenteri, V. pectenicida and V. wodanis appear to be exclusively associated with a particular host or geographical region. Three main categories of isolates could be distinguished: (1) isolates with genomes related (i.e. with > or =45% FAFLP pattern similarity) to one of the known type strains; (2) isolates clustering (> or =45% pattern similarity) with more than one type strain; (3) isolates with genomes unrelated (<45% pattern similarity) to any of the type strains. The latter group consisted of 236 isolates distributed in 31 clusters indicating that many culturable taxa of the Vibrionaceae remain as yet to be described.

  3. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes.

    Science.gov (United States)

    Slamovits, Claudio H; Saldarriaga, Juan F; Larocque, Allen; Keeling, Patrick J

    2007-09-14

    The mitochondrial genome and the expression of the genes within it have evolved to be highly unusual in several lineages. Within alveolates, apicomplexans and dinoflagellates share the most reduced mitochondrial gene content on record, but differ from one another in organisation and function. To clarify how these characteristics originated, we examined mitochondrial genome form and expression in a key lineage that arose close to the divergence of apicomplexans and dinoflagellates, Oxyrrhis marina. We show that Oxyrrhis is a basal member of the dinoflagellate lineage whose mitochondrial genome has some unique characteristics while sharing others with apicomplexans or dinoflagellates. Specifically, Oxyrrhis has the smallest gene complement known, with several rRNA fragments and only two protein coding genes, cox1 and a cob-cox3 fusion. The genome appears to be highly fragmented, like that of dinoflagellates, but genes are frequently arranged as tandem copies, reminiscent of the repeating nature of the Plasmodium genome. In dinoflagellates and Oxyrrhis, genes are found in many arrangements, but the Oxyrrhis genome appears to be more structured, since neighbouring genes or gene fragments are invariably the same: cox1 and the cob-cox3 fusion were never found on the same genomic fragment. Analysing hundreds of cDNAs for both genes and circularized mRNAs from cob-cox3 showed that neither uses canonical start or stop codons, although a UAA terminator is created in the cob-cox3 fusion mRNA by post-transcriptional oligoadenylation. mRNAs from both genes also use a novel 5' oligo(U) cap. Extensive RNA editing is characteristic of dinoflagellates, but we find no editing in Oxyrrhis. Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes.

  4. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

    Science.gov (United States)

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-09-24

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.

  5. Large genomic fragment deletions and insertions in mouse using CRISPR/Cas9.

    Directory of Open Access Journals (Sweden)

    Luqing Zhang

    Full Text Available ZFN, TALENs and CRISPR/Cas9 system have been used to generate point mutations and large fragment deletions and insertions in genomic modifications. CRISPR/Cas9 system is the most flexible and fast developing technology that has been extensively used to make mutations in all kinds of organisms. However, the most mutations reported up to date are small insertions and deletions. In this report, CRISPR/Cas9 system was used to make large DNA fragment deletions and insertions, including entire Dip2a gene deletion, about 65kb in size, and β-galactosidase (lacZ reporter gene insertion of larger than 5kb in mouse. About 11.8% (11/93 are positive for 65kb deletion from transfected and diluted ES clones. High targeting efficiencies in ES cells were also achieved with G418 selection, 46.2% (12/26 and 73.1% (19/26 for left and right arms respectively. Targeted large fragment deletion efficiency is about 21.4% of live pups or 6.0% of injected embryos. Targeted insertion of lacZ reporter with NEO cassette showed 27.1% (13/48 of targeting rate by ES cell transfection and 11.1% (2/18 by direct zygote injection. The procedures have bypassed in vitro transcription by directly co-injection of zygotes or co-transfection of embryonic stem cells with circular plasmid DNA. The methods are technically easy, time saving, and cost effective in generating mouse models and will certainly facilitate gene function studies.

  6. Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

    Directory of Open Access Journals (Sweden)

    Berendzen Joel

    2012-08-01

    Full Text Available Abstract Background Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers. Results At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database. Conclusions Classification by exact matching against a precomputed list of signature

  7. Genome-wide macrosynteny among Fusarium species in the Gibberella fujikuroi complex revealed by amplified fragment length polymorphisms.

    Science.gov (United States)

    De Vos, Lieschen; Steenkamp, Emma T; Martin, Simon H; Santana, Quentin C; Fourie, Gerda; van der Merwe, Nicolaas A; Wingfield, Michael J; Wingfield, Brenda D

    2014-01-01

    The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including Fusarium circinatum, Fusarium fujikuroi and Fusarium verticillioides, each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between Fusarium temperatum and F. circinatum, together with genomic sequence data, was utilized to consider the level of synteny between the three Fusarium genomes. Regions that are homologous amongst the Fusarium genomes examined were identified using in silico and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to F. fujikuroi and F. verticillioides. This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in F. verticillioides and F. fujikuroi, as well as to assign two previously unmapped supercontigs of F. verticillioides to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of F. circinatum and F. temperatum. Overall, a remarkable level of macrosynteny was observed among the three Fusarium genomes, when comparing AFLP fragments. This study not only demonstrates how in silico AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.

  8. Large fragment Bst DNA polymerase for whole genome amplification of DNA from formalin-fixed paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Watson Spencer K

    2006-12-01

    Full Text Available Abstract Background Formalin-fixed paraffin-embedded (FFPE tissues represent the largest source of archival biological material available for genomic studies of human cancer. Therefore, it is desirable to develop methods that enable whole genome amplification (WGA using DNA extracted from FFPE tissues. Multiple-strand Displacement Amplification (MDA is an isothermal method for WGA that uses the large fragment of Bst DNA polymerase. To date, MDA has been feasible only for genomic DNA isolated from fresh or snap-frozen tissue, and yields a representational distortion of less than threefold. Results We amplified genomic DNA of five FFPE samples of normal human lung tissue with the large fragment of Bst DNA polymerase. Using quantitative PCR, the copy number of 7 genes was evaluated in both amplified and original DNA samples. Four neuroblastoma xenograft samples derived from cell lines with known N-myc gene copy number were also evaluated, as were 7 samples of non-small cell lung cancer (NSCLC tumors with known Skp2 gene amplification. In addition, we compared the array comparative genomic hybridization (CGH-based genome profiles of two NSCLC samples before and after Bst MDA. A median 990-fold amplification of DNA was achieved. The DNA amplification products had a very high molecular weight (> 23 Kb. When the gene content of the amplified samples was compared to that of the original samples, the representational distortion was limited to threefold. Array CGH genome profiles of amplified and non-amplified FFPE DNA were similar. Conclusion Large fragment Bst DNA polymerase is suitable for WGA of DNA extracted from FFPE tissues, with an expected maximal representational distortion of threefold. Amplified DNA may be used for the detection of gene copy number changes by quantitative realtime PCR and genome profiling by array CGH.

  9. Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing

    Directory of Open Access Journals (Sweden)

    Leterrier Christine

    2010-07-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism for genomic DNA, and EST (Expressed Sequence Tag for the transcribed fraction of the genome. Findings The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. Conclusions Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA.

  10. A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus.

    Science.gov (United States)

    Woloszynska, Magdalena; Bocer, Tomasz; Mackiewicz, Pawel; Janska, Hanna

    2004-11-01

    The mitochondrial genomes of some Phaseolus species contain a fragment of chloroplast trnA gene intron, named pvs-trnA for its location within the Phaseolus vulgaris sterility sequence (pvs). The purpose of this study was to determine the type of transfer (intracellular or horizontal) that gave rise to pvs-trnA. Using a PCR approach we could not find the respective portion of the trnA gene as a part of pvs outside the Phaseolus genus. However, a BLAST search revealed longer fragments of trnA present in the mitochondrial genomes of some Citrus species, Helianthus annuus and Zea mays. Basing on the identity or near-identity between these mitochondrial sequences and their chloroplast counterparts we concluded that they had relocated from chloroplasts to mitochondria via recent, independent, intracellular DNA transfers. In contrast, pvs-trnA displayed a relatively higher sequence divergence when compared with its chloroplast counterpart from Phaseolus vulgaris. Alignment of pvs-trnA with corresponding trnA fragments from 35 plant species as well as phylogenetic analysis revealed that pvs-trnA grouped with non-eudicot sequences and was well separated from all Fabales sequences. In conclusion, we propose that pvs-trnA arose via horizontal transfer of a trnA intron fragment from chloroplast of a non-eudicot plant to Phaseolus mitochondria. This is the first example of horizontal transfer of a chloroplast sequence to the mitochondrial genome in higher plants.

  11. Amplified fragment length polymorphism: an adept technique for genome mapping, genetic differentiation, and intraspecific variation in protozoan parasites.

    Science.gov (United States)

    Kumar, Awanish; Misra, Pragya; Dube, Anuradha

    2013-02-01

    With the advent of polymerase chain reaction (PCR), genetic markers are now accessible for all organisms, including parasites. Amplified fragment length polymorphism (AFLP) is a PCR-based marker for the rapid screening of genetic diversity and intraspecific variation. It is a potent fingerprinting technique for genomic DNAs of any origin or complexity and rapidly generates a number of highly replicable markers that allow high-resolution genotyping. AFLPs are convenient and reliable in comparison to other markers like random amplified polymorphic DNA, restriction fragment length polymorphism, and simple sequence repeat in terms of time and cost efficiency, reproducibility, and resolution as it does not require template DNA sequencing. In addition, AFLP essentially probes the entire genome at random, without prior sequence knowledge. So, AFLP markers have emerged as an advance type of genetic marker with broad application in genomic mapping, population genetics, and DNA fingerprinting and are ideally suited as screening tool for molecular markers linked with biological and clinical traits. This review describes the AFLP procedure and its applications and overview in the fingerprinting of a genome, which has been currently used in parasite genome research. We outline the AFLP procedure adapted for Leishmania genome study and discuss the benefits of AFLPs for assessing genetic variation and genome mapping over other existing molecular techniques. We highlight the possible use of AFLPs as genetic markers with its broad application in parasitological research because it allows random screening of the entire genome for linkage with genetic and clinical properties of the parasite. In this review, we have taken a pragmatic approach on the study of AFLP for genome mapping and polymorphism in protozoan parasites and conclude that AFLP is a very useful tool.

  12. Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking.

    Directory of Open Access Journals (Sweden)

    Jiabing Ji

    Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well.

  13. Identification and cloning of a new category of DNA fragments which are poorly represented in human genomic libraries.

    Science.gov (United States)

    Wong, P; Myal, Y; Shui, R; Tenniswood, M

    1993-01-29

    We have developed an alternative strategy for the preparation of genomic libraries that ensures better representation of genomic sequences commonly underrepresented in genomic libraries constructed using standard protocols. To overcome the apparent bias against genomic sequences containing clusters of restriction sites we have used nonoptimized restriction digestions to generate a mixture of DNA fragments which have been cloned into the EMBL3 vector. To validate this protocol we have screened the EMBL3 library to identify a full length genomic clone of the prolactin-inducible gene (PIP). Screening 4 other, commercially available, genomic libraries prepared using standard protocols for restriction digestion of the genomic DNA failed to identify any full length clones. We show that this increase in the representation of the full length PIP gene in the EMBL3 genomic library is attributable to the method of insert preparation used and suggests that an additional subset of sequences that may be poorly represented in, or absent from, established libraries may be cloned using this modified protocol.

  14. A specific DNA fragment of Gahai parthenogenesis Artemia genome%尕海孤雌生殖卤虫基因组的特异DNA片段

    Institute of Scientific and Technical Information of China (English)

    曾辉; 陈成彬; 刘凤岐; 宋文芹; 陈瑞阳

    2004-01-01

    Artemia is not only valuable for aquaculture but also exhibits unique biological characters. In this study, based on the silkworm Bmdsx gene, a pair of primers was designed. After amplification with these primers, a DNA fragment Apdsx900 from parthenogenesis Artemia genomic DNA was obtained. The following Southern blotting and FISH analysis also proved the fragment was specific for Gahai parthenogenesis Artemia genome. To our knowledge, this is the first report of parthenogenesis genome specific DNA fragments. Apdsxg00 shares little similarity with the silkworm Bmdsx gene. [Acta Zoologica Sinica 50 (3): 470-474, 2004].

  15. Soluble heparan sulfate fragments generated by heparanase trigger the release of pro-inflammatory cytokines through TLR-4.

    Directory of Open Access Journals (Sweden)

    Katharine J Goodall

    Full Text Available Heparanase is a β-D-endoglucuronidase that cleaves heparan sulfate (HS, facilitating degradation of the extracellular matrix (ECM and the release of HS-bound biomolecules including cytokines. The remodeling of the ECM by heparanase is important for various physiological and pathological processes, including inflammation, wound healing, tumour angiogenesis and metastasis. Although heparanase has been proposed to facilitate leukocyte migration through degradation of the ECM, its role in inflammation by regulating the expression and release of cytokines has not been fully defined. In this study, the role of heparanase in regulating the expression and release of cytokines from human and murine immune cells was examined. Human peripheral blood mononuclear cells treated ex vivo with heparanase resulted in the release of a range of pro-inflammatory cytokines including IL-1β, IL-6, IL-8, IL-10 and TNF. In addition, mouse splenocytes treated ex vivo with heparanase resulted in the release of IL-6, MCP-1 and TNF. A similar pattern of cytokine release was also observed when cells were treated with soluble HS. Furthermore, heparanase-induced cytokine release was abolished by enzymatic-inhibitors of heparanase, suggesting this process is mediated via the enzymatic release of cell surface HS fragments. As soluble HS can signal through the Toll-like receptor (TLR pathway, heparanase may promote the upregulation of cytokines through the generation of heparanase-cleaved fragments of HS. In support of this hypothesis, mouse spleen cells lacking the key TLR adaptor molecule MyD88 demonstrated an abolition of cytokine release after heparanase stimulation. Furthermore, TLR4-deficient spleen cells showed reduced cytokine release in response to heparanase treatment, suggesting that TLR4 is involved in this response. Consistent with these observations, the pathway involved in cytokine upregulation was identified as being NF-κB-dependent. These data identify a new

  16. Replication-Coupled PCNA Unloading by the Elg1 Complex Occurs Genome-wide and Requires Okazaki Fragment Ligation

    Directory of Open Access Journals (Sweden)

    Takashi Kubota

    2015-08-01

    Full Text Available The sliding clamp PCNA is a crucial component of the DNA replication machinery. Timely PCNA loading and unloading are central for genome integrity and must be strictly coordinated with other DNA processing steps during replication. Here, we show that the S. cerevisiae Elg1 replication factor C-like complex (Elg1-RLC unloads PCNA genome-wide following Okazaki fragment ligation. In the absence of Elg1, PCNA is retained on chromosomes in the wake of replication forks, rather than at specific sites. Degradation of the Okazaki fragment ligase Cdc9 leads to PCNA accumulation on chromatin, similar to the accumulation caused by lack of Elg1. We demonstrate that Okazaki fragment ligation is the critical prerequisite for PCNA unloading, since Chlorella virus DNA ligase can substitute for Cdc9 in yeast and simultaneously promotes PCNA unloading. Our results suggest that Elg1-RLC acts as a general PCNA unloader and is dependent upon DNA ligation during chromosome replication.

  17. Novel extraction method of genomic DNA suitable for long-fragment amplification from small amounts of milk.

    Science.gov (United States)

    Liu, Y F; Gao, J L; Yang, Y F; Ku, T; Zan, L S

    2014-11-01

    Isolation of genomic DNA is a prerequisite for assessment of milk quality. As a source of genomic DNA, milk somatic cells from milking ruminants are practical, animal friendly, and cost-effective sources. Extracting DNA from milk can avoid the stress response caused by blood and tissue sampling of cows. In this study, we optimized a novel DNA extraction method for amplifying long (>1,000 bp) DNA fragments and used it to evaluate the isolation of DNA from small amounts of milk. The techniques used for the separation of milk somatic cell were explored and combined with a sodium dodecyl sulfate (SDS)-phenol method for optimizing DNA extraction from milk. Spectrophotometry was used to determine the concentration and purity of the extracted DNA. Gel electrophoresis and DNA amplification technologies were used for to determine DNA size and quality. The DNA of 112 cows was obtained from milk (samples of 13 ± 1 mL) and the corresponding optical density ratios at 260:280 nm were between 1.65 and 1.75. Concentrations were between 12 and 45 μg/μL and DNA size and quality were acceptable. The specific PCR amplification of 1,019- and 729-bp bovine DNA fragments was successfully carried out. This novel method can be used as a practical, fast, and economical mean for long genomic DNA extraction from a small amount of milk. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  18. The Cambrian explosion triggered by critical turning point in genome size evolution.

    Science.gov (United States)

    Li, Dirson Jian; Zhang, Shengli

    2010-02-05

    The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are many conflicts on nature and timing of metazoan origins. The crux of the matter is that an entire roadmap of the evolution is missing to discern the biological complexity transition and to evaluate the critical role of the Cambrian explosion in the overall evolutionary context. Here, we calculate the time of the Cambrian explosion by a "C-value clock"; our result quite fits the fossil records. We clarify that the intrinsic reason of genome evolution determined the Cambrian explosion. A general formula for evaluating genome size of different species has been found, by which the genome size evolution can be illustrated. The Cambrian explosion, as a major transition of biological complexity, essentially corresponds to a critical turning point in genome size evolution.

  19. Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments

    DEFF Research Database (Denmark)

    Wang, Y.; van der Hoeven, R. S.; Nielsen, Rasmus

    2005-01-01

    A collection of 9,990 single-pass nuclear genomic sequences, corresponding to 5 Mb of tomato DNA, were obtained using methylation filtration (MF) strategy and reduced to 7,053 unique undermethylated genomic islands (UGIs) distributed as follows: (1) 59% non-coding sequences, (2) 28% coding...... sequences, (3) 12% transposons-96% of which are class I retroelements, and (4) 1% organellar sequences integrated into the nuclear genome over the past approximately 100 million years. A more detailed analysis of coding UGIs indicates that the unmethylated portion of tomato genes extends as far as 676 bp...... upstream and 766 bp downstream of coding regions with an average of 174 and 171 bp, respectively. Based on the analysis of the UGI copy distribution, the undermethylated portion of the tomato genome is determined to account for the majority of the unmethylated genes in the genome and is estimated...

  20. Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Milbury Coren A

    2010-09-01

    Full Text Available Abstract Background Discontinuous genes have been observed in bacteria, archaea, and eukaryotic nuclei, mitochondria and chloroplasts. Gene discontinuity occurs in multiple forms: the two most frequent forms result from introns that are spliced out of the RNA and the resulting exons are spliced together to form a single transcript, and fragmented gene transcripts that are not covalently attached post-transcriptionally. Within the past few years, fragmented ribosomal RNA (rRNA genes have been discovered in bilateral metazoan mitochondria, all within a group of related oysters. Results In this study, we have characterized this fragmentation with comparative analysis and experimentation. We present secondary structures, modeled using comparative sequence analysis of the discontinuous mitochondrial large subunit rRNA genes of the cupped oysters C. virginica, C. gigas, and C. hongkongensis. Comparative structure models for the large subunit rRNA in each of the three oyster species are generally similar to those for other bilateral metazoans. We also used RT-PCR and analyzed ESTs to determine if the two fragmented LSU rRNAs are spliced together. The two segments are transcribed separately, and not spliced together although they still form functional rRNAs and ribosomes. Conclusions Although many examples of discontinuous ribosomal genes have been documented in bacteria and archaea, as well as the nuclei, chloroplasts, and mitochondria of eukaryotes, oysters are some of the first characterized examples of fragmented bilateral animal mitochondrial rRNA genes. The secondary structures of the oyster LSU rRNA fragments have been predicted on the basis of previous comparative metazoan mitochondrial LSU rRNA structure models.

  1. Mitochondrial genome rearrangements in glomus species triggered by homologous recombination between distinct mtDNA haplotypes.

    Science.gov (United States)

    Beaudet, Denis; Terrat, Yves; Halary, Sébastien; de la Providencia, Ivan Enrique; Hijri, Mohamed

    2013-01-01

    Comparative mitochondrial genomics of arbuscular mycorrhizal fungi (AMF) provide new avenues to overcome long-lasting obstacles that have hampered studies aimed at understanding the community structure, diversity, and evolution of these multinucleated and genetically polymorphic organisms.AMF mitochondrial (mt) genomes are homogeneous within isolates, and their intergenic regions harbor numerous mobile elements that have rapidly diverged, including homing endonuclease genes, small inverted repeats, and plasmid-related DNA polymerase genes (dpo), making them suitable targets for the development of reliable strain-specific markers. However, these elements may also lead to genome rearrangements through homologous recombination, although this has never previously been reported in this group of obligate symbiotic fungi. To investigate whether such rearrangements are present and caused by mobile elements in AMF, the mitochondrial genomes from two Glomeraceae members (i.e., Glomus cerebriforme and Glomus sp.) with substantial mtDNA synteny divergence,were sequenced and compared with available glomeromycotan mitochondrial genomes. We used an extensive nucleotide/protein similarity network-based approach to investigated podiversity in AMF as well as in other organisms for which sequences are publicly available. We provide strong evidence of dpo-induced inter-haplotype recombination, leading to a reshuffled mitochondrial genome in Glomus sp. These findings raise questions as to whether AMF single spore cultivations artificially underestimate mtDNA genetic diversity.We assessed potential dpo dispersal mechanisms in AMF and inferred a robust phylogenetic relationship with plant mitochondrial plasmids. Along with other indirect evidence, our analyses indicate that members of the Glomeromycota phylum are potential donors of mitochondrial plasmids to plants.

  2. A Survey of 6,300 Genomic Fragments for cis-Regulatory Activity in the Imaginal Discs of Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Aurélie Jory

    2012-10-01

    Full Text Available Over 6,000 fragments from the genome of Drosophila melanogaster were analyzed for their ability to drive expression of GAL4 reporter genes in the third-instar larval imaginal discs. About 1,200 reporter genes drove expression in the eye, antenna, leg, wing, haltere, or genital imaginal discs. The patterns ranged from large regions to individual cells. About 75% of the active fragments drove expression in multiple discs; 20% were expressed in ventral, but not dorsal, discs (legs, genital, and antenna, whereas ∼23% were expressed in dorsal but not ventral discs (wing, haltere, and eye. Several patterns, for example, within the leg chordotonal organ, appeared a surprisingly large number of times. Unbiased searches for DNA sequence motifs suggest candidate transcription factors that may regulate enhancers with shared activities. Together, these expression patterns provide a valuable resource to the community and offer a broad overview of how transcriptional regulatory information is distributed in the Drosophila genome.

  3. RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) ANALYSIS OF GENOMIC DNA OF 5 STRAINS OF TRICHINELLA SPIRALIS IN CHINA

    Institute of Scientific and Technical Information of China (English)

    王虹; 张月清; 劳为德; 吴赵永

    1995-01-01

    Five restriction endonucleases were used to digest genomic DNA from 5 isolates of Trichinella spiralis obtained from Changchun,Tianjin,Xian,Henan and Yunnan.All the isolates were secured from pigs ex-cept the Changchun strain which came from dog.The DNA fragments digested by endonuclease were sepa-mted by agarose gel electrophoesis.The DNA fragments digested by endonuclease were sepa-rated by agarose gel electrophoresis.The Changchun is olate had a EcoRI band at 1.12kb and a Dral band at 1.97kb which were unique to this isolate.A cloned specific repetitive DNA sequence(1.12kb) from the Changchun strain was selected to prepare a probe for the Southern blotting of EcoRI restriction DNA frag-ments for the 5 isolates.The 1.12kb hybridizing band did not appear except in the Changchun isolate.These results seem to indicate that there are differences between the isolates obtained from hosts in differ-ent geographical regions.

  4. Genomic variations of Mycoplasma capricolum subsp capripneumoniae detected by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Bolske, G.; Ahrens, Peter;

    2000-01-01

    The genetic diversity of Mycoplasma capricolum subsp. capripneumoniae strains based on determination of amplified fragment length polymorphisms (AFLP) is described. AFLP fingerprints of 38 strains derived from different countries in Africa and the Middle East consisted of over 100 bands in the size...... found by 16S rDNA analysis. The present data support previous observations regarding genetic homogeneity of M. capricolum subsp. capripneumoniae, and confirm the two evolutionary lines of descent found by analysis of 16S rRNA genes....

  5. Mutation of mitochondria genome: trigger of somatic cell transforming to cancer cell

    OpenAIRE

    Jianping, Du

    2010-01-01

    Nearly 80 years ago, scientist Otto Warburg originated a hypothesis that the cause of cancer is primarily a defect in energy metabolism. Following studies showed that mitochondria impact carcinogenesis to remodel somatic cells to cancer cells through modifying the genome, through maintenance the tumorigenic phenotype, and through apoptosis. And the Endosymbiotic Theory explains the origin of mitochondria and eukaryotes, on the other hands, the mitochondria also can fall back. Compared to chro...

  6. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments

    Science.gov (United States)

    Dahl, Fredrik; Gullberg, Mats; Stenberg, Johan; Landegren, Ulf; Nilsson, Mats

    2005-01-01

    We present a method to specifically select large sets of DNA sequences for parallel amplification by PCR using target-specific oligonucleotide constructs, so-called selectors. The selectors are oligonucleotide duplexes with single-stranded target-complementary end-sequences that are linked by a general sequence motif. In the selection process, a pool of selectors is combined with denatured restriction digested DNA. Each selector hybridizes to its respective target, forming individual circular complexes that are covalently closed by enzymatic ligation. Non-circularized fragments are removed by exonucleolysis, enriching for the selected fragments. The general sequence that is introduced into the circularized fragments allows them to be amplified in parallel using a universal primer pair. The procedure avoids amplification artifacts associated with conventional multiplex PCR where two primers are used for each target, thereby reducing the number of amplification reactions needed for investigating large sets of DNA sequences. We demonstrate the specificity, reproducibility and flexibility of this process by performing a 96-plex amplification of an arbitrary set of specific DNA sequences, followed by hybridization to a cDNA microarray. Eighty-nine percent of the selectors generated PCR products that hybridized to the expected positions on the array, while little or no amplification artifacts were observed. PMID:15860768

  7. Comparative analysis of acidobacterial genomic fragments from terrestrial and aquatic metagenomic libraries, with emphasis on acidobacteria subdivision 6.

    Science.gov (United States)

    Kielak, Anna M; van Veen, Johannes A; Kowalchuk, George A

    2010-10-01

    The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.

  8. Genomic diversity among Danish field strains of Mycoplasma hyosynoviae assessed by amplified fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, Niels F.; Nielsen, Elisabeth O.;

    2002-01-01

    ) were concurrently examined for variance in BglII-MfeI and EcoRI-Csp6I-A AFLP markers. A total of 56 different genomic fingerprints having an overall similarity between 77 and 96% were detected. No correlation between AFLP variability and period of isolation or anatomical site of isolation could...

  9. The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity.

    Science.gov (United States)

    Dapprich, Johannes; Ferriola, Deborah; Mackiewicz, Kate; Clark, Peter M; Rappaport, Eric; D'Arcy, Monica; Sasson, Ariella; Gai, Xiaowu; Schug, Jonathan; Kaestner, Klaus H; Monos, Dimitri

    2016-07-09

    The ability to capture and sequence large contiguous DNA fragments represents a significant advancement towards the comprehensive characterization of complex genomic regions. While emerging sequencing platforms are capable of producing several kilobases-long reads, the fragment sizes generated by current DNA target enrichment technologies remain a limiting factor, producing DNA fragments generally shorter than 1 kbp. The DNA enrichment methodology described herein, Region-Specific Extraction (RSE), produces DNA segments in excess of 20 kbp in length. Coupling this enrichment method to appropriate sequencing platforms will significantly enhance the ability to generate complete and accurate sequence characterization of any genomic region without the need for reference-based assembly. RSE is a long-range DNA target capture methodology that relies on the specific hybridization of short (20-25 base) oligonucleotide primers to selected sequence motifs within the DNA target region. These capture primers are then enzymatically extended on the 3'-end, incorporating biotinylated nucleotides into the DNA. Streptavidin-coated beads are subsequently used to pull-down the original, long DNA template molecules via the newly synthesized, biotinylated DNA that is bound to them. We demonstrate the accuracy, simplicity and utility of the RSE method by capturing and sequencing a 4 Mbp stretch of the major histocompatibility complex (MHC). Our results show an average depth of coverage of 164X for the entire MHC. This depth of coverage contributes significantly to a 99.94 % total coverage of the targeted region and to an accuracy that is over 99.99 %. RSE represents a cost-effective target enrichment method capable of producing sequencing templates in excess of 20 kbp in length. The utility of our method has been proven to generate superior coverage across the MHC as compared to other commercially available methodologies, with the added advantage of producing longer sequencing

  10. ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts.

    Science.gov (United States)

    Wei, Guifang; Pan, Li; Du, Huimin; Chen, Junyi; Zhao, Liping

    2004-10-01

    Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.

  11. CCQM-K86/P113.1: Relative quantification of genomic DNA fragments extracted from a biological tissue

    Science.gov (United States)

    Corbisier, P.; Vincent, S.; Schimmel, H.; Kortekaas, A.-M.; Trapmann, S.; Burns, M.; Bushell, C.; Akgoz, M.; Akyürek, S.; Dong, L.; Fu, B.; Zhang, L.; Wang, J.; Pérez Urquiza, M.; Bautista, J. L.; Garibay, A.; Fuller, B.; Baoutina, A.; Partis, L.; Emslie, K.; Holden, M.; Chum, W. Y.; Kim, H.-H.; Phunbua, N.; Milavec, M.; Zel, J.; Vonsky, M.; Konopelko, L. A.; Lau, T. L. T.; Yang, B.; Hui, M. H. K.; Yu, A. C. H.; Viroonudomphol, D.; Prawettongsopon, C.; Wiangnon, K.; Takabatake, R.; Kitta, K.; Kawaharasaki, M.; Parkes, H.

    2012-01-01

    Key comparison CCQM-K86 was performed to demonstrate and document the capacity of interested national metrology institutes (NMIs) and designated institutes (DIs) in the determination of the relative quantity of two specific genomic DNA fragments present in a biological tissue. The study provides the support for the following measurement claim: "Quantification of the ratio of the number of copies of specified intact sequence fragments of a length in the range of 70 to 100 nucleotides in a single genomic DNA extract from ground maize seed materials". The study was carried out under the auspices of the Bioanalysis Working Group (BAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) and was piloted by the Institute for Reference Materials and Methods (IRMM) in Geel (Belgium). The following laboratories (in alphabetical order) participated in this key comparison: AIST (Japan), CENAM (Mexico), DMSc (Thailand), GLHK (Hong Kong), IRMM (European Union), KRISS (Republic of Korea), LGC (United Kingdom), MIRS/NIB (Slovenia), NIM (PR China), NIST (USA), NMIA (Australia), TÜBITAK UME (Turkey) and VNIIM (Russian Federation). The following laboratories (in alphabetical order) participated in a pilot study that was organized in parallel: LGC (United Kingdom), PKU (PR China), NFRI (Japan) and NIMT (Thailand). Good agreement was observed between the reported results of eleven participants. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  12. Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes.

    Science.gov (United States)

    Thierry, A; Dujon, B

    1992-11-11

    We have developed a new method for the physical mapping of genomes and the rapid sorting of genomic libraries which is based on chromosome fragmentation by the meganuclease I-Sce I, the first available member of a new class of endonucleases with very long recognition sequences. I-Sce I allows complete cleavage at a single artificially inserted site in an entire genome. Sites can be inserted by homologous recombination using specific cassettes containing selectable markers or, at random, using transposons. This method has been applied to the physical mapping of chromosome XI (620 kb) of Saccharomyces cerevisi and to the sorting of a cosmid library. Our strategy has potential applications to various genome mapping projects. A set of transgenic yeast strains carrying the I-Sce I sites at various locations along a chromosome defines physical intervals against which new genes, DNA fragments or clones can be mapped directly by simple hybridizations.

  13. Genomic Fingerprinting of the Vaccine Strain of Clostridium Tetani by Restriction Fragment Length Polymorphism Technique

    Directory of Open Access Journals (Sweden)

    Naser Harzandi

    2013-05-01

    Full Text Available Background: Clostridium tetani or Nicolaier’s bacillus is an obligatory anaerobic, Gram-positive, movable with terminal or sub terminal spore. The chromosome of C. tetani contains 2,799,250 bp with a G+C content of 28.6%. The aim of this study was identification and genomic fingerprinting of the vaccine strain of C. tetani.Materials and Methods: The vaccine strain of C. tetani was provided by Razi Vaccine and Serum Research Institute. The seeds were inoculated into Columbia blood agar and grown for 72 h and transferred to the thioglycolate broth medium for further 36 h culturing. The cultures were incubated at 35ºC in anaerobic conditions. DNA extraction with phenol/ chloroform method was performed. After extraction, the consistency of DNA was assayed. Next, the vaccine strain was digested using pvuII enzyme and incubated at 37ºC for overnight. The digested DNA was gel-electrophoresed by 1% agarose for a short time. Then, the gel was studied with Gel Doc system and transferred to Hybond N+membrane using standard DNA blotting techniques.Results: The vaccine strain of C. tetani genome was fingerprinted by RFLP technique. Our preliminary results showed no divergence exists in the vaccine strain used for the production tetanus toxoid during the periods of 1990-2011.Conclusion: Observation suggests that there is lack of significant changes in RFLP genomic fingerprinting profile of the vaccine strain. Therefore, this strain did not lose its efficiency in tetanus vaccine production. RFLP analysis is worthwhile in investigating the nature of the vaccine strain C. tetani.

  14. MALT1-ubiquitination triggers non-genomic NF-κB/IKK signaling upon platelet activation.

    Science.gov (United States)

    Karim, Zubair A; Vemana, Hari Priya; Khasawneh, Fadi T

    2015-01-01

    We have recently shown that IKK complex plays an important non-genomic role in platelet function, i.e., regulates SNARE machinery-dependent membrane fusion. In this connection, it is well known that MALT1, whose activity is modulated by proteasome, plays an important role in the regulation of IKK complex. Therefore, the present studies investigated the mechanism by which IKK signaling is regulated in the context of the platelet proteasome. It was found that platelets express a functional proteasome, and form CARMA/MALT1/Bcl10 (CBM) complex when activated. Using a pharmacological inhibitor, the proteasome was found to regulate platelet function (aggregation, integrin activation, secretion, phosphatidylserine exposure and changes in intracellular calcium). It was also found to regulate thrombogenesis and physiologic hemostasis. We also observed, upon platelet activation, that MALT1 is ubiquitinated, and this coincides with the activation of the IKK/NF-κB-signaling pathway. Finally, we observed that the proteasome inhibitor blocks CBM complex formation and the interaction of IKKγ and MALT1; abrogates SNARE formation, and the association of MALT1 with TAK1 and TAB2, which are upstream of the CBM complex. Thus, our data demonstrate that MALT1 ubiquitination is critical for the engagement of CBM and IKK complexes, thereby directing platelet signals to the NF-κB pathway.

  15. MALT1-ubiquitination triggers non-genomic NF-κB/IKK signaling upon platelet activation.

    Directory of Open Access Journals (Sweden)

    Zubair A Karim

    Full Text Available We have recently shown that IKK complex plays an important non-genomic role in platelet function, i.e., regulates SNARE machinery-dependent membrane fusion. In this connection, it is well known that MALT1, whose activity is modulated by proteasome, plays an important role in the regulation of IKK complex. Therefore, the present studies investigated the mechanism by which IKK signaling is regulated in the context of the platelet proteasome. It was found that platelets express a functional proteasome, and form CARMA/MALT1/Bcl10 (CBM complex when activated. Using a pharmacological inhibitor, the proteasome was found to regulate platelet function (aggregation, integrin activation, secretion, phosphatidylserine exposure and changes in intracellular calcium. It was also found to regulate thrombogenesis and physiologic hemostasis. We also observed, upon platelet activation, that MALT1 is ubiquitinated, and this coincides with the activation of the IKK/NF-κB-signaling pathway. Finally, we observed that the proteasome inhibitor blocks CBM complex formation and the interaction of IKKγ and MALT1; abrogates SNARE formation, and the association of MALT1 with TAK1 and TAB2, which are upstream of the CBM complex. Thus, our data demonstrate that MALT1 ubiquitination is critical for the engagement of CBM and IKK complexes, thereby directing platelet signals to the NF-κB pathway.

  16. Affinity chromatography—dependent selection (ACDS) of genomic DNA fragments bound specifically to bacterial synthesized Myc/Myn proteins

    Institute of Scientific and Technical Information of China (English)

    SHICAN; PEIWANG; 等

    1995-01-01

    This paper describes an approach to seek for mouse c-Myc/Myn proteins-bound specific sequences among genomic DNA.cDNA fragment of myn gene was obtained through RT-PCR technique from RNA of NIH3T3 cells.DNA fragments encoding BR/HLH/LZ structure of Myc and Myn proteins were cloned in frame into pGEX-2T vector respectively.Fusion GST-Myc and GST-Myn synthesized in E.coli hosts showed affinity to CACGTG E-box DNA and subsequently interacted with genomic fragments prepared through whole-genome-PCR.A PCR-assisted procedure which combines protein-DNA interaction and affinity chromatography was designed to enrich Myc/Myn bound DNA.At least two genomic DNA fragments obtained exhibit specifical binding capacity to Myc/Myn complex but not to GST alone.Significance of the work and of the technique itself as well asidentification of the DNAs are discussed.

  17. Identification of a nuclear-localized nuclease from wheat cells undergoing programmed cell death that is able to trigger DNA fragmentation and apoptotic morphology on nuclei from human cells.

    Science.gov (United States)

    Domínguez, Fernando; Cejudo, Francisco J

    2006-08-01

    PCD (programmed cell death) in plants presents important morphological and biochemical differences compared with apoptosis in animal cells. This raises the question of whether PCD arose independently or from a common ancestor in plants and animals. In the present study we describe a cell-free system, using wheat grain nucellar cells undergoing PCD, to analyse nucleus dismantling, the final stage of PCD. We have identified a Ca2+/Mg2+ nuclease and a serine protease localized to the nucleus of dying nucellar cells. Nuclear extracts from nucellar cells undergoing PCD triggered DNA fragmentation and other apoptotic morphology in nuclei from different plant tissues. Inhibition of the serine protease did not affect DNA laddering. Furthermore, we show that the nuclear extracts from plant cells triggered DNA fragmentation and apoptotic morphology in nuclei from human cells. The inhibition of the nucleolytic activity with Zn2+ or EDTA blocked the morphological changes of the nucleus. Moreover, nuclear extracts from apoptotic human cells triggered DNA fragmentation and apoptotic morphology in nuclei from plant cells. These results show that degradation of the nucleus is morphologically and biochemically similar in plant and animal cells. The implication of this finding on the origin of PCD in plants and animals is discussed.

  18. Modeling the fine fragmentation following the triggering stage of a vapor explosion; Modelisation de la fragmentaton fine lors de la phase de declenchement d`une explosion de vapeur

    Energy Technology Data Exchange (ETDEWEB)

    Darbord, I. [CEA Grenoble, 38 (France). Service d`Etudes et de Modelisation Thermohydraulique

    1997-06-11

    In the frame of PWR severe accidents, where the core melt, this thesis studies one of the stages of an FCI (fuel coolant interaction) or vapor explosion. An FCI is a rapid evaporation of a coolant when it comes into contact with a hot liquid. More precisely, the subject of this study is the triggering stage of the FCI, when a fuel drop of diameter around one centimeter breaks up into many fragments, diameter of which is around a hundred micrometers. The model describes the cyclic collapse and growth of a vapor bubble around the fuel droplet and its fragmentation. The main features of the model are: - the destabilization of the film or the vapor bubble due to the growth of Rayleigh-Taylor instabilities (those form coolant jets that contact the fuel surface); - The mechanisms of fragmentation, following the contacts (in the case of entrapment of a certain amount of coolant in the fuel, the entrapped coolant evaporates violently after it has been heated to the homogeneous nucleation temperature); - the transient heat transfer from the fragments to the coolant and the elevated vapor production, which leads to an important expansion of the bubble (about this point, the cooling of the fragments has been described by a transient heat transfer coefficient linked to nucleate boiling). The results of the model show good agreement with experimental data. (Author) 68 refs.

  19. The Depoliticisation and 'ASEANisation' of Counter-Terrorism Policies in South-East Asia: A Weak Trigger for a Fragmented Version of Human Security

    Directory of Open Access Journals (Sweden)

    Alfred Gerstl

    2010-01-01

    Full Text Available This article applies a modified version of the theoretical approach of the Copenhagen School to demonstrate that the Association of Southeast Asian Nations (ASEAN has since 2001 reacted in a twofold way to the complex political obstacles to closer counter-terrorism co-operation: First, it has responded with securitising terrorism as a transnational crime and, second, with a depoliticisation and ‘ASEANisation’ of its counter-terrorism policies. Depoliticisation and ‘ASEANisation’, i.e. the framing of a security threat under the ASEAN Way values, are both deliberate political actions. They enable politicians to base co-operation among the ASEAN members and with outside powers on a non-political, technical basis. Contradicting an assumption of the Copenhagen School, this study argues that in South-East Asia where sovereignty and non- interference are still core principles this approach can offer better political opportunities to resolve a security threat than a ‘classic’ securitisation. Furthermore, this article demonstrates that ASEAN’s anti-terrorism policies reflect its fragmented version of human security, which is based on national and regime rather than individual security. As counter-terrorism does not enjoy political priority in the region, these policies can only be a weak trigger for the implementation of ASEAN’s notion of human security. ----- Dieser Artikel wendet eine leicht modifizierte Version der Copenhagen School an, um aufzuzeigen, wie die Vereinigung südostasiatischer Nationen (ASEAN seit 2001 auf die vielfältigen politischen Hindernisse für eine engere regionale Anti-Terrorismus-Zusammenarbeit reagiert hat. ASEAN hat, erstens, eine Sekuritisierung des Terrorismus als transnationales Verbrechen und, zweitens, eine Depolitisierung und „ASEANisierung“ (die Kontextualisierung einer sicherheitspolitischen Bedrohung unter den Werten des ASEAN Way ihrer Anti-Terrorismus-Politik vorgenommen. Sowohl

  20. [Isolation and characteristics of DNA fragments for the region of the tissue plasminogen activator genes and areas adjacent to it in the human genome].

    Science.gov (United States)

    Sarafanov, A G; Timofeeva, M Ia; Aleshkov, S B; Kupriianova, N S; Bannikov, V M; Zakhar'ev, V M; Baev, A A

    1994-01-01

    Fragments overlapping the tPA gene and its 5'- and 3'-flanking regions were isolated from human liver DNA library cloned in lambda Charon4A vector. A BglII fragment comprising the 3' end and the adjacent genomic region (total length 3.7 kb) was subcloned in plasmid pUC19 and its restriction map was determined. The nucleotide sequence of the 5' region of this fragment was compared with the 3' end region of the tPA gene and the corresponding regions of five published variants of tPA mRNA cDNA from different tissues; discrepancies in seven positions were revealed, which might be caused by intragenomic polymorphism.

  1. Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes.

    Science.gov (United States)

    Ranade, Sonali Sachin; García-Gil, María Rosario; Rosselló, Josep A

    2016-04-01

    Many genes have been lost from the prokaryote plastidial genome during the early events of endosymbiosis in eukaryotes. Some of them were definitively lost, but others were relocated and functionally integrated to the host nuclear genomes through serial events of gene transfer during plant evolution. In gymnosperms, plastid genome sequencing has revealed the loss of ndh genes from several species of Gnetales and Pinaceae, including Norway spruce (Picea abies). This study aims to trace the ndh genes in the nuclear and organellar Norway spruce genomes. The plastid genomes of higher plants contain 11 ndh genes which are homologues of mitochondrial genes encoding subunits of the proton-pumping NADH-dehydrogenase (nicotinamide adenine dinucleotide dehydrogenase) or complex I (electron transport chain). Ndh genes encode 11 NDH polypeptides forming the Ndh complex (analogous to complex I) which seems to be primarily involved in chloro-respiration processes. We considered ndh genes from the plastidial genome of four gymnosperms (Cryptomeria japonica, Cycas revoluta, Ginkgo biloba, Podocarpus totara) and a single angiosperm species (Arabidopsis thaliana) to trace putative homologs in the nuclear and organellar Norway spruce genomes using tBLASTn to assess the evolutionary fate of ndh genes in Norway spruce and to address their genomic location(s), structure, integrity and functionality. The results obtained from tBLASTn were subsequently analyzed by performing homology search for finding ndh specific conserved domains using conserved domain search. We report the presence of non-functional plastid ndh gene fragments, excepting ndhE and ndhG genes, in the nuclear genome of Norway spruce. Regulatory transcriptional elements like promoters, TATA boxes and enhancers were detected in the upstream regions of some ndh fragments. We also found transposable elements in the flanking regions of few ndh fragments suggesting nuclear rearrangements in those regions. These evidences

  2. Targeting Mcl-1 for multiple myeloma (MM) therapy: drug-induced generation of Mcl-1 fragment Mcl-1(128-350) triggers MM cell death via c-Jun upregulation.

    Science.gov (United States)

    Fan, Fengjuan; Tonon, Giovanni; Bashari, Muhammad Hasan; Vallet, Sonia; Antonini, Elena; Goldschmidt, Hartmut; Schulze-Bergkamen, Henning; Opferman, Joseph T; Sattler, Martin; Anderson, Kenneth C; Jäger, Dirk; Podar, Klaus

    2014-02-28

    Myeloid cell leukemia-1 (Mcl-1, HGNC: 6943), a pro-survival member of the Bcl-2 family, plays a crucial role in Multiple Myeloma (MM) pathogenesis and drug resistance, thus representing a promising therapeutic target in MM. A novel strategy to inhibit Mcl-1 activity is the induction of ubiquitin-independent Mcl-1 degradation. Our own and other previous studies have demonstrated caspase-dependent generation of a 28kDa Mcl-1 fragment, Mcl-1(128-350), which inhibits MM cell proliferation and survival. Here, we show that similar to bortezomib, the novel proteasome inhibitors carfilzomib and ixazomib, as well as staurosporine and adaphostin, induce the generation of Mcl-1(128-350) in MM cells. Next, the molecular sequelae downstream of Mcl-1(128-350), which mediate its pro-apoptotic activity, were delineated. Surprisingly, we observed nuclear accumulation of drug-induced or exogenously overexpressed Mcl-1(128-350), followed by elevated mRNA and protein levels of c-Jun, as well as enhanced AP-1 reporter activity. Moreover, drug-induced AP-1 activity was blocked after introducing a point mutation into the highly conserved Mcl-1 caspase-cleavage site Asp127, but not Asp157. Consequently, drug-triggered cell death was significantly decreased in MM cells transfected with Mcl-1 D127A, but not with Mcl-1 D157A. Consistent with these data, treatment with bortezomib triggered c-Jun upregulation followed by apoptosis in Mcl-1(wt/wt), but not Mcl-1(Δ/null) murine embryonic fibroblasts (MEFs). Transfection of a plasmid carrying Mcl-1(wt) into Mcl-1(Δ/null) MEFs restored bortezomib-induced Mcl-1 fragmentation, c-Jun upregulation and AP-1 reporter activity. Finally, our data indicate that drug-induced generation of a pro-apoptotic Mcl-1 fragment followed by c-Jun upregulation may also be a novel therapeutic approach in other tumor entities.

  3. Does personalized melanoma genomic risk information trigger conversations about skin cancer prevention and skin examination with family, friends and health professionals?

    Science.gov (United States)

    Smit, A K; Keogh, L A; Newson, A J; Butow, P N; Dunlop, K; Morton, R L; Kirk, J; Espinoza, D; Cust, A E

    2017-09-01

    Receiving information about genomic risk of melanoma might trigger conversations about skin cancer prevention and skin examinations. To explore conversations prompted by receiving personalized genomic risk of melanoma with family, friends and health professionals. We used a mixed-methods approach. Participants without a personal history and unselected for a family history of melanoma (n = 103, aged 21-69 years, 53% women) completed questionnaires 3 months after receiving a personalized melanoma genomic risk assessment. Semistructured interviews were undertaken with 30 participants in high, average and low genomic risk categories, and data were analysed thematically. From the questionnaires, 74% of participants communicated their genomic risk information with family, and 49% with friends. Communication with a health professional differed by risk level: 41%, 16% and 12% for high, average and low risk, respectively (P = 0·01). Qualitative analysis showed that perceived 'shared risk' and perceived interest of family and friends were motivations for discussing risk or prevention behaviours. The information prompted conversations with family and health professionals about sun protection and skin checks, and general conversations about melanoma risk with friends. Reasons for not discussing with family included existing personal or family health concerns, or existing high levels of sun protection behaviour among family members. Personalized melanoma genomic risk information can prompt risk-appropriate discussions about skin cancer prevention and skin examinations with family and health professionals. Sharing this information with others might increase its impact on melanoma prevention and skin examination behaviours, and this process could be used to encourage healthy behaviour change within families. © 2017 British Association of Dermatologists.

  4. Co-barcoded sequence reads from long DNA fragments: A cost-effective solution for Perfect Genome sequencing

    Directory of Open Access Journals (Sweden)

    Brock A Peters

    2015-01-01

    Full Text Available Next generation sequencing (NGS technologies, primarily based on massively parallel sequencing (MPS, have touched and radically changed almost all aspects of research worldwide. These technologies have allowed for the rapid analysis, to date, of the genomes of more than 2,000 different species. In humans, NGS has arguably had the largest impact. Over 100,000 genomes of individual humans (based on various estimates have been sequenced allowing for deep insights into what makes individuals and families unique and what causes disease in each of us. Despite all of this progress, the current state of the art in sequence technology is far from generating a perfect genome sequence and much remains to be understood in the biology of human and other organisms’ genomes. In the article that follows we outline, why the perfect genome in humans is important, what is lacking from current human whole genome sequences, and a potential strategy for achieving the perfect genome in a cost effective manner.

  5. [Conformational polymorphysm of G-rich fragments of DNA Alu-repeats. II. the putative role of G-quadruplex structures in genomic rearrangements].

    Science.gov (United States)

    Varizhuk, A M; Sekridova, A V; Tankevich, M V; Podgorsky, V S; Smirnov, I P; Pozmogova, G E

    2016-11-01

    Three evolutionary conserved sites of Alu repeats (PQS2, PQS3 and PQS4) were shown to form stable inter- and intramolecular G-quadruplexes (GQs) in vitro. Structures and topologies of these GQs were elucidated using spectral methods. Self-association of G-rich Alu fragments was studied. Dimeric GQ formation from two distal identical or different putative quadruplex sites - (PQS2)2, (PQS3)2 or PQS2-PQS3 - within one lengthy DNA strand was demonstrated by a FRET-based method. Oligomer PQS4 (folded into a parallel intramolecular GQ) was shown to form stacks of quadruplexes that are stabilized by stacking interactions of external G-tetrads (this was confirmed by DOSY NMR, AFM microscopy and differential CD spectroscopy). Comparative analysis of the properties of various GQs allowed us to put forward a hypothesis of two general mechanisms of intermolecular GQ-dependant genomic rearrangements: 1) formation of a dimeric GQs; 2) association of pre-folded intramolecular parallel GQs from different strands into GQ-stacks. Thus, the observed co-localization of G-rich motifs of Alu elements with double-strand break hotspots and rearrangement hotspots may be accounted for by the specific secondary structure of these motifs. At the same time, this is likely primarily due to high abundance of such G-rich Alu fragments in the genome.

  6. Genome Sequence of Rhizobacterium Serratia marcescens Strain 90-166, Which Triggers Induced Systemic Resistance and Plant Growth Promotion.

    Science.gov (United States)

    Jeong, Haeyoung; Kloepper, Joseph W; Ryu, Choong-Min

    2015-06-18

    The rhizobacterium Serratia marcescens strain 90-166 elicits induced systemic resistance against plant pathogens and herbivores and promotes plant growth under greenhouse and field conditions. Strain 90-166 secretes volatile compounds, siderophores, salicylic acid, and quorum-sensing autoinducers as bacterial determinants toward plant health. Herein, we present its draft genome sequence.

  7. Genome Sequence of the Plant Endophyte Bacillus pumilus INR7, Triggering Induced Systemic Resistance in Field Crops.

    Science.gov (United States)

    Jeong, Haeyoung; Choi, Soo-Keun; Kloepper, Joseph W; Ryu, Choong-Min

    2014-10-30

    Bacillus pumilus INR7 is an endophytic bacterium that has been commercialized as a biological control product against soilborne pathogens as well as foliar pathogens by direct antagonism and induction of systemic resistance. In the current study, we provide the genome sequence and a possible explanation of the function of strain INR7.

  8. Lawrence Livermore National Laboratory- Completing the Human Genome Project and Triggering Nearly $1 Trillion in U.S. Economic Activity

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, Jeffrey S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-07-28

    The success of the Human Genome project is already nearing $1 Trillion dollars of U.S. economic activity. Lawrence Livermore National Laboratory (LLNL) was a co-leader in one of the biggest biological research effort in history, sequencing the Human Genome Project. This ambitious research effort set out to sequence the approximately 3 billion nucleotides in the human genome, an effort many thought was nearly impossible. Deoxyribonucleic acid (DNA) was discovered in 1869, and by 1943 came the discovery that DNA was a molecule that encodes the genetic instructions used in the development and functioning of living organisms and many viruses. To make full use of the information, scientists needed to first sequence the billions of nucleotides to begin linking them to genetic traits and illnesses, and eventually more effective treatments. New medical discoveries and improved agriculture productivity were some of the expected benefits. While the potential benefits were vast, the timeline (over a decade) and cost ($3.8 Billion) exceeded what the private sector would normally attempt, especially when this would only be the first phase toward the path to new discoveries and market opportunities. The Department of Energy believed its best research laboratories could meet this Grand Challenge and soon convinced the National Institute of Health to formally propose the Human Genome project to the federal government. The U.S. government accepted the risk and challenge to potentially create new healthcare and food discoveries that could benefit the world and the U.S. Industry.

  9. Genome Sequence of the Plant Endophyte Bacillus pumilus INR7, Triggering Induced Systemic Resistance in Field Crops

    OpenAIRE

    Jeong, Haeyoung; Choi, Soo-Keun; Joseph W Kloepper; Ryu, Choong-Min

    2014-01-01

    Bacillus pumilus INR7 is an endophytic bacterium that has been commercialized as a biological control product against soilborne pathogens as well as foliar pathogens by direct antagonism and induction of systemic resistance. In the current study, we provide the genome sequence and a possible explanation of the function of strain INR7.

  10. Prediction of Protein-Protein Interactions by NanoLuc-Based Protein-Fragment Complementation Assay | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at Emory has developed a new NanoLuc®-based protein-fragment complementation assay (NanoPCA) which allows the detection of novel protein-protein interactions (PPI). NanoPCA allows the study of PPI dynamics with reversible interactions.  Read the abstract. Experimental Approaches Read the detailed Experimetnal Approaches. 

  11. The telomeric sync model of speciation: species-wide telomere erosion triggers cycles of transposon-mediated genomic rearrangements, which underlie the saltatory appearance of nonadaptive characters.

    Science.gov (United States)

    Stindl, Reinhard

    2014-03-01

    Charles Darwin knew that the fossil record is not overwhelmingly supportive of genetic and phenotypic gradualism; therefore, he developed the core of his theory on the basis of breeding experiments. Here, I present evidence for the existence of a cell biological mechanism that strongly points to the almost forgotten European concept of saltatory evolution of nonadaptive characters, which is in perfect agreement with the gaps in the fossil record. The standard model of chromosomal evolution has always been handicapped by a paradox, namely, how speciation can occur by spontaneous chromosomal rearrangements that are known to decrease the fertility of heterozygotes in a population. However, the hallmark of almost all closely related species is a differing chromosome complement and therefore chromosomal rearrangements seem to be crucial for speciation. Telomeres, the caps of eukaryotic chromosomes, erode in somatic tissues during life, but have been thought to remain stable in the germline of a species. Recently, a large human study spanning three healthy generations clearly found a cumulative telomere effect, which is indicative of transgenerational telomere erosion in the human species. The telomeric sync model of speciation presented here is based on telomere erosion between generations, which leads to identical fusions of chromosomes and triggers a transposon-mediated genomic repatterning in the germline of many individuals of a species. The phenotypic outcome of the telomere-triggered transposon activity is the saltatory appearance of nonadaptive characters simultaneously in many individuals. Transgenerational telomere erosion is therefore the material basis of aging at the species level.

  12. The telomeric sync model of speciation: species-wide telomere erosion triggers cycles of transposon-mediated genomic rearrangements, which underlie the saltatory appearance of nonadaptive characters

    Science.gov (United States)

    Stindl, Reinhard

    2014-03-01

    Charles Darwin knew that the fossil record is not overwhelmingly supportive of genetic and phenotypic gradualism; therefore, he developed the core of his theory on the basis of breeding experiments. Here, I present evidence for the existence of a cell biological mechanism that strongly points to the almost forgotten European concept of saltatory evolution of nonadaptive characters, which is in perfect agreement with the gaps in the fossil record. The standard model of chromosomal evolution has always been handicapped by a paradox, namely, how speciation can occur by spontaneous chromosomal rearrangements that are known to decrease the fertility of heterozygotes in a population. However, the hallmark of almost all closely related species is a differing chromosome complement and therefore chromosomal rearrangements seem to be crucial for speciation. Telomeres, the caps of eukaryotic chromosomes, erode in somatic tissues during life, but have been thought to remain stable in the germline of a species. Recently, a large human study spanning three healthy generations clearly found a cumulative telomere effect, which is indicative of transgenerational telomere erosion in the human species. The telomeric sync model of speciation presented here is based on telomere erosion between generations, which leads to identical fusions of chromosomes and triggers a transposon-mediated genomic repatterning in the germline of many individuals of a species. The phenotypic outcome of the telomere-triggered transposon activity is the saltatory appearance of nonadaptive characters simultaneously in many individuals. Transgenerational telomere erosion is therefore the material basis of aging at the species level.

