DNA end resection by CtIP and exonuclease 1 prevents genomic instability

DEFF Research Database (Denmark)

Eid, Wassim; Steger, Martin; El-Shemerly, Mahmoud

2010-01-01

End resection of DNA-which is essential for the repair of DNA double-strand breaks (DSBs) by homologous recombination-relies first on the partnership between MRE11-RAD50-NBS1 (MRN) and CtIP, followed by a processive step involving helicases and exonucleases such as exonuclease 1 (EXO1). In this s......End resection of DNA-which is essential for the repair of DNA double-strand breaks (DSBs) by homologous recombination-relies first on the partnership between MRE11-RAD50-NBS1 (MRN) and CtIP, followed by a processive step involving helicases and exonucleases such as exonuclease 1 (EXO1...... of DNA-PK-dependent radial chromosome formation. Thus, our study identifies new functions of CtIP and EXO1 in DNA end resection and provides new information on the regulation of DSB repair pathways, which is a key factor in the maintenance of genome integrity....

Nature of the end groups of breaks induced by ionizing radiation in dna in vivo

Energy Technology Data Exchange (ETDEWEB)

Gaziev, A I [AN SSSR, Pushchino-na-Oke. Inst. Biologicheskoj Fiziki

1975-01-01

DNA of gamma-irradiated E.coli cells contains singlestranded breaks with 5'Oh, 5'PO/sub 4/ and 3'OH ends assayed by phosphatase, polynucleotide kinase and DNA-ligase reactions. The number of breaks with 5'OH ends corresponds to the breaks detected by DNA sedimentation in alkaline sucrose gradient. The relative amount of breaks with different ends varies with the dose of irradiation. The majority of single-stranded breaks with 5'PO/sub 4/ and 3'OH ends in sealed by ligase.

End-specific strategies of attachment of long double stranded DNA onto gold-coated nanofiber arrays

International Nuclear Information System (INIS)

Peckys, Diana B; De Jonge, Niels; Simpson, Michael L; McKnight, Timothy E

2008-01-01

We report the effective and site-specific binding of long double stranded (ds)DNA to high aspect ratio carbon nanofiber arrays. The carbon nanofibers were first coated with a thin gold layer to provide anchorage for two controllable binding methods. One method was based on the direct binding of thiol end-labeled dsDNA. The second and enhanced method used amine end-labeled dsDNA bound with crosslinkers to a carboxyl-terminated self-assembled monolayer. The bound dsDNA was first visualized with a fluorescent, dsDNA-intercalating dye. The specific binding onto the carbon nanofiber was verified by a high resolution detection method using scanning electron microscopy in combination with the binding of neutravidin-coated fluorescent microspheres to the immobilized and biotinylated dsDNA. Functional activity of thiol end-labeled dsDNA on gold-coated nanofiber arrays was verified with a transcriptional assay, whereby Chinese hamster lung cells (V79) were impaled upon the DNA-modified nanofibers and scored for transgene expression of the tethered template. Thiol end-labeled dsDNA demonstrated significantly higher expression levels than nanofibers prepared with control dsDNA that lacked a gold-binding end-label. Employing these site-specific and robust techniques of immobilization of dsDNA onto nanodevices can be of advantage for the study of DNA/protein interactions and for gene delivery applications.

Nonhomologous DNA End Joining in Cell-Free Extracts

Directory of Open Access Journals (Sweden)

Sheetal Sharma

2010-01-01

Full Text Available Among various DNA damages, double-strand breaks (DSBs are considered as most deleterious, as they may lead to chromosomal rearrangements and cancer when unrepaired. Nonhomologous DNA end joining (NHEJ is one of the major DSB repair pathways in higher organisms. A large number of studies on NHEJ are based on in vitro systems using cell-free extracts. In this paper, we summarize the studies on NHEJ performed by various groups in different cell-free repair systems.

The Ku Heterodimer and the Metabolism of Single-Ended DNA Double-Strand Breaks

NARCIS (Netherlands)

A. Balestrini (Alessia); D. Ristic (Dejan); I. Dionne (Isabelle); X.Z. Liu (Xiao); C. Wyman (Claire); R.J. Wellinger (Raymund); J.H.J. Petrini (John)

2013-01-01

textabstractSingle-ended double-strand breaks (DSBs) are a common form of spontaneous DNA break, generated when the replisome encounters a discontinuity in the DNA template. Given their prevalence, understanding the mechanisms governing the fate(s) of single-ended DSBs is important. We describe the

The Ku80 carboxy terminus stimulates joining and artemis-mediated processing of DNA ends.

Science.gov (United States)

Weterings, Eric; Verkaik, Nicole S; Keijzers, Guido; Florea, Bogdan I; Wang, Shih-Ya; Ortega, Laura G; Uematsu, Naoya; Chen, David J; van Gent, Dik C

2009-03-01

Repair of DNA double-strand breaks (DSBs) is predominantly mediated by nonhomologous end joining (NHEJ) in mammalian cells. NHEJ requires binding of the Ku70-Ku80 heterodimer (Ku70/80) to the DNA ends and subsequent recruitment of the DNA-dependent protein kinase catalytic subunit (DNA-PK(CS)) and the XRCC4/ligase IV complex. Activation of the DNA-PK(CS) serine/threonine kinase requires an interaction with Ku70/80 and is essential for NHEJ-mediated DSB repair. In contrast to previous models, we found that the carboxy terminus of Ku80 is not absolutely required for the recruitment and activation of DNA-PK(CS) at DSBs, although cells that harbored a carboxy-terminal deletion in the Ku80 gene were sensitive to ionizing radiation and showed reduced end-joining capacity. More detailed analysis of this repair defect showed that DNA-PK(CS) autophosphorylation at Thr2647 was diminished, while Ser2056 was phosphorylated to normal levels. This resulted in severely reduced levels of Artemis nuclease activity in vivo and in vitro. We therefore conclude that the Ku80 carboxy terminus is important to support DNA-PK(CS) autophosphorylation at specific sites, which facilitates DNA end processing by the Artemis endonuclease and the subsequent joining reaction.

Interplay between Ku and Replication Protein A in the Restriction of Exo1-mediated DNA Break End Resection*

Science.gov (United States)

Krasner, Danielle S.; Daley, James M.; Sung, Patrick; Niu, Hengyao

2015-01-01

DNA double-strand breaks can be eliminated via non-homologous end joining or homologous recombination. Non-homologous end joining is initiated by the association of Ku with DNA ends. In contrast, homologous recombination entails nucleolytic resection of the 5′-strands, forming 3′-ssDNA tails that become coated with replication protein A (RPA). Ku restricts end access by the resection nuclease Exo1. It is unclear how partial resection might affect Ku engagement and Exo1 restriction. Here, we addressed these questions in a reconstituted system with yeast proteins. With blunt-ended DNA, Ku protected against Exo1 in a manner that required its DNA end-binding activity. Despite binding poorly to ssDNA, Ku could nonetheless engage a 5′-recessed DNA end with a 40-nucleotide (nt) ssDNA overhang, where it localized to the ssDNA-dsDNA junction and efficiently blocked resection by Exo1. Interestingly, RPA could exclude Ku from a partially resected structure with a 22-nt ssDNA tail and thus restored processing by Exo1. However, at a 40-nt tail, Ku remained stably associated at the ssDNA-dsDNA junction, and RPA simultaneously engaged the ssDNA region. We discuss a model in which the dynamic equilibrium between Ku and RPA binding to a partially resected DNA end influences the timing and efficiency of the resection process. PMID:26067273

End to End Travel

Data.gov (United States)

US Agency for International Development — E2 Solutions is a web based end-to-end travel management tool that includes paperless travel authorization and voucher document submissions, document approval...

End-to-side and end-to-end anastomoses give similar results in cervical oesophagogastrostomy.

Science.gov (United States)

Pierie, J P; De Graaf, P W; Poen, H; Van Der Tweel, I; Obertop, H

1995-12-01

To find out if there were any differences in healing between end-to-end and end-to-side anastomoses for oesophagogastrostomy. Open study with historical controls. University hospital, The Netherlands. 28 patients with end-to-end and 90 patients with end-to-side anastomoses after transhiatal oesophagectomy and partial gastrectomy for cancer of the oesophagus or oesophagogastric junction, with gastric tube reconstruction and cervical anastomosis. Leak and stricture rates, and the number of dilatations needed to relieve dysphagia. There were no significant differences in leak rates (end-to-end 4/28, 14%, and end-to-side 13/90, 14%) or anastomotic strictures (end-to-end 9/28, 32%, and end-to-side 26/90, 29%). The median number of dilatations needed to relieve dysphagia was 7 (1-33) after end-to-end and 9 (1-113) after end-to-side oesophagogastrostomy. There were no differences between the two methods of suture of cervical oesophagogastrostomy when leakage, stricture, and number of dilatations were used as criteria of good healing.

A method for filling in the cohesive ends of double-stranded DNA using Pfu DNA polymerase.

Science.gov (United States)

Yang, Shaohui; Li, Xin; Ding, Dongfeng; Hou, Jianhua; Jin, Zhaoxia; Yu, Xinchun; Bo, Tao; Li, Weidong; Li, Minggang

2005-12-01

The present paper reports a highly efficient method of making blunt ends from cohesive ends of double-stranded DNA. Klenow fragment and Pfu DNA polymerases were used to fill in the cohesive ends. Since the transformation efficiency can directly reflect the filling-in efficiency, similar ligation and transformation conditions were used, and the filling-in efficiency was compared with the corresponding transformation efficiency. The results indicate that the filling-in efficiency of Pfu DNA polymerase was 1.96 times that of Klenow fragment and its efficiency was markedly higher than that of Klenow fragment (P<0.01). The optimization experiments on reaction conditions indicate, when the pH is 8.5 and the temperature is 74 degrees C, that the filling-in efficiency was highest upon using a buffer containing 3 mM MgSO4 and 300 microM dNTP.

Unsolved mystery: the role of BRCA1 in DNA end-joining

International Nuclear Information System (INIS)

Saha, Janapriya; Davis, Anthony J.

2016-01-01

Heritable mutations in the tumor suppressor gene BRCA1 increase a woman's lifetime risk of developing breast and ovarian cancer. BRCA1's tumor suppressor function is directly linked to its myriad of functions in the cellular response to DNA double-strand breaks (DSBs). BRCA1 interacts with an extensive array of DNA damage responsive proteins and plays important roles in DSB repair, mediated by the homologous recombination pathway, and in the activation of cell cycle checkpoints. However, the role of BRCA1 in the other two DSB repair pathways, classical non-homologous end-joining (C-NHEJ) and alternative NHEJ (A-NHEJ), remains unclear. In this review, we will discuss the current literature on BRCA1's potential role(s) in modulating both C-NHEJ and A-NHEJ. We also present a model showing that BRCA1 contributes to genomic maintenance by promoting precise DNA repair across all cell cycle phases via the direct modulation of DNA end-joining

Standardizing an End-to-end Accounting Service

Science.gov (United States)

Greenberg, Edward; Kazz, Greg

2006-01-01

Currently there are no space system standards available for space agencies to accomplish end-to-end accounting. Such a standard does not exist for spacecraft operations nor for tracing the relationship between the mission planning activities, the command sequences designed to perform those activities, the commands formulated to initiate those activities and the mission data and specifically the mission data products created by those activities. In order for space agencies to cross-support one another for data accountability/data tracing and for inter agency spacecraft to interoperate with each other, an international CCSDS standard for end-to-end data accountability/tracing needs to be developed. We will first describe the end-to-end accounting service model and functionality that supports the service. This model will describe how science plans that are ultimately transformed into commands can be associated with the telemetry products generated as a result of their execution. Moreover, the interaction between end-to-end accounting and service management will be explored. Finally, we will show how the standard end-to-end accounting service can be applied to a real life flight project i.e., the Mars Reconnaissance Orbiter project.

Human SIRT6 promotes DNA end resection through CtIP deacetylation

DEFF Research Database (Denmark)

Kaidi, Abderrahmane; Weinert, Brian T; Choudhary, Chunaram

2010-01-01

SIRT6 belongs to the sirtuin family of protein lysine deacetylases, which regulate aging and genome stability. We found that human SIRT6 has a role in promoting DNA end resection, a crucial step in DNA double-strand break (DSB) repair by homologous recombination. SIRT6 depletion impaired the accu...

Distinct DNA repair pathways involving RecA and nonhomologous end joining in Mycobacterium smegmatis.

OpenAIRE

Korycka-Machala, M; Brzostek, A; Rozalska, S; Rumijowska-Galewicz, A; Dziedzic, R; Bowater, R; Dziadek, J

2006-01-01

Mycobacterium smegmatis was used to study the relationship between DNA repair processes involving RecA and nonhomologous end joining (NHEJ). The effect of gene deletions in recA and/or in two genes involved in NHEJ (ku and ligD) was tested on the ability of bacteria to join breaks in plasmids transformed into them and in their response to chemicals that damage DNA. The results provide in vivo evidence that only NHEJ is required for the repair of noncompatible DNA ends. By contrast, the respon...

Influence of reduced glutathione on end-joining of DNA double-strand breaks: Cytogenetical and molecular approach

Energy Technology Data Exchange (ETDEWEB)

Ghoshal, Nitin [Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya-793022 (India); Sharma, Sheetal [Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012 (India); Banerjee, Atanu; Kurkalang, Sillarine [Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya-793022 (India); Raghavan, Sathees C. [Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012 (India); Chatterjee, Anupam, E-mail: chatterjeeanupam@hotmail.com [Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya-793022 (India)

2017-01-15

Highlights: • DNA lesions induced by Blem and radiation interact well and form higher frequency of exchange aberrations. • Cellular level of glutathione does influence such interaction of DNA lesions. • Oligomer-based cell-free assay system demonstrated better end-joining efficiency at higher level of endogenous GSH. - Abstract: Radiation induced DNA double-strand breaks (DSB) are the major initial lesions whose misrejoining may lead to exchange aberrations. However, the role of glutathione (GSH), a major cellular thiol, in regulating cell’s sensitivity to DNA damaging agents is not well understood. Influence of endogenous GSH on the efficiency of X-rays and bleomycin (Blem) induced DNA DSBs end-joining has been tested here cytogenetically, in human lymphocytes and Hct116 cells. In another approach, oligomeric DNA (75 bp) containing 5′-compatible and non-compatible overhangs mimicking the endogenous DSB were for rejoining in presence of cell-free extracts from cells having different endogenous GSH levels. Frequency of aberrations, particularly exchange aberrations, was significantly increased when Blem was combined with radiation. The exchange aberration frequency was further enhanced when combined treatment was given at 4 °C since DNA lesions are poorly repaired at 4 °C so that a higher number of DNA breaks persist and interact when shifted from 4 °C to 37 °C. The exchange aberrations increased further when the combined treatment was given to Glutathione-ester (GE) pre-treated cells, indicating more frequent rejoining of DNA lesions in presence of higher cellular GSH. This is further supported by the drastic reduction in frequency of exchange aberrations but significant increase in incidences of deletions when combined treatment was given to GSH-depleted cells. End-joining efficiency of DNA DSBs with compatible ends was better than for non-compatible ends. End-joining efficiency of testicular and MCF7 cell extracts was better than that of lungs and

Monophosphate end groups produced in radiation induced strand breakage in DNA

International Nuclear Information System (INIS)

Kay, E.; Ward, J.F.

1976-01-01

A solution of DNA was gamma-irradiated and treated with monophosphatase for studies on the amount of inorganic phosphate released as a function of time. Studies were also conducted on: effect of alkali on yield of monophosphate end groups; induction of DNA strand breaks by treatment with DNAase; initial G values for monophosphate termini; and effect of alkali on radioinduced DNA damage

OISI dynamic end-to-end modeling tool

Science.gov (United States)

Kersten, Michael; Weidler, Alexander; Wilhelm, Rainer; Johann, Ulrich A.; Szerdahelyi, Laszlo

2000-07-01

The OISI Dynamic end-to-end modeling tool is tailored to end-to-end modeling and dynamic simulation of Earth- and space-based actively controlled optical instruments such as e.g. optical stellar interferometers. `End-to-end modeling' is meant to denote the feature that the overall model comprises besides optical sub-models also structural, sensor, actuator, controller and disturbance sub-models influencing the optical transmission, so that the system- level instrument performance due to disturbances and active optics can be simulated. This tool has been developed to support performance analysis and prediction as well as control loop design and fine-tuning for OISI, Germany's preparatory program for optical/infrared spaceborne interferometry initiated in 1994 by Dornier Satellitensysteme GmbH in Friedrichshafen.

Determination and analysis of site-specific 125I decay-induced DNA double-strand break end-group structures.

Science.gov (United States)

Datta, Kamal; Weinfeld, Michael; Neumann, Ronald D; Winters, Thomas A

2007-02-01

End groups contribute to the structural complexity of radiation-induced DNA double-strand breaks (DSBs). As such, end-group structures may affect a cell's ability to repair DSBs. The 3'-end groups of strand breaks caused by gamma radiation, or oxidative processes, under oxygenated aqueous conditions have been shown to be distributed primarily between 3'-phosphoglycolate and 3'-phosphate, with 5'-phosphate ends in both cases. In this study, end groups of the high-LET-like DSBs caused by 125I decay were investigated. Site-specific DNA double-strand breaks were produced in plasmid pTC27 in the presence or absence of 2 M DMSO by 125I-labeled triplex-forming oligonucleotide targeting. End-group structure was assessed enzymatically as a function of the DSB end to serve as a substrate for ligation and various forms of end labeling. Using this approach, we have demonstrated 3'-hydroxyl (3'-OH) and 3'-phosphate (3'-P) end groups and 5'-ends (> or = 42%) terminated by phosphate. A 32P postlabeling assay failed to detect 3'-phosphoglycolate in a restriction fragment terminated by the 125I-induced DNA double-strand break, and this is likely due to restricted oxygen diffusion during irradiation as a frozen aqueous solution. Even so, end-group structure and relative distribution varied as a function of the free radical scavenging capacity of the irradiation buffer.

Functional intersection of ATM and DNA-dependent protein kinase catalytic subunit in coding end joining during V(D)J recombination

DEFF Research Database (Denmark)

Lee, Baeck-Seung; Gapud, Eric J; Zhang, Shichuan

2013-01-01

V(D)J recombination is initiated by the RAG endonuclease, which introduces DNA double-strand breaks (DSBs) at the border between two recombining gene segments, generating two hairpin-sealed coding ends and two blunt signal ends. ATM and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) ar......V(D)J recombination is initiated by the RAG endonuclease, which introduces DNA double-strand breaks (DSBs) at the border between two recombining gene segments, generating two hairpin-sealed coding ends and two blunt signal ends. ATM and DNA-dependent protein kinase catalytic subunit (DNA......-PKcs) are serine-threonine kinases that orchestrate the cellular responses to DNA DSBs. During V(D)J recombination, ATM and DNA-PKcs have unique functions in the repair of coding DNA ends. ATM deficiency leads to instability of postcleavage complexes and the loss of coding ends from these complexes. DNA...... when ATM is present and its kinase activity is intact. The ability of ATM to compensate for DNA-PKcs kinase activity depends on the integrity of three threonines in DNA-PKcs that are phosphorylation targets of ATM, suggesting that ATM can modulate DNA-PKcs activity through direct phosphorylation of DNA...

Distinct DNA repair pathways involving RecA and nonhomologous end joining in Mycobacterium smegmatis.

Science.gov (United States)

Korycka-Machala, Malgorzata; Brzostek, Anna; Rozalska, Sylwia; Rumijowska-Galewicz, Anna; Dziedzic, Renata; Bowater, Richard; Dziadek, Jaroslaw

2006-05-01

Mycobacterium smegmatis was used to study the relationship between DNA repair processes involving RecA and nonhomologous end joining (NHEJ). The effect of gene deletions in recA and/or in two genes involved in NHEJ (ku and ligD) was tested on the ability of bacteria to join breaks in plasmids transformed into them and in their response to chemicals that damage DNA. The results provide in vivo evidence that only NHEJ is required for the repair of noncompatible DNA ends. By contrast, the response of mycobacteria to mitomycin C preferentially involved a RecA-dependent pathway.

DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch.

Directory of Open Access Journals (Sweden)

Michael Feiss

Full Text Available During DNA replication by the λ-like bacteriophages, immature concatemeric DNA is produced by rolling circle replication. The concatemers are processed into mature chromosomes with cohesive ends, and packaged into prohead shells, during virion assembly. Cohesive ends are generated by the viral enzyme terminase, which introduces staggered nicks at cos, an approx. 200 bp-long sequence containing subsites cosQ, cosN and cosB. Interactions of cos subsites of immature concatemeric DNA with terminase orchestrate DNA processing and packaging. To initiate DNA packaging, terminase interacts with cosB and nicks cosN. The cohesive ends of N15 DNA differ from those of λ at 2/12 positions. Genetic experiments show that phages with chromosomes containing mismatched cohesive ends are functional. In at least some infections, the cohesive end mismatch persists through cyclization and replication, so that progeny phages of both allelic types are produced in the infected cell. N15 possesses an asymmetric packaging specificity: N15 DNA is not packaged by phages λ or 21, but surprisingly, N15-specific terminase packages λ DNA. Implications for genetic interactions among λ-like bacteriophages are discussed.

DNA-dependent protein kinase in nonhomologous end joining: a lock with multiple keys?

Science.gov (United States)

Weterings, Eric; Chen, David J

2007-10-22

The DNA-dependent protein kinase (DNA-PK) is one of the central enzymes involved in DNA double-strand break (DSB) repair. It facilitates proper alignment of the two ends of the broken DNA molecule and coordinates access of other factors to the repair complex. We discuss the latest findings on DNA-PK phosphorylation and offer a working model for the regulation of DNA-PK during DSB repair.

Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica.

Science.gov (United States)

Hickman, Alison B; Ewis, Hosam E; Li, Xianghong; Knapp, Joshua A; Laver, Thomas; Doss, Anna-Louise; Tolun, Gökhan; Steven, Alasdair C; Grishaev, Alexander; Bax, Ad; Atkinson, Peter W; Craig, Nancy L; Dyda, Fred

2014-07-17

Hermes is a member of the hAT transposon superfamily that has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species. The crystal structure of the Hermes transposase-DNA complex reveals that Hermes forms an octameric ring organized as a tetramer of dimers. Although isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple nonspecific DNA binding surfaces for target capture. The unusual assembly explains the basis of bipartite DNA recognition at hAT transposon ends, provides a rationale for transposon end asymmetry, and suggests how the avidity provided by multiple sites of interaction could allow a transposase to locate its transposon ends amidst a sea of chromosomal DNA. Copyright © 2014 Elsevier Inc. All rights reserved.

Sleep/wake scheduling scheme for minimizing end-to-end delay in multi-hop wireless sensor networks

Directory of Open Access Journals (Sweden)

Madani Sajjad

2011-01-01

Full Text Available Abstract We present a sleep/wake schedule protocol for minimizing end-to-end delay for event driven multi-hop wireless sensor networks. In contrast to generic sleep/wake scheduling schemes, our proposed algorithm performs scheduling that is dependent on traffic loads. Nodes adapt their sleep/wake schedule based on traffic loads in response to three important factors, (a the distance of the node from the sink node, (b the importance of the node's location from connectivity's perspective, and (c if the node is in the proximity where an event occurs. Using these heuristics, the proposed scheme reduces end-to-end delay and maximizes the throughput by minimizing the congestion at nodes having heavy traffic load. Simulations are carried out to evaluate the performance of the proposed protocol, by comparing its performance with S-MAC and Anycast protocols. Simulation results demonstrate that the proposed protocol has significantly reduced the end-to-end delay, as well as has improved the other QoS parameters, like average energy per packet, average delay, packet loss ratio, throughput, and coverage lifetime.

End-to-end self-assembly of gold nanorods in isopropanol solution: experimental and theoretical studies

Energy Technology Data Exchange (ETDEWEB)

Gordel, M., E-mail: marta.gordel@pwr.edu.pl [Wrocław University of Technology, Advanced Materials Engineering and Modelling Group, Faculty of Chemistry (Poland); Piela, K., E-mail: katarzyna.piela@pwr.edu.pl [Wrocław University of Technology, Department of Physical and Quantum Chemistry (Poland); Kołkowski, R. [Wrocław University of Technology, Advanced Materials Engineering and Modelling Group, Faculty of Chemistry (Poland); Koźlecki, T. [Wrocław University of Technology, Department of Chemical Engineering, Faculty of Chemistry (Poland); Buckle, M. [CNRS, École Normale Supérieure de Cachan, Laboratoire de Biologie et Pharmacologie Appliquée (France); Samoć, M. [Wrocław University of Technology, Advanced Materials Engineering and Modelling Group, Faculty of Chemistry (Poland)

2015-12-15

We describe here a modification of properties of colloidal gold nanorods (NRs) resulting from the chemical treatment used to carry out their transfer into isopropanol (IPA) solution. The NRs acquire a tendency to attach one to another by their ends (end-to-end assembly). We focus on the investigation of the change in position and shape of the longitudinal surface plasmon (l-SPR) band after self-assembly. The experimental results are supported by a theoretical calculation, which rationalizes the dramatic change in optical properties when the NRs are positioned end-to-end at short distances. The detailed spectroscopic characterization performed at the consecutive stages of transfer of the NRs from water into IPA solution revealed the features of the interaction between the polymers used as ligands and their contribution to the final stage, when the NRs were dispersed in IPA solution. The efficient method of aligning the NRs detailed here may facilitate applications of the self-assembled NRs as building blocks for optical materials and biological sensing.Graphical Abstract.

Sleep/wake scheduling scheme for minimizing end-to-end delay in multi-hop wireless sensor networks

OpenAIRE

Madani Sajjad; Nazir Babar; Hasbullah Halabi

2011-01-01

Abstract We present a sleep/wake schedule protocol for minimizing end-to-end delay for event driven multi-hop wireless sensor networks. In contrast to generic sleep/wake scheduling schemes, our proposed algorithm performs scheduling that is dependent on traffic loads. Nodes adapt their sleep/wake schedule based on traffic loads in response to three important factors, (a) the distance of the node from the sink node, (b) the importance of the node's location from connectivity's perspective, and...

FANCD2 Binds CtIP and Regulates DNA-End Resection during DNA Interstrand Crosslink Repair

Directory of Open Access Journals (Sweden)

Junya Unno

2014-05-01

Full Text Available The Fanconi anemia (FA pathway is critically involved in the maintenance of hematopoietic stem cells and the suppression of carcinogenesis. A key FA protein, FANCD2, is monoubiquitinated and accumulates in chromatin in response to DNA interstrand crosslinks (ICLs, where it coordinates DNA repair through mechanisms that are still poorly understood. Here, we report that CtIP protein directly interacts with FANCD2. A region spanning amino acids 166 to 273 of CtIP and monoubiquitination of FANCD2 are both essential for the FANCD2-CtIP interaction and mitomycin C (MMC-induced CtIP foci. Remarkably, both FANCD2 and CtIP are critical for MMC-induced RPA2 hyperphosphorylation, an event that accompanies end resection of double-strand breaks. Collectively, our results reveal a role of monoubiquitinated FANCD2 in end resection that depends on its binding to CtIP during ICL repair.

A Bayes Theory-Based Modeling Algorithm to End-to-end Network Traffic

OpenAIRE

Zhao Hong-hao; Meng Fan-bo; Zhao Si-wen; Zhao Si-hang; Lu Yi

2016-01-01

Recently, network traffic has exponentially increasing due to all kind of applications, such as mobile Internet, smart cities, smart transportations, Internet of things, and so on. the end-to-end network traffic becomes more important for traffic engineering. Usually end-to-end traffic estimation is highly difficult. This paper proposes a Bayes theory-based method to model the end-to-end network traffic. Firstly, the end-to-end network traffic is described as a independent identically distrib...

A Bayes Theory-Based Modeling Algorithm to End-to-end Network Traffic

Directory of Open Access Journals (Sweden)

Zhao Hong-hao

2016-01-01

Full Text Available Recently, network traffic has exponentially increasing due to all kind of applications, such as mobile Internet, smart cities, smart transportations, Internet of things, and so on. the end-to-end network traffic becomes more important for traffic engineering. Usually end-to-end traffic estimation is highly difficult. This paper proposes a Bayes theory-based method to model the end-to-end network traffic. Firstly, the end-to-end network traffic is described as a independent identically distributed normal process. Then the Bases theory is used to characterize the end-to-end network traffic. By calculating the parameters, the model is determined correctly. Simulation results show that our approach is feasible and effective.

Modeling Non-homologous End Joining

Science.gov (United States)

Li, Yongfeng

2013-01-01

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss

Directory of Open Access Journals (Sweden)

Adrian G. Glover

2015-12-01

Full Text Available Recent years have seen increased survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ, central Pacific Ocean abyss, driven by commercial interests from contractors in the potential extraction of polymetallic nodules in the region. Part of the International Seabed Authority (ISA regulatory requirements are that these contractors undertake environmental research expeditions to their CCZ exploration claims following guidelines approved by the ISA Legal and Technical Commission (ISA, 2010. Section 9 (e of these guidelines instructs contractors to “…collect data on the sea floor communities specifically relating to megafauna, macrofauna, meiofauna, microfauna, nodule fauna and demersal scavengers”. There are a number of methodological challenges to this, including the water depth (4000–5000 m, extremely warm surface waters (~28 °C compared to bottom water (~1.5 °C and great distances to ports requiring a large and long seagoing expedition with only a limited number of scientists. Both scientists and regulators have recently realized that a major gap in our knowledge of the region is the fundamental taxonomy of the animals that live there; this is essential to inform our knowledge of the biogeography, natural history and ultimately our stewardship of the region. Recognising this, the ISA is currently sponsoring a series of taxonomic workshops on the CCZ fauna and to assist in this process we present here a series of methodological pipelines for DNA taxonomy (incorporating both molecular and morphological data of the macrofauna and megafauna from the CCZ benthic habitat in the recent ABYSSLINE cruise program to the UK-1 exploration claim. A major problem on recent CCZ cruises has been the collection of high-quality samples suitable for both morphology and DNA taxonomy, coupled with a workflow that ensures these data are made available. The DNA sequencing techniques themselves are relatively standard, once good samples have been

Automatic detection of end-diastole and end-systole from echocardiography images using manifold learning

International Nuclear Information System (INIS)

Gifani, Parisa; Behnam, Hamid; Shalbaf, Ahmad; Sani, Zahra Alizadeh

2010-01-01

The automatic detection of end-diastole and end-systole frames of echocardiography images is the first step for calculation of the ejection fraction, stroke volume and some other features related to heart motion abnormalities. In this paper, the manifold learning algorithm is applied on 2D echocardiography images to find out the relationship between the frames of one cycle of heart motion. By this approach the nonlinear embedded information in sequential images is represented in a two-dimensional manifold by the LLE algorithm and each image is depicted by a point on reconstructed manifold. There are three dense regions on the manifold which correspond to the three phases of cardiac cycle ('isovolumetric contraction', 'isovolumetric relaxation', 'reduced filling'), wherein there is no prominent change in ventricular volume. By the fact that the end-systolic and end-diastolic frames are in isovolumic phases of the cardiac cycle, the dense regions can be used to find these frames. By calculating the distance between consecutive points in the manifold, the isovolumic frames are mapped on the three minimums of the distance diagrams which were used to select the corresponding images. The minimum correlation between these images leads to detection of end-systole and end-diastole frames. The results on six healthy volunteers have been validated by an experienced echo cardiologist and depict the usefulness of the presented method

FANCI-FANCD2 stabilizes the RAD51-DNA complex by binding RAD51 and protects the 5′-DNA end

Science.gov (United States)

Sato, Koichi; Shimomuki, Mayo; Katsuki, Yoko; Takahashi, Daisuke; Kobayashi, Wataru; Ishiai, Masamichi; Miyoshi, Hiroyuki; Takata, Minoru; Kurumizaka, Hitoshi

2016-01-01

The FANCI-FANCD2 (I-D) complex is considered to work with RAD51 to protect the damaged DNA in the stalled replication fork. However, the means by which this DNA protection is accomplished have remained elusive. In the present study, we found that the I-D complex directly binds to RAD51, and stabilizes the RAD51-DNA filament. Unexpectedly, the DNA binding activity of FANCI, but not FANCD2, is explicitly required for the I-D complex-mediated RAD51-DNA filament stabilization. The RAD51 filament stabilized by the I-D complex actually protects the DNA end from nucleolytic degradation by an FA-associated nuclease, FAN1. This DNA end protection is not observed with the RAD51 mutant from FANCR patient cells. These results clearly answer the currently enigmatic question of how RAD51 functions with the I-D complex to prevent genomic instability at the stalled replication fork. PMID:27694619

End-to-End Security for Personal Telehealth

NARCIS (Netherlands)

Koster, R.P.; Asim, M.; Petkovic, M.

2011-01-01

Personal telehealth is in rapid development with innovative emerging applications like disease management. With personal telehealth people participate in their own care supported by an open distributed system with health services. This poses new end-to-end security and privacy challenges. In this

Cyberinfrastructure for End-to-End Environmental Explorations

Science.gov (United States)

Merwade, V.; Kumar, S.; Song, C.; Zhao, L.; Govindaraju, R.; Niyogi, D.

2007-12-01

The design and implementation of a cyberinfrastructure for End-to-End Environmental Exploration (C4E4) is presented. The C4E4 framework addresses the need for an integrated data/computation platform for studying broad environmental impacts by combining heterogeneous data resources with state-of-the-art modeling and visualization tools. With Purdue being a TeraGrid Resource Provider, C4E4 builds on top of the Purdue TeraGrid data management system and Grid resources, and integrates them through a service-oriented workflow system. It allows researchers to construct environmental workflows for data discovery, access, transformation, modeling, and visualization. Using the C4E4 framework, we have implemented an end-to-end SWAT simulation and analysis workflow that connects our TeraGrid data and computation resources. It enables researchers to conduct comprehensive studies on the impact of land management practices in the St. Joseph watershed using data from various sources in hydrologic, atmospheric, agricultural, and other related disciplines.

Comparison of Direct Side-to-End and End-to-End Hypoglossal-Facial Anastomosis for Facial Nerve Repair.

Science.gov (United States)

Samii, Madjid; Alimohamadi, Maysam; Khouzani, Reza Karimi; Rashid, Masoud Rafizadeh; Gerganov, Venelin

2015-08-01

The hypoglossal facial anastomosis (HFA) is the gold standard for facial reanimation in patients with severe facial nerve palsy. The major drawbacks of the classic HFA technique are lingual morbidities due to hypoglossal nerve transection. The side-to-end HFA is a modification of the classic technique with fewer tongue-related morbidities. In this study we compared the outcome of the classic end-to-end and the direct side-to-end HFA surgeries performed at our center in regards to the facial reanimation success rate and tongue-related morbidities. Twenty-six successive cases of HFA were enrolled. In 9 of them end-to-end anastomoses were performed, and 17 had direct side-to-end anastomoses. The House-Brackmann (HB) and Pitty and Tator (PT) scales were used to document surgical outcome. The hemiglossal atrophy, swallowing, and hypoglossal nerve function were assessed at follow-up. The original pathology was vestibular schwannoma in 15, meningioma in 4, brain stem glioma in 4, and other pathologies in 3. The mean interval between facial palsy and HFA was 18 months (range: 0-60). The median follow-up period was 20 months. The PT grade at follow-up was worse in patients with a longer interval from facial palsy and HFA (P value: 0.041). The lesion type was the only other factor that affected PT grade (the best results in vestibular schwannoma and the worst in the other pathologies group, P value: 0.038). The recovery period for facial tonicity was longer in patients with radiation therapy before HFA (13.5 vs. 8.5 months) and those with a longer than 2-year interval from facial palsy to HFA (13.5 vs. 8.5 months). Although no significant difference between the side-to-end and the end-to-end groups was seen in terms of facial nerve functional recovery, patients from the side-to-end group had a significantly lower rate of lingual morbidities (tongue hemiatrophy: 100% vs. 5.8%, swallowing difficulty: 55% vs. 11.7%, speech disorder 33% vs. 0%). With the side-to-end HFA

Tandemly repeated sequence in 5'end of mtDNA control region of ...

African Journals Online (AJOL)

Extensive length variability was observed in 5' end sequence of the mitochondrial DNA control region of the Japanese Spanish mackerel (Scomberomorus niphonius). This length variability was due to the presence of varying numbers of a 56-bp tandemly repeated sequence and a 46-bp insertion/deletion (indel).

Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification

Directory of Open Access Journals (Sweden)

Gontran Sonet

2013-12-01

Full Text Available Identification by DNA barcoding is more likely to be erroneous when it is based on a large distance between the query (the barcode sequence of the specimen to identify and its best match in a reference barcode library. The number of such false positive identifications can be decreased by setting a distance threshold above which identification has to be rejected. To this end, we proposed recently to use an ad hoc distance threshold producing identifications with an estimated relative error probability that can be fixed by the user (e.g. 5%. Here we introduce two R functions that automate the calculation of ad hoc distance thresholds for reference libraries of DNA barcodes. The scripts of both functions, a user manual and an example file are available on the JEMU website (http://jemu.myspecies.info/computer-programs as well as on the comprehensive R archive network (CRAN, http://cran.r-project.org.

Measurements and analysis of end-to-end Internet dynamics

Energy Technology Data Exchange (ETDEWEB)

Paxson, Vern [Univ. of California, Berkeley, CA (United States). Computer Science Division

1997-04-01

Accurately characterizing end-to-end Internet dynamics - the performance that a user actually obtains from the lengthy series of network links that comprise a path through the Internet - is exceptionally difficult, due to the network`s immense heterogeneity. At the heart of this work is a `measurement framework` in which a number of sites around the Internet host a specialized measurement service. By coordinating `probes` between pairs of these sites one can measure end-to-end behavior along O(N<sup>2</sup>) paths for a framework consisting of N sites. Consequently, one obtains a superlinear scaling that allows measuring a rich cross-section of Internet behavior without requiring huge numbers of observation points. 37 sites participated in this study, allowing the author to measure more than 1,000 distinct Internet paths. The first part of this work looks at the behavior of end-to-end routing: the series of routers over which a connection`s packets travel. Based on 40,000 measurements made using this framework, the author analyzes: routing `pathologies` such as loops, outages, and flutter; the stability of routes over time; and the symmetry of routing along the two directions of an end-to-end path. The author finds that pathologies increased significantly over the course of 1995 and that Internet paths are heavily dominated by a single route. The second part of this work studies end-to-end Internet packet dynamics. The author analyzes 20,000 TCP transfers of 100 Kbyte each to investigate the performance of both the TCP endpoints and the Internet paths. The measurements used for this part of the study are much richer than those for the first part, but require a great degree of attention to issues of calibration, which are addressed by applying self-consistency checks to the measurements whenever possible. The author finds that packet filters are capable of a wide range of measurement errors, some of which, if undetected, can significantly taint subsequent analysis.

Atomic Structure and Nonhomologous End-Joining Function of the Polymerase Component of Bacterial DNA Ligase D

Energy Technology Data Exchange (ETDEWEB)

Zhu,H.; Nandakumar, J.; Aniukwu, J.; Wang, L.; Glickman, M.; Lima, C.; Shuman, S.

2006-01-01

DNA ligase D (LigD) is a large polyfunctional protein that participates in a recently discovered pathway of nonhomologous end-joining in bacteria. LigD consists of an ATP-dependent ligase domain fused to a polymerase domain (Pol) and a phosphoesterase module. The Pol activity is remarkable for its dependence on manganese, its ability to perform templated and nontemplated primer extension reactions, and its preference for adding ribonucleotides to blunt DNA ends. Here we report the 1.5- Angstroms crystal structure of the Pol domain of Pseudomonas LigD and its complexes with manganese and ATP-dATP substrates, which reveal a minimized polymerase with a two-metal mechanism and a fold similar to that of archaeal DNA primase. Mutational analysis highlights the functionally relevant atomic contacts in the active site. Although distinct nucleoside conformations and contacts for ATP versus dATP are observed in the cocrystals, the functional analysis suggests that the ATP-binding mode is the productive conformation for dNMP and rNMP incorporation. We find that a mutation of Mycobacterium LigD that uniquely ablates the polymerase activity results in increased fidelity of blunt-end double-strand break repair in vivo by virtue of eliminating nucleotide insertions at the recombination junctions. Thus, LigD Pol is a direct catalyst of mutagenic nonhomologous end-joining in vivo. Our studies underscore a previously uncharacterized role for the primase-like polymerase family in DNA repair.

Experience of using MOSFET detectors for dose verification measurements in an end-to-end 192Ir brachytherapy quality assurance system.

Science.gov (United States)

Persson, Maria; Nilsson, Josef; Carlsson Tedgren, Åsa

Establishment of an end-to-end system for the brachytherapy (BT) dosimetric chain could be valuable in clinical quality assurance. Here, the development of such a system using MOSFET (metal oxide semiconductor field effect transistor) detectors and experience gained during 2 years of use are reported with focus on the performance of the MOSFET detectors. A bolus phantom was constructed with two implants, mimicking prostate and head & neck treatments, using steel needles and plastic catheters to guide the 192 Ir source and house the MOSFET detectors. The phantom was taken through the BT treatment chain from image acquisition to dose evaluation. During the 2-year evaluation-period, delivered doses were verified a total of 56 times using MOSFET detectors which had been calibrated in an external 60 Co beam. An initial experimental investigation on beam quality differences between 192 Ir and 60 Co is reported. The standard deviation in repeated MOSFET measurements was below 3% in the six measurement points with dose levels above 2 Gy. MOSFET measurements overestimated treatment planning system doses by 2-7%. Distance-dependent experimental beam quality correction factors derived in a phantom of similar size as that used for end-to-end tests applied on a time-resolved measurement improved the agreement. MOSFET detectors provide values stable over time and function well for use as detectors for end-to-end quality assurance purposes in 192 Ir BT. Beam quality correction factors should address not only distance from source but also phantom dimensions. Copyright © 2017 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining

International Nuclear Information System (INIS)

Wang, Chen; Lees-Miller, Susan P.

2013-01-01

DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation

Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining

Energy Technology Data Exchange (ETDEWEB)

Wang, Chen [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada); Lees-Miller, Susan P., E-mail: leesmill@ucalgary.ca [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)

2013-07-01

DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.

High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.

Directory of Open Access Journals (Sweden)

Shin-ichi Hashimoto

Full Text Available Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5'-end transcriptome workflow for the SOLiD system and demonstrate the advantages in sensitivity and dynamic range offered by this tag-based application over traditional approaches for the study of whole genome gene expression. 5'-end transcriptome analysis was used to study whole genome gene expression within a colon cancer cell line, HT-29, treated with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5Aza. More than 20 million 25-base 5'-end tags were obtained from untreated and 5Aza-treated cells and matched to sequences within the human genome. Seventy three percent of the mapped unique tags were associated with RefSeq cDNA sequences, corresponding to approximately 14,000 different protein-coding genes in this single cell type. The level of expression of these genes ranged from 0.02 to 4,704 transcripts per cell. The sensitivity of a single sequence run of the SOLiD platform was 100-1,000 fold greater than that observed from 5'end SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5'end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology.

Multi-institutional evaluation of end-to-end protocol for IMRT/VMAT treatment chains utilizing conventional linacs.

Science.gov (United States)

Loughery, Brian; Knill, Cory; Silverstein, Evan; Zakjevskii, Viatcheslav; Masi, Kathryn; Covington, Elizabeth; Snyder, Karen; Song, Kwang; Snyder, Michael

2018-03-20

We conducted a multi-institutional assessment of a recently developed end-to-end monthly quality assurance (QA) protocol for external beam radiation therapy treatment chains. This protocol validates the entire treatment chain against a baseline to detect the presence of complex errors not easily found in standard component-based QA methods. Participating physicists from 3 institutions ran the end-to-end protocol on treatment chains that include Imaging and Radiation Oncology Core (IROC)-credentialed linacs. Results were analyzed in the form of American Association of Physicists in Medicine (AAPM) Task Group (TG)-119 so that they may be referenced by future test participants. Optically stimulated luminescent dosimeter (OSLD), EBT3 radiochromic film, and A1SL ion chamber readings were accumulated across 10 test runs. Confidence limits were calculated to determine where 95% of measurements should fall. From calculated confidence limits, 95% of measurements should be within 5% error for OSLDs, 4% error for ionization chambers, and 4% error for (96% relative gamma pass rate) radiochromic film at 3% agreement/3 mm distance to agreement. Data were separated by institution, model of linac, and treatment protocol (intensity-modulated radiation therapy [IMRT] vs volumetric modulated arc therapy [VMAT]). A total of 97% of OSLDs, 98% of ion chambers, and 93% of films were within the confidence limits; measurements were found outside these limits by a maximum of 4%, consistent despite institutional differences in OSLD reading equipment and radiochromic film calibration techniques. Results from this test may be used by clinics for data comparison. Areas of improvement were identified in the end-to-end protocol that can be implemented in an updated version. The consistency of our data demonstrates the reproducibility and ease-of-use of such tests and suggests a potential role for their use in broad end-to-end QA initiatives. Copyright © 2018 American Association of Medical

End-Users, Front Ends and Librarians.

Science.gov (United States)

Bourne, Donna E.

1989-01-01

The increase in end-user searching, the advantages and limitations of front ends, and the role of the librarian in end-user searching are discussed. It is argued that librarians need to recognize that front ends can be of benefit to themselves and patrons, and to assume the role of advisors and educators for end-users. (37 references) (CLB)

Agrobacterium May Delay Plant Nonhomologous End-Joining DNA Repair via XRCC4 to Favor T-DNA Integration[W

Science.gov (United States)

Vaghchhipawala, Zarir E.; Vasudevan, Balaji; Lee, Seonghee; Morsy, Mustafa R.; Mysore, Kirankumar S.

2012-01-01

Agrobacterium tumefaciens is a soilborne pathogen that causes crown gall disease in many dicotyledonous plants by transfer of a portion of its tumor-inducing plasmid (T-DNA) into the plant genome. Several plant factors that play a role in Agrobacterium attachment to plant cells and transport of T-DNA to the nucleus have been identified, but the T-DNA integration step during transformation is poorly understood and has been proposed to occur via nonhomologous end-joining (NHEJ)–mediated double-strand DNA break (DSB) repair. Here, we report a negative role of X-RAY CROSS COMPLEMENTATION GROUP4 (XRCC4), one of the key proteins required for NHEJ, in Agrobacterium T-DNA integration. Downregulation of XRCC4 in Arabidopsis and Nicotiana benthamiana increased stable transformation due to increased T-DNA integration. Overexpression of XRCC4 in Arabidopsis decreased stable transformation due to decreased T-DNA integration. Interestingly, XRCC4 directly interacted with Agrobacterium protein VirE2 in a yeast two-hybrid system and in planta. VirE2-expressing Arabidopsis plants were more susceptible to the DNA damaging chemical bleomycin and showed increased stable transformation. We hypothesize that VirE2 titrates or excludes active XRCC4 protein available for DSB repair, thus delaying the closure of DSBs in the chromosome, providing greater opportunity for T-DNA to integrate. PMID:23064322

SV40 Utilizes ATM Kinase Activity to Prevent Non-homologous End Joining of Broken Viral DNA Replication Products

Science.gov (United States)

Sowd, Gregory A.; Mody, Dviti; Eggold, Joshua; Cortez, David; Friedman, Katherine L.; Fanning, Ellen

2014-01-01

Simian virus 40 (SV40) and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PKcs kinase activity, facilitates some aspects of double strand break (DSB) repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR) and do not colocalize with non-homologous end joining (NHEJ) factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PKcs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5′ to 3′ end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication. PMID:25474690

SV40 utilizes ATM kinase activity to prevent non-homologous end joining of broken viral DNA replication products.

Directory of Open Access Journals (Sweden)

Gregory A Sowd

2014-12-01

Full Text Available Simian virus 40 (SV40 and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PK(cs kinase activity, facilitates some aspects of double strand break (DSB repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR and do not colocalize with non-homologous end joining (NHEJ factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PK(cs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5' to 3' end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication.

Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases lambda and mu for nonhomologous end joining in human whole-cell extracts.

Science.gov (United States)

Akopiants, Konstantin; Zhou, Rui-Zhe; Mohapatra, Susovan; Valerie, Kristoffer; Lees-Miller, Susan P; Lee, Kyung-Jong; Chen, David J; Revy, Patrick; de Villartay, Jean-Pierre; Povirk, Lawrence F

2009-07-01

XLF/Cernunnos is a core protein of the nonhomologous end-joining pathway of DNA double-strand break repair. To better define the role of Cernunnos in end joining, whole-cell extracts were prepared from Cernunnos-deficient human cells. These extracts effected little joining of DNA ends with cohesive 5' or 3' overhangs, and no joining at all of partially complementary 3' overhangs that required gap filling prior to ligation. Assays in which gap-filled but unligated intermediates were trapped using dideoxynucleotides revealed that there was no gap filling on aligned DSB ends in the Cernunnos-deficient extracts. Recombinant Cernunnos protein restored gap filling and end joining of partially complementary overhangs, and stimulated joining of cohesive ends more than twentyfold. XLF-dependent gap filling was nearly eliminated by immunodepletion of DNA polymerase lambda, but was restored by addition of either polymerase lambda or polymerase mu. Thus, Cernunnos is essential for gap filling by either polymerase during nonhomologous end joining, suggesting that it plays a major role in aligning the two DNA ends in the repair complex.

TRF2 Protein Interacts with Core Histones to Stabilize Chromosome Ends.

Science.gov (United States)

Konishi, Akimitsu; Izumi, Takashi; Shimizu, Shigeomi

2016-09-23

Mammalian chromosome ends are protected by a specialized nucleoprotein complex called telomeres. Both shelterin, a telomere-specific multi-protein complex, and higher order telomeric chromatin structures combine to stabilize the chromosome ends. Here, we showed that TRF2, a component of shelterin, binds to core histones to protect chromosome ends from inappropriate DNA damage response and loss of telomeric DNA. The N-terminal Gly/Arg-rich domain (GAR domain) of TRF2 directly binds to the globular domain of core histones. The conserved arginine residues in the GAR domain of TRF2 are required for this interaction. A TRF2 mutant with these arginine residues substituted by alanine lost the ability to protect telomeres and induced rapid telomere shortening caused by the cleavage of a loop structure of the telomeric chromatin. These findings showed a previously unnoticed interaction between the shelterin complex and nucleosomal histones to stabilize the chromosome ends. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

TRF2 Protein Interacts with Core Histones to Stabilize Chromosome Ends*

Science.gov (United States)

Izumi, Takashi; Shimizu, Shigeomi

2016-01-01

Mammalian chromosome ends are protected by a specialized nucleoprotein complex called telomeres. Both shelterin, a telomere-specific multi-protein complex, and higher order telomeric chromatin structures combine to stabilize the chromosome ends. Here, we showed that TRF2, a component of shelterin, binds to core histones to protect chromosome ends from inappropriate DNA damage response and loss of telomeric DNA. The N-terminal Gly/Arg-rich domain (GAR domain) of TRF2 directly binds to the globular domain of core histones. The conserved arginine residues in the GAR domain of TRF2 are required for this interaction. A TRF2 mutant with these arginine residues substituted by alanine lost the ability to protect telomeres and induced rapid telomere shortening caused by the cleavage of a loop structure of the telomeric chromatin. These findings showed a previously unnoticed interaction between the shelterin complex and nucleosomal histones to stabilize the chromosome ends. PMID:27514743

Automatic provisioning of end-to-end QoS into the home

DEFF Research Database (Denmark)

Brewka, Lukasz Jerzy; Skoldström, Pontus; Nelis, Jelle

2011-01-01

Due to a growing number of high bandwidth applications today (such as HDTV), and an increasing amount of network and cloud based applications, service providers need to pay attention to QoS in their networks. We believe there is a need for an end-to-end approach reaching into the home as well....... The Home Gateway (HG) as a key component of the home network is crucial for enabling the end-to-end solutions. UPnP-QoS has been proposed as an inhome solution for resource reservations. In this paper we assess a solution for automatic QoS reservations, on behalf of non-UPnP-QoS aware applications....... Additionally we focus on an integrated end-to-end solution, combining GMPLS-based reservations in e.g., access/metro and UPnP-QoS based reservation in the home network....

End-to-end tests using alanine dosimetry in scanned proton beams

Science.gov (United States)

Carlino, A.; Gouldstone, C.; Kragl, G.; Traneus, E.; Marrale, M.; Vatnitsky, S.; Stock, M.; Palmans, H.

2018-03-01

This paper describes end-to-end test procedures as the last fundamental step of medical commissioning before starting clinical operation of the MedAustron synchrotron-based pencil beam scanning (PBS) therapy facility with protons. One in-house homogeneous phantom and two anthropomorphic heterogeneous (head and pelvis) phantoms were used for end-to-end tests at MedAustron. The phantoms were equipped with alanine detectors, radiochromic films and ionization chambers. The correction for the ‘quenching’ effect of alanine pellets was implemented in the Monte Carlo platform of the evaluation version of RayStation TPS. During the end-to-end tests, the phantoms were transferred through the workflow like real patients to simulate the entire clinical workflow: immobilization, imaging, treatment planning and dose delivery. Different clinical scenarios of increasing complexity were simulated: delivery of a single beam, two oblique beams without and with range shifter. In addition to the dose comparison in the plastic phantoms the dose obtained from alanine pellet readings was compared with the dose determined with the Farmer ionization chamber in water. A consistent systematic deviation of about 2% was found between alanine dosimetry and the ionization chamber dosimetry in water and plastic materials. Acceptable agreement of planned and delivered doses was observed together with consistent and reproducible results of the end-to-end testing performed with different dosimetric techniques (alanine detectors, ionization chambers and EBT3 radiochromic films). The results confirmed the adequate implementation and integration of the new PBS technology at MedAustron. This work demonstrates that alanine pellets are suitable detectors for end-to-end tests in proton beam therapy and the developed procedures with customized anthropomorphic phantoms can be used to support implementation of PBS technology in clinical practice.

Influence of suture technique and suture material selection on the mechanics of end-to-end and end-to-side anastomoses.

Science.gov (United States)

Baumgartner, N; Dobrin, P B; Morasch, M; Dong, Q S; Mrkvicka, R

1996-05-01

Experiments were performed in dogs to evaluate the mechanics of 26 end-to-end and 42 end-to-side artery-vein graft anastomoses constructed with continuous polypropylene sutures (Surgilene; Davis & Geck, Division of American Cyanamid Co., Danbury, Conn.), continuous polybutester sutures (Novafil; Davis & Geck), and interrupted stitches with either suture material. After construction, the grafts and adjoining arteries were excised, mounted in vitro at in situ length, filled with a dilute barium sulfate suspension, and pressurized in 25 mm Hg steps up to 200 mm Hg. Radiographs were obtained at each pressure. The computed cross-sectional areas of the anastomoses were compared with those of the native arteries at corresponding pressures. Results showed that for the end-to-end anastomoses at 100 mm Hg the cross-sectional areas of the continuous Surgilene anastomoses were 70% of the native artery cross-sectional areas, the cross-sectional areas of the continuous Novafil anastomoses were 90% of the native artery cross-sectional areas, and the cross-sectional areas of the interrupted anastomoses were 107% of the native artery cross-sectional areas (p anastomoses demonstrated no differences in cross-sectional areas or compliance for the three suture techniques. This suggests that, unlike with end-to-end anastomoses, when constructing an end-to-side anastomosis in patients any of the three suture techniques may be acceptable.

Lipofection and nucleofection of substrate plasmid can generate widely different readings of DNA end-joining efficiency in different cell lines.

Science.gov (United States)

Magin, Simon; Saha, Janapriya; Wang, Minli; Mladenova, Veronika; Coym, Nadine; Iliakis, George

2013-02-01

In vivo plasmid end-joining assays are valuable tools for dissecting important qualitative and quantitative aspects of non-homologous end-joining (NHEJ)--a key mechanism for the repair of DNA double-strand breaks (DSBs) in higher eukaryotes. They enable the use of defined DNA ends as substrates for end-joining and the analysis by sequencing of the resulting junctions to identify the repair pathways engaged. Yet, plasmid assays have generated divergent results of end-joining capacity in the same DSB repair mutants when used under different conditions, which implies contributions from undefined and therefore uncontrolled parameters. To help standardize these assays, we searched for parameters underpinning these variations and identified transfection method as an important determinant. Here, we compare a lipid-based transfection method, lipofection, with an electroporation method, nucleofection, and find large, unanticipated and cell line-dependent differences in percent end-joining without recognizable trends. For example, in rodent cells, transfection using lipofection gives nearly WT end-joining in DNA-PKcs mutants and only mildly inhibited end-joining in Lig4 and Ku mutants. In contrast, transfection using nucleofection shows marked end-joining inhibition in all NHEJ mutants tested as compared to the WT. In human HCT116 cells, end-joining after nucleofection is strongly suppressed even in the WT and the differences to the mutants are small. After lipofection, in contrast, end-joining is high in WT cells and markedly suppressed in the mutants. We conclude that better understanding and control of the physicochemical/biological and analytical parameters underpinning these differences will be required to generate with plasmid assays results with quantitative power comparable to that of well-established methods of DSB analysis such as pulsed-field gel electrophoresis or γ-H2AX foci scoring. Until then, caution is needed in the interpretation of the results obtained

End-to-End Availability Analysis of IMS-Based Networks

DEFF Research Database (Denmark)

Kamyod, Chayapol; Nielsen, Rasmus Hjorth; Prasad, Neeli R.

2013-01-01

Generation Networks (NGNs). In this paper, an end-to-end availability model is proposed and evaluated using a combination of Reliability Block Diagrams (RBD) and a proposed five-state Markov model. The overall availability for intra- and inter domain communication in IMS is analyzed, and the state...

Utilizing Domain Knowledge in End-to-End Audio Processing

DEFF Research Database (Denmark)

Tax, Tycho; Antich, Jose Luis Diez; Purwins, Hendrik

2017-01-01

to learn the commonly-used log-scaled mel-spectrogram transformation. Secondly, we demonstrate that upon initializing the first layers of an end-to-end CNN classifier with the learned transformation, convergence and performance on the ESC-50 environmental sound classification dataset are similar to a CNN......-based model trained on the highly pre-processed log-scaled mel-spectrogram features....

Ku must load directly onto the chromosome end in order to mediate its telomeric functions.

Directory of Open Access Journals (Sweden)

Christopher R Lopez

2011-08-01

Full Text Available The Ku heterodimer associates with the Saccharomyces cerevisiae telomere, where it impacts several aspects of telomere structure and function. Although Ku avidly binds DNA ends via a preformed channel, its ability to associate with telomeres via this mechanism could be challenged by factors known to bind directly to the chromosome terminus. This has led to uncertainty as to whether Ku itself binds directly to telomeric ends and whether end association is crucial for Ku's telomeric functions. To address these questions, we constructed DNA end binding-defective Ku heterodimers by altering amino acid residues in Ku70 and Ku80 that were predicted to contact DNA. These mutants continued to associate with their known telomere-related partners, such as Sir4, a factor required for telomeric silencing, and TLC1, the RNA component of telomerase. Despite these interactions, we found that the Ku mutants had markedly reduced association with telomeric chromatin and null-like deficiencies for telomere end protection, length regulation, and silencing functions. In contrast to Ku null strains, the DNA end binding defective Ku mutants resulted in increased, rather than markedly decreased, imprecise end-joining proficiency at an induced double-strand break. This result further supports that it was the specific loss of Ku's telomere end binding that resulted in telomeric defects rather than global loss of Ku's functions. The extensive telomere defects observed in these mutants lead us to propose that Ku is an integral component of the terminal telomeric cap, where it promotes a specific architecture that is central to telomere function and maintenance.

Ku must load directly onto the chromosome end in order to mediate its telomeric functions.

Science.gov (United States)

Lopez, Christopher R; Ribes-Zamora, Albert; Indiviglio, Sandra M; Williams, Christopher L; Haricharan, Svasti; Bertuch, Alison A

2011-08-01

The Ku heterodimer associates with the Saccharomyces cerevisiae telomere, where it impacts several aspects of telomere structure and function. Although Ku avidly binds DNA ends via a preformed channel, its ability to associate with telomeres via this mechanism could be challenged by factors known to bind directly to the chromosome terminus. This has led to uncertainty as to whether Ku itself binds directly to telomeric ends and whether end association is crucial for Ku's telomeric functions. To address these questions, we constructed DNA end binding-defective Ku heterodimers by altering amino acid residues in Ku70 and Ku80 that were predicted to contact DNA. These mutants continued to associate with their known telomere-related partners, such as Sir4, a factor required for telomeric silencing, and TLC1, the RNA component of telomerase. Despite these interactions, we found that the Ku mutants had markedly reduced association with telomeric chromatin and null-like deficiencies for telomere end protection, length regulation, and silencing functions. In contrast to Ku null strains, the DNA end binding defective Ku mutants resulted in increased, rather than markedly decreased, imprecise end-joining proficiency at an induced double-strand break. This result further supports that it was the specific loss of Ku's telomere end binding that resulted in telomeric defects rather than global loss of Ku's functions. The extensive telomere defects observed in these mutants lead us to propose that Ku is an integral component of the terminal telomeric cap, where it promotes a specific architecture that is central to telomere function and maintenance.

End-to-end System Performance Simulation: A Data-Centric Approach

Science.gov (United States)

Guillaume, Arnaud; Laffitte de Petit, Jean-Luc; Auberger, Xavier

2013-08-01

In the early times of space industry, the feasibility of Earth observation missions was directly driven by what could be achieved by the satellite. It was clear to everyone that the ground segment would be able to deal with the small amount of data sent by the payload. Over the years, the amounts of data processed by the spacecrafts have been increasing drastically, leading to put more and more constraints on the ground segment performances - and in particular on timeliness. Nowadays, many space systems require high data throughputs and short response times, with information coming from multiple sources and involving complex algorithms. It has become necessary to perform thorough end-to-end analyses of the full system in order to optimise its cost and efficiency, but even sometimes to assess the feasibility of the mission. This paper presents a novel framework developed by Astrium Satellites in order to meet these needs of timeliness evaluation and optimisation. This framework, named ETOS (for “End-to-end Timeliness Optimisation of Space systems”), provides a modelling process with associated tools, models and GUIs. These are integrated thanks to a common data model and suitable adapters, with the aim of building suitable space systems simulators of the full end-to-end chain. A big challenge of such environment is to integrate heterogeneous tools (each one being well-adapted to part of the chain) into a relevant timeliness simulation.

System of end-to-end symmetric database encryption

Science.gov (United States)

Galushka, V. V.; Aydinyan, A. R.; Tsvetkova, O. L.; Fathi, V. A.; Fathi, D. V.

2018-05-01

The article is devoted to the actual problem of protecting databases from information leakage, which is performed while bypassing access control mechanisms. To solve this problem, it is proposed to use end-to-end data encryption, implemented at the end nodes of an interaction of the information system components using one of the symmetric cryptographic algorithms. For this purpose, a key management method designed for use in a multi-user system based on the distributed key representation model, part of which is stored in the database, and the other part is obtained by converting the user's password, has been developed and described. In this case, the key is calculated immediately before the cryptographic transformations and is not stored in the memory after the completion of these transformations. Algorithms for registering and authorizing a user, as well as changing his password, have been described, and the methods for calculating parts of a key when performing these operations have been provided.

Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

Institute of Scientific and Technical Information of China (English)

Xiao-Rong Wu; Chen-Wei Wu; Fei Ding; Cheng Tian; Wen Jiang; Cheng-De Mao; Chuan Zhang

2017-01-01

Discrete and symmetric three-dimensional (3D) DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization (e.g.dye molecules,proteins,inorganic nanoparticles,etc.) to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA pointstar motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron (E-TET),rhombic dodecahedron (R-DOD),and rhombic triacontahedron (R-TRI) are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis (PAGE),atomic force microscope (AFM) imaging,and cryogenic transmission electron microscope imaging (cryo-TEM) associated with single particle reconstruction.

Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases ? and ? for nonhomologous end joining in human whole-cell extracts

OpenAIRE

Akopiants, Konstantin; Zhou, Rui-Zhe; Mohapatra, Susovan; Valerie, Kristoffer; Lees-Miller, Susan P.; Lee, Kyung-Jong; Chen, David J.; Revy, Patrick; de Villartay, Jean-Pierre; Povirk, Lawrence F.

2009-01-01

XLF/Cernunnos is a core protein of the nonhomologous end-joining pathway of DNA double-strand break repair. To better define the role of Cernunnos in end joining, whole-cell extracts were prepared from Cernunnos-deficient human cells. These extracts effected little joining of DNA ends with cohesive 5? or 3? overhangs, and no joining at all of partially complementary 3? overhangs that required gap filling prior to ligation. Assays in which gap-filled but unligated intermediates were trapped us...

SU-F-J-177: A Novel Image Analysis Technique (center Pixel Method) to Quantify End-To-End Tests

Energy Technology Data Exchange (ETDEWEB)

Wen, N; Chetty, I [Henry Ford Health System, Detroit, MI (United States); Snyder, K [Henry Ford Hospital System, Detroit, MI (United States); Scheib, S [Varian Medical System, Barton (Switzerland); Qin, Y; Li, H [Henry Ford Health System, Detroit, Michigan (United States)

2016-06-15

Purpose: To implement a novel image analysis technique, “center pixel method”, to quantify end-to-end tests accuracy of a frameless, image guided stereotactic radiosurgery system. Methods: The localization accuracy was determined by delivering radiation to an end-to-end prototype phantom. The phantom was scanned with 0.8 mm slice thickness. The treatment isocenter was placed at the center of the phantom. In the treatment room, CBCT images of the phantom (kVp=77, mAs=1022, slice thickness 1 mm) were acquired to register to the reference CT images. 6D couch correction were applied based on the registration results. Electronic Portal Imaging Device (EPID)-based Winston Lutz (WL) tests were performed to quantify the errors of the targeting accuracy of the system at 15 combinations of gantry, collimator and couch positions. The images were analyzed using two different methods. a) The classic method. The deviation was calculated by measuring the radial distance between the center of the central BB and the full width at half maximum of the radiation field. b) The center pixel method. Since the imager projection offset from the treatment isocenter was known from the IsoCal calibration, the deviation was determined between the center of the BB and the central pixel of the imager panel. Results: Using the automatic registration method to localize the phantom and the classic method of measuring the deviation of the BB center, the mean and standard deviation of the radial distance was 0.44 ± 0.25, 0.47 ± 0.26, and 0.43 ± 0.13 mm for the jaw, MLC and cone defined field sizes respectively. When the center pixel method was used, the mean and standard deviation was 0.32 ± 0.18, 0.32 ± 0.17, and 0.32 ± 0.19 mm respectively. Conclusion: Our results demonstrated that the center pixel method accurately analyzes the WL images to evaluate the targeting accuracy of the radiosurgery system. The work was supported by a Research Scholar Grant, RSG-15-137-01-CCE from the American

REASONING IN THE FUZZY FRONT END OF INNOVATION:

DEFF Research Database (Denmark)

Haase, Louise Møller; Laursen, Linda Nhu

2018-01-01

in the fuzzy front end is the reasoning process: innovation teams are faced with open-ended, ill-defined problems, where they need to make decisions about an unknown future but have only incomplete, ambiguous and contradicting insights available. We study the reasoning of experts, how they frame to make sense...... of all the insights and create a basis for decision-making in relation to a new project. Based on case studies of five innovative products from various industries, we propose a Product DNA model for understanding the reasoning in the fuzzy front end of innovation. The Product DNA Model explains how...... experts reason and what direct their reasoning....

Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin

Science.gov (United States)

Bandaria, Jigar N.; Qin, Peiwu; Berk, Veysel; Chu, Steven; Yildiz, Ahmet

2016-01-01

SUMMARY Telomeres, repetitive DNA sequences at chromosome ends, are shielded against the DNA damage response (DDR) by the shelterin complex. To understand how shelterin protects telomere ends, we investigated the structural organization of telomeric chromatin in human cells using super-resolution microscopy. We found that telomeres form compact globular structures through a complex network of interactions between shelterin subunits and telomeric DNA, and not by DNA methylation, histone deacetylation or histone trimethylation at telomeres and subtelomeric regions. Mutations that abrogate shelterin assembly or removal of individual subunits from telomeres cause up to a 10-fold increase in telomere volume. Decompacted telomeres become more accessible to telomere-associated proteins and accumulate DDR signals. Recompaction of telomeric chromatin using an orthogonal method displaces DDR signals from telomeres. These results reveal the chromatin remodeling activity of shelterin and demonstrate that shelterin-mediated compaction of telomeric chromatin provides robust protection of chromosome ends against the DDR machinery. PMID:26871633

Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea.

Science.gov (United States)

Rzechorzek, Neil J; Blackwood, John K; Bray, Sian M; Maman, Joseph D; Pellegrini, Luca; Robinson, Nicholas P

2014-11-25

The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.

Means-end chains - A means to which end?

DEFF Research Database (Denmark)

Grunert, Klaus G.

2010-01-01

This paper describes the development of the means-end chain concept in consumer behaviour research, starting from the original proposal by Gutman in 1982. A lack of theoretical development - as opposed to a refinement of methodology - is argued to by the main reason why the concept, after....... This reinterpretation leads to three goals for research that could establish means-end chains as a useful theoretical concept in consumer behaviour research....

IDENTIFYING ELUSIVE ELECTROMAGNETIC COUNTERPARTS TO GRAVITATIONAL WAVE MERGERS: AN END-TO-END SIMULATION

International Nuclear Information System (INIS)

Nissanke, Samaya; Georgieva, Alexandra; Kasliwal, Mansi

2013-01-01

Combined gravitational wave (GW) and electromagnetic (EM) observations of compact binary mergers should enable detailed studies of astrophysical processes in the strong-field gravity regime. This decade, ground-based GW interferometers promise to routinely detect compact binary mergers. Unfortunately, networks of GW interferometers have poor angular resolution on the sky and their EM signatures are predicted to be faint. Therefore, a challenging goal will be to unambiguously pinpoint the EM counterparts of GW mergers. We perform the first comprehensive end-to-end simulation that focuses on: (1) GW sky localization, distance measures, and volume errors with two compact binary populations and four different GW networks; (2) subsequent EM detectability by a slew of multiwavelength telescopes; and (3) final identification of the merger counterpart amidst a sea of possible astrophysical false positives. First, we find that double neutron star binary mergers can be detected out to a maximum distance of 400 Mpc (or 750 Mpc) by three (or five) detector GW networks, respectively. Neutron-star-black-hole binary mergers can be detected a factor of 1.5 further out; their median to maximum sky localizations are 50-170 deg 2 (or 6-65 deg 2 ) for a three (or five) detector GW network. Second, by optimizing depth, cadence, and sky area, we quantify relative fractions of optical counterparts that are detectable by a suite of different aperture-size telescopes across the globe. Third, we present five case studies to illustrate the diversity of scenarios in secure identification of the EM counterpart. We discuss the case of a typical binary, neither beamed nor nearby, and the challenges associated with identifying an EM counterpart at both low and high Galactic latitudes. For the first time, we demonstrate how construction of low-latency GW volumes in conjunction with local universe galaxy catalogs can help solve the problem of false positives. We conclude with strategies that would

STS/DBS power subsystem end-to-end stability margin

Science.gov (United States)

Devaux, R. N.; Vattimo, R. J.; Peck, S. R.; Baker, W. E.