  13. Genome Transfer Prevents Fragmentation and Restores Developmental Potential of Developmentally Compromised Postovulatory Aged Mouse Oocytes

    Directory of Open Access Journals (Sweden)

    Mitsutoshi Yamada

    2017-03-01

    Full Text Available Changes in oocyte quality can have great impact on the developmental potential of early embryos. Here we test whether nuclear genome transfer from a developmentally incompetent to a developmentally competent oocyte can restore developmental potential. Using in vitro oocyte aging as a model system we performed nuclear transfer in mouse oocytes at metaphase II or at the first interphase, and observed that development to the blastocyst stage and to term was as efficient as in control embryos. The increased developmental potential is explained primarily by correction of abnormal cytokinesis at anaphase of meiosis and mitosis, by a reduction in chromosome segregation errors, and by normalization of the localization of chromosome passenger complex components survivin and cyclin B1. These observations demonstrate that developmental decline is primarily due to abnormal function of cytoplasmic factors involved in cytokinesis, while the genome remains developmentally fully competent.

  14. Identification of the major structural and nonstructural proteins encoded by human parvovirus B19 and mapping of their genes by procaryotic expression of isolated genomic fragments

    Energy Technology Data Exchange (ETDEWEB)

    Cotmore, S.F.; McKie, V.C.; Anderson, L.J.; Astell, C.R.; Tattersall, P.

    1986-11-01

    Plasma from a child with homozygous sickle-cell disease, sampled during the early phase of an aplastic crisis, contained human parvovirus B19 virions. Plasma taken 10 days later (during the convalescent phase) contained both immunoglobulin M and immunoglobulin G antibodies directed against two viral polypeptides with apparent molecular weights for 83,000 and 58,000 which were present exclusively in the particulate fraction of the plasma taken during the acute phase. These two protein species comigrated at 110S on neutral sucrose velocity gradients with the B19 viral DNA and thus appear to constitute the viral capsid polypeptides. The B19 genome was molecularly cloned into a bacterial plasmid vector. Two expression constructs containing B19 sequences from different halves of the viral genome were obtained, which directed the synthesis, in bacteria, of segments of virally encoded protein. These polypeptide fragments were then purified and used to immunize rabbits. Antibodies against a protein sequence specified between nucleotides 2897 and 3749 recognized both the 83- and 58-kilodalton capsid polypeptides in aplastic plasma taken during the acute phase and detected similar proteins in the similar proteins in the tissues of a stillborn fetus which had been infected transplacentally with B19. Antibodies against a protein sequence encoded in the other half of the B19 genome (nucleotides 1072 through 2044) did not react specifically with any protein in plasma taken during the acute phase but recognized three nonstructural polypeptides of 71, 63, and 52 kilodaltons present in the liver and, at lower levels, in some other tissues of the transplacentally infected fetus.

  15. Dynamic triggering

    Science.gov (United States)

    Hill, David P.; Prejean, Stephanie; Schubert, Gerald

    2015-01-01

    Dynamic stresses propagating as seismic waves from large earthquakes trigger a spectrum of responses at global distances. In addition to locally triggered earthquakes in a variety of tectonic environments, dynamic stresses trigger tectonic (nonvolcanic) tremor in the brittle–plastic transition zone along major plate-boundary faults, activity changes in hydrothermal and volcanic systems, and, in hydrologic domains, changes in spring discharge, water well levels, soil liquefaction, and the eruption of mud volcanoes. Surface waves with periods of 15–200 s are the most effective triggering agents; body-wave trigger is less frequent. Triggering dynamic stresses can be < 1 kPa.

  16. The Armc10/SVH gene: genome context, regulation of mitochondrial dynamics and protection against Aβ-induced mitochondrial fragmentation

    Science.gov (United States)

    Serrat, R; Mirra, S; Figueiro-Silva, J; Navas-Pérez, E; Quevedo, M; López-Doménech, G; Podlesniy, P; Ulloa, F; Garcia-Fernàndez, J; Trullas, R; Soriano, E

    2014-01-01

    Mitochondrial function and dynamics are essential for neurotransmission, neural function and neuronal viability. Recently, we showed that the eutherian-specific Armcx gene cluster (Armcx1–6 genes), located in the X chromosome, encodes for a new family of proteins that localise to mitochondria, regulating mitochondrial trafficking. The Armcx gene cluster evolved by retrotransposition of the Armc10 gene mRNA, which is present in all vertebrates and is considered to be the ancestor gene. Here we investigate the genomic organisation, mitochondrial functions and putative neuroprotective role of the Armc10 ancestor gene. The genomic context of the Armc10 locus shows considerable syntenic conservation among vertebrates, and sequence comparisons and CHIP-data suggest the presence of at least three conserved enhancers. We also show that the Armc10 protein localises to mitochondria and that it is highly expressed in the brain. Furthermore, we show that Armc10 levels regulate mitochondrial trafficking in neurons, but not mitochondrial aggregation, by controlling the number of moving mitochondria. We further demonstrate that the Armc10 protein interacts with the KIF5/Miro1-2/Trak2 trafficking complex. Finally, we show that overexpression of Armc10 in neurons prevents Aβ-induced mitochondrial fission and neuronal death. Our data suggest both conserved and differential roles of the Armc10/Armcx gene family in regulating mitochondrial dynamics in neurons, and underscore a protective effect of the Armc10 gene against Aβ-induced toxicity. Overall, our findings support a further degree of regulation of mitochondrial dynamics in the brain of more evolved mammals. PMID:24722288

  17. Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential

    Directory of Open Access Journals (Sweden)

    Yukio Kurihara

    2014-12-01

    Full Text Available Several transcription factors (TFs coordinate to regulate expression of specific genes at the transcriptional level. In Arabidopsis thaliana it is estimated that approximately 10% of all genes encode TFs or TF-like proteins. It is important to identify target genes that are directly regulated by TFs in order to understand the complete picture of a plant’s transcriptome profile. Here, we investigate the role of the LONG HYPOCOTYL5 (HY5 transcription factor that acts as a regulator of photomorphogenesis. We used an in vitro genomic DNA binding assay coupled with immunoprecipitation and next-generation sequencing (gDB-seq instead of the in vivo chromatin immunoprecipitation (ChIP-based methods. The results demonstrate that the HY5-binding motif predicted here was similar to the motif reported previously and that in vitro HY5-binding loci largely overlapped with the HY5-targeted candidate genes identified in previous ChIP-chip analysis. By combining these results with microarray analysis, we identified hundreds of HY5-binding genes that were differentially expressed in hy5. We also observed delayed induction of some transcripts of HY5-binding genes in hy5 mutants in response to blue-light exposure after dark treatment. Thus, an in vitro gDNA-binding assay coupled with sequencing is a convenient and powerful method to bridge the gap between identifying TF binding potential and establishing function.

  18. Characterization of the genome of molluscum contagiosum virus type 1 between the genome coordinates 0.045 and 0.075 by DNA nucleotide sequence analysis of a 5.6-kb HindIII/MluI DNA fragment.

    Science.gov (United States)

    Hadasch, R P; Bugert, J J; Janssen, W; Darai, G

    1993-01-01

    The complete DNA nucleotide sequence of a HindIII/MluI genomic DNA fragment (0.045-0.075 viral map units) from molluscum contagiosum virus type 1 (MCV-1) was determined. The HindIII/MluI DNA fragment comprises 5,646 bp with a base composition of 64.4% G + C and 35.6% A + T. The DNA sequence contains many perfect direct repeats. A cluster of three repetitive DNA elements R1, R2 and R3, with a complex structural arrangement was detected between nucleotide positions 1802 and 2107. The unit length (box) of the repetitive DNA sequences was found to be 6 bp (15 boxes) and 9 bp (24 boxes) for R1 and R2, respectively. The repetitive DNA element R3 is organized in fifteen boxes (15 bp) in which a unit length of R1 is combined with a unit length of R2. The arrangement of the repetition R3 within the DNA sequences of this particular region of the MCV-1 genome was found to be (5 x R3) + (2 x R2) + (1 x R3) + (6 x R2) + (1 x R3) + (1 x R2) + (8 x R3). Twenty-three open reading frames (ORFs) of 60-1,175 amino acid (AA) residues were detected. The largest ORF (number 17) comprises 1,175 AA with a predicted molecular weight of 126 kD. This ORF harbors a promoter signal which is located 21 nucleotides upstream from the start codon and is very similar to the early promoter signals known for vaccinia virus. This putative protein contains glutamine-enriched regions between AA residues 427 and 682 which show homologies to the corresponding glutamine-enriched regions of a variety of cellular genes like human transcriptional initiation factor (TFIID: TATA box factor).

  19. Brassica napus genome possesses extraordinary high number of CAMTA genes and CAMTA3 contributes to PAMP triggered immunity and resistance to Sclerotinia sclerotiorum

    Directory of Open Access Journals (Sweden)

    Hafizur eRahman

    2016-05-01

    Full Text Available Calmodulin-binding transcription activators (CAMTAs play important roles in various plant biological processes including disease resistance and abiotic stress tolerance. Oilseed rape (Brassica napus L. is one of the most important oil-producing crops worldwide. To date, compositon of CAMTAs in genomes of Brassica species and role of CAMTAs in resistance to the devastating necrotrophic fungal pathogen Sclerotinia sclerotiorum are still unknown. In this study, 18 CAMTA genes were identified in oilseed rape genome through bioinformatics analyses, which were inherited from the nine copies each in its progenitors B. rapa and B. oleracea and represented the highest number of CAMTAs in a given plant species identified so far. Gene structure, protein domain organization and phylogentic analyses showed that the oilseed rape CAMTAs were structurally similar and clustered into three major groups as other plant CAMTAs, but had expanded subgroups CAMTA3 and CAMTA4 genes uniquely in rosids species occurring before formation of oilseed rape. A large number of stress response-related cis-elements existed in the 1.5 kb promoter regions of the BnCAMTA genes. BnCAMTA genes were expressed differentially in various organs and in response to treatments with plant hormones and the toxin oxalic acid (OA secreted by S. sclerotiorum as well as the pathogen inoculation. Remarkably, the expression of BnCAMTA3A1 and BnCAMTA3C1 was drastically induced in early phase of S. sclerotiorum infection, indicating their potential role in the interactions between oilseed rape and S. sclerotiorum. Furthermore, inoculation analyses using Arabidopsis camta mutants demonstrated that Atcamta3 mutant plants exhibited significantly smaller disease lesions than wild-type and other Atcamta mutant plants. In addition, compared with wild-type plants, Atcamta3 plants accumulated obviously more hydrogen peroxide in response to the PAMP chitin and exhibited much higher expression of the CGCG

  20. 乙型肝炎病毒基因组中罕见大片段缺失突变的分析%Analysis of rare mutation of large fragment deletion in the genome of hepatitis B virus

    Institute of Scientific and Technical Information of China (English)

    俞杨; 邬兰; 焦杰; 杜同信; 王自正; 颜宁

    2013-01-01

    目的 对来源于一例慢性乙型肝炎患者的包含罕见大片段缺失的乙肝病毒(HBV)全基因组进行序列分析.方法 提取乙肝病毒基因组DNA,扩增全长基因组,通过单克隆化分析不同准种中大片段缺失的位点和长度;将包含两段缺失突变的片段分别进行扩增,通过扩增产物的序列分析验证准种分析的结果.结果 该标本的HBV基因组中的确存在超过1.4 kb的大片段缺失突变,其中P基因上存在nt2449~489的1256bp的缺失突变,C基因上存在大约nt2088~2298的209bp的缺失突变.结论 该患者HBV基因组中存在罕见大片段缺失突变.%Objective To analyze the whole genome sequence of hepatitis B virus(HBV) including rare large fragment deletion from a patient with chronic hepatitis B.Methods Genomic DNA was extracted from HBV and the whole genome was amplified.The sites and sizes of large fragment deletion in different quasispecies were subjected to monoclonal analysis.Fragments including two deletion mutations were amplified respectively,and the results of quasispecies analysis were confirmed by sequencing analysis of amplified products.Results Mutation of over 1.4 kb large fragment deletion exactly existed in HBV genome of this sample,with 1 256 bp nt2449-489 mutation in P gene and about 209 bp nt2088-2298 deletion mutation in C gene.Conclusion There is a mutation of rare large fragment deletion in HBV genome of the patient.

  1. A mechanism of gene amplification driven by small DNA fragments.

    Directory of Open Access Journals (Sweden)

    Kuntal Mukherjee

    Full Text Available DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene(s. Although gene amplification is frequently observed in cancer and other degenerative disorders, the molecular mechanisms involved in the process of DNA copy number increase remain largely unknown. We hypothesized that small DNA fragments could be the trigger of DNA amplification events. Following our findings that small fragments of DNA in the form of DNA oligonucleotides can be highly recombinogenic, we have developed a system in the yeast Saccharomyces cerevisiae to capture events of chromosomal DNA amplification initiated by small DNA fragments. Here we demonstrate that small DNAs can amplify a chromosomal region, generating either tandem duplications or acentric extrachromosomal DNA circles. Small fragment-driven DNA amplification (SFDA occurs with a frequency that increases with the length of homology between the small DNAs and the target chromosomal regions. SFDA events are triggered even by small single-stranded molecules with as little as 20-nt homology with the genomic target. A double-strand break (DSB external to the chromosomal amplicon region stimulates the amplification event up to a factor of 20 and favors formation of extrachromosomal circles. SFDA is dependent on Rad52 and Rad59, partially dependent on Rad1, Rad10, and Pol32, and independent of Rad51, suggesting a single-strand annealing mechanism. Our results reveal a novel molecular model for gene amplification, in which small DNA fragments drive DNA amplification and define the boundaries of the amplicon region. As DNA fragments are frequently found both inside cells and in the extracellular environment, such as the serum of patients with cancer or other degenerative disorders, we propose that SFDA may be a common mechanism for DNA amplification in cancer cells, as well as a more general cause of DNA copy number variation

  2. Quantum fragmentation

    CERN Document Server

    Peschanski, R

    1993-01-01

    Phenomenological and theoretical aspects of fragmentation for elementary particles (resp. nuclei) are discussed. It is shown that some concepts of classical fragmentation remain relevant in a microscopic framework, exhibiting non-trivial properties of quantum relativistic field theory (resp. lattice percolation). Email contact: pesch@amoco.saclay.cea.fr

  3. Triggering Klystrons

    Energy Technology Data Exchange (ETDEWEB)

    Stefan, Kelton D.; /Purdue U. /SLAC

    2010-08-25

    To determine if klystrons will perform to the specifications of the LCLS (Linac Coherent Light Source) project, a new digital trigger controller is needed for the Klystron/Microwave Department Test Laboratory. The controller needed to be programmed and Windows based user interface software needed to be written to interface with the device over a USB (Universal Serial Bus). Programming the device consisted of writing logic in VHDL (VHSIC (Very High Speed Integrated Circuits) hardware description language), and the Windows interface software was written in C++. Xilinx ISE (Integrated Software Environment) was used to compile the VHDL code and program the device, and Microsoft Visual Studio 2005 was used to compile the C++ based Windows software. The device was programmed in such a way as to easily allow read/write operations to it using a simple addressing model, and Windows software was developed to interface with the device over a USB connection. A method of setting configuration registers in the trigger device is absolutely necessary to the development of a new triggering system, and the method developed will fulfill this need adequately. More work is needed before the new trigger system is ready for use. The configuration registers in the device need to be fully integrated with the logic that will generate the RF signals, and this system will need to be tested extensively to determine if it meets the requirements for low noise trigger outputs.

  4. 毛竹大片段双元细菌人工染色体基因组文库的构建%Construction of a large genomic DNA fragments,BIBAC library for Phyllostachys pubescens

    Institute of Scientific and Technical Information of China (English)

    管雨; 杨洋; 张智俊; 罗淑萍; 汤定钦

    2011-01-01

    One plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library was constructed which represents the first large genomic DNA fragment library generated for Phyllostachys pubescens. High-quality, genomic DNA extracted from young leaves of Phyllostachys pubescens was gradiently enzyme-digested with a gradient using BamH I. Desirable DNA fragments were isolated by pulsed field gel electrophoresis, ligated to the dephosphorylatedion carrier Pcld04541 with a mass ratio of 3:1, and then transformed to Escherichia coli DH10B competent cells. This was followed by blue-white screening with establishment of a binary bacterial artificial chromosome (BIBAC) genome library. Results showed a high recombination positive colony from which a BIB AC genome library, consisting of 104 clones with an average insert fragment size of about 105 kb after detection with a pulsed field gel electrophoresis, was constructed. The BIBAC library was 5 times larger than the Phyllostachys pubescens genome. The construction of this BIBAC genome library laid a good foundation for related genome research.%从毛竹Phyllostachys pubescens幼嫩叶片中提取纯化得到高质量的基因组DNA,经限制性内切酶BamH I对它们进行梯度酶切,脉冲场电泳选择合适酶切DNA片段,与脱磷酸化处理过的质粒载体pCLD04541按质量比3∶1相互连接,转化大肠杆菌Escherichia coli DH10B感受态细胞进行蓝白斑筛选,挑取白色克隆,获得重组率较高的阳性克隆,构建了含有104个克隆的双元细菌人工染色体(BIBAC)基因组文库,并通过脉冲场电泳检测分析后确定,所构建的毛竹BIBAC文库平均插入片段为105 kb,约覆盖5倍毛竹基因组.该文库的构建为毛竹基因组研究做好了前期的基础工作.

  5. Fragmented Authoritarianism or Integrated Fragmentation

    DEFF Research Database (Denmark)

    Brødsgaard, Kjeld Erik

    of these business leaders prompts the question of whether we are seeing the development of distinct interest groups that could challenge Party and state authority and create a fragmented polity. However, through the nomenklatura system the Party has an important instrument of control to wield over business groups...... and the Party-state, I suggest the notion of integrated fragmentation....

  6. Magma Fragmentation

    Science.gov (United States)

    Gonnermann, Helge M.

    2015-05-01

    Magma fragmentation is the breakup of a continuous volume of molten rock into discrete pieces, called pyroclasts. Because magma contains bubbles of compressible magmatic volatiles, decompression of low-viscosity magma leads to rapid expansion. The magma is torn into fragments, as it is stretched into hydrodynamically unstable sheets and filaments. If the magma is highly viscous, resistance to bubble growth will instead lead to excess gas pressure and the magma will deform viscoelastically by fracturing like a glassy solid, resulting in the formation of a violently expanding gas-pyroclast mixture. In either case, fragmentation represents the conversion of potential energy into the surface energy of the newly created fragments and the kinetic energy of the expanding gas-pyroclast mixture. If magma comes into contact with external water, the conversion of thermal energy will vaporize water and quench magma at the melt-water interface, thus creating dynamic stresses that cause fragmentation and the release of kinetic energy. Lastly, shear deformation of highly viscous magma may cause brittle fractures and release seismic energy.

  7. Framing Fragmentation

    DEFF Research Database (Denmark)

    Bundgaard, Charlotte

    2009-01-01

    , contain distinctive architectural traits, not only based on rational repetition, but also supporting composition and montage as dynamic concepts. Prefab architecture is an architecture of fragmentation, individualization and changeability, and this sets up new challenges for the architect. This paper...... into separate parts or systems: skeleton, skin, services, internal cladding, etc. Each building part/system is being conceived, produced, delivered and maintained by different construction companies. Basically the building is being fragmented into separate parts living their separate lives. The architect has...... to create architectural meaning and give character to an architecture of fragmentation. Layers are both seen as conceptual as well as material frames which define certain strong properties or meanings in the architectural work. Defining layers is a way of separating and organizing; it both defines...

  8. AKT1, LKB1, and YAP1 revealed as MYC interactors with NanoLuc-based protein-fragment complementation assay. | Office of Cancer Genomics

    Science.gov (United States)

    The c-Myc (MYC) transcription factor is a major cancer driver and a well-validated therapeutic target. However, directly targeting MYC has been challenging. Thus, identifying proteins that interact with and regulate MYC may provide alternative strategies to inhibit its oncogenic activity. Here we report the development of a NanoLuc®-based protein-fragment complementation assay (NanoPCA) and mapping of the MYC protein interaction hub in live mammalian cells.

  9. Pilot Sequencing of Onion Genomic DNA Reveals Fragments of Transposable Elements, Low Gene Densities, and Significant Gene Enrichment After Methyl Filtration

    Science.gov (United States)

    Onion (Allium cepa) is a diploid (2n=2x=16) monocot with one of the largest nuclear genomes among cultivated plants, over 6 and 16 times that of maize and rice, respectively. In this study, we sequenced onion BACs to estimate gene densities and investigate the nature and distribution of repetitive ...

  10. Synthetic RNAs Mimicking Structural Domains in the Foot-and-Mouth Disease Virus Genome Elicit a Broad Innate Immune Response in Porcine Cells Triggered by RIG-I and TLR Activation.

    Science.gov (United States)

    Borrego, Belén; Rodríguez-Pulido, Miguel; Revilla, Concepción; Álvarez, Belén; Sobrino, Francisco; Domínguez, Javier; Sáiz, Margarita

    2015-07-17

    The innate immune system is the first line of defense against viral infections. Exploiting innate responses for antiviral, therapeutic and vaccine adjuvation strategies is being extensively explored. We have previously described, the ability of small in vitro RNA transcripts, mimicking the sequence and structure of different domains in the non-coding regions of the foot-and-mouth disease virus (FMDV) genome (ncRNAs), to trigger a potent and rapid innate immune response. These synthetic non-infectious molecules have proved to have a broad-range antiviral activity and to enhance the immunogenicity of an FMD inactivated vaccine in mice. Here, we have studied the involvement of pattern-recognition receptors (PRRs) in the ncRNA-induced innate response and analyzed the antiviral and cytokine profiles elicited in swine cultured cells, as well as peripheral blood mononuclear cells (PBMCs).

  11. Synthetic RNAs Mimicking Structural Domains in the Foot-and-Mouth Disease Virus Genome Elicit a Broad Innate Immune Response in Porcine Cells Triggered by RIG-I and TLR Activation

    Directory of Open Access Journals (Sweden)

    Belén Borrego

    2015-07-01

    Full Text Available The innate immune system is the first line of defense against viral infections. Exploiting innate responses for antiviral, therapeutic and vaccine adjuvation strategies is being extensively explored. We have previously described, the ability of small in vitro RNA transcripts, mimicking the sequence and structure of different domains in the non-coding regions of the foot-and-mouth disease virus (FMDV genome (ncRNAs, to trigger a potent and rapid innate immune response. These synthetic non-infectious molecules have proved to have a broad-range antiviral activity and to enhance the immunogenicity of an FMD inactivated vaccine in mice. Here, we have studied the involvement of pattern-recognition receptors (PRRs in the ncRNA-induced innate response and analyzed the antiviral and cytokine profiles elicited in swine cultured cells, as well as peripheral blood mononuclear cells (PBMCs.

  12. Synthetic RNAs Mimicking Structural Domains in the Foot-and-Mouth Disease Virus Genome Elicit a Broad Innate Immune Response in Porcine Cells Triggered by RIG-I and TLR Activation

    Science.gov (United States)

    Borrego, Belén; Rodríguez-Pulido, Miguel; Revilla, Concepción; Álvarez, Belén; Sobrino, Francisco; Domínguez, Javier; Sáiz, Margarita

    2015-01-01

    The innate immune system is the first line of defense against viral infections. Exploiting innate responses for antiviral, therapeutic and vaccine adjuvation strategies is being extensively explored. We have previously described, the ability of small in vitro RNA transcripts, mimicking the sequence and structure of different domains in the non-coding regions of the foot-and-mouth disease virus (FMDV) genome (ncRNAs), to trigger a potent and rapid innate immune response. These synthetic non-infectious molecules have proved to have a broad-range antiviral activity and to enhance the immunogenicity of an FMD inactivated vaccine in mice. Here, we have studied the involvement of pattern-recognition receptors (PRRs) in the ncRNA-induced innate response and analyzed the antiviral and cytokine profiles elicited in swine cultured cells, as well as peripheral blood mononuclear cells (PBMCs). PMID:26193305

  13. Bespoke Fragments

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2016-01-01

    The Ph.D. -project Bespoke Fragments seeks to explore and utilise the space emerging between the potentials of digital drawing and fabrication and the field of materials and their properties and capacities. Within this span, the project is situated in a shuttling between the virtual and the actual......, the emergence of virtual space is no longer limited to the computer's digital world, but extends into the materials' world. Creation and uncertainty are allowed as virtual parameters in both the digital and reality. Based on this notion the project suggests utilising that exact potential to develop...

  14. Conserved TAAATG sequence at the transcriptional and translational initiation sites of vaccinia virus late genes deduced by structural and functional analysis of the HindIII H genome fragment.

    Science.gov (United States)

    Rosel, J L; Earl, P L; Weir, J P; Moss, B

    1986-11-01

    The sequence of the 8,600-base-pair HindIII H fragment, located at the center of the vaccinia virus genome, was determined to analyze several late genes. Seven major complete open reading frames (ORFs) and two that started from or continued into adjacent DNA segments were identified. ORFs were closely spaced and present on both DNA strands. Some adjacent ORFs had oppositely oriented overlapping termination codons or contiguous stop and start codons. Nucleotide compositional analysis indicated that the A-T frequency was consistently lowest in the first codon position. The sizes of the polypeptides predicted from the DNA sequence were compared with those determined by polyacrylamide gel electrophoresis of cell-free translation products of mRNAs selected by hybridization to cloned single-stranded DNA segments or synthesized in vitro by bacteriophage T7 RNA polymerase. Six transcripts that initiated within the HindIII H DNA fragment were detected, and of these, four were synthesized only at late times, one was synthesized only early, and one was synthesized early and late. The sites on the genome corresponding to the 5' ends of the transcripts were located by high-resolution nuclease S1 analysis. For late genes, the transcriptional and translational initiation sites mapped within a few nucleotides of each other, and in each case the sequence TAAATGG occurred at the start of the ORF. The extremely short leader and the absence of A or G in the -3 position, relative to the first nucleotide of the initiation codon, distinguishes the majority of vaccinia virus late genes from eucaryotic and vaccinia virus early genes.

  15. Environmentally triggered genomic plasticity and capsular polysaccharide formation are involved in increased ethanol and acetic acid tolerance in Kozakia baliensis NBRC 16680.

    Science.gov (United States)

    Brandt, Julia U; Born, Friederike-Leonie; Jakob, Frank; Vogel, Rudi F

    2017-08-10

    Kozakia baliensis NBRC 16680 secretes a gum-cluster derived heteropolysaccharide and forms a surface pellicle composed of polysaccharides during static cultivation. Furthermore, this strain exhibits two colony types on agar plates; smooth wild-type (S) and rough mutant colonies (R). This switch is caused by a spontaneous transposon insertion into the gumD gene of the gum-cluster, resulting in a heteropolysaccharide secretion deficient, rough phenotype. To elucidate, whether this is a directed switch triggered by environmental factors, we checked the number of R and S colonies under different growth conditions including ethanol and acetic acid supplementation. Furthermore, we investigated the tolerance of R and S strains against ethanol and acetic acid in shaking and static growth experiments. To get new insights into the composition and function of the pellicle polysaccharide, the polE gene of the R strain was additionally deleted, as it was reported to be involved in pellicle formation in other acetic acid bacteria. The number of R colonies was significantly increased upon growth on acetic acid and especially ethanol. The morphological change from K. baliensis NBRC 16680 S to R strain was accompanied by changes in the sugar contents of the produced pellicle EPS. The R:ΔpolE mutant strain was not able to form a regular pellicle anymore, but secreted an EPS into the medium, which exhibited a similar sugar monomer composition as the pellicle polysaccharide isolated from the R strain. The R strain had a markedly increased tolerance towards acetic acid and ethanol compared to the other NBRC 16680 strains (S, R:ΔpolE). A relatively high intrinsic acetic acid tolerance was also observable for K. baliensis DSM 14400(T), which might indicate diverse adaptation mechanisms of different K. baliensis strains in altering natural habitats. The results suggest that the genetically triggered R phenotype formation is directly related to increased acetic acid and ethanol

  16. Characterization of nosocomial Serratia marcescens isolates: comparison of Fourier-transform infrared spectroscopy with pulsed-field gel electrophoresis of genomic DNA fragments and multilocus enzyme electrophoresis.

    Science.gov (United States)

    Irmscher, H M; Fischer, R; Beer, W; Seltmann, G

    1999-07-01

    A total of 66 Serratia marcescens isolates from 46 patients was investigated by macrorestriction using XbaI followed by pulsed-field gel electrophoresis. 7 restriction fragment patterns attributable to more than one patient and 9 individual patterns were identified. The isolates were additionally characterized by multilocus enzyme electrophoresis and Fourier-transform infrared spectroscopy. The macrorestriction patterns and the multilocus enzyme electrophoresis patterns corresponded fairly well while the classifications derived from these methods were not completely congruent. The grouping achieved by Fourier-transform infrared spectroscopy on the basis of high (> 1000) and moderately high heterogeneity values (300) was consistent with the macrorestriction results. Grouping on a lower heterogeneity level did not contribute to further discrimination. In general, Fourier-transform infrared spectroscopy was less discriminatory than the two other methods, but easier to perform. Therefore, laboratories equipped with the necessary devices may use it to rapidly select bacterial isolates for macrorestriction or other well established characterization procedures.

  17. Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical application to genomic and metagenomic projects

    Directory of Open Access Journals (Sweden)

    Marchesi Julian R

    2007-03-01

    Full Text Available Abstract Background The question of how a circle or line segment becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. The number of uncovered gaps is of particular interest. Approximate distributions for the number of gaps have been given in the literature, one motivation being ease of computation. Error bounds for these approximate distributions have not been given. Results We give bounds on the probability distribution of the number of gaps when a circle is covered by fragments of fixed size. The absolute error in the approximation is typically on the order of 0.1% at 10× coverage depth. The method can be applied to coverage problems on the interval, including edge effects, and applications are given to metagenomic libraries and shotgun sequencing.

  18. Common Asthma Triggers

    Science.gov (United States)

    ... Film Asthma Clinical Guidelines Air Pollution & Respiratory Health Common Asthma Triggers Recommend on Facebook Tweet Share Compartir ... t avoid the triggers. Some of the most common triggers are: Tobacco Smoke Tobacco smoke is unhealthy ...

  19. A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP array

    Directory of Open Access Journals (Sweden)

    Bailey Dione K

    2007-05-01

    Full Text Available Abstract Background DNA copy number aberration (CNA is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH, the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required. Results We have developed a highly sensitive algorithm for the edge detection of copy number data which is especially suitable for the SNP array-based copy number data. The method consists of an over-sensitive edge-detection step and a test-based forward-backward edge selection step. Conclusion Using simulations constructed from real experimental data, the method shows high sensitivity and specificity in detecting small copy number changes in focused regions. The method is implemented in an R package FASeg, which includes data processing and visualization utilities, as well as libraries for processing Affymetrix SNP array data.

  20. Spontaneous deletion of a 209-kilobase-pair fragment from the Escherichia coli genome occurs with acquisition of resistance to an assortment of infectious phages.

    Science.gov (United States)

    Tanji, Yasunori; Hattori, Kenji; Suzuki, Kohichi; Miyanaga, Kazuhiko

    2008-07-01

    To breed resistance to an assortment of infectious phages, continuous cultures of Escherichia coli JM109 grown in a chemostat were exposed to phage mixtures prepared from sewage influent. Four sequential chemostat-grown cultures were each infected with a different phage mixture. At the end of a chemostat run, one phage-resistant colony was isolated and used to inoculate the subsequent culture. This process was repeated, and increased phage resistance of the input bacterial strain resulted from the successive challenges with different phage cocktails. Multiple mutations apparently accumulated progressively. A mutant isolated at the end of the four runs, designated D198, showed resistance to 38 of 40 phages that infect the parent strain, JM109. D198 produced less outer membrane protein C (OmpC) than JM109. However, restoration of the OmpC protein by plasmid-mediated complementation did not completely restore the susceptibility of D198 to the 38 phages. Therefore, alterations beyond the level of OmpC protein production contribute to the phage resistance of D198. PCR-based genetic analysis revealed that D198 has a genome that is 209 kbp (about 200 genes) smaller than JM109. The deletion includes the chromosomal section from ompC to wbbL that encodes the rhamnosyl transferase involved in lipopolysaccharide biosynthesis. Strains D198 and JM109 were comparable in their growth characteristics and their abilities to express a recombinant protein.

  1. High-throughput on-chip DNA fragmentation

    NARCIS (Netherlands)

    Shui, Lingling; Jin, Mingliang; Bomer, Johan G.; Carlen, Edwin; van den Berg, Albert; Abelmann, Leon; Abelmann, L.; Groenland, J.P.J.; van Honschoten, J.W.

    2010-01-01

    free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Genomic DNA has been reproducibly fragmented with 2-10 kbp fragment lengths by applying hydraulic pressure ΔP across micromachined constrictions in the microfluidic channels. The utilization of a

  2. Fragmentation and Hadronization

    OpenAIRE

    Webber, B. R.

    1999-01-01

    Experimental data, theoretical ideas and models concerning jet fragmentation and the hadronization process are reviewed, concentrating on the following topics: factorization and small-x resummation of fragmentation functions, hadronization models, single-particle yields and spectra in Z decay, comparisons between quark and gluon jets, current and target fragmentation in deep inelastic scattering, heavy quark fragmentation, Bose-Einstein correlations and WW fragmentation.

  3. DNA fragment editing of genomes by CRISPR/Cas9%CRISPR/Cas9系统在基因组DNA片段编辑中的应用

    Institute of Scientific and Technical Information of China (English)

    李金环; 寿佳; 吴强

    2015-01-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system from bacteria and archaea emerged recently as a new powerful technology of genome editing in vir-tually any organism. Due to its simplicity and cost effectiveness, a revolutionary change of genetics has occurred. Here, we summarize the recent development of DNA fragment editing methods by CRISPR/Cas9 and describe tar-geted DNA fragment deletions, inversions, duplications, insertions, and translocations. The efficient method of DNA fragment editing provides a powerful tool for studying gene function, regulatory elements, tissue development, and disease progression. Finally, we discuss the prospects of CRISPR/Cas9 system and the potential applications of other types of CRISPR system.%源于细菌和古菌的Ⅱ型成簇规律间隔短回文重复系统[Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9(Cas9),CRISPR/Cas9]近年被改造成为基因组定点编辑的新技术。由于它具有设计简单、操作方便、费用低廉等巨大优势,给遗传操作领域带来了一场革命性的改变。本文重点介绍了CRISPR/Cas9系统在基因组DNA片段靶向编辑方面的研究和应用,主要包括DNA片段的删除、反转、重复、插入和易位,这一有效的DNA片段编辑方法为研究基因功能、调控元件、组织发育和疾病发生发展提供了有力手段。本文最后展望了Ⅱ型CRISPR/Cas9系统的应用前景和其他类型CRISPR系统的应用潜力,为开展利用基因组DNA片段靶向编辑进行基因调控和功能研究提供参考。

  4. Identifying asthma triggers.

    Science.gov (United States)

    McCarty, Justin C; Ferguson, Berrylin J

    2014-02-01

    Asthma has many triggers including rhinosinusitis; allergy; irritants; medications (aspirin in aspirin-exacerbated respiratory disease); and obesity. Paradoxic vocal fold dysfunction mimics asthma and may be present along with asthma. This article reviews each of these triggers, outlining methods of recognizing the trigger and then its management. In many patients more than one trigger may be present. Full appreciation of the complexity of these relationships and targeted therapy to the trigger is needed to best care for the patient with asthma.

  5. CpG-island fragments from the HNRPA2B1/CBX3 genomic locus reduce silencing and enhance transgene expression from the hCMV promoter/enhancer in mammalian cells

    Directory of Open Access Journals (Sweden)

    Irvine Alistair

    2005-06-01

    Full Text Available Abstract Background The hCMV promoter is very commonly used for high level expression of transgenes in mammalian cells, but its utility is hindered by transcriptional silencing. Large genomic fragments incorporating the CpG island region of the HNRPA2B1 locus are resistant to transcriptional silencing. Results In this report we describe studies on the use of a novel series of vectors combining the HNRPA2B1 CpG island with the hCMV promoter for expression of transgenes in CHO-K1 cells. We show that the CpG island gives at least twenty-fold increases in the levels of EGFP and EPO observed in pools of transfectants, and that transgene expression levels remain high in such pools for more than 100 generations. These novel vectors also allow facile isolation of clonal CHO-K1 cell lines showing stable, high-level transgene expression. Conclusion Vectors incorporating the hnRPA2B1 CpG island give major benefits in transgene expression from the hCMV promoter, including substantial improvements in the level and stability of expression. The utility of these vectors for the improved production of recombinant proteins in CHO cells has been demonstrated.

  6. The Central Trigger Processor (CTP)

    CERN Multimedia

    Franchini, Matteo

    2016-01-01

    The Central Trigger Processor (CTP) receives trigger information from the calorimeter and muon trigger processors, as well as from other sources of trigger. It makes the Level-1 decision (L1A) based on a trigger menu.

  7. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  8. Asthma triggers (image)

    Science.gov (United States)

    ... things make your asthma worse. These are called asthma "triggers". Avoiding them is your first step toward feeling better. The most common asthma triggers are mold, pets, dust, grasses, pollen, cockroaches, odors ...

  9. Asthma Triggers: Gain Control

    Science.gov (United States)

    ... Search Asthma Contact Us Share Asthma Triggers: Gain Control Breathing Freely: Controlling Asthma Triggers This video features ... Air Quality: Biological Pollutants Help Your Child Gain Control Over Asthma Top of Page Molds About Molds ...

  10. The KLOE trigger system

    Energy Technology Data Exchange (ETDEWEB)

    Adinolfi, M.; Aloisio, A.; Ambrosino, F.; Andryakov, A.; Antonelli, A.; Antonelli, M.; Anulli, F.; Bacci, C.; Bankamp, A.; Barbiellini, G.; Bellini, F.; Bencivenni, G.; Bertolucci, S.; Bini, C.; Bloise, C.; Bocci, V.; Bossi, F.; Branchini, P.; Bulychjov, S.A.; Cabibbo, G.; Calcaterra, A.; Caloi, R.; Campana, P.; Capon, G.; Carboni, G.; Cardini, A.; Casarsa, M.; Cataldi, G.; Ceradini, F.; Cervelli, F.; Cevenini, F.; Chiefari, G.; Ciambrone, P.; Conetti, S.; Conticelli, S.; De Lucia, E.; De Robertis, G.; De Sangro, R.; De Simone, P.; De Zorzi, G.; Dell' Agnello, S.; Denig, E.; Di Domenico, A.; Di Donato, C.; Di Falco, S.; Doria, A.; Drago, E.; Elia, V.; Erriquez, O.; Farilla, A.; Felici, G.; Ferrari, A.; Ferrer, M.L.; Finocchiaro, G.; Forti, C.; Franceschi, A.; Franzini, P.; Gao, M.L.; Gatti, C.; Gauzzi, P.; Giovannella, S.; Golovatyuk, V.; Gorini, E.; Grancagnolo, F.; Grandegger, W.; Graziani, E.; Guarnaccia, P.; Hagel, U. von; Han, H.G.; Han, S.W.; Huang, X.; Incagli, M.; Ingrosso, L.; Jang, Y.Y.; Kim, W.; Kluge, W.; Kulikov, V.; Lacava, F.; Lanfranchi, G.; Lee-Franzini, J.; Lomtadze, F.; Luisi, C.; Mao, C.S.; Martemianov, M.; Matsyuk, M.; Mei, W.; Merola, L.; Messi, R.; Miscetti, S.; Moalem, A.; Moccia, S.; Moulson, M.; Mueller, S.; Murtas, F.; Napolitano, M.; Nedosekin, A.; Panareo, M.; Pacciani, L.; Pages, P.; Palutan, M.; Paoluzi, L.; Pasqualucci, E.; Passalacqua, L.; Passaseo, M.; Passeri, A.; Patera, V.; Petrolo, E.; Petrucci, G.; Picca, D.; Pirozzi, G.; Pistillo, C.; Pollack, M.; Pontecorvo, L.; Primavera, M.; Ruggieri, F.; Santangelo, P.; Santovetti, E.; Saracino, G.; Schamberger, R.D.; Schwick, C.; Sciascia, B. E-mail: barbara.sciascia@romal.infn.it; Sciubba, A.; Scuri, F.; Sfiligoi, I.; Shan, J.; Silano, P.; Spadaro, T.; Spagnolo, S.; Spiriti, E.; Stanescu, C.; Tong, G.L.; Tortora, L.; Valente, E.; Valente, P.; Valeriani, B.; Venanzoni, G.; Veneziano, S.; Wu, Y.; Xie, Y.G.; Zhao, P.P.; Zhou, Y

    2001-04-01

    A double-level trigger system has been developed for the KLOE experiment. Custom electronics asserts a trigger in a 2 {mu}s decision time. The decision is based on the combined information of the electromagnetic calorimeter and the drift chamber. The entire trigger system is continuously monitored, and data flowing from the trigger system have allowed both an efficient online monitoring of the detector and an online luminosity measurement.

  11. Oscillating Filaments: I - Oscillation and Geometrical Fragmentation

    CERN Document Server

    Gritschneder, Matthias; Burkert, Andreas

    2016-01-01

    We study the stability of filaments in equilibrium between gravity and internal as well as external pressure using the grid based AMR-code RAMSES. A homogeneous, straight cylinder below a critical line mass is marginally stable. However, if the cylinder is bent, e.g. with a slight sinusoidal perturbation, an otherwise stable configuration starts to oscillate, is triggered into fragmentation and collapses. This previously unstudied behavior allows a filament to fragment at any given scale, as long as it has slight bends. We call this process `geometrical fragmentation'. In our realization the spacing between the cores matches the wavelength of the sinusoidal perturbation, whereas up to now, filaments were thought to be only fragmenting on the characteristical scale set by the mass-to-line ratio. Using first principles, we derive the oscillation period as well as the collapse timescale analytically. To enable a direct comparison with observations, we study the line-of-sight velocity for different inclinations. ...

  12. Triggering trigeminal neuralgia.

    Science.gov (United States)

    Di Stefano, Giulia; Maarbjerg, Stine; Nurmikko, Turo; Truini, Andrea; Cruccu, Giorgio

    2017-01-01

    Introduction Although it is widely accepted that facial pain paroxysms triggered by innocuous stimuli constitute a hallmark sign of trigeminal neuralgia, very few studies to date have systematically investigated the role of the triggers involved. In the recently published diagnostic classification, triggered pain is an essential criterion for the diagnosis of trigeminal neuralgia but no study to date has been designed to address this issue directly. In this study, we set out to determine, in patients with trigeminal neuralgia, how frequently triggers are present, which manoeuvres activate them and where cutaneous and mucosal trigger zones are located. Methods Clinical characteristics focusing on trigger factors were collected from 140 patients with trigeminal neuralgia, in a cross-sectional study design. Results Provocation of paroxysmal pain by various trigger manoeuvres was reported by 136 of the 140 patients. The most frequent manoeuvres were gentle touching of the face (79%) and talking (54%). Trigger zones were predominantly reported in the perioral and nasal region. Conclusion This study confirms that in trigeminal neuralgia, paroxysmal pain is associated with triggers in virtually all patients and supports the use of triggers as an essential diagnostic feature of trigeminal neuralgia.

  13. Metagenome Fragment Classification Using -Mer Frequency Profiles

    Directory of Open Access Journals (Sweden)

    Gail Rosen

    2008-01-01

    Full Text Available A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique -mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable to identify any fragment from hundreds of genomes. It also performs quite well at the strain, species, and genera levels and achieves strain resolution despite classifying ubiquitous genomic fragments (gene and nongene regions. Cross-validation analysis demonstrates that species-accuracy achieves 90% for highly-represented species containing an average of 8 strains. We demonstrate that such a tool can be used on the Sargasso Sea dataset, and our analysis shows that NBC can be further enhanced.

  14. Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath.

    Directory of Open Access Journals (Sweden)

    Sandeep K Kasoji

    Full Text Available A perfluorocarbon nanodroplet formulation is shown to be an effective cavitation enhancement agent, enabling rapid and consistent fragmentation of genomic DNA in a standard ultrasonic water bath. This nanodroplet-enhanced method produces genomic DNA libraries and next-generation sequencing results indistinguishable from DNA samples fragmented in dedicated commercial acoustic sonication equipment, and with higher throughput. This technique thus enables widespread access to fast bench-top genomic DNA fragmentation.

  15. Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath

    Science.gov (United States)

    Malc, Ewa P.; Jayakody, Chatura N.; Tsuruta, James K.; Mieczkowski, Piotr A.; Janzen, William P.; Dayton, Paul A.

    2015-01-01

    A perfluorocarbon nanodroplet formulation is shown to be an effective cavitation enhancement agent, enabling rapid and consistent fragmentation of genomic DNA in a standard ultrasonic water bath. This nanodroplet-enhanced method produces genomic DNA libraries and next-generation sequencing results indistinguishable from DNA samples fragmented in dedicated commercial acoustic sonication equipment, and with higher throughput. This technique thus enables widespread access to fast bench-top genomic DNA fragmentation. PMID:26186461

  16. AMY trigger system

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, Yoshihide [National Laboratory for High Energy Physics, Tsukuba, Ibaraki (Japan)

    1989-04-01

    A trigger system of the AMY detector at TRISTAN e{sup +}e{sup -} collider is described briefly. The system uses simple track segment and shower cluster counting scheme to classify events to be triggered. It has been operating successfully since 1987.

  17. Correlation measurements of fission-fragment properties

    Science.gov (United States)

    Oberstedt, S.; Belgya, T.; Billnert, R.; Borcea, R.; Cano-Ott, D.; Göök, A.; Hambsch, F.-J.; Karlsson, J.; Kis, Z.; Martinez, T.; Oberstedt, A.; Szentmiklosi, L.; Takác, K.

    2010-10-01

    For the development of future nuclear fission applications and for a responsible handling of nuclear waste the a-priori assessment of the fission-fragments' heat production and toxicity is a fundamental necessity. The success of an indispensable modelling of the fission process strongly depends on a good understanding of the particular mechanism of scission, the mass fragmentation and partition of excitation energy. Experimental observables are fission-fragment properties like mass- and energy-distributions, and the prompt neutron as well as γ-ray multiplicities and emission spectra. The latter quantities should preferably be known as a function of fragment mass and excitation energy. Those data are highly demanded as published by the OECD-NEA in its high priority data request list. With the construction of the double (v, E) spectrometer VERDI we aim at measuring pre- and post-neutron masses directly and simultaneously to avoid prompt neutron corrections. From the simultaneous measurement of pre- and post-neutron fission-fragment data the prompt neutron multiplicity may then be inferred fully correlated with fragment mass yield and total kinetic energy. Using an ultra-fast fission event trigger spectral prompt fission γ-ray measurements may be performed. For that purpose recently developed lanthanum-halide detectors, with excellent timing characteristics, were coupled to the VERDI spectrometer allowing for a very good discrimination of fission γ-rays and prompt neutrons due to their different time-of-flight.

  18. Research on seismic stress triggering

    Institute of Scientific and Technical Information of China (English)

    万永革; 吴忠良; 周公威; 黄静; 秦立新

    2002-01-01

    This paper briefly reviews basic theory of seismic stress triggering. Recent development on seismic stress triggering has been reviewed in the views of seismic static and dynamic stress triggering, application of viscoelastic model in seismic stress triggering, the relation between earthquake triggering and volcanic eruption or explosion, other explanation of earthquake triggering, etc. And some suggestions for further study on seismic stress triggering in near future are given.

  19. Fragmentation of Kozai–Lidov Disks

    Science.gov (United States)

    Fu, Wen; Lubow, Stephen H.; Martin, Rebecca G.

    2017-02-01

    We analyze the gravitational instability (GI) of a locally isothermal inclined disk around one component of a binary system. Such a disk can undergo global Kozai–Lidov (KL) cycles if the initial disk tilt is above the critical KL angle (of about 40◦). During these cycles, an initially circular disk exchanges its inclination for eccentricity, and vice versa. Self-gravity may suppress the cycles under some circumstances. However, with hydrodynamic simulations that include self-gravity, we show that for a sufficiently high initial disk tilts and for certain disk masses, disks can undergo KL oscillations and fragment due to GI, even when the Toomre Q value for an equivalent undisturbed disk is well within the stable regime (Q> 2). We suggest that KL triggered disk fragmentation provides a mechanism for the efficient formation of giant planets in binary systems and may enhance the fragmentation of disks in massive black hole binaries.

  20. Mechanisms in Impact Fragmentation

    OpenAIRE

    Wittel, Falk K.; Carmona, Humberto A.; Kun, Ferenc; Herrmann, Hans J.

    2015-01-01

    The brittle fragmentation of spheres is studied numerically by a 3D Discrete Element Model. Large scale computer simulations are performed with models that consist of agglomerates of many spherical particles, interconnected by beam-truss elements. We focus on a detailed description of the fragmentation process and study several fragmentation mechanisms involved. The evolution of meridional cracks is studied in detail. These cracks are found to initiate in the inside of the specimen with quasi...

  1. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis. Elegant biochemical work identified the DNA fragmentation factor (DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro. Genetic studies in mice support the importance of DFF in DNA fragmentation and possibly in apoptosis in vivo. Recent work also suggests the existence of additional endonucleases for DNA degradation. Understanding the roles of individual endonucleases in apoptosis, and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis, as well as in various diseased states, will be a major research focus in the near future.

  2. Endogenous viral elements in algal genomes

    Institute of Scientific and Technical Information of China (English)

    WANG Liang; YU Jun; WU Shuangxiu; LIU Tao; SUN Jing; CHI Shan; LIU Cui; LI Xingang; YIN Jinlong; WANG Xumin

    2014-01-01

    Endogenous viral elements (EVEs) are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analy-sis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes. We classified the EVE fragments into three categories according to the length of EVE fragments. Due to the probability of sequence similarity by chance, we ignored the potential function of medium-length EVE fragments. However, long-length EVE fragments probably had capability to encode protein domains or even entire proteins, and some short-length EVE fragments had high similarity with host's siRNA sequences and possibly served functions of small RNAs. Therefore, short and long EVE fragments might provide regulomic and proteomic novelty to the host's metabolism and adaptation. We also found several EVE fragments shared by more than 3 algal genomes. By phylogenetic analysis of the shared EVEs and their corresponding species, we found that the integration of viral fragments into host genomes was an ancient event, possibly before the divergence of Chlorophytes and Ochrophytes. Our findings show that there is a frequent genetic flow from viruses to algal genomes. Moreover, study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems.

  3. Calo trigger acquisition system

    CERN Multimedia

    Franchini, Matteo

    2016-01-01

    Calo trigger acquisition system - Evolution of the acquisition system from a multiple boards system (upper, orange cables) to a single board one (below, light blue cables) where all the channels are collected in a single board.

  4. Aspartame-Triggered Migraine

    OpenAIRE

    J Gordon Millichap

    2001-01-01

    Two patients with known aspartame-triggered and rizatriptan-responsive migraine had their headaches worsened following use of an aspartame-containing formulation of rizatriptan (Maxalt-MLT), in a report from Albert Einstein College of Medicine, Bronx, NY.

  5. Calorimetry triggering in ATLAS

    CERN Document Server

    Igonkina, O; Adragna, P; Aharrouche, M; Alexandre, G; Andrei, V; Anduaga, X; Aracena, I; Backlund, S; Baines, J; Barnett, B M; Bauss, B; Bee, C; Behera, P; Bell, P; Bendel, M; Benslama, K; Berry, T; Bogaerts, A; Bohm, C; Bold, T; Booth, J R A; Bosman, M; Boyd, J; Bracinik, J; Brawn, I, P; Brelier, B; Brooks, W; Brunet, S; Bucci, F; Casadei, D; Casado, P; Cerri, A; Charlton, D G; Childers, J T; Collins, N J; Conde Muino, P; Coura Torres, R; Cranmer, K; Curtis, C J; Czyczula, Z; Dam, M; Damazio, D; Davis, A O; De Santo, A; Degenhardt, J; Delsart, P A; Demers, S; Demirkoz, B; Di Mattia, A; Diaz, M; Djilkibaev, R; Dobson, E; Dova, M, T; Dufour, M A; Eckweiler, S; Ehrenfeld, W; Eifert, T; Eisenhandler, E; Ellis, N; Emeliyanov, D; Enoque Ferreira de Lima, D; Faulkner, P J W; Ferland, J; Flacher, H; Fleckner, J E; Flowerdew, M; Fonseca-Martin, T; Fratina, S; Fhlisch, F; Gadomski, S; Gallacher, M P; Garitaonandia Elejabarrieta, H; Gee, C N P; George, S; Gillman, A R; Goncalo, R; Grabowska-Bold, I; Groll, M; Gringer, C; Hadley, D R; Haller, J; Hamilton, A; Hanke, P; Hauser, R; Hellman, S; Hidvgi, A; Hillier, S J; Hryn'ova, T; Idarraga, J; Johansen, M; Johns, K; Kalinowski, A; Khoriauli, G; Kirk, J; Klous, S; Kluge, E-E; Koeneke, K; Konoplich, R; Konstantinidis, N; Kwee, R; Landon, M; LeCompte, T; Ledroit, F; Lei, X; Lendermann, V; Lilley, J N; Losada, M; Maettig, S; Mahboubi, K; Mahout, G; Maltrana, D; Marino, C; Masik, J; Meier, K; Middleton, R P; Mincer, A; Moa, T; Monticelli, F; Moreno, D; Morris, J D; Mller, F; Navarro, G A; Negri, A; Nemethy, P; Neusiedl, A; Oltmann, B; Olvito, D; Osuna, C; Padilla, C; Panes, B; Parodi, F; Perera, V J O; Perez, E; Perez Reale, V; Petersen, B; Pinzon, G; Potter, C; Prieur, D P F; Prokishin, F; Qian, W; Quinonez, F; Rajagopalan, S; Reinsch, A; Rieke, S; Riu, I; Robertson, S; Rodriguez, D; Rogriquez, Y; Rhr, F; Saavedra, A; Sankey, D P C; Santamarina, C; Santamarina Rios, C; Scannicchio, D; Schiavi, C; Schmitt, K; Schultz-Coulon, H C; Schfer, U; Segura, E; Silverstein, D; Silverstein, S; Sivoklokov, S; Sjlin, J; Staley, R J; Stamen, R; Stelzer, J; Stockton, M C; Straessner, A; Strom, D; Sushkov, S; Sutton, M; Tamsett, M; Tan, C L A; Tapprogge, S; Thomas, J P; Thompson, P D; Torrence, E; Tripiana, M; Urquijo, P; Urrejola, P; Vachon, B; Vercesi, V; Vorwerk, V; Wang, M; Watkins, P M; Watson, A; Weber, P; Weidberg, T; Werner, P; Wessels, M; Wheeler-Ellis, S; Whiteson, D; Wiedenmann, W; Wielers, M; Wildt, M; Winklmeier, F; Wu, X; Xella, S; Zhao, L; Zobernig, H; de Seixas, J M; dos Anjos, A; Asman, B; Özcan, E

    2009-01-01

    The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 105 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

  6. Topological Trigger Developments

    CERN Document Server

    Likhomanenko, Tatiana

    2015-01-01

    The main b-physics trigger algorithm used by the LHCb experiment is the so-called topological trigger. The topological trigger selects vertices which are a) detached from the primary proton-proton collision and b) compatible with coming from the decay of a b-hadron. In the LHC Run 1, this trigger utilized a custom boosted decision tree algorithm, selected an almost 100% pure sample of b-hadrons with a typical efficiency of 60-70%, and its output was used in about 60% of LHCb papers. This talk presents studies carried out to optimize the topological trigger for LHC Run 2. In particular, we have carried out a detailed comparison of various machine learning classifier algorithms, e.g., AdaBoost, MatrixNet and uBoost. The topological trigger algorithm is designed to select all "interesting" decays of b-hadrons, but cannot be trained on every such decay. Studies have therefore been performed to determine how to optimize the performance of the classification algorithm on decays not used in the training. These inclu...

  7. LHCb Topological Trigger Reoptimization

    CERN Document Server

    Likhomanenko, Tatiana; Khairullin, Egor; Rogozhnikov, Alex; Ustyuzhanin, Andrey; Williams, Michael

    2015-01-01

    The main b-physics trigger algorithm used by the LHCb experiment is the so-called topological trigger. The topological trigger selects vertices which are a) detached from the primary proton-proton collision and b) compatible with coming from the decay of a b-hadron. In the LHC Run 1, this trigger, which utilized a custom boosted decision tree algorithm, selected a nearly 100% pure sample of b-hadrons with a typical efficiency of 60-70%; its output was used in about 60% of LHCb papers. This talk presents studies carried out to optimize the topological trigger for LHC Run 2. In particular, we have carried out a detailed comparison of various machine learning classifier algorithms, e.g., AdaBoost, MatrixNet and neural networks. The topological trigger algorithm is designed to select all "interesting" decays of b-hadrons, but cannot be trained on every such decay. Studies have therefore been performed to determine how to optimize the performance of the classification algorithm on decays not used in the training. ...

  8. Electromagnetic calorimeter trigger at Belle

    CERN Document Server

    Cheon, B G; Lee, S H; Won, E; Park, I C; Hur, T W; Park, C S; Kim, S K; Kim, H J; Kim, H O; Chu, T H; Usov, Y V; Aulchenko, V M; Kuzmin, A S; Bondar, A E; Shwartz, B A; Eidelman, S; Krokovnyi, P P; Hayashii, H; Sagawa, H; Fukushima, M

    2002-01-01

    The performance of CsI(Tl) electromagnetic calorimeter trigger system in the Belle experiment is described. Two kinds of trigger schemes have been taken into account, namely a total energy trigger and a cluster counting trigger which are complementary to each other. In addition, the system has provided the online/offline luminosity information using the Bhabha event trigger scheme. An upgrade of the trigger is discussed.

  9. Correlation measurements of fission-fragment properties

    Directory of Open Access Journals (Sweden)

    Oberstedt A.

    2010-10-01

    Full Text Available For the development of future nuclear fission applications and for a responsible handling of nuclear waste the a-priori assessment of the fission-fragments’ heat production and toxicity is a fundamental necessity. The success of an indispensable modelling of the fission process strongly depends on a good understanding of the particular mechanism of scission, the mass fragmentation and partition of excitation energy. Experimental observables are fission-fragment properties like mass- and energy-distributions, and the prompt neutron as well as γ-ray multiplicities and emission spectra. The latter quantities should preferably be known as a function of fragment mass and excitation energy. Those data are highly demanded as published by the OECD-NEA in its high priority data request list. With the construction of the double (v, E spectrometer VERDI we aim at measuring pre- and post-neutron masses directly and simultaneously to avoid prompt neutron corrections. From the simultaneous measurement of pre- and post-neutron fission-fragment data the prompt neutron multiplicity may then be inferred fully correlated with fragment mass yield and total kinetic energy. Using an ultra-fast fission event trigger spectral prompt fission γ-ray measurements may be performed. For that purpose recently developed lanthanum-halide detectors, with excellent timing characteristics, were coupled to the VERDI spectrometer allowing for a very good discrimination of fission γ-rays and prompt neutrons due to their different time-of-flight.

  10. String fragmentation; La fragmentation des cordes

    Energy Technology Data Exchange (ETDEWEB)

    Drescher, H.J.; Werner, K. [Laboratoire de Physique Subatomique et des Technologies Associees - SUBATECH, Centre National de la Recherche Scientifique, 44 - Nantes (France)

    1997-10-01

    The classical string model is used in VENUS as a fragmentation model. For the soft domain simple 2-parton strings were sufficient, whereas for higher energies up to LHC, the perturbative regime of the QCD gives additional soft gluons, which are mapped on the string as so called kinks, energy singularities between the leading partons. The kinky string model is chosen to handle fragmentation of these strings by application of the Lorentz invariant area law. The `kinky strings` model, corresponding to the perturbative gluons coming from pQCD, takes into consideration this effect by treating the partons and gluons on the same footing. The decay law is always the Artru-Menessier area law which is the most realistic since it is invariant to the Lorentz and gauge transformations. For low mass strings a manipulation of the rupture point is necessary if the string corresponds already to an elementary particle determined by the mass and the flavor content. By means of the fragmentation model it will be possible to simulate the data from future experiments at LHC and RHIC 3 refs.

  11. Fragmentation trees reloaded.

    Science.gov (United States)

    Böcker, Sebastian; Dührkop, Kai

    2016-01-01

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring). We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our method, as well as other methods for this task. SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods.Graphical abstractWe present a new scoring for computing fragmentation trees from tandem mass spectrometry data based on Bayesian statistics. The best scoring fragmentation tree most likely explains the molecular formula of the measured parent ion.

  12. Fragmentation of monoclonal antibodies

    Science.gov (United States)

    Vlasak, Josef

    2011-01-01

    Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5–6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule. PMID:21487244

  13. The CMS trigger system

    Energy Technology Data Exchange (ETDEWEB)

    Khachatryan, Vardan; et al.

    2016-09-08

    This paper describes the CMS trigger system and its performance during Run 1 of the LHC. The trigger system consists of two levels designed to select events of potential physics interest from a GHz (MHz) interaction rate of proton-proton (heavy ion) collisions. The first level of the trigger is implemented in hardware, and selects events containing detector signals consistent with an electron, photon, muon, tau lepton, jet, or missing transverse energy. A programmable menu of up to 128 object-based algorithms is used to select events for subsequent processing. The trigger thresholds are adjusted to the LHC instantaneous luminosity during data taking in order to restrict the output rate to 100 kHz, the upper limit imposed by the CMS readout electronics. The second level, implemented in software, further refines the purity of the output stream, selecting an average rate of 400 Hz for offline event storage. The objectives, strategy and performance of the trigger system during the LHC Run 1 are described.

  14. The CMS trigger system

    CERN Document Server

    Khachatryan, Vardan; Tumasyan, Armen; Adam, Wolfgang; Aşılar, Ece; Bergauer, Thomas; Brandstetter, Johannes; Brondolin, Erica; Dragicevic, Marko; Erö, Janos; Flechl, Martin; Friedl, Markus; Fruehwirth, Rudolf; Ghete, Vasile Mihai; Hartl, Christian; Hörmann, Natascha; Hrubec, Josef; Jeitler, Manfred; Knünz, Valentin; König, Axel; Krammer, Manfred; Krätschmer, Ilse; Liko, Dietrich; Matsushita, Takashi; Mikulec, Ivan; Rabady, Dinyar; Rahbaran, Babak; Rohringer, Herbert; Schieck, Jochen; Schöfbeck, Robert; Strauss, Josef; Treberer-Treberspurg, Wolfgang; Waltenberger, Wolfgang; Wulz, Claudia-Elisabeth; Mossolov, Vladimir; Shumeiko, Nikolai; Suarez Gonzalez, Juan; Alderweireldt, Sara; Cornelis, Tom; De Wolf, Eddi A; Janssen, Xavier; Knutsson, Albert; Lauwers, Jasper; Luyckx, Sten; Van De Klundert, Merijn; Van Haevermaet, Hans; Van Mechelen, Pierre; Van Remortel, Nick; Van Spilbeeck, Alex; Abu Zeid, Shimaa; Blekman, Freya; D'Hondt, Jorgen; Daci, Nadir; De Bruyn, Isabelle; Deroover, Kevin; Heracleous, Natalie; Keaveney, James; Lowette, Steven; Moreels, Lieselotte; Olbrechts, Annik; Python, Quentin; Strom, Derek; Tavernier, Stefaan; Van Doninck, Walter; Van Mulders, Petra; Van Onsem, Gerrit Patrick; Van Parijs, Isis; Barria, Patrizia; Brun, Hugues; Caillol, Cécile; Clerbaux, Barbara; De Lentdecker, Gilles; Fasanella, Giuseppe; Favart, Laurent; Grebenyuk, Anastasia; Karapostoli, Georgia; Lenzi, Thomas; Léonard, Alexandre; Maerschalk, Thierry; Marinov, Andrey; Perniè, Luca; Randle-conde, Aidan; Reis, Thomas; Seva, Tomislav; Vander Velde, Catherine; Vanlaer, Pascal; Yonamine, Ryo; Zenoni, Florian; Zhang, Fengwangdong; Beernaert, Kelly; Benucci, Leonardo; Cimmino, Anna; Crucy, Shannon; Dobur, Didar; Fagot, Alexis; Garcia, Guillaume; Gul, Muhammad; Mccartin, Joseph; Ocampo Rios, Alberto Andres; Poyraz, Deniz; Ryckbosch, Dirk; Salva Diblen, Sinem; Sigamani, Michael; Strobbe, Nadja; Tytgat, Michael; Van Driessche, Ward; Yazgan, Efe; Zaganidis, Nicolas; Basegmez, Suzan; Beluffi, Camille; Bondu, Olivier; Brochet, Sébastien; Bruno, Giacomo; Caudron, Adrien; Ceard, Ludivine; Da Silveira, Gustavo Gil; Delaere, Christophe; Favart, Denis; Forthomme, Laurent; Giammanco, Andrea; Hollar, Jonathan; Jafari, Abideh; Jez, Pavel; Komm, Matthias; Lemaitre, Vincent; Mertens, Alexandre; Musich, Marco; Nuttens, Claude; Perrini, Lucia; Pin, Arnaud; Piotrzkowski, Krzysztof; Popov, Andrey; Quertenmont, Loic; Selvaggi, Michele; Vidal Marono, Miguel; Beliy, Nikita; Hammad, Gregory Habib; Aldá Júnior, Walter Luiz; Alves, Fábio Lúcio; Alves, Gilvan; Brito, Lucas; Correa Martins Junior, Marcos; Hamer, Matthias; Hensel, Carsten; Mora Herrera, Clemencia; Moraes, Arthur; Pol, Maria Elena; Rebello Teles, Patricia; Belchior Batista Das Chagas, Ewerton; Carvalho, Wagner; Chinellato, Jose; Custódio, Analu; Melo Da Costa, Eliza; De Jesus Damiao, Dilson; De Oliveira Martins, Carley; Fonseca De Souza, Sandro; Huertas Guativa, Lina Milena; Malbouisson, Helena; Matos Figueiredo, Diego; Mundim, Luiz; Nogima, Helio; Prado Da Silva, Wanda Lucia; Santoro, Alberto; Sznajder, Andre; Tonelli Manganote, Edmilson José; Vilela Pereira, Antonio; Ahuja, Sudha; Bernardes, Cesar Augusto; De Souza Santos, Angelo; Dogra, Sunil; Tomei, Thiago; De Moraes Gregores, Eduardo; Mercadante, Pedro G; Moon, Chang-Seong; Novaes, Sergio F; Padula, Sandra; Romero Abad, David; Ruiz Vargas, José Cupertino; Aleksandrov, Aleksandar; Hadjiiska, Roumyana; Iaydjiev, Plamen; Rodozov, Mircho; Stoykova, Stefka; Sultanov, Georgi; Vutova, Mariana; Dimitrov, Anton; Glushkov, Ivan; Litov, Leander; Pavlov, Borislav; Petkov, Peicho; Ahmad, Muhammad; Bian, Jian-Guo; Chen, Guo-Ming; Chen, He-Sheng; Chen, Mingshui; Cheng, Tongguang; Du, Ran; Jiang, Chun-Hua; Plestina, Roko; Romeo, Francesco; Shaheen, Sarmad Masood; Spiezia, Aniello; Tao, Junquan; Wang, Chunjie; Wang, Zheng; Zhang, Huaqiao; Asawatangtrakuldee, Chayanit; Ban, Yong; Li, Qiang; Liu, Shuai; Mao, Yajun; Qian, Si-Jin; Wang, Dayong; Xu, Zijun; Avila, Carlos; Cabrera, Andrés; Chaparro Sierra, Luisa Fernanda; Florez, Carlos; Gomez, Juan Pablo; Gomez Moreno, Bernardo; Sanabria, Juan Carlos; Godinovic, Nikola; Lelas, Damir; Puljak, Ivica; Ribeiro Cipriano, Pedro M; Antunovic, Zeljko; Kovac, Marko; Brigljevic, Vuko; Kadija, Kreso; Luetic, Jelena; Micanovic, Sasa; Sudic, Lucija; Attikis, Alexandros; Mavromanolakis, Georgios; Mousa, Jehad; Nicolaou, Charalambos; Ptochos, Fotios; Razis, Panos A; Rykaczewski, Hans; Bodlak, Martin; Finger, Miroslav; Finger Jr, Michael; Assran, Yasser; El Sawy, Mai; Elgammal, Sherif; Ellithi Kamel, Ali; Mahmoud, Mohammed; Calpas, Betty; Kadastik, Mario; Murumaa, Marion; Raidal, Martti; Tiko, Andres; Veelken, Christian; Eerola, Paula; Pekkanen, Juska; Voutilainen, Mikko; Härkönen, Jaakko; Karimäki, Veikko; Kinnunen, Ritva; Lampén, Tapio; Lassila-Perini, Kati; Lehti, Sami; Lindén, Tomas; Luukka, Panja-Riina; Mäenpää, Teppo; Peltola, Timo; Tuominen, Eija; Tuominiemi, Jorma; Tuovinen, Esa; Wendland, Lauri; Talvitie, Joonas; Tuuva, Tuure; Besancon, Marc; Couderc, Fabrice; Dejardin, Marc; Denegri, Daniel; Fabbro, Bernard; Faure, Jean-Louis; Favaro, Carlotta; Ferri, Federico; Ganjour, Serguei; Givernaud, Alain; Gras, Philippe; Hamel de Monchenault, Gautier; Jarry, Patrick; Locci, Elizabeth; Machet, Martina; Malcles, Julie; Rander, John; Rosowsky, André; Titov, Maksym; Zghiche, Amina; Antropov, Iurii; Baffioni, Stephanie; Beaudette, Florian; Busson, Philippe; Cadamuro, Luca; Chapon, Emilien; Charlot, Claude; Dahms, Torsten; Davignon, Olivier; Filipovic, Nicolas; Florent, Alice; Granier de Cassagnac, Raphael; Lisniak, Stanislav; Mastrolorenzo, Luca; Miné, Philippe; Naranjo, Ivo Nicolas; Nguyen, Matthew; Ochando, Christophe; Ortona, Giacomo; Paganini, Pascal; Pigard, Philipp; Regnard, Simon; Salerno, Roberto; Sauvan, Jean-Baptiste; Sirois, Yves; Strebler, Thomas; Yilmaz, Yetkin; Zabi, Alexandre; Agram, Jean-Laurent; Andrea, Jeremy; Aubin, Alexandre; Bloch, Daniel; Brom, Jean-Marie; Buttignol, Michael; Chabert, Eric Christian; Chanon, Nicolas; Collard, Caroline; Conte, Eric; Coubez, Xavier; Fontaine, Jean-Charles; Gelé, Denis; Goerlach, Ulrich; Goetzmann, Christophe; Le Bihan, Anne-Catherine; Merlin, Jeremie Alexandre; Skovpen, Kirill; Van Hove, Pierre; Gadrat, Sébastien; Beauceron, Stephanie; Bernet, Colin; Boudoul, Gaelle; Bouvier, Elvire; Carrillo Montoya, Camilo Andres; Chierici, Roberto; Contardo, Didier; Courbon, Benoit; Depasse, Pierre; El Mamouni, Houmani; Fan, Jiawei; Fay, Jean; Gascon, Susan; Gouzevitch, Maxime; Ille, Bernard; Lagarde, Francois; Laktineh, Imad Baptiste; Lethuillier, Morgan; Mirabito, Laurent; Pequegnot, Anne-Laure; Perries, Stephane; Ruiz Alvarez, José David; Sabes, David; Sgandurra, Louis; Sordini, Viola; Vander Donckt, Muriel; Verdier, Patrice; Viret, Sébastien; Toriashvili, Tengizi; Tsamalaidze, Zviad; Autermann, Christian; Beranek, Sarah; Edelhoff, Matthias; Feld, Lutz; Heister, Arno; Kiesel, Maximilian Knut; Klein, Katja; Lipinski, Martin; Ostapchuk, Andrey; Preuten, Marius; Raupach, Frank; Schael, Stefan; Schulte, Jan-Frederik; Verlage, Tobias; Weber, Hendrik; Wittmer, Bruno; Zhukov, Valery; Ata, Metin; Brodski, Michael; Dietz-Laursonn, Erik; Duchardt, Deborah; Endres, Matthias; Erdmann, Martin; Erdweg, Sören; Esch, Thomas; Fischer, Robert; Güth, Andreas; Hebbeker, Thomas; Heidemann, Carsten; Hoepfner, Kerstin; Klingebiel, Dennis; Knutzen, Simon; Kreuzer, Peter; Merschmeyer, Markus; Meyer, Arnd; Millet, Philipp; Olschewski, Mark; Padeken, Klaas; Papacz, Paul; Pook, Tobias; Radziej, Markus; Reithler, Hans; Rieger, Marcel; Scheuch, Florian; Sonnenschein, Lars; Teyssier, Daniel; Thüer, Sebastian; Cherepanov, Vladimir; Erdogan, Yusuf; Flügge, Günter; Geenen, Heiko; Geisler, Matthias; Hoehle, Felix; Kargoll, Bastian; Kress, Thomas; Kuessel, Yvonne; Künsken, Andreas; Lingemann, Joschka; Nehrkorn, Alexander; Nowack, Andreas; Nugent, Ian Michael; Pistone, Claudia; Pooth, Oliver; Stahl, Achim; Aldaya Martin, Maria; Asin, Ivan; Bartosik, Nazar; Behnke, Olaf; Behrens, Ulf; Bell, Alan James; Borras, Kerstin; Burgmeier, Armin; Campbell, Alan; Choudhury, Somnath; Costanza, Francesco; Diez Pardos, Carmen; Dolinska, Ganna; Dooling, Samantha; Dorland, Tyler; Eckerlin, Guenter; Eckstein, Doris; Eichhorn, Thomas; Flucke, Gero; Gallo, Elisabetta; Garay Garcia, Jasone; Geiser, Achim; Gizhko, Andrii; Gunnellini, Paolo; Hauk, Johannes; Hempel, Maria; Jung, Hannes; Kalogeropoulos, Alexis; Karacheban, Olena; Kasemann, Matthias; Katsas, Panagiotis; Kieseler, Jan; Kleinwort, Claus; Korol, Ievgen; Lange, Wolfgang; Leonard, Jessica; Lipka, Katerina; Lobanov, Artur; Lohmann, Wolfgang; Mankel, Rainer; Marfin, Ihar; Melzer-Pellmann, Isabell-Alissandra; Meyer, Andreas Bernhard; Mittag, Gregor; Mnich, Joachim; Mussgiller, Andreas; Naumann-Emme, Sebastian; Nayak, Aruna; Ntomari, Eleni; Perrey, Hanno; Pitzl, Daniel; Placakyte, Ringaile; Raspereza, Alexei; Roland, Benoit; Sahin, Mehmet Özgür; Saxena, Pooja; Schoerner-Sadenius, Thomas; Schröder, Matthias; Seitz, Claudia; Spannagel, Simon; Trippkewitz, Karim Damun; Walsh, Roberval; Wissing, Christoph; Blobel, Volker; Centis Vignali, Matteo; Draeger, Arne-Rasmus; Erfle, Joachim; Garutti, Erika; Goebel, Kristin; Gonzalez, Daniel; Görner, Martin; Haller, Johannes; Hoffmann, Malte; Höing, Rebekka Sophie; Junkes, Alexandra; Klanner, Robert; Kogler, Roman; Kovalchuk, Nataliia; Lapsien, Tobias; Lenz, Teresa; Marchesini, Ivan; Marconi, Daniele; Meyer, Mareike; Nowatschin, Dominik; Ott, Jochen; Pantaleo, Felice; Peiffer, Thomas; Perieanu, Adrian; Pietsch, Niklas; Poehlsen, Jennifer; Rathjens, Denis; Sander, Christian; Scharf, Christian; Schettler, Hannes; Schleper, Peter; Schlieckau, Eike; Schmidt, Alexander; Schwandt, Joern; Sola, Valentina; Stadie, Hartmut; Steinbrück, Georg; Tholen, Heiner; Troendle, Daniel; Usai, Emanuele; Vanelderen, Lukas; Vanhoefer, Annika; Vormwald, Benedikt; Akbiyik, Melike; Barth, Christian; Baus, Colin; Berger, Joram; Böser, Christian; Butz, Erik; Chwalek, Thorsten; Colombo, Fabio; De Boer, Wim; Descroix, Alexis; Dierlamm, Alexander; Fink, Simon; Frensch, Felix; Friese, Raphael; Giffels, Manuel; Gilbert, Andrew; Haitz, Dominik; Hartmann, Frank; Heindl, Stefan Michael; Husemann, Ulrich; Katkov, Igor; Kornmayer, Andreas; Lobelle Pardo, Patricia; Maier, Benedikt; Mildner, Hannes; Mozer, Matthias Ulrich; Müller, Thomas; Müller, Thomas; Plagge, Michael; Quast, Gunter; Rabbertz, Klaus; Röcker, Steffen; Roscher, Frank; Sieber, Georg; Simonis, Hans-Jürgen; Stober, Fred-Markus Helmut; Ulrich, Ralf; Wagner-Kuhr, Jeannine; Wayand, Stefan; Weber, Marc; Weiler, Thomas; Wöhrmann, Clemens; Wolf, Roger; Anagnostou, Georgios; Daskalakis, Georgios; Geralis, Theodoros; Giakoumopoulou, Viktoria Athina; Kyriakis, Aristotelis; Loukas, Demetrios; Psallidas, Andreas; Topsis-Giotis, Iasonas; Agapitos, Antonis; Kesisoglou, Stilianos; Panagiotou, Apostolos; Saoulidou, Niki; Tziaferi, Eirini; Evangelou, Ioannis; Flouris, Giannis; Foudas, Costas; Kokkas, Panagiotis; Loukas, Nikitas; Manthos, Nikolaos; Papadopoulos, Ioannis; Paradas, Evangelos; Strologas, John; Bencze, Gyorgy; Hajdu, Csaba; Hazi, Andras; Hidas, Pàl; Horvath, Dezso; Sikler, Ferenc; Veszpremi, Viktor; Vesztergombi, Gyorgy; Zsigmond, Anna Julia; Beni, Noemi; Czellar, Sandor; Karancsi, János; Molnar, Jozsef; Szillasi, Zoltan; Bartók, Márton; Makovec, Alajos; Raics, Peter; Trocsanyi, Zoltan Laszlo; Ujvari, Balazs; Mal, Prolay; Mandal, Koushik; Sahoo, Deepak Kumar; Sahoo, Niladribihari; Swain, Sanjay Kumar; Bansal, Sunil; Beri, Suman Bala; Bhatnagar, Vipin; Chawla, Ridhi; Gupta, Ruchi; Bhawandeep, Bhawandeep; Kalsi, Amandeep Kaur; Kaur, Anterpreet; Kaur, Manjit; Kumar, Ramandeep; Mehta, Ankita; Mittal, Monika; Singh, Jasbir; Walia, Genius; Kumar, Ashok; Bhardwaj, Ashutosh; Choudhary, Brajesh C; Garg, Rocky Bala; Kumar, Ajay; Malhotra, Shivali; Naimuddin, Md; Nishu, Nishu; Ranjan, Kirti; Sharma, Ramkrishna; Sharma, Varun; Bhattacharya, Satyaki; Chatterjee, Kalyanmoy; Dey, Sourav; Dutta, Suchandra; Jain, Sandhya; Majumdar, Nayana; Modak, Atanu; Mondal, Kuntal; Mukherjee, Swagata; Mukhopadhyay, Supratik; Roy, Ashim; Roy, Debarati; Roy Chowdhury, Suvankar; Sarkar, Subir; Sharan, Manoj; Abdulsalam, Abdulla; Chudasama, Ruchi; Dutta, Dipanwita; Jha, Vishwajeet; Kumar, Vineet; Mohanty, Ajit Kumar; Pant, Lalit Mohan; Shukla, Prashant; Topkar, Anita; Aziz, Tariq; Banerjee, Sudeshna; Bhowmik, Sandeep; Chatterjee, Rajdeep Mohan; Dewanjee, Ram Krishna; Dugad, Shashikant; Ganguly, Sanmay; Ghosh, Saranya; Guchait, Monoranjan; Gurtu, Atul; Kole, Gouranga; Kumar, Sanjeev; Mahakud, Bibhuprasad; Maity, Manas; Majumder, Gobinda; Mazumdar, Kajari; Mitra, Soureek; Mohanty, Gagan Bihari; Parida, Bibhuti; Sarkar, Tanmay; Sur, Nairit; Sutar, Bajrang; Wickramage, Nadeesha; Chauhan, Shubhanshu; Dube, Sourabh; Kothekar, Kunal; Sharma, Seema; Bakhshiansohi, Hamed; Behnamian, Hadi; Etesami, Seyed Mohsen; Fahim, Ali; Goldouzian, Reza; Khakzad, Mohsen; Mohammadi Najafabadi, Mojtaba; Naseri, Mohsen; Paktinat Mehdiabadi, Saeid; Rezaei Hosseinabadi, Ferdos; Safarzadeh, Batool; Zeinali, Maryam; Felcini, Marta; Grunewald, Martin; Abbrescia, Marcello; Calabria, Cesare; Caputo, Claudio; Colaleo, Anna; Creanza, Donato; Cristella, Leonardo; De Filippis, Nicola; De Palma, Mauro; Fiore, Luigi; Iaselli, Giuseppe; Maggi, Giorgio; Maggi, Marcello; Miniello, Giorgia; My, Salvatore; Nuzzo, Salvatore; Pompili, Alexis; Pugliese, Gabriella; Radogna, Raffaella; Ranieri, Antonio; Selvaggi, Giovanna; Silvestris, Lucia; Venditti, Rosamaria; Verwilligen, Piet; Abbiendi, Giovanni; Battilana, Carlo; Benvenuti, Alberto; Bonacorsi, Daniele; Braibant-Giacomelli, Sylvie; Brigliadori, Luca; Campanini, Renato; Capiluppi, Paolo; Castro, Andrea; Cavallo, Francesca Romana; Chhibra, Simranjit Singh; Codispoti, Giuseppe; Cuffiani, Marco; Dallavalle, Gaetano-Marco; Fabbri, Fabrizio; Fanfani, Alessandra; Fasanella, Daniele; Giacomelli, Paolo; Grandi, Claudio; Guiducci, Luigi; Marcellini, Stefano; Masetti, Gianni; Montanari, Alessandro; Navarria, Francesco; Perrotta, Andrea; Rossi, Antonio; Rovelli, Tiziano; Siroli, Gian Piero; Tosi, Nicolò; Travaglini, Riccardo; Cappello, Gigi; Chiorboli, Massimiliano; Costa, Salvatore; Di Mattia, Alessandro; Giordano, Ferdinando; Potenza, Renato; Tricomi, Alessia; Tuve, Cristina; Barbagli, Giuseppe; Ciulli, Vitaliano; Civinini, Carlo; D'Alessandro, Raffaello; Focardi, Ettore; Gonzi, Sandro; Gori, Valentina; Lenzi, Piergiulio; Meschini, Marco; Paoletti, Simone; Sguazzoni, Giacomo; Tropiano, Antonio; Viliani, Lorenzo; Benussi, Luigi; Bianco, Stefano; Fabbri, Franco; Piccolo, Davide; Primavera, Federica; Calvelli, Valerio; Ferro, Fabrizio; Lo Vetere, Maurizio; Monge, Maria Roberta; Robutti, Enrico; Tosi, Silvano; Brianza, Luca; Dinardo, Mauro Emanuele; Fiorendi, Sara; Gennai, Simone; Gerosa, Raffaele; Ghezzi, Alessio; Govoni, Pietro; Malvezzi, Sandra; Manzoni, Riccardo Andrea; Marzocchi, Badder; Menasce, Dario; Moroni, Luigi; Paganoni, Marco; Pedrini, Daniele; Ragazzi, Stefano; Redaelli, Nicola; Tabarelli de Fatis, Tommaso; Buontempo, Salvatore; Cavallo, Nicola; Di Guida, Salvatore; Esposito, Marco; Fabozzi, Francesco; Iorio, Alberto Orso Maria; Lanza, Giuseppe; Lista, Luca; Meola, Sabino; Merola, Mario; Paolucci, Pierluigi; Sciacca, Crisostomo; Thyssen, Filip; Bacchetta, Nicola; Bellato, Marco; Benato, Lisa; Bisello, Dario; Boletti, Alessio; Carlin, Roberto; Checchia, Paolo; Dall'Osso, Martino; Dosselli, Umberto; Gasparini, Fabrizio; Gasparini, Ugo; Gozzelino, Andrea; Lacaprara, Stefano; Margoni, Martino; Meneguzzo, Anna Teresa; Montecassiano, Fabio; Passaseo, Marina; Pazzini, Jacopo; Pegoraro, Matteo; Pozzobon, Nicola; Simonetto, Franco; Torassa, Ezio; Tosi, Mia; Vanini, Sara; Ventura, Sandro; Zanetti, Marco; Zotto, Pierluigi; Zucchetta, Alberto; Zumerle, Gianni; Braghieri, Alessandro; Magnani, Alice; Montagna, Paolo; Ratti, Sergio P; Re, Valerio; Riccardi, Cristina; Salvini, Paola; Vai, Ilaria; Vitulo, Paolo; Alunni Solestizi, Luisa; Biasini, Maurizio; Bilei, Gian Mario; Ciangottini, Diego; Fanò, Livio; Lariccia, Paolo; Mantovani, Giancarlo; Menichelli, Mauro; Saha, Anirban; Santocchia, Attilio; Androsov, Konstantin; Azzurri, Paolo; Bagliesi, Giuseppe; Bernardini, Jacopo; Boccali, Tommaso; Castaldi, Rino; Ciocci, Maria Agnese; Dell'Orso, Roberto; Donato, Silvio; Fedi, Giacomo; Foà, Lorenzo; Giassi, Alessandro; Grippo, Maria Teresa; Ligabue, Franco; Lomtadze, Teimuraz; Martini, Luca; Messineo, Alberto; Palla, Fabrizio; Rizzi, Andrea; Savoy-Navarro, Aurore; Serban, Alin Titus; Spagnolo, Paolo; Tenchini, Roberto; Tonelli, Guido; Venturi, Andrea; Verdini, Piero Giorgio; Barone, Luciano; Cavallari, Francesca; D'imperio, Giulia; Del Re, Daniele; Diemoz, Marcella; Gelli, Simone; Jorda, Clara; Longo, Egidio; Margaroli, Fabrizio; Meridiani, Paolo; Organtini, Giovanni; Paramatti, Riccardo; Preiato, Federico; Rahatlou, Shahram; Rovelli, Chiara; Santanastasio, Francesco; Traczyk, Piotr; Amapane, Nicola; Arcidiacono, Roberta; Argiro, Stefano; Arneodo, Michele; Bellan, Riccardo; Biino, Cristina; Cartiglia, Nicolo; Costa, Marco; Covarelli, Roberto; Degano, Alessandro; Demaria, Natale; Finco, Linda; Kiani, Bilal; Mariotti, Chiara; Maselli, Silvia; Migliore, Ernesto; Monaco, Vincenzo; Monteil, Ennio; Obertino, Maria Margherita; Pacher, Luca; Pastrone, Nadia; Pelliccioni, Mario; Pinna Angioni, Gian Luca; Ravera, Fabio; Romero, Alessandra; Ruspa, Marta; Sacchi, Roberto; Solano, Ada; Staiano, Amedeo; Tamponi, Umberto; Belforte, Stefano; Candelise, Vieri; Casarsa, Massimo; Cossutti, Fabio; Della Ricca, Giuseppe; Gobbo, Benigno; La Licata, Chiara; Marone, Matteo; Schizzi, Andrea; Zanetti, Anna; Kropivnitskaya, Anna; Nam, Soon-Kwon; Kim, Dong Hee; Kim, Gui Nyun; Kim, Min Suk; Kong, Dae Jung; Lee, Sangeun; Oh, Young Do; Sakharov, Alexandre; Son, Dong-Chul; Brochero Cifuentes, Javier Andres; Kim, Hyunsoo; Kim, Tae Jeong; Song, Sanghyeon; Choi, Suyong; Go, Yeonju; Gyun, Dooyeon; Hong, Byung-Sik; Jo, Mihee; Kim, Hyunchul; Kim, Yongsun; Lee, Byounghoon; Lee, Kisoo; Lee, Kyong Sei; Lee, Songkyo; Park, Sung Keun; Roh, Youn; Yoo, Hwi Dong; Choi, Minkyoo; Kim, Hyunyong; Kim, Ji Hyun; Lee, Jason Sang Hun; Park, Inkyu; Ryu, Geonmo; Ryu, Min Sang; Choi, Young-Il; Goh, Junghwan; Kim, Donghyun; Kwon, Eunhyang; Lee, Jongseok; Yu, Intae; Dudenas, Vytautas; Juodagalvis, Andrius; Vaitkus, Juozas; Ahmed, Ijaz; Ibrahim, Zainol Abidin; Komaragiri, Jyothsna Rani; Md Ali, Mohd Adli Bin; Mohamad Idris, Faridah; Wan Abdullah, Wan Ahmad Tajuddin; Yusli, Mohd Nizam; Casimiro Linares, Edgar; Castilla-Valdez, Heriberto; De La Cruz-Burelo, Eduard; Heredia-De La Cruz, Ivan; Hernandez-Almada, Alberto; Lopez-Fernandez, Ricardo; Sánchez Hernández, Alberto; Carrillo Moreno, Salvador; Vazquez Valencia, Fabiola; Pedraza, Isabel; Salazar Ibarguen, Humberto Antonio; Morelos Pineda, Antonio; Krofcheck, David; Butler, Philip H; Ahmad, Ashfaq; Ahmad, Muhammad; Hassan, Qamar; Hoorani, Hafeez R; Khan, Wajid Ali; Khurshid, Taimoor; Shoaib, Muhammad; Bialkowska, Helena; Bluj, Michal; Boimska, Bożena; Frueboes, Tomasz; Górski, Maciej; Kazana, Malgorzata; Nawrocki, Krzysztof; Romanowska-Rybinska, Katarzyna; Szleper, Michal; Zalewski, Piotr; Brona, Grzegorz; Bunkowski, Karol; Byszuk, Adrian; Doroba, Krzysztof; Kalinowski, Artur; Konecki, Marcin; Krolikowski, Jan; Misiura, Maciej; Olszewski, Michal; Pozniak, Krzysztof; Walczak, Marek; Bargassa, Pedrame; Beirão Da Cruz E Silva, Cristóvão; Di Francesco, Agostino; Faccioli, Pietro; Ferreira Parracho, Pedro Guilherme; Gallinaro, Michele; Leonardo, Nuno; Lloret Iglesias, Lara; Nguyen, Federico; Rodrigues Antunes, Joao; Seixas, Joao; Toldaiev, Oleksii; Vadruccio, Daniele; Varela, Joao; Vischia, Pietro; Afanasiev, Serguei; Bunin, Pavel; Gavrilenko, Mikhail; Golutvin, Igor; Gorbunov, Ilya; Kamenev, Alexey; Karjavin, Vladimir; Konoplyanikov, Viktor; Lanev, Alexander; Malakhov, Alexander; Matveev, Viktor; Moisenz, Petr; Palichik, Vladimir; Perelygin, Victor; Shmatov, Sergey; Shulha, Siarhei; Skatchkov, Nikolai; Smirnov, Vitaly; Zarubin, Anatoli; Golovtsov, Victor; Ivanov, Yury; Kim, Victor; Kuznetsova, Ekaterina; Levchenko, Petr; Murzin, Victor; Oreshkin, Vadim; Smirnov, Igor; Sulimov, Valentin; Uvarov, Lev; Vavilov, Sergey; Vorobyev, Alexey; Andreev, Yuri; Dermenev, Alexander; Gninenko, Sergei; Golubev, Nikolai; Karneyeu, Anton; Kirsanov, Mikhail; Krasnikov, Nikolai; Pashenkov, Anatoli; Tlisov, Danila; Toropin, Alexander; Epshteyn, Vladimir; Gavrilov, Vladimir; Lychkovskaya, Natalia; Popov, Vladimir; Pozdnyakov, Ivan; Safronov, Grigory; Spiridonov, Alexander; Vlasov, Evgueni; Zhokin, Alexander; Bylinkin, Alexander; Andreev, Vladimir; Azarkin, Maksim; Dremin, Igor; Kirakosyan, Martin; Leonidov, Andrey; Mesyats, Gennady; Rusakov, Sergey V; Baskakov, Alexey; Belyaev, Andrey; Boos, Edouard; Dubinin, Mikhail; Dudko, Lev; Ershov, Alexander; Gribushin, Andrey; Kaminskiy, Alexandre; Klyukhin, Vyacheslav; Kodolova, Olga; Lokhtin, Igor; Miagkov, Igor; Obraztsov, Stepan; Petrushanko, Sergey; Savrin, Viktor; Azhgirey, Igor; Bayshev, Igor; Bitioukov, Sergei; Kachanov, Vassili; Kalinin, Alexey; Konstantinov, Dmitri; Krychkine, Victor; Petrov, Vladimir; Ryutin, Roman; Sobol, Andrei; Tourtchanovitch, Leonid; Troshin, Sergey; Tyurin, Nikolay; Uzunian, Andrey; Volkov, Alexey; Adzic, Petar; Milosevic, Jovan; Rekovic, Vladimir; Alcaraz Maestre, Juan; Calvo, Enrique; Cerrada, Marcos; Chamizo Llatas, Maria; Colino, Nicanor; De La Cruz, Begona; Delgado Peris, Antonio; Domínguez Vázquez, Daniel; Escalante Del Valle, Alberto; Fernandez Bedoya, Cristina; Fernández Ramos, Juan Pablo; Flix, Jose; Fouz, Maria Cruz; Garcia-Abia, Pablo; Gonzalez Lopez, Oscar; Goy Lopez, Silvia; Hernandez, Jose M; Josa, Maria Isabel; Navarro De Martino, Eduardo; Pérez-Calero Yzquierdo, Antonio María; Puerta Pelayo, Jesus; Quintario Olmeda, Adrián; Redondo, Ignacio; Romero, Luciano; Santaolalla, Javier; Senghi Soares, Mara; Albajar, Carmen; de Trocóniz, Jorge F; Missiroli, Marino; Moran, Dermot; Cuevas, Javier; Fernandez Menendez, Javier; Folgueras, Santiago; Gonzalez Caballero, Isidro; Palencia Cortezon, Enrique; Vizan Garcia, Jesus Manuel; Cabrillo, Iban Jose; Calderon, Alicia; Castiñeiras De Saa, Juan Ramon; De Castro Manzano, Pablo; Duarte Campderros, Jordi; Fernandez, Marcos; Garcia-Ferrero, Juan; Gomez, Gervasio; Lopez Virto, Amparo; Marco, Jesus; Marco, Rafael; Martinez Rivero, Celso; Matorras, Francisco; Munoz Sanchez, Francisca Javiela; Piedra Gomez, Jonatan; Rodrigo, Teresa; Rodríguez-Marrero, Ana Yaiza; Ruiz-Jimeno, Alberto; Scodellaro, Luca; Trevisani, Nicolò; Vila, Ivan; Vilar Cortabitarte, Rocio; Abbaneo, Duccio; Auffray, Etiennette; Auzinger, Georg; Bachtis, Michail; Baillon, Paul; Ball, Austin; Barney, David; Benaglia, Andrea; Bendavid, Joshua; Benhabib, Lamia; Benitez, Jose F; Berruti, Gaia Maria; Bloch, Philippe; Bocci, Andrea; Bonato, Alessio; Botta, Cristina; Breuker, Horst; Camporesi, Tiziano; Castello, Roberto; Cerminara, Gianluca; D'Alfonso, Mariarosaria; D'Enterria, David; Dabrowski, Anne; Daponte, Vincenzo; David Tinoco Mendes, Andre; De Gruttola, Michele; De Guio, Federico; De Roeck, Albert; De Visscher, Simon; Di Marco, Emanuele; Dobson, Marc; Dordevic, Milos; Dorney, Brian; Du Pree, Tristan; Dünser, Marc; Dupont, Niels; Elliott-Peisert, Anna; Franzoni, Giovanni; Funk, Wolfgang; Gigi, Dominique; Gill, Karl; Giordano, Domenico; Girone, Maria; Glege, Frank; Guida, Roberto; Gundacker, Stefan; Guthoff, Moritz; Hammer, Josef; Harris, Philip; Hegeman, Jeroen; Innocente, Vincenzo; Janot, Patrick; Kirschenmann, Henning; Kortelainen, Matti J; Kousouris, Konstantinos; Krajczar, Krisztian; Lecoq, Paul; Lourenco, Carlos; Lucchini, Marco Toliman; Magini, Nicolo; Malgeri, Luca; Mannelli, Marcello; Martelli, Arabella; Masetti, Lorenzo; Meijers, Frans; Mersi, Stefano; Meschi, Emilio; Moortgat, Filip; Morovic, Srecko; Mulders, Martijn; Nemallapudi, Mythra Varun; Neugebauer, Hannes; Orfanelli, Styliani; Orsini, Luciano; Pape, Luc; Perez, Emmanuelle; Peruzzi, Marco; Petrilli, Achille; Petrucciani, Giovanni; Pfeiffer, Andreas; Piparo, Danilo; Racz, Attila; Rolandi, Gigi; Rovere, Marco; Ruan, Manqi; Sakulin, Hannes; Schäfer, Christoph; Schwick, Christoph; Seidel, Markus; Sharma, Archana; Silva, Pedro; Simon, Michal; Sphicas, Paraskevas; Steggemann, Jan; Stieger, Benjamin; Stoye, Markus; Takahashi, Yuta; Treille, Daniel; Triossi, Andrea; Tsirou, Andromachi; Veres, Gabor Istvan; Wardle, Nicholas; Wöhri, Hermine Katharina; Zagoździńska, Agnieszka; Zeuner, Wolfram Dietrich; Bertl, Willi; Deiters, Konrad; Erdmann, Wolfram; Horisberger, Roland; Ingram, Quentin; Kaestli, Hans-Christian; Kotlinski, Danek; Langenegger, Urs; Renker, Dieter; Rohe, Tilman; Bachmair, Felix; Bäni, Lukas; Bianchini, Lorenzo; Casal, Bruno; Dissertori, Günther; Dittmar, Michael; Donegà, Mauro; Eller, Philipp; Grab, Christoph; Heidegger, Constantin; Hits, Dmitry; Hoss, Jan; Kasieczka, Gregor; Lustermann, Werner; Mangano, Boris; Marionneau, Matthieu; Martinez Ruiz del Arbol, Pablo; Masciovecchio, Mario; Meister, Daniel; Micheli, Francesco; Musella, Pasquale; Nessi-Tedaldi, Francesca; Pandolfi, Francesco; Pata, Joosep; Pauss, Felicitas; Perrozzi, Luca; Quittnat, Milena; Rossini, Marco; Starodumov, Andrei; Takahashi, Maiko; Tavolaro, Vittorio Raoul; Theofilatos, Konstantinos; Wallny, Rainer; Aarrestad, Thea Klaeboe; Amsler, Claude; Caminada, Lea; Canelli, Maria Florencia; Chiochia, Vincenzo; De Cosa, Annapaola; Galloni, Camilla; Hinzmann, Andreas; Hreus, Tomas; Kilminster, Benjamin; Lange, Clemens; Ngadiuba, Jennifer; Pinna, Deborah; Robmann, Peter; Ronga, Frederic Jean; Salerno, Daniel; Yang, Yong; Cardaci, Marco; Chen, Kuan-Hsin; Doan, Thi Hien; Jain, Shilpi; Khurana, Raman; Konyushikhin, Maxim; Kuo, Chia-Ming; Lin, Willis; Lu, Yun-Ju; Yu, Shin-Shan; Kumar, Arun; Bartek, Rachel; Chang, Paoti; Chang, You-Hao; Chang, Yu-Wei; Chao, Yuan; Chen, Kai-Feng; Chen, Po-Hsun; Dietz, Charles; Fiori, Francesco; Grundler, Ulysses; Hou, George Wei-Shu; Hsiung, Yee; Liu, Yueh-Feng; Lu, Rong-Shyang; Miñano Moya, Mercedes; Petrakou, Eleni; Tsai, Jui-fa; Tzeng, Yeng-Ming; Asavapibhop, Burin; Kovitanggoon, Kittikul; Singh, Gurpreet; Srimanobhas, Norraphat; Suwonjandee, Narumon; Adiguzel, Aytul; Bakirci, Mustafa Numan; Demiroglu, Zuhal Seyma; Dozen, Candan; Eskut, Eda; Girgis, Semiray; Gokbulut, Gul; Guler, Yalcin; Gurpinar, Emine; Hos, Ilknur; Kangal, Evrim Ersin; Onengut, Gulsen; Ozdemir, Kadri; Polatoz, Ayse; Sunar Cerci, Deniz; Tali, Bayram; Topakli, Huseyin; Vergili, Mehmet; Zorbilmez, Caglar; Akin, Ilina Vasileva; Bilin, Bugra; Bilmis, Selcuk; Isildak, Bora; Karapinar, Guler; Yalvac, Metin; Zeyrek, Mehmet; Gülmez, Erhan; Kaya, Mithat; Kaya, Ozlem; Yetkin, Elif Asli; Yetkin, Taylan; Cakir, Altan; Cankocak, Kerem; Sen, Sercan; Vardarlı, Fuat Ilkehan; Grynyov, Boris; Levchuk, Leonid; Sorokin, Pavel; Aggleton, Robin; Ball, Fionn; Beck, Lana; Brooke, James John; Clement, Emyr; Cussans, David; Flacher, Henning; Goldstein, Joel; Grimes, Mark; Heath, Greg P; Heath, Helen F; Jacob, Jeson; Kreczko, Lukasz; Lucas, Chris; Meng, Zhaoxia; Newbold, Dave M; Paramesvaran, Sudarshan; Poll, Anthony; Sakuma, Tai; Seif El Nasr-storey, Sarah; Senkin, Sergey; Smith, Dominic; Smith, Vincent J; Bell, Ken W; Belyaev, Alexander; Brew, Christopher; Brown, Robert M; Calligaris, Luigi; Cieri, Davide; Cockerill, David JA; Coughlan, John A; Harder, Kristian; Harper, Sam; Olaiya, Emmanuel; Petyt, David; Shepherd-Themistocleous, Claire; Thea, Alessandro; Tomalin, Ian R; Williams, Thomas; Womersley, William John; Worm, Steven; Baber, Mark; Bainbridge, Robert; Buchmuller, Oliver; Bundock, Aaron; Burton, Darren; Casasso, Stefano; Citron, Matthew; Colling, David; Corpe, Louie; Cripps, Nicholas; Dauncey, Paul; Davies, Gavin; De Wit, Adinda; Della Negra, Michel; Dunne, Patrick; Elwood, Adam; Ferguson, William; Fulcher, Jonathan; Futyan, David; Hall, Geoffrey; Iles, Gregory; Kenzie, Matthew; Lane, Rebecca; Lucas, Robyn; Lyons, Louis; Magnan, Anne-Marie; Malik, Sarah; Nash, Jordan; Nikitenko, Alexander; Pela, Joao; Pesaresi, Mark; Petridis, Konstantinos; Raymond, David Mark; Richards, Alexander; Rose, Andrew; Seez, Christopher; Tapper, Alexander; Uchida, Kirika; Vazquez Acosta, Monica; Virdee, Tejinder; Zenz, Seth Conrad; Cole, Joanne; Hobson, Peter R; Khan, Akram; Kyberd, Paul; Leggat, Duncan; Leslie, Dawn; Reid, Ivan; Symonds, Philip; Teodorescu, Liliana; Turner, Mark; Borzou, Ahmad; Call, Kenneth; Dittmann, Jay; Hatakeyama, Kenichi; Liu, Hongxuan; Pastika, Nathaniel; Charaf, Otman; Cooper, Seth; Henderson, Conor; Rumerio, Paolo; Arcaro, Daniel; Avetisyan, Aram; Bose, Tulika; Fantasia, Cory; Gastler, Daniel; Lawson, Philip; Rankin, Dylan; Richardson, Clint; Rohlf, James; St John, Jason; Sulak, Lawrence; Zou, David; Alimena, Juliette; Berry, Edmund; Bhattacharya, Saptaparna; Cutts, David; Dhingra, Nitish; Ferapontov, Alexey; Garabedian, Alex; Hakala, John; Heintz, Ulrich; Laird, Edward; Landsberg, Greg; Mao, Zaixing; Narain, Meenakshi; Piperov, Stefan; Sagir, Sinan; Syarif, Rizki; Breedon, Richard; Breto, Guillermo; Calderon De La Barca Sanchez, Manuel; Chauhan, Sushil; Chertok, Maxwell; Conway, John; Conway, Rylan; Cox, Peter Timothy; Erbacher, Robin; Gardner, Michael; Ko, Winston; Lander, Richard; Mulhearn, Michael; Pellett, Dave; Pilot, Justin; Ricci-Tam, Francesca; Shalhout, Shalhout; Smith, John; Squires, Michael; Stolp, Dustin; Tripathi, Mani; Wilbur, Scott; Yohay, Rachel; Cousins, Robert; Everaerts, Pieter; Farrell, Chris; Hauser, Jay; Ignatenko, Mikhail; Saltzberg, David; Takasugi, Eric; Valuev, Vyacheslav; Weber, Matthias; Burt, Kira; Clare, Robert; Ellison, John Anthony; Gary, J William; Hanson, Gail; Heilman, Jesse; Paneva, Mirena Ivova; Jandir, Pawandeep; Kennedy, Elizabeth; Lacroix, Florent; Long, Owen Rosser; Luthra, Arun; Malberti, Martina; Olmedo Negrete, Manuel; Shrinivas, Amithabh; Wei, Hua; Wimpenny, Stephen; Yates, Brent; Branson, James G; Cerati, Giuseppe Benedetto; Cittolin, Sergio; D'Agnolo, Raffaele Tito; Derdzinski, Mark; Holzner, André; Kelley, Ryan; Klein, Daniel; Letts, James; Macneill, Ian; Olivito, Dominick; Padhi, Sanjay; Pieri, Marco; Sani, Matteo; Sharma, Vivek; Simon, Sean; Tadel, Matevz; Vartak, Adish; Wasserbaech, Steven; Welke, Charles; Würthwein, Frank; Yagil, Avraham; Zevi Della Porta, Giovanni; Bradmiller-Feld, John; Campagnari, Claudio; Dishaw, Adam; Dutta, Valentina; Flowers, Kristen; Franco Sevilla, Manuel; Geffert, Paul; George, Christopher; Golf, Frank; Gouskos, Loukas; Gran, Jason; Incandela, Joe; Mccoll, Nickolas; Mullin, Sam Daniel; Richman, Jeffrey; Stuart, David; Suarez, Indara; West, Christopher; Yoo, Jaehyeok; Anderson, Dustin; Apresyan, Artur; Bornheim, Adolf; Bunn, Julian; Chen, Yi; Duarte, Javier; Mott, Alexander; Newman, Harvey B; Pena, Cristian; Pierini, Maurizio; Spiropulu, Maria; Vlimant, Jean-Roch; Xie, Si; Zhu, Ren-Yuan; Andrews, Michael Benjamin; Azzolini, Virginia; Calamba, Aristotle; Carlson, Benjamin; Ferguson, Thomas; Paulini, Manfred; Russ, James; Sun, Menglei; Vogel, Helmut; Vorobiev, Igor; Cumalat, John Perry; Ford, William T; Gaz, Alessandro; Jensen, Frank; Johnson, Andrew; Krohn, Michael; Mulholland, Troy; Nauenberg, Uriel; Stenson, Kevin; Wagner, Stephen Robert; Alexander, James; Chatterjee, Avishek; Chaves, Jorge; Chu, Jennifer; Dittmer, Susan; Eggert, Nicholas; Mirman, Nathan; Nicolas Kaufman, Gala; Patterson, Juliet Ritchie; Rinkevicius, Aurelijus; Ryd, Anders; Skinnari, Louise; Soffi, Livia; Sun, Werner; Tan, Shao Min; Teo, Wee Don; Thom, Julia; Thompson, Joshua; Tucker, Jordan; Weng, Yao; Wittich, Peter; Abdullin, Salavat; Albrow, Michael; Anderson, Jacob; Apollinari, Giorgio; Banerjee, Sunanda; Bauerdick, Lothar AT; Beretvas, Andrew; Berryhill, Jeffrey; Bhat, Pushpalatha C; Bolla, Gino; Burkett, Kevin; Butler, Joel Nathan; Cheung, Harry; Chlebana, Frank; Cihangir, Selcuk; Elvira, Victor Daniel; Fisk, Ian; Freeman, Jim; Gottschalk, Erik; Gray, Lindsey; Green, Dan; Grünendahl, Stefan; Gutsche, Oliver; Hanlon, Jim; Hare, Daryl; Harris, Robert M; Hasegawa, Satoshi; Hirschauer, James; Hu, Zhen; Jayatilaka, Bodhitha; Jindariani, Sergo; Johnson, Marvin; Joshi, Umesh; Jung, Andreas Werner; Klima, Boaz; Kreis, Benjamin; Kwan, Simon; Lammel, Stephan; Linacre, Jacob; Lincoln, Don; Lipton, Ron; Liu, Tiehui; Lopes De Sá, Rafael; Lykken, Joseph; Maeshima, Kaori; Marraffino, John Michael; Martinez Outschoorn, Verena Ingrid; Maruyama, Sho; Mason, David; McBride, Patricia; Merkel, Petra; Mishra, Kalanand; Mrenna, Stephen; Nahn, Steve; Newman-Holmes, Catherine; O'Dell, Vivian; Pedro, Kevin; Prokofyev, Oleg; Rakness, Gregory; Sexton-Kennedy, Elizabeth; Soha, Aron; Spalding, William J; Spiegel, Leonard; Taylor, Lucas; Tkaczyk, Slawek; Tran, Nhan Viet; Uplegger, Lorenzo; Vaandering, Eric Wayne; Vernieri, Caterina; Verzocchi, Marco; Vidal, Richard; Weber, Hannsjoerg Artur; Whitbeck, Andrew; Yang, Fan; Acosta, Darin; Avery, Paul; Bortignon, Pierluigi; Bourilkov, Dimitri; Carnes, Andrew; Carver, Matthew; Curry, David; Das, Souvik; Di Giovanni, Gian Piero; Field, Richard D; Furic, Ivan-Kresimir; Gleyzer, Sergei V; Hugon, Justin; Konigsberg, Jacobo; Korytov, Andrey; Low, Jia Fu; Ma, Peisen; Matchev, Konstantin; Mei, Hualin; Milenovic, Predrag; Mitselmakher, Guenakh; Rank, Douglas; Rossin, Roberto; Shchutska, Lesya; Snowball, Matthew; Sperka, David; Terentyev, Nikolay; Thomas, Laurent; Wang, Jian; Wang, Sean-Jiun; Yelton, John; Hewamanage, Samantha; Linn, Stephan; Markowitz, Pete; Martinez, German; Rodriguez, Jorge Luis; Ackert, Andrew; Adams, Jordon Rowe; Adams, Todd; Askew, Andrew; Bochenek, Joseph; Diamond, Brendan; Haas, Jeff; Hagopian, Sharon; Hagopian, Vasken; Johnson, Kurtis F; Khatiwada, Ajeeta; Prosper, Harrison; Weinberg, Marc; Baarmand, Marc M; Bhopatkar, Vallary; Colafranceschi, Stefano; Hohlmann, Marcus; Kalakhety, Himali; Noonan, Daniel; Roy, Titas; Yumiceva, Francisco; Adams, Mark Raymond; Apanasevich, Leonard; Berry, Douglas; Betts, Russell Richard; Bucinskaite, Inga; Cavanaugh, Richard; Evdokimov, Olga; Gauthier, Lucie; Gerber, Cecilia Elena; Hofman, David Jonathan; Kurt, Pelin; O'Brien, Christine; Sandoval Gonzalez, Irving Daniel; Silkworth, Christopher; Turner, Paul; Varelas, Nikos; Wu, Zhenbin; Zakaria, Mohammed; Bilki, Burak; Clarida, Warren; Dilsiz, Kamuran; Durgut, Süleyman; Gandrajula, Reddy Pratap; Haytmyradov, Maksat; Khristenko, Viktor; Merlo, Jean-Pierre; Mermerkaya, Hamit; Mestvirishvili, Alexi; Moeller, Anthony; Nachtman, Jane; Ogul, Hasan; Onel, Yasar; Ozok, Ferhat; Penzo, Aldo; Snyder, Christina; Tiras, Emrah; Wetzel, James; Yi, Kai; Anderson, Ian; Barnett, Bruce Arnold; Blumenfeld, Barry; Eminizer, Nicholas; Fehling, David; Feng, Lei; Gritsan, Andrei; Maksimovic, Petar; Martin, Christopher; Osherson, Marc; Roskes, Jeffrey; Cocoros, Alice; Sarica, Ulascan; Swartz, Morris; Xiao, Meng; Xin, Yongjie; You, Can; Baringer, Philip; Bean, Alice; Benelli, Gabriele; Bruner, Christopher; Kenny III, Raymond Patrick; Majumder, Devdatta; Malek, Magdalena; Murray, Michael; Sanders, Stephen; Stringer, Robert; Wang, Quan; Ivanov, Andrew; Kaadze, Ketino; Khalil, Sadia; Makouski, Mikhail; Maravin, Yurii; Mohammadi, Abdollah; Saini, Lovedeep Kaur; Skhirtladze, Nikoloz; Toda, Sachiko; Lange, David; Rebassoo, Finn; Wright, Douglas; Anelli, Christopher; Baden, Drew; Baron, Owen; Belloni, Alberto; Calvert, Brian; Eno, Sarah Catherine; Ferraioli, Charles; Gomez, Jaime; Hadley, Nicholas John; Jabeen, Shabnam; Kellogg, Richard G; Kolberg, Ted; Kunkle, Joshua; Lu, Ying; Mignerey, Alice; Shin, Young Ho; Skuja, Andris; Tonjes, Marguerite; Tonwar, Suresh C; Apyan, Aram; Barbieri, Richard; Baty, Austin; Bierwagen, Katharina; Brandt, Stephanie; Busza, Wit; Cali, Ivan Amos; Demiragli, Zeynep; Di Matteo, Leonardo; Gomez Ceballos, Guillelmo; Goncharov, Maxim; Gulhan, Doga; Iiyama, Yutaro; Innocenti, Gian Michele; Klute, Markus; Kovalskyi, Dmytro; Lai, Yue Shi; Lee, Yen-Jie; Levin, Andrew; Luckey, Paul David; Marini, Andrea Carlo; Mcginn, Christopher; Mironov, Camelia; Narayanan, Siddharth; Niu, Xinmei; Paus, Christoph; Ralph, Duncan; Roland, Christof; Roland, Gunther; Salfeld-Nebgen, Jakob; Stephans, George; Sumorok, Konstanty; Varma, Mukund; Velicanu, Dragos; Veverka, Jan; Wang, Jing; Wang, Ta-Wei; Wyslouch, Bolek; Yang, Mingming; Zhukova, Victoria; Dahmes, Bryan; Evans, Andrew; Finkel, Alexey; Gude, Alexander; Hansen, Peter; Kalafut, Sean; Kao, Shih-Chuan; Klapoetke, Kevin; Kubota, Yuichi; Lesko, Zachary; Mans, Jeremy; Nourbakhsh, Shervin; Ruckstuhl, Nicole; Rusack, Roger; Tambe, Norbert; Turkewitz, Jared; Acosta, John Gabriel; Oliveros, Sandra; Avdeeva, Ekaterina; Bloom, Kenneth; Bose, Suvadeep; Claes, Daniel R; Dominguez, Aaron; Fangmeier, Caleb; Gonzalez Suarez, Rebeca; Kamalieddin, Rami; Keller, Jason; Knowlton, Dan; Kravchenko, Ilya; Meier, Frank; Monroy, Jose; Ratnikov, Fedor; Siado, Joaquin Emilo; Snow, Gregory R; Alyari, Maral; Dolen, James; George, Jimin; Godshalk, Andrew; Harrington, Charles; Iashvili, Ia; Kaisen, Josh; Kharchilava, Avto; Kumar, Ashish; Rappoccio, Salvatore; Roozbahani, Bahareh; Alverson, George; Barberis, Emanuela; Baumgartel, Darin; Chasco, Matthew; Hortiangtham, Apichart; Massironi, Andrea; Morse, David Michael; Nash, David; Orimoto, Toyoko; Teixeira De Lima, Rafael; Trocino, Daniele; Wang, Ren-Jie; Wood, Darien; Zhang, Jinzhong; Hahn, Kristan Allan; Kubik, Andrew; Mucia, Nicholas; Odell, Nathaniel; Pollack, Brian; Pozdnyakov, Andrey; Schmitt, Michael Henry; Stoynev, Stoyan; Sung, Kevin; Trovato, Marco; Velasco, Mayda; Brinkerhoff, Andrew; Dev, Nabarun; Hildreth, Michael; Jessop, Colin; Karmgard, Daniel John; Kellams, Nathan; Lannon, Kevin; Lynch, Sean; Marinelli, Nancy; Meng, Fanbo; Mueller, Charles; Musienko, Yuri; Pearson, Tessa; Planer, Michael; Reinsvold, Allison; Ruchti, Randy; Smith, Geoffrey; Taroni, Silvia; Valls, Nil; Wayne, Mitchell; Wolf, Matthias; Woodard, Anna; Antonelli, Louis; Brinson, Jessica; Bylsma, Ben; Durkin, Lloyd Stanley; Flowers, Sean; Hart, Andrew; Hill, Christopher; Hughes, Richard; Ji, Weifeng; Kotov, Khristian; Ling, Ta-Yung; Liu, Bingxuan; Luo, Wuming; Puigh, Darren; Rodenburg, Marissa; Winer, Brian L; Wulsin, Howard Wells; Driga, Olga; Elmer, Peter; Hardenbrook, Joshua; Hebda, Philip; Koay, Sue Ann; Lujan, Paul; Marlow, Daniel; Medvedeva, Tatiana; Mooney, Michael; Olsen, James; Palmer, Christopher; Piroué, Pierre; Saka, Halil; Stickland, David; Tully, Christopher; Zuranski, Andrzej; Malik, Sudhir; Barnes, Virgil E; Benedetti, Daniele; Bortoletto, Daniela; Gutay, Laszlo; Jha, Manoj; Jones, Matthew; Jung, Kurt; Miller, David Harry; Neumeister, Norbert; Radburn-Smith, Benjamin Charles; Shi, Xin; Shipsey, Ian; Silvers, David; Sun, Jian; Svyatkovskiy, Alexey; Wang, Fuqiang; Xie, Wei; Xu, Lingshan; Parashar, Neeti; Stupak, John; Adair, Antony; Akgun, Bora; Chen, Zhenyu; Ecklund, Karl Matthew; Geurts, Frank JM; Guilbaud, Maxime; Li, Wei; Michlin, Benjamin; Northup, Michael; Padley, Brian Paul; Redjimi, Radia; Roberts, Jay; Rorie, Jamal; Tu, Zhoudunming; Zabel, James; Betchart, Burton; Bodek, Arie; de Barbaro, Pawel; Demina, Regina; Eshaq, Yossof; Ferbel, Thomas; Galanti, Mario; Garcia-Bellido, Aran; Han, Jiyeon; Harel, Amnon; Hindrichs, Otto; Khukhunaishvili, Aleko; Petrillo, Gianluca; Tan, Ping; Verzetti, Mauro; Arora, Sanjay; Barker, Anthony; Chou, John Paul; Contreras-Campana, Christian; Contreras-Campana, Emmanuel; Duggan, Daniel; Ferencek, Dinko; Gershtein, Yuri; Gray, Richard; Halkiadakis, Eva; Hidas, Dean; Hughes, Elliot; Kaplan, Steven; Kunnawalkam Elayavalli, Raghav; Lath, Amitabh; Nash, Kevin; Panwalkar, Shruti; Park, Michael; Salur, Sevil; Schnetzer, Steve; Sheffield, David; Somalwar, Sunil; Stone, Robert; Thomas, Scott; Thomassen, Peter; Walker, Matthew; Foerster, Mark; Riley, Grant; Rose, Keith; Spanier, Stefan; York, Andrew; Bouhali, Othmane; Castaneda Hernandez, Alfredo; Dalchenko, Mykhailo; De Mattia, Marco; Delgado, Andrea; Dildick, Sven; Eusebi, Ricardo; Gilmore, Jason; Kamon, Teruki; Krutelyov, Vyacheslav; Mueller, Ryan; Osipenkov, Ilya; Pakhotin, Yuriy; Patel, Rishi; Perloff, Alexx; Rose, Anthony; Safonov, Alexei; Tatarinov, Aysen; Ulmer, Keith; Akchurin, Nural; Cowden, Christopher; Damgov, Jordan; Dragoiu, Cosmin; Dudero, Phillip Russell; Faulkner, James; Kunori, Shuichi; Lamichhane, Kamal; Lee, Sung Won; Libeiro, Terence; Undleeb, Sonaina; Volobouev, Igor; Appelt, Eric; Delannoy, Andrés G; Greene, Senta; Gurrola, Alfredo; Janjam, Ravi; Johns, Willard; Maguire, Charles; Mao, Yaxian; Melo, Andrew; Ni, Hong; Sheldon, Paul; Snook, Benjamin; Tuo, Shengquan; Velkovska, Julia; Xu, Qiao; Arenton, Michael Wayne; Cox, Bradley; Francis, Brian; Goodell, Joseph; Hirosky, Robert; Ledovskoy, Alexander; Li, Hengne; Lin, Chuanzhe; Neu, Christopher; Sinthuprasith, Tutanon; Sun, Xin; Wang, Yanchu; Wolfe, Evan; Wood, John; Xia, Fan; Clarke, Christopher; Harr, Robert; Karchin, Paul Edmund; Kottachchi Kankanamge Don, Chamath; Lamichhane, Pramod; Sturdy, Jared; Belknap, Donald; Carlsmith, Duncan; Cepeda, Maria; Dasu, Sridhara; Dodd, Laura; Duric, Senka; Gomber, Bhawna; Grothe, Monika; Hall-Wilton, Richard; Herndon, Matthew; Hervé, Alain; Klabbers, Pamela; Lanaro, Armando; Levine, Aaron; Long, Kenneth; Loveless, Richard; Mohapatra, Ajit; Ojalvo, Isabel; Perry, Thomas; Pierro, Giuseppe Antonio; Polese, Giovanni; Ruggles, Tyler; Sarangi, Tapas; Savin, Alexander; Sharma, Archana; Smith, Nicholas; Smith, Wesley H; Taylor, Devin; Woods, Nathaniel

    2017-01-01

    This paper describes the CMS trigger system and its performance during Run 1 of the LHC. The trigger system consists of two levels designed to select events of potential physics interest from a GHz (MHz) interaction rate of proton-proton (heavy ion) collisions. The first level of the trigger is implemented in hardware, and selects events containing detector signals consistent with an electron, photon, muon, $\\tau$ lepton, jet, or missing transverse energy. A programmable menu of up to 128 object-based algorithms is used to select events for subsequent processing. The trigger thresholds are adjusted to the LHC instantaneous luminosity during data taking in order to restrict the output rate to 100 kHz, the upper limit imposed by the CMS readout electronics. The second level, implemented in software, further refines the purity of the output stream, selecting an average rate of 400 Hz for offline event storage. The objectives, strategy and performance of the trigger system during the LHC Run 1 are described.