Attention is given to a full-up end-to-end subsystem stability test which was performed with a flight solar array providing power to a fully operational spacecraft. The solar array simulator is described, and a comparison is made between test results obtained with the simulator and those obtained with the actual array. It is concluded that stability testing with a fully integrated spacecraft is necessary to ensure that all elements have been adequately modeled.

Mycobacterium tuberculosis and Mycobacterium marinum non-homologous end-joining proteins can function together to join DNA ends in Escherichia coli.

Science.gov (United States)

Wright, Douglas G; Castore, Reneau; Shi, Runhua; Mallick, Amrita; Ennis, Don G; Harrison, Lynn

2017-03-01

Mycobacterium tuberculosis and Mycobacterium smegmatis express a Ku protein and a DNA ligase D and are able to repair DNA double strand breaks (DSBs) by non-homologous end-joining (NHEJ). This pathway protects against DNA damage when bacteria are in stationary phase. Mycobacterium marinum is a member of this mycobacterium family and like M. tuberculosis is pathogenic. M. marinum lives in water, forms biofilms and infects fish and frogs. M. marinum is a biosafety level 2 (BSL2) organism as it can infect humans, although infections are limited to the skin. M. marinum is accepted as a model to study mycobacterial pathogenesis, as M. marinum and M. tuberculosis are genetically closely related and have similar mechanisms of survival and persistence inside macrophage. The aim of this study was to determine whether M. marinum could be used as a model to understand M. tuberculosis NHEJ repair. We identified and cloned the M. marinum genes encoding NHEJ proteins and generated E. coli strains that express the M. marinum Ku (Mm-Ku) and ligase D (Mm-Lig) individually or together (LHmKumLig strain) from expression vectors integrated at phage attachment sites in the genome. We demonstrated that Mm-Ku and Mm-Lig are both required to re-circularize Cla I-linearized plasmid DNA in E. coli. We compared repair of strain LHmKumLig with that of an E. coli strain (BWKuLig#2) expressing the M. tuberculosis Ku (Mt-Ku) and ligase D (Mt-Lig), and found that LHmKumLig performed 3.5 times more repair and repair was more accurate than BWKuLig#2. By expressing the Mm-Ku with the Mt-Lig, or the Mt-Ku with the Mm-Lig in E. coli, we have shown that the NHEJ proteins from M. marinum and M. tuberculosis can function together to join DNA DSBs. NHEJ repair is therefore conserved between the two species. Consequently, M. marinum is a good model to study NHEJ repair during mycobacterial pathogenesis. © The Author 2016. Published by Oxford University Press on behalf of the UK Environmental Mutagen

End-to-End Operations in the ELT Era

Science.gov (United States)

Hainaut, O. R.; Bierwirth, T.; Brillant, S.; Mieske, S.; Patat, F.; Rejkuba, M.; Romaniello, M.; Sterzik, M.

2018-03-01

The Data Flow System is the infrastructure on which Very Large Telescope (VLT) observations are performed at the Observatory, before and after the observations themselves take place. Since its original conception in the late 1990s, it has evolved to accommodate new observing modes and new instruments on La Silla and Paranal. Several updates and upgrades are needed to overcome its obsolescence and to integrate requirements from the new instruments from the community and, of course, from ESO's Extremely Large Telescope (ELT), which will be integrated into Paranal's operations. We describe the end-to-end operations and the resulting roadmap guiding their further development.

Optimizing End-to-End Big Data Transfers over Terabits Network Infrastructure

International Nuclear Information System (INIS)

Kim, Youngjae; Vallee, Geoffroy R.; Lee, Sangkeun; Shipman, Galen M.

2016-01-01

While future terabit networks hold the promise of significantly improving big-data motion among geographically distributed data centers, significant challenges must be overcome even on today's 100 gigabit networks to realize end-to-end performance. Multiple bottlenecks exist along the end-to-end path from source to sink, for instance, the data storage infrastructure at both the source and sink and its interplay with the wide-area network are increasingly the bottleneck to achieving high performance. In this study, we identify the issues that lead to congestion on the path of an end-to-end data transfer in the terabit network environment, and we present a new bulk data movement framework for terabit networks, called LADS. LADS exploits the underlying storage layout at each endpoint to maximize throughput without negatively impacting the performance of shared storage resources for other users. LADS also uses the Common Communication Interface (CCI) in lieu of the sockets interface to benefit from hardware-level zero-copy, and operating system bypass capabilities when available. It can further improve data transfer performance under congestion on the end systems using buffering at the source using flash storage. With our evaluations, we show that LADS can avoid congested storage elements within the shared storage resource, improving input/output bandwidth, and data transfer rates across the high speed networks. We also investigate the performance degradation problems of LADS due to I/O contention on the parallel file system (PFS), when multiple LADS tools share the PFS. We design and evaluate a meta-scheduler to coordinate multiple I/O streams while sharing the PFS, to minimize the I/O contention on the PFS. Finally, with our evaluations, we observe that LADS with meta-scheduling can further improve the performance by up to 14 percent relative to LADS without meta-scheduling.

Development of a Dynamic, End-to-End Free Piston Stirling Convertor Model

Science.gov (United States)

Regan, Timothy F.; Gerber, Scott S.; Roth, Mary Ellen

2003-01-01

A dynamic model for a free-piston Stirling convertor is being developed at the NASA Glenn Research Center. The model is an end-to-end system model that includes the cycle thermodynamics, the dynamics, and electrical aspects of the system. The subsystems of interest are the heat source, the springs, the moving masses, the linear alternator, the controller and the end-user load. The envisioned use of the model will be in evaluating how changes in a subsystem could affect the operation of the convertor. The model under development will speed the evaluation of improvements to a subsystem and aid in determining areas in which most significant improvements may be found. One of the first uses of the end-to-end model will be in the development of controller architectures. Another related area is in evaluating changes to details in the linear alternator.

Experimental demonstration of software defined data center optical networks with Tbps end-to-end tunability

Science.gov (United States)

Zhao, Yongli; Zhang, Jie; Ji, Yuefeng; Li, Hui; Wang, Huitao; Ge, Chao

2015-10-01

The end-to-end tunability is important to provision elastic channel for the burst traffic of data center optical networks. Then, how to complete the end-to-end tunability based on elastic optical networks? Software defined networking (SDN) based end-to-end tunability solution is proposed for software defined data center optical networks, and the protocol extension and implementation procedure are designed accordingly. For the first time, the flexible grid all optical networks with Tbps end-to-end tunable transport and switch system have been online demonstrated for data center interconnection, which are controlled by OpenDayLight (ODL) based controller. The performance of the end-to-end tunable transport and switch system has been evaluated with wavelength number tuning, bit rate tuning, and transmit power tuning procedure.

Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end.

Science.gov (United States)

Merkiene, Egle; Gaidamaviciute, Edita; Riauba, Laurynas; Janulaitis, Arvydas; Lagunavicius, Arunas

2010-08-01

We improved the target RNA-primed RCA technique for direct detection and analysis of RNA in vitro and in situ. Previously we showed that the 3' --> 5' single-stranded RNA exonucleolytic activity of Phi29 DNA polymerase converts the target RNA into a primer and uses it for RCA initiation. However, in some cases, the single-stranded RNA exoribonucleolytic activity of the polymerase is hindered by strong double-stranded structures at the 3'-end of target RNAs. We demonstrate that in such hampered cases, the double-stranded RNA-specific Escherichia coli RNase III efficiently assists Phi29 DNA polymerase in converting the target RNA into a primer. These observations extend the target RNA-primed RCA possibilities to test RNA sequences distanced far from the 3'-end and customize this technique for the inner RNA sequence analysis.

End-to-end network models encompassing terrestrial, wireless, and satellite components

Science.gov (United States)

Boyarko, Chandler L.; Britton, John S.; Flores, Phil E.; Lambert, Charles B.; Pendzick, John M.; Ryan, Christopher M.; Shankman, Gordon L.; Williams, Ramon P.

2004-08-01

Development of network models that reflect true end-to-end architectures such as the Transformational Communications Architecture need to encompass terrestrial, wireless and satellite component to truly represent all of the complexities in a world wide communications network. Use of best-in-class tools including OPNET, Satellite Tool Kit (STK), Popkin System Architect and their well known XML-friendly definitions, such as OPNET Modeler's Data Type Description (DTD), or socket-based data transfer modules, such as STK/Connect, enable the sharing of data between applications for more rapid development of end-to-end system architectures and a more complete system design. By sharing the results of and integrating best-in-class tools we are able to (1) promote sharing of data, (2) enhance the fidelity of our results and (3) allow network and application performance to be viewed in the context of the entire enterprise and its processes.

Apparatus and method for applying an end plug to a fuel rod tube end

International Nuclear Information System (INIS)

Rieben, S.L.; Wylie, M.E.

1987-01-01

An apparatus is described for applying an end plug to a hollow end of a nuclear fuel rod tube, comprising: support means mounted for reciprocal movement between remote and adjacent positions relative to a nuclear fuel rod tube end to which an end plug is to be applied; guide means supported on the support means for movement; and drive means coupled to the support means and being actuatable for movement between retracted and extended positions for reciprocally moving the support means between its respective remote and adjacent positions. A method for applying an end plug to a hollow end of a nuclear fuel rod tube is also described

DNA-activated protein kinase (DNA-PK) and significance in its responses to radiation. The end is the beginning of the story

International Nuclear Information System (INIS)

Matsumoto, Yoshihisa

1996-01-01

This review described findings hitherto and future perspective on the DNA-PK. The enzyme was activated by double-strand DNA, required the end of the DNA and was the major component of p350 protein. Ku-antigen (an autoimmune antigen) was found a subunit. It phosphorylated p53, c-Myc, RPAp34, DNA ligase I, DNA topoisomerase I and II. Therefore DNA-PK can be a trigger factor which recognizes DNA break induced by radiation, and phosphorylates proteins participating in the DNA repair, cell cycle regulation and cell death. Recently p350 was found to be a responsible gene product to SCID syndrome of mice hypersensitive to ionizing radiation. The review included; On the DNA-PK: Discovery, relation to Ku antigen and molecular properties. On the DNA-PK and radiation sensitivity, and V(D)J recombination: Ku80 was the product of X-ray repair cross-complementing (XRCC). p350 was found the gene product whose lack causing SCID syndrome of radiosensitive mice. On the significance of phosphorylation of DNA-PK and the substrate: p53. RPA (replication protein A, alias RF-A or SSB). P1/MCM3, a possible substrate. On the other properties of DNA-PK: DNA-helicase activity. Suppression of transcription by RNA polymerase. DNA-PKp350 and ATM (ataxia-telangiectasia). Family molecules of p53 and ATM (MEI-41, Tel1p and Mec1p, and Rad3). (H.O). 70 refs

Building dialogue POMDPs from expert dialogues an end-to-end approach

CERN Document Server

Chinaei, Hamidreza

2016-01-01

This book discusses the Partially Observable Markov Decision Process (POMDP) framework applied in dialogue systems. It presents POMDP as a formal framework to represent uncertainty explicitly while supporting automated policy solving. The authors propose and implement an end-to-end learning approach for dialogue POMDP model components. Starting from scratch, they present the state, the transition model, the observation model and then finally the reward model from unannotated and noisy dialogues. These altogether form a significant set of contributions that can potentially inspire substantial further work. This concise manuscript is written in a simple language, full of illustrative examples, figures, and tables. Provides insights on building dialogue systems to be applied in real domain Illustrates learning dialogue POMDP model components from unannotated dialogues in a concise format Introduces an end-to-end approach that makes use of unannotated and noisy dialogue for learning each component of dialogue POM...

End-to-end delay analysis in wireless sensor networks with service vacation

KAUST Repository

Alabdulmohsin, Ibrahim; Hyadi, Amal; Afify, Laila H.; Shihada, Basem

2014-01-01

In this paper, a delay-sensitive multi-hop wireless sensor network is considered, employing an M/G/1 with vacations framework. Sensors transmit measurements to a predefined data sink subject to maximum end-to-end delay constraint. In order to prolong the battery lifetime, a sleeping scheme is adopted throughout the network nodes. The objective of our proposed framework is to present an expression for maximum hop-count as well as an approximate expression of the probability of blocking at the sink node upon violating certain end-to-end delay threshold. Using numerical simulations, we validate the proposed analytical model and demonstrate that the blocking probability of the system for various vacation time distributions matches the simulation results.

End-to-end delay analysis in wireless sensor networks with service vacation

KAUST Repository

Alabdulmohsin, Ibrahim

2014-04-01

In this paper, a delay-sensitive multi-hop wireless sensor network is considered, employing an M/G/1 with vacations framework. Sensors transmit measurements to a predefined data sink subject to maximum end-to-end delay constraint. In order to prolong the battery lifetime, a sleeping scheme is adopted throughout the network nodes. The objective of our proposed framework is to present an expression for maximum hop-count as well as an approximate expression of the probability of blocking at the sink node upon violating certain end-to-end delay threshold. Using numerical simulations, we validate the proposed analytical model and demonstrate that the blocking probability of the system for various vacation time distributions matches the simulation results.

End-to-end Configuration of Wireless Realtime Communication over Heterogeneous Protocols

DEFF Research Database (Denmark)

Malinowsky, B.; Grønbæk, Jesper; Schwefel, Hans-Peter

2015-01-01

This paper describes a wireless real-time communication system design using two Time Division Multiple Access (TDMA) protocols. Messages are subject to prioritization and queuing. For this interoperation scenario, we show a method for end-to-end configuration of protocols and queue sizes. Such co...

Design and end-to-end modelling of a deployable telescope

Science.gov (United States)

Dolkens, Dennis; Kuiper, Hans

2017-09-01

Deployable optics have the potential of revolutionizing the field of high resolution Earth Observation. By offering the same resolutions as a conventional telescope, while using a much smaller launch volume and mass, the costs of high resolution image data can be brought down drastically. In addition, the technology will ultimately enable resolutions that are currently unattainable due to limitations imposed by the size of launcher fairings. To explore the possibilities and system complexities of a deployable telescope, a concept study was done to design a competitive deployable imager. A deployable telescope was designed for a ground sampling distance of 25 cm from an orbital altitude of 550 km. It offers an angular field of view of 0.6° and has a panchromatic channel as well as four multispectral bands in the visible and near infrared spectrum. The optical design of the telescope is based on an off-axis Korsch Three Mirror Anastigmat. A freeform tertiary mirror is used to ensure a diffraction limited image quality for all channels, while maintaining a compact design. The segmented primary mirror consists of four tapered aperture segments, which can be folded down during launch, while the secondary mirror is mounted on a deployable boom. In its stowed configuration, the telescope fits within a quarter of the volume of a conventional telescope reaching the same resolution. To reach a diffraction limited performance while operating in orbit, the relative position of each individual mirror segment must be controlled to a fraction of a wavelength. Reaching such tolerances with deployable telescope challenging, due to inherent uncertainties in the deployment mechanisms. Adding to the complexity is the fact that the telescope will be operating in a Low Earth Orbit (LEO) where it will be exposed to very dynamic thermal conditions. Therefore, the telescope will be equipped with a robust calibration system. Actuators underneath the primary mirror will be controlled using

N-(2-chloroethyl)-N-nitrosoureas covalently bound to nonionic and monocationic lexitropsin dipeptides. Synthesis, DNA affinity binding characteristics, and reactions with 32P-end-labeled DNA

International Nuclear Information System (INIS)

Church, K.M.; Wurdeman, R.L.; Zhang, Yi; Chen, Faxian; Gold, B.

1990-01-01

The synthesis and characterization of a series of compounds that contain an N-alkyl-N-nitrosourea functionality linked to DNA minor groove binding bi- and tripeptides (lexitropsins or information-reading peptides) based on methylpyrrole-2-carboxamide subunits are described. The lexitropsins (lex) synthesized have either a 3-(dimethylamino)propyl or propyl substituent on the carboxyl terminus. The preferred DNA affinity binding sequences of these compounds were footprinted in 32 P-end-labeled restriction fragments with methidiumpropyl-EDTA·Fe(II), and in common with other structural analogues, e.g., distamycin and netropsin, these nitrosoureas recognize A-T-rich runs. The affinity binding of the compound with the dimethylamino terminus, which is ionized at near-neutral pH, appeared stronger than that observed for the neutral dipeptide. The sequence specificity for DNA alkylation by (2-chloroethyl)nitrosourea-lex dipeptides (Cl-ENU-lex), with neutral and charged carboxyl termini, using 32 P-end-labeled restriction fragments, was determined by the conversion of the adducted sites into single-strand breaks by sequential heating at neutral pH and exposure to base. The DNA cleavage sites were visualized by polyacrylamide gel electrophoresis and autoradiography. Linking the Cl-ENU moiety to minor groove binders is a viable strategy to qualitatively and quantitatively control the delivery and release of the ultimate DNA alkylating agent in a sequence-dependent fashion

End-to-End Delay Model for Train Messaging over Public Land Mobile Networks

Directory of Open Access Journals (Sweden)

Franco Mazzenga

2017-11-01

Full Text Available Modern train control systems rely on a dedicated radio network for train to ground communications. A number of possible alternatives have been analysed to adopt the European Rail Traffic Management System/European Train Control System (ERTMS/ETCS control system on local/regional lines to improve transport capacity. Among them, a communication system based on public networks (cellular&satellite provides an interesting, effective and alternative solution to proprietary and expensive radio networks. To analyse performance of this solution, it is necessary to model the end-to-end delay and message loss to fully characterize the message transfer process from train to ground and vice versa. Starting from the results of a railway test campaign over a 300 km railway line for a cumulative 12,000 traveled km in 21 days, in this paper, we derive a statistical model for the end-to-end delay required for delivering messages. In particular, we propose a two states model allowing for reproducing the main behavioral characteristics of the end-to-end delay as observed experimentally. Model formulation has been derived after deep analysis of the recorded experimental data. When it is applied to model a realistic scenario, it allows for explicitly accounting for radio coverage characteristics, the received power level, the handover points along the line and for the serving radio technology. As an example, the proposed model is used to generate the end-to-end delay profile in a realistic scenario.

End-to-end plasma bubble PIC simulations on GPUs

Science.gov (United States)

Germaschewski, Kai; Fox, William; Matteucci, Jackson; Bhattacharjee, Amitava

2017-10-01

Accelerator technologies play a crucial role in eventually achieving exascale computing capabilities. The current and upcoming leadership machines at ORNL (Titan and Summit) employ Nvidia GPUs, which provide vast computational power but also need specifically adapted computational kernels to fully exploit them. In this work, we will show end-to-end particle-in-cell simulations of the formation, evolution and coalescence of laser-generated plasma bubbles. This work showcases the GPU capabilities of the PSC particle-in-cell code, which has been adapted for this problem to support particle injection, a heating operator and a collision operator on GPUs.

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

Science.gov (United States)

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data.

Science.gov (United States)

Miller, Mark P; Knaus, Brian J; Mullins, Thomas D; Haig, Susan M

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25 bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

Model outputs - Developing end-to-end models of the Gulf of California

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the northern Gulf of California, linking oceanography, biogeochemistry, food web...

Coupling of a single quantum emitter to end-to-end aligned silver nanowires

DEFF Research Database (Denmark)

Kumar, Shailesh; Huck, Alexander; Chen, Yuntian

2013-01-01

We report on the observation of coupling a single nitrogen vacancy (NV) center in a nanodiamond crystal to a propagating plasmonic mode of silver nanowires. The nanocrystal is placed either near the apex of a single silver nanowire or in the gap between two end-to-end aligned silver nanowires. We...

End-to-End Flow Control for Visual-Haptic Communication under Bandwidth Change

Science.gov (United States)

Yashiro, Daisuke; Tian, Dapeng; Yakoh, Takahiro

This paper proposes an end-to-end flow controller for visual-haptic communication. A visual-haptic communication system transmits non-real-time packets, which contain large-size visual data, and real-time packets, which contain small-size haptic data. When the transmission rate of visual data exceeds the communication bandwidth, the visual-haptic communication system becomes unstable owing to buffer overflow. To solve this problem, an end-to-end flow controller is proposed. This controller determines the optimal transmission rate of visual data on the basis of the traffic conditions, which are estimated by the packets for haptic communication. Experimental results confirm that in the proposed method, a short packet-sending interval and a short delay are achieved under bandwidth change, and thus, high-precision visual-haptic communication is realized.

An Analysis of the Radiation Damage to the ATLAS Semiconductor Tracker End-Caps

CERN Document Server

Millar, Declan; Moretti, Stefano

The motivation, theoretical principles and analytical procedure for an assessment of the radiation damage to the ATLAS SCT end-caps is presented. An analysis of the leakage current across end-cap modules is performed for 2011 and 2012 data. A comparison between the observed and expected leakage current is made, with measurements favouring the shape of the theoretical evolution. Measured data is found to be systematically lower than predicted for a large subset of end-cap modules, while the remainder show surface current effects which interfere with bulk current observation. Uniform differences for modules at different radial distances suggest a radial temperature distribution in the end-caps, with absolute silicon sensor temperature to be established in further analysis.

Human pro. cap alpha. 1(III) collagen: cDNA sequence for the 3' end

Energy Technology Data Exchange (ETDEWEB)

Mankoo, B S; Dalgleish, R

1988-03-25

The authors have previously isolated two overlapping cDNA clones, pIII-21 and pIII-33, which encode the C-terminal end of human type III procollagen. They now present the sequence of 2520 bases encoded in these cDNAs which overlaps other previously published sequences for the same gene. The sequence presented differs from previously published sequences at five positions.

AN ANALYSIS OF THE APPLICATION END TO END QUALITY OF SERVICE ON 3G TELECOMMUNICATION NETWORK

Directory of Open Access Journals (Sweden)

Cahya Lukito

2012-05-01

Full Text Available End to End Quality of Service is a way to provide data package service in a telecommunication network that based on Right Price, Right Service Level, and Right Quality. The goal of this research is to analyze the impact of End to End QoS use on 3G telecommunication network for voice service and data. This research uses an analysis method by doing the application on the lab. The result that is achieved in this research shows that End to End QoS is very influental to the Service Level Agreement to the users of the telecommunication service.Keywords: End to End Qos, SLA, Diffserv

DNA ligase C1 mediates the LigD-independent nonhomologous end-joining pathway of Mycobacterium smegmatis.

Science.gov (United States)

Bhattarai, Hitesh; Gupta, Richa; Glickman, Michael S

2014-10-01

Nonhomologous end joining (NHEJ) is a recently described bacterial DNA double-strand break (DSB) repair pathway that has been best characterized for mycobacteria. NHEJ can religate transformed linear plasmids, repair ionizing radiation (IR)-induced DSBs in nonreplicating cells, and seal I-SceI-induced chromosomal DSBs. The core components of the mycobacterial NHEJ machinery are the DNA end binding protein Ku and the polyfunctional DNA ligase LigD. LigD has three autonomous enzymatic modules: ATP-dependent DNA ligase (LIG), DNA/RNA polymerase (POL), and 3' phosphoesterase (PE). Although genetic ablation of ku or ligD abolishes NHEJ and sensitizes nonreplicating cells to ionizing radiation, selective ablation of the ligase activity of LigD in vivo only mildly impairs NHEJ of linearized plasmids, indicating that an additional DNA ligase can support NHEJ. Additionally, the in vivo role of the POL and PE domains in NHEJ is unclear. Here we define a LigD ligase-independent NHEJ pathway in Mycobacterium smegmatis that requires the ATP-dependent DNA ligase LigC1 and the POL domain of LigD. Mycobacterium tuberculosis LigC can also support this backup NHEJ pathway. We also demonstrate that, although dispensable for efficient plasmid NHEJ, the activities of the POL and PE domains are required for repair of IR-induced DSBs in nonreplicating cells. These findings define the genetic requirements for a LigD-independent NHEJ pathway in mycobacteria and demonstrate that all enzymatic functions of the LigD protein participate in NHEJ in vivo. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Reversible end-to-end assembly of gold nanorods using a disulfide-modified polypeptide

International Nuclear Information System (INIS)

Walker, David A; Gupta, Vinay K

2008-01-01

Directing the self-assembly of colloidal particles into nanostructures is of great interest in nanotechnology. Here, reversible end-to-end assembly of gold nanorods (GNR) is induced by pH-dependent changes in the secondary conformation of a disulfide-modified poly(L-glutamic acid) (SSPLGA). The disulfide anchoring group drives chemisorption of the polyacid onto the end of the gold nanorods in an ethanolic solution. A layer of poly(vinyl pyrrolidone) is adsorbed on the positively charged, surfactant-stabilized GNR to screen the surfactant bilayer charge and provide stability for dispersion of the GNR in ethanol. For comparison, irreversible end-to-end assembly using a bidentate ligand, namely 1,6-hexanedithiol, is also performed. Characterization of the modified GNR and its end-to-end linking behavior using SSPLGA and hexanedithiol is performed using dynamic light scattering (DLS), UV-vis absorption spectroscopy and transmission electron microscopy (TEM). Experimental results show that, in a colloidal solution of GNR-SSPLGA at a pH∼3.5, where the PLGA is in an α-helical conformation, the modified GNR self-assemble into one-dimensional nanostructures. The linking behavior can be reversed by increasing the pH (>8.5) to drive the conformation of the polypeptide to a random coil and this reversal with pH occurs rapidly within minutes. Cycling the pH multiple times between low and high pH values can be used to drive the formation of the nanostructures of the GNR and disperse them in solution.

Redundant function of DNA ligase 1 and 3 in alternative end-joining during immunoglobulin class switch recombination.

Science.gov (United States)

Masani, Shahnaz; Han, Li; Meek, Katheryn; Yu, Kefei

2016-02-02

Nonhomologous end-joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammals and resolves the DSBs generated during both V(D)J recombination in developing lymphocytes and class switch recombination (CSR) in antigen-stimulated B cells. In contrast to the absolute requirement for NHEJ to resolve DSBs associated with V(D)J recombination, DSBs associated with CSR can be resolved in NHEJ-deficient cells (albeit at a reduced level) by a poorly defined alternative end-joining (A-EJ) pathway. Deletion of DNA ligase IV (Lig4), a core component of the NHEJ pathway, reduces CSR efficiency in a mouse B-cell line capable of robust cytokine-stimulated CSR in cell culture. Here, we report that CSR levels are not further reduced by deletion of either of the two remaining DNA ligases (Lig1 and nuclear Lig3) in Lig4(-/-) cells. We conclude that in the absence of Lig4, Lig1, and Lig3 function in a redundant manner in resolving switch region DSBs during CSR.

End to end adaptive congestion control in TCP/IP networks

CERN Document Server

Houmkozlis, Christos N

2012-01-01

This book provides an adaptive control theory perspective on designing congestion controls for packet-switching networks. Relevant to a wide range of disciplines and industries, including the music industry, computers, image trading, and virtual groups, the text extensively discusses source oriented, or end to end, congestion control algorithms. The book empowers readers with clear understanding of the characteristics of packet-switching networks and their effects on system stability and performance. It provides schemes capable of controlling congestion and fairness and presents real-world app

Testing Application (End-to-End Performance of Networks With EFT Traffic

Directory of Open Access Journals (Sweden)

Vlatko Lipovac

2009-01-01

Full Text Available This paper studies how end-to-end application peiformance(of Electronic Financial Transaction traffic, in particulardepends on the actual protocol stacks, operating systemsand network transmission rates. With this respect, the respectivesimulation tests of peiformance of TCP and UDP protocolsrunning on various operating systems, ranging from Windows,Sun Solmis, to Linux have been implemented, and thedifferences in peiformance addressed focusing on throughputand response time.

In vivo blunt-end cloning through CRISPR/Cas9-facilitated non-homologous end-joining

Science.gov (United States)

Geisinger, Jonathan M.; Turan, Sören; Hernandez, Sophia; Spector, Laura P.; Calos, Michele P.

2016-01-01

The CRISPR/Cas9 system facilitates precise DNA modifications by generating RNA-guided blunt-ended double-strand breaks. We demonstrate that guide RNA pairs generate deletions that are repaired with a high level of precision by non-homologous end-joining in mammalian cells. We present a method called knock-in blunt ligation for exploiting these breaks to insert exogenous PCR-generated sequences in a homology-independent manner without loss of additional nucleotides. This method is useful for making precise additions to the genome such as insertions of marker gene cassettes or functional elements, without the need for homology arms. We successfully utilized this method in human and mouse cells to insert fluorescent protein cassettes into various loci, with efficiencies up to 36% in HEK293 cells without selection. We also created versions of Cas9 fused to the FKBP12-L106P destabilization domain in an effort to improve Cas9 performance. Our in vivo blunt-end cloning method and destabilization-domain-fused Cas9 variant increase the repertoire of precision genome engineering approaches. PMID:26762978

The mechanism of non-homologous end-joining: a synopsis of synapsis.

Science.gov (United States)

Weterings, Eric; van Gent, Dik C

2004-11-02

Repair of DNA double-strand breaks (DSBs) by non-homologous end-joining (NHEJ) is required for resistance to genotoxic agents, such as ionizing radiation, but also for proper development of the vertebrate immune system. Much progress has been made in identifying the factors that are involved in this repair pathway. We are now entering the phase in which we begin to understand basic concepts of the reaction mechanism and regulation of non-homologous end-joining. This review concentrates on novel insights into damage recognition and subsequent tethering, processing and joining of DNA ends.

Anchoring a Defined Sequence to the 55' Ends of mRNAs : The Bolt to Clone Rare Full Length mRNAs and Generate cDNA Libraries porn a Few Cells.

Science.gov (United States)

Baptiste, J; Milne Edwards, D; Delort, J; Mallet, J

1993-01-01

Among numerous applications, the polymerase chain reaction (PCR) (1,2) provides a convenient means to clone 5' ends of rare mRNAs and to generate cDNA libraries from tissue available in amounts too low to be processed by conventional methods. Basically, the amplification of cDNAs by the PCR requires the availability of the sequences of two stretches of the molecule to be amplified. A sequence can easily be imposed at the 5' end of the first-strand cDNAs (corresponding to the 3' end of the mRNAs) by priming the reverse transcription with a specific primer (for cloning the 5' end of rare messenger) or with an oligonucleotide tailored with a poly (dT) stretch (for cDNA library construction), taking advantage of the poly (A) sequence that is located at the 3' end of mRNAs. Several strategies have been devised to tag the 3' end of the ss-cDNAs (corresponding to the 55' end of the mRNAs). We (3) and others have described strategies based on the addition of a homopolymeric dG (4,5) or dA (6,7) tail using terminal deoxyribonucleotide transferase (TdT) ("anchor-PCR" [4]). However, this strategy has important limitations. The TdT reaction is difficult to control and has a low efficiency (unpublished observations). But most importantly, the return primers containing a homopolymeric (dC or dT) tail generate nonspecific amplifications, a phenomenon that prevents the isolation of low abundance mRNA species and/or interferes with the relative abundance of primary clones in the library. To circumvent these drawbacks, we have used two approaches. First, we devised a strategy based on a cRNA enrichment procedure, which has been useful to eliminate nonspecific-PCR products and to allow detection and cloning of cDNAs of low abundance (3). More recently, to avoid the nonspecific amplification resulting from the annealing of the homopolymeric tail oligonucleotide, we have developed a novel anchoring strategy that is based on the ligation of an oligonucleotide to the 35' end of ss

End-to-end learning for digital hologram reconstruction

Science.gov (United States)

Xu, Zhimin; Zuo, Si; Lam, Edmund Y.

2018-02-01

Digital holography is a well-known method to perform three-dimensional imaging by recording the light wavefront information originating from the object. Not only the intensity, but also the phase distribution of the wavefront can then be computed from the recorded hologram in the numerical reconstruction process. However, the reconstructions via the traditional methods suffer from various artifacts caused by twin-image, zero-order term, and noise from image sensors. Here we demonstrate that an end-to-end deep neural network (DNN) can learn to perform both intensity and phase recovery directly from an intensity-only hologram. We experimentally show that the artifacts can be effectively suppressed. Meanwhile, our network doesn't need any preprocessing for initialization, and is comparably fast to train and test, in comparison with the recently published learning-based method. In addition, we validate that the performance improvement can be achieved by introducing a prior on sparsity.

Sirt6 Promotes DNA End Joining in iPSCs Derived from Old Mice

Directory of Open Access Journals (Sweden)

Wen Chen

2017-03-01

Full Text Available Induced pluripotent stem cells (iPSCs have great potential for treating age-related diseases, but the genome integrity of iPSCs is critically important. Here, we demonstrate that non-homologous end joining (NHEJ, rather than homologous recombination (HR, is less efficient in iPSCs from old mice than young mice. We further find that Sirt6 is downregulated in iPSCs from old mice. Sirt6 directly binds to Ku80 and facilitates the Ku80/DNA-PKcs interaction, thus promoting DNA-PKcs phosphorylation at residue S2056, leading to efficient NHEJ. Rescue experiments show that introducing a combination of Sirt6 and the Yamanaka factors during reprogramming significantly promotes DNA double-strand break (DSB repair by activating NHEJ in iPSCs derived from old mice. Thus, our study suggests a strategy to improve the quality of iPSCs derived from old donors by activating NHEJ and stabilizing the genome.

Advanced Camera Image Cropping Approach for CNN-Based End-to-End Controls on Sustainable Computing

Directory of Open Access Journals (Sweden)

Yunsick Sung

2018-03-01

Full Text Available Recent research on deep learning has been applied to a diversity of fields. In particular, numerous studies have been conducted on self-driving vehicles using end-to-end approaches based on images captured by a single camera. End-to-end controls learn the output vectors of output devices directly from the input vectors of available input devices. In other words, an end-to-end approach learns not by analyzing the meaning of input vectors, but by extracting optimal output vectors based on input vectors. Generally, when end-to-end control is applied to self-driving vehicles, the steering wheel and pedals are controlled autonomously by learning from the images captured by a camera. However, high-resolution images captured from a car cannot be directly used as inputs to Convolutional Neural Networks (CNNs owing to memory limitations; the image size needs to be efficiently reduced. Therefore, it is necessary to extract features from captured images automatically and to generate input images by merging the parts of the images that contain the extracted features. This paper proposes a learning method for end-to-end control that generates input images for CNNs by extracting road parts from input images, identifying the edges of the extracted road parts, and merging the parts of the images that contain the detected edges. In addition, a CNN model for end-to-end control is introduced. Experiments involving the Open Racing Car Simulator (TORCS, a sustainable computing environment for cars, confirmed the effectiveness of the proposed method for self-driving by comparing the accumulated difference in the angle of the steering wheel in the images generated by it with those of resized images containing the entire captured area and cropped images containing only a part of the captured area. The results showed that the proposed method reduced the accumulated difference by 0.839% and 0.850% compared to those yielded by the resized images and cropped images

QoS Modeling for End-to-End Performance Evaluation over Networks with Wireless Access

Directory of Open Access Journals (Sweden)

Gómez Gerardo

2010-01-01

Full Text Available This paper presents an end-to-end Quality of Service (QoS model for assessing the performance of data services over networks with wireless access. The proposed model deals with performance degradation across protocol layers using a bottom-up strategy, starting with the physical layer and moving on up to the application layer. This approach makes it possible to analytically assess performance at different layers, thereby facilitating a possible end-to-end optimization process. As a representative case, a scenario where a set of mobile terminals connected to a streaming server through an IP access node has been studied. UDP, TCP, and the new TCP-Friendly Rate Control (TFRC protocols were analyzed at the transport layer. The radio interface consisted of a variable-rate multiuser and multichannel subsystem, including retransmissions and adaptive modulation and coding. The proposed analytical QoS model was validated on a real-time emulator of an end-to-end network with wireless access and proved to be very useful for the purposes of service performance estimation and optimization.