  15. Cygnus Trigger System

    Energy Technology Data Exchange (ETDEWEB)

    G. Corrow, M. Hansen, D. Henderson, C. Mitton

    2008-02-01

    The Cygnus Dual Beam Radiographic Facility consists of two radiographic sources (Cygnus 1, Cygnus 2) each with a dose rating of 4 rads at 1 m, and a 1-mm diameter spot size. The electrical specifications are: 2.25 MV, 60 kA, 60 ns. This facility is located in an underground environment at the Nevada Test Site (NTS). These sources were developed as a primary diagnostic for subcritical tests, which are single-shot, high-value events. In such an application there is an emphasis on reliability and reproducibility. A robust, low-jitter trigger system is a key element for meeting these goals. The trigger system was developed with both commercial and project-specific equipment. In addition to the traditional functions of a trigger system there are novel features added to protect the investment of a high-value shot. Details of the trigger system, including elements designed specifically for a subcritical test application, will be presented. The individual electronic components have their nominal throughput, and when assembled have a system throughput with a measured range of jitter. The shot-to-shot jitter will be assessed both individually and in combination. Trigger reliability and reproducibility results will be presented for a substantial number of shots executed at the NTS.

  16. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2014-01-01

    Physics processes involving tau leptons play a crucial role in understanding particle physics at the high energy frontier. The ability to efficiently trigger on events containing hadronic tau decays is therefore of particular importance to the ATLAS experiment. During the 2012 run, the Large Hadronic Collder (LHC) reached instantaneous luminosities of nearly $10^{34} cm^{-2}s^{-1}$ with bunch crossings occurring every $50 ns$. This resulted in a huge event rate and a high probability of overlapping interactions per bunch crossing (pile-up). With this in mind it was necessary to design an ATLAS tau trigger system that could reduce the event rate to a manageable level, while efficiently extracting the most interesting physics events in a pile-up robust manner. In this poster the ATLAS tau trigger is described, its performance during 2012 is presented, and the outlook for the LHC Run II is briefly summarized.

  17. Microfabricated triggered vacuum switch

    Science.gov (United States)

    Roesler, Alexander W.; Schare, Joshua M.; Bunch, Kyle

    2010-05-11

    A microfabricated vacuum switch is disclosed which includes a substrate upon which an anode, cathode and trigger electrode are located. A cover is sealed over the substrate under vacuum to complete the vacuum switch. In some embodiments of the present invention, a metal cover can be used in place of the trigger electrode on the substrate. Materials used for the vacuum switch are compatible with high vacuum, relatively high temperature processing. These materials include molybdenum, niobium, copper, tungsten, aluminum and alloys thereof for the anode and cathode. Carbon in the form of graphitic carbon, a diamond-like material, or carbon nanotubes can be used in the trigger electrode. Channels can be optionally formed in the substrate to mitigate against surface breakdown.

  18. Embedded Fragments Registry (EFR)

    Data.gov (United States)

    Department of Veterans Affairs — In 2009, the Department of Defense estimated that approximately 40,000 service members who served in OEF/OIF may have embedded fragment wounds as the result of small...

  19. Fragmentation in Biaxial Tension

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, G H; Archbold, G C; Hurricane, O A; Miller, P L

    2006-06-13

    We have carried out an experiment that places a ductile stainless steel in a state of biaxial tension at a high rate of strain. The loading of the ductile metal spherical cap is performed by the detonation of a high explosive layer with a conforming geometry to expand the metal radially outwards. Simulations of the loading and expansion of the metal predict strain rates that compare well with experimental observations. A high percentage of the HE loaded material was recovered through a soft capture process and characterization of the recovered fragments provided high quality data, including uniform strain prior to failure and fragment size. These data were used with a modified fragmentation model to determine a fragmentation energy.

  20. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  1. Fragmentation Main Model

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The fragmentation model combines patch size and patch continuity with diversity of vegetation types per patch and rarity of vegetation types per patch. A patch was...

  2. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  3. ALICE High Level Trigger

    CERN Multimedia

    Alt, T

    2013-01-01

    The ALICE High Level Trigger (HLT) is a computing farm designed and build for the real-time, online processing of the raw data produced by the ALICE detectors. Events are fully reconstructed from the raw data, analyzed and compressed. The analysis summary together with the compressed data and a trigger decision is sent to the DAQ. In addition the reconstruction of the events allows for on-line monitoring of physical observables and this information is provided to the Data Quality Monitor (DQM). The HLT can process event rates of up to 2 kHz for proton-proton and 200 Hz for Pb-Pb central collisions.

  4. Fragment Merger: An Online Tool to Merge Overlapping Long Sequence Fragments

    Directory of Open Access Journals (Sweden)

    Anna Kramvis

    2013-03-01

    Full Text Available While PCR amplicons extend to a few thousand bases, the length of sequences from direct Sanger sequencing is limited to 500–800 nucleotides. Therefore, several fragments may be required to cover an amplicon, a gene or an entire genome. These fragments are typically sequenced in an overlapping fashion and assembled by manually sliding and aligning the sequences visually. This is time-consuming, repetitive and error-prone, and further complicated by circular genomes. An online tool merging two to twelve long overlapping sequence fragments was developed. Either chromatograms or FASTA files are submitted to the tool, which trims poor quality ends of chromatograms according to user-specified parameters. Fragments are assembled into a single sequence by repeatedly calling the EMBOSS merger tool in a consecutive manner. Output includes the number of trimmed nucleotides, details of each merge, and an optional alignment to a reference sequence. The final merge sequence is displayed and can be downloaded in FASTA format. All output files can be downloaded as a ZIP archive. This tool allows for easy and automated assembly of overlapping sequences and is aimed at researchers without specialist computer skills. The tool is genome- and organism-agnostic and has been developed using hepatitis B virus sequence data.

  5. Disambiguating Syntactic Triggers

    Science.gov (United States)

    Sakas, William Gregory; Fodor, Janet Dean

    2012-01-01

    We present data from an artificial language domain that suggest new contributions to the theory of syntactic triggers. Whether a learning algorithm is capable of matching the achievements of child learners depends in part on how much parametric ambiguity there is in the input. For practical reasons this cannot be established for the domain of all…

  6. Dealing with Asthma Triggers

    Science.gov (United States)

    ... irritants include perfumes and aerosol (say: AIR-uh-sol) sprays, such as hair spray and cleaners. Other irritants include wood and tobacco smoke, the smell given off by paint or gas, and air pollution. If you notice that an irritant triggers your ...

  7. The ALFA Trigger Simulator

    CERN Document Server

    Dziedzic B

    2015-01-01

    The paper presents basic information about ALFA detectors used in the ATLAS experiment, and the structure of currently developed device used to test a new ALFA trigger interface. It discusses the block diagram of the device, principle of its operation, implementation details and future plans for developing the Simulator.

  8. Short read DNA fragment anchoring algorithm.

    Science.gov (United States)

    Wang, Wendi; Zhang, Peiheng; Liu, Xinchun

    2009-01-30

    The emerging next-generation sequencing method based on PCR technology boosts genome sequencing speed considerably, the expense is also get decreased. It has been utilized to address a broad range of bioinformatics problems. Limited by reliable output sequence length of next-generation sequencing technologies, we are confined to study gene fragments with 30 - 50 bps in general and it is relatively shorter than traditional gene fragment length. Anchoring gene fragments in long reference sequence is an essential and prerequisite step for further assembly and analysis works. Due to the sheer number of fragments produced by next-generation sequencing technologies and the huge size of reference sequences, anchoring would rapidly becoming a computational bottleneck. We compared algorithm efficiency on BLAT, SOAP and EMBF. The efficiency is defined as the count of total output results divided by time consumed to retrieve them. The data show that our algorithm EMBF have 3 - 4 times efficiency advantage over SOAP, and at least 150 times over BLAT. Moreover, when the reference sequence size is increased, the efficiency of SOAP will get degraded as far as 30%, while EMBF have preferable increasing tendency. In conclusion, we deem that EMBF is more suitable for short fragment anchoring problem where result completeness and accuracy is predominant and the reference sequences are relatively large.

  9. Detecting Cortex Fragments During Bacterial Spore Germination.

    Science.gov (United States)

    Francis, Michael B; Sorg, Joseph A

    2016-06-25

    The process of endospore germination in Clostridium difficile, and other Clostridia, increasingly is being found to differ from the model spore-forming bacterium, Bacillus subtilis. Germination is triggered by small molecule germinants and occurs without the need for macromolecular synthesis. Though differences exist between the mechanisms of spore germination in species of Bacillus and Clostridium, a common requirement is the hydrolysis of the peptidoglycan-like cortex which allows the spore core to swell and rehydrate. After rehydration, metabolism can begin and this, eventually, leads to outgrowth of a vegetative cell. The detection of hydrolyzed cortex fragments during spore germination can be difficult and the modifications to the previously described assays can be confusing or difficult to reproduce. Thus, based on our recent report using this assay, we detail a step-by-step protocol for the colorimetric detection of cortex fragments during bacterial spore germination.

  10. Oscillating Filaments. I. Oscillation and Geometrical Fragmentation

    Science.gov (United States)

    Gritschneder, Matthias; Heigl, Stefan; Burkert, Andreas

    2017-01-01

    We study the stability of filaments in equilibrium between gravity and internal as well as external pressure using the grid-based AMR code RAMSES. A homogeneous, straight cylinder below a critical line mass is marginally stable. However, if the cylinder is bent, such as with a slight sinusoidal perturbation, an otherwise stable configuration starts to oscillate, is triggered into fragmentation, and collapses. This previously unstudied behavior allows a filament to fragment at any given scale, as long as it has slight bends. We call this process “geometrical fragmentation.” In our realization, the spacing between the cores matches the wavelength of the sinusoidal perturbation, whereas up to now, filaments were thought to be only fragmenting on the characteristic scale set by the mass-to-line ratio. Using first principles, we derive the oscillation period as well as the collapse timescale analytically. To enable a direct comparison with observations, we study the line-of-sight velocity for different inclinations. We show that the overall oscillation pattern can hide the infall signature of cores.

  11. Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (Indica) and Nipponbare (Japonica)

    Institute of Scientific and Technical Information of China (English)

    CAI Xingxing; LIU Jing; QIU Yinqiu; ZHAO Wei; SONG Zhiping; LU Baorong

    2007-01-01

    DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers.To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species,we studied 49 Indica,43 Japonica,and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs.Results indicated that of the 45 InDel primer pairs,41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%.The scatter plotting data of the principal component analysis (PCA) indicated that:(i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties,in addition to revealing their genetic differentiation;(ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties;and (iii)the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types.It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying lndica and Japonica rice varieties,and for studying genetic relationships of wild rice species,particularly in terms of the Indica-Japonica differentiation.

  12. Fluctuations of fragment observables

    CERN Document Server

    Gulminelli, F

    2006-01-01

    This contribution presents a review of our present theoretical as well as experimental knowledge of different fluctuation observables relevant to nuclear multifragmentation. The possible connection between the presence of a fluctuation peak and the occurrence of a phase transition or a critical phenomenon is critically analyzed. Many different phenomena can lead both to the creation and to the suppression of a fluctuation peak. In particular, the role of constraints due to conservation laws and to data sorting is shown to be essential. From the experimental point of view, a comparison of the available fragmentation data reveals that there is a good agreement between different data sets of basic fluctuation observables, if the fragmenting source is of comparable size. This compatibility suggests that the fragmentation process is largely independent of the reaction mechanism (central versus peripheral collisions, symmetric versus asymmetric systems, light ions versus heavy ion induced reactions). Configurationa...

  13. Triggering of dendritic cell apoptosis by xanthohumol.

    Science.gov (United States)

    Xuan, Nguyen Thi; Shumilina, Ekaterina; Gulbins, Erich; Gu, Shuchen; Götz, Friedrich; Lang, Florian

    2010-07-01

    Xanthohumol, a flavonoid from beer with anticancer activity is known to trigger apoptosis in a variety of tumor cells. Xanthohumol further has anti-inflammatory activity. However, little is known about the effect of xanthohumol on survival and function of immune cells. The present study thus addressed the effect of xanthohumol on dendritic cells (DCs), key players in the regulation of innate and adaptive immunity. To this end, mouse bone marrow-derived DCs were treated with xanthohumol with subsequent assessment of enzymatic activity of acid sphingomyelinase (Asm), ceramide formation determined with anti-ceramide antibodies in FACS and immunohistochemical analysis, caspase activity utilizing FITC conjugated anti-active caspase 8 or caspase 3 antibodies in FACS and by Western blotting, DNA fragmentation by determining the percentage of cells in the sub-G1 phase and cell membrane scrambling by annexin V binding in FACS analysis. As a result, xanthohumol stimulated Asm, enhanced ceramide formation, activated caspases 8 and 3, triggered DNA fragmentation and led to cell membrane scrambling, all effects virtually absent in DCs from gene targeted mice lacking functional Asm or in wild-type cells treated with sphingomyelinase inhibitor amitriptyline. In conclusion, xanthohumol stimulated Asm leading to caspase activation and apoptosis of bone marrow-derived DCs.

  14. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.

    Science.gov (United States)

    Huang, Chao-Li; Pu, Pei-Hua; Huang, Hao-Jen; Sung, Huang-Mo; Liaw, Hung-Jiun; Chen, Yi-Min; Chen, Chien-Ming; Huang, Ming-Ban; Osada, Naoki; Gojobori, Takashi; Pai, Tun-Wen; Chen, Yu-Tin; Hwang, Chi-Chuan; Chiang, Tzen-Yuh

    2015-03-15

    Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification.

  15. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

    KAUST Repository

    Huang, Chao-Li

    2015-03-15

    Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Results: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Conclusion: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification. © Huang et al.

  16. Fragments of Time

    DEFF Research Database (Denmark)

    Christiansen, Steen Ledet

    Time travel films necessarily fragment linear narratives, as scenes are revisited with differences from the first time we saw it. Popular films such as Back to the Future mine comedy from these visitations, but there are many different approaches. One extreme is Chris Marker's La Jetée - a film...... made almost completely of still images, recounting the end of the world. These stills can be viewed as fragments that have survived the end of the world and now provide the only access to the events that occured. Shane Carruth's Primer has a different approach to time travel, the narrative diegesis...

  17. The Serendipity of Fragmentation

    DEFF Research Database (Denmark)

    Leixnering, Stephan; Meyer, Renate E.

    , it was the central government’s task to coordinate, steer and control the newly emerged decentralized organizations. This raises questions about the overall design of the public sector at present. Our paper engages with the prevalent public governance phenomenon of fragmentation from a design perspective in order...... form of organizing between networks and formal organization: lacking a single center and featuring multiplex and multifaceted relations within the politico-administrative apparatus and between government and PSOs, high fragmentation, local and robust action, but latent structures of significant formal...

  18. IMPACT fragmentation model developments

    Science.gov (United States)

    Sorge, Marlon E.; Mains, Deanna L.

    2016-09-01

    The IMPACT fragmentation model has been used by The Aerospace Corporation for more than 25 years to analyze orbital altitude explosions and hypervelocity collisions. The model is semi-empirical, combining mass, energy and momentum conservation laws with empirically derived relationships for fragment characteristics such as number, mass, area-to-mass ratio, and spreading velocity as well as event energy distribution. Model results are used for several types of analysis including assessment of short-term risks to satellites from orbital altitude fragmentations, prediction of the long-term evolution of the orbital debris environment and forensic assessments of breakup events. A new version of IMPACT, version 6, has been completed and incorporates a number of advancements enabled by a multi-year long effort to characterize more than 11,000 debris fragments from more than three dozen historical on-orbit breakup events. These events involved a wide range of causes, energies, and fragmenting objects. Special focus was placed on the explosion model, as the majority of events examined were explosions. Revisions were made to the mass distribution used for explosion events, increasing the number of smaller fragments generated. The algorithm for modeling upper stage large fragment generation was updated. A momentum conserving asymmetric spreading velocity distribution algorithm was implemented to better represent sub-catastrophic events. An approach was developed for modeling sub-catastrophic explosions, those where the majority of the parent object remains intact, based on estimated event energy. Finally, significant modifications were made to the area-to-mass ratio distribution to incorporate the tendencies of different materials to fragment into different shapes. This ability enabled better matches between the observed area-to-mass ratios and those generated by the model. It also opened up additional possibilities for post-event analysis of breakups. The paper will discuss

  19. Optically triggered infrared photodetector.

    Science.gov (United States)

    Ramiro, Íñigo; Martí, Antonio; Antolín, Elisa; López, Esther; Datas, Alejandro; Luque, Antonio; Ripalda, José M; González, Yolanda

    2015-01-14

    We demonstrate a new class of semiconductor device: the optically triggered infrared photodetector (OTIP). This photodetector is based on a new physical principle that allows the detection of infrared light to be switched ON and OFF by means of an external light. Our experimental device, fabricated using InAs/AlGaAs quantum-dot technology, demonstrates normal incidence infrared detection in the 2-6 μm range. The detection is optically triggered by a 590 nm light-emitting diode. Furthermore, the detection gain is achieved in our device without an increase of the noise level. The novel characteristics of OTIPs open up new possibilities for third generation infrared imaging systems ( Rogalski, A.; Antoszewski, J.; Faraone, L. J. Appl. Phys. 2009, 105 (9), 091101).

  20. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2013-01-01

    The tau lepton plays a crucial role in understanding particle physics at the Tera scale. One of the most promising probes of the Higgs boson coupling to fermions is with detector signatures involving taus. In addition, many theories beyond the Standard Model, such as supersymmetry and exotic particles (Wʹ′ and Zʹ′), predict new physics with large couplings to taus. The ability to trigger on hadronic tau decays is therefore critical to achieving the physics goals of the ATLAS experiment. The higher instantaneous luminosities of proton-proton collisions achieved by the Large Hadron Collider (LHC) in 2012 resulted in a larger probability of overlap (pile-up) between bunch crossings, and so it was critical for ATLAS to have an effective tau trigger strategy. The details of this strategy are summarized in this poster, and the latest performance measurements are presented.

  1. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2013-01-01

    The tau lepton plays a crucial role in understanding particle physics at the Tera scale. One of the most promising probes of the Higgs boson coupling to fermions is with detector signatures involving taus. In addition, many theories beyond the Standard Model, such as supersymmetry and exotic particles (Wʹ and Zʹ), predict new physics with large couplings to taus. The ability to trigger on hadronic tau decays is therefore critical to achieving the physics goals of the ATLAS experiment. The higher instantaneous luminosities of proton-proton collisions achieved by the Large Hadron Collider (LHC) in 2012 resulted in a larger probability of overlap (pile-up) between bunch crossings, and so it was critical for ATLAS to have an effective tau trigger strategy. The details of this strategy are summarized in this paper, and the results of the latest performance measurements are presented.

  2. Neural networks for triggering

    Energy Technology Data Exchange (ETDEWEB)

    Denby, B. (Fermi National Accelerator Lab., Batavia, IL (USA)); Campbell, M. (Michigan Univ., Ann Arbor, MI (USA)); Bedeschi, F. (Istituto Nazionale di Fisica Nucleare, Pisa (Italy)); Chriss, N.; Bowers, C. (Chicago Univ., IL (USA)); Nesti, F. (Scuola Normale Superiore, Pisa (Italy))

    1990-01-01

    Two types of neural network beauty trigger architectures, based on identification of electrons in jets and recognition of secondary vertices, have been simulated in the environment of the Fermilab CDF experiment. The efficiencies for B's and rejection of background obtained are encouraging. If hardware tests are successful, the electron identification architecture will be tested in the 1991 run of CDF. 10 refs., 5 figs., 1 tab.

  3. The ARGUS vertex trigger

    CERN Document Server

    Koch, N; Kolanoski, H; Siegmund, T; Bergter, J; Eckstein, P; Schubert, Klaus R; Waldi, R; Imhof, M; Ressing, D; Weiss, U; Weseler, S

    1995-01-01

    A fast second level trigger has been developed for the ARGUS experiment which recognizes tracks originating from the interaction region. The processor compares the hits in the ARGUS Micro Vertex Drift Chamber to 245760 masks stored in random access memories. The masks which are fully defined in three dimensions are able to reject tracks originating in the wall of the narrow beampipe of 10.5\\,mm radius.

  4. Unligated Okazaki Fragments Induce PCNA Ubiquitination and a Requirement for Rad59-Dependent Replication Fork Progression.

    Directory of Open Access Journals (Sweden)

    Hai Dang Nguyen

    Full Text Available Deficiency in DNA ligase I, encoded by CDC9 in budding yeast, leads to the accumulation of unligated Okazaki fragments and triggers PCNA ubiquitination at a non-canonical lysine residue. This signal is crucial to activate the S phase checkpoint, which promotes cell cycle delay. We report here that a pol30-K107 mutation alleviated cell cycle delay in cdc9 mutants, consistent with the idea that the modification of PCNA at K107 affects the rate of DNA synthesis at replication forks. To determine whether PCNA ubiquitination occurred in response to nicks or was triggered by the lack of PCNA-DNA ligase interaction, we complemented cdc9 cells with either wild-type DNA ligase I or a mutant form, which fails to interact with PCNA. Both enzymes reversed PCNA ubiquitination, arguing that the modification is likely an integral part of a novel nick-sensory mechanism and not due to non-specific secondary mutations that could have occurred spontaneously in cdc9 mutants. To further understand how cells cope with the accumulation of nicks during DNA replication, we utilized cdc9-1 in a genome-wide synthetic lethality screen, which identified RAD59 as a strong negative interactor. In comparison to cdc9 single mutants, cdc9 rad59Δ double mutants did not alter PCNA ubiquitination but enhanced phosphorylation of the mediator of the replication checkpoint, Mrc1. Since Mrc1 resides at the replication fork and is phosphorylated in response to fork stalling, these results indicate that Rad59 alleviates nick-induced replication fork slowdown. Thus, we propose that Rad59 promotes fork progression when Okazaki fragment processing is compromised and counteracts PCNA-K107 mediated cell cycle arrest.

  5. Isolating Triggered Star Formation

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Elizabeth J.; Arnold, Jacob A.; /UC, Irvine; Zentner, Andrew R.; /KICP, Chicago /Chicago U., EFI; Bullock, James S.; /UC, Irvine; Wechsler, Risa H.; /KIPAC, Menlo

    2007-09-12

    Galaxy pairs provide a potentially powerful means of studying triggered star formation from galaxy interactions. We use a large cosmological N-body simulation coupled with a well-tested semi-analytic substructure model to demonstrate that the majority of galaxies in close pairs reside within cluster or group-size halos and therefore represent a biased population, poorly suited for direct comparison to 'field' galaxies. Thus, the frequent observation that some types of galaxies in pairs have redder colors than 'field' galaxies is primarily a selection effect. We use our simulations to devise a means to select galaxy pairs that are isolated in their dark matter halos with respect to other massive subhalos (N= 2 halos) and to select a control sample of isolated galaxies (N= 1 halos) for comparison. We then apply these selection criteria to a volume-limited subset of the 2dF Galaxy Redshift Survey with M{sub B,j} {le} -19 and obtain the first clean measure of the typical fraction of galaxies affected by triggered star formation and the average elevation in the star formation rate. We find that 24% (30.5 %) of these L* and sub-L* galaxies in isolated 50 (30) h{sup -1} kpc pairs exhibit star formation that is boosted by a factor of {approx}> 5 above their average past value, while only 10% of isolated galaxies in the control sample show this level of enhancement. Thus, 14% (20 %) of the galaxies in these close pairs show clear triggered star formation. Our orbit models suggest that 12% (16%) of 50 (30) h{sup -1} kpc close pairs that are isolated according to our definition have had a close ({le} 30 h{sup -1} kpc) pass within the last Gyr. Thus, the data are broadly consistent with a scenario in which most or all close passes of isolated pairs result in triggered star formation. The isolation criteria we develop provide a means to constrain star formation and feedback prescriptions in hydrodynamic simulations and a very general method of understanding

  6. Fragmented Work Stories

    DEFF Research Database (Denmark)

    Humle, Didde Maria; Reff Pedersen, Anne

    2015-01-01

    by exploring how different types of fragmentation create meanings. This is done by studying the work stories of job and personnel consultants and by drawing on the results of a narrative, ethnographic study of a consultancy. The analysis demonstrates how work stories are social practices negotiated, retold...

  7. Picking Up (On) Fragments

    NARCIS (Netherlands)

    Ellis, Phil

    2015-01-01

    abstractThis article discusses the implications for archival and media archaeological research and reenactment artwork relating to a recent arts practice project: reenacttv: 30 lines / 60 seconds. It proposes that archival material is unstable but has traces and fragments that are full of creative p

  8. Fragments of the Past

    Directory of Open Access Journals (Sweden)

    Peter Szende

    2016-10-01

    Full Text Available With travel being made more accessible throughout the decades, the hospitality industry constantly evolved their practices as society and technology progressed. Hotels looked for news ways up service their customers, which led to the invention of the Servidor in 1918. Once revolutionary innovations have gone extinct, merely becoming fragments of the past.

  9. Cryobiology of coral fragments.

    Science.gov (United States)

    Hagedorn, Mary; Farrell, Ann; Carter, Virginia L

    2013-02-01

    Around the world, coral reefs are dying due to human influences, and saving habitat alone may not stop this destruction. This investigation focused on the biological processes that will provide the first steps in understanding the cryobiology of whole coral fragments. Coral fragments are a partnership of coral tissue and endosymbiotic algae, Symbiodinium sp., commonly called zooxanthellae. These data reflected their separate sensitivities to chilling and a cryoprotectant (dimethyl sulfoxide) for the coral Pocillopora damicornis, as measured by tissue loss and Pulse Amplitude Modulated fluorometry 3weeks post-treatment. Five cryoprotectant treatments maintained the viability of the coral tissue and zooxanthellae at control values (1M dimethyl sulfoxide at 1.0, 1.5 and 2.0h exposures, and 1.5M dimethyl sulfoxide at 1.0 and 1.5h exposures, P>0.05, ANOVA), whereas 2M concentrations did not (Pcoral tissue, but not in the zooxanthellae. During the winter when the fragments were chilled, the coral tissue remained relatively intact (∼25% loss) post-treatment, but the zooxanthellae numbers in the tissue declined after 5min of chilling (Pcoral tissue (∼75% loss) and zooxanthellae numbers declined in response to chilling alone (Pcoral against tissue loss after 45min of cryoprotectant exposure (P>0.05, ANOVA), but it did not protect against the loss of zooxanthellae (Pcoral fragment complex and future cryopreservation protocols must be guided by their greater sensitivity. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Picking Up (On) Fragments

    NARCIS (Netherlands)

    Ellis, Phil

    2015-01-01

    abstractThis article discusses the implications for archival and media archaeological research and reenactment artwork relating to a recent arts practice project: reenacttv: 30 lines / 60 seconds. It proposes that archival material is unstable but has traces and fragments that are full of creative p

  11. Wildlife habitat fragmentation.

    Science.gov (United States)

    John. Lehmkuhl

    2005-01-01

    A primary issue in forest wildlife management is habitat fragmentation and its effects on viability, which is the "bottom line" for plant and animal species of conservation concern. Population viability is the likelihood that a population will be able to maintain itself (remain viable) over a long period of time-usually 100 years or more. Though it is true...

  12. Amplified-fragment length polymorphism fingerprinting of Mycoplasma species

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, N.F.; Jensen, J.S.

    1999-01-01

    Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including......I restriction endonucleases and subsequent ligation of corresponding site-specific adapters. The amplification of AFLP templates with a single set of nonselective primers resulted in reproducible fingerprints of approximately 60 to 80 fragments in the size range of 50 to 500 bp, The method was able...

  13. Carbon Fragmentation Cross Sections for Hadrontherapy and Space Radiation Protection

    Science.gov (United States)

    De Napoli, M.; Agodi, C.; Cirrone, G. A. P.; Cuttone, G.; Nicolosi, D.; Pandola, L.; Raciti, G.; Romano, F.; Sardina, D.; Scuderi, V.; Tropea, S.; Bondì, M.; Cappuzzello, F.; Carbone, D.; Cavallaro, M.

    2014-05-01

    Fragmentation reactions represent a serious complication in hadrontherapy and space radiation protection. In order to predict their effects, both reliable Monte Carlo codes and experimental data are needed. The shortage of precise measurements, especially of double differential cross sections, has triggered many dedicated experiments at relativistic energies. Aiming to explore the Fermi energy regime, as well, where different reaction mechanisms are involved, we measured the 12C fragmentation at 62 AMeV on a 12C and a 197Au target. A high granularity Si-CsI hodoscope allowed to identify the charge and the mass of detected fragments and measure their energy and emission angle. In this work we report the double differential cross sections for the production of different fragments as a function of the emission angle. Experimental results are compared with the GEANT-4 Monte Carlo predictions performed using two reaction models, the Quantum Molecular Dynamic and the Binary Light Ion Cascade.

  14. Triggering filamentation using turbulence

    CERN Document Server

    Eeltink, D; Marchiando, N; Hermelin, S; Gateau, J; Brunetti, M; Wolf, J P; Kasparian, J

    2016-01-01

    We study the triggering of single filaments due to turbulence in the beam path for a laser of power below the filamenting threshold. Turbulence can act as a switch between the beam not filamenting and producing single filaments. This 'positive' effect of turbulence on the filament probability, combined with our observation of off-axis filaments suggests the underlying mechanism is modulation instability caused by transverse perturbations. We hereby experimentally explore the interaction of modulation instability and turbulence, commonly associated with multiple-filaments, in the single-filament regime.

  15. The NA48 trigger supervisor

    CERN Document Server

    Arcidiacono, R; Berotto, F; Bertolino, F; Govi, G; Menichetti, E; Sozzi, M

    2000-01-01

    The NA48 experiment aims to measure direct CP violation in the K/sub L//sup 0/ decays system with an accuracy of 2*10/sup -4/. High performances are required to the trigger and acquisition systems. This paper describes the NA48 Trigger Supervisor, a 40 MHz pipelined hardware system which correlates and processes trigger informations from local trigger sources, searching for interesting patterns. The trigger packet include a timestamp information used by the readout systems to retrieve detector data. The design architecture and functionality during 98 data taking are described. (5 refs).

  16. [Landscape and ecological genomics].

    Science.gov (United States)

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment.

  17. The ATLAS tau trigger

    CERN Document Server

    Tsuno, S; The ATLAS collaboration

    2009-01-01

    The ATLAS tau trigger has three levels: the first one (L1) is hardware based and uses FPGAs, while the second (L2) and third levels (EF -Event Filter-) are software based and use commodity computers (2 x Intel Harpertown quad-core 2.5 GHz), running scientific linux 4. In this contribution we discuss both the physics characteristics of tau leptons and the technical solutions to quick data access and fast algorithms. We show that L1 selects narrow jets in the calorimeter with an overall rejection against QCD jets of 300, whilst L2 and EF (referred together as High Level Trigger -HLT-) use all the detectors with full granularity and apply a typical rejection of 15 within the stringent timing requirements of the LHC. In the HLT there are two complementary approaches: specialized, fast algorithms are used at L2, while more refined and sophisticated algorithms, imported from the offline, are utilized in the EF.

  18. ATLAS Tau Trigger

    CERN Document Server

    Belanger-Champagne, C; Bosman, M; Brenner, R; Casado, MP; Czyczula, Z; Dam, M; Demers, S; Farrington, S; Igonkina, O; Kalinowski, A; Kanaya, N; Osuna, C; Pérez, E; Ptacek, E; Reinsch, A; Saavedra, A; Sopczak, A; Strom, D; Torrence, E; Tsuno, S; Vorwerk, V; Watson, A; Xella, S

    2008-01-01

    Moving to the high energy scale of the LHC, the identification of tau leptons will become a necessary and very powerful tool, allowing a discovery of physics beyond Standard Model. Many models, among them light SM Higgs and various SUSY models, predict an abundant production of taus with respect to other leptons. The reconstruction of hadronic tau decays, although a very challenging task in hadronic enviroments, allows to increase a signal efficiency by at least of factor 2, and provides an independent control sample to disantangle lepton tau decays from prompt electrons and muons. Thanks to the advanced calorimetry and tracking, the ATLAS experiment has developed tools to efficiently identify hadronic taus at the trigger level. In this presentation we will review the characteristics of taus and the methods to suppress low-multiplicity, low-energy jets contributions as well as we will address the tau trigger chain which provide a rejection rate of 10^5. We will further present plans for commissioning the ATLA...

  19. Minimum Bias Trigger in ATLAS

    CERN Document Server

    Kwee, R E; The ATLAS collaboration

    2010-01-01

    Since the restart of the LHC in November 2009, ATLAS has collected inelastic pp-collisions to perform first measurements on charged particle densities. These measurements will help to constrain various models describing phenomenologically soft parton interactions. Understanding the trigger efficiencies for different event types are therefore crucial to minimize any possible bias in the event selection. ATLAS uses two main minimum bias triggers, featuring complementary detector components and trigger levels. While a hardware based first trigger level situated in the forward regions with 2.09 < |eta| < 3.8 has been proven to select pp-collisions very efficiently, the Inner Detector based minimum bias trigger uses a random seed on filled bunches and central tracking detectors for the event selection. Both triggers were essential for the analysis of kinematic spectra of charged particles. Their performance and trigger efficiency measurements as well as studies on possible bias sources will be presen...

  20. Electroeluting DNA fragments.

    Science.gov (United States)

    Zarzosa-Alvarez, Ana L; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L; Bermudez-Cruz, Rosa M

    2010-09-05

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The electroelution procedure allows one to purify very clean DNA to be used in a large number of applications (sequencing, radiolabeling, enzymatic restriction, enzymatic modification, cloning etc). This procedure consists in placing DNA band-containing agarose or acrylamide slices into sample wells of the electroeluter, then applying current will make the DNA fragment to leave the agarose and thus be trapped in a cushion salt to be recovered later by ethanol precipitation.

  1. Microevolutionary Effects of Habitat Fragmentation on Plant-Animal Interactions

    Directory of Open Access Journals (Sweden)

    Francisco E. Fontúrbel

    2014-01-01

    Full Text Available Plant-animal interactions are a key component for biodiversity maintenance, but they are currently threatened by human activities. Habitat fragmentation might alter ecological interactions due to demographic changes, spatial discontinuities, and edge effects. Also, there are less evident effects of habitat fragmentation that potentially alter selective forces and compromise the fitness of the interacting species. Changes in the mutualistic and antagonistic interactions in fragmented habitats could significantly influence the plant reproductive output and the fauna assemblage associated with. Fragmented habitats may trigger contemporary evolution processes and open new evolutionary opportunities. Interacting parties with a diffuse and asymmetric relationship are less susceptible to local extinction but more prone to evolve towards new interactions or autonomy. However, highly specialized mutualisms are likely to disappear. On the other hand, ecological interactions may mutually modulate their response in fragmented habitats, especially when antagonistic interactions disrupt mutualistic ones. Ecoevolutionary issues of habitat fragmentation have been little explored, but the empiric evidence available suggests that the complex modification of ecological interactions in fragmented habitats might lead to nonanalogous communities on the long term.

  2. Metagenome fragment classification using N-mer frequency profiles.

    Science.gov (United States)

    Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino; Polikar, Robi; Sokhansanj, Bahrad

    2008-01-01

    A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique N-mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC) that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable to identify any fragment from hundreds of genomes. It also performs quite well at the strain, species, and genera levels and achieves strain resolution despite classifying ubiquitous genomic fragments (gene and nongene regions). Cross-validation analysis demonstrates that species-accuracy achieves 90% for highly-represented species containing an average of 8 strains. We demonstrate that such a tool can be used on the Sargasso Sea dataset, and our analysis shows that NBC can be further enhanced.

  3. Latent myofascial trigger points.

    Science.gov (United States)

    Ge, Hong-You; Arendt-Nielsen, Lars

    2011-10-01

    A latent myofascial trigger point (MTP) is defined as a focus of hyperirritability in a muscle taut band that is clinically associated with local twitch response and tenderness and/or referred pain upon manual examination. Current evidence suggests that the temporal profile of the spontaneous electrical activity at an MTP is similar to focal muscle fiber contraction and/or muscle cramp potentials, which contribute significantly to the induction of local tenderness and pain and motor dysfunctions. This review highlights the potential mechanisms underlying the sensory-motor dysfunctions associated with latent MTPs and discusses the contribution of central sensitization associated with latent MTPs and the MTP network to the spatial propagation of pain and motor dysfunctions. Treating latent MTPs in patients with musculoskeletal pain may not only decrease pain sensitivity and improve motor functions, but also prevent latent MTPs from transforming into active MTPs, and hence, prevent the development of myofascial pain syndrome.

  4. Heavy meson fragmentation at LHC

    Directory of Open Access Journals (Sweden)

    M. A. Gomshi Nobary

    2003-06-01

    Full Text Available   Large Hadron Collider (LHC at CERN will provide excellent opportunity to study the production and decay of heavy mesons and baryons with high statistics. We aim at the heavy mesons in this work and calculate their fragmentation functions consistent with this machine and present their total fragmentation probabilities and average fragmentation parameters.

  5. SCALING AND 4-QUARK FRAGMENTATION

    NARCIS (Netherlands)

    SCHOLTEN, O; BOSVELD, GD

    1991-01-01

    The conditions for a scaling behaviour from the fragmentation process leading to slow protons are discussed- The scaling referred to implies that the fragmentation functions depend on the light-cone momentum fraction only. It is shown that differences in the fragmentation functions for valence- and

  6. The Study of TVS Trigger Geometry and Triggered Vacuum Conditions

    CERN Document Server

    Park, Wung-Hoa; Son, Yoon-Kyoo; Frank, Klaus; Lee, Byung-Joon

    2016-01-01

    This presentation focuses on the optimization of the trigger unit of a six-rod TVS. The different configurations of the trigger pin and of the trigger electrode have been considered to study the electric field distribution at the triple points of the unit embedded in the cathode. To optimize the field enhancement, electric field simulations with a planar and a circular heads of the trigger pin in combinations with a convex and a concave shaped trigger electrodes have been done. The simulations were done with an applied trigger pulse voltage of Utrigger = 5 kV and with a discharge voltage the main switch of Uswitch = 20 kV. The experimental values had been Utrigger = 40 kV and Uswitch = 5 kV. The simulation results show that the combination of a circular trigger pin head and a concave trigger electrode yields the highest electric field of 9.6 .106 V/m at the triple point. In-parallel experiments have been performed with those four trigger configurations. The results of the experiments however cannot yet clearl...

  7. High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System

    Science.gov (United States)

    Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C. T.; Shui, Lingling

    2017-01-01

    DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1-10 Kbp fragment lengths with a yield of 75.30-91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

  8. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility

    NARCIS (Netherlands)

    Badali, H.; Yazdanparast, S.A.; Bonifaz, A.; Mousavi, B.; de Hoog, G.S.; Klaassen, C.H.W.; Meis, J.F.G.M.

    2013-01-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated in

  9. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility

    NARCIS (Netherlands)

    Badali, H.; Yazdanparast, S.A.; Bonifaz, A.; Mousavi, B.; de Hoog, G.S.; Klaassen, C.H.W.; Meis, J.F.G.M.

    2013-01-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated in

  10. Picking Up (On Fragments

    Directory of Open Access Journals (Sweden)

    Phil Ellis

    2015-09-01

    Full Text Available This article discusses the implications for archival and media archaeological research and reenactment artwork relating to a recent arts practice project: reenacttv: 30 lines / 60 seconds. It proposes that archival material is unstable but has traces and fragments that are full of creative potential to re-think and re-examine past media historical events through a media archaeological approach to reenactment. The article contains images and links to videos from the final reenactment artworks as well as from rehearsals in Vienna and Bradford.

  11. An Archeology of Fragments

    Directory of Open Access Journals (Sweden)

    Gerald L. Bruns

    2014-10-01

    Full Text Available This is a short (fragmentary history of fragmentary writing from the German Romantics (F. W. Schlegel, Friedrich Hölderlin to modern and contemporary concrete or visual poetry. Such writing is (often deliberately a critique of the logic of subsumption that tries to assimilate whatever is singular and irreducible into totalities of various categorical or systematic sorts. Arguably, the fragment (parataxis is the distinctive feature of literary Modernism, which is a rejection, not of what precedes it, but of what Max Weber called “the rationalization of the world” (or Modernity whose aim is to keep everything, including all that is written, under surveillance and control.

  12. Generic behaviours in impact fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Sator, N.; Mechkov, S.; Sausset, F. [Paris-6 Univ. Pierre et Marie Curie, Lab. de Physique Theorique de la Matiere Condensee, UMR CNRS 7600, 75 - Paris (France); Mechkov, S. [Ecole Normale Superieure, Lab. de Physique Statistique, 75 - Paris (France)

    2008-02-15

    From atomic nuclei to supernovae, including plates and rocks, every cohesive system can be broken into fragments, provided that the deposited energy is sufficiently large compared to its cohesive energy. We present a simple numerical model for investigating the general properties of fragmentation. By use of molecular dynamics simulations, we study the impact fragmentation of a solid disk of interacting particles with a wall. Regardless of the particular form of the interaction potential, the fragment size distribution exhibits a power law behaviour with an exponent that increases logarithmically with the energy deposited in the system, in agreement with experiments. We expect this behaviour to be generic in fragmentation phenomena. (authors)

  13. The CMS High Level Trigger

    CERN Document Server

    Adam, W; Deldicque, C; Ero, J; Frühwirth, R; Jeitler, Manfred; Kastner, K; Köstner, S; Neumeister, N; Porth, M; Padrta P; Rohringer, H; Sakulinb, H; Strauss, J; Taurok, A; Walzel, G; Wulz, C E; Lowette, S; Van De Vyver, B; De Lentdecker, G; Vanlaer, P; Delaere, C; Lemaître, V; Ninane, A; van der Aa, O; Damgov, J; Karimäki, V; Kinnunen, R; Lampen, T; Lassila-Perini, K M; Lehti, S; Nysten, J; Tuominiemi, J; Busson, P; Todorov, T; Schwering, G; Gras, P; Daskalakis, G; Sfyrla, A; Barone, M; Geralis, T; Markou, C; Zachariadou, K; Hidas, P; Banerjee, S; Mazumdara, K; Abbrescia, M; Colaleoa, A; D'Amato, N; De Filippis, N; Giordano, D; Loddo, F; Maggi, M; Silvestris, L; Zito, G; Arcelli, S; Bonacorsi, D; Capiluppi, P; Dallavalle, G M; Fanfani, A; Grandi, C; Marcellini, S; Montanari, A; Odorici, F; Travaglini, R; Costa, S; Tricomi, A; Ciulli, a V; Magini, N; Ranieri, R; Berti, L; Biasotto, M; Gulminia, M; Maron, G; Toniolo, N; Zangrando, L; Bellato, M; Gasparini, U; Lacaprara, S; Parenti, A; Ronchese, P; Vanini, S; Zotto, S; Ventura P L; Perugia; Benedetti, D; Biasini, M; Fano, L; Servoli, L; Bagliesi, a G; Boccali, T; Dutta, S; Gennai, S; Giassi, A; Palla, F; Segneri, G; Starodumov, A; Tenchini, R; Meridiani, P; Organtini, G; Amapane, a N; Bertolino, F; Cirio, R; Kim, J Y; Lim, I T; Pac, Y; Joo, K; Kim, S B; Suwon; Choi, Y I; Yu, I T; Cho, K; Chung, J; Ham, S W; Kim, D H; Kim, G N; Kim, W; CKim, J; Oh, S K; Park, H; Ro, S R; Son, D C; Suh, J S; Aftab, Z; Hoorani, H; Osmana, A; Bunkowski, K; Cwiok, M; Dominik, Wojciech; Doroba, K; Kazana, M; Królikowski, J; Kudla, I; Pietrusinski, M; Pozniak, Krzysztof T; Zabolotny, W M; Zalipska, J; Zych, P; Goscilo, L; Górski, M; Wrochna, G; Zalewski, P; Alemany-Fernandez, R; Almeida, C; Almeida, N; Da Silva, J C; Santos, M; Teixeira, I; Teixeira, J P; Varelaa, J; Vaz-Cardoso, N; Konoplyanikov, V F; Urkinbaev, A R; Toropin, A; Gavrilov, V; Kolosov, V; Krokhotin, A; Oulianov, A; Stepanov, N; Kodolova, O L; Vardanyan, I; Ilic, J; Skoro, G P; Albajar, C; De Troconiz, J F; Calderón, A; López-Virto, M A; Marco, R; Martínez-Rivero, C; Matorras, F; Vila, I; Cucciarelli, S; Konecki, M; Ashby, S; Barney, D; Bartalini, P; Benetta, R; Brigljevic, V; Bruno, G; Cano, E; Cittolin, S; Della Negra, M; de Roeck, A; Favre, P; Frey, A; Funk, W; Futyan, D; Gigi, D; Glege, F; Gutleber, J; Hansen, M; Innocente, V; Jacobs, C; Jank, W; Kozlovszky, Miklos; Larsen, H; Lenzi, M; Magrans, I; Mannelli, M; Meijers, F; Meschi, E; Mirabito, L; Murray, S J; Oh, A; Orsini, L; Palomares-Espiga, C; Pollet, L; Rácz, A; Reynaud, S; Samyn, D; Scharff-Hansen, P; Schwick, C; Sguazzoni, G; Sinanis, N; Sphicas, P; Spiropulu, M; Strandlie, A; Taylor, B G; Van Vulpen, I; Wellisch, J P; Winkler, M; Villigen; Kotlinski, D; Zurich; Prokofiev, K; Speer, T; Dumanoglu, I; Bristol; Bailey, S; Brooke, J J; Cussans, D; Heath, G P; Machin, D; Nash, S J; Newbold, D; Didcot; Coughlan, A; Halsall, R; Haynes, W J; Tomalin, I R; Marinelli, N; Nikitenko, A; Rutherford, S; Seeza, C; Sharif, O; Antchev, G; Hazen, E; Rohlf, J; Wu, S; Breedon, R; Cox, P T; Murray, P; Tripathi, M; Cousins, R; Erhan, S; Hauser, J; Kreuzer, P; Lindgren, M; Mumford, J; Schlein, P E; Shi, Y; Tannenbaum, B; Valuev, V; Von der Mey, M; Andreevaa, I; Clare, R; Villa, S; Bhattacharya, S; Branson, J G; Fisk, I; Letts, J; Mojaver, M; Paar, H P; Trepagnier, E; Litvine, V; Shevchenko, S; Singh, S; Wilkinson, R; Aziz, S; Bowden, M; Elias, J E; Graham, G; Green, D; Litmaath, M; Los, S; O'Dell, V; Ratnikova, N; Suzuki, I; Wenzel, H; Acosta, D; Bourilkov, D; Korytov, A; Madorsky, A; Mitselmakher, G; Rodríguez, J L; Scurlock, B; Abdullin, S; Baden, D; Eno, S; Grassi, T; Kunori, S; Pavlon, S; Sumorok, K; Tether, S; Cremaldi, L M; Sanders, D; Summers, D; Osborne, I; Taylor, L; Tuura, L; Fisher,W C; Mans6, J; Stickland, D P; Tully, C; Wildish, T; Wynhoff, S; Padley, B P; Chumney, P; Dasu, S; Smith, W H; CMS Trigger Data Acquisition Group

    2006-01-01

    At the Large Hadron Collider at CERN the proton bunches cross at a rate of 40MHz. At the Compact Muon Solenoid experiment the original collision rate is reduced by a factor of O (1000) using a Level-1 hardware trigger. A subsequent factor of O(1000) data reduction is obtained by a software-implemented High Level Trigger (HLT) selection that is executed on a multi-processor farm. In this review we present in detail prototype CMS HLT physics selection algorithms, expected trigger rates and trigger performance in terms of both physics efficiency and timing.

  14. Genomics spurs rapid advances in our understanding of the biology of vascular wilt pathogens in the genus Verticillium

    NARCIS (Netherlands)

    Klimes, A.; Dobinson, K.F.; Thomma, B.; Klosterman, S.J.

    2015-01-01

    The availability of genomic sequences of several Verticillium species triggered an explosion of genome-scale investigations of mechanisms fundamental to the Verticillium life cycle and disease process. Comparative genomics studies have revealed evolutionary mechanisms, such as hybridization and inte

  15. The PHENIX Muon Trigger Upgrade Level-1 Trigger System

    Science.gov (United States)

    Lajoie, John; Kempel, Todd

    2010-02-01

    The PHENIX Muon Trigger Upgrade adds a set of Level-1 trigger detectors to the existing muon spectrometers and will enhance the ability of the experiment to pursue a rich program of spin physics in polarized proton collisions. The upgrade will allow the experiment to select high momentum muons from the decay of W bosons and reject both beam-associated and low-momentum collision background, enabling the study of quark and antiquark polarization in the proton. The Muon Trigger Upgrade will add momentum and timing information to the present muon Level-1 trigger, which only makes use of tracking in the PHENIX muon identifier (MuID) panels. Signals from new Resistive Plate Chambers (RPCs) and re-instrumented planes in the existing muon tracking (MuTr) chambers will provide momentum and timing information for the new Level-1 trigger. An RPC timing resolution of ˜2 ns will permit rejection of beam related backgrounds while tracking information from the RPCs and MuTr station will be used by the trigger to select events with high momentum muon candidates. The RPC and MuTr hit information will be sent by optical fibers to a set of Level-1 trigger processors that will make use of cutting edge FPGA technology to provide very high data densities in a compact form factor. The layout of the upgrade, details of the Level-1 electronics and trigger algorithm development will be presented. )

  16. Isolating Triggered Star Formation

    CERN Document Server

    Barton, Elizabeth J; Zentner, Andrew R; Bullock, James S; Wechsler, Risa H

    2007-01-01

    Galaxy pairs provide a potentially powerful means of studying triggered star formation from galaxy interactions. We use a large cosmological N-body simulation coupled with a well-tested semi-analytic substructure model to demonstrate that the majority of galaxies in close pairs reside within cluster or group-size halos and therefore represent a biased population, poorly suited for direct comparison to ``field'' galaxies. Thus, the frequent observation that some types of galaxies in pairs have redder colors than ``field'' galaxies is primarily a selection effect. We select galaxy pairs that are isolated in their dark matter halos with respect to other massive subhalos (N=2 halos) and a control sample of isolated galaxies (N=1 halos) for comparison. We then apply these selection criteria to a volume-limited subset of the 2dF Galaxy Redshift Survey with M_Bj ~ 5 above their average past value, while only 10% of isolated galaxies in the control sample show this level of enhancement. Thus, 14% (20 %) of the galaxi...

  17. Upgrade trigger: Biannual performance update

    CERN Document Server

    Aaij, Roel; Couturier, Ben; Esen, Sevda; De Cian, Michel; De Vries, Jacco Andreas; Dziurda, Agnieszka; Fitzpatrick, Conor; Fontana, Marianna; Grillo, Lucia; Hasse, Christoph; Jones, Christopher Rob; Le Gac, Renaud; Matev, Rosen; Neufeld, Niko; Nikodem, Thomas; Polci, Francesco; Del Buono, Luigi; Quagliani, Renato; Schwemmer, Rainer; Seyfert, Paul; Stahl, Sascha; Szumlak, Tomasz; Vesterinen, Mika Anton; Wanczyk, Joanna; Williams, Mark Richard James; Yin, Hang; Zacharjasz, Emilia Anna

    2017-01-01

    This document presents the performance of the LHCb Upgrade trigger reconstruction sequence, incorporating changes to the underlying reconstruction algorithms and detector description since the Trigger and Online Upgrade TDR. An updated extrapolation is presented using the most recent example of an Event Filter Farm node.

  18. Cryopreservation increases DNA fragmentation in spermatozoa of smokers.

    Science.gov (United States)

    Aydin, Mehmet Serif; Senturk, Gozde Erkanli; Ercan, Feriha

    2013-05-01

    Smoking causes subfertility due to deterioration of spermatozoa including decreased concentration and abnormal morphology. Although evidence on the deleterious effects of smoking on spermatozoa parameters is well known, its interference with cryopreservation is not clear. This study aimed to investigate the effects of cryopreservation on sperm parameters and DNA fragmentation in non-smokers and smokers. Semen samples were obtained from 40 normospermic male volunteers of whom 20 were non-smokers and 20 smokers. Samples were analyzed in terms of motility, concentration, morphology, and DNA fragmentation before freezing and 1 and 3 months after freezing and thawing. Ultrastructural alterations were investigated by transmission electron microscopy. Sperm morphology seemed to be more affected after cryopreservation in samples obtained from smokers. Ultrastructural examination showed alterations in the integrity of the membranes and increased subacrosomal swelling. Before freezing, the increase in DNA fragmentation rate in smokers was not statistically significant compared to that of non-smokers. However, after thawing, the DNA fragmentation rates were significantly high in both non-smokers and smokers compared to their respective rates before freezing. The extent of the increase in DNA fragmentation rate was significantly higher in smokers after thawing compared to that of non-smokers. In conclusion, cryopreservation causes alterations in membrane integrity and increases DNA fragmentation, thus triggering relatively negative effects on the sperm samples of smokers compared to that of non-smokers. Copyright © 2012 Elsevier GmbH. All rights reserved.

  19. Stone fragmentation by ultrasound

    Indian Academy of Sciences (India)

    S K Shrivastava; Kailash

    2004-08-01

    The presence of kidney stone in the kidney causes discomfort to patients. Hence, removal of such stones is important which is commonly done these days, non-destructively, with lithotripters without surgery. Commercially, lithotripters like extra-corporeal shock wave lithotripters (ESWL) made by Siemens etc are in routine use. These methods are very cumbersome and expensive. Treatment of the patients also takes comparatively more time because of more number of sittings. Some delicate nerves and fibres in the surrounding areas of the stones present in the kidney are also damaged by high ultrasonic intensity used in such systems. In the present work, enhancement of the kidney stone fragmentation by using ultrasound is studied. The cavitation bubbles are found to implode faster, with more disintegration efficiency of the lithotripters, which give better treatment to the patients.

  20. Physical map of polyoma viral DNA fragments produced by cleavage with a restriction enzyme from Haemophilus aegyptius, endonuclease R-HaeIII.

    Science.gov (United States)

    Summers, J

    1975-04-01

    Digestion of polyoma viral DNA with a restriction enzyme from Haemophilus aegyptius generates at least 22 unique fragments. The fragments have been characterized with respect to size and physical order on the polyoma genome, and the 5' to 3' orientation of the (+) and (-) strands has been determined. A method for specific radiolabeling of adjacent fragments was employed to establish the fragment order. This technique may be useful for ordering the fragments produced by digestion of complex DNAs.

  1. GnRH agonist triggering

    DEFF Research Database (Denmark)

    Kol, Shahar; Humaidan, Peter; Al Humaidan, Peter Samir Heskjær

    2013-01-01

    The concept that a bolus of gonadotrophin-releasing hormone agonist (GnRHa) can replace human chorionic gonadotrophin (HCG) as a trigger of final oocyte maturation was introduced several years ago. Recent developments in the area strengthen this premise. GnRHa trigger offers important advantages...... triggering concept should be challenged and that the GnRHa trigger is the way to move forward with thoughtful consideration of the needs, safety and comfort of our patients. Routinely, human chorionic gonadotrophin (HCG) is used to induce ovulation in fertility treatments. This approach deviates...... significantly from physiology and often results in insufficient hormonal support in early pregnancy and in ovarian hyperstimulation syndrome (OHSS). An alternative approach is to use a gonadotrophin-releasing hormone (GnRH) agonist which allows a more physiological trigger of ovulation and, most importantly...

  2. Triggering requirements for SSC physics

    Energy Technology Data Exchange (ETDEWEB)

    Gilchriese, M.G.D. [Lawrence Berkeley Lab., CA (United States)

    1989-04-01

    Some aspects of triggering requirements for high P{sub T} physics processes at the Superconducting Super Collider (SSC) are described. A very wide range of trigger types will be required to enable detection of the large number of potential physics signatures possible at the SSC. Although in many cases trigger rates are not now well understood, it is possible to conclude that the ability to trigger on transverse energy, number and energy of jets, number and energy of leptons (electrons and muons), missing energy and combinations of these will be required. An SSC trigger system must be both highly flexible and redundant to ensure reliable detection of many new physics processes at the SSC.

  3. CONTROL OF FRAGMENTATION BY BLASTING

    Directory of Open Access Journals (Sweden)

    Branko Božić

    1998-12-01

    Full Text Available The degree of fragmentation influences the economy of the excavation operations. Characteristics of blasted rock such as fragment size, volume and mass are fundamental variables effecting the economics of a mining operation and are in effect the basis for evaluating the quality of a blast. The properties of fragmentation, such as size and shape, are very important information for the optimization of production. Three factors control the fragment size distribution: the rock structure, the quantity of explosive and its distribution within the rock mass. Over the last decade there have been considerable advances in our ability to measure and analyze blasting performance. These can now be combined with the continuing growth in computing power to develop a more effective description of rock fragmentation for use by future blasting practitioners. The paper describes a view of the fragmentation problem by blasting and the need for a new generation of engineering tools to guide the design and implementation of blasting operations.

  4. Rewriting the blueprint of life by synthetic genomics and genome engineering

    OpenAIRE

    Annaluru, Narayana; Ramalingam, Sivaprakash; Chandrasegaran, Srinivasan

    2015-01-01

    Advances in DNA synthesis and assembly methods over the past decade have made it possible to construct genome-size fragments from oligonucleotides. Early work focused on synthesis of small viral genomes, followed by hierarchical synthesis of wild-type bacterial genomes and subsequently on transplantation of synthesized bacterial genomes into closely related recipient strains. More recently, a synthetic designer version of yeast Saccharomyces cerevisiae chromosome III has been generated, with ...

  5. Progress towards construction of a total restriction fragment map of a human chromosome.

    NARCIS (Netherlands)

    H. Vissing; F.G. Grosveld (Frank); E. Solomon; G. Moore; N. Lench; N. Shennan; R. Williamson

    1987-01-01

    textabstractWe present an approach to the construction of an overlapping restriction fragment map of a single human chromosome. A genomic cosmid library genome was constructed from a mouse-human hybrid cell line containing chromosome 17 as its only human genetic component. Cosmids containing human i

  6. Triggered Release from Polymer Capsules

    Energy Technology Data Exchange (ETDEWEB)

    Esser-Kahn, Aaron P. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Chemistry; Odom, Susan A. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Chemistry; Sottos, Nancy R. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Materials Science and Engineering; White, Scott R. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Aerospace Engineering; Moore, Jeffrey S. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Chemistry

    2011-07-06

    Stimuli-responsive capsules are of interest in drug delivery, fragrance release, food preservation, and self-healing materials. Many methods are used to trigger the release of encapsulated contents. Here we highlight mechanisms for the controlled release of encapsulated cargo that utilize chemical reactions occurring in solid polymeric shell walls. Triggering mechanisms responsible for covalent bond cleavage that result in the release of capsule contents include chemical, biological, light, thermal, magnetic, and electrical stimuli. We present methods for encapsulation and release, triggering methods, and mechanisms and conclude with our opinions on interesting obstacles for chemically induced activation with relevance for controlled release.

  7. Thermodynamical string fragmentation

    Science.gov (United States)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  8. Thermodynamical String Fragmentation

    CERN Document Server

    Fischer, Nadine

    2016-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from...

  9. Fragmentation Considered Poisonous

    CERN Document Server

    Herzberg, Amir

    2012-01-01

    We present practical poisoning and name-server block- ing attacks on standard DNS resolvers, by off-path, spoofing adversaries. Our attacks exploit large DNS responses that cause IP fragmentation; such long re- sponses are increasingly common, mainly due to the use of DNSSEC. In common scenarios, where DNSSEC is partially or incorrectly deployed, our poisoning attacks allow 'com- plete' domain hijacking. When DNSSEC is fully de- ployed, attacker can force use of fake name server; we show exploits of this allowing off-path traffic analy- sis and covert channel. When using NSEC3 opt-out, attacker can also create fake subdomains, circumvent- ing same origin restrictions. Our attacks circumvent resolver-side defenses, e.g., port randomisation, IP ran- domisation and query randomisation. The (new) name server (NS) blocking attacks force re- solver to use specific name server. This attack allows Degradation of Service, traffic-analysis and covert chan- nel, and also facilitates DNS poisoning. We validated the attac...

  10. An Algebra for Program Fragments

    DEFF Research Database (Denmark)

    Kristensen, Bent Bruun; Madsen, Ole Lehrmann; Møller-Pedersen, Birger

    1985-01-01

    Program fragments are described either by strings in the concrete syntax or by constructor applications in the abstract syntax. By defining conversions between these forms, both may be intermixed. Program fragments are constructed by terminal and nonterminal symbols from the grammar and by variab...

  11. Complete axiomatizations for XPath fragments

    NARCIS (Netherlands)

    ten Cate, B.; Litak, T.; Marx, M.

    2010-01-01

    We provide complete axiomatizations for several fragments of Core XPath, the navigational core of XPath 1.0 introduced by Gottlob, Koch and Pichler. A complete axiomatization for a given fragment is a set of equivalences from which every other valid equivalence is derivable; equivalences can be thou

  12. FERMIGTRIG - Fermi GBM Trigger Catalog

    Data.gov (United States)

    National Aeronautics and Space Administration — This table lists all of the triggers observed by one or more of the 14 GBM detectors (12 NaI and 2 BGO). Note that there are two Browse catalogs resulting from GBM...

  13. The ATLAS Trigger Muon "Vertical Slice"

    CERN Document Server

    Sidoti, A; Biglietti, M; Carlino, G; Cataldi, G; Conventi, F; Del Prete, T; Di Mattia, A; Falciano, S; Gorini, S; Kanaya, N; Kohno, T; Krasznahorkay, A; Lagouri, T; Luci, C; Luminari, L; Marzano, F; Nagano, K; Nisati, A; Panikashvili, N; Pasqualucci, E; Primavera, M; Scannicchio, D A; Spagnolo, S; Tarem, S; Tarem, Z; Tokushuku, K; Usai, G; Ventura, A; Vercesi, V; Yamazaki, Y; 10th Pisa Meeting on Advanced Detectors : Frontier Detectors For Frontier Physics

    2007-01-01

    The muon trigger system is a fundamental component of the ATLAS detector at the LHC collider. In this paper we describe the ATLAS multi-level trigger selecting events with muons: the Muon Trigger Slice.

  14. Isomeric signatures in the fragmentation of pyridazine and pyrimidine induced by fast ion impact

    Energy Technology Data Exchange (ETDEWEB)

    Wolff, Wania, E-mail: wania@if.ufrj.br; Luna, Hugo; Montenegro, Eduardo C. [Instituto de Física, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil)

    2015-07-28

    We present fast proton impact induced fragmentations of pyrimidine and pyridazine as an experimental resource to investigate isomeric signatures. Major isomeric imprints are identified for few fragment ions and differences of more than an order of magnitude for the cross sections of fragments of the same mass were measured. The observation of the molecular structure of these isomers gives no apparent indication for the reasons for such substantial differences. It is verified that the simple displacement of the position of one nitrogen atom strongly inhibits or favors the production of some ionic fragment species. The dependency of the fragmentation cross sections on the proton impact energy, investigated by means of time of flight mass spectroscopy and of a model calculation based in first order perturbation theory, allows us to disentangle the complex collision dynamics of the ionic fragments. The proton-induced fragmentation discriminates rather directly the association between a molecular orbital ionization and the fragment-ions creation and abundance, as well as how the redistribution of the energy imparted to the molecules takes place, triggering not only single but also double vacancy and leads to specific fragmentation pathways.

  15. Driven fragmentation of granular gases.

    Science.gov (United States)

    Cruz Hidalgo, Raúl; Pagonabarraga, Ignacio

    2008-06-01

    The dynamics of homogeneously heated granular gases which fragment due to particle collisions is analyzed. We introduce a kinetic model which accounts for correlations induced at the grain collisions and analyze both the kinetics and relevant distribution functions these systems develop. The work combines analytical and numerical studies based on direct simulation Monte Carlo calculations. A broad family of fragmentation probabilities is considered, and its implications for the system kinetics are discussed. We show that generically these driven materials evolve asymptotically into a dynamical scaling regime. If the fragmentation probability tends to a constant, the grain number diverges at a finite time, leading to a shattering singularity. If the fragmentation probability vanishes, then the number of grains grows monotonously as a power law. We consider different homogeneous thermostats and show that the kinetics of these systems depends weakly on both the grain inelasticity and driving. We observe that fragmentation plays a relevant role in the shape of the velocity distribution of the particles. When the fragmentation is driven by local stochastic events, the long velocity tail is essentially exponential independently of the heating frequency and the breaking rule. However, for a Lowe-Andersen thermostat, numerical evidence strongly supports the conjecture that the scaled velocity distribution follows a generalized exponential behavior f(c) approximately exp(-cn) , with n approximately 1.2 , regarding less the fragmentation mechanisms.

  16. Flexible trigger menu implementation on the Global Trigger for the CMS Level-1 trigger upgrade

    CERN Document Server

    Matsushita, Takashi

    2017-01-01

    The CMS experiment at the Large Hadron Collider (LHC) has continued to explore physics at the high-energy frontier in 2016. The integrated luminosity delivered by the LHC in 2016 was 41~fb$^{-1}$ with a peak luminosity of 1.5 $\\times$ 10$^{34}$ cm$^{-2}$s$^{-1}$ and peak mean pile-up of about 50, all exceeding the initial estimations for 2016. The CMS experiment has upgraded its hardware-based Level-1 trigger system to maintain its performance for new physics searches and precision measurements at high luminosities. The Global Trigger is the final step of the CMS \\mbox{Level-1} trigger and implements a trigger menu, a set of selection requirements applied to the final list of objects from calorimeter and muon triggers, for reducing the 40 MHz collision rate to 100 kHz. The Global Trigger has been upgraded with state-of-the-art FPGA processors on Advanced Mezzanine Cards with optical links running at 10 GHz in a MicroTCA crate. The powerful processing resources of the upgraded system enable implemen...

  17. The spectroscopy of fission fragments

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, W.R. [Department of Physics and Astronomy, University of Manchester, Manchester, M13 9PL (United Kingdom); Collaboration: La Direction des Sciences de la Matiere du CEA (FR); Le Fonds National de la Recherche Scientifique de Belgique (BE)

    1998-12-31

    High-resolution measurements on {gamma} rays from fission fragments have provided a rich source of information, unobtainable at the moment in any other way, on the spectroscopy of neutron-rich nuclei. In recent years important data have been obtained on the yrast- and near yrast-structure of neutron-rich fission fragments. We discuss the scope of measurements which can be made on prompt gamma rays from secondary fission fragments, the techniques used in the experiments and some results recently obtained. (author) 24 refs., 8 figs., 1 tab.

  18. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.

    Directory of Open Access Journals (Sweden)

    Estienne C Swart

    Full Text Available The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5% of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10%, encode 2-8 genes, have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size that vary from 469 bp to 66 kb long (mean ∼3.2 kb and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%, suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing

  19. Anthropogenic triggering of large earthquakes.

    Science.gov (United States)

    Mulargia, Francesco; Bizzarri, Andrea

    2014-08-26

    The physical mechanism of the anthropogenic triggering of large earthquakes on active faults is studied on the basis of experimental phenomenology, i.e., that earthquakes occur on active tectonic faults, that crustal stress values are those measured in situ and, on active faults, comply to the values of the stress drop measured for real earthquakes, that the static friction coefficients are those inferred on faults, and that the effective triggering stresses are those inferred for real earthquakes. Deriving the conditions for earthquake nucleation as a time-dependent solution of the Tresca-Von Mises criterion applied in the framework of poroelasticity yields that active faults can be triggered by fluid overpressures oil and gas production and storage may trigger destructive earthquakes on active faults at a few tens of kilometers. Fluid pressure propagates as slow stress waves along geometric paths operating in a drained condition and can advance the natural occurrence of earthquakes by a substantial amount of time. Furthermore, it is illusory to control earthquake triggering by close monitoring of minor "foreshocks", since the induction may occur with a delay up to several years.

  20. Review Document: Full Software Trigger

    CERN Document Server

    Albrecht, J; Raven, G

    2014-01-01

    This document presents a trigger system for the upgraded LHCb detector, scheduled to begin operation in 2020. This document serves as input for the internal review towards the "DAQ, online and trigger TDR". The proposed trigger system is implemented entirely in software. In this document we show that track reconstruction of a similar quality to that available in the offline algorithms can be performed on the full inelastic $pp$-collision rate, without prior event selections implemented in custom hardware and without relying upon a partial event reconstruction. A track nding eciency of 98.8 % relative to oine can be achieved for tracks with $p_T >$ 500 MeV/$c$. The CPU time required for this reconstruction is about 40 % of the available budget. Proof-of-principle selections are presented which demonstrate that excellent performance is achievable using an inclusive beauty trigger, in addition to exclusive beauty and charm triggers. Finally, it is shown that exclusive beauty and charm selections that do not intr...

  1. Plastid-like Seq in mt Genome - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available erences for individual fragments is available. Data file...t were migrated from the plastid genome to the mitochondrial genome. Information on sizes, positions, gene names, homologies and diff

  2. Industrial accidents triggered by lightning.

    Science.gov (United States)

    Renni, Elisabetta; Krausmann, Elisabeth; Cozzani, Valerio

    2010-12-15

    Natural disasters can cause major accidents in chemical facilities where they can lead to the release of hazardous materials which in turn can result in fires, explosions or toxic dispersion. Lightning strikes are the most frequent cause of major accidents triggered by natural events. In order to contribute towards the development of a quantitative approach for assessing lightning risk at industrial facilities, lightning-triggered accident case histories were retrieved from the major industrial accident databases and analysed to extract information on types of vulnerable equipment, failure dynamics and damage states, as well as on the final consequences of the event. The most vulnerable category of equipment is storage tanks. Lightning damage is incurred by immediate ignition, electrical and electronic systems failure or structural damage with subsequent release. Toxic releases and tank fires tend to be the most common scenarios associated with lightning strikes. Oil, diesel and gasoline are the substances most frequently released during lightning-triggered Natech accidents.

  3. Genome chaos: survival strategy during crisis.

    Science.gov (United States)

    Liu, Guo; Stevens, Joshua B; Horne, Steven D; Abdallah, Batoul Y; Ye, Karen J; Bremer, Steven W; Ye, Christine J; Chen, David J; Heng, Henry H

    2014-01-01

    Genome chaos, a process of complex, rapid genome re-organization, results in the formation of chaotic genomes, which is followed by the potential to establish stable genomes. It was initially detected through cytogenetic analyses, and recently confirmed by whole-genome sequencing efforts which identified multiple subtypes including "chromothripsis", "chromoplexy", "chromoanasynthesis", and "chromoanagenesis". Although genome chaos occurs commonly in tumors, both the mechanism and detailed aspects of the process are unknown due to the inability of observing its evolution over time in clinical samples. Here, an experimental system to monitor the evolutionary process of genome chaos was developed to elucidate its mechanisms. Genome chaos occurs following exposure to chemotherapeutics with different mechanisms, which act collectively as stressors. Characterization of the karyotype and its dynamic changes prior to, during, and after induction of genome chaos demonstrates that chromosome fragmentation (C-Frag) occurs just prior to chaotic genome formation. Chaotic genomes seem to form by random rejoining of chromosomal fragments, in part through non-homologous end joining (NHEJ). Stress induced genome chaos results in increased karyotypic heterogeneity. Such increased evolutionary potential is demonstrated by the identification of increased transcriptome dynamics associated with high levels of karyotypic variance. In contrast to impacting on a limited number of cancer genes, re-organized genomes lead to new system dynamics essential for cancer evolution. Genome chaos acts as a mechanism of rapid, adaptive, genome-based evolution that plays an essential role in promoting rapid macroevolution of new genome-defined systems during crisis, which may explain some unwanted consequences of cancer treatment.

  4. Mutant DNA quantification by digital PCR can be confounded by heating during DNA fragmentation.

    Science.gov (United States)

    Kang, Qing; Parkin, Brian; Giraldez, Maria D; Tewari, Muneesh

    2016-04-01

    Digital PCR (dPCR) is gaining popularity as a DNA mutation quantification method for clinical specimens. Fragmentation prior to dPCR is required for non-fragmented genomic DNA samples; however, the effect of fragmentation on DNA analysis has not been well-studied. Here we evaluated three fragmentation methods for their effects on dPCR point mutation assay performance. Wild-type (WT) human genomic DNA was fragmented by heating, restriction digestion, or acoustic shearing using a Covaris focused-ultrasonicator. dPCR was then used to determine the limit of blank (LoB) by quantifying observed WT and mutant allele counts of the proto-oncogenes KRAS and BRAF in the WT DNA sample. DNA fragmentation by heating to 95°C, while the simplest and least expensive method, produced a high background mutation frequency for certain KRAS mutations relative to the other methods. This was due to heat-induced mutations, specifically affecting dPCR assays designed to interrogate guanine to adenine (G>A) mutations. Moreover, heat-induced fragmentation overestimated gene copy number, potentially due to denaturation and partition of single-stranded DNA into different droplets. Covaris acoustic shearing and restriction enzyme digestion showed similar LoBs and gene copy number estimates to one another. It should be noted that moderate heating, commonly used in genomic DNA extraction protocols, did not significantly increase observed KRAS mutation counts.

  5. Upgrade trigger: Bandwidth strategy proposal

    CERN Document Server

    Boettcher, Thomas Julian; Meloni, Simone; Whitehead, Mark Peter; Williams, Mark Richard James

    2017-01-01

    This document describes a proposed selection strategy for the upgrade trigger using charm signals as a benchmark. The Upgrade trigger uses a 'Run2-like' sequence consisting of a first and second stage, in between which the calibration and alignment is performed. The first stage, HLT1, uses an inclusive strategy to select beauty and charm, while the second stage uses offline-quality exclusive selections. A novel genetic algorithm-based bandwidth division is performed at the second stage to maximise the output of useful physics events, and a range of possible signal efficiencies are presented as a function of the available bandwidth.

  6. ATLAS FTK Fast Track Trigger

    CERN Document Server

    Iizawa, T; The ATLAS collaboration

    2014-01-01

    The Fast TracKer (FTK) will perform global track reconstruction after each Level-1 trigger accept signal to enable the software-based higher level trigger to have early access to tracking information. FTK is a dedicated processor based on a mixture of advanced technologies. Modern, powerful Field Programmable Gate Arrays (FPGAs) form an important part of the system architecture, and the large level of computing power required for pattern recognition is provided by incorporating standard-cell ASICs named Associative Memory (AM). Motivation and the architecture of the FTK system will be presented, and the status of hardware and simulation will be following.

  7. Upgrade trigger: Bandwidth strategy proposal

    CERN Document Server

    Fitzpatrick, Conor; Meloni, Simone; Boettcher, Thomas Julian; Whitehead, Mark Peter; Dziurda, Agnieszka; Vesterinen, Mika Anton

    2017-01-01

    This document describes a selection strategy for the upgrade trigger using charm signals as a benchmark. The Upgrade trigger uses a 'Run 2-like' sequence consisting of a first and second stage, in between which the calibration and alignment is performed. The first stage, HLT1, uses an inclusive strategy to select beauty and charm decays, while the second stage uses offline-quality exclusive selections. A novel genetic algorithm-based bandwidth division is performed at the second stage to distribute the output bandwidth among different physics channels, maximising the efficiency for useful physics events. The performance is then studied as a function of the available output bandwidth.

  8. LHCb Run 2 Trigger Performance

    CERN Document Server

    Sciascia, Barbara

    2016-01-01

    During the first long shutdown of the LHC (2013-2014, LS1), the LHCb detector remained essentially unchanged, while the trigger system has been completely revisited. Upgrades to the LHCb computing infrastructure have allowed for high quality decay information to be calculated by the software trigger making a separate offline event reconstruction unnecessary. Reaching the ultimate precision of the LHCb experiment already in real time as the data arrive has the power to transform the experimental approach to processing large quantities of data

  9. Binding-site assessment by virtual fragment screening.

    Directory of Open Access Journals (Sweden)

    Niu Huang

    Full Text Available The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock approximately 11,000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors.

  10. The ATLAS Hadronic Tau Trigger

    CERN Document Server

    Brost, E; The ATLAS collaboration

    2014-01-01

    As proton-proton collisions at the LHC reach luminosities close to 10$^{\\mathrm{34}}$ cm$^{\\mathrm{-2}}$ s $^{\\mathrm{-1}}$, the strategies for triggering have become more important than ever for physics analyses. Simplistic single tau lepton triggers suffer from severe rate limitation, despite the sophisticated algorithms used in the tau identification. The development of further fast algorithms and the design of topological selections are the main challenges to allow a large program of physics analysis. The tau triggers provide many opportunities to study new physics beyond the Standard Model, and to get precise measurements of the properties of the Higgs boson decaying to tau-leptons. We present the performance of the hadronic tau trigger taken in Run 1 data with the ATLAS detector at $\\sqrt{s}$ = 8 TeV pp collision. One of the major challenges is to sustain high efficiencies in events with multiple interactions. To do this we introduced faster tracking methods, multivariate selection techniques, and new t...

  11. Etiology of myofascial trigger points

    NARCIS (Netherlands)

    Bron, C.; Dommerholt, J.D.

    2012-01-01

    Myofascial pain syndrome (MPS) is described as the sensory, motor, and autonomic symptoms caused by myofascial trigger points (TrPs). Knowing the potential causes of TrPs is important to prevent their development and recurrence, but also to inactivate and eliminate existing TrPs. There is general

  12. Etiology of myofascial trigger points

    NARCIS (Netherlands)

    Bron, C.; Dommerholt, J.D.

    2012-01-01

    Myofascial pain syndrome (MPS) is described as the sensory, motor, and autonomic symptoms caused by myofascial trigger points (TrPs). Knowing the potential causes of TrPs is important to prevent their development and recurrence, but also to inactivate and eliminate existing TrPs. There is general ag

  13. Suicide Triggers Described by Herodotus

    Science.gov (United States)

    Auchincloss, Stephane; Ahmadi, Jamshid

    2016-01-01

    Objective: The aim of this study was to better understand the triggers of suicide, particularly among the ancient Greek and Persian soldiers and commanders. Method: ‘Herodotus:TheHistories’ is a history of the rulers and soldiery who participated in the Greco-Persian wars (492-449 BCE). A new translation (2013) of this manuscript was studied. Accounts of suicide were collected and collated, with descriptions of circumstances, methods, and probable triggers. Results: Nine accounts of suicide were identified. Eight of these were named individuals (4 Greeks and 4 Persians); of whom, seven were male. Only one (not the female) appeared to act in response to a mental disorder. Other triggers of suicide included guilt, avoidance of dishonour/punishment and altruism. Cutting/ stabbing was the most common method; others included hanging, jumping, poison, and burning (the single female). Conclusion: While soldiers at a time of war do not reflect the general community, they are nevertheless members of their society. Thus, this evidence demonstrates that suicide triggered by burdensome circumstances (in addition to mental disorder) was known to the Greek and Persian people more than two millennia ago. PMID:27437010

  14. Insights into structural variations and genome rearrangements in prokaryotic genomes.

    Science.gov (United States)

    Periwal, Vinita; Scaria, Vinod

    2015-01-01

    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing.

  15. ALIS-FLP: Amplified ligation selected fragment-length polymorphism method for microbial genotyping

    DEFF Research Database (Denmark)

    Brillowska-Dabrowska, A.; Wianecka, M.; Dabrowski, Slawomir

    2008-01-01

    in that only one specific restriction enzyme (TspRI) is used. The cohesive ends of the DNA fragments are ligated with two types of oligonucleotide. A long oligonucleotide containing the primer site and the specific 9 nt 3 prime end, which is complementary to specific 9 nt, cohesive 3 prime end of the Tsp......RI genomic DNA fragment, and a short, degenerated, oligonucleotide covering the remaining TspRI cohesive ends. Other cohesive ends are covered by a short degenerated oligonucleotide lacking the primer site. The ligation mixture is used as a template for amplification using a single primer corresponding...... to the 5 prime end of the long, specific oligonucleotide. The selection of TspRI digested genomic DNA fragments for amplification is achieved by sequence selective ligation of the specific long oligonucleotide carrying the primer site to both ends of the specific target fragment. This technique allows...

  16. Nuclear energy release from fragmentation

    CERN Document Server

    Li, Cheng; Tsang, M B; Zhang, Feng-Shou

    2015-01-01

    Nuclear energy released by splitting Uranium and Thorium isotopes into two, three, four, up to eight fragments with nearly equal size are studied. We found that the energy released come from equally splitting the $^{235,238}$U and $^{230,232}$Th nuclei into to three fragments is largest. The statistical multifragmentation model is employed to calculate the probability of different breakup channels for the excited nuclei. Weighing the the probability distributions of fragments multiplicity at different excitation energies for the $^{238}$U nucleus, we found that an excitation energy between 1.2 and 2 MeV/u is optimal for the $^{235}$U, $^{238}$U, $^{230}$Th and $^{232}$Th nuclei to release nuclear energy of about 0.7-0.75 MeV/u.

  17. Trigger electronics for the ALICE PHOS detector

    CERN Document Server

    Müller, H; Musa, L; Yin, Z; Röhrich, D; Skaali, B; Sibiryak, Yu; Budnikov, D L

    2004-01-01

    The Photon Spectrometer of ALICE consists of 5 identical modules of 56 multiplied by 64 PWO crystals with a total of 100 degree azimuthal coverage of the barrel. The electronics required for implementing both the L0 trigger for high luminosity p-p physics and the L1 trigger for high p//T Pb+Pb physics has been studied. A full integration of the trigger logic into the detector's enclosure is based on analog transmission of fast trigger sums between stacks of front-end boards and trigger-router units. The latter contain 112 digitizer channels of 10bit, which are mapped into a single FPGA per trigger unit, covering areas of 24 multiplied by 16 crystals. The running modes allow for Level-0 trigger at 800ns and Level-1 at 6200ns trigger latencies. The design and status of the PHOS trigger electronics are outlined.

  18. Gene prediction in metagenomic fragments: A large scale machine learning approach

    Directory of Open Access Journals (Sweden)

    Morgenstern Burkhard

    2008-04-01

    Full Text Available Abstract Background Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. In contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous sequencing reads. One of the aims of all metagenomic sequencing projects is the identification of novel genes. Short length, for example, Sanger sequencing yields on average 700 bp fragments, and unknown phylogenetic origin of most fragments require approaches to gene prediction that are different from the currently available methods for genomes of single species. In particular, the large size of metagenomic samples requires fast and accurate methods with small numbers of false positive predictions. Results We introduce a novel gene prediction algorithm for metagenomic fragments based on a two-stage machine learning approach. In the first stage, we use linear discriminants for monocodon usage, dicodon usage and translation initiation sites to extract features from DNA sequences. In the second stage, an artificial neural network combines these features with open reading frame length and fragment GC-content to compute the probability that this open reading frame encodes a protein. This probability is used for the classification and scoring of gene candidates. With large scale training, our method provides fast single fragment predictions with good sensitivity and specificity on artificially fragmented genomic DNA. Additionally, this method is able to predict translation initiation sites accurately and distinguishes complete from incomplete genes with high reliability. Conclusion Large scale machine learning methods are well-suited for gene

  19. Hands as markers of fragmentation

    Directory of Open Access Journals (Sweden)

    A. Barnard

    2005-07-01

    Full Text Available Margaret Atwood is an internationally read, translated, and critiqued writer whose novels have established her as one of the most esteemed authors in English (McCombs & Palmer, 1991:1. Critical studies of her work deal mainly with notions of identity from psychoanalytical perspectives. This study has identified a gap in current critical studies on Atwood’s works, namely the challenging of textual unity which is paralleled in the challenging of the traditional (single narrative voice. The challenging of textual unity and the single narrative voice brings about the fragmentation of both. This article will focus on the role that hands play as markers of fragmentation in “The Blind Assassin” (2000. In the novel, the writing hand destabilises the narrative voice, since it is not connected to the voice of a single author. If the author of the text – the final signified – is eliminated, the text becomes fragmentary and open, inviting the reader to contribute to the creation of meaning. Hands play a signficant role in foregrounding the narrator’s fragmented identity, and consequently, the fragmentation of the text. We will investigate this concept in the light of Roland Barthes’ notion of the scriptor, whose hand is metaphorically severed from his or her “voice”. Instead of the text being a unified entity, it becomes unstable and it displays the absence of hierarchical textual levels. Based mainly on Barthes’ writings, this article concludes that hands foreground the narrator’s fragmented identity, which is paralleled in the fragmented text.

  20. 基于线粒体基因片段核苷酸多态性的亚洲栽培稻起源进化研究%Study on the Origin and Evolution of Asian Cultivated Rice Based on Gene Fragment Nucleotides Diversity of Mitochondrial Genome

    Institute of Scientific and Technical Information of China (English)

    曹立荣; 魏鑫; 黄娟; 乔卫华; 张万霞; 杨庆文

    2013-01-01

    亚洲栽培稻的祖先是普通野生稻,已成为世界公认的观点,然而亚洲栽培稻的2个亚种:粳稻和籼稻是一次起源还是二次起源仍存在很大争议,其起源地是国内还是国外依然是国际学者间争论的焦点.本文通过对184份亚洲栽培稻和203份普通野生稻3段基因序列cox3、cox1、orf 224和2段基因间序列ssv-39/178、rps2-trnfM的多样性研究,验证了以下观点:1)粳稻起源于中国,籼稻起源于中国和国外;2)亚洲栽培稻的起源为二次起源,即普通野生稻存在偏籼和偏粳2种类型,亚洲栽培稻的2个亚种籼稻和粳稻在进化过程中分别由偏籼型的普通野生稻和偏粳型的普通野生稻进化而来.%Wild rice ( Oryza rufipogon ) has been recognized as the ancestor of Asian cultivated rice ( Oryza sati-va). However, where and how cultivated rice originated from wild rice has been debated for a long time in the world. Moreover,whether the two subspecies of Asian cultivated rice, indica and japonica, were domesticated with the ways of single origin or multiple origins was still considerably controversial, and whether they originated from China or aboard was still the focus of debate among international scholars. In this study, 184 accessions of Asian cultivated rice and 203 accessions of Oryza rufipogon to be sequenced with 3 gene fragments (cox3 ,coxl, orf 224) and two inter gene regions( ssv-39/178 ,rps2-trnfM) in mitochondrial genome of rice were collected. Through the study of gene diversity of the five fragments, the following propositions were verified. First,the origin of japonica was in China, and the origin of indica was not only in China but also in foreign countries. Second,the subspecies of Asian cultivated rice were domesticated with two origins. In other words,common wild rice contained the indica-like and japonica-like types, and the two subspecies were evolved from the indica -like wild rice and the japonica-like wild rice respectively.

  1. Phenomenology of Dihadron Fragmentation Function

    CERN Document Server

    Courtoy, A

    2016-01-01

    We report on the phenomenological results obtained through Dihadron Fragmentation Functions related processes. In 2015, an update on the fitting techniques for the Dihadron Fragmentation Functions has led to an improved extraction of the transversity PDF and, as a consequence, the nucleon tensor charge. We discuss the impact of the determination of the latter on search for physics Beyond the Standard Model, focusing on the error treatment. We also comment on the future of the extraction of the subleading-twist PDF $e(x)$ from JLab soon-to-be-released Beam Spin Asymmetry data.

  2. Transversity and dihadron fragmentation functions

    CERN Document Server

    Bacchetta, A; Bacchetta, Alessandro; Radici, Marco

    2005-01-01

    The observation of the quark transversity distribution requires another soft object sensitive to the quark's transverse spin. Dihadron fragmentation functions represent a convenient tool to analyze partonic spin, which can influence the angular distribution of the two hadrons. In particular, the so-called interference fragmentation functions can be used to probe transversity both in semi-inclusive deep inelastic scattering as well as proton-proton collisions. We discuss two single-spin asymmetries sensitive to transversity in the these two processes, at leading twist and leading order in alpha_S.

  3. RIA Fragmentation Line Beam Dumps

    Energy Technology Data Exchange (ETDEWEB)

    Stein, W

    2003-08-08

    The Rare Isotope Accelerator project involves generating heavy-element ion beams for use in a fragmentation target line to produce beams for physics research. The main beam, after passing through the fragmentation target, may be dumped into a beam dump located in the vacuum cavity of the first dipole magnet. For a dump beam power of 100 kW, cooling is required to avoid excessive high temperatures. The proposed dump design involves rotating cylinders to spread out the energy deposition and turbulent subcooled water flow through internal water cooling passages to obtain high, nonboiling, cooling rates.

  4. Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Baroukh, Nadine; Rubin, Edward M.

    2003-05-15

    Deciphering the genetic code embedded within the human genome remains a significant challenge despite the human genome consortium's recent success at defining its linear sequence (Lander et al. 2001; Venter et al. 2001). While useful strategies exist to identify a large percentage of protein encoding regions, efforts to accurately define functional sequences in the remaining {approx}97 percent of the genome lag. Our primary interest has been to utilize the evolutionary relationship and the universal nature of genomic sequence information in vertebrates to reveal functional elements in the human genome. This has been achieved through the combined use of vertebrate comparative genomics to pinpoint highly conserved sequences as candidates for biological activity and transgenic mouse studies to address the functionality of defined human DNA fragments. Accordingly, we describe strategies and insights into functional sequences in the human genome through the use of comparative genomics coupled wit h functional studies in the mouse.

  5. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  6. A thermodynamic theory of dynamic fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Yew, Ching H. [Texas Univ., Austin, TX (United States); Taylor, P.A. [Sandia National Labs., Albuquerque, NM (United States)

    1993-08-01

    We present a theory of dynamic fragmentation of brittle materials based on thermodynamic arguments. We recover the expressions for average fragment size and number as originally derived by Grady. We extend the previous work by obtaining descriptions of fragment size distribution and compressibility change due to the fragmentation process. The size distribution is assumed to be proportional to the spectral power of the strain history and a sample distribution is presented for a fragmentation process corresponding to a constant rate strain history. The description of compressibility change should be useful in computational studies of fragmentation. These results should provide insight into the process of fragmentation of brittle materials from hypervelocity impact.

  7. The trigger system of the NOMAD experiment

    CERN Document Server

    Altegoer, J; Boyd, S; Cardini, A; Farthouat, Philippe; Ferrari, R; Geppert, D; Gössling, C; Huta, W; Hyett, N; Koch, N; Lanza, A; Long, J; Moorhead, G F; Poolmann, D; Poulsen, C; Rubbia, André; Schmidt, B; Soler, F J P; Steele, D; Varvell, K E; Weisse, T; Winton, L J; Yabsley, B D; Voullieme, A

    1999-01-01

    The NOMAD trigger system is described in the present paper. It is made up of a largearea plastic scintillator veto system, two trigger scintillator planes inside a 0.4~Tmagnetic field and their associated trigger electronics. Special features of the systemconsist of the use of proximity mesh photomultipliers which allow the trigger scintillators to operate in the magnetic field, and the use of custom-built VME moduleswhich perform the trigger logic decisions, the signal synchronisation and gate generation,event counting and livetime calculations. This paper also includes a description of each of the NOMAD triggers, with their calculated and measured rates, efficiencies and livetimes.

  8. The ALICE high level trigger

    Science.gov (United States)

    Alt, T.; Grastveit, G.; Helstrup, H.; Lindenstruth, V.; Loizides, C.; Röhrich, D.; Skaali, B.; Steinbeck, T.; Stock, R.; Tilsner, H.; Ullaland, K.; Vestbø, A.; Vik, T.; Wiebalck, A.; the ALICE Collaboration

    2004-08-01

    The ALICE experiment at LHC will implement a high-level trigger system for online event selection and/or data compression. The largest computing challenge is posed by the TPC detector, which requires real-time pattern recognition. The system entails a very large processing farm that is designed for an anticipated input data stream of 25 GB s-1. In this paper, we present the architecture of the system and the current state of the tracking methods and data compression applications.

  9. ATLAS FTK: Fast Track Trigger

    CERN Document Server

    Volpi, Guido; The ATLAS collaboration

    2015-01-01

    An overview of the ATLAS Fast Tracker processor is presented, reporting the design of the system, its expected performance, and the integration status. The next LHC runs, with a significant increase in instantaneous luminosity, will provide a big challenge to the trigger and data acquisition systems of all the experiments. An intensive use of the tracking information at the trigger level will be important to keep high efficiency in interesting events, despite the increase in multiple p-p collisions per bunch crossing (pile-up). In order to increase the use of tracks within the High Level Trigger (HLT), the ATLAS experiment planned the installation of an hardware processor dedicated to tracking: the Fast TracKer (FTK) processor. The FTK is designed to perform full scan track reconstruction at every Level-1 accept. To achieve this goal, the FTK uses a fully parallel architecture, with algorithms designed to exploit the computing power of custom VLSI chips, the Associative Memory, as well as modern FPGAs. The FT...

  10. Development of autonomous triggering instrumentation

    Science.gov (United States)

    Watkins, Steve E.; Swift, Theresa M.; Fonda, James W.

    2008-03-01

    Triggering instrumentation for autonomous monitoring of load-induced strain is described for economical, fast bridge inspection. The development addresses one aspect for the management of transportation infrastructure - bridge monitoring and inspection. The objectives are to provide quantitative performance information from a load test, to minimize the setup time at the bridge, and to minimize the closure time to traffic. Multiple or networked measurements can be made for a prescribed loading sequence. The proposed smart system consists of in-situ strain sensors, an embedded data acquisition module, and a measurement triggering system. A companion control unit is mounted on the truck serving as the load. As the truck moves to the proper position, the desired measurement is automatically relayed back to the control unit. In this work, the testing protocol is developed and the performance parameters for the triggering and data acquisition are measured. The test system uses a dedicated wireless sensor mote and an infrared positioning system. The electronic procedure offers improvements in available information and economics.

  11. Stimulus conflict triggers behavioral avoidance.

    Science.gov (United States)

    Dignath, David; Eder, Andreas B

    2015-12-01

    According to a recent extension of the conflict-monitoring theory, conflict between two competing response tendencies is registered as an aversive event and triggers a motivation to avoid the source of conflict. In the present study, we tested this assumption. Over five experiments, we examined whether conflict is associated with an avoidance motivation and whether stimulus conflict or response conflict triggers an avoidance tendency. Participants first performed a color Stroop task. In a subsequent motivation test, participants responded to Stroop stimuli with approach- and avoidance-related lever movements. These results showed that Stroop-conflict stimuli increased the frequency of avoidance responses in a free-choice motivation test, and also increased the speed of avoidance relative to approach responses in a forced-choice test. High and low proportions of response conflict in the Stroop task had no effect on avoidance in the motivation test. Avoidance of conflict was, however, obtained even with new conflict stimuli that had not been presented before in a Stroop task, and when the Stroop task was replaced with an unrelated filler task. Taken together, these results suggest that stimulus conflict is sufficient to trigger avoidance.

  12. Short-term genetic consequences of habitat loss and fragmentation for the neotropical palm Oenocarpus bataua.

    Science.gov (United States)

    Browne, L; Ottewell, K; Karubian, J

    2015-11-01

    Habitat loss and fragmentation may impact animal-mediated dispersal of seed and pollen, and a key question is how the genetic attributes of plant populations respond to these changes. Theory predicts that genetic diversity may be less sensitive to such disruptions in the short term, whereas inbreeding and genetic structure may respond more strongly. However, results from studies to date vary in relation to species, context and the parameter being assessed, triggering calls for more empirical studies, especially from the tropics, where plant-animal dispersal mutualisms are both disproportionately common and at risk. We compared the genetic characteristics of adults and recruits in a long-lived palm Oenocarpus bataua in a recently fragmented landscape (fragments and one nearby continuous forest. Our goal was to assess short-term consequences of fragmentation, with a focus on how well empirical data from this system follow theoretical expectations. Mostly congruent with predictions, we found stronger genetic differentiation and fine-scale spatial genetic structure among recruits in fragments compared with recruits in continuous forest, but we did not record differences in genetic diversity or inbreeding, nor did we record any differences between adults in fragments and adults in continuous forest. Our findings suggest that genetic characteristics of populations vary in their sensitivity to change in response to habitat loss and fragmentation, and that fine-scale spatial genetic structure may be a particularly useful indicator of genetic change in recently fragmented landscapes.

  13. Population pressure and farm fragmentation:

    African Journals Online (AJOL)

    user

    small but farms are further fragmented into diminutive size fields due to ... terms of household characteristics; land use and performance indicators; technology adoption .... 'best' unit of measurement of farm size, and size of enterprises within farms will ..... less common, accounting for 18 percent (3 percent) and 10 percent (7.

  14. Nuclear energy release from fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Li, Cheng [The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Beijing Radiation Center, Beijing 100875 (China); Souza, S.R. [Instituto de Física, Universidade Federal do Rio de Janeiro Cidade Universitária, Caixa Postal 68528, 21945-970 Rio de Janeiro (Brazil); Tsang, M.B. [The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Beijing Radiation Center, Beijing 100875 (China); National Superconducting Cyclotron Laboratory and Physics and Astronomy Department, Michigan State University, East Lansing, MI 48824 (United States); Zhang, Feng-Shou, E-mail: fszhang@bnu.edu.cn [The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Beijing Radiation Center, Beijing 100875 (China); Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000 (China)

    2016-08-15

    It is well known that binary fission occurs with positive energy gain. In this article we examine the energetics of splitting uranium and thorium isotopes into various numbers of fragments (from two to eight) with nearly equal size. We find that the energy released by splitting {sup 230,232}Th and {sup 235,238}U into three equal size fragments is largest. The statistical multifragmentation model (SMM) is applied to calculate the probability of different breakup channels for excited nuclei. By weighing the probability distributions of fragment multiplicity at different excitation energies, we find the peaks of energy release for {sup 230,232}Th and {sup 235,238}U are around 0.7–0.75 MeV/u at excitation energy between 1.2 and 2 MeV/u in the primary breakup process. Taking into account the secondary de-excitation processes of primary fragments with the GEMINI code, these energy peaks fall to about 0.45 MeV/u.

  15. Nuclear energy release from fragmentation

    Science.gov (United States)

    Li, Cheng; Souza, S. R.; Tsang, M. B.; Zhang, Feng-Shou

    2016-08-01

    It is well known that binary fission occurs with positive energy gain. In this article we examine the energetics of splitting uranium and thorium isotopes into various numbers of fragments (from two to eight) with nearly equal size. We find that the energy released by splitting 230,232Th and 235,238U into three equal size fragments is largest. The statistical multifragmentation model (SMM) is applied to calculate the probability of different breakup channels for excited nuclei. By weighing the probability distributions of fragment multiplicity at different excitation energies, we find the peaks of energy release for 230,232Th and 235,238U are around 0.7-0.75 MeV/u at excitation energy between 1.2 and 2 MeV/u in the primary breakup process. Taking into account the secondary de-excitation processes of primary fragments with the GEMINI code, these energy peaks fall to about 0.45 MeV/u.

  16. The Fragmentation of Literary Theory

    Science.gov (United States)

    Howard, Jennifer

    2005-01-01

    Syllabi from some 20 colleges and universities were reviewed with prominent English and literature departments and a discussion was held with a number of professors who teach literary theory. It is suggested that devolution and fragmentation of theory might be a survival strategy, an adaptation to the new realties of academic institutions.

  17. Fragmented nature : consequences for biodiversity

    NARCIS (Netherlands)

    Olff, Han; Ritchie, Mark E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  18. Fragmented nature: consequences for biodiversity

    NARCIS (Netherlands)

    Olff, H.; Ritchie, M.E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  19. Fragmented nature : consequences for biodiversity

    NARCIS (Netherlands)

    Olff, Han; Ritchie, Mark E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  20. Fragmented nature: consequences for biodiversity

    NARCIS (Netherlands)

    Olff, H.; Ritchie, M.E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  1. The VERDI fission fragment spectrometer

    Science.gov (United States)

    Frégeau, M. O.; Bryś, T.; Gamboni, Th.; Geerts, W.; Oberstedt, S.; Oberstedt, A.; Borcea, R.

    2013-12-01

    The VERDI time-of-flight spectrometer is dedicated to measurements of fission product yields and of prompt neutron emission data. Pre-neutron fission-fragment masses will be determined by the double time-of-flight (TOF) technique. For this purpose an excellent time resolution is required. The time of flight of the fragments will be measured by electrostatic mirrors located near the target and the time signal coming from silicon detectors located at 50 cm on both sides of the target. This configuration, where the stop detector will provide us simultaneously with the kinetic energy of the fragment and timing information, significantly limits energy straggling in comparison to legacy experimental setup where a thin foil was usually used as a stop detector. In order to improve timing resolution, neutron transmutation doped silicon will be used. The high resistivity homogeneity of this material should significantly improve resolution in comparison to standard silicon detectors. Post-neutron fission fragment masses are obtained form the time-of-flight and the energy signal in the silicon detector. As an intermediary step a diamond detector will also be used as start detector located very close to the target. Previous tests have shown that poly-crystalline chemical vapour deposition (pCVD) diamonds provides a coincidence time resolution of 150 ps not allowing complete separation between very low-energy fission fragments, alpha particles and noise. New results from using artificial single-crystal diamonds (sCVD) show similar time resolution as from pCVD diamonds but also sufficiently good energy resolution.

  2. The VERDI fission fragment spectrometer

    Directory of Open Access Journals (Sweden)

    Frégeau M.O.

    2013-12-01

    Full Text Available The VERDI time-of-flight spectrometer is dedicated to measurements of fission product yields and of prompt neutron emission data. Pre-neutron fission-fragment masses will be determined by the double time-of-flight (TOF technique. For this purpose an excellent time resolution is required. The time of flight of the fragments will be measured by electrostatic mirrors located near the target and the time signal coming from silicon detectors located at 50 cm on both sides of the target. This configuration, where the stop detector will provide us simultaneously with the kinetic energy of the fragment and timing information, significantly limits energy straggling in comparison to legacy experimental setup where a thin foil was usually used as a stop detector. In order to improve timing resolution, neutron transmutation doped silicon will be used. The high resistivity homogeneity of this material should significantly improve resolution in comparison to standard silicon detectors. Post-neutron fission fragment masses are obtained form the time-of-flight and the energy signal in the silicon detector. As an intermediary step a diamond detector will also be used as start detector located very close to the target. Previous tests have shown that poly-crystalline chemical vapour deposition (pCVD diamonds provides a coincidence time resolution of 150 ps not allowing complete separation between very low-energy fission fragments, alpha particles and noise. New results from using artificial single-crystal diamonds (sCVD show similar time resolution as from pCVD diamonds but also sufficiently good energy resolution.

  3. Novel Proresolving Aspirin-Triggered DHA Pathway

    National Research Council Canada - National Science Library

    Serhan, Charles N; Fredman, Gabrielle; Yang, Rong; Karamnov, Sergey; Belayev, Ludmila S; Bazan, Nicolas G; Zhu, Min; Winkler, Jeremy W; Petasis, Nicos A

    2011-01-01

    .... We report an aspirin-triggered DHA metabolome that biosynthesizes a potent product in inflammatory exudates and human leukocytes, namely aspirin-triggered Neuroprotectin D1/Protectin D1 [AT-(NPD1/PD1...

  4. Event Builder and Level 3 trigger at the CDF experiment

    Science.gov (United States)

    Anikeev, K.; Bauer, G.; Furić, I.; Holmgren, D.; Korn, A.; Kravchenko, I.; Mulhearn, M.; Ngan, P.; Paus, Ch.; Rakitin, A.; Rechenmacher, R.; Shah, T.; Sphicas, P.; Sumorok, K.; Tether, S.; Tseng, J.; Wüerthwein, F.

    2001-10-01

    The Event Builder and Level 3 trigger systems of the CDF experiment at Fermilab are required to process about 300 events per second, with an average event size of ˜200 KB. In the event building process the event is assembled from 15 sources supplying event fragments with roughly equal sizes of 12-16 KB. In the subsequent commercial processor-based Level 3 trigger, the events are reconstructed and trigger algorithms are applied. The CPU power required for filtering such a high data throughput rate exceeds 45 000 MIPS. To meet these requirements a distributed and scalable architecture has been chosen. It is based on commodity components: VME-based CPU's for the data read out, an ATM switch for the event building and Pentium-based personal computers running the Linux operating system for the event processing. Event flow through ATM is controlled by a reflective memory ring. The roughly homogeneous distribution of the expected load allows the use of 100 Mbps Ethernet for event distribution and collection within the Level 3 system. Preliminary results from a test system obtained during the last year are presented.

  5. Triggers for a high sensitivity charm experiment

    Energy Technology Data Exchange (ETDEWEB)

    Christian, D.C.

    1994-07-01

    Any future charm experiment clearly should implement an E{sub T} trigger and a {mu} trigger. In order to reach the 10{sup 8} reconstructed charm level for hadronic final states, a high quality vertex trigger will almost certainly also be necessary. The best hope for the development of an offline quality vertex trigger lies in further development of the ideas of data-driven processing pioneered by the Nevis/U. Mass. group.

  6. Fragmentation

    Science.gov (United States)

    K.H. Riitters

    2009-01-01

    Effective resource management takes into account the administrative and biophysical settings within which natural resources occur. A setting may be described in many ways; for example, by forest land ownership, by reserved and roadless designation, or by the distribution of human populations in relation to forest (chapter 3). The physical arrangement of forest in a...

  7. DNA fragmentation of spermatozoa and assisted reproduction technology.

    Science.gov (United States)

    Henkel, Ralf; Kierspel, Eva; Hajimohammad, Marjam; Stalf, Thomas; Hoogendijk, Christiaan; Mehnert, Claas; Menkveld, Roelof; Schill, Wolf-Bernhard; Kruger, Thinus F

    2003-01-01

    Despite the ever-increasing knowledge of the fertilization process, there is still a need for better understanding of the causes of sperm DNA fragmentation and its impact on fertilization and pregnancy. For this reason, human sperm DNA fragmentation was investigated by means of the terminal deoxynucleotidyl transferase-mediated dUDP nick-end labelling (TUNEL) assay and the production of reactive oxygen species (ROS) in the ejaculate and in the spermatozoa themselves. These data were correlated with fertilization and pregnancy data from IVF and intracytoplasmic sperm injection (ICSI) patients. Sperm DNA fragmentation did not correlate with fertilization rate, but there was a significantly reduced pregnancy rate in IVF patients inseminated with TUNEL-positive spermatozoa. ICSI patients exhibited the same tendency. This implies that spermatozoa with damaged DNA are able to fertilize an oocyte, but at the time the paternal genome is switched on, further development stops. The determination of ROS in the ejaculate and the percentage of ROS-producing spermatozoa revealed markedly stronger correlations between sperm functions (i.e. motility) and the percentage of ROS-producing spermatozoa. The influence of seminal leukocytes, known to produce large amounts of oxidants, on sperm DNA fragmentation should not be neglected.

  8. [Genome editing of industrial microorganism].

    Science.gov (United States)

    Zhu, Linjiang; Li, Qi

    2015-03-01

    Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

  9. Efficient and accurate fragmentation methods.

    Science.gov (United States)

    Pruitt, Spencer R; Bertoni, Colleen; Brorsen, Kurt R; Gordon, Mark S

    2014-09-16

    Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum

  10. Infrasonic Observations from Triggered Lightning

    Science.gov (United States)

    Arechiga, R. O.; Johnson, J. B.; Edens, H. E.; Rison, W.; Thomas, R. J.; Eack, K.; Eastvedt, E. M.

    2009-12-01

    We measured acoustic signals during both triggered and natural lightning. A comparative analysis of simultaneous data from the Lightning Mapping Array (LMA), acoustic measurements and digital high-speed photography operating in the same area was made. Acoustic emissions, providing quantitative estimates of acoustic power and spectral content, will complement coincident investigations, such as X-ray emissions. Most cloud-to-ground lightning flashes lower negative charge to ground, but flashes that lower positive charge to ground are often unusually destructive and are less understood. The New Mexico Tech Lightning Mapping Array (LMA) locates the sources of impulsive RF radiation produced by lightning flashes in three spatial dimensions and time, operating in the 60 - 66 MHz television band. However, positive breakdown is rarely detected by the LMA and positive leader channels are outlined only by recoil events. Positive cloud-to-ground (CG) channels are usually not mapped (or partially mapped because they may have recoil events). Acoustic and electric field instruments are a good complement to the LMA, since they can detect both negative and positive leaders. An array of five stations was deployed during the Summer of 2009 (July 20 to August 13) in the Magdalena mountains of New Mexico, to monitor infrasound (below 20 Hz) and audio range sources due to natural and triggered lightning. The stations were located at close (57 m), medium (303 and 537 m) and far (1403 and 2556 m) distances surrounding the triggering site. Each station consisted of five sensors, one infrasonic and one in the audio range at the center, and three infrasonic in a triangular configuration. This research will provide a more complete picture, and provide further insight into the nature of lightning.

  11. The ALICE high level trigger

    Energy Technology Data Exchange (ETDEWEB)

    Alt, T [Kirchhoff Institute for Physics, University of Heidelberg (Germany); Grastveit, G [Department of Physics and Technology, University of Bergen (Norway); Helstrup, H [Faculty of Engineering, Bergen University College (Norway); Lindenstruth, V [Kirchhoff Institute for Physics, University of Heidelberg (Germany); Loizides, C [Institute for Nuclear Physics, University of Frankfurt (Germany); Roehrich, D [Department of Physics and Technology, University of Bergen (Norway); Skaali, B [Department of Physics, University of Oslo (Norway); Steinbeck, T [Kirchhoff Institute for Physics, University of Heidelberg (Germany); Stock, R [Institute for Nuclear Physics, University of Frankfurt (Germany); Tilsner, H [Kirchhoff Institute for Physics, University of Heidelberg (Germany); Ullaland, K [Department of Physics and Technology, University of Bergen (Norway); Vestboe, A [Faculty of Engineering, Bergen University College (Norway); Vik, T [Department of Physics, University of Oslo (Norway); Wiebalck, A [Kirchhoff Institute for Physics, University of Heidelberg (Germany)

    2004-08-01

    The ALICE experiment at LHC will implement a high-level trigger system for online event selection and/or data compression. The largest computing challenge is posed by the TPC detector, which requires real-time pattern recognition. The system entails a very large processing farm that is designed for an anticipated input data stream of 25 GB s{sup -1}. In this paper, we present the architecture of the system and the current state of the tracking methods and data compression applications.