ABI Base Recall: Automatic Correction and Ends Trimming of DNA Sequences.

Science.gov (United States)

Elyazghi, Zakaria; Yazouli, Loubna El; Sadki, Khalid; Radouani, Fouzia

2017-12-01

Automated DNA sequencers produce chromatogram files in ABI format. When viewing chromatograms, some ambiguities are shown at various sites along the DNA sequences, because the program implemented in the sequencing machine and used to call bases cannot always precisely determine the right nucleotide, especially when it is represented by either a broad peak or a set of overlaying peaks. In such cases, a letter other than A, C, G, or T is recorded, most commonly N. Thus, DNA sequencing chromatograms need manual examination: checking for mis-calls and truncating the sequence when errors become too frequent. The purpose of this paper is to develop a program allowing the automatic correction of these ambiguities. This application is a Web-based program powered by Shiny and runs under R platform for an easy exploitation. As a part of the interface, we added the automatic ends clipping option, alignment against reference sequences, and BLAST. To develop and test our tool, we collected several bacterial DNA sequences from different laboratories within Institut Pasteur du Maroc and performed both manual and automatic correction. The comparison between the two methods was carried out. As a result, we note that our program, ABI base recall, accomplishes good correction with a high accuracy. Indeed, it increases the rate of identity and coverage and minimizes the number of mismatches and gaps, hence it provides solution to sequencing ambiguities and saves biologists' time and labor.

Lithium chloride protects retinal neurocytes from nutrient deprivation by promoting DNA non-homologous end-joining

International Nuclear Information System (INIS)

Zhuang Jing; Li Fan; Liu Xuan; Liu Zhiping; Lin Jianxian; Ge Yihong; Kaminski, Joseph M.; Summers, James Bradley; Wang Zhichong; Ge Jian; Yu Keming

2009-01-01

Lithium chloride is a therapeutic agent for treatment of bipolar affective disorders. Increasing numbers of studies have indicated that lithium has neuroprotective effects. However, the molecular mechanisms underlying the actions of lithium have not been fully elucidated. This study aimed to investigate whether lithium chloride produces neuroprotective function by improving DNA repair pathway in retinal neurocyte. In vitro, the primary cultured retinal neurocytes (85.7% are MAP-2 positive cells) were treated with lithium chloride, then cultured with serum-free media to simulate the nutrient deprived state resulting from ischemic insult. The neurite outgrowth of the cultured cells increased significantly in a dose-dependent manner when exposed to different levels of lithium chloride. Genomic DNA electrophoresis demonstrated greater DNA integrity of retinal neurocytes when treated with lithium chloride as compared to the control. Moreover, mRNA and protein levels of Ligase IV (involved in DNA non-homologous end-joining (NHEJ) pathway) in retinal neurocytes increased with lithium chloride. The end joining activity assay was performed to determine the role of lithium on NHEJ in the presence of extract from retinal neurocytes. The rejoining levels in retinal neurocytes treated with lithium were significantly increased as compared to the control. Furthermore, XRCC4, the Ligase IV partner, and the transcriptional factor, CREB and CTCF, were up-regulated in retinal cells after treating with 1.0 mM lithium chloride. Therefore, our data suggest that lithium chloride protects the retinal neural cells from nutrient deprivation in vitro, which may be similar to the mechanism of cell death in glaucoma. The improvement in DNA repair pathway involving in Ligase IV might have an important role in lithium neuroprotection. This study provides new insights into the neural protective mechanisms of lithium chloride.

Circular myotomy as an aid to resection and end-to-end anastomosis of the esophagus.

Science.gov (United States)

Attum, A A; Hankins, J R; Ngangana, J; McLaughlin, J S

1979-08-01

Segments ranging from 40 to 70% of the thoracic esophagus were resected in 80 mongrel dogs. End-to-end anastomosis was effected after circular myotomy either proximal or distal, or both proximal and distal, to the anastomosis. Among dogs undergoing resection of 60% of the esophagus, distal myotomy enabled 6 of 8 animals to survive, and combined proximal and distal myotomy permitted 8 of 10 to survive. Cineesophagography was performed in a majority of the 50 surviving animals and showed no appreciable delay of peristalsis at the myotomy sites. When these sites were examined at postmortem examination up to 13 months after operation, 1 dog showed a small diverticulum but none showed dilatation or stricture. It is concluded that circular myotomy holds real promise as a means of extending the clinical application of esophageal resection with end-to-end anastomosis.

Increasing operations profitability using an end-to-end, wireless internet, gas monitoring system

Energy Technology Data Exchange (ETDEWEB)

McDougall, M. [Northrock Resources Ltd., AB (Canada); Benterud, K. [zed.i solutions, inc., Calgary, AB (Canada)

2004-10-01

Implementation by Northrock Resources Ltd., a wholly-owned subsidiary of Unocal Corporation, of a fully integrated end-to-end gas measurement and production analysis system, is discussed. The system, dubbed Smart-Alek(TM), utilizes public wireless communications and a web browser only delivery system to provide seamless well visibility to a desk-top computer. Smart-Alek(TM) is an example of a new type of end-to-end electronic gas flow measurement system, known as FINE(TM), which is an acronym for Field Intelligence Network and End-User Interface. The system delivers easy-to-use, complete, reliable and cost effective production information, far more effective than is possible to obtain with conventional SCADA technology. By installing the system, Northrock was able to increase gas volumes with more accurate electronic flow measurement in place of mechanical charts, with very low technical maintenance, and at a reduced operating cost. It is emphasized that deploying the technology alone will produce only partial benefits; to realize full benefits it is also essential to change grass roots operating practices, aiming at timely decision-making at the field level. 5 refs., 5 figs.

The endless tale of non-homologous end-joining.

Science.gov (United States)

Weterings, Eric; Chen, David J

2008-01-01

DNA double-strand breaks (DSBs) are introduced in cells by ionizing radiation and reactive oxygen species. In addition, they are commonly generated during V(D)J recombination, an essential aspect of the developing immune system. Failure to effectively repair these DSBs can result in chromosome breakage, cell death, onset of cancer, and defects in the immune system of higher vertebrates. Fortunately, all mammalian cells possess two enzymatic pathways that mediate the repair of DSBs: homologous recombination and non-homologous end-joining (NHEJ). The NHEJ process utilizes enzymes that capture both ends of the broken DNA molecule, bring them together in a synaptic DNA-protein complex, and finally repair the DNA break. In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented.

Mung Bean nuclease mapping of RNAs 3' end

Directory of Open Access Journals (Sweden)

Barbieri Rainer

2009-05-01

Full Text Available Abstract A method is described that allows an accurate mapping of 3' ends of RNAs. In this method a labeled DNA probe, containing the presumed 3' end of the RNA under analysis is allowed to anneals to the RNA itself. Mung-bean nuclease is then used to digest single strands of both RNA and DNA. Electrophoretic fractionation of "protected" undigested, labeled DNA is than performed using a sequence reaction of a known DNA as length marker. This procedure was applied to the analysis of both a polyA RNA (Interleukin 10 mRNA and non polyA RNAs (sea urchin 18S and 26S rRNAs. This method might be potentially relevant for the evaluation of the role of posttrascriptional control of IL-10 in the pathogenesis of the immune and inflammatory mediated diseases associated to ageing. This might allow to develop new strategies to approach to the diagnosis and therapy of age related diseases.

Kinetics of end-to-end collision in short single-stranded nucleic acids.

Science.gov (United States)

Wang, Xiaojuan; Nau, Werner M

2004-01-28

A novel fluorescence-based method, which entails contact quenching of the long-lived fluorescent state of 2,3-diazabicyclo[2.2.2]-oct-2-ene (DBO), was employed to measure the kinetics of end-to-end collision in short single-stranded oligodeoxyribonucleotides of the type 5'-DBO-(X)n-dG with X = dA, dC, dT, or dU and n = 2 or 4. The fluorophore was covalently attached to the 5' end and dG was introduced as an efficient intrinsic quencher at the 3' terminus. The end-to-end collision rates, which can be directly related to the efficiency of intramolecular fluorescence quenching, ranged from 0.1 to 9.0 x 10(6) s(-1). They were strongly dependent on the strand length, the base sequence, as well as the temperature. Oligonucleotides containing dA in the backbone displayed much slower collision rates and significantly higher positive activation energies than strands composed of pyrimidine bases, suggesting a higher intrinsic rigidity of oligoadenylate. Comparison of the measured collision rates in short single-stranded oligodeoxyribonucleotides with the previously reported kinetics of hairpin formation indicates that the intramolecular collision is significantly faster than the nucleation step of hairpin closing. This is consistent with the configurational diffusion model suggested by Ansari et al. (Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc.Natl. Acad. Sci. USA 2001, 98, 7771-7776), in which the formation of misfolded loops is thought to slow hairpin formation.

Specific interaction of the nonstructural protein NS1 of minute virus of mice (MVM) with [ACCA](2) motifs in the centre of the right-end MVM DNA palindrome induces hairpin-primed viral DNA replication.

Science.gov (United States)

Willwand, Kurt; Moroianu, Adela; Hörlein, Rita; Stremmel, Wolfgang; Rommelaere, Jean

2002-07-01

The linear single-stranded DNA genome of minute virus of mice (MVM) is replicated via a double-stranded replicative form (RF) intermediate DNA. Amplification of viral RF DNA requires the structural transition of the right-end palindrome from a linear duplex into a double-hairpin structure, which serves for the repriming of unidirectional DNA synthesis. This conformational transition was found previously to be induced by the MVM nonstructural protein NS1. Elimination of the cognate NS1-binding sites, [ACCA](2), from the central region of the right-end palindrome next to the axis of symmetry was shown to markedly reduce the efficiency of hairpin-primed DNA replication, as measured in a reconstituted in vitro replication system. Thus, [ACCA](2) sequence motifs are essential as NS1-binding elements in the context of the structural transition of the right-end MVM palindrome.

Outcome of end-to-end urethroplasty in post-traumatic stricture of posterior urethra.

Science.gov (United States)

Hussain, Akbar; Pansota, Mudassar Saeed; Rasool, Mumtaz; Tabassum, Shafqat Ali; Ahmad, Iftikhar; Saleem, Muhammad Shahzad

2013-04-01

To determine the outcome of delayed end-to-end anastomotic urethroplasty in blind post-traumatic stricture of posterior urethra at our setup. Case series. Department of Urology and Renal Transplantation, Quaid-e-Azam Medical College/Bahawal Victoria Hospital, Bahawalpur, from January 2009 to June 2011. Adult patients with completely obliterated post-traumatic stricture of posterior urethra ≤ 2 cm were included in the study. Patients with post-prostatectomy (TUR-P, TVP) stricture, stricture more than 2 cm in size or patients of stricture with neurogenic bladder and patients with any perineal disease were excluded from the study. Retrograde urethrogram and voiding cysto-urethrogram was done in every patient to assess stricture length and location. Stricture excision and delayed end-to-end anastomosis of urethra with spatulation was performed in every patient. Minimum followup period was 6 months and maximum 18 months. There were 26 cases with road traffic accident (indirect) and 14 had history of fall/direct trauma to perineum or urethra. Majority of the patients (57.5%) were between 16 to 30 years of age. Twelve (30.0%) patients developed complications postoperatively. Early complications of wound infection occurred in 01 (2.5%) patient. Late complications were seen in 11 (27.5%) patients i.e. stricture recurrence in 7 (17.5%), erectile dysfunction in 2 (5.0%), urethrocutaneous fistula and urinary incontinence in one patient (2.5%) each. Success rate was 70.0% initially and 87.5% overall. Delayed end-to-end anastomotic urethroplasty is an effective procedure for traumatic posterior urethral strictures with success rate of about 87.5%.

Analytical Framework for End-to-End Delay Based on Unidirectional Highway Scenario

Directory of Open Access Journals (Sweden)

Aslinda Hassan

2015-01-01

Full Text Available In a sparse vehicular ad hoc network, a vehicle normally employs a carry and forward approach, where it holds the message it wants to transmit until the vehicle meets other vehicles or roadside units. A number of analyses in the literature have been done to investigate the time delay when packets are being carried by vehicles on both unidirectional and bidirectional highways. However, these analyses are focusing on the delay between either two disconnected vehicles or two disconnected vehicle clusters. Furthermore, majority of the analyses only concentrate on the expected value of the end-to-end delay when the carry and forward approach is used. Using regression analysis, we establish the distribution model for the time delay between two disconnected vehicle clusters as an exponential distribution. Consequently, a distribution is newly derived to represent the number of clusters on a highway using a vehicular traffic model. From there, we are able to formulate end-to-end delay model which extends the time delay model for two disconnected vehicle clusters to multiple disconnected clusters on a unidirectional highway. The analytical results obtained from the analytical model are then validated through simulation results.

Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome.

Science.gov (United States)

Shen, Weiran; Deng, Xuefeng; Zou, Wei; Engelhardt, John F; Yan, Ziying; Qiu, Jianming

2016-09-01

Parvoviruses are single-stranded DNA viruses that use the palindromic structures at the ends of the viral genome for their replication. The mechanism of parvovirus replication has been studied mostly in the dependoparvovirus adeno-associated virus 2 (AAV2) and the protoparvovirus minute virus of mice (MVM). Here, we used human bocavirus 1 (HBoV1) to understand the replication mechanism of bocaparvovirus. HBoV1 is pathogenic to humans, causing acute respiratory tract infections, especially in young children under 2 years old. By using the duplex replicative form of the HBoV1 genome in human embryonic kidney 293 (HEK293) cells, we identified the HBoV1 minimal replication origin at the right-end hairpin (OriR). Mutagenesis analyses confirmed the putative NS1 binding and nicking sites within the OriR. Of note, unlike the large nonstructural protein (Rep78/68 or NS1) of other parvoviruses, HBoV1 NS1 did not specifically bind OriR in vitro, indicating that other viral and cellular components or the oligomerization of NS1 is required for NS1 binding to the OriR. In vivo studies demonstrated that residues responsible for NS1 binding and nicking are within the origin-binding domain. Further analysis identified that the small nonstructural protein NP1 is required for HBoV1 DNA replication at OriR. NP1 and other viral nonstructural proteins (NS1 to NS4) colocalized within the viral DNA replication centers in both OriR-transfected cells and virus-infected cells, highlighting a direct involvement of NP1 in viral DNA replication at OriR. Overall, our study revealed the characteristics of HBoV1 DNA replication at OriR, suggesting novel characteristics of autonomous parvovirus DNA replication. Human bocavirus 1 (HBoV1) causes acute respiratory tract infections in young children. The duplex HBoV1 genome replicates in HEK293 cells and produces progeny virions that are infectious in well-differentiated airway epithelial cells. A recombinant AAV2 vector pseudotyped with an HBoV1

SPoRT - An End-to-End R2O Activity

Science.gov (United States)

Jedlovec, Gary J.

2009-01-01

Established in 2002 to demonstrate the weather and forecasting application of real-time EOS measurements, the Short-term Prediction Research and Transition (SPoRT) program has grown to be an end-to-end research to operations activity focused on the use of advanced NASA modeling and data assimilation approaches, nowcasting techniques, and unique high-resolution multispectral observational data applications from EOS satellites to improve short-term weather forecasts on a regional and local scale. SPoRT currently partners with several universities and other government agencies for access to real-time data and products, and works collaboratively with them and operational end users at 13 WFOs to develop and test the new products and capabilities in a "test-bed" mode. The test-bed simulates key aspects of the operational environment without putting constraints on the forecaster workload. Products and capabilities which show utility in the test-bed environment are then transitioned experimentally into the operational environment for further evaluation and assessment. SPoRT focuses on a suite of data and products from MODIS, AMSR-E, and AIRS on the NASA Terra and Aqua satellites, and total lightning measurements from ground-based networks. Some of the observations are assimilated into or used with various versions of the WRF model to provide supplemental forecast guidance to operational end users. SPoRT is enhancing partnerships with NOAA / NESDIS for new product development and data access to exploit the remote sensing capabilities of instruments on the NPOESS satellites to address short term weather forecasting problems. The VIIRS and CrIS instruments on the NPP and follow-on NPOESS satellites provide similar observing capabilities to the MODIS and AIRS instruments on Terra and Aqua. SPoRT will be transitioning existing and new capabilities into the AWIIPS II environment to continue the continuity of its activities.

SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

Science.gov (United States)

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

The Ku70/80 ring in Non-Homologous End-Joining

DEFF Research Database (Denmark)

Kragelund, Birthe Brandt; Weterings, Eric; Hartmann-Petersen, Rasmus

2016-01-01

/80 heterodimer is a key-player in the NHEJ pathway and binds to DNA termini with high affinity, where it helps to protect DNA ends from degradation and to recruit other NHEJ factors required for repair. The mechanism of Ku70/80 detachment from the DNA helix after completion of DNA repair is incompletely......Non-homologous end-joining (NHEJ) is an essential DNA double strand break repair pathway during all cell cycle stages. Deficiency in NHEJ factors can lead to accumulation of unrepaired DNA breaks or faulty DNA repair, which may ultimately result in cell death, senescence or carcinogenesis. The Ku70...... understood. Some data suggest that certain DNA repair factors are ubiquitylated and targeted for proteasomal degradation after repair. Recent studies suggest that Ku80 is conjugated to lysine48-linked ubiquitin chains by the Skp1-Cullin-F-box (SCF) complex and/or the RING finger protein 8 (RNF8) ubiquitin-protein...

End-to-end operations at the National Radio Astronomy Observatory

Science.gov (United States)

Radziwill, Nicole M.

2008-07-01

In 2006 NRAO launched a formal organization, the Office of End to End Operations (OEO), to broaden access to its instruments (VLA/EVLA, VLBA, GBT and ALMA) in the most cost-effective ways possible. The VLA, VLBA and GBT are mature instruments, and the EVLA and ALMA are currently under construction, which presents unique challenges for integrating software across the Observatory. This article 1) provides a survey of the new developments over the past year, and those planned for the next year, 2) describes the business model used to deliver many of these services, and 3) discusses the management models being applied to ensure continuous innovation in operations, while preserving the flexibility and autonomy of telescope software development groups.

Outcome of end-to-end urethroplasty in post-traumatic stricture of posterior urethra

International Nuclear Information System (INIS)

Hussain, A.; Pansota, M. S.; Rasool, M.; Tabassum, S. A.; Ahmad, I.; Saleem, M. S.

2013-01-01

Objective: To determine the outcome of delayed end-to-end anastomotic urethroplasty in blind post-traumatic stricture of posterior urethra at our setup. Study Design: Case series. Place and Duration of Study: Department of Urology and Renal Transplantation, Quaid-e-Azam Medical College/ Bahawal Victoria Hospital, Bahawalpur, from January 2009 to June 2011. Methodology: Adult patients with completely obliterated post-traumatic stricture of posterior urethra 2 cm/sup 2/ were included in the study. Patients with post-prostatectomy (TUR-P, TVP) stricture, stricture more than 2 cm in size or patients of stricture with neurogenic bladder and patients with any perineal disease were excluded from the study. Retrograde urethrogram and voiding cysto-urethrogram was done in every patient to assess stricture length and location. Stricture excision and delayed end-to-end anastomosis of urethra with spatulation was performed in every patient. Minimum followup period was 6 months and maximum 18 months. Results: There were 26 cases with road traffic accident (indirect) and 14 had history of fall/direct trauma to perineum or urethra. Majority of the patients (57.5%) were between 16 to 30 years of age. Twelve (30.0%) patients developed complications postoperatively. Early complications of wound infection occurred in 01 (2.5%) patient. Late complications were seen in 11 (27.5%) patients i.e. stricture recurrence in 7 (17.5%), erectile dysfunction in 2 (5.0%), urethrocutaneous fistula and urinary incontinence in one patient (2.5%) each. Success rate was 70.0% initially and 87.5% overall. Conclusion: Delayed end-to-end anastomotic urethroplasty is an effective procedure for traumatic posterior urethral strictures with success rate of about 87.5%. (author)

Outcome of end-to-end urethroplasty in post-traumatic stricture of posterior urethra

Energy Technology Data Exchange (ETDEWEB)

Hussain, A.; Pansota, M. S.; Rasool, M.; Tabassum, S. A.; Ahmad, I.; Saleem, M. S. [Bahawal Victoria Hospital, Bahawalpur (Pakistan). Dept. of Urology

2013-04-15

Objective: To determine the outcome of delayed end-to-end anastomotic urethroplasty in blind post-traumatic stricture of posterior urethra at our setup. Study Design: Case series. Place and Duration of Study: Department of Urology and Renal Transplantation, Quaid-e-Azam Medical College/ Bahawal Victoria Hospital, Bahawalpur, from January 2009 to June 2011. Methodology: Adult patients with completely obliterated post-traumatic stricture of posterior urethra 2 cm/sup 2/ were included in the study. Patients with post-prostatectomy (TUR-P, TVP) stricture, stricture more than 2 cm in size or patients of stricture with neurogenic bladder and patients with any perineal disease were excluded from the study. Retrograde urethrogram and voiding cysto-urethrogram was done in every patient to assess stricture length and location. Stricture excision and delayed end-to-end anastomosis of urethra with spatulation was performed in every patient. Minimum followup period was 6 months and maximum 18 months. Results: There were 26 cases with road traffic accident (indirect) and 14 had history of fall/direct trauma to perineum or urethra. Majority of the patients (57.5%) were between 16 to 30 years of age. Twelve (30.0%) patients developed complications postoperatively. Early complications of wound infection occurred in 01 (2.5%) patient. Late complications were seen in 11 (27.5%) patients i.e. stricture recurrence in 7 (17.5%), erectile dysfunction in 2 (5.0%), urethrocutaneous fistula and urinary incontinence in one patient (2.5%) each. Success rate was 70.0% initially and 87.5% overall. Conclusion: Delayed end-to-end anastomotic urethroplasty is an effective procedure for traumatic posterior urethral strictures with success rate of about 87.5%. (author)

QoC-based Optimization of End-to-End M-Health Data Delivery Services

NARCIS (Netherlands)

Widya, I.A.; van Beijnum, Bernhard J.F.; Salden, Alfons

2006-01-01

This paper addresses how Quality of Context (QoC) can be used to optimize end-to-end mobile healthcare (m-health) data delivery services in the presence of alternative delivery paths, which is quite common in a pervasive computing and communication environment. We propose min-max-plus based

Designing EEG Neurofeedback Procedures to Enhance Open-Ended versus Closed-Ended Creative Potentials

Science.gov (United States)

Lin, Wei-Lun; Shih, Yi-Ling

2016-01-01

Recent empirical evidence demonstrated that open-ended creativity (which refers to creativity measures that require various and numerous responses, such as divergent thinking) correlated with alpha brain wave activation, whereas closed-ended creativity (which refers to creativity measures that ask for one final correct answer, such as insight…

Multi-geohazards of Ende city area

Directory of Open Access Journals (Sweden)

Igan Supriatman Sutawidjaja

2014-06-01

Full Text Available http://dx.doi.org/10.17014/ijog.vol2no4.20073The Ende City is a steep mountainous area, of which the height of their peaks are above 1500 m asl. It has the limited extent of plain places, without coastal plains. Due to this condition, large parts of the area are vulnerable to mass-movements mainly debris flows, rock-falls and shallow translational and rotational landslides. On the other hand, Flores Island is a segment of the Banda Arc that contains eleven very active volcanoes and numerous inactive volcanic cones. Two of them, Mount Iya and Mount Kelimutu are included to Ende Regency. The northern foot of Mount Iya is only about 1 km away from the southern outskirts of Ende city. But the presence of Mount Meja and Mount Roja as the barrier, and the orientation of the active crater (K2, the highly explosive eruption of Iya Volcano may not directly endanger the city of Ende. Most pyroclastic flows of previous eruptions and other eruptive material emplaced into the sea, but due to a short horizontal distance between Mount Iya and Ende City, the ejected rock fragments can endanger the city of Ende especially its southern parts. A crack has developed around the active crater (K2 of Iya Volcano. It seems that the crack indicates a major weakness within the volcano, which could result in a giant landslide, entering the sea in future eruptions of Iya Volcano. The kinetic energy which is transmitted through the water may probably generate a tsunami. The Ende City also experienced significant damages in the 1992 earthquake. Luckily this city is located on a solid rock instead of alluvial sediments which can potentially undergo liquefaction.  

Physical oceanography - Developing end-to-end models of the California Current Large Marine Ecosystem

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

Hybrid monitoring scheme for end-to-end performance enhancement of multicast-based real-time media

Science.gov (United States)

Park, Ju-Won; Kim, JongWon

2004-10-01

As real-time media applications based on IP multicast networks spread widely, end-to-end QoS (quality of service) provisioning for these applications have become very important. To guarantee the end-to-end QoS of multi-party media applications, it is essential to monitor the time-varying status of both network metrics (i.e., delay, jitter and loss) and system metrics (i.e., CPU and memory utilization). In this paper, targeting the multicast-enabled AG (Access Grid) a next-generation group collaboration tool based on multi-party media services, the applicability of hybrid monitoring scheme that combines active and passive monitoring is investigated. The active monitoring measures network-layer metrics (i.e., network condition) with probe packets while the passive monitoring checks both application-layer metrics (i.e., user traffic condition by analyzing RTCP packets) and system metrics. By comparing these hybrid results, we attempt to pinpoint the causes of performance degradation and explore corresponding reactions to improve the end-to-end performance. The experimental results show that the proposed hybrid monitoring can provide useful information to coordinate the performance improvement of multi-party real-time media applications.

Lower end fitting debris collector and end cap spacer grid

International Nuclear Information System (INIS)

Bryan, W.J.

1990-01-01

This patent describes a nuclear reactor having fuel assemblies including an upper end fitting and spaced nuclear fuel rod spacer grids for supporting and spacing a plurality of elongated nuclear fuel rods. Each includes a hollow active portion of nuclear fuel filled cladding intermediate the rod ends and tapering end cap of solid material with a circumferential groove on the rod end which first encounters reactor coolant flow, a lower end filtering debris collector and end cap spacer grid for capturing and retaining deleterious debris carried by reactor coolant before it enters the active region of a fuel assembly and creates fuel rod cladding damage

Plugger guide for aligning an end plug and a fuel rod tube end

International Nuclear Information System (INIS)

Klapper, K.K.; Boatwright, D.A.

1987-01-01

A pin driving tool is described for inserting or removing pins from teeth on a digging means, comprising: fuel rod tube toward an end plug for application of the end plug into the tube end, the apparatus comprising: (a) a guide housing having an elongated central longitudinal bore with one end for receiving the end plug and an opposite end for receiving the fuel rod tube end; (b) sets of rolling elements disposed in the housing at axially spaced positions along and about the bore thereof. The rolling elements in each set are positioned in fixed relation with respect to one another to receive the fuel rod tube end therebetween and align the tube end with the end plug as the tube end is moved through the bore and into engagement with the end plug; and (c) retaining means disposed adjacent to the open end of the housing bore for engaging the end plug so as to maintain it in a stationary seated position at the one end of the housing bore

Open-ended education

DEFF Research Database (Denmark)

Nørgård, Rikke Toft; Paaskesen, Rikke Berggreen

2016-01-01

THE ARTICLE DESCRIBES OPEN-ENDED EDUCATION FOR 21ST CENTURY LEARNING AS THE COMING TOGETHER OF OPEN-ENDED TECHNOLOGY, OPEN-ENDED PROJECTS, AND OPEN-ENDED INSTITUTIONS IN WAYS THAT FOSTER AND PROMOTE FUTURE EDUCATION FOR CITIZENSHIP IN SOCIETY. THROUGH THE CASE OF THE CODING PIRATES FUTURE ISLAND......, THE ARTICLE DEMONSTRATES HOW OPEN-ENDED EDUCATION CAN BE PRACTICED TO FOSTER AND PROMOTE TECHNOLOGICAL IMAGINATION, ENTERPRISING, AND PARTICIPATION. THIS PRACTICE IS THEN DEVELOPED INTO A THEORETICAL MODEL FOR THE CONCEPT OF OPEN-ENDED EDUCATION AS A WAY OF AND FRAMEWORK FOR PRACTICING FUTURE EDUCATION FOR 21......ST CENTURY LEARNING WITH NEW TECHNOLOGIES. THE ARTICLE PRESENTS AN ANSWER TO THE CALL FOR 21ST CENTURY LEARNING AS THOROUGHLY COLLABORATIVE, COMMUNICATIVE, CREATIVE, AND CRITICALLY REFLECTIVE THROUGH THE CASE AND THE CONCEPT OF OPEN-ENDED EDUCATION. IT OUTLINES THE IMPLICATIONS OF THIS CALL...

Screening California Current fishery management scenarios using the Atlantis end-to-end ecosystem model

Science.gov (United States)

Kaplan, Isaac C.; Horne, Peter J.; Levin, Phillip S.

2012-09-01

End-to-end marine ecosystem models link climate and oceanography to the food web and human activities. These models can be used as forecasting tools, to strategically evaluate management options and to support ecosystem-based management. Here we report the results of such forecasts in the California Current, using an Atlantis end-to-end model. We worked collaboratively with fishery managers at NOAA’s regional offices and staff at the National Marine Sanctuaries (NMS) to explore the impact of fishery policies on management objectives at different spatial scales, from single Marine Sanctuaries to the entire Northern California Current. In addition to examining Status Quo management, we explored the consequences of several gear switching and spatial management scenarios. Of the scenarios that involved large scale management changes, no single scenario maximized all performance metrics. Any policy choice would involve trade-offs between stakeholder groups and policy goals. For example, a coast-wide 25% gear shift from trawl to pot or longline appeared to be one possible compromise between an increase in spatial management (which sacrificed revenue) and scenarios such as the one consolidating bottom impacts to deeper areas (which did not perform substantially differently from Status Quo). Judged on a coast-wide scale, most of the scenarios that involved minor or local management changes (e.g. within Monterey Bay NMS only) yielded results similar to Status Quo. When impacts did occur in these cases, they often involved local interactions that were difficult to predict a priori based solely on fishing patterns. However, judged on the local scale, deviation from Status Quo did emerge, particularly for metrics related to stationary species or variables (i.e. habitat and local metrics of landed value or bycatch). We also found that isolated management actions within Monterey Bay NMS would cause local fishers to pay a cost for conservation, in terms of reductions in landed

Financing the End-to-end Supply Chain: A Reference Guide to Supply Chain Finance

OpenAIRE

Templar, Simon; Hofmann, Erik; Findlay, Charles

2016-01-01

Financing the End to End Supply Chain provides readers with a real insight into the increasingly important area of supply chain finance. It demonstrates the importance of the strategic relationship between the physical supply of goods and services and the associated financial flows. The book provides a clear introduction, demonstrating the importance of the strategic relationship between supply chain and financial communities within an organization. It contains vital information on how supply...

End-to-End Airplane Detection Using Transfer Learning in Remote Sensing Images

Directory of Open Access Journals (Sweden)

Zhong Chen

2018-01-01

Full Text Available Airplane detection in remote sensing images remains a challenging problem due to the complexity of backgrounds. In recent years, with the development of deep learning, object detection has also obtained great breakthroughs. For object detection tasks in natural images, such as the PASCAL (Pattern Analysis, Statistical Modelling and Computational Learning VOC (Visual Object Classes Challenge, the major trend of current development is to use a large amount of labeled classification data to pre-train the deep neural network as a base network, and then use a small amount of annotated detection data to fine-tune the network for detection. In this paper, we use object detection technology based on deep learning for airplane detection in remote sensing images. In addition to using some characteristics of remote sensing images, some new data augmentation techniques have been proposed. We also use transfer learning and adopt a single deep convolutional neural network and limited training samples to implement end-to-end trainable airplane detection. Classification and positioning are no longer divided into multistage tasks; end-to-end detection attempts to combine them for optimization, which ensures an optimal solution for the final stage. In our experiment, we use remote sensing images of airports collected from Google Earth. The experimental results show that the proposed algorithm is highly accurate and meaningful for remote sensing object detection.

Network analysis on skype end-to-end video quality

NARCIS (Netherlands)

Exarchakos, Georgios; Druda, Luca; Menkovski, Vlado; Liotta, Antonio

2015-01-01

Purpose – This paper aims to argue on the efficiency of Quality of Service (QoS)-based adaptive streamingwith regards to perceived quality Quality of Experience (QoE). Although QoS parameters are extensivelyused even by high-end adaptive streaming algorithms, achieved QoE fails to justify their use

Modeling and simulation of satellite subsystems for end-to-end spacecraft modeling

Science.gov (United States)

Schum, William K.; Doolittle, Christina M.; Boyarko, George A.

2006-05-01

During the past ten years, the Air Force Research Laboratory (AFRL) has been simultaneously developing high-fidelity spacecraft payload models as well as a robust distributed simulation environment for modeling spacecraft subsystems. Much of this research has occurred in the Distributed Architecture Simulation Laboratory (DASL). AFRL developers working in the DASL have effectively combined satellite power, attitude pointing, and communication link analysis subsystem models with robust satellite sensor models to create a first-order end-to-end satellite simulation capability. The merging of these two simulation areas has advanced the field of spacecraft simulation, design, and analysis, and enabled more in-depth mission and satellite utility analyses. A core capability of the DASL is the support of a variety of modeling and analysis efforts, ranging from physics and engineering-level modeling to mission and campaign-level analysis. The flexibility and agility of this simulation architecture will be used to support space mission analysis, military utility analysis, and various integrated exercises with other military and space organizations via direct integration, or through DOD standards such as Distributed Interaction Simulation. This paper discusses the results and lessons learned in modeling satellite communication link analysis, power, and attitude control subsystems for an end-to-end satellite simulation. It also discusses how these spacecraft subsystem simulations feed into and support military utility and space mission analyses.

Foraging conditions 'at the end of the world' in the context of long-distance migration and population declines in red knots

NARCIS (Netherlands)

Escudero, Graciela; Navedo, Juan G.; Piersma, Theunis; De Goeij, Petra; Edelaar, Pim

The long-distance migrant red knot (Calidris canutus ssp. rufa Scolopacidae) alternates between the northern and southern ends of the New World, one of the longest yearly migrations of any bird and paradoxically overflying apparently suitable habitat at lower latitudes. This subspecies is sharply

Foraging conditions 'at the end of the world' in the context of long-distance migration and population declines in red knots

NARCIS (Netherlands)

Escudero, G.; Navedo, J.G.; Piersma, T.; de Goeij, P.; Edelaar, P.

2012-01-01

The long-distance migrant red knot (Calidris canutus ssp. rufa Scolopacidae) alternates between the northern and southern ends of the New World, one of the longest yearly migrations of any bird and paradoxically overflying apparently suitable habitat at lower latitudes. This subspecies is sharply

Classroom-based and distance learning education and training courses in end-of-life care for health and social care staff: a systematic review.

Science.gov (United States)

Pulsford, David; Jackson, Georgina; O'Brien, Terri; Yates, Sue; Duxbury, Joy

2013-03-01

Staff from a range of health and social care professions report deficits in their knowledge and skills when providing end-of-life and palliative care, and education and training has been advocated at a range of levels. To review the literature related to classroom-based and distance learning education and training initiatives for health and social care staff in end-of-life and palliative care, in terms of their target audience, extent, modes of delivery, content and teaching and learning strategies, and to identify the most effective educational strategies for enhancing care. A systematic review of the literature evaluating classroom-based and distance learning education and training courses for health and social care staff in end-of-life and palliative care. Online databases CINAHL, MEDLINE, EMBASE and PSYCHINFO between January 2000 and July 2010. Studies were selected that discussed specific education and training initiatives and included pre-and post-test evaluation of participants' learning. 30 studies met eligibility criteria. The majority reported successful outcomes, though there were some exceptions. Level of prior experience and availability of practice reinforcement influenced learning. Participative and interactive learning strategies were predominantly used along with discussion of case scenarios. Multi-professional learning was infrequently reported and service user and carer input to curriculum development and delivery was reported in only one study. Classroom-based education and training is useful for enhancing professionals' skills and perceived preparedness for delivering end-of-life care but should be reinforced by actual practice experience.