  12. Trigger efficiencies at BES III

    CERN Document Server

    Berger, N; Liu, Z A; Jin, D P; Xu, H; Gong, W X; Wang, K; Cao, G F

    2010-01-01

    Trigger efficiencies at BES III were determined for both the J/psi and psi' data taking of 2009. Both dedicated runs and physics datasets are used; efficiencies are presented for Bhabha-scattering events, generic hadronic decay events involving charged tracks, dimuon events and psi' -> pi+pi-J/psi, J/psi -> l+l- events (l an electron or muon). The efficiencies are found to lie well above 99% for all relevant physics cases, thus fulfilling the BES III design specifications.

  13. Capturing Biological Activity in Natural Product Fragments by Chemical Synthesis.

    Science.gov (United States)

    Crane, Erika A; Gademann, Karl

    2016-03-14

    Natural products have had an immense influence on science and have directly led to the introduction of many drugs. Organic chemistry, and its unique ability to tailor natural products through synthesis, provides an extraordinary approach to unlock the full potential of natural products. In this Review, an approach based on natural product derived fragments is presented that can successfully address some of the current challenges in drug discovery. These fragments often display significantly reduced molecular weights, reduced structural complexity, a reduced number of synthetic steps, while retaining or even improving key biological parameters such as potency or selectivity. Examples from various stages of the drug development process up to the clinic are presented. In addition, this process can be leveraged by recent developments such as genome mining, antibody-drug conjugates, and computational approaches. All these concepts have the potential to identify the next generation of drug candidates inspired by natural products.

  14. Fragmentation in the biopharmaceutical industry.

    Science.gov (United States)

    Goldsmith, Andrew D; Varela, Francisco E

    2017-02-01

    The large number of biopharmaceutical mergers and acquisitions (M&A) that occurred over the past decade has generated questions about whether the industry is consolidating around too-few players, negatively impacting both the number of medicines developed and overall innovation. However, closer examination of the level of biopharmaceutical consolidation by prescription sales shows that the industry was more fragmented in 2015 than in 2003. The trend towards increasing fragmentation is also observed across noncommercial and independent metrics over the same time period. The number and size of M&A deals has masked an active and competitive marketplace in which market growth and the number of companies entering the market exceeded the apparent reduction in the number of players caused by acquisitions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Fragment separator momentum compression schemes

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, Laura, E-mail: bandura@anl.gov [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Erdelyi, Bela [Argonne National Laboratory, Argonne, IL 60439 (United States); Northern Illinois University, DeKalb, IL 60115 (United States); Hausmann, Marc [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Kubo, Toshiyuki [RIKEN Nishina Center, RIKEN, Wako (Japan); Nolen, Jerry [Argonne National Laboratory, Argonne, IL 60439 (United States); Portillo, Mauricio [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Sherrill, Bradley M. [National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States)

    2011-07-21

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  16. Fragment separator momentum compression schemes.

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, L.; Erdelyi, B.; Hausmann, M.; Kubo, T.; Nolen, J.; Portillo, M.; Sherrill, B.M. (Physics); (MSU); (Northern Illinois Univ.); (RIKEN)

    2011-07-21

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  17. Fragment correlations from NAUTILUS multidetector

    Energy Technology Data Exchange (ETDEWEB)

    Bizard, G. [Caen Univ., 14 (France). Lab. de Physique Corpusculaire

    1995-12-31

    It is shown on a few examples how heavy fragment correlations, induced either by conservation laws or by Coulomb interaction can bring physical information on nuclear reactions. All the experimental data discussed have been obtained at GANIL using the NAUTILUS gaseous multi detectors DELF and XYZT, which - due to their good spatial and time resolution and their large solid angle coverage - have proved to be efficient tools for multifragment correlation studies. Different reactions of Ar, Kr, Xe, and Pb beams on Au targets are discussed. It is shown that velocity and angular correlations between fragments provide a powerful clock to scrutinize the details of the hot nuclei decay history. (K.A.). 18 refs., 6 figs.

  18. Fragmentation in filamentary molecular clouds

    CERN Document Server

    Contreras, Yanett; Rathborne, Jill M; Sanhueza, Patricio

    2015-01-01

    Recent surveys of dust continuum emission at sub-mm wavelengths have shown that filamentary molecular clouds are ubiquitous along the Galactic plane. These structures are inhomogeneous, with over-densities that are sometimes associated with infrared emission and active of star formation. To investigate the connection between filaments and star formation, requires an understanding of the processes that lead to the fragmentation of filaments and a determination of the physical properties of the over-densities (clumps). In this paper, we present a multi-wavelength study of five filamentary molecular clouds, containing several clumps in different evolutionary stages of star formation. We analyse the fragmentation of the filaments and derive the physical properties of their clumps. We find that the clumps in all filaments have a characteristic spacing consistent with the prediction of the `sausage' instability theory, regardless of the complex morphology of the filaments or their evolutionary stage. We also find t...

  19. Fragmentering og korridorer i landskabet

    DEFF Research Database (Denmark)

    Hammershøj, M.; Madsen, A. B.

    , at fragmentering af habitater resulterer i en reduktion og isolering af mange plante- og dyrepopulationer. Det er desuden vist, at korridorer har en funktion som habitater, hvilket er medvirkende til, at et område med korridorer kan huse flere arter og individer end et tilsvarende område uden korridorer. Der......Rapporten indeholder en litteraturudredning, der er baseret på en bearbejdning af den tilgængelige nationale og internationale litteratur omhandlende fragmentering og korridorer på det botaniske og zoologiske område. I alt 1.063 titler ligger til grund for udredningen. Udredningen har vist...... mangler dog entydige beviser for, at korridorer kan være af afgørende betydning for rekolonisering af habitater, i hvilke en given art er forsvundet. Afslutningsvis gives en liste med forskningsbehov samt en række anbefalinger....

  20. Asymmetry effects in fragment production

    Science.gov (United States)

    Kaur, Manpreet; Kaur, Varinderjit

    2016-05-01

    The production of different fragments has been studied by taking into account the mass asymmetry of the reaction and employing the momentum dependent interactions. Two different set of asymmetric reactions have been analyzed while keeping Atotal fixed using soft momentum dependent equation of state. Our results indicate that the impact of momentum dependent interactions is different in lighter projectile systems as compared to heavier ones. The comparative analysis of IQMD simulations with the experimental data in case of heavier projectile and lighter target system for the reaction of 197Au+27Al (η = 0.7) at E = 600 MeV/nucleon shows that with the inclusion of MDI we are able, upto some extent, to reproduce the experimental universality of rise and fall of intermediate mass fragments (IMFs).

  1. The fragmentation of Kosmos 2163

    Science.gov (United States)

    1992-01-01

    On 6 Dec. 1991 Kosmos 2163, a maneuverable Soviet spacecraft which had been in orbit for 58 days, experienced a major breakup at an altitude of approximately 210 km. Although numerous pieces of debris were created, the fragments decayed rapidly leaving no long-term impact on the near-Earth environment. The assessed cause of the event is the deliberate detonation of an explosive device. Details of this event are presented.

  2. Modeling of Fragmentation of Asteroids

    Science.gov (United States)

    Agrawal, Parul; Prabhu, Dinesh K.; Carlozzi, Alexander; Hart, Kenneth; Bryson, Katie; Sears, Derek

    2015-01-01

    The objective of this study is to understand fragmentation and fracture of a given asteroid and mechanisms of break-up. The focus of the present work is to develop modeling techniques for stony asteroids in 10m-100m range to answer two questions: 1) What is the role of material makeup of an asteroid in the stress distribution? 2)How is stress distribution altered in the presence of pre-existing defects?

  3. Fragmentation measurement using image processing

    Directory of Open Access Journals (Sweden)

    Farhang Sereshki

    2016-12-01

    Full Text Available In this research, first of all, the existing problems in fragmentation measurement are reviewed for the sake of its fast and reliable evaluation. Then, the available methods used for evaluation of blast results are mentioned. The produced errors especially in recognizing the rock fragments in computer-aided methods, and also, the importance of determination of their sizes in the image analysis methods are described. After reviewing the previous work done, an algorithm is proposed for the automated determination of rock particles’ boundary in the Matlab software. This method can determinate automatically the particles boundary in the minimum time. The results of proposed method are compared with those of Split Desktop and GoldSize software in two automated and manual states. Comparing the curves extracted from different methods reveals that the proposed approach is accurately applicable in measuring the size distribution of laboratory samples, while the manual determination of boundaries in the conventional software is very time-consuming, and the results of automated netting of fragments are very different with the real value due to the error in separation of the objects.

  4. Residual Fragments after Percutaneous Nephrolithotomy

    Directory of Open Access Journals (Sweden)

    Kaan Özdedeli

    2012-09-01

    Full Text Available Clinically insignificant residual fragments (CIRFs are described as asymptomatic, noninfectious and nonobstructive stone fragments (≤4 mm remaining in the urinary system after the last session of any intervention (ESWL, URS or PCNL for urinary stones. Their insignificance is questionable since CIRFs could eventually become significant, as their presence may result in recurrent stone growth and they may cause pain and infection due to urinary obstruction. They may become the source of persistent infections and a significant portion of the patients will have a stone-related event, requiring auxilliary interventions. CT seems to be the ultimate choice of assessment. Although there is no concensus about the timing, recent data suggests that it may be performed one month after the procedure. However, imaging can be done in the immediate postoperative period, if there are no tubes blurring the assessment. There is some evidence indicating that selective medical therapy may have an impact on decreasing stone formation rates. Retrograde intrarenal surgery, with its minimally invasive nature, seems to be the best way to deal with residual fragments.

  5. The Database Driven ATLAS Trigger Configuration System

    CERN Document Server

    Martyniuk, Alex; The ATLAS collaboration

    2015-01-01

    This contribution describes the trigger selection configuration system of the ATLAS low- and high-level trigger (HLT) and the upgrades it received in preparation for LHC Run 2. The ATLAS trigger configuration system is responsible for applying the physics selection parameters for the online data taking at both trigger levels and the proper connection of the trigger lines across those levels. Here the low-level trigger consists of the already existing central trigger (CT) and the new Level-1 Topological trigger (L1Topo), which has been added for Run 2. In detail the tasks of the configuration system during the online data taking are Application of the selection criteria, e.g. energy cuts, minimum multiplicities, trigger object correlation, at the three trigger components L1Topo, CT, and HLT On-the-fly, e.g. rate-dependent, generation and application of prescale factors to the CT and HLT to adjust the trigger rates to the data taking conditions, such as falling luminosity or rate spikes in the detector readout ...

  6. Chlamydia causes fragmentation of the Golgi compartment to ensure reproduction.

    Science.gov (United States)

    Heuer, Dagmar; Rejman Lipinski, Anette; Machuy, Nikolaus; Karlas, Alexander; Wehrens, Andrea; Siedler, Frank; Brinkmann, Volker; Meyer, Thomas F

    2009-02-05

    The obligate intracellular bacterium Chlamydia trachomatis survives and replicates within a membrane-bound vacuole, termed the inclusion, which intercepts host exocytic pathways to obtain nutrients. Like many other intracellular pathogens, C. trachomatis has a marked requirement for host cell lipids, such as sphingolipids and cholesterol, produced in the endoplasmic reticulum and the Golgi apparatus. However, the mechanisms by which intracellular pathogens acquire host cell lipids are not well understood. In particular, no host cell protein responsible for transporting Golgi-derived lipids to the chlamydial inclusions has yet been identified. Here we show that Chlamydia infection in human epithelial cells induces Golgi fragmentation to generate Golgi ministacks surrounding the bacterial inclusion. Ministack formation is triggered by the proteolytic cleavage of the Golgi matrix protein golgin-84. Inhibition of golgin-84 truncation prevents Golgi fragmentation, causing a block in lipid acquisition and maturation of C. trachomatis. Golgi fragmentation by means of RNA-interference-mediated knockdown of distinct Golgi matrix proteins before infection enhances bacterial maturation. Our data functionally connect bacteria-induced golgin-84 cleavage, Golgi ministack formation, lipid acquisition and intracellular pathogen growth. We show that C. trachomatis subverts the structure and function of an entire host cell organelle for its own advantage.

  7. Triggering with the ALICE TRD

    CERN Document Server

    Klein, Jochen

    2011-01-01

    We discuss how a level-1 trigger, about 8 us after a hadron-hadron collision, can be derived from the Transition Radiation Detector (TRD) in A Large Ion Collider Experiment (ALICE) at the LHC. Chamber-wise track segments from fast on-detector reconstruction are read out with position, angle and electron likelihood. In the Global Tracking Unit up to 6 tracklets from a particle traversing the detector layers are matched and used for the reconstruction of transverse momentum and electron identification. Such tracks form the basis for versatile and flexible trigger conditions, e.g. single high-pt hadron, single high-pt electron, di-electron (J/Psi, Upsilon) and at least n close high-pt tracks (jet). The need for low-latency on-line reconstruction poses challenges on the detector operation. The calibration for gain (pad-by-pad) and drift velocity must be applied already in the front-end electronics. Due to changes in pressure and gas composition an on-line monitoring and feedback loop for these parameters is requi...

  8. The UA1 trigger processor

    CERN Document Server

    Grayer, G H

    1981-01-01

    Experiment UA1 is a large multipurpose spectrometer at the CERN proton-antiproton collider. The principal trigger is formed on the basis of the energy deposition in calorimeters. A trigger decision taken in under 2.4 microseconds can avoid dead-time losses due to the bunched nature of the beam. To achieve this fast 8-bit charge to digital converters have been built followed by two identical digital processors tailored to the experiment. The outputs of groups of the 2440 photomultipliers in the calorimeters are summed to form a total of 288 input channels to the ADCs. A look-up table in RAM is used to convert the digitised photomultiplier signals to energy in one processor, and to transverse energy in the other. Each processor forms four sums from a chosen combination of input channels, and also counts the number of clusters with electromagnetic or hadronic energy above pre-determined levels. Up to twelve combinations of these conditions, together with external information, may be combined in coincidence or in...

  9. Energy parasites trigger oncogene mutation.

    Science.gov (United States)

    Pokorný, Jiří; Pokorný, Jan; Jandová, Anna; Kobilková, Jitka; Vrba, Jan; Vrba, Jan

    2016-10-01

    Cancer initialization can be explained as a result of parasitic virus energy consumption leading to randomized genome chemical bonding. Analysis of experimental data on cell-mediated immunity (CMI) containing about 12,000 cases of healthy humans, cancer patients and patients with precancerous cervical lesions disclosed that the specific cancer and the non-specific lactate dehydrogenase-elevating (LDH) virus antigen elicit similar responses. The specific antigen is effective only in cancer type of its origin but the non-specific antigen in all examined cancers. CMI results of CIN patients display both healthy and cancer state. The ribonucleic acid (RNA) of the LDH virus parasitizing on energy reduces the ratio of coherent/random oscillations. Decreased effect of coherent cellular electromagnetic field on bonding electrons in biological macromolecules leads to elevating probability of random genome reactions. Overlapping of wave functions in biological macromolecules depends on energy of the cellular electromagnetic field which supplies energy to bonding electrons for selective chemical bonds. CMI responses of cancer and LDH virus antigens in all examined healthy, precancerous and cancer cases point to energy mechanism in cancer initiation. Dependence of the rate of biochemical reactions on biological electromagnetic field explains yet unknown mechanism of genome mutation.

  10. Hadronic triggers and trigger object-level analysis at ATLAS

    CERN Document Server

    Zaripovas, Donatas Ramilas; The ATLAS collaboration

    2017-01-01

    Hadronic signatures are critical to the high energy physics analysis program at the Large Hadron Collider (LHC), and are broadly used for both Standard Model measurements and searches for new physics. These signatures include generic quark and gluon jets, as well as jets originating from b-quarks or the decay of massive particles (such as electroweak bosons or top quarks). Additionally missing transverse momentum from non-interacting particles provides an interesting probe in the search for new physics beyond the Standard Model. Developing trigger selections that target these events is a huge challenge at the LHC due to the enormous event rates associated with these signatures. This challenge is exacerbated by the amount of pile-up activity, which continues to grow. In order to address these challenges, several new techniques have been developed during the past year in order to significantly improve the potential of the 2017 dataset and overcome the limiting factors, such as storage and computing requirements...

  11. Hadronic Triggers and trigger-object level analysis at ATLAS

    CERN Document Server

    Zaripovas, Donatas Ramilas; The ATLAS collaboration

    2017-01-01

    Hadronic signatures are critical to the high energy physics analysis program, and are broadly used for both Standard Model measurements and searches for new physics. These signatures include generic quark and gluon jets, as well as jets originating from b-quarks or the decay of massive particles (such as electroweak bosons or top quarks). Additionally missing transverse momentum from non-interacting particles provides an interesting probe in the search for new physics beyond the Standard Model. Developing trigger selections that target these events is a huge challenge at the LHC due to the enormous rates associated with these signatures. This challenge is exacerbated by the amount of pile-up activity, which continues to grow. In order to address these challenges, several new techniques have been developed during the past year in order to significantly improve the potential of the 2017 dataset and overcome the limiting factors to more deeply probing for new physics, such as storage and computing requirements f...

  12. Augmenting Tractable Fragments of Abstract Argumentation

    CERN Document Server

    Ordyniak, Sebastian

    2011-01-01

    We present a new and compelling approach to the efficient solution of important computational problems that arise in the context of abstract argumentation. Our approach makes known algorithms defined for restricted fragments generally applicable, at a computational cost that scales with the distance from the fragment. Thus, in a certain sense, we gradually augment tractable fragments. Surprisingly, it turns out that some tractable fragments admit such an augmentation and that others do not. More specifically, we show that the problems of credulous and skeptical acceptance are fixed-parameter tractable when parameterized by the distance from the fragment of acyclic argumentation frameworks. Other tractable fragments such as the fragments of symmetrical and bipartite frameworks seem to prohibit an augmentation: the acceptance problems are already intractable for frameworks at distance 1 from the fragments. For our study we use a broad setting and consider several different semantics. For the algorithmic results...

  13. Efficient multi-site-directed mutagenesis directly from genomic template

    Indian Academy of Sciences (India)

    Fengtao Luo; Xiaolan Du; Tujun Weng; Xuan Wen; Junlan Huang; Lin Chen

    2012-12-01

    In this article, the traditional multi-site-directed mutagenesis method based on overlap extension PCR was improved specifically for complicated templates, such as genomic sequence or complementary DNA. This method was effectively applied for multi-site-directed mutagenesis directly from mouse genomic DNA, as well as for combination, deletion or insertion of DNA fragments.

  14. A gapless genome sequence of the fungus Botrytis cinerea

    NARCIS (Netherlands)

    Kan, Van Jan A.L.; Stassen, Joost H.M.; Mosbach, Andreas; Lee, Van Der Theo A.J.; Faino, Luigi; Farmer, Andrew D.; Papasotiriou, Dimitrios G.; Zhou, Shiguo; Seidl, Michael F.; Cottam, Eleanor; Edel, Dominique; Hahn, Matthias; Schwartz, David C.; Dietrich, Robert A.; Widdison, Stephanie; Scalliet, Gabriel

    2016-01-01

    Following earlier incomplete and fragmented versions of a genome sequence for the grey mould Botrytis cinerea, a gapless, near-finished genome sequence for B. cinerea strain B05.10 is reported. The assembly comprised 18 chromosomes and was confirmed by an optical map and a genetic map based on ap

  15. De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

    Directory of Open Access Journals (Sweden)

    Iorizzo Massimo

    2012-05-01

    Full Text Available Abstract Background Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. Conclusions This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

  16. Screening for metronidazole-resistance associated gene fragments of H pylori by suppression subtractive hybridization

    Institute of Scientific and Technical Information of China (English)

    Ai-Qing Li; Ning Dai; Jie Yan; Yong-Liang Zhu

    2007-01-01

    AIM:To screen for metronidazole (MTZ)-resistance associated gene fragments of H pylori by suppression subtractive hybridization (SSH).METHODS:Five MTZ-resistant (tester,T) and 1 MTZ-susceptible (driver,D) clinical H pylori isolates were selected. Genomic DMAs were prepared and submitted to Rsa I digestion. Then two different adaptors were ligated respectively to the 5'-end of two aliquots of the tester DNA fragments and SSH was made between the tester and driver DNAs. The specific inserts of tester strains were screened and MTZ-resistance related gene fragments were identified by dot blotting.RESULTS:Among the randomly selected 120 subtractive colonies,37 DNA fragments had a different number of DNA copies (≥2 times) in resistant and susceptible strains and 17 of them had a significantly different number of DNA copies (≥3 times). Among the sequences obtained from the 17 DNA fragments,new sequences were found in 10 DNA fragments and duplicated sequences in 7 DNA fragments,representing respectively the sequences of depeptide ABC transporter periplasmic dipeptide-binding protein (dppA),permease protein (dppB),ribosomal protein S4 (rps4),ribonuclease in (rnc),protease (pqqE),diaminopimelate epimerase (dapF),acetatekinase (ackA),H pylori plasmid pHPSl and H pylori gene 1334.CONCLUSION:Gene fragments specific to MTZ-resistant H pylori strains can be screened by SSH and may be associated with MTZ-resistant H pylori.

  17. Energy-loss distributions of fission fragments

    Energy Technology Data Exchange (ETDEWEB)

    Demidovich, N.N.; Nakhutin, I.E.; Shatunov, V.G.

    1976-03-05

    The f-f coincidence method was used to investigate the change in the form of the energy-loss distributions of Cf/sup 252/ fission fragments in air, down to fragment energies approx.0.8 MeV. A theoretical model is considered for the estimate of the mean-squared deviations of the fragment energy-loss distributions. (AIP)

  18. Self-organized criticality in fragmenting

    DEFF Research Database (Denmark)

    Oddershede, L.; Dimon, P.; Bohr, J.

    1993-01-01

    The measured mass distributions of fragments from 26 fractured objects of gypsum, soap, stearic paraffin, and potato show evidence of obeying scaling laws; this suggests the possibility of self-organized criticality in fragmenting. The probability of finding a fragment scales inversely to a power...

  19. Low pressure microfluidic-based DNA fragmentation

    NARCIS (Netherlands)

    Shui, Lingling; Sparreboom, Wouter; Bomer, Johan G.; Jin, Mingliang; Carlen, Edwin; van den Berg, Albert

    2011-01-01

    We report a low-pressure microfluidic deoxyribonucleic acid (DNA) fragmentation device based on a combination of me-chanical hydrodynamic shearing and low temperature sample heating. Conventional DNA fragmentation based on hydrody-namic shearing is capable of achieving fragment lengths (FL) < 10k bp

  20. Scaling and four-quark fragmentation

    NARCIS (Netherlands)

    Scholten, O.; Bosveld, G. D.

    1991-01-01

    The conditions for a scaling behaviour from the fragmentation process leading to slow protons are discussed. The scaling referred to implies that the fragmentation functions depend on the light-cone momentum fraction only. It is shown that differences in the fragmentation functions for valence- and

  1. Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.

    Science.gov (United States)

    García-López, Rodrigo; Vázquez-Castellanos, Jorge Francisco; Moya, Andrés

    2015-01-01

    Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the degree of fragmentation of each genome in the sample, which is dependent on the sequencing effort and the genome length. Depending on ecological, biological, or procedural biases, some fragments have a higher prevalence, or coverage, in the assembly. However, assemblers must face challenges, such as the formation of chimerical structures and intra-species variability. Diversity calculation relies on the classification of the sequences that comprise a metagenomic dataset. Whenever the corresponding genomic and taxonomic information is available, contigs matching the same species can be classified accordingly and the coverage of its genome can be calculated for that species. This may be used to compare populations by estimating abundance and assessing species distribution from this data. Nevertheless, the coverage does not take into account the degree of fragmentation, or else genome completeness, and is not necessarily representative of actual species distribution in the samples. Furthermore, undetermined sequences are abundant in viral metagenomic datasets, resulting in several independent contigs that cannot be assigned by homology or genomic information. These may only be classified as different operational taxonomic units (OTUs), sometimes remaining inadvisably unrelated. Thus

  2. Infectious triggers of pediatric asthma.

    Science.gov (United States)

    Gern, James E; Lemanske, Robert F

    2003-06-01

    Respiratory infections can cause wheezing illnesses in children of all ages and also can influence the causation and disease activity of asthma. For years it has been recognized that respiratory syncytial virus infections often produce the first episode of wheezing in children who go on to develop chronic asthma. More recently, it has been proposed that repeated infections with other common childhood viral pathogens might help the immune system develop in such a way as to prevent the onset of allergic diseases and possibly asthma. In addition to the effects of viral infections, infections with certain intracellular pathogens, such as chlamydia and mycoplasma, may cause acute and chronic wheezing in some individuals, whereas common cold and acute sinus infections can trigger acute symptoms of asthma. In this article, the epidemiologic, mechanistic, and treatment implications of the association between respiratory infections and asthma are discussed.

  3. Infectious Agents Trigger Trophic Cascades.

    Science.gov (United States)

    Buck, Julia C; Ripple, William J

    2017-09-01

    Most demonstrated trophic cascades originate with predators, but infectious agents can also cause top-down indirect effects in ecosystems. Here we synthesize the literature on trophic cascades initiated by infectious agents including parasitoids, pathogens, parasitic castrators, macroparasites, and trophically transmitted parasites. Like predators, infectious agents can cause density-mediated and trait-mediated indirect effects through their direct consumptive and nonconsumptive effects respectively. Unlike most predators, however, infectious agents are not fully and immediately lethal to their victims, so their consumptive effects can also trigger trait-mediated indirect effects. We find that the frequency of trophic cascades reported for different consumer types scales with consumer lethality. Furthermore, we emphasize the value of uniting predator-prey and parasite-host theory under a general consumer-resource framework. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Episodic tremor triggers small earthquakes

    Science.gov (United States)

    Balcerak, Ernie

    2011-08-01

    It has been suggested that episodic tremor and slip (ETS), the weak shaking not associated with measurable earthquakes, could trigger nearby earthquakes. However, this had not been confirmed until recently. Vidale et al. monitored seismicity in the 4-month period around a 16-day episode of episodic tremor and slip in March 2010 in the Cascadia region. They observed five small earthquakes within the subducting slab during the ETS episode. They found that the timing and locations of earthquakes near the tremor suggest that the tremor and earthquakes are related. Furthermore, they observed that the rate of earthquakes across the area was several times higher within 2 days of tremor activity than at other times, adding to evidence of a connection between tremor and earthquakes. (Geochemistry, Geophysics, Geosystems, doi:10.1029/2011GC003559, 2011)

  5. Landslide triggering by rain infiltration

    Science.gov (United States)

    Iverson, Richard M.

    2000-01-01

    Landsliding in response to rainfall involves physical processes that operate on disparate timescales. Relationships between these timescales guide development of a mathematical model that uses reduced forms of Richards equation to evaluate effects of rainfall infiltration on landslide occurrence, timing, depth, and acceleration in diverse situations. The longest pertinent timescale is A/D0, where D0 is the maximum hydraulic diffusivity of the soil and A is the catchment area that potentially affects groundwater pressures at a prospective landslide slip surface location with areal coordinates x, y and depth H. Times greater than A/D0 are necessary for establishment of steady background water pressures that develop at (x, y, H) in response to rainfall averaged over periods that commonly range from days to many decades. These steady groundwater pressures influence the propensity for landsliding at (x, y, H), but they do not trigger slope failure. Failure results from rainfall over a typically shorter timescale H2/D0 associated with transient pore pressure transmission during and following storms. Commonly, this timescale ranges from minutes to months. The shortest timescale affecting landslide responses to rainfall is √(H/g), where g is the magnitude of gravitational acceleration. Postfailure landslide motion occurs on this timescale, which indicates that the thinnest landslides accelerate most quickly if all other factors are constant. Effects of hydrologic processes on landslide processes across these diverse timescales are encapsulated by a response function, R(t*) = √(t*/π) exp (-1/t*) - erfc (1/√t*), which depends only on normalized time, t*. Use of R(t*) in conjunction with topographic data, rainfall intensity and duration information, an infinite-slope failure criterion, and Newton's second law predicts the timing, depth, and acceleration of rainfall-triggered landslides. Data from contrasting landslides that exhibit rapid, shallow motion and slow, deep

  6. Understanding of myofascial trigger points

    Institute of Scientific and Technical Information of China (English)

    Zhuang Xiaoqiang; Tan Shusheng; Huang Qiangmin

    2014-01-01

    Objective To investigate the current practice of myofascial pain syndrome (MPS) including current epidemiology,pathology,diagnosis and treatment.Data sources The data analyzed in this review were mainly from relevant articles without restriction on the publication date reported in PubMed,MedSci,Google scholar.The terms "myofasial trigger points" and "myofacial pain syndrome" were used for the literature search.Study selection Original articles with no limitation of research design and critical reviews containing data relevant to myofascial trigger points (MTrPs) and MPS were retrieved,reviewed,analyzed and summarized.Results Myofascial pain syndrome (MPS) is characterized by painful taut band,referred pain,and local response twitch with a prevalence of 85% to 95% of incidence.Several factors link to the etiology of MTrPs,such as the chronic injury and overload of muscles.Other factors,such as certain nutrient and hormone insufficiency,comorbidities,and muscle imbalance may also maintain the MTrP in an active status and induce recurrent pain.The current pathology is that an extra leakage acetylcholine at the neuromuscular junction induces persistent contracture knots,relative to some hypotheses of integration,muscle spindle discharges,spinal segment sensitization,ect.MTrPs can be diagnosed and localized based on a few subjective criteria.Several approaches,including both direct and supplementary treatments,can inactivate MTrPs.Direct treatments are categorized into invasive and conservative.Conclusion This review provides a clear understanding of MTrP pain and introduces the most useful treatment approaches in China.

  7. Disaster triggers disaster: Earthquake triggering by tropical cyclones

    Science.gov (United States)

    Wdowinski, S.; Tsukanov, I.

    2011-12-01

    Three recent devastating earthquakes, the 1999 M=7.6 Chi-Chi (Taiwan), 2010 M=7.0 Leogane (Haiti), 2010 M=6.4 Kaohsiung (Taiwan), and additional three moderate size earthquakes (6cyclones (hurricane or typhoon) hit the very same area. The most familiar example is Haiti, which was hit during the late summer of 2008 by two hurricanes and two tropical storms (Fay, Gustav, Hanna and Ike) within 25 days. A year an a half after this very wet hurricane season, the 2010 Leogane earthquake occurred in the mountainous Haiti's southern peninsula and caused the death of more than 300,000 people. The other cases are from Taiwan, which is characterized by a high seismicity level and frequent typhoon landfall. The three wettest typhoons in Taiwan's past 50 years were Morakot (in 2009, with 2885 mm or rain), Flossie (1969, 2162 mm) and Herb (1996, 1987 mm)[Lin et al., 2010]. Each of this three very wet storms was followed by one or two main-shock M>6 earthquake that occurred in the central mountainous area of Taiwan within three years after the typhoon. The 2009 Morakot typhoon was followed by 2009 M=6.2 Nantou and 2010 M=6.4 Kaohsiung earthquakes; the 1969 Flossie typhoon was followed by an M=6.3 earthquake in 1972; and the 1996 Herb typhoon by the 1998 M=6.2 Rueyli and 1999 M=7.6 Chi-Chi earthquakes. The earthquake catalog of Taiwan lists only two other M>6 main-shocks that occurred in Taiwan's central mountainous belt, one of them was in 1964 only four months after the wet Typhoon Gloria poured heavy rain in the same area. We suggest that the close proximity in time and space between wet tropical cyclones and earthquakes reflects a physical link between the two hazard types in which these earthquakes were triggered by rapid erosion induced by tropical cyclone's heavy rain. Based on remote sensing observations, meshfree finite element modeling, and Coulomb failure stress analysis, we show that the erosion induced by very wet cyclones increased the failure stresses at the

  8. High-Diversity Genes in the Arabidopsis Genome

    OpenAIRE

    Cork, Jennifer M.; Purugganan, Michael D.

    2005-01-01

    High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana Ler ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 gen...

  9. Isoscaling of projectile-like fragments

    Institute of Scientific and Technical Information of China (English)

    Zhong Chen; Chen Jin-Hui; Guo Wei; Ma Chun-Wang; Ma Guo-Liang; Su Qian-Min; Yan Ting-Zhi; Zuo Jia-Xu; Ma Yu-Gang; Fang De-Qing; Cai Xiang-Zhou; Chen Jin-Gen; Shen Wen-Qing; Tian Wen-Dong; Wang Kun; Wei Yi-Bin

    2006-01-01

    In this paper, the isotopic and isotonic distributions of projectile fragmentation products have been simulated by a modified statistical abrasion-ablation model and the isoscaling behaviour of projectile-like fragments has been discussed. The isoscaling parameters α andβ have been extracted respectively, for hot fragments before evaporation and cold fragments after evaporation. It looks that the evaporation has stronger effect on α than β. For cold fragments,a monotonic increase of α and |β| with the increase of Z and N is observed. The relation between isoscaling parameter and the change of isospin content is discussed.

  10. Smart trigger logic for focal plane arrays

    Science.gov (United States)

    Levy, James E; Campbell, David V; Holmes, Michael L; Lovejoy, Robert; Wojciechowski, Kenneth; Kay, Randolph R; Cavanaugh, William S; Gurrieri, Thomas M

    2014-03-25

    An electronic device includes a memory configured to receive data representing light intensity values from pixels in a focal plane array and a processor that analyzes the received data to determine which light values correspond to triggered pixels, where the triggered pixels are those pixels that meet a predefined set of criteria, and determines, for each triggered pixel, a set of neighbor pixels for which light intensity values are to be stored. The electronic device also includes a buffer that temporarily stores light intensity values for at least one previously processed row of pixels, so that when a triggered pixel is identified in a current row, light intensity values for the neighbor pixels in the previously processed row and for the triggered pixel are persistently stored, as well as a data transmitter that transmits the persistently stored light intensity values for the triggered and neighbor pixels to a data receiver.

  11. Tracking triggers for the upgraded DOe detector

    Energy Technology Data Exchange (ETDEWEB)

    Glenn, S. [California Univ., Davis (United States); Bloom, P. [California Univ., Davis (United States); Mani, S. [California Univ., Davis (United States); Pellett, D. [California Univ., Davis (United States); Costa, J. [CBPF/LAFEX, Rio de Janeiro (Brazil); Moreira, L. [CBPF/LAFEX, Rio de Janeiro (Brazil); Baumbaugh, A. [Fermi National Accelerator Laboratory, Batavia, IL (United States); Blazey, G. [Fermi National Accelerator Laboratory, Batavia, IL (United States); Borcherding, F. [Fermi National Accelerator Laboratory, Batavia, IL (United States); Johnson, M. [Fermi National Accelerator Laboratory, Batavia, IL (United States); Wilcox, J. [Northeastern University, Boston, MA (United States)

    1995-06-01

    The high luminosity environment of the upgraded Tevatron will require not only the upgrade of various DOe subdetectors, but the trigger system as well. With respect to the present system, the upgraded trigger system must operate faster and provide a higher degree of background rejection while extending the physics acceptance beyond that of the current system. This will be accomplished in part by incorporating the scintillating fiber tracker and the preshower detector into the Level 1 trigger. Track logic, implemented in commercial FPGAs, will be used to identify tracks in the scintillating fiber tracker with P{sub T}>1.5 GeV/c and electron candidates in the preshower detector. Integration of the trigger logic and readout electronics permits the identification of all tracks in a few hundred nanoseconds. Here, preliminary designs for the readout and trigger electronics are presented along with simulation results for trigger efficiencies and rejection factors. (orig.).

  12. Importance of direct and indirect triggered seismicity

    CERN Document Server

    Helmstetter, A; Helmstetter, Agnes; Sornette, Didier

    2003-01-01

    Using the simple ETAS branching model of seismicity, which assumes that each earthquake can trigger other earthquakes, we quantify the role played by the cascade of triggered seismicity in controlling the rate of aftershock decay as well as in the overall level of seismicity in the presence of a constant external seismicity source. We show that, in this model, the proportion of triggered seismicity is equal to the proportion of secondary plus later-generation aftershocks, and is given by the average number of triggered events per earthquake. Based on these results and on the observation that a large fraction of seismicity are triggered earthquakes, we conclude that similarly a large fraction of aftershocks occurring a few hours or days after a mainshock are triggered indirectly by the mainshock.

  13. The ATLAS b-jet Trigger

    CERN Document Server

    Ferreira de Lima, D E; The ATLAS collaboration

    2011-01-01

    The ATLAS b-jet Trigger The online event selection is crucial to reject most of the events containing uninteresting background collisions while preserving as much as possible the interesting physical signals. The b-jet selection is part of the trigger strategy of the ATLAS experiment and a set of dedicated triggers is presently contributing to the event selection for the 2011 running. The b-jets acceptance is increased and the background reduced by lowering jet transverse energy thresholds at the first trigger level and applying b-tagging techniques at the subsequent levels. Different physics channels, especially topologies containing more than one b-jet where higher rejection factors are achieved, benefit from requesting this trigger to be fired. An overview of the status-of-art of the b-jet trigger menu and performance on real data is presented in this poster.

  14. Online software trigger at PANDA/FAIR

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Donghee [Mainz Univ. (Germany). Inst. fuer Kernphysik; Collaboration: PANDA-Collaboration

    2013-07-01

    The PANDA experiment at the FAIR facility will employ a novel trigger-less readout concept. PANDA will have no first level hardware trigger and apply a high level software trigger to do fast event selection based on the physics properties of reconstructed events. A trigger-less data stream implies that an event selection requires track reconstruction and pattern recognition to be performed online, analysing data under real time condition at the event rates up to 40 MHz. A significant event rate reduction is required to reject effectively background events, while retaining the interesting events at the same time. The projected reduction factor is 10{sup -3}. Real time event selection in this environment is very challenging and rely on sophisticated algorithms in the software trigger. This presentation shows the implementation and performance tests of the online high level physics trigger algorithms. The impact of parameters such as momentum, mass resolution, and PID probability for the event filtering are presented.

  15. Star Formation Triggered by Low-Mass Clump Collisions

    Science.gov (United States)

    Kitsionas, Spyridon; Whitworth, Anthony P.

    We investigate by means of high-resolution numerical simulations the phenomenology of star formation triggered by low-velocity collisions between low-mass molecular clumps. The simulations are performed using an SPH code which satisfies the Jeans condition by invoking On-the-Fly Particle Splitting (Kitsionas & Whitworth 2002). The efficiency of star formation appears to increase with increasing clump mass and/or decreasing impact parameter b and/or increasing clump velocity. For bcompressed layers which fragment into filaments that break up into cores. Protostellar objects then condense out of the cores and accrete from them. The resulting accretion rates are comparable to those of Class 0 objects. The densities in the filaments are sufficient that they could be mapped in ammonia or CS line radiation in nearby star formation regions. The phenomenology of star formation observed in our simulations compares rather well with the observed filamentary distribution of young stars in Taurus (Hartmann 2002).

  16. Chromosome loss caused by DNA fragmentation induced in main nuclei and micronuclei of human lymphoblastoid cells treated with colcemid.

    Science.gov (United States)

    Yamamoto, Mika; Wakata, Akihiro; Aoki, Yoshinobu; Miyamae, Yoichi; Kodama, Seiji

    2014-04-01

    Aneuploidy, a change in the number of chromosomes, plays an essential role in tumorigenesis. Our previous study demonstrated that a loss of a whole chromosome is induced in human lymphocytes by colcemid, a well-known aneugen. Here, to clarify the mechanism for colcemid-induced chromosome loss, we investigated the relationship between chromosome loss and DNA fragmentation in human lymphoblastoid cells treated with colcemid (an aneugen) compared with methyl methanesulfonate (MMS; a clastogen). We analyzed the number of fluorescence in situ hybridization (FISH) signals targeted for a whole chromosome 2 in cytokinesis-blocked binucleated TK6 cells and WTK-1 cells treated with colcemid and MMS, and concurrently detected DNA fragmentation by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. Results revealed that DNA fragmentation occurred in 60% of all binucleated TK6 cells harboring colcemid-induced chromosome loss (30% of micronuclei and 30% of main nuclei). DNA fragmentation was observed in colcemid-induced micronuclei containing a whole chromosome but not in MMS-induced micronuclei containing chromosome fragments. In contrast, colcemid-induced nondisjunction had no effect on induction of DNA fragmentation, suggesting that DNA fragmentation was triggered by micronuclei containing a whole chromosome but not by micronuclei containing chromosome fragments or nondisjunction. In addition, the frequency of binucleated cells harboring chromosome loss with DNA fragmentation in micronuclei or main nuclei was higher in wild-type p53 TK6 cells than in mutated-p53 WTK-1 cells treated with colcemid. Taken together, these present and previous results suggest that colcemid-induced chromosome loss is caused by DNA fragmentation, which is triggered by a micronucleus with a whole chromosome and controlled by the p53-dependent pathway. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Analysis of Transmissions Scheduling with Packet Fragmentation

    Directory of Open Access Journals (Sweden)

    Nir Menakerman

    2001-12-01

    Full Text Available We investigate a scheduling problem in which packets, or datagrams, may be fragmented. While there are a few applications to scheduling with datagram fragmentation, our model of the problem is derived from a scheduling problem present in data over CATV networks. In the scheduling problem datagrams of variable lengths must be assigned (packed into fixed length time slots. One of the capabilities of the system is the ability to break a datagram into several fragments. When a datagram is fragmented, extra bits are added to the original datagram to enable the reassembly of all the fragments. We convert the scheduling problem into the problem of bin packing with item fragmentation, which we define in the following way: we are asked to pack a list of items into a minimum number of unit capacity bins. Each item may be fragmented in which case overhead units are added to the size of every fragment. The cost associated with fragmentation renders the problem NP-hard, therefore an approximation algorithm is needed. We define a version of the well-known Next-Fit algorithm, capable of fragmenting items, and investigate its performance. We present both worst case and average case results and compare them to the case where fragmentation is not allowed.

  18. Impact of numerical models on fragmentation processes

    Science.gov (United States)

    Renouf, Mathieu; Gezahengn, Belien; Abbas, Micheline; Bourgeois, Florent

    2013-06-01

    Simulated fragmentation process in granular assemblies is a challenging problem which date back the beginning of the 90'. If first approaches have focus on the fragmentation on a single particle, with the development of robust, fast numerical method is is possible today to simulated such process in a large collection of particles. But the question of the fragmentation problem is still open: should the fragmentation be done dynamically (one particle becoming two fragments) and according which criterion or should the fragment paths be defined initially and which is the impact of the discretization and the model of fragments? The present contribution proposes to investigate the second aspect i.e. the impact of fragment modeling on the fragmentation processes. First to perform such an analysis, the geometry of fragments (disks/sphere or polygon/polyhedra), their behavior (rigid/deformable) and the law governing their interactions are investigated. Then such model will be used in a grinding application where the evolution of fragments and impact on the behavior of the whole packing are investigate.

  19. Efficient Distribution of Triggered Synchronous Block Diagrams

    Science.gov (United States)

    2011-10-21

    called a trigger. At a given synchronous step, if the trigger is true , the block fires normally; otherwise, the block stutters , that is, keeps its...outputs have the same value as in the previous step, but they are still transmitted to downstream blocks. In this paper we present an implementation...optimizations that apply to general Triggered SBDs, we also present further optimizations for the case of Timed SBDs. 1.1 Motivating Examples Fig. 1

  20. Genomic and polyploid evolution in genus Avena as revealed by RFLPs of repeated DNA sequences.

    Science.gov (United States)

    Morikawa, Toshinobu; Nishihara, Miho

    2009-06-01

    Phylogenetic relationships and genome affinities were investigated by utilizing all the biological Avena species consisting of 11 diploid species (15 accessions), 8 tetraploid species (9 accessions) and 4 hexaploid species (5 accessions). Genomic DNA regions of As120a, avenin, and globulin were amplified by PCR. A total of 130 polymorphic fragments were detected out of 156 fragments generated by digesting the PCR-amplified fragments with 11 restriction enzymes. The number of fragments generated by PCR-amplification followed by digestion with restriction enzymes was almost the same as those among the three repeated DNA sequences. A high level of genetic distance was detected between A. damascena (Ad) and A. canariensis (Ac) genomes, which reflected their different morphology and reproductive isolation. The A. longiglumis (Al) and A. prostrata (Ap) genomes were closely related to the As genome group. The AB genome species formed a cluster with the AsAs genome artificial autotetraploid and the As genome diploids indicating near-autotetraploid origin. The A. macrostachya is an outbreeding autotetraploid closely related with the C genome diploid and the AC genome tetraploid species. The differences of genetic distances estimated from the repeated DNA sequence divergence among the Avena species were consistent with genome divergences and it was possible to compare the genetic intra- and inter-ploidy relationships produced by RFLPs. These results suggested that the PCR-mediated analysis of repeated DNA polymorphism can be used as a tool to examine genomic relationships of polyploidy species.

  1. The formation of planets by disc fragmentation

    Directory of Open Access Journals (Sweden)

    Stamatellos Dimitris

    2013-04-01

    Full Text Available I discuss the role that disc fragmentation plays in the formation of gas giant and terrestrial planets, and how this relates to the formation of brown dwarfs and low-mass stars, and ultimately to the process of star formation. Protostellar discs may fragment, if they are massive enough and can cool fast enough, but most of the objects that form by fragmentation are brown dwarfs. It may be possible that planets also form, if the mass growth of a proto-fragment is stopped (e.g. if this fragment is ejected from the disc, or suppressed and even reversed (e.g by tidal stripping. I will discuss if it is possible to distinguish whether a planet has formed by disc fragmentation or core accretion, and mention of a few examples of observed exoplanets that are suggestive of formation by disc fragmentation.

  2. Reframing landscape fragmentation's effects on ecosystem services.

    Science.gov (United States)

    Mitchell, Matthew G E; Suarez-Castro, Andrés F; Martinez-Harms, Maria; Maron, Martine; McAlpine, Clive; Gaston, Kevin J; Johansen, Kasper; Rhodes, Jonathan R

    2015-04-01

    Landscape structure and fragmentation have important effects on ecosystem services, with a common assumption being that fragmentation reduces service provision. This is based on fragmentation's expected effects on ecosystem service supply, but ignores how fragmentation influences the flow of services to people. Here we develop a new conceptual framework that explicitly considers the links between landscape fragmentation, the supply of services, and the flow of services to people. We argue that fragmentation's effects on ecosystem service flow can be positive or negative, and use our framework to construct testable hypotheses about the effects of fragmentation on final ecosystem service provision. Empirical efforts to apply and test this framework are critical to improving landscape management for multiple ecosystem services.

  3. Extraction of 16th Century Calender Fragments

    DEFF Research Database (Denmark)

    Holck, Jakob Povl; Etheridge, Christian

    at the Cultural Heritage & Archaeometric Research Team, SDU. Upon finding medieval manuscript fragments in the university library’s special collections, scholars at the Centre for Medieval Literature are consulted. In most cases, digital pictures of the finds will circulate in the international community...... of medieval scholars. Thousands of 16th and 17th Century books are stored in the University Library of Southern Denmark. One out of five of these books is expected to contain medieval manuscript fragments or fragments of rare prints, e.g. incunabula....... fragments may require extensive use of Big Data and other forms of analysis in order to be identified. Usually, the university library prefers not to remove the fragments from their “fragment carriers”. In order to read fragments that are only partially visible or invisible, x-ray technology may be deployed...

  4. Dihadron Fragmentation Functions and Transversity

    CERN Document Server

    Radici, Marco; Bacchetta, Alessandro

    2014-01-01

    We present preliminary results for an updated extraction of the transversity parton distribution based on the analysis of pion-pair production in deep-inelastic scattering off transversely polarized targets in collinear factorization. Data for proton and deuteron targets by HERMES and COMPASS allow for a flavor separation of the valence components of transversity, while di-hadron fragmentation functions are taken from the semi-inclusive production of two pion pairs in back-to-back jets in $e^+ e^-$ annihilation. The latter data from Belle have been reanalyzed using the replica method and a more realistic estimate of the uncertainties on the chiral-odd interference fragmentation function has been obtained. After encoding this piece of information into the deep-inelastic scattering cross section, the transversity has been re-extracted by using the most recent and more precise COMPASS data for proton target. This picture represents the current most realistic estimate of the uncertainties on our knowledge of tran...

  5. Dihadron Fragmentation Functions and Transversity

    Directory of Open Access Journals (Sweden)

    Radici Marco

    2015-01-01

    Full Text Available We present preliminary results for an updated extraction of the transversity parton distribution based on the analysis of pion-pair production in deep-inelastic scattering off transversely polarized targets in collinear factorization. Data for proton and deuteron targets by HERMES and COMPASS allow for a flavor separation of the valence components of transversity, while di-hadron fragmentation functions are taken from the semi-inclusive production of two pion pairs in back-to-back jets in e+e− annihilation. The latter data from Belle have been reanalyzed using the replica method and a more realistic estimate of the uncertainties on the chiral-odd interference fragmentation function has been obtained. After encoding this piece of information into the deep-inelastic scattering cross section, the transversity has been re-extracted by using the most recent and more precise COMPASS data for proton target. This picture represents the current most realistic estimate of the uncertainties on our knowledge of transversity. The preliminary results indicate that the valence up component seems smaller and with a narrower error band than in previous extraction.

  6. Fragmentation Speed and Permeability of hot Volcanic Rocks

    Science.gov (United States)

    Scheu, B.; Mueller, S.; Spieler, O.; Dingwell, D. B.

    2002-12-01

    The speed of fragmentation may control the explosive behaviour of silicic volcanoes. It is directly affected by the gas pressure within the volcano, which else influences the eruptive behaviour of the volcano. We used two techniques to analyse the speed of fragmentation. At both the fragmentation is triggered by the rapid decompression inside a high-pressure autoclave. Firstly at room temperature a set of two pressure transducers record the differential pressure loss above and below the cylindrical sample (d = 25mm, l = 60 mm). Secondly at temperatures of 850°C two platinum wires are inserted at known distance into the sample cylinder and used as electrical conductors to record the rupture time. The recorded time difference and the distance between the conductors are used to recalculate the speed of the fragmentation wave. This speed depends on porosity, texture and initial pressure difference. Further, the results show a decrease of fragmentation speed while propagating through the rock sample. We propose this effect to be linked to the density changes of the gas and therefore the reducing flow rates through the rock sample (gas permeability). Up to today permeability measurements have only been performed on cold porous rocks (e.g. Eichelberger et al. 1986, Klug & Cashman 1996), because measurements with higher temperatures are not possible with common gas permeameters. Investigating the permeability of volcanic rocks in a hot state (up to 850°C) provides a better insight into the degassing processes under natural conditions. Therefore, any new experimental set-up is expected to yield information about the temperature dependency of permeability in volcanic rocks. The present experiments have been performed on samples with a wide range of porosities, collected from block-and-ash flows on Merapi (Indonesia), Unzen (Japan) and from pumices on Lipari Island (Italy). Permeability was measured using a modified set-up of the fragmentation apparatus. Below the sample a

  7. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  8. The first-level trigger of ATLAS

    CERN Document Server

    Haller, J; Aielli, G; Aloisio, A; Alviggi, M G; Aprodu, V; Ask, S; Barnett, B M; Bartos, D; Bauss, B; Belkin, A; Benhammou, Ya; Bocci, V; Booth, J R A; Brambilla, Elena; Brawn, I P; Bressler, S; Buda, S; Bohm, C; Canale, V; Caracinha, D; Cardarelli, R; Carlino, G; Cataldi, G; Charlton, D G; Chiodi, G; Ciapetti, G; Constantin, S; Conventi, F; Davis, A O; De Asmundis, R; De Pedis, D; De Seixas, J M; Della Pietra, M; Della Volpe, D; Di Ciaccio, A; Di Girolamo, A; Di Mattia, A; Di Simone, A; Distante, L; Dogaru, M; Edwards, J; Eisenhandler, E F; Ellis, Nick; Etzion, E; Farthouat, P; Fukunaga, C; Föhlisch, F; Gee, C N P; Gennari, E; Geweniger, C; Gillman, A R; Gorini, E; Grancagnolo, F; Gällnö, P; Haas, S; Hanke, P; Harel, A; Hasegawa, Y; Hellman, S; Hidvegi, A; Hillier, S J; Ichimiya, R; Iengo, P; Ikeno, M; Ishino, M; Iwasaki, H; Izzo, V; Kagawa, S; Kanaya, N; Kawagoe, K; Kawamoto, T; Kiyamura, H; Kluge, E -E; Kobayashi, T; Krasznahorkay, A; Kurashige, H; Kuwabara, T; Landon, M; Lellouch, D; Levinson, L; Lifshitz, R; Luci, C; Lupu, N; Magureanu, C; Mahboubi, K; Mahout, G; Meier, K; Migliaccio, A; Mikenberg, G; Mirea, A; Moye, T H; Nagano, K; Nisati, A; Nomachi, M; Nomoto, H; Nozaki, M; Ochi, A; Ogata, T; Omachi, C; Oshita, H; Pasqualucci, E; Pastore, F; Patricelli, S; Pauly, T; Pectu, M; Perantoni, M; Perera, V J O; Perrino, R; Pessoa-Lima, H; Petrolo, E; Primavera, M; Prodan, L; Qian, W; Rieke, S; Rusu, A; Rühr, F; Sakamoto, H; Salamon, A; Sankey, D P C; Santonico, R; Sasaki, O; Schmitt, K; Schuler, G; Schultz-Coulon, H C; Schäfer, U; Sekhniaidze, G; Silverstein, S; Spagnolo, S; Spila, F; Spiwoks, R; Staley, R J; Sugaya, Y; Sugimoto, T; Takeda, H; Takeshita, T; Tanaka, S; Tapprogge, S; Tarem, S; Thomas, J P; Trefzger, T; Typaldos, D; Uroseviteanu, C; Vari, R; Veneziano, Stefano; Watkins, P M; Watson, A; Weber, G A; Weber, P; Wengler, T; Woerling, E E; Yamaguchi, Y; Yasu, Y; Zanello, L

    2006-01-01

    Due to the huge interaction rates and the tough experimental environment of pp collisions at a centre-of-mass energy sqrt(s)=14 TeV and luminosities of up to 10^34cm^-2s^-1, one of the experimental challenges at the LHC is the triggering of interesting events. In the ATLAS experiment a three-level trigger system is foreseen for this purpose. The first-level trigger is implemented in custom hardware and has been designed to reduce the data rate from the initial bunch-crossing rate of 40MHz to around 75 kHz. Its event selection is based on information from the calorimeters and dedicated muon detectors. This article gives an overview over the full first-level trigger system including the Calorimeter Trigger, the Muon Trigger and the Central Trigger Processor. In addition, recent results are reported that have been obtained from test-beam studies performed at CERN where the full first-level trigger chain was established successfully for the first time and used to trigger the read-out of up to nine ATLAS sub-detec...

  9. Data analysis at Level-1 Trigger level

    CERN Document Server

    Wittmann, Johannes; Aradi, Gregor; Bergauer, Herbert; Jeitler, Manfred; Wulz, Claudia; Apanasevich, Leonard; Winer, Brian; Puigh, Darren Michael

    2017-01-01

    With ever increasing luminosity at the LHC, optimum online data selection is getting more and more important. While in the case of some experiments (LHCb and ALICE) this task is being completely transferred to computer farms, the others - ATLAS and CMS - will not be able to do this in the medium-term future for technological, detector-related reasons. Therefore, these experiments pursue the complementary approach of migrating more and more of the offline and High-Level Trigger intelligence into the trigger electronics. This paper illustrates how the Level-1 Trigger of the CMS experiment and in particular its concluding stage, the Global Trigger, take up this challenge.

  10. The Run-2 ATLAS Trigger System

    Science.gov (United States)

    Ruiz Martínez, A.; ATLAS Collaboration

    2016-10-01

    The ATLAS trigger successfully collected collision data during the first run of the LHC between 2009-2013 at different centre-of-mass energies between 900 GeV and 8TeV. The trigger system consists of a hardware Level-1 and a software-based high level trigger (HLT) that reduces the event rate from the design bunch-crossing rate of 40 MHz to an average recording rate of a few hundred Hz. In Run-2, the LHC will operate at centre-of-mass energies of 13 and 14 TeV and higher luminosity, resulting in up to five times higher rates of processes of interest. A brief review of the ATLAS trigger system upgrades that were implemented between Run-1 and Run-2, allowing to cope with the increased trigger rates while maintaining or even improving the efficiency to select physics processes of interest, will be given. This includes changes to the Level-1 calorimeter and muon trigger systems, the introduction of a new Level-1 topological trigger module and the merging of the previously two-level HLT system into a single event processing farm. A few examples will be shown, such as the impressive performance improvements in the HLT trigger algorithms used to identify leptons, hadrons and global event quantities like missing transverse energy. Finally, the status of the commissioning of the trigger system and its performance during the 2015 run will be presented.

  11. CSC Trigger Primitive Rates in ORCA

    CERN Document Server

    Cousins, Robert; Valuev, S

    2002-01-01

    Recent work in ORCA has prompted us to make a new estimate of the background rates in the Level-1 CSC Trigger Primitives. We report our findings for SimHit, digi, and LCT rates, as well as the input LCT rates in the Muon Port Cards. We compare our estimates with two earlier results (Level-1 Trigger TDR, and ``Background LCT Rates by CSC Type Using the Forward Muon Trigger Simulation in CMS100'' by Breedon, Fisyak, Ko and Rowe), and observe some differences attributed to geometry changes, improved shielding, and improved CSC and Level-1 Trigger simulation. % and larger statistics in the present study.

  12. Sequence-specific double strand breaks trigger P-TEFb-dependent Rpb1-CTD hyperphosphorylation

    Energy Technology Data Exchange (ETDEWEB)

    Napolitano, Giuliana; Amente, Stefano; Lavadera, Miriam Lubrano; Di Palo, Giacomo; Ambrosio, Susanna; Lania, Luigi [Department of Biology, University of Naples ‘Federico II’, Naples (Italy); Dellino, Gaetano Ivan; Pelicci, Pier Giuseppe [Department of Experimental Oncology, European Institute of Oncology, Milan (Italy); Majello, Barbara, E-mail: majello@unina.it [Department of Biology, University of Naples ‘Federico II’, Naples (Italy)

    2013-09-15

    Highlights: • Using an inducible restriction enzyme, hundreds of site-specific DSBs are generated across the genome. • Site-specific DSBs trigger activation of P-TEFb and consequent Rpb1-CTD hyperphosphorylation. • Site-specific DSBs induce activation of p53-transcriptional axis. - Abstract: Double strand DNA breaks (DSBs) are one of the most challenging forms of DNA damage which, if left unrepaired, can trigger cellular death and can contribute to cancer. A number of studies have been focused on DNA-damage response (DDR) mechanisms, and most of them rely on the induction of DSBs triggered by chemical compounds or radiations. However, genotoxic drugs and radiation treatments of cultured cell lines induce random DSBs throughout the genome, thus heterogeneously across the cell population, leading to variability of the cellular response. To overcome this aspect, we used here a recently described cell-based DSBs system whereby, upon induction of an inducible restriction enzyme, hundreds of site-specific DSBs are generated across the genome. We show here that sequence-specific DSBs are sufficient to activate the positive transcription elongation factor b (P-TEFb), to trigger hyperphosphorylation of the largest RNA polymerase II carboxyl-terminal-domain (Rpb1-CTD) and to induce activation of p53-transcriptional axis resulting in cell cycle arrest.

  13. An integrated restriction fragment length polymorphism--amplified fragment length polymorphism linkage map for cultivated sunflower.

    Science.gov (United States)

    Gedil, M A; Wye, C; Berry, S; Segers, B; Peleman, J; Jones, R; Leon, A; Slabaugh, M B; Knapp, S J

    2001-04-01

    Restriction fragment length polymorphism (RFLP) maps have been constructed for cultivated sunflower (Helianthus annuus L.) using three independent sets of RFLP probes. The aim of this research was to integrate RFLP markers from two sets with RFLP markers for resistance gene candidate (RGC) and amplified fragment length polymorphism (AFLP) markers. Genomic DNA samples of HA370 and HA372, the parents of the F2 population used to build the map, were screened for AFLPs using 42 primer combinations and RFLPs using 136 cDNA probes (RFLP analyses were performed on DNA digested with EcoRI, HindIII, EcoRV, or DraI). The AFLP primers produced 446 polymorphic and 1101 monomorphic bands between HA370 and HA372. The integrated map was built by genotyping 296 AFLP and 104 RFLP markers on 180 HA370 x HA372 F2 progeny (the AFLP marker assays were performed using 18 primer combinations). The HA370 x HA372 map comprised 17 linkage groups, presumably corresponding to the 17 haploid chromosomes of sunflower, had a mean density of 3.3 cM, and was 1326 cM long. Six RGC RFLP loci were polymorphic and mapped to three linkage groups (LG8, LG13, and LG15). AFLP markers were densely clustered on several linkage groups, and presumably reside in centromeric regions where recombination is reduced and the ratio of genetic to physical distance is low. Strategies for targeting markers to euchromatic DNA need to be tested in sunflower. The HA370 x HA372 map integrated 14 of 17 linkage groups from two independent RFLP maps. Three linkage groups were devoid of RFLP markers from one of the two maps.

  14. Accurate phylogenetic classification of DNA fragments based onsequence composition

    Energy Technology Data Exchange (ETDEWEB)

    McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis; Hugenholtz, Philip; Rigoutsos, Isidore

    2006-05-01

    Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequence characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.

  15. Bacterial genome reengineering.

    Science.gov (United States)

    Zhou, Jindan; Rudd, Kenneth E

    2011-01-01

    The web application PrimerPair at ecogene.org generates large sets of paired DNA sequences surrounding- all protein and RNA genes of Escherichia coli K-12. Many DNA fragments, which these primers amplify, can be used to implement a genome reengineering strategy using complementary in vitro cloning and in vivo recombineering. The integration of a primer design tool with a model organism database increases the level of quality control. Computer-assisted design of gene primer pairs relies upon having highly accurate genomic DNA sequence information that exactly matches the DNA of the cells being used in the laboratory to ensure predictable DNA hybridizations. It is equally crucial to have confidence that the predicted start codons define the locations of genes accurately. Annotations in the EcoGene database are queried by PrimerPair to eliminate pseudogenes, IS elements, and other problematic genes before the design process starts. These projects progressively familiarize users with the EcoGene content, scope, and application interfaces that are useful for genome reengineering projects. The first protocol leads to the design of a pair of primer sequences that were used to clone and express a single gene. The N-terminal protein sequence was experimentally verified and the protein was detected in the periplasm. This is followed by instructions to design PCR primer pairs for cloning gene fragments encoding 50 periplasmic proteins without their signal peptides. The design process begins with the user simply designating one pair of forward and reverse primer endpoint positions relative to all start and stop codon positions. The gene name, genomic coordinates, and primer DNA sequences are reported to the user. When making chromosomal deletions, the integrity of the provisional primer design is checked to see whether it will generate any unwanted double deletions with adjacent genes. The bad designs are recalculated and replacement primers are provided alongside the

  16. Rewriting the blueprint of life by synthetic genomics and genome engineering.

    Science.gov (United States)

    Annaluru, Narayana; Ramalingam, Sivaprakash; Chandrasegaran, Srinivasan

    2015-06-16

    Advances in DNA synthesis and assembly methods over the past decade have made it possible to construct genome-size fragments from oligonucleotides. Early work focused on synthesis of small viral genomes, followed by hierarchical synthesis of wild-type bacterial genomes and subsequently on transplantation of synthesized bacterial genomes into closely related recipient strains. More recently, a synthetic designer version of yeast Saccharomyces cerevisiae chromosome III has been generated, with numerous changes from the wild-type sequence without having an impact on cell fitness and phenotype, suggesting plasticity of the yeast genome. A project to generate the first synthetic yeast genome--the Sc2.0 Project--is currently underway.

  17. Dinoflagellates: a mitochondrial genome all at sea.

    Science.gov (United States)

    Nash, Edmund A; Nisbet, R Ellen R; Barbrook, Adrian C; Howe, Christopher J

    2008-07-01

    Dinoflagellate algae are notorious for their highly unusual organization of nuclear and chloroplast genomes. Early studies on the dinoflagellate mitochondrial genome indicated that it encodes the same three protein-coding genes found in Plasmodium spp., but with a complex organization and transcript editing. Recent work has extended this view, showing that the dinoflagellate mitochondrial genome contains a wide array of gene fragments and genes interspersed with noncoding inverted repeats. The genome seems to require noncanonical start and stop codons, as well as high levels of editing, trans-splicing and the addition of oligonucleotide caps at the 5' and 3' ends of transcripts. Despite its small coding content, the dinoflagellate mitochondrial genome is one of the most complex known.

  18. The Video Genome

    CERN Document Server

    Bronstein, Alexander M; Kimmel, Ron

    2010-01-01

    Fast evolution of Internet technologies has led to an explosive growth of video data available in the public domain and created unprecedented challenges in the analysis, organization, management, and control of such content. The problems encountered in video analysis such as identifying a video in a large database (e.g. detecting pirated content in YouTube), putting together video fragments, finding similarities and common ancestry between different versions of a video, have analogous counterpart problems in genetic research and analysis of DNA and protein sequences. In this paper, we exploit the analogy between genetic sequences and videos and propose an approach to video analysis motivated by genomic research. Representing video information as video DNA sequences and applying bioinformatic algorithms allows to search, match, and compare videos in large-scale databases. We show an application for content-based metadata mapping between versions of annotated video.

  19. Purification of Lamins and Soluble Fragments of NETs.

    Science.gov (United States)

    Makarov, Alexandr A; Rizzotto, Andrea; Meinke, Peter; Schirmer, Eric C

    2016-01-01

    Lamins and associated nuclear envelope transmembrane proteins (NETs) present unique problems for biochemical studies. Lamins form insoluble intermediate filament networks, associate with chromatin, and are also connected via specific NETs to the cytoskeleton, thus further complicating their isolation and purification from mammalian cells. Adding to this complexity, NETs at the inner nuclear membrane function in three distinct environments: (a) their nucleoplasmic domain(s) can bind lamins, chromatin, and transcriptional regulators; (b) they possess one or more integral transmembrane domains; and (c) their lumenal domain(s) function in the unique reducing environment of the nuclear envelope/ER lumen. This chapter describes strategic considerations and protocols to facilitate biochemical studies of lamins and NET proteins in vitro. Studying these proteins in vitro typically involves first expressing specific polypeptide fragments in bacteria and optimizing conditions to purify each fragment. We describe parameters for choosing specific fragments and designing purification strategies and provide detailed purification protocols. Biochemical studies can provide fundamental knowledge including binding strengths and the molecular consequences of disease-causing mutations that will be essential to understand nuclear envelope-genome interactions and nuclear envelope linked disease mechanisms.

  20. Immunogenic properties of Streptococcus agalactiae FbsA fragments.

    Directory of Open Access Journals (Sweden)

    Salvatore Papasergi

    Full Text Available Several species of Gram-positive bacteria can avidly bind soluble and surface-associated fibrinogen (Fng, a property that is considered important in the pathogenesis of human infections. To gain insights into the mechanism by which group B Streptococcus (GBS, a frequent neonatal pathogen, interacts with Fng, we have screened two phage displayed genomic GBS libraries. All of the Fng-binding phage clones contained inserts encoding fragments of FbsA, a protein displaying multiple repeats. Since the functional role of this protein is only partially understood, representative fragments were recombinantly expressed and analyzed for Fng binding affinity and ability to induce immune protection against GBS infection. Maternal immunization with 6pGST, a fragment containing five repeats, significantly protected mouse pups against lethal GBS challenge and these protective effects could be recapitulated by administration of anti-6pGST serum from adult animals. Notably, a monoclonal antibody that was capable of neutralizing Fng binding by 6pGST, but not a non-neutralizing antibody, could significantly protect pups against lethal GBS challenge. These data suggest that FbsA-Fng interaction promotes GBS pathogenesis and that blocking such interaction is a viable strategy to prevent or treat GBS infections.

  1. Mechanism study on mitochondrial fragmentation under oxidative stress caused by high-fluence low-power laser irradiation

    Science.gov (United States)

    Wu, Shengnan; Zhou, Feifan; Xing, Da

    2012-03-01

    Mitochondria are dynamic organelles that undergo continual fusion and fission to maintain their morphology and functions, but the mechanism involved is still not clear. Here, we investigated the effect of mitochondrial oxidative stress triggered by high-fluence low-power laser irradiation (HF-LPLI) on mitochondrial dynamics in human lung adenocarcinoma cells (ASTC-a-1). Upon HF-LPLI-triggered oxidative stress, mitochondria displayed a fragmented structure, which was abolished by exposure to dehydroascorbic acid (DHA), a reactive oxygen species scavenger, indicating that oxidative stress can induce mitochondrial fragmentation. Mitochondrial translocation of the profission protein dynamin-related protein 1 (Drp1) was observed following HF-LPLI, demonstrating apoptosis-related activation of Drp1. Notably, DHA pre-treatment prevented HF-LPLI-induced Drp1 activation. We conclude that mitochondrial oxidative stress through activation of Drp1 causes mitochondrial fragmentation.

  2. Nonlinear dynamical triggering of slow slip

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Paul A [Los Alamos National Laboratory; Knuth, Matthew W [WISCONSIN; Kaproth, Bryan M [PENN STATE; Carpenter, Brett [PENN STATE; Guyer, Robert A [Los Alamos National Laboratory; Le Bas, Pierre - Yves [Los Alamos National Laboratory; Daub, Eric G [Los Alamos National Laboratory; Marone, Chris [PENN STATE

    2010-12-10

    Among the most fascinating, recent discoveries in seismology have been the phenomena of triggered slip, including triggered earthquakes and triggered-tremor, as well as triggered slow, silent-slip during which no seismic energy is radiated. Because fault nucleation depths cannot be probed directly, the physical regimes in which these phenomena occur are poorly understood. Thus determining physical properties that control diverse types of triggered fault sliding and what frictional constitutive laws govern triggered faulting variability is challenging. We are characterizing the physical controls of triggered faulting with the goal of developing constitutive relations by conducting laboratory and numerical modeling experiments in sheared granular media at varying load conditions. In order to simulate granular fault zone gouge in the laboratory, glass beads are sheared in a double-direct configuration under constant normal stress, while subject to transient perturbation by acoustic waves. We find that triggered, slow, silent-slip occurs at very small confining loads ({approx}1-3 MPa) that are smaller than those where dynamic earthquake triggering takes place (4-7 MPa), and that triggered slow-slip is associated with bursts of LFE-like acoustic emission. Experimental evidence suggests that the nonlinear dynamical response of the gouge material induced by dynamic waves may be responsible for the triggered slip behavior: the slip-duration, stress-drop and along-strike slip displacement are proportional to the triggering wave amplitude. Further, we observe a shear-modulus decrease corresponding to dynamic-wave triggering relative to the shear modulus of stick-slips. Modulus decrease in response to dynamical wave amplitudes of roughly a microstrain and above is a hallmark of elastic nonlinear behavior. We believe that the dynamical waves increase the material non-affine elastic deformation during shearing, simultaneously leading to instability and slow-slip. The inferred

  3. A novel whole genome amplification method using type IIS restriction enzymes to create overhangs with random sequences.

    Science.gov (United States)

    Pan, Xiaoming; Wan, Baihui; Li, Chunchuan; Liu, Yu; Wang, Jing; Mou, Haijin; Liang, Xingguo

    2014-08-20

    Ligation-mediated polymerase chain reaction (LM-PCR) is a whole genome amplification (WGA) method, for which genomic DNA is cleaved into numerous fragments and then all of the fragments are amplified by PCR after attaching a universal end sequence. However, the self-ligation of these fragments could happen and may cause biased amplification and restriction of its application. To decrease the self-ligation probability, here we use type IIS restriction enzymes to digest genomic DNA into fragments with 4-5nt long overhangs with random sequences. After ligation to an adapter with random end sequences to above fragments, PCR is carried out and almost all present DNA sequences are amplified. In this study, whole genome of Vibrio parahaemolyticus was amplified and the amplification efficiency was evaluated by quantitative PCR. The results suggested that our approach could provide sufficient genomic DNA with good quality to meet requirements of various genetic analyses.

  4. Intrasaccadic perception triggers pupillary constriction

    Directory of Open Access Journals (Sweden)

    Sebastiaan Mathôt

    2015-08-01

    Full Text Available It is commonly believed that vision is impaired during saccadic eye movements. However, here we report that some visual stimuli are clearly visible during saccades, and trigger a constriction of the eye’s pupil. Participants viewed sinusoid gratings that changed polarity 150 times per second (every 6.67 ms. At this rate of flicker, the gratings were perceived as homogeneous surfaces while participants fixated. However, the flickering gratings contained ambiguous motion: rightward and leftward motion for vertical gratings; upward and downward motion for horizontal gratings. When participants made a saccade perpendicular to the gratings’ orientation (e.g., a leftward saccade for a vertical grating, the eye’s peak velocity matched the gratings’ motion. As a result, the retinal image was approximately stable for a brief moment during the saccade, and this gave rise to an intrasaccadic percept: A normally invisible stimulus became visible when eye velocity was maximal. Our results confirm and extend previous studies by demonstrating intrasaccadic perception using a reflexive measure (pupillometry that does not rely on subjective report. Our results further show that intrasaccadic perception affects all stages of visual processing, from the pupillary response to visual awareness.

  5. Draft Genome Sequence of Anammox Bacterium "Candidatus Scalindua brodae," Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments

    NARCIS (Netherlands)

    Speth, Daan R; Russ, Lina; Kartal, Boran; Op den Camp, Huub J M; Dutilh, Bas E; Jetten, Mike S M

    2015-01-01

    We present the draft genome of anammox bacterium "Candidatus Scalindua brodae," which at 282 contigs is a major improvement over the highly fragmented genome assembly of related species "Ca. Scalindua profunda" (1,580 contigs) which was previously published.

  6. Draft Genome Sequence of Anammox Bacterium "Candidatus Scalindua brodae," Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments

    NARCIS (Netherlands)

    Speth, Daan R; Russ, Lina; Kartal, Boran; Op den Camp, Huub J M; Dutilh, Bas E; Jetten, Mike S M

    2015-01-01

    We present the draft genome of anammox bacterium "Candidatus Scalindua brodae," which at 282 contigs is a major improvement over the highly fragmented genome assembly of related species "Ca. Scalindua profunda" (1,580 contigs) which was previously published.

  7. Single chain Fab (scFab fragment

    Directory of Open Access Journals (Sweden)

    Brenneis Mariam

    2007-03-01

    Full Text Available Abstract Background The connection of the variable part of the heavy chain (VH and and the variable part of the light chain (VL by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd and the light chain (LC, resulting in the formation of a single chain Fab fragment (scFab, can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC connecting the constant part 1 of the heavy chain (CH1 and the constant part of the light chain (CL were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of

  8. Fluid fragmentation from hospital toilets

    CERN Document Server

    Traverso, G; Lu, C -C; Maa, R; Langer, R; Bourouiba, L

    2013-01-01

    Hospital-acquired infections represent significant health and financial burdens to society. Clostridium difficile (C. difficile) is a particularly challenging bacteria with the potential to cause severe diarrhea and death. One mode of transmission for C. difficile, as well as other pathogens, which has received little attention is the potential air contamination by pathogen-bearing droplets emanating from toilets. In the fluid dynamics video submitted to the APS DFD Gallery of Fluid Motion 2013, we present flow visualizations via high-speed recordings showing the capture of the product of the fluid fragmentation generated by hospital toilet high-pressure flushes. Important quantities of both large and small droplets are observed. We illustrate how high-pressure flushes and cleaning products currently used in hospital toilets result in aggravating, rather than alleviating, the suspension and recirculation of tenacious airborne pathogen-bearing droplets.

  9. Fragmentation in Carbon Therapy Beams

    CERN Document Server

    Charara, Y M

    2010-01-01

    The state of the art Monte Carlo code HETC-HEDS was used to simulate spallation products, secondary neutron, and secondary proton production in A-150 Tissue Equivalent Plastic phantoms to investigate fragmentation of carbon therapy beams. For a 356 MeV/Nucleon carbon ion beam, production of charged particles heavier than protons was 0.24 spallation products per incident carbon ion with atomic numbers ranging from 1 through 5 (hydrogen to boron). In addition, there were 4.73 neutrons and 2.95 protons produced per incident carbon ion. Furthermore, as the incident energy increases, the neutron production rate increases at a rate of 20% per 10 MeV/nucleon. Secondary protons were created at a rate between 2.62-2.87 per carbon ion, while spallation products were created at a rate between 0.20-0.24 per carbon ion.

  10. Nonlinear Inflaton Fragmentation after Preheating

    CERN Document Server

    Felder, G N; Felder, Gary N.; Kofman, Lev

    2007-01-01

    We consider the nonlinear dynamics of inflaton fragmentation during and after preheating in the simplest model of chaotic inflation. While the earlier regime of parametric resonant particle production and the later turbulent regime of interacting fields evolving towards equilibrium are well identified and understood, the short intermediate stage of violent nonlinear dynamics remains less explored. Lattice simulations of fully nonlinear preheating dynamics show specific features of this intermediate stage: occupation numbers of the scalar particles are peaked, scalar fields become significantly non-gaussian and the field dynamics become chaotic and irreversible. Visualization of the field dynamics in configuration space reveals that nonlinear interactions generate non-gaussian inflaton inhomogeneities with very fast growing amplitudes. The peaks of the inflaton inhomogeneities coincide with the peaks of the scalar field(s) produced by parametric resonance. When the inflaton peaks reach their maxima, they stop ...

  11. Experimental Study of Remotely Triggered Rockburst Induced by a Tunnel Axial Dynamic Disturbance Under True-Triaxial Conditions

    Science.gov (United States)

    Su, Guoshao; Feng, Xiating; Wang, Jinhuan; Jiang, Jianqing; Hu, Lihua

    2017-08-01

    During deep underground excavation, dynamic ejection failure of a highly stressed rock mass near an excavated boundary is easily triggered by a dynamic disturbance in the tunnel axial direction, induced by blasting on the tunnel face. Such a dynamic ejection failure is usually called remotely triggered rockburst, and it poses a threat to underground construction. To clarify the characteristics of remotely triggered rockburst, the development of remotely triggered rockbursts of granite rock specimens was investigated using an improved true-triaxial test system. Experimental results show that with increasing static Z-direction stress (i.e., in situ tangential stress on the cross section of the tunnel), rockburst is triggered more easily and the kinetic energy of ejected fragments increases. Under other constant static stresses and dynamic disturbance, with increasing horizontal stress including X-direction stress (i.e., in situ axial stress) or Y-direction stress (i.e., in situ radial stress on the cross section of the tunnel), rockburst is more difficult to trigger and the kinetic energy of the ejected fragments decreases. Under constant static stresses, once the amplitude and frequency of the dynamic loading exceed their thresholds, the rockburst intensity increases rapidly and the rockburst can be triggered much more easily with small increments of the amplitude and frequency. Furthermore, Z-direction strain increases during the dynamic disturbance process, indicating that the ultimate energy-storage capacity of the specimen decreases with increasing damage. When the elastic strain energy is greater than the ultimate energy-storage capacity of the damaged specimen, part of the residual elastic energy is converted into kinetic energy of the ejected fragments.

  12. Microfluidic chip for stacking, separation and extraction of multiple DNA fragments.

    Science.gov (United States)

    Wu, Ruige; Seah, Y P; Wang, Zhiping

    2016-03-11

    A disposable integrated microfluidic device was developed for rapid sample stacking, separation and extraction of multiple DNA fragments from a relatively large amount of sample. Isotachophoresis hyphenated gel electrophoresis (ITP-GE) was used to pre-concentrate and separate DNA fragments, followed by extraction of pure DNA fragments with electroelution on-chip. DNA fragments of 200bp, 500bp and 1kbp were successfully separated and collected in the extraction chamber within 25min. The extraction efficiency obtained from the chip was 49.9%, 52.1% and 53.7% for 200bp, 500bp and 1kbp DNA fragments, respectively. The extracted DNA fragments exhibited compatibility with downstream enzymatic reactions, for example PCR. The chip was also used to extract DNA fragments with specific size range from sheared genomic DNA and demonstrated similar performance to that using traditional gel cutting method. The whole assay can finish in 32min, 6 times faster than traditional method. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Intelligent trigger processor for the crystal box

    CERN Document Server

    Sanders, G H; Cooper, M D; Hart, G W; Hoffman, C M; Hogan, G E; Hughes, E B; Matis, H S; Rolfe, J; Sandberg, V D; Williams, R A; Wilson, S; Zeman, H

    1981-01-01

    A large solid angle angular modular NaI(Tl) detector with 432 phototubes and 88 trigger scintillators is being used to search simultaneously for three lepton flavor-changing decays of the muon. A beam of up to 10/sup 6/ muons stopping per second with a 6% duty factor would yield up to 1000 triggers per second from random triple coincidences. A reduction of the trigger rate to 10 Hz is required from a hardwired primary trigger processor. Further reduction to <1 Hz is achieved by a microprocessor-based secondary trigger processor. The primary trigger hardware imposes voter coincidence logic, stringent timing requirements, and a non-adjacency requirement in the trigger scintillators defined by hardwired circuits. Sophisticated geometric requirements are imposed by a PROM-based matrix logic, and energy and vector-momentum cuts are imposed by a hardwired processor using LSI flash ADC's and digital arithmetic logic. The secondary trigger employs four satellite microprocessors to do a sparse data scan, multiplex ...

  14. The LVL2 trigger goes online

    CERN Document Server

    David Berge

    On Friday, the 9th of February, the ATLAS TDAQ community reached an important milestone. In a successful integration test, cosmic-ray muons were recorded with parts of the muon spectrometer, the central-trigger system and a second-level trigger algorithm. This was actually the first time that a full trigger slice all the way from the first-level trigger muon chambers up to event building after event selection by the second-level trigger ran online with cosmic rays. The ATLAS trigger and data acquisition system has a three-tier structure that is designed to cope with the enormous demands of proton-proton collisions at a bunch-crossing frequency of 40 MHz, with a typical event size of 1-2 MB. The online event selection has to reduce the incoming rate by a factor of roughly 200,000 to 200 Hz, a rate digestible by the archival-storage and offline-processing facilities. ATLAS has a mixed system: the first-level trigger (LVL1) is in hardware, while the other two consecutive levels, the second-level trigger (LVL2)...

  15. The ATLAS Level-1 Topological Trigger Performance

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00371751; The ATLAS collaboration

    2016-01-01

    The LHC will collide protons in the ATLAS detector with increasing luminosity through 2016, placing stringent operational and physical requirements to the ATLAS trigger system in order to reduce the 40 MHz collision rate to a manageable event storage rate of 1 kHz, while not rejecting interesting physics events. The Level-1 trigger is the first rate-reducing step in the ATLAS trigger system with an output rate of 100 kHz and decision latency smaller than 2.5 μs. It consists of a calorimeter trigger, muon trigger and a central trigger processor. During the LHC shutdown after the Run 1 finished in 2013, the Level-1 trigger system was upgraded including hardware, firmware and software updates. In particular, new electronics modules were introduced in the real-time data processing path: the Topological Processor System (L1Topo). It consists of a single AdvancedCTA shelf equipped with two Level-1 topological processor blades. They receive real-time information from the Level-1 calorimeter and muon triggers, which...

  16. The Run-2 ATLAS Trigger System

    CERN Document Server

    Ruiz-Martinez, Aranzazu; The ATLAS collaboration

    2016-01-01

    The ATLAS trigger has been successfully collecting collision data during the first run of the LHC between 2009-2013 at a centre-of-mass energy between 900 GeV and 8 TeV. The trigger system consists of a hardware Level-1 (L1) and a software based high-level trigger (HLT) that reduces the event rate from the design bunch-crossing rate of 40 MHz to an average recording rate of a few hundred Hz. In Run-2, the LHC will operate at centre-of-mass energies of 13 and 14 TeV resulting in roughly five times higher trigger rates. We will briefly review the ATLAS trigger system upgrades that were implemented during the shutdown, allowing us to cope with the increased trigger rates while maintaining or even improving our efficiency to select relevant physics processes. This includes changes to the L1 calorimeter and muon trigger systems, the introduction of a new L1 topological trigger module and the merging of the previously two-level HLT system into a single event filter farm. At hand of a few examples, we will show the ...

  17. Trigger factors for familial hemiplegic migraine

    DEFF Research Database (Denmark)

    Hansen, Jakob Møller; Hauge, Anne Werner; Ashina, Messoud

    2011-01-01

    The aim was to identify and describe migraine trigger factors in patients with familial hemiplegic migraine (FHM) from a population-based sample.......The aim was to identify and describe migraine trigger factors in patients with familial hemiplegic migraine (FHM) from a population-based sample....

  18. The ATLAS Level-1 Central Trigger Processor

    CERN Document Server

    Pauly, T; Ellis, Nick; Farthouat, P; Gällnö, P; Haller, J; Krasznahorkay, A; Maeno, T; Pessoa-Lima, H; Resurreccion-Arcas, I; Schuler, G; De Seixas, J M; Spiwoks, R; Torga-Teixeira, R; Wengler, T; 14th IEEE-NPSS Real Time Conference 2005

    2005-01-01

    ATLAS is a multi-purpose particle physics detector at CERN’s Large Hadron Collider where two pulsed beams of protons are brought to collision at very high energy. There are collisions every 25 ns, corresponding to a rate of 40 MHz. A three-level trigger system reduces this rate to about 200 Hz while keeping bunch crossings which potentially contain interesting processes. The Level-1 trigger, implemented in electronics and firmware, makes an initial selection in under 2.5 us with an output rate of less than 100 kHz. A key element of this is the Central Trigger Processor (CTP) which combines trigger information from the calorimeter and muon trigger processors to make the final Level-1 accept decision in under 100 ns on the basis of lists of selection criteria, implemented as a trigger menu. Timing and trigger signals are fanned out to all sub-detectors, while busy signals from all sub-detector read-out systems are collected and fed into the CTP in order to throttle the generation of Level-1 triggers.

  19. Do episodes of anger trigger myocardial infarction?

    DEFF Research Database (Denmark)

    Möller, J; Hallqvist, J; Diderichsen, Finn

    1999-01-01

    Our objectives were to study anger as a trigger of acute myocardial infarction (MI) and to explore potential effect modification by usual behavioral patterns related to hostility.......Our objectives were to study anger as a trigger of acute myocardial infarction (MI) and to explore potential effect modification by usual behavioral patterns related to hostility....

  20. Trigger factors for familial hemiplegic migraine

    DEFF Research Database (Denmark)

    Hansen, Jakob Møller; Hauge, Anne Werner; Ashina, Messoud

    2011-01-01

    The aim was to identify and describe migraine trigger factors in patients with familial hemiplegic migraine (FHM) from a population-based sample.......The aim was to identify and describe migraine trigger factors in patients with familial hemiplegic migraine (FHM) from a population-based sample....

  1. The Run-2 ATLAS Trigger System

    CERN Document Server

    Ruiz-Martinez, Aranzazu; The ATLAS collaboration

    2016-01-01

    The ATLAS trigger successfully collected collision data during the first run of the LHC between 2009-2013 at different centre-of-mass energies between 900 GeV and 8 TeV. The trigger system consists of a hardware Level-1 and a software-based high level trigger (HLT) that reduces the event rate from the design bunch-crossing rate of 40 MHz to an average recording rate of a few hundred Hz. In Run-2, the LHC will operate at centre-of-mass energies of 13 and 14 TeV and higher luminosity, resulting in roughly five times higher trigger rates. A brief review of the ATLAS trigger system upgrades that were implemented between Run-1 and Run-2, allowing to cope with the increased trigger rates while maintaining or even improving the efficiency to select physics processes of interest, will be given. This includes changes to the Level-1 calorimeter and muon trigger systems, the introduction of a new Level-1 topological trigger module and the merging of the previously two-level HLT system into a single event filter farm. A ...

  2. Corticosteroid injection for trigger finger in adults

    NARCIS (Netherlands)

    Peters-Veluthamaningal, Cyriac; van der Windt, Danielle A. W. M.; Winters, Jan C.; Meyboom-de Jong, Betty

    2009-01-01

    Background Trigger finger is a disease of the tendons of the hand leading to triggering (locking) of affected fingers, dysfunction and pain. Available treatments include local injection with corticosteroids, surgery, or splinting. Objectives To summarize the evidence on the efficacy and safety of

  3. High yield DNA fragmentation using cyclical hydrodynamic shearing

    NARCIS (Netherlands)

    Shui, Lingling; Sparreboom, Wouter; Spang, Peter; Roeser, Tina; Nieto, Benjamin; Guasch, Francesc; Corbera, Antoni Homs; van den Berg, Albert; Carlen, Edwin

    2013-01-01

    We report a new DNA fragmentation technique that significantly simplifies conventional hydrodynamic shearing fragmentation by eliminating the need for sample recirculation while maintaining high fragmentation yield and low fragment length variation, and therefore, reduces instrument complexity and c

  4. High yield DNA fragmentation using cyclical hydrodynamic shearing

    NARCIS (Netherlands)

    Shui, Lingling; Sparreboom, Wouter; Spang, Peter; Roeser, Tina; Nieto, Benjamin; Guasch, Francesc; Corbera, Antoni Homs; van den Berg, Albert; Carlen, Edwin

    2013-01-01

    We report a new DNA fragmentation technique that significantly simplifies conventional hydrodynamic shearing fragmentation by eliminating the need for sample recirculation while maintaining high fragmentation yield and low fragment length variation, and therefore, reduces instrument complexity and

  5. DNA large restriction fragment patterns of sporadic and epidemic nosocomial strains of Mycobacterium chelonae and Mycobacterium abscessus.

    OpenAIRE

    Wallace, R J; Zhang, Y; Brown, B.A.; Fraser, V; Mazurek, G H; S. Maloney

    1993-01-01

    Large restriction fragment (LRF) pattern analysis of genomic DNA using pulsed-field gel electrophoresis was performed on three reference strains, 32 sporadic isolates, and 92 nosocomial isolates from 12 epidemics of Mycobacterium chelonae and Mycobacterium abscessus. Only 17 of 30 (57%) unrelated strains of M. abscessus, compared with 10 of 11 (91%) of M. chelonae strains, gave satisfactory DNA extractions, with the remainder resulting in highly fragmented DNA. DraI, AsnI, XbaI, and SpeI gave...

  6. A Novel in situ Trigger Combination Method

    CERN Document Server

    Buzatu, Adrian; Krumnack, Nils; Yao, Wei-Ming

    2012-01-01

    Searches for rare physics processes using particle detectors in high-luminosity colliding hadronic beam environments require the use of multi-level trigger systems to reject colossal background rates in real time. In analyses like the search for the Higgs boson, there is a need to maximize the signal acceptance by combining multiple different trigger chains when forming the offline data sample. In such statistically limited searches, datasets are often amassed over periods of several years, during which the trigger characteristics evolve and their performance can vary significantly. Reliable production cross-section measurements and upper limits must take into account a detailed understanding of the effective trigger inefficiency for every selected candidate event. We present as an example the complex situation of three trigger chains, based on missing energy and jet energy, to be combined in the context of the search for the Higgs (H) boson produced in association with a W boson at the Collider Detector at F...

  7. The LHCb trigger and its upgrade

    Science.gov (United States)

    Dziurda, A.

    2016-07-01

    The current LHCb trigger system consists of a hardware level, which reduces the LHC inelastic collision rate of 30 MHz, at which the entire detector is read out. In a second level, implemented in a farm of 20 k parallel-processing CPUs, the event rate is reduced to about 5 kHz. We review the performance of the LHCb trigger system during Run I of the LHC. Special attention is given to the use of multivariate analyses in the High Level Trigger. The major bottleneck for hadronic decays is the hardware trigger. LHCb plans a major upgrade of the detector and DAQ system in the LHC shutdown of 2018, enabling a purely software based trigger to process the full 30 MHz of inelastic collisions delivered by the LHC. We demonstrate that the planned architecture will be able to meet this challenge.

  8. MR imaging findings of trigger thumb

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Eric Y.; Chen, Karen C.; Chung, Christine B. [VA San Diego Healthcare System, Radiology Service, San Diego, CA (United States); University of California, San Diego Medical Center, Department of Radiology, San Diego, CA (United States)

    2015-08-15

    Trigger finger (or trigger thumb), also known as sclerosing tenosynovitis, is a common clinical diagnosis that rarely presents for imaging. Because of this selection bias, many radiologists may not be familiar with the process. Furthermore, patients who do present for imaging frequently have misleading examination indications. To our knowledge, magnetic resonance (MR) imaging findings of trigger thumb have not been previously reported in the literature. In this article, we review the entity of trigger thumb, the anatomy involved, and associated imaging findings, which include flexor pollicis longus tendinosis with a distinct nodule, A1 pulley thickening, and tenosynovitis. In addition, in some cases, an abnormal Av pulley is apparent. In the rare cases of trigger finger that present for MR imaging, accurate diagnosis by the radiologist can allow initiation of treatment and avoid further unnecessary workup. (orig.)

  9. Concept of the CMS Trigger Supervisor

    CERN Document Server

    Magrans de Abril, Ildefons; Varela, Joao

    2006-01-01

    The Trigger Supervisor is an online software system designed for the CMS experiment at CERN. Its purpose is to provide a framework to set up, test, operate and monitor the trigger components on one hand and to manage their interplay and the information exchange with the run control part of the data acquisition system on the other. The Trigger Supervisor is conceived to provide a simple and homogeneous client interface to the online software infrastructure of the trigger subsystems. This document specifies the functional and non-functional requirements, design and operational details, and the components that will be delivered in order to facilitate a smooth integration of the trigger software in the context of CMS.

  10. The ATLAS b-Jet Trigger

    CERN Document Server

    Hansson Adrian, Per

    2011-01-01

    The online event selection is crucial to reject most of the events containing uninteresting background collisions while preserving as much as possible the interesting physical signals. The b-jet selection is part of the trigger strategy of the ATLAS experiment and a set of dedicated triggers was contributing to the event selection for the 2011 running. The b-jets acceptance is increased and the background reduced by lowering jet transverse energy thresholds at the first trigger level and applying b-tagging techniques at the subsequent levels. Different physics channels, especially topologies containing more than one b-jet where higher rejection factors are achieved, benefit from using the b-jet trigger. An overview of the b-jet trigger menu and performance on data is presented.

  11. The ATLAS b-jet Trigger

    CERN Document Server

    Hansson Adrian, P; The ATLAS collaboration

    2011-01-01

    The online event selection is crucial to reject most of the events containing uninteresting background collisions while preserving as much as possible the interesting physical signals. The b-jet selection is part of the trigger strategy of the ATLAS experiment and a set of dedicated triggers is presently contributing to the event selection for the 2011 running. The b-jets acceptance is increased and the background reduced by lowering jet transverse energy thresholds at the first trigger level and applying b-tagging techniques at the subsequent levels. Different physics channels, especially topologies containing more than one b-jet where higher rejection factors are achieved, benefit from requesting this trigger to be fired. An overview of the status-of-art of the b-jet trigger menu and performance on real data is presented in this contribution.

  12. The LHCb Trigger: Present and Future

    CERN Document Server

    Aaij, R

    2012-01-01

    LHCb is a single arm spectrometer covering the pseudo-rapidity range between 1.9 and 4.9, and has been optimised to perform flavour physics measurements at the LHC. The present two stage trigger system is able to select charm and beauty decay products with high efficiency due the highly inclusive approach of triggering on partially reconstructed decays and the use of a novel multivariate classifier at the second stage. The trigger can select both leptonic and purely hadronic decays. The performance of the trigger is determined from the data itself without having to rely on Monte-Carlo simulation and is presented. LHCb has recently submitted their upgrade LOI, which mainly aims at profiting from much larger luminosities by moving towards a single fully software based trigger. The upgrade strategy and expected performance are presented.

  13. ATLAS jet trigger performance in 2015 data

    CERN Document Server

    Herwig, Theodor Christian; The ATLAS collaboration

    2016-01-01

    The ATLAS experiment at the LHC uses a two-level trigger system to preferentially select events with a predefined topology of interest for future analysis. The hadronic jet trigger is used to select several different topologies containing different types and multiplicities of hadronic jets, thus supporting many different physics searches and measurements. The hadronic jet trigger efficiency for proton-proton collision data at a centre-of-mass energy of 13 TeV is presented. The efficient selection of events containing hadronic jets requires the characteristics of trigger-level jets and offline jets to be very similar. A comparison of relevant characteristics demonstrates that trigger-level jets and offline jets are in excellent agreement.

  14. ATLAS jet trigger performance in 2016 data

    CERN Document Server

    Herwig, Theodor Christian; The ATLAS collaboration

    2016-01-01

    The ATLAS experiment at the LHC uses a two-level trigger system to preferentially select events with a predefined topology of interest for future analysis. The hadronic jet trigger is used to select several different topologies containing different types and multiplicities of hadronic jets, thus supporting many different physics searches and measurements. The hadronic jet trigger efficiency for proton-proton collision data at a centre-of-mass energy of 13 TeV is presented. The efficient selection of events containing hadronic jets requires the characteristics of trigger-level jets and offline jets to be very similar. A comparison of relevant characteristics demonstrates that trigger-level jets and offline jets are in excellent agreement.

  15. Generalized fragmentation functions for fractal jet observables

    Science.gov (United States)

    Elder, Benjamin T.; Procura, Massimiliano; Thaler, Jesse; Waalewijn, Wouter J.; Zhou, Kevin

    2017-06-01

    We introduce a broad class of fractal jet observables that recursively probe the collective properties of hadrons produced in jet fragmentation. To describe these collinear-unsafe observables, we generalize the formalism of fragmentation functions, which are important objects in QCD for calculating cross sections involving identified final-state hadrons. Fragmentation functions are fundamentally nonperturbative, but have a calculable renormalization group evolution. Unlike ordinary fragmentation functions, generalized fragmentation functions exhibit nonlinear evolution, since fractal observables involve correlated subsets of hadrons within a jet. Some special cases of generalized fragmentation functions are reviewed, including jet charge and track functions. We then consider fractal jet observables that are based on hierarchical clustering trees, where the nonlinear evolution equations also exhibit tree-like structure at leading order. We develop a numeric code for performing this evolution and study its phenomenological implications. As an application, we present examples of fractal jet observables that are useful in discriminating quark jets from gluon jets.

  16. Coal char fragmentation during pulverized coal combustion

    Energy Technology Data Exchange (ETDEWEB)

    Baxter, L.L.

    1995-07-01

    A series of investigations of coal and char fragmentation during pulverized coal combustion is reported for a suite of coals ranging in rank from lignite to low-volatile (lv) bituminous coal under combustion conditions similar to those found in commercial-scale boilers. Experimental measurements are described that utilize identical particle sizing characteristics to determine initial and final size distributions. Mechanistic interpretation of the data suggest that coal fragmentation is an insignificant event and that char fragmentation is controlled by char structure. Chars forming cenospheres fragment more extensively than solid chars. Among the chars that fragment, large particles produce more fine material than small particles. In all cases, coal and char fragmentation are seen to be sufficiently minor as to be relatively insignificant factors influencing fly ash size distribution, particle loading, and char burnout.

  17. Designing signal-enriched triggers for boosted jets.

    CERN Document Server

    Toumazou, Marina

    2017-01-01

    Triggers designed to favour the selection of hadronically decaying massive particles have been studied. Both triggers using solely ET and mass cuts (similar to new 2017 triggers) and triggers exploiting polarization information have been studied. The mass cut triggers show substantial gains in rate reduction, while the benefits of polarization triggers are less obvious. The final conclusion is that it is more useful to identify and trigger on generic boosted decays, irrespective of the polarization of the decaying particle

  18. Fragmentation processes during explosion welding (review)

    Science.gov (United States)

    Grinberg, B. A.; Ivanov, M. A.; Rybin, V. V.; Elkina, O. A.; Patselov, A. M.; Antonova, O. V.; Inozemtsev, A. V.; Tolmachev, T. P.

    2013-10-01

    The fragmentation during explosion welding is briefly reviewed. Fragmentation of partitioning type (FPT), which consists in partitioning into particles that either fly away or join each other, is detected. FPT is an analog of the fragmentation during an explosion that was studied by Mott. In both cases, the flight of particles (fragments) takes place, and the integrity of the material is retained in FPT. FPT is a powerful channel for the dissipation of supplied energy, since the surface of flying particles has a large total area.

  19. Molecular energies from an incremental fragmentation method

    Science.gov (United States)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  20. A Note on Convex Renorming and Fragmentability

    Indian Academy of Sciences (India)

    A K Mirmostafaee

    2005-05-01

    Using the game approach to fragmentability, we give new and simpler proofs of the following known results: (a) If the Banach space admits an equivalent Kadec norm, then its weak topology is fragmented by a metric which is stronger than the norm topology. (b) If the Banach space admits an equivalent rotund norm, then its weak topology is fragmented by a metric. (c) If the Banach space is weakly locally uniformly rotund, then its weak topology is fragmented by a metric which is stronger than the norm topology.

  1. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  2. Identification and characterization of CACTA transposable elements capturing gene fragments in maize

    Institute of Scientific and Technical Information of China (English)

    LI Qing; LI Lin; DAI JingRui; LI JianSheng; YAN JianBing

    2009-01-01

    Transposable elements (TEs)-mediated gene sequence movement is thought to play an important role in genome expansion and origin of genes with novel functions. In this study, a gene, HGGT, involved in vitamin E synthesis was used in a case study to discover and characterize transposons carrying gene fragments in maize. A total of 69 transposons that are distributed across the 10 chromosomes and have an average length of 3689 bp were identified from the maize sequence database by using the BLAST search algorithm. Three of these carry gene fragments from the progenitor HGGT gene, while the rest (66) contain gene fragments from other cellular genes. Nine of the 69 transposons contain fragments derived from two locations in the genome. By querying the maize Expressed Sequence Tag (EST) da-tabase, we found that at least thirteen out of the 69 TEs had corresponding transcripts. More interest-ingly, two transposons that carry gene fragments from two different chromosomal loci could be ex-pressed as chimeric transcripts.

  3. [Novel bidirectional promoter from human genome].

    Science.gov (United States)

    Orekhova, A S; Sverdlova, P S; Spirin, P V; Leonova, O G; Popenko, V I; Prasolov, V S; Rubtsov, P M

    2011-01-01

    In human and other mammalian genomes a number of closely linked gene pairs transcribed in opposite directions are found. According to bioinformatic analysis up to 10% of human genes are arranged in this way. In present work the fragment of human genome was cloned that separates genes localized at 2p13.1 and oriented "head-to-head", coding for hypothetical proteins with unknown functions--CCDC (Coiled Coil Domain Containing) 142 and TTC (TetraTricopeptide repeat Containing) 31. Intergenic CCDC142-TTC31 region overlaps with CpG-island and contains a number of potential binding sites for transcription factors. This fragment functions as bidirectional promoter in the system ofluciferase reporter gene expression upon transfection of human embryonic kidney (HEK293) cells. The vectors containing genes of two fluorescent proteins--green (EGFP) and red (DsRed2) in opposite orientations separated by the fragment of CCDC142-TTC31 intergenic region were constructed. In HEK293 cells transfected with these vectors simultaneous expression of two fluorescent proteins is observed. Truncated versions of intergenic region were obtained and their promoter activity measured. Minimal promoter fragment contains elements Inr, BRE, DPE characteristic for TATA-less promoters. Thus, from the human genome the novel bidirectional promoter was cloned that can be used for simultaneous constitutive expression of two genes in human cells.

  4. GnRHa trigger for final oocyte maturation: is HCG trigger history?

    DEFF Research Database (Denmark)

    Humaidan, Peter; Alsbjerg, Birgit

    2014-01-01

    gonadotrophin (HCG) trigger. Early trials showed a severe luteal phase insufficiency after GnRHa trigger despite the application of standard luteal phase support protocols. Subsequent research has led to modifications of the luteal phase support, resulting in reproductive outcome comparable to that seen after...... HCG trigger in normal- and high-responders. GnRHa trigger facilitates a tailored approach to subsequent luteal phase support, taking into account the ovarian response to stimulation. In the future, GnRHa is likely to be used for trigger in all women co-treated with GnRH antagonists....

  5. Spatial- and Time-Correlated Detection of Fission Fragments

    Directory of Open Access Journals (Sweden)

    Platkevic M.

    2012-02-01

    Full Text Available With the goal to measure angular correlations of fission fragments in rare fission decay (e.g. ternary and quaternary fission, a multi-detector coincidence system based on two and up to four position sensitive pixel detectors Timepix has been built. In addition to the high granularity, wide dynamic range and per pixel signal threshold, these devices are equipped with per pixel energy and time sensitivity providing more information (position, energy, time, enhances particle-type identification and selectivity of event-by-event detection. Operation of the device with the integrated USB 2.0 based readout interface FITPix and the control and data acquisition software tool Pixelman enables online visualization and flexible/adjustable operation for a different type of experiments. Spatially correlated fission fragments can be thus registered in coincidence. Similarly triggered measurements are performed using an integrated spectrometric module with analogue signal chain electronics. The current status of development together with demonstration of the technique with a 252Cf source is presented.

  6. Fragmentation of wall rock garnets during deep crustal earthquakes

    Science.gov (United States)

    Austrheim, Håkon; Dunkel, Kristina G.; Plümper, Oliver; Ildefonse, Benoit; Liu, Yang; Jamtveit, Bjørn

    2017-01-01

    Fractures and faults riddle the Earth’s crust on all scales, and the deformation associated with them is presumed to have had significant effects on its petrological and structural evolution. However, despite the abundance of directly observable earthquake activity, unequivocal evidence for seismic slip rates along ancient faults is rare and usually related to frictional melting and the formation of pseudotachylites. We report novel microstructures from garnet crystals in the immediate vicinity of seismic slip planes that transected lower crustal granulites during intermediate-depth earthquakes in the Bergen Arcs area, western Norway, some 420 million years ago. Seismic loading caused massive dislocation formations and fragmentation of wall rock garnets. Microfracturing and the injection of sulfide melts occurred during an early stage of loading. Subsequent dilation caused pervasive transport of fluids into the garnets along a network of microfractures, dislocations, and subgrain and grain boundaries, leading to the growth of abundant mineral inclusions inside the fragmented garnets. Recrystallization by grain boundary migration closed most of the pores and fractures generated by the seismic event. This wall rock alteration represents the initial stages of an earthquake-triggered metamorphic transformation process that ultimately led to reworking of the lower crust on a regional scale.

  7. Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

    Directory of Open Access Journals (Sweden)

    Langdon Tim

    2009-06-01

    Full Text Available Abstract Background Helitrons are a class of transposable elements which have been identified in a number of species of plants, animals and fungi. They are unique in their proposed rolling-circle mode of replication, have a highly variable copy-number and have been implicated in the restructuring of coding sequences both by their insertion into existing genes and by their incorporation of transcriptionally competent gene fragments. Helitron discovery depends on identifying associated DNA signature sequences and comprehensive evaluation of helitron contribution to a particular genome requires detailed computational analysis of whole genome sequence. Therefore, the role which helitrons have played in modelling non-model plant genomes is largely unknown. Results Cloning of the flowering gene GIGANTEA (GI from a BAC library of the Pooideae grass Lolium perenne (perennial ryegrass identified the target gene and several GI pseudogene fragments spanning the first five exons. Analysis of genomic sequence 5' and 3' of one these GI fragments revealed motifs consistent with helitron-type transposon insertion, specifically a putative 5'-A↓T-3' insertion site containing 5'-TC and CTAG-3' borders with a sub-terminal 16 bp hairpin. Screening of a BAC library of the closely related grass species Festuca pratensis (meadow fescue indicated similar helitron-associated GI fragments present in this genome, as well as non-helitron associated GI fragments derived from the same region of GI. In order to investigate the possible extent of ancestral helitron-activity in L. perenne, a methylation-filtered GeneThresher® genomic library developed from this species was screened for potential helitron 3' hairpin sequences associated with a 3'-CTRR motif. This identified 7 potential helitron hairpin-types present between at least 9 and 51 times within the L. perenne methylation-filtered library. Conclusion This represents evidence for a possible ancestral role for helitrons

  8. Cleavage of Tau by calpain in Alzheimer's disease: the quest for the toxic 17 kD fragment.

    Science.gov (United States)

    Garg, Sarika; Timm, Thomas; Mandelkow, Eva-Maria; Mandelkow, Eckhard; Wang, Yipeng

    2011-01-01

    The amyloid cascade hypothesis of Alzheimer's disease (AD) posits that the generation of β-amyloid (Aβ) triggers Tau neurofibrillary pathology. Recently a "17 kD" calpain-induced Tau fragment, comprising residues 45-230 (molecular weight [MW], 18.7 kD), was proposed to mediate Aβ-induced toxicity. Here, we demonstrate that the "17 kD" fragment is actually much smaller, containing residues 125-230 (molecular weight, 10.7 kD). Inducing Tau phosphorylation by okadaic acid or mimicking phosphorylation by Glu mutations at the epitopes of Alzheimer-diagnostic antibodies AT100/AT8/PHF1 could not prevent the generation of this fragment. The fragment can be induced not only by Aβ oligomers, but also by other cell stressors, e.g., thapsigargin (a Ca(2+)-ATPase inhibitor) or glutamate (an excitatory neurotransmitter). However, overexpression of neither Tau(45-230) nor Tau(125-230) fragment is toxic to Chinese hamster ovary (CHO) cells, neuroblastoma cells (N2a) or primary hippocampal neurons. Finally, the calpain-induced fragment can be observed both in Alzheimer's disease brains and in control normal human brains. We conclude that the 17 kD Tau fragment is not a mediator of Aβ-induced toxicity, leaving open the possibility that upstream calpain activation might cause both Tau fragmentation and toxicity.

  9. Comparison by restriction fragment pattern analyses and molecular characterization of some European isolates of Suid herpesvirus 1: A contribution to strain differentiation of European isolates

    DEFF Research Database (Denmark)

    Christensen, Laurids Siig

    1988-01-01

    Eleven European isolates of Suid herpesvirus type 1 (SHV-1) were compared by restriction fragment pattern analyses and Southern blot hybridization using different genomic probes. The presence of strain discriminative 4 major genome types and several subtypes as well as the molecular distinctions ...

  10. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  11. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  12. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  13. Climatic triggers for peatland initiation

    Science.gov (United States)

    Morris, Paul J.; Swindles, Graeme T.; Valdes, Paul J.; Ivanovic, Ruza F.; Gregoire, Lauren J.; Smith, Mark W.; Tarasov, Lev; Haywood, Alan M.; Bacon, Karen L.

    2017-04-01

    Peatlands are carbon-dense wetlands characterised by waterlogged, organic-rich soils. Modern-day peatlands have formed mainly since the Last Glacial Maximum (LGM), and despite covering only 3 % of the Earth's land surface are thought to store more than a third of all global soil carbon in the form of poorly decomposed plant detritus. Concern exists that this globally important carbon store may be vulnerable to near-future warming and changes in precipitation patterns, although the links between peatland development and climate are contested. The climatic and other environmental conditions that facilitate the initiation of peat are particularly poorly understood. We present the results of a novel, global study into the climate space of peat initiation since the LGM. We compiled a catalogue of radiocarbon dates of peat initiation from 942 sites that span a range of latitudes and biomes. We used the locations and ages of these peatlands to interrogate downscaled climate hindcasts at 500-yr intervals from a coupled atmosphere-ocean-vegetation general circulation model, HadCM3. This powerful combination of modelling and observational data provides a globally-consistent, temporally-extensive estimate of the climate spaces of peat initiation. In particular, it allows us to identify local and regional climatic changes that may have acted as triggers for peat formation. Peatlands in mid- and high-latitudes of both hemispheres, particularly in maritime locations, developed shortly after local increases in the time integral of growing season temperatures, and were seemingly not influenced by rainfall regime. Peat initiation at such sites appears to have been stimulated by temperature-driven increases in plant productivity in cold, postglacial landscapes, and was not water limited. The exception is the large peatland complex of the Western Siberian Lowlands, which was not glaciated during the last glacial period, and which appears to have been prompted instead by a strong

  14. Upgrade of the CMS Global Muon Trigger

    CERN Document Server

    Lingemann, Joschka; Sakulin, Hannes; Jeitler, Manfred; Stahl, Achim

    2015-01-01

    The increase in center-of-mass energy and luminosity for Run 2 of the Large Hadron Collider pose new challenges for the trigger systems of the experiments. To keep triggering with a similar performance as in Run 1, the CMS muon trigger is currently being upgraded. The new algorithms will provide higher resolution, especially for the muon transverse momentum and will make use of isolation criteria that combine calorimeter with muon information already in the level-1 trigger. The demands of the new algorithms can only be met by upgrading the level-1 trigger system to new powerful FPGAs with high bandwidth I/O. The processing boards will be based on the new microTCA standard. We report on the planned algorithms for the upgraded Global Muon Trigger (GMT) which combines information from the muon trigger sub-systems and assigns the isolation variable. The upgraded GMT will be implemented using a Master Processor 7 card, built by Imperial College, that features a large Xilinx Virtex 7 FPGA. Up to 72 optical links at...

  15. The Uses of Dynamic Earthquake Triggering

    Science.gov (United States)

    Brodsky, Emily E.; van der Elst, Nicholas J.

    2014-05-01

    Dynamic triggering of earthquakes by seismic waves is a robustly observed phenomenon with well-documented examples from over 30 major earthquakes. We are now in a position to use dynamic triggering as a natural experiment to probe the reaction of faults to the known stresses from seismic waves. We show here that dynamic triggering can be used to investigate the distribution of stresses required for failure on faults. In some regions, faults appear to be uniformly distributed over their loading cycles with equal numbers at all possible stresses from failure. Regions under tectonic extension, at the interface between locked and creeping faults, or subject to anthropogenic forcing are most prone to triggered failure. Predictions of future seismicity rates based on seismic wave amplitudes are theoretically possible and may provide similar results to purely stochastic prediction schemes. The underlying mechanisms of dynamic triggering are still unknown. The prolonged triggered sequences require a multistage process such as shear failure from rate-state friction coupled to aseismic creep or continued triggering through a secondary cascade. Permeability enhancement leading to drainage or pore pressure redistribution on faults is an alternative possibility.

  16. The ATLAS Trigger Menu: Design and Performance

    CERN Document Server

    Bernius, C; The ATLAS collaboration

    2012-01-01

    The ATLAS trigger is a three-tiered system designed to select events of interest for the diverse ATLAS physics program such as Higgs Boson decays. At the same time the rate of events has to be reduced in order to stay within the limitations of available resources such as the output bandwidth, processing power and recording rate. At design capacity, the LHC has a bunch-crossing rate of 40 MHz whereas ATLAS detector has an average recording rate of about 300Hz. The decision to record an event is based on physics signatures found in the event such as energetic jets, leptons or large missing energy. The ATLAS trigger menu consists of several hundred trigger chains which are used during data taking. Each chain defines the selection criteria at each of the three trigger levels for a single physics signature. Additionally, the trigger menu specifies, depending on the physics purpose of the trigger, at which given rate the trigger is running. The continuously increasing luminosities together with optimisations of alg...

  17. Upgrade of the CMS Global Muon Trigger

    CERN Document Server

    Jeitler, Manfred; Rabady, Dinyar; Sakulin, Hannes; Stahl, Achim

    2015-01-01

    The increase in center-of-mass energy and luminosity for Run-II of the Large Hadron Collider poses new challenges for the trigger systems of the experiments. To keep triggering with a similar performance as in Run-I, the CMS muon trigger is currently being upgraded. The new algorithms will provide higher resolution, especially for the muon transverse momentum and will make use of isolation criteria that combine calorimeter with muon information already in the level-1 trigger. The demands of the new algorithms can only be met by upgrading the level-1 trigger system to new powerful FPGAs with high bandwidth I/O. The processing boards will be based on the new μTCA standard. We report on the planned algorithms for the upgraded Global Muon Trigger (μGMT) which sorts and removes duplicates from boundaries of the muon trigger sub-systems. Furthermore, it determines how isolated the muon candidates are based on calorimetric energy deposits. The μGMT will be implemented using a processing board that features a larg...