Providing end-to-end QoS for multimedia applications in 3G wireless networks

Science.gov (United States)

Guo, Katherine; Rangarajan, Samapth; Siddiqui, M. A.; Paul, Sanjoy

2003-11-01

As the usage of wireless packet data services increases, wireless carriers today are faced with the challenge of offering multimedia applications with QoS requirements within current 3G data networks. End-to-end QoS requires support at the application, network, link and medium access control (MAC) layers. We discuss existing CDMA2000 network architecture and show its shortcomings that prevent supporting multiple classes of traffic at the Radio Access Network (RAN). We then propose changes in RAN within the standards framework that enable support for multiple traffic classes. In addition, we discuss how Session Initiation Protocol (SIP) can be augmented with QoS signaling for supporting end-to-end QoS. We also review state of the art scheduling algorithms at the base station and provide possible extensions to these algorithms to support different classes of traffic as well as different classes of users.

End-to-End Adversarial Retinal Image Synthesis.

Science.gov (United States)

Costa, Pedro; Galdran, Adrian; Meyer, Maria Ines; Niemeijer, Meindert; Abramoff, Michael; Mendonca, Ana Maria; Campilho, Aurelio

2018-03-01

In medical image analysis applications, the availability of the large amounts of annotated data is becoming increasingly critical. However, annotated medical data is often scarce and costly to obtain. In this paper, we address the problem of synthesizing retinal color images by applying recent techniques based on adversarial learning. In this setting, a generative model is trained to maximize a loss function provided by a second model attempting to classify its output into real or synthetic. In particular, we propose to implement an adversarial autoencoder for the task of retinal vessel network synthesis. We use the generated vessel trees as an intermediate stage for the generation of color retinal images, which is accomplished with a generative adversarial network. Both models require the optimization of almost everywhere differentiable loss functions, which allows us to train them jointly. The resulting model offers an end-to-end retinal image synthesis system capable of generating as many retinal images as the user requires, with their corresponding vessel networks, by sampling from a simple probability distribution that we impose to the associated latent space. We show that the learned latent space contains a well-defined semantic structure, implying that we can perform calculations in the space of retinal images, e.g., smoothly interpolating new data points between two retinal images. Visual and quantitative results demonstrate that the synthesized images are substantially different from those in the training set, while being also anatomically consistent and displaying a reasonable visual quality.

Segregation of chain ends to polymer melt surfaces and interfaces

International Nuclear Information System (INIS)

Zhao, W.; Zhao, X.; Rafailovich, M.H.; Sokolov, J.; Composto, R.J.; Smith, S.D.; Satkowski, M.; Russell, T.P.; Dozier, W.D.; Mansfield, T.

1993-01-01

The conformation of polymer chains in the melt near an impenetrable boundary has recently been studied by molecular dynamics and off-lattice Monte Carlo simulations. Both types of calculations show an enhancement of the chain end density within a distance of approximately two polymer segment lengths of the interface relative to the bulk. In the absence of preferential interactions between monomers and the interface, the segregation arises from minimizing the loss of conformational entropy near an impenetrable boundary; i.e., by positioning an end near the surface, only one unit rather than two is reflected. In order to obtain an experimental measure of this effect, monodisperse polystyrene (PS) chains of molecular weight 63 000 with short blocks of deuterated polystyrene (dPS) at each end were prepared. The block length was kept as short as possible, while yet producing sufficient neutron scattering contrast in order to minimize any preferential surface segregation due to isotopic effects. The synthesis was carried out via living anionic polymerization of a purified styrene monomer in cyclohexane at 60 C, utilizing sec-butyllithium as the initiator. The process was terminated using degassed methanol

Induction and repair of DNA double strand breaks: The increasing spectrum of non-homologous end joining pathways

International Nuclear Information System (INIS)

Mladenov, Emil; Iliakis, George

2011-01-01

A defining characteristic of damage induced in the DNA by ionizing radiation (IR) is its clustered character that leads to the formation of complex lesions challenging the cellular repair mechanisms. The most widely investigated such complex lesion is the DNA double strand break (DSB). DSBs undermine chromatin stability and challenge the repair machinery because an intact template strand is lacking to assist restoration of integrity and sequence in the DNA molecule. Therefore, cells have evolved a sophisticated machinery to detect DSBs and coordinate a response on the basis of inputs from various sources. A central function of cellular responses to DSBs is the coordination of DSB repair. Two conceptually different mechanisms can in principle remove DSBs from the genome of cells of higher eukaryotes. Homologous recombination repair (HRR) uses as template a homologous DNA molecule and is therefore error-free; it functions preferentially in the S and G2 phases. Non-homologous end joining (NHEJ), on the other hand, simply restores DNA integrity by joining the two ends, is error prone as sequence is only fortuitously preserved and active throughout the cell cycle. The basis of DSB repair pathway choice remains unknown, but cells of higher eukaryotes appear programmed to utilize preferentially NHEJ. Recent work suggests that when the canonical DNA-PK dependent pathway of NHEJ (D-NHEJ), becomes compromised an alternative NHEJ pathway and not HRR substitutes in a quasi-backup function (B-NHEJ). Here, we outline aspects of DSB induction by IR and review the mechanisms of their processing in cells of higher eukaryotes. We place particular emphasis on backup pathways of NHEJ and summarize their increasing significance in various cellular processes, as well as their potential contribution to carcinogenesis.

Ferromagnetic interaction in an asymmetric end-to-end azido double-bridged copper(II) dinuclear complex: a combined structure, magnetic, polarized neutron diffraction and theoretical study.

Science.gov (United States)

Aronica, Christophe; Jeanneau, Erwann; El Moll, Hani; Luneau, Dominique; Gillon, Béatrice; Goujon, Antoine; Cousson, Alain; Carvajal, Maria Angels; Robert, Vincent

2007-01-01

A new end-to-end azido double-bridged copper(II) complex [Cu(2)L(2)(N(3))2] (1) was synthesized and characterized (L=1,1,1-trifluoro-7-(dimethylamino)-4-methyl-5-aza-3-hepten-2-onato). Despite the rather long Cu-Cu distance (5.105(1) A), the magnetic interaction is ferromagnetic with J= +16 cm(-1) (H=-JS(1)S(2)), a value that has been confirmed by DFT and high-level correlated ab initio calculations. The spin distribution was studied by using the results from polarized neutron diffraction. This is the first such study on an end-to-end system. The experimental spin density was found to be localized mainly on the copper(II) ions, with a small degree of delocalization on the ligand (L) and terminal azido nitrogens. There was zero delocalization on the central nitrogen, in agreement with DFT calculations. Such a picture corresponds to an important contribution of the d(x2-y2) orbital and a small population of the d(z2) orbital, in agreement with our calculations. Based on a correlated wavefunction analysis, the ferromagnetic behavior results from a dominant double spin polarization contribution and vanishingly small ionic forms.

Flexible End2End Workflow Automation of Hit-Discovery Research.

Science.gov (United States)

Holzmüller-Laue, Silke; Göde, Bernd; Thurow, Kerstin

2014-08-01

The article considers a new approach of more complex laboratory automation at the workflow layer. The authors purpose the automation of end2end workflows. The combination of all relevant subprocesses-whether automated or manually performed, independently, and in which organizational unit-results in end2end processes that include all result dependencies. The end2end approach focuses on not only the classical experiments in synthesis or screening, but also on auxiliary processes such as the production and storage of chemicals, cell culturing, and maintenance as well as preparatory activities and analyses of experiments. Furthermore, the connection of control flow and data flow in the same process model leads to reducing of effort of the data transfer between the involved systems, including the necessary data transformations. This end2end laboratory automation can be realized effectively with the modern methods of business process management (BPM). This approach is based on a new standardization of the process-modeling notation Business Process Model and Notation 2.0. In drug discovery, several scientific disciplines act together with manifold modern methods, technologies, and a wide range of automated instruments for the discovery and design of target-based drugs. The article discusses the novel BPM-based automation concept with an implemented example of a high-throughput screening of previously synthesized compound libraries. © 2014 Society for Laboratory Automation and Screening.

The Ku70/80 ring in Non-Homologous End-Joining: easy to slip on, hard to remove.

Science.gov (United States)

Kragelund, Birthe B; Weterings, Eric; Hartmann-Petersen, Rasmus; Keijzers, Guido

2016-01-01

Non-homologous end-joining (NHEJ) is an essential DNA double strand break repair pathway during all cell cycle stages. Deficiency in NHEJ factors can lead to accumulation of unrepaired DNA breaks or faulty DNA repair, which may ultimately result in cell death, senescence or carcinogenesis. The Ku70/80 heterodimer is a key-player in the NHEJ pathway and binds to DNA termini with high affinity, where it helps to protect DNA ends from degradation and to recruit other NHEJ factors required for repair. The mechanism of Ku70/80 detachment from the DNA helix after completion of DNA repair is incompletely understood. Some data suggest that certain DNA repair factors are ubiquitylated and targeted for proteasomal degradation after repair. Recent studies suggest that Ku80 is conjugated to lysine48-linked ubiquitin chains by the Skp1-Cullin-F-box (SCF) complex and/or the RING finger protein 8 (RNF8) ubiquitin-protein ligases, followed by rapid proteasomal degradation. In this review we address the structure and function of the Ku70/80 heterodimer and how ubiquitylation may affect the release of Ku70/80 from chromatin and its subsequent degradation via the ubiquitin-proteasome system.

Mechanics of spatulated end-to-end artery-to-vein anastomoses.

Science.gov (United States)

Morasch, M D; Dobrin, P B; Dong, Q S; Mrkvicka, R

1998-01-01

It previously has been shown that in straight end-to-end artery-to-vein anastomoses, maximum dimensions are obtained with an interrupted suture line. Nearly equivalent dimensions are obtained with a continuous compliant polybutester suture (Novafil), and the smallest dimensions are obtained with a continuous noncompliant polypropylene suture (Surgilene). The present study was undertaken to examine these suture techniques in a spatulated or beveled anastomosis in living dogs. Anastomoses were constructed using continuous 6-0 polypropylene (Surgilene), continuous 6-0 polybutester (Novafil), or interrupted 6-0 polypropylene or polybutester. Thirty minutes after construction, the artery, vein, and beveled anastomoses were excised, restored to in situ length and pressurized with the lumen filled with a dilute suspension of barium sulfate. High resolution radiographs were obtained at 25 mmHg pressure increments up to 200 mmHg. Dimensions and compliance were determined from the radiographic images. Results showed that, unlike straight artery-to-vein anastomoses, there were no differences in the dimensions or compliance of spatulated anastomoses with continuous Surgilene, continuous Novafil, or interrupted suture techniques. Therefore a continuous suture technique is acceptable when constructing spatulated artery-to-vein anastomoses in patients.

Location Assisted Vertical Handover Algorithm for QoS Optimization in End-to-End Connections

DEFF Research Database (Denmark)

Dam, Martin S.; Christensen, Steffen R.; Mikkelsen, Lars M.

2012-01-01

implementation on Android based tablets. The simulations cover a wide range of scenarios for two mobile users in an urban area with ubiquitous cellular coverage, and shows our algorithm leads to increased throughput, with fewer handovers, when considering the end-to-end connection than to other handover schemes...

An end to end secure CBIR over encrypted medical database.

Science.gov (United States)

Bellafqira, Reda; Coatrieux, Gouenou; Bouslimi, Dalel; Quellec, Gwenole

2016-08-01

In this paper, we propose a new secure content based image retrieval (SCBIR) system adapted to the cloud framework. This solution allows a physician to retrieve images of similar content within an outsourced and encrypted image database, without decrypting them. Contrarily to actual CBIR approaches in the encrypted domain, the originality of the proposed scheme stands on the fact that the features extracted from the encrypted images are themselves encrypted. This is achieved by means of homomorphic encryption and two non-colluding servers, we however both consider as honest but curious. In that way an end to end secure CBIR process is ensured. Experimental results carried out on a diabetic retinopathy database encrypted with the Paillier cryptosystem indicate that our SCBIR achieves retrieval performance as good as if images were processed in their non-encrypted form.

An end-to-end secure patient information access card system.

Science.gov (United States)

Alkhateeb, A; Singer, H; Yakami, M; Takahashi, T

2000-03-01

The rapid development of the Internet and the increasing interest in Internet-based solutions has promoted the idea of creating Internet-based health information applications. This will force a change in the role of IC cards in healthcare card systems from a data carrier to an access key medium. At the Medical Informatics Department of Kyoto University Hospital we are developing a smart card patient information project where patient databases are accessed via the Internet. Strong end-to-end data encryption is performed via Secure Socket Layers, transparent to transmit patient information. The smart card is playing the crucial role of access key to the database: user authentication is performed internally without ever revealing the actual key. For easy acceptance by healthcare professionals, the user interface is integrated as a plug-in for two familiar Web browsers, Netscape Navigator and MS Internet Explorer.

Atlantis model outputs - Developing end-to-end models of the California Current Large Marine Ecosystem

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

Weighted-DESYNC and Its Application to End-to-End Throughput Fairness in Wireless Multihop Network

Directory of Open Access Journals (Sweden)

Ui-Seong Yu

2017-01-01

Full Text Available The end-to-end throughput of a routing path in wireless multihop network is restricted by a bottleneck node that has the smallest bandwidth among the nodes on the routing path. In this study, we propose a method for resolving the bottleneck-node problem in multihop networks, which is based on multihop DESYNC (MH-DESYNC algorithm that is a bioinspired resource allocation method developed for use in multihop environments and enables fair resource allocation among nearby (up to two hops neighbors. Based on MH-DESYNC, we newly propose weighted-DESYNC (W-DESYNC as a tool artificially to control the amount of resource allocated to the specific user and thus to achieve throughput fairness over a routing path. Proposed W-DESYNC employs the weight factor of a link to determine the amount of bandwidth allocated to a node. By letting the weight factor be the link quality of a routing path and making it the same across a routing path via Cucker-Smale flocking model, we can obtain throughput fairness over a routing path. The simulation results show that the proposed algorithm achieves throughput fairness over a routing path and can increase total end-to-end throughput in wireless multihop networks.

WiMAX security and quality of service an end-to-end perspective

CERN Document Server

Tang, Seok-Yee; Sharif, Hamid

2010-01-01

WiMAX is the first standard technology to deliver true broadband mobility at speeds that enable powerful multimedia applications such as Voice over Internet Protocol (VoIP), online gaming, mobile TV, and personalized infotainment. WiMAX Security and Quality of Service, focuses on the interdisciplinary subject of advanced Security and Quality of Service (QoS) in WiMAX wireless telecommunication systems including its models, standards, implementations, and applications. Split into 4 parts, Part A of the book is an end-to-end overview of the WiMAX architecture, protocol, and system requirements.

On end-to-end performance of MIMO multiuser in cognitive radio networks

KAUST Repository

Yang, Yuli

2011-12-01

In this paper, a design for the multiple-input-multiple-output (MIMO) multiuser transmission in the cognitive radio network is developed and its end-to-end performance is investigated under spectrum-sharing constraints. Firstly, the overall average packet error rate is analyzed by considering the channel state information feedback delay and the multiuser scheduling. Then, we provide corresponding numerical results to measure the performance evaluation for several separate scenarios, which presents a convenient tool for the cognitive radio network design with multiple secondary MIMO users. © 2011 IEEE.

On end-to-end performance of MIMO multiuser in cognitive radio networks

KAUST Repository

Yang, Yuli; Aissa, Sonia

2011-01-01

In this paper, a design for the multiple-input-multiple-output (MIMO) multiuser transmission in the cognitive radio network is developed and its end-to-end performance is investigated under spectrum-sharing constraints. Firstly, the overall average packet error rate is analyzed by considering the channel state information feedback delay and the multiuser scheduling. Then, we provide corresponding numerical results to measure the performance evaluation for several separate scenarios, which presents a convenient tool for the cognitive radio network design with multiple secondary MIMO users. © 2011 IEEE.

Security Considerations around End-to-End Security in the IP-based Internet of Things

NARCIS (Netherlands)

Brachmann, M.; Garcia-Mochon, O.; Keoh, S.L.; Kumar, S.S.

2012-01-01

The IP-based Internet of Things refers to the interconnection of smart objects in a Low-power and Lossy Network (LLN) with the Internetby means of protocols such as 6LoWPAN or CoAP. The provisioning of an end-to-end security connection is the key to ensure basic functionalities such as software

Rear end collision: Causes and avoidance techniques

NARCIS (Netherlands)

Nekovee, Maziar; Bie, Jing; Naja, Rola

2013-01-01

Rear-end collision is one of the most frequent accidents occurring on roadways. This chapter investigates how vehicle’s local parameters in a platoon of cars (i.e., perception and information collection, vehicle speed, safe distance, braking parameters) affect the global behavior of the traffic

An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data

Directory of Open Access Journals (Sweden)

Wilson Zoe A

2010-02-01

Full Text Available Abstract Background ChIP-Seq, which combines chromatin immunoprecipitation (ChIP with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. However, to maximize the effectiveness of data analysis of such sequences requires the development of new algorithms that are able to accurately predict DNA-protein binding sites. Results Here, we present SIPeS (Site Identification from Paired-end Sequencing, a novel algorithm for precise identification of binding sites from short reads generated by paired-end solexa ChIP-Seq technology. In this paper we used ChIP-Seq data from the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS, which is expressed within the anther during pollen development, the results show that SIPeS has better resolution for binding site identification compared to two existing ChIP-Seq peak detection algorithms, Cisgenome and MACS. Conclusions When compared to Cisgenome and MACS, SIPeS shows better resolution for binding site discovery. Moreover, SIPeS is designed to calculate the mappable genome length accurately with the fragment length based on the paired-end reads. Dynamic baselines are also employed to effectively discriminate closely adjacent binding sites, for effective binding sites discovery, which is of particular value when working with high-density genomes.

Performance Enhancements of UMTS networks using end-to-end QoS provisioning

DEFF Research Database (Denmark)

Wang, Haibo; Prasad, Devendra; Teyeb, Oumer

2005-01-01

This paper investigates the end-to-end(E2E) quality of service(QoS) provisioning approaches for UMTS networks together with DiffServ IP network. The effort was put on QoS classes mapping from DiffServ to UMTS, Access Control(AC), buffering and scheduling optimization. The DiffServ Code Point (DSCP......) was utilized in the whole UMTS QoS provisioning to differentiate different type of traffics. The overall algorithm was optimized to guarantee the E2E QoS parameters of each service class, especially for realtime applications, as well as to improve the bandwidth utilization. Simulation shows that the enhanced...

Fuel rod end plug

International Nuclear Information System (INIS)

McGeary, R.K.; Bucher, G.D.

1989-01-01

This patent describes an end plug for welded disposition within the end of a tube. It comprises a circumferentially extending, axially oriented land surface, having a radial extent defined by means of a first predetermined dimension, for disposition within the end of the tube; a circumferentially extending, axially oriented land surface, having a radial extent defined by means of a second predetermined dimension which is greater than the first predetermined dimension, for disposition outside of the end of the tube. The second land surface being disposed upstream of the first land surface; an annularly extending, radially oriented shoulder portion, defined at the downstream end of the second land surface and having a radially inward depth which is greater than the difference defined between the first and second radial dimensions of the first and second land surfaces, for engaging the end of the tube in a butt contact fashion; and annular groove means defined between the upstream end of the first land surface and the shoulder portion of the end plug, for eliminating porosity defects normally developed within a weldment defined between the tube end and the end plug when the end plug is welded within the tube end, and including a conical surface which extends radially outwardly from the innermost radial depth extent of the shoulder portion to the upstream end of the first land surface

Rectovaginal fistula following colectomy with an end-to-end anastomosis stapler for a colorectal adenocarcinoma.

Science.gov (United States)

Klein, A; Scotti, S; Hidalgo, A; Viateau, V; Fayolle, P; Moissonnier, P

2006-12-01

An 11-year-old, female neutered Labrador retriever was presented with a micro-invasive differentiated papillar adenocarcinoma at the colorectal junction. A colorectal end-to-end anastomosis stapler device was used to perform resection and anastomosis using a transanal technique. A rectovaginal fistula was diagnosed two days later. An exploratory laparotomy was conducted and the fistula was identified and closed. Early dehiscence of the colon was also suspected and another colorectal anastomosis was performed using a manual technique. Comparison to a conventional manual technique of intestinal surgery showed that the use of an automatic staple device was quicker and easier. To the authors' knowledge, this is the first report of a rectovaginal fistula occurring after end-to-end anastomosis stapler colorectal resection-anastomosis in the dog. To minimise the risk of this potential complication associated with the limited surgical visibility, adequate tissue retraction and inspection of the anastomosis site are essential.

Load factors to end March 1989

International Nuclear Information System (INIS)

Howles, L.

1989-01-01

Load factors for nuclear reactors of 150MWe gross and above for the 12 month period up to the end of March 1989, and over their lifetimes, are tabulated. Units which have been in operation for more than one year as of end March 1989 are ranked in order of annual load factor; cumulative load factors are also shown, measured from first synchronization to the grid not from start of commercial operation. New reactors which had operated for less than 12 months as of end of March 1989 are listed separately. With the exception of the four Paks units in Hungary, Comecon reactors are excluded due to lack of data. (author)

GROWTH OF THE HYPOPLASTIC AORTIC-ARCH AFTER SIMPLE COARCTATION RESECTION AND END-TO-END ANASTOMOSIS

NARCIS (Netherlands)

BROUWER, MHJ; CROMMEDIJKHUIS, AH; EBELS, T; EIJGELAAR, A

Surgical treatment of a hypoplastic aortic arch associated with an aortic coarctation is controversial. The controversy concerns the claimed need to surgically enlarge the diameter of the hypoplastic arch, in addition to resection and end-to-end anastomosis. The purpose of this prospective study is

Noncanonical substrate preference of lambda exonuclease for 5'-nonphosphate-ended dsDNA and a mismatch-induced acceleration effect on the enzymatic reaction.

Science.gov (United States)

Wu, Tongbo; Yang, Yufei; Chen, Wei; Wang, Jiayu; Yang, Ziyu; Wang, Shenlin; Xiao, Xianjin; Li, Mengyuan; Zhao, Meiping

2018-04-06

Lambda exonuclease (λ exo) plays an important role in the resection of DNA ends for DNA repair. Currently, it is also a widely used enzymatic tool in genetic engineering, DNA-binding protein mapping, nanopore sequencing and biosensing. Herein, we disclose two noncanonical properties of this enzyme and suggest a previously undescribed hydrophobic interaction model between λ exo and DNA substrates. We demonstrate that the length of the free portion of the substrate strand in the dsDNA plays an essential role in the initiation of digestion reactions by λ exo. A dsDNA with a 5' non-phosphorylated, two-nucleotide-protruding end can be digested by λ exo with very high efficiency. Moreover, we show that when a conjugated structure is covalently attached to an internal base of the dsDNA, the presence of a single mismatched base pair at the 5' side of the modified base may significantly accelerate the process of digestion by λ exo. A detailed comparison study revealed additional π-π stacking interactions between the attached label and the amino acid residues of the enzyme. These new findings not only broaden our knowledge of the enzyme but will also be very useful for research on DNA repair and in vitro processing of nucleic acids.

DNA double-strand break response factors influence end-joining features of IgH class switch and general translocation junctions.

Science.gov (United States)

Panchakshari, Rohit A; Zhang, Xuefei; Kumar, Vipul; Du, Zhou; Wei, Pei-Chi; Kao, Jennifer; Dong, Junchao; Alt, Frederick W

2018-01-23

Ig heavy chain (IgH) class switch recombination (CSR) in B lymphocytes switches IgH constant regions to change antibody functions. CSR is initiated by DNA double-strand breaks (DSBs) within a donor IgH switch (S) region and a downstream acceptor S region. CSR is completed by fusing donor and acceptor S region DSB ends by classical nonhomologous end-joining (C-NHEJ) and, in its absence, by alternative end-joining that is more biased to use longer junctional microhomologies (MHs). Deficiency for DSB response (DSBR) factors, including ataxia telangiectasia-mutated (ATM) and 53BP1, variably impair CSR end-joining, with 53BP1 deficiency having the greatest impact. However, studies of potential impact of DSBR factor deficiencies on MH-mediated CSR end-joining have been technically limited. We now use a robust DSB joining assay to elucidate impacts of deficiencies for DSBR factors on CSR and chromosomal translocation junctions in primary mouse B cells and CH12F3 B-lymphoma cells. Compared with wild-type, CSR and c-myc to S region translocation junctions in the absence of 53BP1, and, to a lesser extent, other DSBR factors, have increased MH utilization; indeed, 53BP1-deficient MH profiles resemble those associated with C-NHEJ deficiency. However, translocation junctions between c-myc DSB and general DSBs genome-wide are not MH-biased in ATM-deficient versus wild-type CH12F3 cells and are less biased in 53BP1- and C-NHEJ-deficient cells than CSR junctions or c-myc to S region translocation junctions. We discuss potential roles of DSBR factors in suppressing increased MH-mediated DSB end-joining and features of S regions that may render their DSBs prone to MH-biased end-joining in the absence of DSBR factors.

A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica

Directory of Open Access Journals (Sweden)

Anne-Catherine Portmann

2018-03-01

Full Text Available Whole genome sequencing (WGS, using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations. Despite its increased use, no standards or guidelines are available today for the use of WGS in outbreak and/or trace-back investigations. Here we present a validation of our complete (end-to-end WGS workflow for Listeria monocytogenes and Salmonella enterica including: subculture of isolates, DNA extraction, sequencing and bioinformatics analysis. This end-to-end WGS workflow was evaluated according to the following performance criteria: stability, repeatability, reproducibility, discriminatory power, and epidemiological concordance. The current study showed that few single nucleotide polymorphism (SNPs were observed for L. monocytogenes and S. enterica when comparing genome sequences from five independent colonies from the first subculture and five independent colonies after the tenth subculture. Consequently, the stability of the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite the few genomic variations that can occur during subculturing steps. Repeatability and reproducibility were also demonstrated. The WGS workflow was shown to have a high discriminatory power and has the ability to show genetic relatedness. Additionally, the WGS workflow was able to reproduce published outbreak investigation results, illustrating its capability of showing epidemiological concordance. The current study proposes a validation approach comprising all steps of a WGS workflow and demonstrates that the workflow can be applied to L. monocytogenes or S. enterica.

Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments.

Science.gov (United States)

Moukhtar, Julien; Faivre-Moskalenko, Cendrine; Milani, Pascale; Audit, Benjamin; Vaillant, Cedric; Fontaine, Emeline; Mongelard, Fabien; Lavorel, Guillaume; St-Jean, Philippe; Bouvet, Philippe; Argoul, Françoise; Arneodo, Alain

2010-04-22

Sequence dependency of DNA intrinsic bending properties has been emphasized as a possible key ingredient to in vivo chromatin organization. We use atomic force microscopy (AFM) in air and liquid to image intrinsically straight (synthetic), uncorrelated (hepatitis C RNA virus) and persistent long-range correlated (human) DNA fragments in various ionic conditions such that the molecules freely equilibrate on the mica surface before being captured in a particular conformation. 2D thermodynamic equilibrium is experimentally verified by a detailed statistical analysis of the Gaussian nature of the DNA bend angle fluctuations. We show that the worm-like chain (WLC) model, commonly used to describe the average conformation of long semiflexible polymers, reproduces remarkably well the persistence length estimates for the first two molecules as consistently obtained from (i) mean square end-to-end distance measurement and (ii) mean projection of the end-to-end vector on the initial orientation. Whatever the operating conditions (air or liquid, concentration of metal cations Mg(2+) and/or Ni(2+)), the persistence length found for the uncorrelated viral DNA underestimates the value obtained for the straight DNA. We show that this systematic difference is the signature of the presence of an uncorrelated structural intrinsic disorder in the hepatitis C virus (HCV) DNA fragment that superimposes on local curvatures induced by thermal fluctuations and that only the entropic disorder depends upon experimental conditions. In contrast, the WLC model fails to describe the human DNA conformations. We use a mean-field extension of the WLC model to account for the presence of long-range correlations (LRC) in the intrinsic curvature disorder of human genomic DNA: the stronger the LRC, the smaller the persistence length. The comparison of AFM imaging of human DNA with LRC DNA simulations confirms that the rather small mean square end-to-end distance observed, particularly for G

Experimental research on end-to-side anastomosis of peripheral nerves and effect of FK506 on end-to-side anastomosis.

Science.gov (United States)

Yang, L M; Wu, Y X; Zhang, X P; Li, X H

2014-01-01

To study the effects of end-to-side anastomosis of initially-denatured nerves at different times. 60 male Wistar albino rats were used to fabricate animal models for the experiment on end-to-side anastomosis of peripheral nerves and 50 female Wistar albino rats were used to fabricate animal models for the experiment on the effect of FK506 on end-to-side anastomosis. Bilateral common peroneal nerve, tibialis anterior muscle electrophysiological and histological examinations, tibialis anterior muscle wet muscle weight determination, and motor end plate examination were performed 3 months after operation. All recovery rates of action potential, single muscle contraction force and tetanic contraction force of the FK506 experimental group are significantly higher than those of the control group and the sectional area of muscle fiber is also higher than that of the control group of normal saline. The best time for end-to-side anastomosis of nerves should be controlled within 2 weeks and the effect of end-to-side anastomosis of nerves will gradually become unsatisfactory. FK506 plays a role in promoting functional rehabilitation following nerve end-to-side anastomosis (Tab. 7, Fig. 4, Ref. 31).

Double 90 Degrees Counterrotated End-to-End-Anastomosis: An Experimental Study of an Intestinal Anastomosis Technique.

Science.gov (United States)

Holzner, Philipp; Kulemann, Birte; Seifert, Gabriel; Glatz, Torben; Chikhladze, Sophia; Höppner, Jens; Hopt, Ulrich; Timme, Sylvia; Bronsert, Peter; Sick, Olivia; Zhou, Cheng; Marjanovic, Goran

2015-06-01

The aim of the article is to investigate a new anastomotic technique compared with standardized intestinal anastomotic procedures. A total of 32 male Wistar rats were randomized to three groups. In the Experimental Group (n = 10), the new double 90 degrees inversely rotated anastomosis was used, in the End Group (n = 10) a single-layer end-to-end anastomosis, and in the Side Group (n = 12) a single-layer side-to-side anastomosis. All anastomoses were done using interrupted sutures. On postoperative day 4, rats were relaparotomized. Bursting pressure, hydroxyproline concentration, a semiquantitative adhesion score and two histological anastomotic healing scores (mucosal healing according to Chiu and overall anastomotic healing according to Verhofstad) were collected. Most data are presented as median (range). p < 0.05 was considered significant. Anastomotic insufficiency occurred only in one rat of the Side Group. Median bursting pressure in the Experimental Group was 105 mm Hg (range = 72-161 mm Hg), significantly higher in the End Group (164 mm Hg; range = 99-210 mm Hg; p = 0.021) and lower in the Side Group by trend (81 mm Hg; range = 59-122 mm Hg; p = 0.093). Hydroxyproline concentration did not differ significantly in between the groups. The adhesion score was 2.5 (range = 1-3) in the Experimental Group, 2 (range = 1-2) in the End Group, but there were significantly more adhesions in the Side Group (range = 3-4); p = 0.020 versus Experimental Group, p < 0.001 versus End Group. The Chiu Score showed the worst mucosal healing in the Experimental Group. The overall Verhofstad Score was significantly worse (mean = 2.032; standard deviation [SD] = 0.842) p = 0.031 and p = 0.002 in the Experimental Group, compared with the Side Group (mean = 1.729; SD = 0.682) and the End Group (mean = 1.571; SD = 0.612). The new anastomotic technique is feasible and did not show any relevant complication. Even though it was superior to the side-to-side anastomosis by trend with

Alternative end-joining of DNA breaks

NARCIS (Netherlands)

Schendel, Robin van

2016-01-01

DNA is arguably the most important molecule found in any organism, as it contains all information to perform cellular functions and enables continuity of species. It is continuously exposed to DNA-damaging agents both from endogenous and exogenous sources. To protect DNA against these sources of DNA

DNA with Parallel Strand Orientation: A Nanometer Distance Study with Spin Labels in the Watson-Crick and the Reverse Watson-Crick Double Helix.

Science.gov (United States)

Wunnicke, Dorith; Ding, Ping; Yang, Haozhe; Seela, Frank; Steinhoff, Heinz-Jürgen

2015-10-29

Parallel-stranded (ps) DNA characterized by its sugar-phosphate backbones pointing in the same direction represents an alternative pairing system to antiparallel-stranded (aps) DNA with the potential to inhibit transcription and translation. 25-mer oligonucleotides were selected containing only dA·dT base pairs to compare spin-labeled nucleobase distances over a range of 10 or 15 base pairs in ps DNA with those in aps DNA. By means of the copper(I)-catalyzed Huisgen-Meldal-Sharpless alkyne-azide cycloaddition, the spin label 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl was clicked to 7-ethynyl-7-deaza-2'-deoxyadenosine or 5-ethynyl-2'-deoxyuridine to yield 25-mer oligonucleotides incorporating two spin labels. The interspin distances between spin labeled residues were determined by pulse EPR spectroscopy. The results reveal that in ps DNA these distances are between 5 and 10% longer than in aps DNA when the labeled DNA segment is located near the center of the double helix. The interspin distance in ps DNA becomes shorter compared with aps DNA when one of the spin labels occupies a position near the end of the double helix.

Role for Artemis nuclease in the repair of radiation-induced DNA double strand breaks by alternative end joining.

Science.gov (United States)

Moscariello, Mario; Wieloch, Radi; Kurosawa, Aya; Li, Fanghua; Adachi, Noritaka; Mladenov, Emil; Iliakis, George

2015-07-01

Exposure of cells to ionizing radiation or radiomimetic drugs generates DNA double-strand breaks that are processed either by homologous recombination repair (HRR), or by canonical, DNA-PKcs-dependent non-homologous end-joining (C-NHEJ). Chemical or genetic inactivation of factors involved in C-NHEJ or HRR, but also their local failure in repair proficient cells, promotes an alternative, error-prone end-joining pathway that serves as backup (A-EJ). There is evidence for the involvement of Artemis endonuclease, a protein deficient in a human radiosensitivity syndrome associated with severe immunodeficiency (RS-SCID), in the processing of subsets of DSBs by HRR or C-NHEJ. It is thought that within HRR or C-NHEJ Artemis processes DNA termini at complex DSBs. Whether Artemis has a role in A-EJ remains unknown. Here, we analyze using pulsed-field gel electrophoresis (PFGE) and specialized reporter assays, DSB repair in wild-type pre-B NALM-6 lymphocytes, as well as in their Artemis(-/-), DNA ligase 4(-/-) (LIG4(-/-)), and LIG4(-/-)/Artemis(-/-) double mutant counterparts, under conditions allowing evaluation of A-EJ. Our results substantiate the suggested roles of Artemis in C-NHEJ and HRR, but also demonstrate a role for the protein in A-EJ that is confirmed in Artemis deficient normal human fibroblasts. We conclude that Artemis is a nuclease participating in DSB repair by all major repair pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

Analytical solutions to SSC coil end design

International Nuclear Information System (INIS)

Bossert, R.C.; Brandt, J.S.; Carson, J.A.; Fulton, H.J.; Lee, G.C.; Cook, J.M.

1989-03-01

As part of the SCC magnet effort, Fermilab will build and test a series of one meter model SSC magnets. The coils in these magnets will be constructed with several different end configurations. These end designs must satisfy both mechanical and magnetic criteria. Only the mechanical problem will be addressed. Solutions will attempt to minimize stresses and provide internal support for the cable. Different end designs will be compared in an attempt to determine which is most appropriate for the SSC dipole. The mathematics required to create each end configuration will be described. The computer aided design, programming and machine technology needed to make the parts will be reviewed. 2 refs., 10 figs

Armazenamento refrigerado sob atmosfera modificada de pedúnculos de cajueiro-anão-precoce dos clones CCP-76, end-157, end-183 e end-189 Storage of cashew apples from dwarf clones CCP-76, end-157, end-183 and end-189 under refrigeration and modified atmosphere

Directory of Open Access Journals (Sweden)

Auricélia de Souza Morais

2002-12-01

Full Text Available Pedúnculos de clones de cajueiro-anão-precoce, dos clones CCP-76, END-157, END-183 e END-189, foram armazenados durante 25 dias, sob refrigeração associada a atmosfera modificada, com o objetivo de avaliar o efeito das condições atualmente utilizadas (5ºC e 85-90% de UR para conservação, transporte e comercialização de cajus in natura. Os pedúnculos foram avaliados a cada 5 dias quanto às seguintes características: perda de peso, firmeza, cor (antocianinas, sólidos e açúcares solúveis, acidez, pH, vitamina C e compostos fenólicos. O uso da refrigeração (5ºC e 85% U.R, associada a atmosfera modificada, proporcionou uma vida útil pós-colheita de 10 dias para o clone END 189, de até 15 dias para o clone END 157 e de até 25 dias para os clones CCP 76 e END 183. A temperatura de 5ºC não se mostrou adequada para armazenamento de pedúnculos de coloração mais intensa (END 157 e END 189 que a testemunha (CCP 76, provocando perda de cor (antocianinas a partir do 10º dia de armazenamento. A atmosfera modificada reduziu significativamente a perda de peso, favorecendo a aparência do produto para comercialização, independentemente do clone estudado.Apples or false fruits from early dwarf cashew clones CCP-76, END-157, END-183 and END-189 were stored for 25 days under refrigeration associated to modified atmosphere with the aim of evaluating the effect of the conditions presently adopted (5ºC and 85-90% RH for conservation, storage and commercialization of fresh cashew apples. The cashew apples were evaluated every 5 days for the following characteristics: weight loss, pulp firmness, color (anthocyannins, acidity, pH, soluble solids, vitamin C and phenolic contents. With the use of refrigeration and modified atmosphere it was possible to attain postharvest storage life of 10 days for clone END 189, 15 days for clone END 157 and up to 25 days for clones CCP 76 and END 183. It was found that 5ºC was not an adequate

Single-Molecule Imaging of DNAs with Sticky Ends at Water/Fused Silica Interface

Energy Technology Data Exchange (ETDEWEB)

Isailovic, Slavica [Iowa State Univ., Ames, IA (United States)

2005-01-01

Total internal reflection fluorescence microscopy (TIRFM) was used to study intermolecular interactions of DNAs with unpaired (sticky) ends of different lengths at water/fused silica interface at the single-molecule level. Evanescent field residence time, linear velocity and adsorption/desorption frequency were measured in a microchannel for individual DNA molecules from T7, Lambda, and PSP3 phages at various pH values. The longest residence times and the highest adsorption/desorption frequencies at the constant flow at pH 5.5 were found for PSP3 DNA, followed by lower values for Lambda DNA, and the lowest values for T7 DNA. Since T7, Lambda, and PSP3 DNA molecules contain none, twelve and nineteen unpaired bases, respectively, it was concluded that the affinity of DNAs for the surface increases with the length of the sticky ends. This confirms that hydrophobic and hydrogen-bonding interactions between sticky ends and fused-silica surface are driving forces for DNA adsorption at the fused-silica surface. Described single-molecule methodology and results therein can be valuable for investigation of interactions in liquid chromatography, as well as for design of DNA hybridization sensors and drug delivery systems.

Direct Involvement of Retinoblastoma Family Proteins in DNA Repair by Non-homologous End-Joining

Directory of Open Access Journals (Sweden)

Rebecca Cook

2015-03-01

Full Text Available Deficiencies in DNA double-strand break (DSB repair lead to genetic instability, a recognized cause of cancer initiation and evolution. We report that the retinoblastoma tumor suppressor protein (RB1 is required for DNA DSB repair by canonical non-homologous end-joining (cNHEJ. Support of cNHEJ involves a mechanism independent of RB1’s cell-cycle function and depends on its amino terminal domain with which it binds to NHEJ components XRCC5 and XRCC6. Cells with engineered loss of RB family function as well as cancer-derived cells with mutational RB1 loss show substantially reduced levels of cNHEJ. RB1 variants disabled for the interaction with XRCC5 and XRCC6, including a cancer-associated variant, are unable to support cNHEJ despite being able to confer cell-cycle control. Our data identify RB1 loss as a candidate driver of structural genomic instability and a causative factor for cancer somatic heterogeneity and evolution.

The effectiveness of sharp end and rounded end bristle toothbrush

OpenAIRE

Paulus Januar; Anastasia Susetyo; Ratih Widyastuti

2010-01-01

Background: Numerous designs of manual toothbrush are available in the market with the claims of superiority in plaque removal. It often makes the public confuse which is the best design. The sharp end bristle toothbrush is a modification that commercially available in the market. Purpose: The objective of the study was to compare the effectiveness in plaque removal of the sharp end bristle toothbrush and the rounded end bristle toothbrush. Methods: This clinical trial was a double blind cros...

3' RNA ligase mediated rapid amplification of cDNA ends for validating viroid induced cleavage at the 3' extremity of the host mRNA.

Science.gov (United States)

Adkar-Purushothama, Charith Raj; Bru, Pierrick; Perreault, Jean-Pierre

2017-12-01

5' RNA ligase-mediated rapid amplification of cDNA ends (5' RLM-RACE) is a widely-accepted method for the validation of direct cleavage of a target gene by a microRNA (miRNA) and viroid-derived small RNA (vd-sRNA). However, this method cannot be used if cleavage takes place in the 3' extremity of the target RNA, as this gives insufficient sequence length to design nested PCR primers for 5' RLM RACE. To overcome this hurdle, we have developed 3' RNA ligase-mediated rapid amplification of cDNA ends (3' RLM RACE). In this method, an oligonucleotide adapter having 5' adenylated and 3' blocked is ligated to the 3' end of the cleaved RNA followed by PCR amplification using gene specific primers. In other words, in 3' RLM RACE, 3' end is mapped using 5' fragment instead of small 3' fragment. The method developed here was verified by examining the bioinformatics predicted and parallel analysis of RNA ends (PARE) proved cleavage sites of chloride channel protein CLC-b-like mRNA in Potato spindle tuber viroid infected tomato plants. The 3' RLM RACE developed in this study has the potential to validate the miRNA and vd-sRNA mediated cleavage of mRNAs at its 3' untranslated region (3' UTR). Copyright © 2017 Elsevier B.V. All rights reserved.

Poly(ethyl glyoxylate)-Poly(ethylene oxide) Nanoparticles: Stimuli-Responsive Drug Release via End-to-End Polyglyoxylate Depolymerization.

Science.gov (United States)

Fan, Bo; Gillies, Elizabeth R

2017-08-07

The ability to disrupt polymer assemblies in response to specific stimuli provides the potential to release drugs selectively at certain sites or conditions in vivo. However, most stimuli-responsive delivery systems require many stimuli-initiated events to release drugs. "Self-immolative polymers" offer the potential to provide amplified responses to stimuli as they undergo complete end-to-end depolymerization following the cleavage of a single end-cap. Herein, linker end-caps were developed to conjugate self-immolative poly(ethyl glyoxylate) (PEtG) with poly(ethylene oxide) (PEO) to form amphiphilic block copolymers. These copolymers were self-assembled to form nanoparticles in aqueous solution. Cleavage of the linker end-caps were triggered by a thiol reducing agent, UV light, H 2 O 2 , and combinations of these stimuli, resulting in nanoparticle disintegration. Low stimuli concentrations were effective in rapidly disrupting the nanoparticles. Nile red, doxorubin, and curcumin were encapsulated into the nanoparticles and were selectively released upon application of the appropriate stimulus. The ability to tune the stimuli-responsiveness simply by changing the linker end-cap makes this new platform highly attractive for applications in drug delivery.

End-to-end simulation of the C-ADS injector Ⅱ with a 3-D field map

International Nuclear Information System (INIS)

Wang Zhijun; He Yuan; Li Chao; Wang Wangsheng; Liu Shuhui; Jia Huan; Xu Xianbo; Chen Ximeng

2013-01-01

The Injector II, one of the two parallel injectors of the high-current superconducting proton driver linac for the China Accelerator-Driven System (C-ADS) project, is being designed and constructed by the Institute of Modern Physics. At present, the design work for the injector is almost finished. End-to-end simulation has been carried out using the TRACK multiparticle simulation code to check the match between each acceleration section and the performance of the injector as a whole. Moreover, multiparticle simulations with all kinds of errors and misalignments have been performed to define the requirements of each device. The simulation results indicate that the lattice design is robust. In this paper, the results of end-to-end simulation and error simulation with a 3-D field map are presented. (authors)

End to end distribution functions for a class of polymer models

International Nuclear Information System (INIS)

Khandekar, D.C.; Wiegel, F.W.

1988-01-01

The two point end-to-end distribution functions for a class of polymer models have been obtained within the first cumulant approximation. The trial distribution function this purpose is chosen to correspond to a general non-local quadratic functional. An Exact expression for the trial distribution function is obtained. It is pointed out that these trial distribution functions themselves can be used to study certain aspects of the configurational behaviours of polymers. These distribution functions are also used to obtain the averaged mean square size 2 > of a polymer characterized by the non-local quadratic potential energy functional. Finally, we derive an analytic expression for 2 > of a polyelectrolyte model and show that for a long polymer a weak electrostatic interaction does not change the behaviour of 2 > from that of a free polymer. (author). 16 refs

Wiretapping End-to-End Encrypted VoIP Calls: Real-World Attacks on ZRTP

Directory of Open Access Journals (Sweden)

Schürmann Dominik

2017-07-01

Full Text Available Voice calls are still one of the most common use cases for smartphones. Often, sensitive personal information but also confidential business information is shared. End-to-end security is required to protect against wiretapping of voice calls. For such real-time communication, the ZRTP key-agreement protocol has been proposed. By verbally comparing a small number of on-screen characters or words, called Short Authentication Strings, the participants can be sure that no one is wiretapping the call. Since 2011, ZRTP is an IETF standard implemented in several VoIP clients.

End-to-end integrated security and performance analysis on the DEGAS Choreographer platform

DEFF Research Database (Denmark)

Buchholtz, Mikael; Gilmore, Stephen; Haenel, Valentin

2005-01-01

We present a software tool platform which facilitates security and performance analysis of systems which starts and ends with UML model descriptions. A UML project is presented to the platform for analysis, formal content is extracted in the form of process calculi descriptions, analysed with the......We present a software tool platform which facilitates security and performance analysis of systems which starts and ends with UML model descriptions. A UML project is presented to the platform for analysis, formal content is extracted in the form of process calculi descriptions, analysed...

miR-19, a component of the oncogenic miR-17∼92 cluster, targets the DNA-end resection factor CtIP

DEFF Research Database (Denmark)

Hühn, D; Kousholt, A N; Sørensen, Claus Storgaard

2014-01-01

MicroRNA-19 (miR-19) was recently identified as the key oncogenic component of the polycistronic miR-17∼92 cluster, also known as oncomiR-1, which is frequently upregulated or amplified in multiple tumor types. However, the gene targets and the pathways underlying the tumor-promoting activity of mi......R-19 still remain largely elusive. CtIP/RBBP8 promotes DNA-end resection, a critical step in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR), and is considered to function as a tumor suppressor. In this study, we show that miR-19 downregulates CtIP expression by binding...... to two highly conserved sequences located in the 3'-untranslated region of CtIP mRNA. We further demonstrate that CtIP expression is repressed by miR-19 during continuous genotoxic stress in a p53-dependent manner. Finally, we report that miR-19 impairs CtIP-mediated DNA-end resection, which results...

An End-to-End Model of Plant Pheromone Channel for Long Range Molecular Communication.

Science.gov (United States)

Unluturk, Bige D; Akyildiz, Ian F

2017-01-01

A new track in molecular communication is using pheromones which can scale up the range of diffusion-based communication from μm meters to meters and enable new applications requiring long range. Pheromone communication is the emission of molecules in the air which trigger behavioral or physiological responses in receiving organisms. The objective of this paper is to introduce a new end-to-end model which incorporates pheromone behavior with communication theory for plants. The proposed model includes both the transmission and reception processes as well as the propagation channel. The transmission process is the emission of pheromones from the leaves of plants. The dispersion of pheromones by the flow of wind constitutes the propagation process. The reception process is the sensing of pheromones by the pheromone receptors of plants. The major difference of pheromone communication from other molecular communication techniques is the dispersion channel acting under the laws of turbulent diffusion. In this paper, the pheromone channel is modeled as a Gaussian puff, i.e., a cloud of pheromone released instantaneously from the source whose dispersion follows a Gaussian distribution. Numerical results on the performance of the overall end-to-end pheromone channel in terms of normalized gain and delay are provided.

Associations of mitochondrial haplogroups and mitochondrial DNA copy numbers with end-stage renal disease in a Han population.

Science.gov (United States)

Zhang, Yuheng; Zhao, Ying; Wen, Shuzhen; Yan, Rengna; Yang, Qinglan; Chen, Huimei

2017-09-01

Mitochondrial DNA (mtDNA) is closely related to mitochondrion function, and variations have been suggested to be involved in pathogenesis of complex diseases. The present study sought to elucidate mitochondrial haplogroups and mtDNA copy number in end-stage renal disease (ESRD) in a Han population. First, the mitochondrial haplogroups of 37 ESRD patients were clustered into several haplogroups, and haplogroup A & D were taken as the candidate risk haplogroups for ESRD. Second, the frequencies of A and D were assessed in 344 ESRD patients and 438 healthy controls, respectively. Haplogroup D was found to be risk maker for ESRD in young subjects (numbers were evaluated with quantitative-PCR. The ESRD patients exhibited greater cell-free mtDNA contents than the healthy controls but less intracellular mtDNA. Haplogroup D exhibited a further increase in cell-free mtDNA content and a decrease in intracellular mtDNA content among the ESRDs patients. Our findings suggest that mtNDA haplogroup D may contributes to pathogenesis of early-onset ESRD through alterations of mtDNA copy numbers.

Minimizing End-to-End Interference in I/O Stacks Spanning Shared Multi-Level Buffer Caches

Science.gov (United States)

Patrick, Christina M.

2011-01-01

This thesis presents an end-to-end interference minimizing uniquely designed high performance I/O stack that spans multi-level shared buffer cache hierarchies accessing shared I/O servers to deliver a seamless high performance I/O stack. In this thesis, I show that I can build a superior I/O stack which minimizes the inter-application interference…

Exploring the requirements for multimodal interaction for mobile devices in an end-to-end journey context.

Science.gov (United States)

Krehl, Claudia; Sharples, Sarah

2012-01-01

The paper investigates the requirements for multimodal interaction on mobile devices in an end-to-end journey context. Traditional interfaces are deemed cumbersome and inefficient for exchanging information with the user. Multimodal interaction provides a different user-centred approach allowing for more natural and intuitive interaction between humans and computers. It is especially suitable for mobile interaction as it can overcome additional constraints including small screens, awkward keypads, and continuously changing settings - an inherent property of mobility. This paper is based on end-to-end journeys where users encounter several contexts during their journeys. Interviews and focus groups explore the requirements for multimodal interaction design for mobile devices by examining journey stages and identifying the users' information needs and sources. Findings suggest that multimodal communication is crucial when users multitask. Choosing suitable modalities depend on user context, characteristics and tasks.

Noncanonical substrate preference of lambda exonuclease for 5′-nonphosphate-ended dsDNA and a mismatch-induced acceleration effect on the enzymatic reaction

Science.gov (United States)

Yang, Yufei; Chen, Wei; Wang, Jiayu; Yang, Ziyu; Wang, Shenlin; Xiao, Xianjin; Li, Mengyuan

2018-01-01

Abstract Lambda exonuclease (λ exo) plays an important role in the resection of DNA ends for DNA repair. Currently, it is also a widely used enzymatic tool in genetic engineering, DNA-binding protein mapping, nanopore sequencing and biosensing. Herein, we disclose two noncanonical properties of this enzyme and suggest a previously undescribed hydrophobic interaction model between λ exo and DNA substrates. We demonstrate that the length of the free portion of the substrate strand in the dsDNA plays an essential role in the initiation of digestion reactions by λ exo. A dsDNA with a 5′ non-phosphorylated, two-nucleotide-protruding end can be digested by λ exo with very high efficiency. Moreover, we show that when a conjugated structure is covalently attached to an internal base of the dsDNA, the presence of a single mismatched base pair at the 5′ side of the modified base may significantly accelerate the process of digestion by λ exo. A detailed comparison study revealed additional π–π stacking interactions between the attached label and the amino acid residues of the enzyme. These new findings not only broaden our knowledge of the enzyme but will also be very useful for research on DNA repair and in vitro processing of nucleic acids. PMID:29490081

Reconstruction of lower end of radius using vascularized upper end of fibula

Directory of Open Access Journals (Sweden)

Koul Ashok

2007-01-01

Full Text Available Background: Giant cell tumor is a fairly common locally invasive tumor in young adults. The lower end of the radius is the second commonest site for this tumor. The most common treatment for this tumor is curettage with or without bone grafting but it carries a significant rate of recurrence. Excision is the treatment of choice, especially for cases in which the cortex has been breached. After excision of the distal end of the radius, different procedures have been described to reconstruct the defect of distal radius. These include partial arthrodesis and hemiarthroplasty using the upper end of the fibula. The upper end of the fibula has a morphological resemblance to the lower end of the radius and has been used to replace the latter. Traditionally it was used as a ′free′ (non-vascularized graft. More recently the upper end of the fibula has been transferred as a vascularized transfer for the same purpose. Though vascularized transfer should be expected to be more physiological, its superiority over the technically simpler non-vascularized transfer has not been conclusively proven. Materials and Methods: Two patients are presented who had giant cell tumor of distal radius. They underwent wide local excision and reconstruction with free vascularized upper end of the fibula. Result: Follow-up period was two and a half years and 12 months respectively. Both patients have returned to routine work. One patient has excellent functional result and the other has a good result. Conclusion: Vascularized upper end of fibula transfer is a reliable method of reconstruction for loss of the distal end of the radius that restores local anatomy and physiology.

The End

DEFF Research Database (Denmark)

Hasse Jørgensen, Stina

2016-01-01

Operaen THE END af den japanske komponist og DJ, Keiichiro Shibuya, skubber radikalt til publikums forventninger om, hvad en opera kan og skal være. THE END byder på 3D animation, surround sound, elektronisk glitch og syntetiske stemmer i en kompromisløs virtuel forestilling med det japanske...

An end-to-end microfluidic platform for engineering life supporting microbes in space exploration missions, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — HJ Science & Technology proposes a programmable, low-cost, and compact microfluidic platform capable of running automated end-to-end processes and optimization...

End-to-End Traffic Flow Modeling of the Integrated SCaN Network

Science.gov (United States)

Cheung, K.-M.; Abraham, D. S.

2012-05-01

In this article, we describe the analysis and simulation effort of the end-to-end traffic flow for the Integrated Space Communications and Navigation (SCaN) Network. Using the network traffic derived for the 30-day period of July 2018 from the Space Communications Mission Model (SCMM), we generate the wide-area network (WAN) bandwidths of the ground links for different architecture options of the Integrated SCaN Network. We also develop a new analytical scheme to model the traffic flow and buffering mechanism of a store-and-forward network. It is found that the WAN bandwidth of the Integrated SCaN Network is an important differentiator of different architecture options, as the recurring circuit costs of certain architecture options can be prohibitively high.

The role of sea ports in end-to-end maritime transport chain emissions

International Nuclear Information System (INIS)

Gibbs, David; Rigot-Muller, Patrick; Mangan, John; Lalwani, Chandra

2014-01-01

This paper's purpose is to investigate the role of sea ports in helping to mitigate the GHG emissions associated with the end-to-end maritime transport chain. The analysis is primarily focused on the UK, but is international in application. The paper is based on both the analysis of secondary data and information on actions taken by ports to reduce their emissions, with the latter data collected for the main UK ports via their published reports and/or via interviews. Only a small number of ports (representing 32% of UK port activity) actually measure and report their carbon emissions in the UK context. The emissions generated by ships calling at these ports are analysed using a method based on Department for Transport Maritime Statistics Data. In addition, a case example (Felixstowe) of emissions associated with HGV movements to and from ports is presented, and data on vessel emissions at berth are also considered. Our analyses indicate that emissions generated by ships during their voyages between ports are of a far greater magnitude than those generated by the port activities. Thus while reducing the ports' own emissions is worthwhile, the results suggest that ports might have more impact through focusing their efforts on reducing shipping emissions. - Highlights: • Investigates role of ports in mitigating GHG emissions in the end-to-end maritime transport chain. • Emissions generated both by ports and by ships calling at ports are analysed. • Shipping's emissions are far greater than those generated by port activities. • Ports may have more impact through focusing efforts on reducing shipping's emissions. • Options for ports to support and drive change in the maritime sector also considered

A new technique for end-to-end ureterostomy in the rat, using an indwelling reabsorbable stent.

Science.gov (United States)

Carmignani, G; Farina, F P; De Stefani, S; Maffezzini, M

1983-01-01

The restoration of the continuity of the urinary tract represents one of the major problems in rat renal transplantation. End-to-end ureterostomy is the most physiologically effective technique; however, it involves noteworthy technical difficulties because of the extremely thin caliber of the ureter in the rat and the high incidence of postoperative hydronephrosis. We describe a new technique for end-to-end ureterostomy in the rat, where the use of an absorbable ureteral stent is recommended. A 5-0 plain catgut thread is used as a stent. The anastomosis is performed under an operating microscope at X 25-40 magnification with interrupted sutures of 11-0 Vicryl. The use of the indwelling stent facilitates the performance of the anastomosis and yields optimal results. The macroscopical, radiological, and histological controls in a group of rats operated on with this technique showed a very high percentage of success with no complications, a result undoubtedly superior to that obtained with conventional methods.

Non-homologous end joining mediated DNA repair is impaired in the NUP98-HOXD13 mouse model for myelodysplastic syndrome.

Science.gov (United States)

Puthiyaveetil, Abdul Gafoor; Reilly, Christopher M; Pardee, Timothy S; Caudell, David L

2013-01-01

Chromosomal translocations typically impair cell differentiation and often require secondary mutations for malignant transformation. However, the role of a primary translocation in the development of collaborating mutations is debatable. To delineate the role of leukemic translocation NUP98-HOXD13 (NHD13) in secondary mutagenesis, DNA break and repair mechanisms in stimulated mouse B lymphocytes expressing NHD13 were analyzed. Our results showed significantly reduced expression of non-homologous end joining (NHEJ)-mediated DNA repair genes, DNA Pkcs, DNA ligase4, and Xrcc4 leading to cell cycle arrest at G2/M phase. Our results showed that expression of NHD13 fusion gene resulted in impaired NHEJ-mediated DNA break repair. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mucociliary clearance following tracheal resection and end-to-end anastomosis.

Science.gov (United States)

Toomes, H; Linder, A

1989-10-01

Mucociliary clearance is an important cleaning system of the bronchial tree. The complex transport system reacts sensitively to medicinal stimuli and inhaled substances. A disturbance causes secretion retention which encourages the development of acute and chronic pulmonary diseases. It is not yet known in which way sectional resection of the central airway effects mucociliary clearance. A large number of the surgical failures are attributable to septic complications in the area of the anastomosis. In order to study the transportation process over the anastomosis, ten dogs underwent a tracheal resection with end-to-end anastomosis, and the mucociliary activity was recorded using a bronchoscopic video-technical method. Recommencement of mucous transport was observed on the third, and transport over the anastomosis from the sixth to tenth, postoperative days. The mucociliary clearance had completely recovered on the twenty-first day in the majority of dogs. Histological examination of the anastomoses nine months postoperatively showed a flat substitute epithelium without cilia-bearing cells in all dogs. This contrasts with the quick restitution of the transport function. In case of undamaged respiratory mucosa, a good adaptation of the resection margins suffices for the mucous film to slide over the anastomosis.

AN AUTOMATED END-TO-END MULTI-AGENT QOS BASED ARCHITECTURE FOR SELECTION OF GEOSPATIAL WEB SERVICES

Directory of Open Access Journals (Sweden)

M. Shah

2012-07-01

With the proliferation of web services published over the internet, multiple web services may provide similar functionality, but with different non-functional properties. Thus, Quality of Service (QoS offers a metric to differentiate the services and their service providers. In a quality-driven selection of web services, it is important to consider non-functional properties of the web service so as to satisfy the constraints or requirements of the end users. The main intent of this paper is to build an automated end-to-end multi-agent based solution to provide the best-fit web service to service requester based on QoS.

Mutagenic effects of carbon ions near the range end in plants

Energy Technology Data Exchange (ETDEWEB)

Hase, Yoshihiro, E-mail: hase.yoshihiro@jaea.go.jp [Ion Beam Mutagenesis Research Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 1233 Watanuki, Takasaki, Gunma 370-1292 (Japan); Yoshihara, Ryouhei; Nozawa, Shigeki; Narumi, Issay [Ion Beam Mutagenesis Research Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 1233 Watanuki, Takasaki, Gunma 370-1292 (Japan)

2012-03-01

To gain insight into the mutagenic effects of accelerated heavy ions in plants, the mutagenic effects of carbon ions near the range end (mean linear energy transfer (LET): 425 keV/{mu}m) were compared with the effects of carbon ions penetrating the seeds (mean LET: 113 keV/{mu}m). Mutational analysis by plasmid rescue of Escherichia coli rpsL from irradiated Arabidopsis plants showed a 2.7-fold increase in mutant frequency for 113 keV/{mu}m carbon ions, whereas no enhancement of mutant frequency was observed for carbon ions near the range end. This suggested that carbon ions near the range end induced mutations that were not recovered by plasmid rescue. An Arabidopsis DNA ligase IV mutant, deficient in non-homologous end-joining repair, showed hyper-sensitivity to both types of carbon-ion irradiation. The difference in radiation sensitivity between the wild type and the repair-deficient mutant was greatly diminished for carbon ions near the range end, suggesting that these ions induce irreparable DNA damage. Mutational analysis of the Arabidopsis GL1 locus showed that while the frequency of generation of glabrous mutant sectors was not different between the two types of carbon-ion irradiation, large deletions (>{approx}30 kb) were six times more frequently induced by carbon ions near the range end. When 352 keV/{mu}m neon ions were used, these showed a 6.4 times increase in the frequency of induced large deletions compared with the 113 keV/{mu}m carbon ions. We suggest that the proportion of large deletions increases with LET in plants, as has been reported for mammalian cells. The nature of mutations induced in plants by carbon ions near the range end is discussed in relation to mutation detection by plasmid rescue and transmissibility to progeny.

Distancing sedation in end-of-life care from physician-assisted suicide and euthanasia

Science.gov (United States)

Soh, Tze Ling Gwendoline Beatrice; Krishna, Lalit Kumar Radha; Sim, Shin Wei; Yee, Alethea Chung Peng

2016-01-01

Lipuma equates continuous sedation until death (CSD) to physician-assisted suicide/euthanasia (PAS/E) based on the premise that iatrogenic unconsciousness negates social function and, thus, personhood, leaving a patient effectively ‘dead’. Others have extrapolated upon this position further, to suggest that any use of sedation and/or opioids at the end of life would be analogous to CSD and thus tantamount to PAS/E. These posits sit diametrically opposite to standard end-of-life care practices. This paper will refute Lipuma’s position and the posits borne from it. We first show that prevailing end-of-life care guidelines require proportional and monitored use of sedatives and/or opioids to attenuate fears that the use of such treatment could hasten death. These guidelines also classify CSD as a last resort treatment, employed only when symptoms prove intractable, and not amenable to all standard treatment options. Furthermore, CSD is applied only when deemed appropriate by a multidisciplinary palliative medicine team. We also show that empirical data based on local views of personhood will discount concerns that iatrogenic unconsciousness is tantamount to a loss of personhood and death. PMID:27211055

Distancing sedation in end-of-life care from physician-assisted suicide and euthanasia.

Science.gov (United States)

Soh, Tze Ling Gwendoline Beatrice; Krishna, Lalit Kumar Radha; Sim, Shin Wei; Yee, Alethea Chung Peng

2016-05-01

Lipuma equates continuous sedation until death (CSD) to physician-assisted suicide/euthanasia (PAS/E) based on the premise that iatrogenic unconsciousness negates social function and, thus, personhood, leaving a patient effectively 'dead'. Others have extrapolated upon this position further, to suggest that any use of sedation and/or opioids at the end of life would be analogous to CSD and thus tantamount to PAS/E. These posits sit diametrically opposite to standard end-of-life care practices. This paper will refute Lipuma's position and the posits borne from it. We first show that prevailing end-of-life care guidelines require proportional and monitored use of sedatives and/or opioids to attenuate fears that the use of such treatment could hasten death. These guidelines also classify CSD as a last resort treatment, employed only when symptoms prove intractable, and not amenable to all standard treatment options. Furthermore, CSD is applied only when deemed appropriate by a multidisciplinary palliative medicine team. We also show that empirical data based on local views of personhood will discount concerns that iatrogenic unconsciousness is tantamount to a loss of personhood and death. Copyright: © Singapore Medical Association.

Evaluation of Techniques to Detect Significant Network Performance Problems using End-to-End Active Network Measurements

Energy Technology Data Exchange (ETDEWEB)

Cottrell, R.Les; Logg, Connie; Chhaparia, Mahesh; /SLAC; Grigoriev, Maxim; /Fermilab; Haro, Felipe; /Chile U., Catolica; Nazir, Fawad; /NUST, Rawalpindi; Sandford, Mark

2006-01-25

End-to-End fault and performance problems detection in wide area production networks is becoming increasingly hard as the complexity of the paths, the diversity of the performance, and dependency on the network increase. Several monitoring infrastructures are built to monitor different network metrics and collect monitoring information from thousands of hosts around the globe. Typically there are hundreds to thousands of time-series plots of network metrics which need to be looked at to identify network performance problems or anomalous variations in the traffic. Furthermore, most commercial products rely on a comparison with user configured static thresholds and often require access to SNMP-MIB information, to which a typical end-user does not usually have access. In our paper we propose new techniques to detect network performance problems proactively in close to realtime and we do not rely on static thresholds and SNMP-MIB information. We describe and compare the use of several different algorithms that we have implemented to detect persistent network problems using anomalous variations analysis in real end-to-end Internet performance measurements. We also provide methods and/or guidance for how to set the user settable parameters. The measurements are based on active probes running on 40 production network paths with bottlenecks varying from 0.5Mbits/s to 1000Mbit/s. For well behaved data (no missed measurements and no very large outliers) with small seasonal changes most algorithms identify similar events. We compare the algorithms' robustness with respect to false positives and missed events especially when there are large seasonal effects in the data. Our proposed techniques cover a wide variety of network paths and traffic patterns. We also discuss the applicability of the algorithms in terms of their intuitiveness, their speed of execution as implemented, and areas of applicability. Our encouraging results compare and evaluate the accuracy of our

Surgical approach to end-stage heart failure.

Science.gov (United States)

Klotz, Stefan; Scheld, Hans H

2011-02-01

End-stage heart failure is a challenging disease with growing incidence. With decreasing heart transplant rates worldwide organ preserving therapies become, again, of interest. The purpose of the present review is to examine the potential challenges of surgical therapies in patients with end-stage heart failure. The gold-standard for end-stage heart failure is and will be cardiac transplantation. However, due to organ shortage this therapy is limited to a few patients. Therefore implantation of ventricular assist devices (VADs) or long-term minimal-invasive partial support devices will increase. Improvements in device design with smaller devices, easier implantation techniques, and modified anticoagulation outcome and long-term success will likely improve. In addition, good quality of life as destination therapy is almost available. Organ conservation surgery (coronary artery bypass grafting and surgical ventricular restoration or surgical repair of mitral valve regurgitation) in end-stage heart failure patients could not prove the expected results. Transcatheter or minimal-invasive approaches of these therapies might become routine in the near future. Due to the overwhelming outcome rates, cardiac transplantation is the most established surgical therapy for end-stage heart failure. VAD therapy is increasing and minimized VADs might further open the market for destination therapy/permanent support.

Understanding Effect of Constraint Release Environment on End-to-End Vector Relaxation of Linear Polymer Chains

KAUST Repository

Shivokhin, Maksim E.

2017-05-30

We propose and verify methods based on the slip-spring (SSp) model [ Macromolecules 2005, 38, 14 ] for predicting the effect of any monodisperse, binary, or ternary environment of topological constraints on the relaxation of the end-to-end vector of a linear probe chain. For this purpose we first validate the ability of the model to consistently predict both the viscoelastic and dielectric response of monodisperse and binary mixtures of type A polymers, based on published experimental data. We also report the synthesis of new binary and ternary polybutadiene systems, the measurement of their linear viscoelastic response, and the prediction of these data by the SSp model. We next clarify the relaxation mechanisms of probe chains in these constraint release (CR) environments by analyzing a set of "toy" SSp models with simplified constraint release rates, by examining fluctuations of the end-to-end vector. In our analysis, the longest relaxation time of the probe chain is determined by a competition between the longest relaxation times of the effective CR motions of the fat and thin tubes and the motion of the chain itself in the thin tube. This picture is tested by the analysis of four model systems designed to separate and estimate every single contribution involved in the relaxation of the probe\\'s end-to-end vector in polydisperse systems. We follow the CR picture of Viovy et al. [ Macromolecules 1991, 24, 3587 ] and refine the effective chain friction in the thin and fat tubes based on Read et al. [ J. Rheol. 2012, 56, 823 ]. The derived analytical equations form a basis for generalizing the proposed methodology to polydisperse mixtures of linear and branched polymers. The consistency between the SSp model and tube model predictions is a strong indicator of the compatibility between these two distinct mesoscopic frameworks.

Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks.

Science.gov (United States)

Stephanou, Nicolas C; Gao, Feng; Bongiorno, Paola; Ehrt, Sabine; Schnappinger, Dirk; Shuman, Stewart; Glickman, Michael S

2007-07-01

Bacterial nonhomologous end joining (NHEJ) is a recently described DNA repair pathway best characterized in mycobacteria. Bacterial NHEJ proteins LigD and Ku have been analyzed biochemically, and their roles in linear plasmid repair in vivo have been verified genetically; yet the contributions of NHEJ to repair of chromosomal DNA damage are unknown. Here we use an extensive set of NHEJ- and homologous recombination (HR)-deficient Mycobacterium smegmatis strains to probe the importance of HR and NHEJ in repairing diverse types of chromosomal DNA damage. An M. smegmatis Delta recA Delta ku double mutant has no apparent growth defect in vitro. Loss of the NHEJ components Ku and LigD had no effect on sensitivity to UV radiation, methyl methanesulfonate, or quinolone antibiotics. NHEJ deficiency had no effect on sensitivity to ionizing radiation in logarithmic- or early-stationary-phase cells but was required for ionizing radiation resistance in late stationary phase in 7H9 but not LB medium. In addition, NHEJ components were required for repair of I-SceI mediated chromosomal double-strand breaks (DSBs), and in the absence of HR, the NHEJ pathway rapidly mutates the chromosomal break site. The molecular outcomes of NHEJ-mediated chromosomal DSB repair involve predominantly single-nucleotide insertions at the break site, similar to previous findings using plasmid substrates. These findings demonstrate that prokaryotic NHEJ is specifically required for DSB repair in late stationary phase and can mediate mutagenic repair of homing endonuclease-generated chromosomal DSBs.