  18. In vivo assembly of DNA-fragments in the moss, Physcomitrella patens

    DEFF Research Database (Denmark)

    King, Brian Christopher; Vavitsas, Konstantinos; Ikram, Nur Kusaira Binti Khairul

    2016-01-01

    Direct assembly of multiple linear DNA fragments via homologous recombination, a phenomenon known as in vivo assembly or transformation associated recombination, is used in biotechnology to assemble DNA constructs ranging in size from a few kilobases to full synthetic microbial genomes. It has also...... enabled the complete replacement of eukaryotic chromosomes with heterologous DNA. The moss Physcomitrella patens, a non-vascular and spore producing land plant (Bryophyte), has a well-established capacity for homologous recombination. Here, we demonstrate the in vivo assembly of multiple DNA fragments...

  19. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  20. Intraplate triggered earthquakes: Observations and interpretation

    Science.gov (United States)

    Hough, S.E.; Seeber, L.; Armbruster, J.G.

    2003-01-01

    We present evidence that at least two of the three 1811-1812 New Madrid, central United States, mainshocks and the 1886 Charleston, South Carolina, earthquake triggered earthquakes at regional distances. In addition to previously published evidence for triggered earthquakes in the northern Kentucky/southern Ohio region in 1812, we present evidence suggesting that triggered events might have occurred in the Wabash Valley, to the south of the New Madrid Seismic Zone, and near Charleston, South Carolina. We also discuss evidence that earthquakes might have been triggered in northern Kentucky within seconds of the passage of surface waves from the 23 January 1812 New Madrid mainshock. After the 1886 Charleston earthquake, accounts suggest that triggered events occurred near Moodus, Connecticut, and in southern Indiana. Notwithstanding the uncertainty associated with analysis of historical accounts, there is evidence that at least three out of the four known Mw 7 earthquakes in the central and eastern United States seem to have triggered earthquakes at distances beyond the typically assumed aftershock zone of 1-2 mainshock fault lengths. We explore the possibility that remotely triggered earthquakes might be common in low-strain-rate regions. We suggest that in a low-strain-rate environment, permanent, nonelastic deformation might play a more important role in stress accumulation than it does in interplate crust. Using a simple model incorporating elastic and anelastic strain release, we show that, for realistic parameter values, faults in intraplate crust remain close to their failure stress for a longer part of the earthquake cycle than do faults in high-strain-rate regions. Our results further suggest that remotely triggered earthquakes occur preferentially in regions of recent and/or future seismic activity, which suggests that faults are at a critical stress state in only some areas. Remotely triggered earthquakes may thus serve as beacons that identify regions of

  1. Remotely triggered earthquakes following moderate main shocks

    Science.gov (United States)

    Hough, S.E.

    2007-01-01

    Since 1992, remotely triggered earthquakes have been identified following large (M > 7) earthquakes in California as well as in other regions. These events, which occur at much greater distances than classic aftershocks, occur predominantly in active geothermal or volcanic regions, leading to theories that the earthquakes are triggered when passing seismic waves cause disruptions in magmatic or other fluid systems. In this paper, I focus on observations of remotely triggered earthquakes following moderate main shocks in diverse tectonic settings. I summarize evidence that remotely triggered earthquakes occur commonly in mid-continent and collisional zones. This evidence is derived from analysis of both historic earthquake sequences and from instrumentally recorded M5-6 earthquakes in eastern Canada. The latter analysis suggests that, while remotely triggered earthquakes do not occur pervasively following moderate earthquakes in eastern North America, a low level of triggering often does occur at distances beyond conventional aftershock zones. The inferred triggered events occur at the distances at which SmS waves are known to significantly increase ground motions. A similar result was found for 28 recent M5.3-7.1 earthquakes in California. In California, seismicity is found to increase on average to a distance of at least 200 km following moderate main shocks. This supports the conclusion that, even at distances of ???100 km, dynamic stress changes control the occurrence of triggered events. There are two explanations that can account for the occurrence of remotely triggered earthquakes in intraplate settings: (1) they occur at local zones of weakness, or (2) they occur in zones of local stress concentration. ?? 2007 The Geological Society of America.

  2. Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

    Energy Technology Data Exchange (ETDEWEB)

    McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

    2005-08-26

    Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

  3. Governmental Fragmentation in Metropolitan Detroit

    Directory of Open Access Journals (Sweden)

    Davis, Kristal D.

    2012-01-01

    Full Text Available At its population peak in the 1950’s, Detroit, Michigan was inhabited by almost two million residents and served as the car capital of the country. Today, however, the population has dropped by more than fifty percent. With the loss of Detroit residents to surrounding cities and counties, the wedge between Detroit and the suburbs has grown wider. Detroit, once considered the crown jewel of the state of Michigan, is now treated as an immovable stain by its surrounding municipalities. What this means for the metro Detroit area is a high level of governmental fragmentation, preventing economic opportunities for both the city and its suburbs. This is especially unfortunate for the economy of the metro Detroit area because of the current economic crisis in the state of Michigan. With the state’s long tradition of home rule and pride in autonomous, municipal decision-making, municipalities in the metro Detroit area might better realize economic opportunities and the relief they can bring to their own local economies by not only collaborating with the city of Detroit, but with neighboring cities as well.

  4. Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations

    Directory of Open Access Journals (Sweden)

    Rodrigo eGarcía-López

    2015-09-01

    Full Text Available Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impact the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using Overlap Layout Consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the degree of fragmentation of each genome in the sample, which is dependent on the sequencing effort and the genome length. Depending on ecological, biological or procedural biases, some fragments have a higher prevalence, or coverage, in the assembly. However, assemblers must face challenges such as the formation of chimerical structures and intra-species variability.Diversity calculation relies on the classification of the sequences that comprise a metagenomic dataset. Whenever the corresponding genomic and taxonomic information is available, contigs matching the same species can be classified accordingly and the coverage of its genome can be calculated for that species. This may be used to compare populations by estimating abundance and assessing species distribution from this data. Nevertheless, the coverage does not take into account the degree of fragmentation, or else genome completeness, and is not necessarily representative of actual species distribution in the samples. Furthermore, undetermined sequences are abundant in viral metagenomic datasets, resulting in several independent contigs that cannot be assigned by homology or genomic information. These may only be classified as different Operational Taxonomic Units (OTUs, sometimes remaining inadvisably

  5. Trigger tracking for the LHCb upgrade

    CERN Multimedia

    Dungs, K

    2014-01-01

    This poster presents a trigger system for the upgraded LHCb detector, scheduled to begin operation in 2020. The proposed trigger system is implemented entirely in software. We show that track reconstruction of a similar quality to that available in the offline algorithms can be performed on the full inelastic pp-collision rate. A track finding efficiency of 98.8% relative to offline can be achieved for good trigger tracks. The CPU time required for this reconstruction is less than 60% of the available budget.

  6. Is Earthquake Triggering Driven by Small Earthquakes?

    CERN Document Server

    Helmstetter, A

    2002-01-01

    Using a catalog of seismicity for Southern California, we measure how the number of triggered earthquakes increases with the earthquake magnitude. The trade-off between this scaling and the distribution of earthquake magnitudes controls the relative role of small compared to large earthquakes. We show that seismicity triggering is driven by the smallest earthquakes, which trigger fewer aftershocks than larger earthquakes, but which are much more numerous. We propose that the non-trivial scaling of the number of aftershocks emerges from the fractal spatial distribution of aftershocks.

  7. The upgrade of the CMS Global Trigger

    CERN Document Server

    Arnold, Bernhard; Jeitler, Manfred; Matsushita, Takashi; Rabady, Dinyar Sebastian; Rahbaran, Babak; Wittmann, Johannes; Wulz, Claudia

    2015-01-01

    The Global Trigger is the final step of the CMS Level-1 Trigger. Previously implemented in VME, it has been redesigned and completely rebuilt in microTCA technology, using the Virtex-7 FPGA chip family. It will allow to implement trigger algorithms close to the final physics selection. The new system is presented, together with performance tests undertaken in parallel operation with the legacy system during the initial months of Run II of the LHC at a beam energy of 13 TeV.

  8. Revisiting Pneumatic Nail Gun Trigger Recommendations.

    Science.gov (United States)

    Albers, James; Lowe, Brian; Lipscomb, Hester; Hudock, Stephen; Dement, John; Evanoff, Bradley; Fullen, Mark; Gillen, Matt; Kaskutas, Vicki; Nolan, James; Patterson, Dennis; Platner, James; Pompeii, Lisa; Schoenfisch, Ashley

    2015-03-01

    Use of a pneumatic nail gun with a sequential actuation trigger (SAT) significantly diminishes the risk for acute traumatic injury compared to use of a contact actuation trigger (CAT) nail gun. A theoretically-based increased risk of work-related musculoskeletal disorders from use of a SAT nail gun, relative to CAT, appears unlikely and remains unproven. Based on current knowledge, the use of CAT nail guns cannot be justified as a safe alternative to SAT nail guns. This letter provides a perspective of ergonomists and occupational safety researchers recommending the use of the sequential actuation trigger for all nail gun tasks in the construction industry.

  9. The LHCb trigger in Run II

    CERN Document Server

    Michielin, Emanuele

    2016-01-01

    The LHCb trigger system has been upgraded to allow alignment, calibration and physics analysis to be performed in real time. An increased CPU capacity and improvements in the software have allowed lifetime unbiased selections of beauty and charm decays in the high level trigger. Thanks to offline quality event reconstruction already available online, physics analyses can be performed directly on this information and for the majority of charm physics selections a reduced event format can be written out. Beauty hadron decays are more efficiently triggered by re-optimised inclusive selections, and the HLT2 output event rate is increased by a factor of three.

  10. Introduction to myofascial trigger points in dogs.

    Science.gov (United States)

    Wall, Rick

    2014-06-01

    In dogs, muscles make up 44%-57% of total body weight and can serve as source of both pain and dysfunction when myofascial trigger points are present. However, rarely is muscle mentioned as a generator of pain in dogs, and even less mentioned is muscle dysfunction. The veterinary practitioner with interest in pain management, rehabilitation, orthopedics, and sports medicine must be familiar with the characteristics, etiology, and precipitating factors of myofascial trigger points. Additionally, the development of examination and treatment skill is needed to effectively manage myofascial trigger points in dogs.

  11. On the fragmentation of biomolecules: fragmentation of alanine dipeptide along the polypeptide chain

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander; Solov'yov, Andrey

    2006-01-01

    . The fragmentation of dipeptide along the polypeptide chain, as well as the interaction between alanines, has been considered. The energy of the system has been analyzed as a function of the distance between fragments for all possible dipeptide fragmentation channels. Analysis of the energy barriers makes...... it possible to estimate the characteristic fragmentation times and to determine the degree of applicability of classical electrodynamics for describing the system energy....

  12. Degradation of paternal mitochondria by fertilization-triggered autophagy in C. elegans embryos.

    Science.gov (United States)

    Sato, Miyuki; Sato, Ken

    2011-11-25

    The mitochondrial genome is believed to be maternally inherited in many eukaryotes. Sperm-derived paternal mitochondria enter the oocyte cytoplasm upon fertilization and then normally disappear during early embryogenesis. However, the mechanism responsible for this clearance has been unknown. Here, we show that autophagy, which delivers cytosolic components to lysosomes for degradation, is required for the elimination of paternal mitochondria in Caenorhabditis elegans. Immediately after fertilization, sperm-derived components trigger the localized induction of autophagy around sperm mitochondria. Autophagosomes engulf paternal mitochondria, resulting in their lysosomal degradation during early embryogenesis. In autophagy-defective zygotes, paternal mitochondria and their genome remain even in the first larval stage. Thus, fertilization-triggered autophagy is required for selective degradation of paternal mitochondria and thereby maternal inheritance of mitochondrial DNA.

  13. Modelling distribution functions and fragmentation functions

    CERN Document Server

    Rodrigues, J; Mulders, P J

    1995-01-01

    We present examples for the calculation of the distribution and fragmentation functions using the representation in terms of non-local matrix elements of quark field operators. As specific examples, we use a simple spectator model to estimate the leading twist quark distribution functions and the fragmentation functions for a quark into a nucleon or a pion.

  14. The Family Circle: A Study in Fragmentation

    Science.gov (United States)

    Bronfenbrenner, Urie

    1976-01-01

    Presents data describing the fragmentation of the family, suggests causes for the fragmentation, and offers suggestions for reversing the trend. The suggestions focus on day care, part-time employment practices, enhancing the position of women, and work and responsibility. (IRT)

  15. The Stellar IMF from turbulent fragmentation

    Science.gov (United States)

    Padoan, P.; Nordlund, A.

    2001-01-01

    In this paper they conclude that turbulent fragmentation is unavoidable in super-sonically turbulent molecular clouds, and given the success of the present model to predict the observed shape of the Stellar IMF, they conclude that turbulent fragmentation is essential to the origin of the stellar IMF.

  16. Baculovirus display of functional antibody Fab fragments.

    Science.gov (United States)

    Takada, Shinya; Ogawa, Takafumi; Matsui, Kazusa; Suzuki, Tasuku; Katsuda, Tomohisa; Yamaji, Hideki

    2015-08-01

    The generation of a recombinant baculovirus that displays antibody Fab fragments on the surface was investigated. A recombinant baculovirus was engineered so that the heavy chain (Hc; Fd fragment) of a mouse Fab fragment was expressed as a fusion to the N-terminus of baculovirus gp64, while the light chain of the Fab fragment was simultaneously expressed as a secretory protein. Following infection of Sf9 insect cells with the recombinant baculovirus, the culture supernatant was analyzed by enzyme-linked immunosorbent assay using antigen-coated microplates and either an anti-mouse IgG or an anti-gp64 antibody. A relatively strong signal was obtained in each case, showing antigen-binding activity in the culture supernatant. In western blot analysis of the culture supernatant using the anti-gp64 antibody, specific protein bands were detected at an electrophoretic mobility that coincided with the molecular weight of the Hc-gp64 fusion protein as well as that of gp64. Flow cytometry using a fluorescein isothiocyanate-conjugated antibody specific to mouse IgG successfully detected the Fab fragments on the surface of the Sf9 cells. These results suggest that immunologically functional antibody Fab fragments can be displayed on the surface of baculovirus particles, and that a fluorescence-activated cell sorter with a fluorescence-labeled antigen can isolate baculoviruses displaying specific Fab fragments. This successful baculovirus display of antibody Fab fragments may offer a novel approach for the efficient selection of specific antibodies.

  17. Pollen and gene flow in fragmented habitats

    NARCIS (Netherlands)

    Kwak, Manja M.; Velterop, Odilia; van Andel, Jelte

    1998-01-01

    . Habitat fragmentation affects both plants and pollinators. Habitat fragmentation leads to changes in species richness, population number and size, density, and shape, thus to changes in the spatial arrangement of flowers. These changes influence the amount of food for flower-visiting insects and t

  18. Pollen and gene flow in fragmented habitats

    NARCIS (Netherlands)

    Kwak, Manja M.; Velterop, Odilia; van Andel, Jelte

    1998-01-01

    . Habitat fragmentation affects both plants and pollinators. Habitat fragmentation leads to changes in species richness, population number and size, density, and shape, thus to changes in the spatial arrangement of flowers. These changes influence the amount of food for flower-visiting insects and t

  19. INTERMITTENCY, A TEST FOR STRING FRAGMENTATION PROCESSES

    NARCIS (Netherlands)

    SCHOLTEN, O

    The Artru-Mennessier and the string fragmentation procedure as implemented in the code VENUS have been compared. The two fragmentation prescriptions predict a similar rapidity spectrum including its energy dependence and event multiplicities, but give rise to very different intermittency results.

  20. Fragmentation of eastern United States forest types

    Science.gov (United States)

    Kurt H. Riitters; John W. Coulston

    2013-01-01

    Fragmentation is a continuing threat to the sustainability of forests in the Eastern United States, where land use changes supporting a growing human population are the primary driver of forest fragmentation (Stein and others 2009). While once mostly forested, approximately 40 percent of the original forest area has been converted to other land uses, and most of the...

  1. The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

    Science.gov (United States)

    Su, Aiguo; Geng, Jianing; Grover, Corrinne E.; Hu, Songnian; Hua, Jinping

    2013-01-01

    Background Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. Methodology/Principal Findings We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. Conclusion The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species. PMID:23940520

  2. The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.

    Directory of Open Access Journals (Sweden)

    Guozheng Liu

    Full Text Available BACKGROUND: Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L. is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt genome could be helpful for the evolution research of plant mt genomes. METHODOLOGY/PRINCIPAL FINDINGS: We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. CONCLUSION: The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.

  3. Long-term effects of fragmentation and fragment properties on bird species richness in Hawaiian forests

    Science.gov (United States)

    David J. Flaspohler; Christian P. Giardina; Gregory P. Asner; Patrick Hart; Jonathan Price; Cassie Ka’apu Lyons; Xeronimo. Castaneda

    2010-01-01

    Forest fragmentation is a common disturbance affecting biological diversity, yet the impacts of fragmentation on many forest processes remain poorly understood. Forest restoration is likely to be more successful when it proceeds with an understanding of how native and exotic vertebrates utilize forest patches of different size. We used a system of forest fragments...

  4. Etude de la production de fragments dans la fission induite par neutrons sur l'uranium 238.

    CERN Document Server

    Casoli, P

    2003-01-01

    Mass and charge distributions of fission fragments from the fission induced on uranium 238 by neutrons from 1 to 150 MeV were studied by experimental data and theoretical calculations. Measurements in prompt gamma and x-ray spectroscopy, completed at the LANSCE laboratory of Los Alamos allowed us to determine the secondary fission fragment production yields. Photovoltaic cells were used as a fission trigger. About one hundred fragments were identified and about thirty excitation functions were extracted. Mass and charge distributions at different incident energies were obtained. The comparison with evaluated data (Wahl systematics) shows that the calculations are consistent with the measurements below 20 MeV but not predictive enough above. A potential energy surface was drawn from microscopic constrained self-consistent HFB calculations. We obtained a fragment mass distribution by solving the dynamic Schrodinger equation on this surface.

  5. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  6. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  7. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  8. CLP-based protein fragment assembly

    CERN Document Server

    Palu', Alessandro Dal; Fogolari, Federico; Pontelli, Enrico; 10.1017/S1471068410000372

    2010-01-01

    The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.

  9. The politics of municipal fragmentation in Ghana

    Directory of Open Access Journals (Sweden)

    Abdulai Kuyini Mohammed

    2015-06-01

    Full Text Available The scholarly debate over the rival merits of local government consolidation and fragmentation is an old but enduring one. However, in this debate very little attention has been focused on the political dimension of council amalgamation and fragmentation – yet political considerations play a central role in both the formulation and outcomes of de-concentration policy. The purpose of this article is to fill a gap in the literature by examining local government fragmentation in Ghana from 1988 to 2014. The article does this by identifying the key players and analysing their interests and gains, as well as the tensions arising from the fragmentation exercise. The implications from the Ghanaian case for more general theories of fragmentation are drawn out.

  10. First principles approach to ionicity of fragments

    Science.gov (United States)

    Pilania, Ghanshyam; Liu, Xiang-Yang; Valone, Steven M.

    2015-02-01

    We develop a first principles approach towards the ionicity of fragments. In contrast to the bond ionicity, the fragment ionicity refers to an electronic property of the constituents of a larger system, which may vary from a single atom to a functional group or a unit cell to a crystal. The fragment ionicity is quantitatively defined in terms of the coefficients of contributing charge states in a superposition of valence configurations of the system. Utilizing the constrained density functional theory-based computations, a practical method to compute the fragment ionicity from valence electron charge densities, suitably decomposed according to the Fragment Hamiltonian (FH) model prescription for those electron densities, is presented for the first time. The adopted approach is illustrated using BeO, MgO and CaO diatomic molecules as simple examples. The results are compared and discussed with respect to the bond ionicity scales of Phillips and Pauling.

  11. The Trigger Processor and Trigger Processor Algorithms for the ATLAS New Small Wheel Upgrade

    CERN Document Server

    Lazovich, Tomo; The ATLAS collaboration

    2015-01-01

    The ATLAS New Small Wheel (NSW) is an upgrade to the ATLAS muon endcap detectors that will be installed during the next long shutdown of the LHC. Comprising both MicroMegas (MMs) and small-strip Thin Gap Chambers (sTGCs), this system will drastically improve the performance of the muon system in a high cavern background environment. The NSW trigger, in particular, will significantly reduce the rate of fake triggers coming from track segments in the endcap not originating from the interaction point. We will present an overview of the trigger, the proposed sTGC and MM trigger algorithms, and the hardware implementation of the trigger. In particular, we will discuss both the heart of the trigger, an ATCA system with FPGA-based trigger processors (using the same hardware platform for both MM and sTGC triggers), as well as the full trigger electronics chain, including dedicated cards for transmission of data via GBT optical links. Finally, we will detail the challenges of ensuring that the trigger electronics can ...

  12. A hypothesis for delayed dynamic earthquake triggering

    Science.gov (United States)

    Parsons, T.

    2005-01-01

    It's uncertain whether more near-field earthquakes are triggered by static or dynamic stress changes. This ratio matters because static earthquake interactions are increasingly incorporated into probabilistic forecasts. Recent studies were unable to demonstrate all predictions from the static-stress-change hypothesis, particularly seismicity rate reductions. However, current dynamic stress change hypotheses do not explain delayed earthquake triggering and Omori's law. Here I show numerically that if seismic waves can alter some frictional contacts in neighboring fault zones, then dynamic triggering might cause delayed triggering and an Omori-law response. The hypothesis depends on faults following a rate/state friction law, and on seismic waves changing the mean critical slip distance (Dc) at nucleation zones.

  13. Timing in the ALICE trigger system

    CERN Document Server

    Lietava, Roman; Evans, D; Jones, G T; Jovanovic, P; Jusko, A; Králik, I; Krivda, M; Pastircák, B; Sándor, L; Urbán, J; Villalobos Baillie, O

    2007-01-01

    In this paper we discuss trigger signals synchronisation and trigger input alignment in the ALICE trigger system. The synchronisation procedure adjusts the phase of the input signals with respect to the local Bunch Crossing (BC) clock and, indirectly, with respect to the LHC bunch crossing instant. The synchronisation delays are within one clock period: 0-25 ns. The alignment assures that the trigger signals originating from the same bunch crossing reach the processor logic in the same clock cycle. It is achieved by delaying signals by an appropriate number of full clock periods. We propose a procedure which will allow us to nd alignment delays during the system con guration, and to monitor them during the data taking.

  14. Developments of the ATLAS Jet Trigger

    CERN Document Server

    Lopes, L; The ATLAS collaboration

    2012-01-01

    There have been a lot of recent changes in the ATLAS jet trigger. The standard strategy, based on Regions Of Interest, is not well-suited for multi-jet events since it leads to pathologies and efficiency losses. This philosophy has been changed for the jet trigger, and we now have the possibility of unpacking the full calorimeter at Event Filter and (even for a small subset of the events) at an intermediate level between Level-1 and Level-2. We also moved to the use of calibrated scale at trigger level, and to the application of noise cuts to reduce rate spikes. We will present the performance of the jet trigger in 2011, when most of these changes were operational

  15. New Fast Interaction Trigger for ALICE

    Science.gov (United States)

    Trzaska, Wladyslaw Henryk

    2017-02-01

    The LHC heavy-ion luminosity and collision rate from 2021 onwards will considerably exceed the design parameters of the present ALICE forward trigger detectors and the introduction of the Muon Forward Tracker (MFT) will significantly reduce the space available for the new trigger detectors. To comply with these conditions a new Fast Interaction Trigger (FIT) will be built. FIT will be the main forward trigger, luminometer, and interaction-time detector. It will also determine multiplicity, centrality, and reaction plane of heavy-ion collisions. FIT will consist of two arrays of Cherenkov quartz radiators with MCP-PMT sensors and of a plastic scintillator ring. By increasing the overall acceptance of FIT, the scintillator will improve centrality and event plane resolution. It will also add sensitivity for the detection of beam-gas events and provide some degree of redundancy. FIT is currently undergoing an intense R&D and prototyping period. It is scheduled for installation in ALICE during 2020.

  16. Application of Vector Triggering Random Decrement

    DEFF Research Database (Denmark)

    Asmussen, J. C.; Ibrahim, S. R.; Brincker, Rune

    This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented in this pa......This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented...... in this paper should be regarded as a further documentation of the technique. The key point in Random Decrement estimation is the formulation of a triggering condition. If the triggering condition is fulfilled a time segment from each measurement is picked out and averaged with previous time segments. The final...

  17. Application of Vector Triggering Random Decrement

    DEFF Research Database (Denmark)

    Asmussen, J. C.; Ibrahim, S. R.; Brincker, Rune

    1997-01-01

    This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented in this pa......This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented...... in this paper should be regarded as a further documentation of the technique. The key point in Random Decrement estimation is the formulation of a triggering condition. If the triggering condition is fulfilled a time segment from each measurement is picked out and averaged with previous time segments. The final...

  18. Graphics Processing Units for HEP trigger systems

    Science.gov (United States)

    Ammendola, R.; Bauce, M.; Biagioni, A.; Chiozzi, S.; Cotta Ramusino, A.; Fantechi, R.; Fiorini, M.; Giagu, S.; Gianoli, A.; Lamanna, G.; Lonardo, A.; Messina, A.; Neri, I.; Paolucci, P. S.; Piandani, R.; Pontisso, L.; Rescigno, M.; Simula, F.; Sozzi, M.; Vicini, P.

    2016-07-01

    General-purpose computing on GPUs (Graphics Processing Units) is emerging as a new paradigm in several fields of science, although so far applications have been tailored to the specific strengths of such devices as accelerator in offline computation. With the steady reduction of GPU latencies, and the increase in link and memory throughput, the use of such devices for real-time applications in high-energy physics data acquisition and trigger systems is becoming ripe. We will discuss the use of online parallel computing on GPU for synchronous low level trigger, focusing on CERN NA62 experiment trigger system. The use of GPU in higher level trigger system is also briefly considered.

  19. The dangers of being trigger--happy

    CERN Document Server

    Dale, J E; Bressert, E

    2015-01-01

    We examine the evidence offered for triggered star formation against the backdrop provided by recent numerical simulations of feedback from massive stars at or below giant molecular cloud sizescales. We compile a catalogue of sixty--seven observational papers, mostly published over the last decade, and examine the signposts most commonly used to infer the presence of triggered star formation. We then determine how well these signposts perform in a recent suite of hydrodynamic simulations of star formation including feedback from O--type stars performed by Dale et al (2012a, b, 2013a, b, 2014). We find that none of the observational markers improve the chances of correctly identifying a given star as triggered by more than factors of two at most. This limits the fidelity of these techniques in interpreting star formation histories. We therefore urge caution in interpreting observations of star formation near feedback--driven structures in terms of triggering.

  20. The second level trigger system of FAST

    CERN Document Server

    Martínez,G; Berdugo, J; Casaus, J; Casella, V; De Laere, D; Deiters, K; Dick, P; Kirkby, J; Malgeri, L; Mañá, C; Marín, J; Pohl, M; Petitjean, C; Sánchez, E; Willmott, C

    2009-01-01

    The Fibre Active Scintillator Target (FAST) experiment is a novel imaging particle detector currently operating in a high-intensity π+ beam at the Paul Scherrer Institute (PSI), Villigen, Switzerland. The detector is designed to perform a high precision measurement of the μ+ lifetime, in order to determine the Fermi constant, Gf, to 1 ppm precision. A dedicated second level (LV2) hardware trigger system has been developed for the experiment. It performs an online analysis of the π/μ decay chain by identifying the stopping position of each beam particle and detecting the subsequent appearance of the muon. The LV2 trigger then records the muon stop pixel and selectively triggers the Time-to-Digital Converters (TDCs) in the vicinity. A detailed description of the trigger system is presented in this paper.

  1. Triggering on W, Z Boson Jets

    CERN Document Server

    Fehr, Armin

    2016-01-01

    The ATLAS trigger performs well for the hadronisation of isolated quarks or gluons, but is not optimised for $\\text{W}^\\pm$ and $\\text{Z}^0$ jets. This can be done with substructure techniques. As the W and Z bosons are highly boosted, the pair of quarks from their decay is heavily collimated and cannot be separated. The result is one single large jet with substructure. As it has two regions in the jet with high energy density (cores), while quarks have only one and gluons have two but a low mass, the existence of two cores plus a mass cut can be used to trigger on the hadronic decay of W and Z. In this project, it was investigated whether an offline tagger for W and Z bosons can be used as a trigger. Trimming, calibration and a tighter mass cut were applied to the jets and the trigger and offline reconstruction performance were compared.

  2. Trigger factors in migraine with aura

    DEFF Research Database (Denmark)

    Hauge, A W; Hauge, Anne Werner; Kirchmann, M

    2010-01-01

    The aim of the present study was to identify trigger factors in migraine with aura (MA). A total of 629 MA patients representative of the Danish population were sent a questionnaire listing 16 trigger factors thought to be relevant as well as space for free text. Distinction was made between...... attacks with or without aura within each patient. The questionnaire was returned by 522 patients of whom 347 had current MA attacks. In total 80% with current attacks (278/347) indicated that at least one factor triggered their migraine, and 67% (187/278) in this group indicated that they were aware...... of at least one factor often or always giving rise to an attack of MA. Forty-one per cent (113/278) had co-occurring attacks of migraine without aura (MO). Stress (following stress), bright light, intense emotional influences, stress (during stress) and sleeping too much or too little were the trigger factors...

  3. Pulling the trigger on LHC electronics

    CERN Document Server

    CERN. Geneva

    2001-01-01

    The conditions at CERN's Large Hadron Collider pose severe challenges for the designers and builders of front-end, trigger and data acquisition electronics. A recent workshop reviewed the encouraging progress so far and discussed what remains to be done. The LHC experiments have addressed level one trigger systems with a variety of high-speed hardware. The CMS Calorimeter Level One Regional Trigger uses 160 MHz logic boards plugged into the front and back of a custom backplane, which provides point-to-point links between the cards. Much of the processing in this system is performed by five types of 160 MHz digital applications-specific integrated circuits designed using Vitesse submicron high-integration gallium arsenide gate array technology. The LHC experiments make extensive use of field programmable gate arrays (FPGAs). These offer programmable reconfigurable logic, which has the flexibility that trigger designers need to be able to alter algorithms so that they can follow the physics and detector perform...

  4. Graphics Processing Units for HEP trigger systems

    Energy Technology Data Exchange (ETDEWEB)

    Ammendola, R. [INFN Sezione di Roma “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Roma (Italy); Bauce, M. [INFN Sezione di Roma “La Sapienza”, P.le A. Moro 2, 00185 Roma (Italy); University of Rome “La Sapienza”, P.lee A.Moro 2, 00185 Roma (Italy); Biagioni, A. [INFN Sezione di Roma “La Sapienza”, P.le A. Moro 2, 00185 Roma (Italy); Chiozzi, S.; Cotta Ramusino, A. [INFN Sezione di Ferrara, Via Saragat 1, 44122 Ferrara (Italy); University of Ferrara, Via Saragat 1, 44122 Ferrara (Italy); Fantechi, R. [INFN Sezione di Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); CERN, Geneve (Switzerland); Fiorini, M. [INFN Sezione di Ferrara, Via Saragat 1, 44122 Ferrara (Italy); University of Ferrara, Via Saragat 1, 44122 Ferrara (Italy); Giagu, S. [INFN Sezione di Roma “La Sapienza”, P.le A. Moro 2, 00185 Roma (Italy); University of Rome “La Sapienza”, P.lee A.Moro 2, 00185 Roma (Italy); Gianoli, A. [INFN Sezione di Ferrara, Via Saragat 1, 44122 Ferrara (Italy); University of Ferrara, Via Saragat 1, 44122 Ferrara (Italy); Lamanna, G., E-mail: gianluca.lamanna@cern.ch [INFN Sezione di Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); INFN Laboratori Nazionali di Frascati, Via Enrico Fermi 40, 00044 Frascati (Roma) (Italy); Lonardo, A. [INFN Sezione di Roma “La Sapienza”, P.le A. Moro 2, 00185 Roma (Italy); Messina, A. [INFN Sezione di Roma “La Sapienza”, P.le A. Moro 2, 00185 Roma (Italy); University of Rome “La Sapienza”, P.lee A.Moro 2, 00185 Roma (Italy); and others

    2016-07-11

    General-purpose computing on GPUs (Graphics Processing Units) is emerging as a new paradigm in several fields of science, although so far applications have been tailored to the specific strengths of such devices as accelerator in offline computation. With the steady reduction of GPU latencies, and the increase in link and memory throughput, the use of such devices for real-time applications in high-energy physics data acquisition and trigger systems is becoming ripe. We will discuss the use of online parallel computing on GPU for synchronous low level trigger, focusing on CERN NA62 experiment trigger system. The use of GPU in higher level trigger system is also briefly considered.

  5. Tracking at High Level Trigger in CMS

    CERN Document Server

    Tosi, Mia

    2014-01-01

    A reduction of several orders of magnitude of the event rate is needed to reach values compatible with detector readout, offline storage and analysis capability. The CMS experiment has been designed with a two-level trigger system: the Level-1 Trigger (L1T), implemented on custom-designed electronics, and the High Level Trigger (HLT), a streamlined version of the CMS offline reconstruction software running on a computer farm. A software trigger system requires a trade-off between the complexity of the algorithms, the sustainable output rate, and the selection efficiency. With the computing power available during the 2012 data taking the maximum reconstruction time at HLT was about 200 ms per event, at the nominal L1T rate of 100 kHz. Track reconstruction algorithms are widely used in the HLT, for the reconstruction of the physics objects as well as in the identification of b-jets and lepton iso...

  6. The trigger system of the CHORUS experiment

    Energy Technology Data Exchange (ETDEWEB)

    Beuzekom, M.G. van [NIKHEF, Amsterdam (Netherlands); Boes, J.C. [NIKHEF, Amsterdam (Netherlands); Born, E.A. van den [NIKHEF, Amsterdam (Netherlands); Jaspers, M.J.F. [NIKHEF, Amsterdam (Netherlands); Konijn, J. [NIKHEF, Amsterdam (Netherlands); Oldeman, R.G.C. [NIKHEF, Amsterdam (Netherlands); Poel, C.A.F.J. van der [NIKHEF, Amsterdam (Netherlands); Reen, T. van [NIKHEF, Amsterdam (Netherlands); Stolte, J. [NIKHEF, Amsterdam (Netherlands); Uiterwijk, J.W.E. [NIKHEF, Amsterdam (Netherlands); Visschers, J.L. [NIKHEF, Amsterdam (Netherlands); Pesen, E. [Middle East Technical University, Ankara (Turkey); Zeyrek, M.T. [Middle East Technical University, Ankara (Turkey); Dewulf, J.P. [Inter-University Institute for High Energies (ULB-VUB), Brussels (Belgium); Bal, F. [CERN, EP Division, 1211 Geneva 23 (Switzerland); Beyer, R. [CERN, EP Division, 1211 Geneva 23 (Switzerland); Gorbunov, P. [CERN, EP Division, 1211 Geneva 23 (Switzerland); Ferreira, R. [CERN, EP Division, 1211 Geneva 23 (Switzerland); Friend, B. [CERN, EP Division, 1211 Geneva 23 (Switzerland); Jong, M. de [CERN, EP Division, 1211 Geneva 23 (Switzerland); Ludovici, L. [CERN, EP Division, 1211 Geneva 23 (Switzerland); Panman, J. [CERN, EP Division, 1211 Geneva 23 (Switzerland); Bonnet, L. [Universite Catholique de Louvain, Louvain-la-Neuve (Belgium); Gregoire, G. [Universite Catholique de Louvain, Louvain-la-Neuve (Belgium)

    1999-05-01

    A new apparatus for detection of {nu}{sub {mu}}{yields}{nu}{sub {tau}} oscillation has been successfully constructed and operated by the CHORUS Collaboration for the CERN-WA95 experiment. The design, implementation and performance of the electronic trigger system is described. A trigger efficiency of 99% was measured for {nu}{sub {mu}} charged-current events and 90% for neutral-current events.

  7. Commissioning of the CMS High Level Trigger

    CERN Document Server

    Agostino, Lorenzo; Beccati, Barbara; Behrens, Ulf; Berryhil, Jeffrey; Biery, Kurt; Bose, Tulika; Brett, Angela; Branson, James; Cano, Eric; Cheung, Harry; Ciganek, Marek; Cittolin, Sergio; Coarasa, Jose Antonio; Dahmes, Bryan; Deldicque, Christian; Dusinberre, Elizabeth; Erhan, Samim; Gigi, Dominique; Glege, Frank; Gomez-Reino, Robert; Gutleber, Johannes; Hatton, Derek; Laurens, Jean-Francois; Loizides, Constantin; Ma, Frank; Meijers, Frans; Meschi, Emilio; Meyer, Andreas; Mommsen, Remigius K; Moser, Roland; O'Dell, Vivian; Oh, Alexander; Orsini, Luciano; Patras, Vaios; Paus, Christoph; Petrucci, Andrea; Pieri, Marco; Racz, Attila; Sakulin, Hannes; Sani, Matteo; Schieferdeckerd, Philipp; Schwick, Christoph; Serrano Margaleff, Josep Francesc; Shpakov, Dennis; Simon, Sean; Sumorok, Konstanty; Sungho Yoon, Andre; Wittich, Peter; Zanetti, Marco

    2009-01-01

    The CMS experiment will collect data from the proton-proton collisions delivered by the Large Hadron Collider (LHC) at a centre-of-mass energy up to 14 TeV. The CMS trigger system is designed to cope with unprecedented luminosities and LHC bunch-crossing rates up to 40 MHz. The unique CMS trigger architecture only employs two trigger levels. The Level-1 trigger is implemented using custom electronics, while the High Level Trigger (HLT) is based on software algorithms running on a large cluster of commercial processors, the Event Filter Farm. We present the major functionalities of the CMS High Level Trigger system as of the starting of LHC beams operations in September 2008. The validation of the HLT system in the online environment with Monte Carlo simulated data and its commissioning during cosmic rays data taking campaigns are discussed in detail. We conclude with the description of the HLT operations with the first circulating LHC beams before the incident occurred the 19th September 2008.

  8. Progress on the Level-1 Calorimeter Trigger

    CERN Multimedia

    Eric Eisenhandler

    The Level-1 Calorimeter Trigger (L1Calo) has recently passed a number of major hurdles. The various electronic modules that make up the trigger are either in full production or are about to be, and preparations in the ATLAS pit are well advanced. L1Calo has three main subsystems. The PreProcessor converts analogue calorimeter signals to digital, associates the rather broad trigger pulses with the correct proton-proton bunch crossing, and does a final calibration in transverse energy before sending digital data streams to the two algorithmic trigger processors. The Cluster Processor identifies and counts electrons, photons and taus, and the Jet/Energy-sum Processor looks for jets and also sums missing and total transverse energy. Readout drivers allow the performance of the trigger to be monitored online and offline, and also send region-of-interest information to the Level-2 Trigger. The PreProcessor (Heidelberg) is the L1Calo subsystem with the largest number of electronic modules (124), and most of its fu...

  9. Level-1 Calorimeter Trigger starts firing

    CERN Multimedia

    Stephen Hillier

    2007-01-01

    L1Calo is one of the major components of ATLAS First Level trigger, along with the Muon Trigger and Central Trigger Processor. It forms all of the first-level calorimeter-based triggers, including electron, jet, tau and missing ET. The final system consists of over 250 custom designed 9U VME boards, most containing a dense array of FPGAs or ASICs. It is subdivided into a PreProcessor, which digitises the incoming trigger signals from the Liquid Argon and Tile calorimeters, and two separate processor systems, which perform the physics algorithms. All of these are highly flexible, allowing the possibility to adapt to beam conditions and luminosity. All parts of the system are read out through Read-Out Drivers, which provide monitoring data and Region of Interest (RoI) information for the Level-2 trigger. Production of the modules is now essentially complete, and enough modules exist to populate the full scale system in USA15. Installation is proceeding rapidly - approximately 90% of the final modules are insta...

  10. The LHCb trigger and data acquisition system

    CERN Document Server

    Dufey, J P; Harris, F; Harvey, J; Jost, B; Mato, P; Müller, E

    2000-01-01

    The LHCb experiment is the most recently approved of the 4 experiments under construction at CERNs LHC accelerator. It is a special purpose experiment designed to precisely measure the CP violation parameters in the B-B system. Triggering poses special problems since the interesting events containing B-mesons are immersed in a large background of inelastic p-p reactions. We therefore decided to implement a 4 level triggering scheme. The LHCb Data Acquisition (DAQ) system will have to cope with an average trigger rate of ~40 kHz, after two levels of hardware triggers, and an average event size of ~100 kB. Thus an event-building network which can sustain an average bandwidth of 4 GB/s is required. A powerful software trigger farm will have to be installed to reduce the rate from the 40 kHz to ~100 Hz of events written to permanent storage. In this paper we outline the general architecture of the Trigger and DAQ system and the readout protocols we plan to implement. First results of simulations of the behavior o...

  11. Level-1 Jets and Sums Trigger Performance

    CERN Document Server

    CMS Collaboration

    2016-01-01

    After the first long shutdown, the LHC has restarted at a centre-of-mass energy of 13 TeV. The LHC is expected to achieve an instantaneous luminosity larger than $10^{34} \\rm{cm}^{-2} \\rm{s}^{-1}$ and an average number of pile-up interactions of at least 40. The CMS Level-1 trigger architecture has undergone a full upgrade in order to maintain and improve the trigger performance under these new conditions. It will allow CMS to keep the trigger rate under control and to avoid a significant increase in trigger thresholds that would have a negative impact on the CMS physics programme. First studies of the performance of the calorimeter trigger upgrade for jets and energy sums are shown. Details of the algorithms and commissioning may be found in CMS-DP-2015-051 and the CMS Technical Design Report for the Level-1 Trigger upgrade: CERN-LHCC-2013-011, CMS-TDR-12 (2013)

  12. The ATLAS Trigger Commissioning with cosmic rays

    CERN Document Server

    Abolins, M; Adragna, P; Aielli, G; Aleksandrov, E; Aleksandrov, I; Aloisio, A; Alviggi, M G; Amorim, A; Anderson, K; Andrei, V; Anduaga, X; Antonelli, S; Aracena, I; Ask, S; Asquith, L; Avolio, G; Backlund, S; Badescu, E; Bahat Treidel, O; Baines, J; Barnett, B M; Barria, P; Bartoldus, R; Batreanu, S; Bauss, B; Beck, H P; Bee, C; Bell, P; Bell, W H; Bellagamba, L; Bellomo, M; Ben Ami, S; Bendel, M; Benhammou, Ya; Benslama, K; Berge, D; Berger, N; Berry, T; Bianco, M; Biglietti, M; Blair, R R; Bogaerts, A; Bohm, C; Bold, T; Booth, J R A; Boscherini, D; Bosman, M; Boyd, J; Brawn, I P; Brelier, B; Bressler, S; Bruni, A; Bruni, G; Buda, S; Burckhart-Chromek, D; Buttar, C; Camarri, P; Campanelli, M; Canale, V; Caprini, M; Caracinha, D; Cardarelli, R; Carlino, G; Casadei, D; Casado, M P; Cataldi, G; Cerri, A; Charlton, D G; Chiodini, G; Ciapetti, G; Cimino, D; Ciobotaru, M; Clements, D; Coccaro, A; Coluccia, M R; Conde-Muíño, P; Constantin, S; Conventi, F; Corso-Radu, A; Costa, M J; Coura Torres, R; Cranfield, R; Cranmer, K; Crone, G; Curtis, C J; Dam, M; Damazio, D; Davis, A O; Dawson, I; Dawson, J; De Almeida Simoes, J; De Cecco, S; De Pedis, D; De Santo, A; DeAsmundis, R; DellaPietra, M; DellaVolpe, D; Delsart, P A; Demers, S; Demirkoz, B; Di Mattia, A; Di Ciaccio, A; Di Girolamo, A; Dionisi, C; Djilkibaev, R; Dobinson, Robert W; Dobson, M; Dogaru, M; Dotti, A; Dova, M; Drake, G; Dufour, M -A; Eckweiler, S; Ehrenfeld, W; Eifert, T; Eisenhandler, E F; Ellis, Nick; Emeliyanov, D; Enoque Ferreira de Lima, D; Ermoline, Y; Eschrich, I; Etzion, E; Facius, K; Falciano, S; Farthouat, P; Faulkner, P J W F; Feng, E; Ferland, J; Ferrari, R; Ferrer, M L; Fischer, G; Fonseca-Martin, T; Francis, D; Fukunaga, C; Föhlisch, F; Gadomski, S; Garitaonandia Elejabarrieta, H; Gaudio, G; Gaumer, O; Gee, C N P; George, S; Geweniger, C; Giagu, S; Gillman, A R; Giusti, P; Goncalo, R; Gorini, B; Gorini, E; Gowdy, S; Grabowska-Bold, I; Grancagnolo, F; Grancagnolo, S; Green, B; Galllno, P; Haas, S; Haberichter, W; Hadavand, H; Haeberli, C; Haller, J; Hamilton, A; Hanke, P; Hansen, J R; Hasegawa, Y; Hauschild, M; Hauser, R; Head, S; Hellman, S; Hidvegi, A; Hillier, S J; Höcker, A; Hrynóva, T; Hughes-Jones, R; Huston, J; Iacobucci, G; Idarraga, J; Iengo, P; Igonkina, O; Ikeno, M; Inada, M; Ishino, M; Iwasaki, H; Izzo, V; Jain, V; Johansen, M; Johns, K; Joos, M; Kadosaka, T; Kajomovitz, E; Kama, S; Kanaya, N; Kawagoe, K; Kawamoto, T; Kazarov, A; Kehoe, R; Khoriauli, G; Kieft, G; Kilvington, G; Kirk, J; Kiyamura, H; Klofver, P; Klous, S; Kluge, E E; Kobayashi, T; Kolos, S; Kono, T; Konstantinidis, N; Korcyl, K; Kordas, K; Kotov, V; Krasznahorkay, A; Kubota, T; Kugel, A; Kuhn, D; Kurashige, H; Kurasige, H; Kuwabara, T; Kwee, R; Landon, M; Lankford, A; LeCompte, T; Leahu, L; Leahu, M; Ledroit, F; Lehmann-Miotto, G; Lei, X; Lellouch, D; Lendermann, V; Levinson, L; Leyton, M; Li, S; Liberti, B; Lifshitz, R; Lim, H; Lohse, T; Losada, M; Luci, C; Luminari, L; Lupu, N; Mahboubi, K; Mahout, G; Mapelli, L; Marchese, F; Martin, B; Martin, B T; Martínez, A; Marzano, F; Masik, J; McMahon, T; McPherson, R; Medinnis, M; Meessen, C; Meier, K; Meirosu, C; Messina, A; Migliaccio, A; Mikenberg, G; Mincer, A; Mineev, M; Misiejuk, A; Mönig, K; Monticelli, F; Moraes, A; Moreno, D; Morettini, P; Murillo Garcia, R; Nagano, K; Nagasaka, Y; Negri, A; Némethy, P; Neusiedl, A; Nisati, A; Niwa, T; Nomachi, M; Nomoto, H; Nozaki, M; Nozicka, M; Ochi, A; Ohm, C; Okumura, Y; Omachi, C; Osculati, B; Oshita, H; Osuna, C; Padilla, C; Panikashvili, N; Parodi, F; Pasqualucci, E; Pastore, F; Patricelli, S; Pauly, T; Pectu, M; Perantoni, M; Perera, V; Perera, V J O; Pérez, E; Pérez-Réale, V; Perrino, R; Pessoa Lima Junior, H; Petersen, J; Petrolo, E; Piegaia, R; Pilcher, J E; Pinto, F; Pinzon, G; Polini, A; Pope, B; Potter, C; Prieur, D P F; Primavera, M; Qian, W; Radescu, V; Rajagopalan, S; Renkel, P; Rescigno, M; Rieke, S; Risler, C; Riu, I; Robertson, S; Roda, C; Rodríguez, D; Rogriquez, Y; Roich, A; Romeo, G; Rosati, S; Ryabov, Yu; Ryan, P; Rühr, F; Sakamoto, H; Salamon, A; Salvatore, D; Sankey, D P C; Santamarina, C; Santamarina-Rios, C; Santonico, R; Sasaki, O; Scannicchio, D; Scannicchio, D A; Schiavi, C; Schlereth, J L; Schmitt, K; Scholtes, I; Schooltz, D; Schuler, G; Schultz-Coulon, H -C; Schäfer, U; Scott, W; Segura, E; Sekhniaidze, G; Shimbo, N; Sidoti, A; Silva, L; Silverstein, S; Siragusa, G; Sivoklokov, S; Sloper, J E; Smizanska, M; Solfaroli, E; Soloviev, I; Soluk, R; Spagnolo, S; Spila, F; Spiwoks, R; Staley, R J; Stamen, R; Stancu, S; Steinberg, P; Stelzer, J; Stradling, A; Strom, D; Strong, J; Su, D; Sugaya, Y; Sugimoto, T; Sushkov, S; Sutton, M; Szymocha, T; Takahashi, Y; Takeda, H; Takeshita, T; Tanaka, S; Tapprogge, S; Tarem, S; Tarem, Z; Teixeira-Dias, P; Thomas, J P; Tokoshuku, K; Tomoto, M; Torrence, E; Touchard, F

    2008-01-01

    The ATLAS detector at CERN's LHC will be exposed to proton-proton collisions from beams crossing at 40 MHz. At the design luminosity there are roughly 23 collisions per bunch crossing. ATLAS has designed a three-level trigger system to select potentially interesting events. The first-level trigger, implemented in custom-built electronics, reduces the incoming rate to less than 100 kHz with a total latency of less than 2.5$\\mu$s. The next two trigger levels run in software on commercial PC farms. They reduce the output rate to 100-200 Hz. In preparation for collision data-taking which is scheduled to commence in May 2008, several cosmic-ray commissioning runs have been performed. Among the first sub-detectors available for commissioning runs are parts of the barrel muon detector including the RPC detectors that are used in the first-level trigger. Data have been taken with a full slice of the muon trigger and readout chain, from the detectors in one sector of the RPC system, to the second-level trigger algorit...

  13. Commissioning of the CMS High Level Trigger

    Energy Technology Data Exchange (ETDEWEB)

    Agostino, Lorenzo; et al.

    2009-08-01

    The CMS experiment will collect data from the proton-proton collisions delivered by the Large Hadron Collider (LHC) at a centre-of-mass energy up to 14 TeV. The CMS trigger system is designed to cope with unprecedented luminosities and LHC bunch-crossing rates up to 40 MHz. The unique CMS trigger architecture only employs two trigger levels. The Level-1 trigger is implemented using custom electronics, while the High Level Trigger (HLT) is based on software algorithms running on a large cluster of commercial processors, the Event Filter Farm. We present the major functionalities of the CMS High Level Trigger system as of the starting of LHC beams operations in September 2008. The validation of the HLT system in the online environment with Monte Carlo simulated data and its commissioning during cosmic rays data taking campaigns are discussed in detail. We conclude with the description of the HLT operations with the first circulating LHC beams before the incident occurred the 19th September 2008.

  14. Upgrade of the trigger system of CMS

    CERN Document Server

    Jeitler, Manfred

    2012-01-01

    Various parts of the CMS trigger and in particular the Level-1 hardware trigger will be upgraded to cope with increasing luminosity, using more selective trigger conditions at Level-1 and improving the reliability of the system. Many trigger subsystems use FPGAs (Field Programmable Gate Arrays) in the electronics and will benefit from developments in this technology, allowing much more logic into a single FPGA chip, thus reducing the number of chips, electronic boards and interconnections and in this way improving reliability. A number of subsystems plan to switch from the old VME bus to the new microTCA crate standard. Using similar approaches, identical modules and common software whereever possible will reduce costs and manpower requirements and improve the serviceability of the whole trigger system. The computer-farm based High-Level Trigger will not only be extended by using increasing numbers of more powerful PCs but there are also concepts for making it more robust and the software easier to maintain, ...

  15. Trigger finger, tendinosis, and intratendinous gene expression.

    Science.gov (United States)

    Lundin, A-C; Aspenberg, P; Eliasson, P

    2014-04-01

    The pathogenesis of trigger finger has generally been ascribed to primary changes in the first annular ligament. In contrast, we recently found histological changes in the tendons, similar to the findings in Achilles tendinosis or tendinopathy. We therefore hypothesized that trigger finger tendons would show differences in gene expression in comparison to normal tendons in a pattern similar to what is published for Achilles tendinosis. We performed quantitative real-time polymerase chain reaction on biopsies from finger flexor tendons, 13 trigger fingers and 13 apparently healthy control tendons, to assess the expression of 10 genes which have been described to be differently expressed in tendinosis (collagen type 1a1, collagen 3a1, MMP-2, MMP-3, ADAMTS-5, TIMP-3, aggrecan, biglycan, decorin, and versican). In trigger finger tendons, collagen types 1a1 and 3a1, aggrecan and biglycan were all up-regulated, and MMP-3and TIMP-3 were down-regulated. These changes were statistically significant and have been previously described for Achilles tendinosis. The remaining four genes were not significantly altered. The changes in gene expression support the hypothesis that trigger finger is a form of tendinosis. Because trigger finger is a common condition, often treated surgically, it could provide opportunities for clinical research on tendinosis. © 2012 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. ATLAS triggers for B-physics

    CERN Document Server

    George, S

    2000-01-01

    The LHC will produce bb events at an unprecedented rate. The number of events recorded by ATLAS will be limited by the rate at which they can be stored offline and subsequently analysed. Despite the huge number of events, the small branching ratios mean that analysis of many of the most interesting channels for CP violation and other measurements will be limited by statistics. The challenge for the Trigger and Data Acquisition (DAQ) system is therefore to maximise the fraction of interesting B decays in the B-physics data stream. The ATLAS Trigger/DAQ system is split into three levels. The initial B-physics selection is made in the first-level trigger by an inclusive low-p/sub t/ muon trigger (~6 GeV). The second-level trigger strategy is based on identifying classes of final states by their partial reconstruction. The muon trigger is confirmed before proceeding to a track search. Electron/hadron separation is given by the transition radiation tracking detector and the electromagnetic calorimeter. Muon identi...

  17. Commissioning of the CMS High Level Trigger

    Energy Technology Data Exchange (ETDEWEB)

    Agostino, Lorenzo; et al.

    2009-08-01

    The CMS experiment will collect data from the proton-proton collisions delivered by the Large Hadron Collider (LHC) at a centre-of-mass energy up to 14 TeV. The CMS trigger system is designed to cope with unprecedented luminosities and LHC bunch-crossing rates up to 40 MHz. The unique CMS trigger architecture only employs two trigger levels. The Level-1 trigger is implemented using custom electronics, while the High Level Trigger (HLT) is based on software algorithms running on a large cluster of commercial processors, the Event Filter Farm. We present the major functionalities of the CMS High Level Trigger system as of the starting of LHC beams operations in September 2008. The validation of the HLT system in the online environment with Monte Carlo simulated data and its commissioning during cosmic rays data taking campaigns are discussed in detail. We conclude with the description of the HLT operations with the first circulating LHC beams before the incident occurred the 19th September 2008.

  18. The Zeus calorimeter first level trigger

    Energy Technology Data Exchange (ETDEWEB)

    Smith, W.J. [Univ. of Wisconsin, Madison, WI (United States)

    1989-04-01

    The design of the Zeus Detector Calorimeter Level Trigger is presented. The Zeus detector is being built for operation at HERA, a new storage ring that will provide collisions between 820 GeV protons and 30 GeV electrons in 1990. The calorimeter is made of depleted uranium plates and plastic scintillator read out by wavelength shifter bars into 12,864 photomultiplier tubes. These signals are combined into 974 trigger towers with separate electromagnetic and hadronic sums. The calorimeter first level trigger is pipelined with a decision provided 5 {mu}sec after each beam crossing, occurring every 96 nsec. The trigger determines the total energy, the total transverse energy, the missing energy, and the energy and number of isolated electrons and muons. It also provides information on the number and energy of clusters. The trigger rate needs to be held to 1 kHz against a rate of proton-beam gas interactions of approximately 500 kHz. The summed trigger tower pulseheights are digitized by flash ADC`s. The digital values are linearized, stored and used for sums and pattern tests.

  19. Enhanced trigger for the NIFFTE fissionTPC in presence of high-rate alpha backgrounds

    Science.gov (United States)

    Bundgaard, Jeremy; Niffte Collaboration

    2015-10-01

    Nuclear physics and nuclear energy communities call for new, high precision measurements to improve existing fission models and design next generation reactors. The Neutron Induced Fission Fragment Tracking experiment (NIFFTE) has developed the fission Time Projection Chamber (fissionTPC) to measure neutron induced fission with unrivaled precision. The fissionTPC is annually deployed to the Weapons Neutron Research facility at Los Alamos Neutron Science Center where it operates with a neutron beam passing axially through the drift volume, irradiating heavy actinide targets to induce fission. The fissionTPC was developed at the Lawrence Livermore National Laboratory's TPC lab, where it measures spontaneous fission from radioactive sources to characterize detector response, improve performance, and evolve the design. To measure 244Cm, we've developed a fission trigger to reduce the data rate from alpha tracks while maintaining a high fission detection efficiency. In beam, alphas from 239Pu are a large background when detecting fission fragments; implementing the fission trigger will greatly reduce this background. The implementation of the cathode fission trigger in the fissionTPC will be presented along with a detailed study of its efficiency.

  20. Predicting minimum-bias trigger-associated dijet correlations in p-p collisions

    CERN Document Server

    Trainor, Thomas A

    2014-01-01

    A method is derived to predict the structure of dijet-related hard components of trigger-associated (TA) hadron correlations from p-p collisions based on measured fragmentation functions (FFs) from e-e or p-pbar collisions and a minimum-bias (MB) jet or scattered-parton spectrum from p-pbar collisions. The method is based on the probability chain rule and Bayes' theorem and relates a trigger-parton--associated-fragment system from reconstructed dijets to a trigger-hadron--associated-hadron system from p-p data. The method is tested in this study by comparisons of FF TA structure with preliminary p-p TA data but can also be applied to p-A, d-A and A-A collisions over a range of energies. Quantitative comparisons of measured TA correlations with FF-derived predictions may confirm a QCD MB dijet mechanism for certain spectrum and correlation structures whose origins are currently questioned and have been attributed by some to collective expansion (flows).