Double Strand Break Repair, one mechanism can hide another: Alternative non-homologous end joining

International Nuclear Information System (INIS)

Rass, E.; Grabarz, A.; Bertrand, P.; Lopez, B.S.

2012-01-01

DNA double strand breaks are major cytotoxic lesions encountered by the cells. They can be induced by ionizing radiation or endogenous stress and can lead to genetic instability. Two mechanisms compete for the repair of DNA double strand breaks: homologous recombination and non-homologous end joining (NHEJ). Homologous recombination requires DNA sequences homology and is initiated by single strand resection. Recently, advances have been made concerning the major steps and proteins involved in resection. NHEJ, in contrast, does not require sequence homology. The existence of a DNA double strand break repair mechanism, independent of KU and ligase IV, the key proteins of the canonical non homologous end joining pathway, has been revealed lately and named alternative non homologous end joining. The hallmarks of this highly mutagenic pathway are deletions at repair junctions and frequent use of distal micro-homologies. This mechanism is also initiated by a single strand resection of the break. The aim of this review is firstly to present recent data on single strand resection, and secondly the alternative NHEJ pathway, including a discussion on the fidelity of NHEJ. Based on current knowledge, canonical NHEJ does not appear as an intrinsically mutagenic mechanism, but in contrast, as a conservative one. The structure of broken DNA ends actually dictates the quality repair of the alternative NHEJ and seems the actual responsible for the mutagenesis attributed beforehand to the canonical NHEJ. The existence of this novel DNA double strand breaks repair mechanism needs to be taken into account in the development of radiosensitizing strategies in order to optimise the efficiency of radiotherapy. (authors)

Debris mitigation measures by satellite design and operational methods - Findings from the DLR space debris End-to-End Service

Science.gov (United States)

Sdunnus, H.; Beltrami, P.; Janovsky, R.; Koppenwallner, G.; Krag, H.; Reimerdes, H.; Schäfer, F.

Debris Mitigation has been recognised as an issue to be addressed by the space faring nations around the world. Currently, there are various activities going on, aiming at the establishment of debris mitigation guidelines on various levels, reaching from the UN down to national space agencies. Though guidelines established on the national level already provide concrete information how things should be done (rather that specifying what should be done or providing fundamental principles) potential users of the guidelines will still have the need to explore the technical, management, and financial implications of the guidelines for their projects. Those questions are addressed by the so called "Space Debris End-to-End Service" project, which has been initiated as a national initiative of the German Aerospace Centre (DLR). Based on a review of already existing mitigation guidelines or guidelines under development and following an identification of needs from a circle of industrial users the "End-to-End Service Gu idelines" have been established for designer and operators of spacecraft. The End-to-End Service Guidelines are based on requirements addressed by the mitigation guidelines and provide recommendations how and when the technical consideration of the mitigation guidelines should take place. By referencing requirements from the mitigation guidelines, the End-to-End Service Guidelines address the consideration of debris mitigation measures by spacecraft design and operational measures. This paper will give an introduction to the End-to-End Service Guidelines. It will focus on the proposals made for mitigation measures by the S/C system design, i.e. on protective design measures inside the spacecraft and on design measures, e.g. innovative protective (shielding) systems. Furthermore, approaches on the analytical optimisation of protective systems will be presented, aiming at the minimisation of shield mass under conservation of the protective effects. On the

Experimental evaluation of end-to-end delay in switched Ethernet application in the automotive domain

OpenAIRE

Beretis , Kostas; Symeonidis , Ieroklis

2013-01-01

International audience; This article presents an approach for deriving upper bound for end-to-end delay in a double star switched Ethernet network. Four traffic classes, following a strict priority queuing policy, were considered. The theoretical analysis was based on network calculus. An experimental setup, which accu-rately reflects an automotive communication network, was implemented in or-der to evaluate the theoretical model. The results obtained by the experiments provided valuable feed...

End-to-End Multimodal Emotion Recognition Using Deep Neural Networks

Science.gov (United States)

Tzirakis, Panagiotis; Trigeorgis, George; Nicolaou, Mihalis A.; Schuller, Bjorn W.; Zafeiriou, Stefanos

2017-12-01

Automatic affect recognition is a challenging task due to the various modalities emotions can be expressed with. Applications can be found in many domains including multimedia retrieval and human computer interaction. In recent years, deep neural networks have been used with great success in determining emotional states. Inspired by this success, we propose an emotion recognition system using auditory and visual modalities. To capture the emotional content for various styles of speaking, robust features need to be extracted. To this purpose, we utilize a Convolutional Neural Network (CNN) to extract features from the speech, while for the visual modality a deep residual network (ResNet) of 50 layers. In addition to the importance of feature extraction, a machine learning algorithm needs also to be insensitive to outliers while being able to model the context. To tackle this problem, Long Short-Term Memory (LSTM) networks are utilized. The system is then trained in an end-to-end fashion where - by also taking advantage of the correlations of the each of the streams - we manage to significantly outperform the traditional approaches based on auditory and visual handcrafted features for the prediction of spontaneous and natural emotions on the RECOLA database of the AVEC 2016 research challenge on emotion recognition.

Primary and secondary structure dependence of peptide flexibility assessed by fluorescence-based measurement of end-to-end collision rates.

Science.gov (United States)

Huang, Fang; Hudgins, Robert R; Nau, Werner M

2004-12-22

The intrachain fluorescence quenching of the fluorophore 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) is measured in short peptide fragments, namely the two strands and the turn of the N-terminal beta-hairpin of ubiquitin. The investigated peptides adopt a random-coil conformation in aqueous solution according to CD and NMR experiments. The combination of quenchers with different quenching efficiencies, namely tryptophan and tyrosine, allows the extrapolation of the rate constants for end-to-end collision rates as well as the dissociation of the end-to-end encounter complex. The measured activation energies for fluorescence quenching demonstrate that the end-to-end collision process in peptides is partially controlled by internal friction within the backbone, while measurements in solvents of different viscosities (H2O, D2O, and 7.0 M guanidinium chloride) suggest that solvent friction is an additional important factor in determining the collision rate. The extrapolated end-to-end collision rates, which are only slightly larger than the experimental rates for the DBO/Trp probe/quencher system, provide a measure of the conformational flexibility of the peptide backbone. The chain flexibility is found to be strongly dependent on the type of secondary structure that the peptides represent. The collision rates for peptides derived from the beta-strand motifs (ca. 1 x 10(7) s(-1)) are ca. 4 times slower than that derived from the beta-turn. The results provide further support for the hypothesis that chain flexibility is an important factor in the preorganization of protein fragments during protein folding. Mutations to the beta-turn peptide show that subtle sequence changes strongly affect the flexibility of peptides as well. The protonation and charge status of the peptides, however, are shown to have no significant effect on the flexibility of the investigated peptides. The meaning and definition of end-to-end collision rates in the context of protein folding are critically

LSPR Coupling and Distribution of Interparticle Distances between Nanoparticles in Hydrogel on Optical Fiber End Face

Directory of Open Access Journals (Sweden)

Harald Ian Muri

2017-11-01

Full Text Available We report on a new localized surface plasmon resonance (LSPR-based optical fiber (OF architecture with a potential in sensor applications. The LSPR-OF system is fabricated by immobilizing gold nanoparticles (GNPs in a hydrogel droplet polymerized on the fiber end face. This design has several advantages over earlier designs. It dramatically increase the number nanoparticles (NP available for sensing, it offers precise control over the NP density, and the NPs are positioned in a true 3D aqueous environment. The OF-hydrogel design is also compatible with low-cost manufacturing. The LSPR-OF platform can measure volumetric changes in a stimuli-responsive hydrogel or measure binding to receptors on the NP surface. It can also be used as a two-parameter sensor by utilizing both effects. We present results from proof-of-concept experiments exploring the properties of LSPR and interparticle distances of the GNP-hydrogel OF design by characterizing the distribution of distances between NPs in the hydrogel, the refractive index of the hydrogel and the LSPR attributes of peak position, amplitude and linewidth for hydrogel deswelling controlled with pH solutions.

End-to-End Neural Optical Music Recognition of Monophonic Scores

Directory of Open Access Journals (Sweden)

Jorge Calvo-Zaragoza

2018-04-01

Full Text Available Optical Music Recognition is a field of research that investigates how to computationally decode music notation from images. Despite the efforts made so far, there are hardly any complete solutions to the problem. In this work, we study the use of neural networks that work in an end-to-end manner. This is achieved by using a neural model that combines the capabilities of convolutional neural networks, which work on the input image, and recurrent neural networks, which deal with the sequential nature of the problem. Thanks to the use of the the so-called Connectionist Temporal Classification loss function, these models can be directly trained from input images accompanied by their corresponding transcripts into music symbol sequences. We also present the Printed Music Scores dataset, containing more than 80,000 monodic single-staff real scores in common western notation, that is used to train and evaluate the neural approach. In our experiments, it is demonstrated that this formulation can be carried out successfully. Additionally, we study several considerations about the codification of the output musical sequences, the convergence and scalability of the neural models, as well as the ability of this approach to locate symbols in the input score.

Semantic Complex Event Processing over End-to-End Data Flows

Energy Technology Data Exchange (ETDEWEB)

Zhou, Qunzhi [University of Southern California; Simmhan, Yogesh; Prasanna, Viktor K.

2012-04-01

Emerging Complex Event Processing (CEP) applications in cyber physical systems like SmartPower Grids present novel challenges for end-to-end analysis over events, flowing from heterogeneous information sources to persistent knowledge repositories. CEP for these applications must support two distinctive features - easy specification patterns over diverse information streams, and integrated pattern detection over realtime and historical events. Existing work on CEP has been limited to relational query patterns, and engines that match events arriving after the query has been registered. We propose SCEPter, a semantic complex event processing framework which uniformly processes queries over continuous and archived events. SCEPteris built around an existing CEP engine with innovative support for semantic event pattern specification and allows their seamless detection over past, present and future events. Specifically, we describe a unified semantic query model that can operate over data flowing through event streams to event repositories. Compile-time and runtime semantic patterns are distinguished and addressed separately for efficiency. Query rewriting is examined and analyzed in the context of temporal boundaries that exist between event streams and their repository to avoid duplicate or missing results. The design and prototype implementation of SCEPterare analyzed using latency and throughput metrics for scenarios from the Smart Grid domain.

Human induced pluripotent cells resemble embryonic stem cells demonstrating enhanced levels of DNA repair and efficacy of nonhomologous end-joining

Energy Technology Data Exchange (ETDEWEB)

Fan Jinshui; Robert, Carine [Department of Radiation Oncology, University of Maryland School of Medicine, 655 West Baltimore Street, BRB 7-023A, Baltimore, MD 21201 (United States); Jang, Yoon-Young; Liu Hua; Sharkis, Saul; Baylin, Stephen Bruce [Johns Hopkins University School of Medicine, Department of Oncology, Baltimore, MD 21231-1000 (United States); Rassool, Feyruz Virgilia, E-mail: frassool@som.umaryland.edu [Department of Radiation Oncology, University of Maryland School of Medicine, 655 West Baltimore Street, BRB 7-023A, Baltimore, MD 21201 (United States)

2011-08-01

Highlights: {yields} iPSC and hESC demonstrate a similar cell cycle profile, with increased S phase cells and decreased G0/G1. {yields} iPSC and hESC increased ROS and decreased DSBs, compared with differentiated parental cells. {yields} iPSC and hESC demonstrate elevated DSB repair activity, including nonhomologous end-joining, compared with differentiated parental cells. {yields} iPSC however show a partial apoptotic response to DNA damage, compared to hESC. {yields} DNA damage responses may constitute important markers for the efficacy of iPSC reprogramming. - Abstract: To maintain the integrity of the organism, embryonic stem cells (ESC) need to maintain their genomic integrity in response to DNA damage. DNA double strand breaks (DSBs) are one of the most lethal forms of DNA damage and can have disastrous consequences if not repaired correctly, leading to cell death, genomic instability and cancer. How human ESC (hESC) maintain genomic integrity in response to agents that cause DSBs is relatively unclear. Adult somatic cells can be induced to 'dedifferentiate' into induced pluripotent stem cells (iPSC) and reprogram into cells of all three germ layers. Whether iPSC have reprogrammed the DNA damage response is a critical question in regenerative medicine. Here, we show that hESC demonstrate high levels of endogenous reactive oxygen species (ROS) which can contribute to DNA damage and may arise from high levels of metabolic activity. To potentially counter genomic instability caused by DNA damage, we find that hESC employ two strategies: First, these cells have enhanced levels of DNA repair proteins, including those involved in repair of DSBs, and they demonstrate elevated nonhomologous end-joining (NHEJ) activity and repair efficacy, one of the main pathways for repairing DSBs. Second, they are hypersensitive to DNA damaging agents, as evidenced by a high level of apoptosis upon irradiation. Importantly, iPSC, unlike the parent cells they are derived

Human induced pluripotent cells resemble embryonic stem cells demonstrating enhanced levels of DNA repair and efficacy of nonhomologous end-joining

International Nuclear Information System (INIS)

Fan Jinshui; Robert, Carine; Jang, Yoon-Young; Liu Hua; Sharkis, Saul; Baylin, Stephen Bruce; Rassool, Feyruz Virgilia

2011-01-01

Highlights: → iPSC and hESC demonstrate a similar cell cycle profile, with increased S phase cells and decreased G0/G1. → iPSC and hESC increased ROS and decreased DSBs, compared with differentiated parental cells. → iPSC and hESC demonstrate elevated DSB repair activity, including nonhomologous end-joining, compared with differentiated parental cells. → iPSC however show a partial apoptotic response to DNA damage, compared to hESC. → DNA damage responses may constitute important markers for the efficacy of iPSC reprogramming. - Abstract: To maintain the integrity of the organism, embryonic stem cells (ESC) need to maintain their genomic integrity in response to DNA damage. DNA double strand breaks (DSBs) are one of the most lethal forms of DNA damage and can have disastrous consequences if not repaired correctly, leading to cell death, genomic instability and cancer. How human ESC (hESC) maintain genomic integrity in response to agents that cause DSBs is relatively unclear. Adult somatic cells can be induced to 'dedifferentiate' into induced pluripotent stem cells (iPSC) and reprogram into cells of all three germ layers. Whether iPSC have reprogrammed the DNA damage response is a critical question in regenerative medicine. Here, we show that hESC demonstrate high levels of endogenous reactive oxygen species (ROS) which can contribute to DNA damage and may arise from high levels of metabolic activity. To potentially counter genomic instability caused by DNA damage, we find that hESC employ two strategies: First, these cells have enhanced levels of DNA repair proteins, including those involved in repair of DSBs, and they demonstrate elevated nonhomologous end-joining (NHEJ) activity and repair efficacy, one of the main pathways for repairing DSBs. Second, they are hypersensitive to DNA damaging agents, as evidenced by a high level of apoptosis upon irradiation. Importantly, iPSC, unlike the parent cells they are derived from, mimic hESC in their ROS levels

Optimized capture section for a muon accelerator front end

Directory of Open Access Journals (Sweden)

Hisham Kamal Sayed

2014-07-01

Full Text Available In a muon accelerator complex, a target is bombarded by a multi-MW proton beam to produce pions, which decay into the muons which are thereafter bunched, cooled, and accelerated. The front end of the complex captures those pions, then manipulates their phase space, and that of the muons into which they decay, to maximize the number of muons within the acceptance of the downstream systems. The secondary pion beam produced at the target is captured by a high field target solenoid that tapers down to a constant field throughout the rest of the front end. In this study we enhance the useful muon flux by introducing a new design of the longitudinal profile of the solenoid field at, and downstream of, the target. We find that the useful muon flux exiting the front end is larger when the field at the target is higher, the distance over which the field tapers down is shorter, and the field at the end of the taper is higher. We describe how the solenoid field profile impacts the transverse and longitudinal phase space of the beam and thereby leads to these dependencies.

Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway

Science.gov (United States)

Weeden, Clare E.; Chen, Yunshun; Ma, Stephen B.; Hu, Yifang; Ramm, Georg; Sutherland, Kate D.; Smyth, Gordon K.

2017-01-01

Lung squamous cell carcinoma (SqCC), the second most common subtype of lung cancer, is strongly associated with tobacco smoking and exhibits genomic instability. The cellular origins and molecular processes that contribute to SqCC formation are largely unexplored. Here we show that human basal stem cells (BSCs) isolated from heavy smokers proliferate extensively, whereas their alveolar progenitor cell counterparts have limited colony-forming capacity. We demonstrate that this difference arises in part because of the ability of BSCs to repair their DNA more efficiently than alveolar cells following ionizing radiation or chemical-induced DNA damage. Analysis of mice harbouring a mutation in the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key enzyme in DNA damage repair by nonhomologous end joining (NHEJ), indicated that BSCs preferentially repair their DNA by this error-prone process. Interestingly, polyploidy, a phenomenon associated with genetically unstable cells, was only observed in the human BSC subset. Expression signature analysis indicated that BSCs are the likely cells of origin of human SqCC and that high levels of NHEJ genes in SqCC are correlated with increasing genomic instability. Hence, our results favour a model in which heavy smoking promotes proliferation of BSCs, and their predilection for error-prone NHEJ could lead to the high mutagenic burden that culminates in SqCC. Targeting DNA repair processes may therefore have a role in the prevention and therapy of SqCC. PMID:28125611

End-to-end models for marine ecosystems: Are we on the precipice of a significant advance or just putting lipstick on a pig?

Directory of Open Access Journals (Sweden)

Kenneth A. Rose

2012-02-01

Full Text Available There has been a rapid rise in the development of end-to-end models for marine ecosystems over the past decade. Some reasons for this rise include need for predicting effects of climate change on biota and dissatisfaction with existing models. While the benefits of a well-implemented end-to-end model are straightforward, there are many challenges. In the short term, my view is that the major role of end-to-end models is to push the modelling community forward, and to identify critical data so that these data can be collected now and thus be available for the next generation of end-to-end models. I think we should emulate physicists and build theoretically-oriented models first, and then collect the data. In the long-term, end-to-end models will increase their skill, data collection will catch up, and end-to-end models will move towards site-specific applications with forecasting and management capabilities. One pathway into the future is individual efforts, over-promise, and repackaging of poorly performing component submodels (“lipstick on a pig”. The other pathway is a community-based collaborative effort, with appropriate caution and thoughtfulness, so that the needed improvements are achieved (“significant advance”. The promise of end-to-end modelling is great. We should act now to avoid missing a great opportunity.

End of Life Issues

Science.gov (United States)

Planning for the end of life can be difficult. But by deciding what end-of-life care best suits your needs when you are healthy, you can ... right choices when the time comes. End-of-life planning usually includes making choices about the following: ...

An End-to-End System to Enable Quick, Easy and Inexpensive Deployment of Hydrometeorological Stations

Science.gov (United States)

Celicourt, P.; Piasecki, M.

2014-12-01

The high cost of hydro-meteorological data acquisition, communication and publication systems along with limited qualified human resources is considered as the main reason why hydro-meteorological data collection remains a challenge especially in developing countries. Despite significant advances in sensor network technologies which gave birth to open hardware and software, low-cost (less than $50) and low-power (in the order of a few miliWatts) sensor platforms in the last two decades, sensors and sensor network deployment remains a labor-intensive, time consuming, cumbersome, and thus expensive task. These factors give rise for the need to develop a affordable, simple to deploy, scalable and self-organizing end-to-end (from sensor to publication) system suitable for deployment in such countries. The design of the envisioned system will consist of a few Sensed-And-Programmed Arduino-based sensor nodes with low-cost sensors measuring parameters relevant to hydrological processes and a Raspberry Pi micro-computer hosting the in-the-field back-end data management. This latter comprises the Python/Django model of the CUAHSI Observations Data Model (ODM) namely DjangODM backed by a PostgreSQL Database Server. We are also developing a Python-based data processing script which will be paired with the data autoloading capability of Django to populate the DjangODM database with the incoming data. To publish the data, the WOFpy (WaterOneFlow Web Services in Python) developed by the Texas Water Development Board for 'Water Data for Texas' which can produce WaterML web services from a variety of back-end database installations such as SQLite, MySQL, and PostgreSQL will be used. A step further would be the development of an appealing online visualization tool using Python statistics and analytics tools (Scipy, Numpy, Pandas) showing the spatial distribution of variables across an entire watershed as a time variant layer on top of a basemap.

RPA accumulation during class switch recombination represents 5'-3' DNA-end resection during the S-G2/M phase of the cell cycle.

Science.gov (United States)

Yamane, Arito; Robbiani, Davide F; Resch, Wolfgang; Bothmer, Anne; Nakahashi, Hirotaka; Oliveira, Thiago; Rommel, Philipp C; Brown, Eric J; Nussenzweig, Andre; Nussenzweig, Michel C; Casellas, Rafael

2013-01-31

Activation-induced cytidine deaminase (AID) promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in the G1 phase. RPA is a single-stranded DNA (ssDNA)-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR), such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here, we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, recombination-activating genes (RAG), or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in the S-G2/M phase is extensive, ATM independent, and associated with Rad51 accumulation. In the S-G2/M phase, RPA increases in nonhomologous-end-joining-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during class switch recombination represents salvage of unrepaired breaks by homology-based pathways during the S-G2/M phase of the cell cycle. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

An end-to-end coupled model ROMS-N 2 P 2 Z 2 D 2 -OSMOSE of ...

African Journals Online (AJOL)

An end-to-end coupled model ROMS-N 2 P 2 Z 2 D 2 -OSMOSE of the southern Benguela foodweb: parameterisation, calibration and pattern-oriented validation. ... We also highlight the capacity of this model for tracking indicators at various hierarchical levels. Keywords: individual-based model, model validation, ...

Crosstalk in an FDM Laboratory Setup and the Athena X-IFU End-to-End Simulator

Science.gov (United States)

den Hartog, R.; Kirsch, C.; de Vries, C.; Akamatsu, H.; Dauser, T.; Peille, P.; Cucchetti, E.; Jackson, B.; Bandler, S.; Smith, S.; Wilms, J.

2018-04-01

The impact of various crosstalk mechanisms on the performance of the Athena X-IFU instrument has been assessed with detailed end-to-end simulations. For the crosstalk in the electrical circuit, a detailed model has been developed. In this contribution, we test this model against measurements made with an FDM laboratory setup and discuss the assumption of deterministic crosstalk in the context of the weak link effect in the detectors. We conclude that crosstalk levels predicted by the model are conservative with respect to the observed levels.

The end-to-end testbed of the optical metrology system on-board LISA Pathfinder

Energy Technology Data Exchange (ETDEWEB)

Steier, F; Cervantes, F Guzman; Marin, A F GarcIa; Heinzel, G; Danzmann, K [Max-Planck-Institut fuer Gravitationsphysik (Albert-Einstein-Institut) and Universitaet Hannover (Germany); Gerardi, D, E-mail: frank.steier@aei.mpg.d [EADS Astrium Satellites GmbH, Friedrichshafen (Germany)

2009-05-07

LISA Pathfinder is a technology demonstration mission for the Laser Interferometer Space Antenna (LISA). The main experiment on-board LISA Pathfinder is the so-called LISA Technology Package (LTP) which has the aim to measure the differential acceleration between two free-falling test masses with an accuracy of 3 x 10{sup -14} ms{sup -2} Hz{sup -1/2} between 1 mHz and 30 mHz. This measurement is performed interferometrically by the optical metrology system (OMS) on-board LISA Pathfinder. In this paper, we present the development of an experimental end-to-end testbed of the entire OMS. It includes the interferometer and its sub-units, the interferometer backend which is a phasemeter and the processing of the phasemeter output data. Furthermore, three-axes piezo-actuated mirrors are used instead of the free-falling test masses for the characterization of the dynamic behaviour of the system and some parts of the drag-free and attitude control system (DFACS) which controls the test masses and the satellite. The end-to-end testbed includes all parts of the LTP that can reasonably be tested on earth without free-falling test masses. At its present status it consists mainly of breadboard components. Some of those have already been replaced by engineering models of the LTP experiment. In the next steps, further engineering and flight models will also be inserted in this testbed and tested against well-characterized breadboard components. The presented testbed is an important reference for the unit tests and can also be used for validation of the on-board experiment during the mission.

Nuclear fuel element end fitting

International Nuclear Information System (INIS)

Jabsen, F.S.

1980-01-01

An invention is described whereby end fittings are formed from lattices of mutually perpendicular plates. At the plate intersections, sockets are secured to the end fittings in a manner that permits the longitudinal axes of each of the sockets to align with the respective lines of intersection of the plates. The sockets all protrude above one of the surfaces of the end fitting. Further, a detent is formed in the proturding sides of each of the sockets. Annular grooves are formed in each of the ends of the fuel rods that are to be mounted between the end fittings. The socket detents protrude into the respective annular grooves, thus engaging the grooves and retaining the fuel rods and end fittings in one integral structure. (auth)

Synthesis of N-methyl-N-nitrosourea linked to a methidium chloride analogue and its reactions with 32P-end-labeled DNA

International Nuclear Information System (INIS)

Konakahara, T.; Wurdeman, R.L.; Gold, B.

1988-01-01

The synthesis and characterization of an N-methyl-N-nitrosourea (MNU) analogue that is covalently linked to methidium nucleus (9) is described. At 37/degrees/C in pH 8.0 buffer 9 hydrolyzes via pseudo-first-order kinetics, with a calculated t/sub 1/2/ = 77 min. By use of polyacrylamide sequencing gels the formation of piperidine-labile N 7 -methylguanine adducts from the reaction of 9 and MNU with 5'- 32 P-end-labeled DNA restriction fragments is reported. DNA methylation by 9 in 10 mM Tris buffer is enhanced with increasing ionic strength (50-200 mM NaCl), which contrasts to the inhibition of MNU-induced cleavage with increasing salt. In addition, 9 methylates all G sites equally, while MNU shows a clear preference for d(G)/sub n/ (n ≥ 3) runs and an asymmetrical methylation pattern within these G-rich regions. The results are discussed in terms of the delivery of the MNU moiety to the DNA target by a non-sequence-specific intercalation process and the subsequent hydrolytic generation of a nondiffusible alkylating intermediate

End-to-End Joint Antenna Selection Strategy and Distributed Compress and Forward Strategy for Relay Channels

Directory of Open Access Journals (Sweden)

Rahul Vaze

2009-01-01

Full Text Available Multihop relay channels use multiple relay stages, each with multiple relay nodes, to facilitate communication between a source and destination. Previously, distributed space-time codes were proposed to maximize the achievable diversity-multiplexing tradeoff; however, they fail to achieve all the points of the optimal diversity-multiplexing tradeoff. In the presence of a low-rate feedback link from the destination to each relay stage and the source, this paper proposes an end-to-end antenna selection (EEAS strategy as an alternative to distributed space-time codes. The EEAS strategy uses a subset of antennas of each relay stage for transmission of the source signal to the destination with amplifying and forwarding at each relay stage. The subsets are chosen such that they maximize the end-to-end mutual information at the destination. The EEAS strategy achieves the corner points of the optimal diversity-multiplexing tradeoff (corresponding to maximum diversity gain and maximum multiplexing gain and achieves better diversity gain at intermediate values of multiplexing gain, versus the best-known distributed space-time coding strategies. A distributed compress and forward (CF strategy is also proposed to achieve all points of the optimal diversity-multiplexing tradeoff for a two-hop relay channel with multiple relay nodes.

How to engage end-users in smart energy behaviour?

Directory of Open Access Journals (Sweden)

Valkering Pieter

2014-01-01

Full Text Available End users will play a crucial role in up-coming smart grids that aim to link end-users and energy providers in a better balanced and more efficient electricity system. Within this context, this paper aims to deliver a coherent view on current good practice in end-user engagement in smart grid projects. It draws from a recent review of theoretical insights from sustainable consumption behaviour, social marketing and innovation systems and empirical insights from recent smart grid projects to create an inventory of common motivators, enablers and barriers of behavioural change, and the end-user engagement principles that can be derived from that. We conclude with identifying current research challenges as input for a research agenda on end-user engagement in smart grids.

End-to-end Information Flow Security Model for Software-Defined Networks

Directory of Open Access Journals (Sweden)

D. Ju. Chaly

2015-01-01

Full Text Available Software-defined networks (SDN are a novel paradigm of networking which became an enabler technology for many modern applications such as network virtualization, policy-based access control and many others. Software can provide flexibility and fast-paced innovations in the networking; however, it has a complex nature. In this connection there is an increasing necessity of means for assuring its correctness and security. Abstract models for SDN can tackle these challenges. This paper addresses to confidentiality and some integrity properties of SDNs. These are critical properties for multi-tenant SDN environments, since the network management software must ensure that no confidential data of one tenant are leaked to other tenants in spite of using the same physical infrastructure. We define a notion of end-to-end security in context of software-defined networks and propose a semantic model where the reasoning is possible about confidentiality, and we can check that confidential information flows do not interfere with non-confidential ones. We show that the model can be extended in order to reason about networks with secure and insecure links which can arise, for example, in wireless environments.The article is published in the authors’ wording.

Automatic detection of end-diastolic and end-systolic frames in 2D echocardiography.

Science.gov (United States)

Zolgharni, Massoud; Negoita, Madalina; Dhutia, Niti M; Mielewczik, Michael; Manoharan, Karikaran; Sohaib, S M Afzal; Finegold, Judith A; Sacchi, Stefania; Cole, Graham D; Francis, Darrel P

2017-07-01

Correctly selecting the end-diastolic and end-systolic frames on a 2D echocardiogram is important and challenging, for both human experts and automated algorithms. Manual selection is time-consuming and subject to uncertainty, and may affect the results obtained, especially for advanced measurements such as myocardial strain. We developed and evaluated algorithms which can automatically extract global and regional cardiac velocity, and identify end-diastolic and end-systolic frames. We acquired apical four-chamber 2D echocardiographic video recordings, each at least 10 heartbeats long, acquired twice at frame rates of 52 and 79 frames/s from 19 patients, yielding 38 recordings. Five experienced echocardiographers independently marked end-systolic and end-diastolic frames for the first 10 heartbeats of each recording. The automated algorithm also did this. Using the average of time points identified by five human operators as the reference gold standard, the individual operators had a root mean square difference from that gold standard of 46.5 ms. The algorithm had a root mean square difference from the human gold standard of 40.5 ms (P<.0001). Put another way, the algorithm-identified time point was an outlier in 122/564 heartbeats (21.6%), whereas the average human operator was an outlier in 254/564 heartbeats (45%). An automated algorithm can identify the end-systolic and end-diastolic frames with performance indistinguishable from that of human experts. This saves staff time, which could therefore be invested in assessing more beats, and reduces uncertainty about the reliability of the choice of frame. © 2017, Wiley Periodicals, Inc.

An overview of recent end-to-end wireless medical video telemedicine systems using 3G.

Science.gov (United States)

Panayides, A; Pattichis, M S; Pattichis, C S; Schizas, C N; Spanias, A; Kyriacou, E

2010-01-01

Advances in video compression, network technologies, and computer technologies have contributed to the rapid growth of mobile health (m-health) systems and services. Wide deployment of such systems and services is expected in the near future, and it's foreseen that they will soon be incorporated in daily clinical practice. This study focuses in describing the basic components of an end-to-end wireless medical video telemedicine system, providing a brief overview of the recent advances in the field, while it also highlights future trends in the design of telemedicine systems that are diagnostically driven.

[End-of-life care and end-of-life medical decisions: the ITAELD study].

Science.gov (United States)

Miccinesi, Guido; Puliti, Donella; Paci, Eugenio

2011-01-01

To describe the attitudes towards end of life care and the practice of end-of-life medical decisions with possible life-shortening effect among Italian physicians. Cross sectional study (last death among the assisted patients in the last 12 months was considered). In the year 2007, 5,710 GPs and 8,950 hospital physicians were invited all over Italy to participate in the ITAELDstudy through anonymous mail questionnaire. Proportion of agreement with statements on end-of-life care issues. Proportion of deaths with an end-of-life medical decision. The response rate was 19.2%. The 65% of respondents agreed with the duty to respect any non-treatment request of the competent patient, the 55% agreed with the same duty in case of advanced directives, the 39% in case of proxy's request. The 53% of respondents agreed with the ethical acceptability of active euthanasia in selected cases. Among 1,850 deaths the 57.7% did not receive any end-of-life medical decision. For a further 21.0% no decision was possible, being sudden and unexpected deaths. In the remaining 21.3% at least one end-of-life medical decision was reported: 0.8% was classified as physician assisted death, 20.5% as non-treatment decision. Among all deceased the 19.6% were reported to have been deeply sedated. Being favourable to the use of opioids in terminal patients was associated to non-treatment decisions with possible but non-intentional life shortening effect; agreeing with the duty to fully respect any actual non-treatment request of the competent patient was associated to end-of life medical decisions with intentional life-shortening effect (adjusted OR>10 in both cases). The life stance and ethical beliefs of physicians determine their behaviour at the end of life wherever specific statements of law are lacking. Therefore education and debate are needed on these issues.

End-to-end interoperability and workflows from building architecture design to one or more simulations

Science.gov (United States)

Chao, Tian-Jy; Kim, Younghun

2015-02-10

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented that communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.

PEAR: a fast and accurate Illumina Paired-End reAd mergeR.

Science.gov (United States)

Zhang, Jiajie; Kobert, Kassian; Flouri, Tomáš; Stamatakis, Alexandros

2014-03-01

The Illumina paired-end sequencing technology can generate reads from both ends of target DNA fragments, which can subsequently be merged to increase the overall read length. There already exist tools for merging these paired-end reads when the target fragments are equally long. However, when fragment lengths vary and, in particular, when either the fragment size is shorter than a single-end read, or longer than twice the size of a single-end read, most state-of-the-art mergers fail to generate reliable results. Therefore, a robust tool is needed to merge paired-end reads that exhibit varying overlap lengths because of varying target fragment lengths. We present the PEAR software for merging raw Illumina paired-end reads from target fragments of varying length. The program evaluates all possible paired-end read overlaps and does not require the target fragment size as input. It also implements a statistical test for minimizing false-positive results. Tests on simulated and empirical data show that PEAR consistently generates highly accurate merged paired-end reads. A highly optimized implementation allows for merging millions of paired-end reads within a few minutes on a standard desktop computer. On multi-core architectures, the parallel version of PEAR shows linear speedups compared with the sequential version of PEAR. PEAR is implemented in C and uses POSIX threads. It is freely available at http://www.exelixis-lab.org/web/software/pear.

End effects on elbows subjected to moment loadings

International Nuclear Information System (INIS)

Rodabaugh, E.C.; Moore, S.E.

1982-01-01

So-called end effects for moment loadings on short-radius and long-radius butt welding elbows of various arc lengths are investigated with a view toward providing more accurate design formulas for critical piping systems. Data developed in this study, along with published information, were used to develop relatively simple design equations for elbows attached at both ends to long sections of straight pipe. These formulas are the basis for an alternate ASME Code procedure for evaluating the bending moment stresses in Class 1 nuclear piping (ASME Code Case N-319). The more complicated problems of elbows with other end conditions, e.g., flanges at one or both ends, are also considered. Comparisons of recently published experimental and theoretical studies with current industrial code design rules for these situations indicate that these rules also need to be improved

End-to-End Beam Simulations for the New Muon G-2 Experiment at Fermilab

Energy Technology Data Exchange (ETDEWEB)

Korostelev, Maxim [Cockcroft Inst. Accel. Sci. Tech.; Bailey, Ian [Lancaster U.; Herrod, Alexander [Liverpool U.; Morgan, James [Fermilab; Morse, William [RIKEN BNL; Stratakis, Diktys [RIKEN BNL; Tishchenko, Vladimir [RIKEN BNL; Wolski, Andrzej [Cockcroft Inst. Accel. Sci. Tech.

2016-06-01

The aim of the new muon g-2 experiment at Fermilab is to measure the anomalous magnetic moment of the muon with an unprecedented uncertainty of 140 ppb. A beam of positive muons required for the experiment is created by pion decay. Detailed studies of the beam dynamics and spin polarization of the muons are important to predict systematic uncertainties in the experiment. In this paper, we present the results of beam simulations and spin tracking from the pion production target to the muon storage ring. The end-to-end beam simulations are developed in Bmad and include the processes of particle decay, collimation (with accurate representation of all apertures) and spin tracking.

Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

Science.gov (United States)

Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

2003-09-01

Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

Home-end and activity-end preferences for access to and egress from train stations in the Copenhagen region

DEFF Research Database (Denmark)

Halldórsdóttir, Katrín; Nielsen, Otto Anker; Prato, Carlo Giacomo

2017-01-01

. Moreover, model results emphasize the role of bicycle parking in terms of the sheer number of spaces to be increased as well as covered places to be offered at the activity end, de facto giving the possibility to leave a bicycle at that end during the night. Lastly, model results show that it is a matter......Increasing public transport use with the aim of improving the sustainability of cities should focus not only on enhancing level and quality of the service offered, but also on understanding determinants of the choice of access and egress modes to and from the railway network. This study analyzes...... the difference in preferences at the home-end and activity-end for travelers who have chosen train as their main travel mode while investigating the effect of policy variables such as car parking availability, bicycle parking availability and type, and bicycle on train possibility. Specifically, this study...

BCR/ABL downregulates DNA-PK(CS)-dependent and upregulates backup non-homologous end joining in leukemic cells.

Science.gov (United States)

Poplawski, Tomasz; Blasiak, Janusz

2010-06-01

Non-homologous end joining (NHEJ) and homologous recombination repair (HRR) are the main mechanisms involved in the processing of DNA double strand breaks (DSBs) in humans. We showed previously that the oncogenic tyrosine kinase BCR/ABL stimulated DSBs repair by HRR. To evaluate the role of BCR/ABL in DSBs repair by NHEJ we examined the ability of leukemic BCR/ABL-expressing cell line BV173 to repair DNA damage induced by two DNA topoisomerase II inhibitors: etoposide and sobuzoxane. DNA lesions induced by sobuzoxane are repaired by a NHEJ pathway which is dependent on the catalytic subunit of protein kinase dependent on DNA (DNA-PK(CS); D-NHEJ), whereas damage evoked by etoposide are repaired by two distinct NHEJ pathways, dependent on or independent of DNA-PK(CS) (backup NHEJ, B-NHEJ). Cells incubated with STI571, a highly specific inhibitor of BCR/ABL, displayed resistance to these agents associated with an accelerated kinetics of DSBs repair, as measured by the neutral comet assay and pulsed field gel electrophoresis. However, in a functional NHEJ assay, cells preincubated with STI571 repaired DSBs induced by a restriction enzyme with a lower efficacy than without the preincubation and addition of wortmannin, a specific inhibitor of DNA-PK(CS), did not change efficacy of the NHEJ reaction. We suggest that BCR/ABL switch on B-NHEJ which is more error-prone then D-NHEJ and in such manner contribute to the increase of the genomic instability of leukemic cells.

Double strand break rejoining by the Ku-dependent mechanism of non-homologous end-joining

International Nuclear Information System (INIS)

Jeggo, P.; Singleton, B.; Beamish, H.; Priestley, A.

1999-01-01

The DNA-dependent protein kinase functions in the repair of DNA double strand breaks (DSBs) and in V(D)J recombination. To gain insight into the function of DNA-PK in this process we have carried out a mutation analysis of Ku80 and DNA-PKcs. Mutations at multiple sites within the N-terminal two thirds of Ku80 result in loss of Ku70/80 interaction, loss of DNA end-binding activity and inability to complement Ku80 defective cell fines. In contrast, mutations in the carboxy terminal region of the protein do not impair DNA end-binding activity but decrease the ability of Ku to activate DNA-PK. To gain insight into important functional domains within DNA-PKcs, we have analysed defective mutants, including the mouse scid cell line, and the rodent mutants, ire-20 and V-3. Mutational changes in the carboxy terminal region have been identified in all cases. Our results strongly suggest that the C-terminus of DNA-PKcs is required for kinase activity. (author)

Chromosome End Repair and Genome Stability in Plasmodium falciparum

Directory of Open Access Journals (Sweden)

Susannah F. Calhoun

2017-08-01

Full Text Available The human malaria parasite Plasmodium falciparum replicates within circulating red blood cells, where it is subjected to conditions that frequently cause DNA damage. The repair of DNA double-stranded breaks (DSBs is thought to rely almost exclusively on homologous recombination (HR, due to a lack of efficient nonhomologous end joining. However, given that the parasite is haploid during this stage of its life cycle, the mechanisms involved in maintaining genome stability are poorly understood. Of particular interest are the subtelomeric regions of the chromosomes, which contain the majority of the multicopy variant antigen-encoding genes responsible for virulence and disease severity. Here, we show that parasites utilize a competitive balance between de novo telomere addition, also called “telomere healing,” and HR to stabilize chromosome ends. Products of both repair pathways were observed in response to DSBs that occurred spontaneously during routine in vitro culture or resulted from experimentally induced DSBs, demonstrating that both pathways are active in repairing DSBs within subtelomeric regions and that the pathway utilized was determined by the DNA sequences immediately surrounding the break. In combination, these two repair pathways enable parasites to efficiently maintain chromosome stability while also contributing to the generation of genetic diversity.

Evaluation of End Mill Coatings

Energy Technology Data Exchange (ETDEWEB)

L. J. Lazarus; R. L. Hester,

2005-08-01

Milling tests were run on families of High Speed Steel (HSS) end mills to determine their lives while machining 304 Stainless Steel. The end mills tested were made from M7, M42 and T15-CPM High Speed Steels. The end mills were also evaluated with no coatings as well as with Titanium Nitride (TiN) and Titanium Carbo-Nitride (TiCN) coatings to determine which combination of HSS and coating provided the highest increase in end mill life while increasing the cost of the tool the least. We found end mill made from M42 gave us the largest increase in tool life with the least increase in cost. The results of this study will be used by Cutting Tool Engineering in determining which end mill descriptions will be dropped from our tool catalog.

End-to-End Assessment of a Large Aperture Segmented Ultraviolet Optical Infrared (UVOIR) Telescope Architecture

Science.gov (United States)

Feinberg, Lee; Bolcar, Matt; Liu, Alice; Guyon, Olivier; Stark,Chris; Arenberg, Jon

2016-01-01

Key challenges of a future large aperture, segmented Ultraviolet Optical Infrared (UVOIR) Telescope capable of performing a spectroscopic survey of hundreds of Exoplanets will be sufficient stability to achieve 10-10 contrast measurements and sufficient throughput and sensitivity for high yield Exo-Earth spectroscopic detection. Our team has collectively assessed an optimized end to end architecture including a high throughput coronagraph capable of working with a segmented telescope, a cost-effective and heritage based stable segmented telescope, a control architecture that minimizes the amount of new technologies, and an Exo-Earth yield assessment to evaluate potential performance.

Automated Design of Propellant-Optimal, End-to-End, Low-Thrust Trajectories for Trojan Asteroid Tours

Science.gov (United States)

Stuart, Jeffrey; Howell, Kathleen; Wilson, Roby

2013-01-01

The Sun-Jupiter Trojan asteroids are celestial bodies of great scientific interest as well as potential resources offering water and other mineral resources for longterm human exploration of the solar system. Previous investigations under this project have addressed the automated design of tours within the asteroid swarm. This investigation expands the current automation scheme by incorporating options for a complete trajectory design approach to the Trojan asteroids. Computational aspects of the design procedure are automated such that end-to-end trajectories are generated with a minimum of human interaction after key elements and constraints associated with a proposed mission concept are specified.

User-oriented end-to-end transport protocols for the real-time distribution of telemetry data from NASA spacecraft

Science.gov (United States)

Hooke, A. J.

1979-01-01

A set of standard telemetry protocols for downlink data flow facilitating the end-to-end transport of instrument data from the spacecraft to the user in real time is proposed. The direct switching of data by autonomous message 'packets' that are assembled by the source instrument on the spacecraft is discussed. The data system consists thus of a format on a message rather than word basis, and such packet telemetry would include standardized protocol headers. Standards are being developed within the NASA End-to-End Data System (NEEDS) program for the source packet and transport frame protocols. The source packet protocol contains identification of both the sequence number of the packet as it is generated by the source and the total length of the packet, while the transport frame protocol includes a sequence count defining the serial number of the frame as it is generated by the spacecraft data system, and a field specifying any 'options' selected in the format of the frame itself.

A tale of two extinctions : converging end-Permian and end-Triassic scenarios

NARCIS (Netherlands)

van de Schootbrugge, Bas; Wignall, Paul B.

The end-Permian (c. 252 Ma) and end-Triassic (c. 201 Ma) mass-extinction events are commonly linked to the emplacement of the large igneous provinces of the Siberia Traps and Central Atlantic Magmatic Province, respectively. Accordingly, scenarios for both extinctions are increasingly convergent and

Agrobacterium tumefaciens T-DNA Integration and Gene Targeting in Arabidopsis thaliana Non-Homologous End-Joining Mutants

Directory of Open Access Journals (Sweden)

Qi Jia

2012-01-01

Full Text Available In order to study the role of AtKu70 and AtKu80 in Agrobacterium-mediated transformation and gene targeting, plant lines with a T-DNA insertion in AtKu80 or AtKu70 genes were functionally characterized. Such plant lines lacked both subunits, indicating that heterodimer formation between AtKu70 and AtKu80 is needed for the stability of the proteins. Homozygous mutants were phenotypically indistinguishable from wild-type plants and were fertile. However, they were hypersensitive to the genotoxic agent bleomycin, resulting in more DSBs as quantified in comet assays. They had lower end-joining efficiency, suggesting that NHEJ is a critical pathway for DSB repair in plants. Both Atku mutants and a previously isolated Atmre11 mutant were impaired in Agrobacterium T-DNA integration via floral dip transformation, indicating that AtKu70, AtKu80, and AtMre11 play an important role in T-DNA integration in Arabidopsis. The frequency of gene targeting was not significantly increased in the Atku80 and Atku70 mutants, but it was increased at least 10-fold in the Atmre11 mutant compared with the wild type.

End of an era?

DEFF Research Database (Denmark)

Abrahamson, Peter

2016-01-01

At the end of 2015, China put an end to the one-child policy (OCP), thereby terminating the largest family planning program in human history. For nearly four decades it had shaped relations between generations and between men and women to an extent never before seen. Today, China struggles with t...... because of the strong preference for boys, which has led to so-called “bare branches:” Chinese men who are not able to find a spouse or have to rely on “mail-order brides.” The paper concludes that the OCP has come to an end, but the unintended consequences prevail.......At the end of 2015, China put an end to the one-child policy (OCP), thereby terminating the largest family planning program in human history. For nearly four decades it had shaped relations between generations and between men and women to an extent never before seen. Today, China struggles...... cultural values and legal prescriptions foresee reciprocal care responsibilities between generations. This has led to an enormous care deficit, which triggers conflicts between both genders and generations. A second major unintended consequence has been a skewed gender ratio of only 18 women per 20 men...

Effect of Cisplatin on the Flexibility of Linear DNA

International Nuclear Information System (INIS)

Ji Chao; Zhang Ling-Yun; Hou Xi-Miao; Dou Shuo-Xing; Wang Peng-Ye

2011-01-01

With the aid of an atomic force microscope (AFM), we study the interaction between linear DNA fragment and cisplatin. For different cisplatin concentrations, the AFM used to observe the conformation of DNA has a gradual change. The contour length, the end-to-end distance and the local bend angles of the linear DNA fragment can be accurately measured. The persistence length of DNA interacting with cisplatin is decreased with the increasing cisplatin concentration. Furthermore, it is demonstrated that the local bend angles of DNA chains are increased by the binding interaction of cisplatin. (cross-disciplinary physics and related areas of science and technology)

Indico front-end: From spaghetti to lasagna

CERN Multimedia

CERN. Geneva

2017-01-01

We will present how we transitioned from legacy spaghetti UI code to a more coherent, easier to understand and maintain ecosystem of front-end technologies and facilities with a strong emphasis in reusable components. In particular, we will share with you: 1) how we use Sass to maintain our home-baked CSS, 2) how we survive in 2017 without front-end Javascript frameworks, and 3) how we use template macros and WTForms for generating consistent HTML transparently.

EndNote 7.0

Directory of Open Access Journals (Sweden)

Eapen Bell

2006-01-01

Full Text Available EndNote is a useful software for online literature search and efficient bibliography management. It helps to format the bibliography according to the citation style of each journal. EndNote stores references in a library file, which can be shared with others. It can connect to online resources like PubMed and retrieve search results as per the search criteria. It can also effortlessly integrate with popular word processors like MS Word. The Indian Journal of Dermatology, Venereology and Leprology website has a provision to import references to EndNote.

KIN17, XPC, DNA-PKCS and XRCC4 proteins in the cellular response to DNA damages. Relations between nucleotide excision repair and non-homologous end joining in a human syn-genic model

International Nuclear Information System (INIS)

Despras, Emmanuelle

2006-01-01

The response to genotoxic stress involves many cellular factors in a complex network of mechanisms that aim to preserve the genetic integrity of the organism. These mechanisms enclose the detection and repair of DNA lesions, the regulation of transcription and replication and, eventually, the setting of cell death. Among the nuclear proteins involved in this response, kin17 proteins are zinc-finger proteins conserved through evolution and activated by ultraviolet (UV) or ionizing radiations (IR). We showed that human kin17 protein (HSAkin17) is found in the cell under a soluble form and a form tightly anchored to nuclear structures. A fraction of HSAkin17 protein is directly associated with chromatin. HSAkin17 protein is recruited to nuclear structures 24 hours after treatment with various agents inducing DNA double-strand breaks (DSB) and/or replication forks blockage. Moreover, the reduction of total HSAkin17 protein level sensitizes RKO cells to IR. We also present evidence for the involvement of HSAkin17 protein in DNA replication. This hypothesis was further confirmed by the biochemical demonstration of its belonging to the replication complex. HSAkin17 protein could link DNA replication and DNA repair, a defect in the HSAkin17 pathway leading to an increased radiosensitivity. In a second part, we studied the interactions between two DNA repair mechanisms: nucleotide excision repair (NER) and non-homologous end joining (NHEJ). NER repairs a wide variety of lesions inducing a distortion of the DNA double helix including UV-induced pyrimidine dimers. NHEJ allows the repair of DSB by direct joining of DNA ends. We used a syn-genic model for DNA repair defects based on RNA interference developed in the laboratory. Epstein-Barr virus-derived vectors (pEBV) allow long-term expression of siRNA and specific extinction of the targeted gene. The reduction of the expression of genes involved in NER (XPA and XPC) or NHEJ (DNA-PKcs and XRCC4) leads to the expected

Processing of DNA double strand breaks by alternative non-homologous end-joining in hyperacetylated chromatin.

Science.gov (United States)

Manova, Vasilissa; Singh, Satyendra K; Iliakis, George

2012-08-22

Mammalian cells employ at least two subpathways of non-homologous end-joining for the repair of ionizing radiation induced DNA double strand breaks: The canonical DNA-PK-dependent form of non-homologous end-joining (D-NHEJ) and an alternative, slowly operating, error-prone backup pathway (B-NHEJ). In contrast to D-NHEJ, which operates with similar efficiency throughout the cell cycle, B-NHEJ operates more efficiently in G2-phase. Notably, B-NHEJ also shows strong and as of yet unexplained dependency on growth activity and is markedly compromised in serum-deprived cells, or in cells that enter the plateau-phase of growth. The molecular mechanisms underpinning this response remain unknown. Since chromatin structure or changes in chromatin structure are prime candidate-B-NHEJ-modulators, we study here the role of chromatin hyperacetylation, either by HDAC2 knockdown or treatment with the HDAC inhibitor TSA, on the repair by B-NHEJ of IR-induced DSBs. siRNA-mediated knockdown of HDAC2 fails to provoke histone hyperacetylation in Lig4-/- MEFs and has no detectable effect on B-NHEJ function. Treatment with TSA that inhibits multiple HDACs causes efficient, reversible chromatin hyperacetylation in Lig4-/- MEFs, as well as in human HCT116 Lig4-/- cells and the human glioma cell line M059K. The IR yield of DSBs in TSA-treated cells remains similar to that of untreated cells despite the expected chromatin relaxation. In addition, chromatin hyperacetylation leaves unchanged repair of DSBs by B-NHEJ in irradiated exponentially growing, or plateau-phase cells. Notably, under the experimental conditions employed here, chromatin hyperacetylation fails to detectably modulate B-NHEJ in M059K cells as well. In summary, the results show that chromatin acetylation or deacetylation does not affect the kinetics of alternative NHEJ in all types of cells examined both in exponentially growing and serum deprived cultures. We conclude that parameters beyond chromatin acetylation determine B

The Open-Ended Approach Framework

Science.gov (United States)

Munroe, Lloyd

2015-01-01

This paper describes a pedagogical framework that teachers can use to support students who are engaged in solving open-ended problems, by explaining how two Japanese expert teachers successfully apply open-ended problems in their mathematics class. The Open-Ended Approach (OPA) framework consists of two main sections: Understanding Mathematical…

Beginning from the End: Strategies of Composition in Lyrical Improvisation with End Rhyme

Directory of Open Access Journals (Sweden)

Venla Sykäri

2017-03-01

Full Text Available This essay examines the basic principles of constructing improvised verses with end rhyme in three contemporary cultures: _mandinadhes_, Mallorcan _gloses_, and Finnish freestyle rap. This study is based on ethnographic interviews, in which improvisers analyze their methods of composition. This knowledge is complemented by a textual analysis of examples of performances in the given traditions. Sykäri shows that competent improvisers master complex cognitive methods when they create their lines that end with the poetic device of end rhyme, and in particular when they structure the discourse so that the strong arguments are situated at the end of the structural unit of composition. This “reversed” method witnesses a tendency to use parallel phonic patterns in a way that is largely the opposite of those employed with semantic (or canonical parallelism.

Circumferential resection and "Z"-shape plastic end-to-end anastomosis of canine trachea.

Science.gov (United States)

Zhao, H; Li, Z; Fang, J; Fang, C

1999-03-01

To prevent anastomotic stricture of the trachea. Forty young mongrel dogs, weighing 5-7 kg, were randomly divided into two groups: experimental group and control group, with 20 dogs in each group. Four tracheal rings were removed from each dog. In the experimental group, two "Z"-shape tracheoplastic anastomoses were performed on each dog, one on the anterior wall and the other on the membranous part of the trachea. In the control group, each dog received only simple end-to-end anastomosis. Vicryl 3-0 absorbable suture and OB fibrin glue were used for both groups. All dogs were killed when their body weight doubled. The average sagittal stenotic ratio were 1.20 +/- 0.12 for the experimental group and 0.83 +/- 0.05 for the control group. The average cross-sectional area stenotic ratio were 0.90 +/- 0.12 and 0.69 +/- 0.09 and T values were 8.71 and 4.57 for the two groups (P anastomosis in preventing anastomotic stricture of canine trachea.

CENTRIFUGE END CAP

Science.gov (United States)

Beams, J.W.; Snoddy, L.B.

1960-08-01

An end cap for ultra-gas centrifuges is designed to impart or remove angular momentum to or from the gas and to bring the entering gas to the temperature of the gas inside the centrifuge. The end cap is provided with slots or fins for adjusting the temperature and the angular momentum of the entering gas to the temperature and momentum of the gas in the centrifuge and is constructed to introduce both the inner and the peripheral stream into the centrifuge.

Partial QoS-Aware Opportunistic Relay Selection Over Two-Hop Channels: End-to-End Performance Under Spectrum-Sharing Requirements

KAUST Repository

Yuli Yang,; Hao Ma,; Aissa, Sonia

2014-01-01

it with transmission constraints imposed on the transmit power budget and interference to other users. By analyzing the statistics of received SNRs in the first and second hops, we obtain the end-to-end PLR of this scheme in closed form under the considered scenario

Human Assisted Robotic Vehicle Studies - A conceptual end-to-end mission architecture

Science.gov (United States)

Lehner, B. A. E.; Mazzotta, D. G.; Teeney, L.; Spina, F.; Filosa, A.; Pou, A. Canals; Schlechten, J.; Campbell, S.; Soriano, P. López

2017-11-01

With current space exploration roadmaps indicating the Moon as a proving ground on the way to human exploration of Mars, it is clear that human-robotic partnerships will play a key role for successful future human space missions. This paper details a conceptual end-to-end architecture for an exploration mission in cis-lunar space with a focus on human-robot interactions, called Human Assisted Robotic Vehicle Studies (HARVeSt). HARVeSt will build on knowledge of plant growth in space gained from experiments on-board the ISS and test the first growth of plants on the Moon. A planned deep space habitat will be utilised as the base of operations for human-robotic elements of the mission. The mission will serve as a technology demonstrator not only for autonomous tele-operations in cis-lunar space but also for key enabling technologies for future human surface missions. The successful approach of the ISS will be built on in this mission with international cooperation. Mission assets such as a modular rover will allow for an extendable mission and to scout and prepare the area for the start of an international Moon Village.

MO-B-BRB-04: 3D Dosimetry in End-To-End Dosimetry QA

Energy Technology Data Exchange (ETDEWEB)

Ibbott, G. [UT MD Anderson Cancer Center (United States)

2016-06-15

irradiated volume can help understand interplay effects during TomoTherapy or VMAT. Titania Juang: Special techniques in the clinic and research Understand the potential for 3D dosimetry in validating dose accumulation in deformable systems, and Observe the benefits of high resolution measurements for precision therapy in SRS and in MicroSBRT for small animal irradiators Geoffrey S. Ibbott: 3D Dosimetry in end-to-end dosimetry QA Understand the potential for 3D dosimetry for end-to-end radiation therapy process validation in the in-house and external credentialing setting. Canadian Institutes of Health Research; L. Schreiner, Modus QA, London, ON, Canada; T. Juang, NIH R01CA100835.

TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data

OpenAIRE

Platzer, Alexander; Nizhynska, Viktoria; Long, Quan

2012-01-01

Transposable elements (TEs) are common mobile DNA elements present in nearly all genomes. Since the movement of TEs within a genome can sometimes have phenotypic consequences, an accurate report of TE actions is desirable. To this end, we developed TE-Locate, a computational tool that uses paired-end reads to identify the novel locations of known TEs. TE-Locate can utilize either a database of TE sequences, or annotated TEs within the reference sequence of interest. This makes TE-Locate usefu...

Welding nuclear reactor fuel rod end plugs

International Nuclear Information System (INIS)

Yeo, D.

1984-01-01

Apparatus for applying a vacuum to a nuclear fuel rod cladding tube's interior through its open end while girth welding an inserted end plug to its other end. An airtight housing has an orifice with a seal which can hermetically engage the tube's open end. A vacuum hose has one end connected to the housing and the other end connected to a vacuum pump. A mechanized device which moves the housing to engage or disengage its seal with the tube's open end includes at least one arm having one end attached to the housing and the other end pivotally attached to a movable table; an arm rotating device to coaxially align the housing's orifice with the welding-positioned tube; and a table moving device to engage the seal of the coaxially aligned orifice with the tube's open end. (author)

West Coast fish, mammal, and bird species diets - Developing end-to-end models of the California Current Large Marine Ecosystem

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

A 3-hydroxy β-end group in xanthophylls is preferentially oxidized to a 3-oxo ε-end group in mammals.

Science.gov (United States)

Nagao, Akihiko; Maoka, Takashi; Ono, Hiroshi; Kotake-Nara, Eiichi; Kobayashi, Miyuki; Tomita, Mie

2015-02-01

We previously found that mice fed lutein accumulated its oxidative metabolites (3'-hydroxy-ε,ε-caroten-3-one and ε,ε-carotene-3,3'-dione) as major carotenoids, suggesting that mammals can convert xanthophylls to keto-carotenoids by the oxidation of hydroxyl groups. Here we elucidated the metabolic activities of mouse liver for several xanthophylls. When lutein was incubated with liver postmitochondrial fraction in the presence of NAD(+), (3'R,6'R)-3'-hydroxy-β,ε-caroten-3-one and (6RS,3'R,6'R)-3'-hydroxy-ε,ε-caroten-3-one were produced as major oxidation products. The former accumulated only at the early stage and was assumed to be an intermediate, followed by isomerization to the latter. The configuration at the C3' and C6' of the ε-end group in lutein was retained in the two oxidation products. These results indicate that the 3-hydroxy β-end group in lutein was preferentially oxidized to a 3-oxo ε-end group via a 3-oxo β-end group. Other xanthophylls such as β-cryptoxanthin and zeaxanthin, which have a 3-hydroxy β-end group, were also oxidized in the same manner as lutein. These keto-carotenoids, derived from dietary xanthophylls, were confirmed to be present in plasma of normal human subjects, and β,ε-caroten-3'-one was significantly increased by the ingestion of β-cryptoxanthin. Thus, humans as well as mice have oxidative activity to convert the 3-hydroxy β-end group of xanthophylls to a 3-oxo ε-end group. Copyright © 2015 by the American Society for Biochemistry and Molecular Biology, Inc.

Increasing gas producer profitability with virtual well visibility via an end-to-end wireless Internet gas monitoring system

Energy Technology Data Exchange (ETDEWEB)

McDougall, M. [Northrock Resources Ltd., Calgary, AB (Canada); Benterud, K. [Zed.i solutions, Calgary, AB (Canada)

2003-07-01

This PowerPoint presentation describes how Northrock Resources Ltd. increased profitability using Smart-Alek{sup TM} while avoiding high implementation costs. Smart-Alek is a new type of fully integrated end-to-end electronic gas flow measurement (GFM) system based on Field Intelligence Network and End User Interference (FINE). Smart-Alek can analyze gas production through public wireless communications and a web-browser delivery system. The system has enabled Northrock to increase gas volumes with more accurate measurement and reduced downtime. In addition, operating costs have decreased because the frequency of well visits has been reduced and the administrative procedures of data collection is more efficient. The real-time well visibility of the tool has proven to be very effective in optimizing business profitability. 7 figs.

Calorimetry end-point predictions

International Nuclear Information System (INIS)

Fox, M.A.

1981-01-01

This paper describes a portion of the work presently in progress at Rocky Flats in the field of calorimetry. In particular, calorimetry end-point predictions are outlined. The problems associated with end-point predictions and the progress made in overcoming these obstacles are discussed. The two major problems, noise and an accurate description of the heat function, are dealt with to obtain the most accurate results. Data are taken from an actual calorimeter and are processed by means of three different noise reduction techniques. The processed data are then utilized by one to four algorithms, depending on the accuracy desired to determined the end-point

Risk Factors for Dehiscence of Stapled Functional End-to-End Intestinal Anastomoses in Dogs: 53 Cases (2001-2012).

Science.gov (United States)

Snowdon, Kyle A; Smeak, Daniel D; Chiang, Sharon

2016-01-01

To identify risk factors for dehiscence in stapled functional end-to-end anastomoses (SFEEA) in dogs. Retrospective case series. Dogs (n = 53) requiring an enterectomy. Medical records from a single institution for all dogs undergoing an enterectomy (2001-2012) were reviewed. Surgeries were included when gastrointestinal (GIA) and thoracoabdominal (TA) stapling equipment was used to create a functional end-to-end anastomosis between segments of small intestine or small and large intestine in dogs. Information regarding preoperative, surgical, and postoperative factors was recorded. Anastomotic dehiscence was noted in 6 of 53 cases (11%), with a mortality rate of 83%. The only preoperative factor significantly associated with dehiscence was the presence of inflammatory bowel disease (IBD). Surgical factors significantly associated with dehiscence included the presence, duration, and number of intraoperative hypotensive periods, and location of anastomosis, with greater odds of dehiscence in anastomoses involving the large intestine. IBD, location of anastomosis, and intraoperative hypotension are risk factors for intestinal anastomotic dehiscence after SFEEA in dogs. Previously suggested risk factors (low serum albumin concentration, preoperative septic peritonitis, and intestinal foreign body) were not confirmed in this study. © Copyright 2015 by The American College of Veterinary Surgeons.

FANCD2 Maintains Fork Stability in BRCA1/2-Deficient Tumors and Promotes Alternative End-Joining DNA Repair

Directory of Open Access Journals (Sweden)

Zeina Kais

2016-06-01

Full Text Available BRCA1/2 proteins function in homologous recombination (HR-mediated DNA repair and cooperate with Fanconi anemia (FA proteins to maintain genomic integrity through replication fork stabilization. Loss of BRCA1/2 proteins results in DNA repair deficiency and replicative stress, leading to genomic instability and enhanced sensitivity to DNA-damaging agents. Recent studies have shown that BRCA1/2-deficient tumors upregulate Polθ-mediated alternative end-joining (alt-EJ repair as a survival mechanism. Whether other mechanisms maintain genomic integrity upon loss of BRCA1/2 proteins is currently unknown. Here we show that BRCA1/2-deficient tumors also upregulate FANCD2 activity. FANCD2 is required for fork protection and fork restart in BRCA1/2-deficient tumors. Moreover, FANCD2 promotes Polθ recruitment at sites of damage and alt-EJ repair. Finally, loss of FANCD2 in BRCA1/2-deficient tumors enhances cell death. These results reveal a synthetic lethal relationship between FANCD2 and BRCA1/2, and they identify FANCD2 as a central player orchestrating DNA repair pathway choice at the replication fork.

Expression of Mycobacterium tuberculosis Ku and Ligase D in Escherichia coli results in RecA and RecB-independent DNA end-joining at regions of microhomology.

Science.gov (United States)

Malyarchuk, Svitlana; Wright, Douglas; Castore, Reneau; Klepper, Emily; Weiss, Bernard; Doherty, Aidan J; Harrison, Lynn

2007-10-01

Unlike Escherichia coli, Mycobacterium tuberculosis (Mt) expresses a Ku-like protein and an ATP-dependent DNA ligase that can perform non-homologous end-joining (NHEJ). We have expressed the Mt-Ku and Mt-Ligase D in E. coli using an arabinose-inducible promoter and expression vectors that integrate into specific sites in the E. coli chromosome. E. coli strains have been generated that express the Mt-Ku and Mt-Ligase D on a genetic background that is wild-type for repair, or deficient in either the RecA or RecB protein. Transformation of these strains with linearized plasmid DNA containing a 2bp overhang has demonstrated that expression of both the Mt-Ku and Mt-Ligase D is required for DNA end-joining and that loss of RecA does not prevent this double-strand break repair. Analysis of the re-joined plasmid has shown that repair is predominantly inaccurate and results in the deletion of sequences. Loss of RecB did not prevent the formation of large deletions, but did increase the amount of end-joining. Sequencing the junctions has revealed that the majority of the ligations occurred at regions of microhomology (1-4bps), eliminating one copy of the homologous sequence at the junction. The Mt-Ku and Mt-Ligase D can therefore function in E. coli to re-circularize linear plasmid.

Including 10-Gigabit-capable Passive Optical Network under End-to-End Generalized Multi-Protocol Label Switching Provisioned Quality of Service

DEFF Research Database (Denmark)

Brewka, Lukasz Jerzy; Gavler, Anders; Wessing, Henrik

2012-01-01

of the network where quality of service signaling is bridged. This article proposes strategies for generalized multi-protocol label switching control over next emerging passive optical network standard, i.e., the 10-gigabit-capable passive optical network. Node management and resource allocation approaches...... are discussed, and possible issues are raised. The analysis shows that consideration of a 10-gigabit-capable passive optical network as a generalized multi-protocol label switching controlled domain is valid and may advance end-to-end quality of service provisioning for passive optical network based customers.......End-to-end quality of service provisioning is still a challenging task despite many years of research and development in this area. Considering a generalized multi-protocol label switching based core/metro network and resource reservation protocol capable home gateways, it is the access part...

The End of ‘the end of impunity’?

DEFF Research Database (Denmark)

Holtermann, Jakob von Holderstein

2010-01-01

With its express intention ‘to put an end to impunity’, the International Criminal Court (ICC) faces a substantial challenge in the shape of conditional amnesties granted in future national truth commissions (TCs)—a challenge that invokes fundamental considerations of criminal justice ethics...

ATLAS end-cap detector

CERN Multimedia

Maximilien Brice

2003-01-01

Three scientists from the Institute of Nuclear Phyiscs at Novossibirsk with one of the end-caps of the ATLAS detector. The end-caps will be used to detect particles produced in the proton-proton collisions at the heart of the ATLAS experiment that are travelling close to the axis of the two beams.

Users’ Perceptions Using Low-End and High-End Mobile-Rendered HMDs: A Comparative Study

Directory of Open Access Journals (Sweden)

M.-Carmen Juan

2018-02-01

Full Text Available Currently, it is possible to combine Mobile-Rendered Head-Mounted Displays (MR HMDs with smartphones to have Augmented Reality platforms. The differences between these types of platforms can affect the user’s experiences and satisfaction. This paper presents a study that analyses the user’s perception when using the same Augmented Reality app with two MR HMD (low-end and high-end. Our study evaluates the user’s experience taking into account several factors (control, sensory, distraction, ergonomics and realism. An Augmalpha-lowerented Reality app was developed to carry out the comparison for two MR HMDs. The application had exactly the same visual appearance and functionality for both devices. Forty adults participated in our study. From the results, there were no statistically significant differences for the users’ experience for the different factors when using the two MR HMDs, except for the ergonomic factors in favour of the high-end MR HMD. Even though the scores for the high-end MR HMD were higher in nearly all of the questions, both MR HMDs provided a very satisfying viewing experience with very high scores. The results were independent of gender and age. The participants rated the high-end MR HMD as the best one. Nevertheless, when they were asked which MR HMD they would buy, the participants chose the low-end MR HMD taking into account its price.

Self-assembled nanogaps via seed-mediated growth of end-to-end linked gold nanorods

DEFF Research Database (Denmark)

Jain, Titoo; Westerlund, Axel Rune Fredrik; Johnson, Erik

2009-01-01

Gold nanorods (AuNRs) are of interest for a wide range of applications, ranging from imaging to molecular electronics, and they have been studied extensively for the past decade. An important issue in AuNR applications is the ability to self-assemble the rods in predictable structures...... on the nanoscale. We here present a new way to end-to-end link AuNRs with a single or few linker molecules. Whereas methods reported in the literature so far rely on modification of the AuNRs after the synthesis, we here dimerize gold nanoparticle seeds with a water-soluble dithiol-functionalized polyethylene...... that a large fraction of the rods are flexible around the hinging molecule in solution, as expected for a molecularly linked nanogap. By using excess of gold nanoparticles relative to the linking dithiol molecule, this method can provide a high probability that a single molecule is connecting the two rods...

End-to-end performance of cooperative relaying in spectrum-sharing systems with quality of service requirements

KAUST Repository

Asghari, Vahid Reza

2011-07-01

We propose adopting a cooperative relaying technique in spectrum-sharing cognitive radio (CR) systems to more effectively and efficiently utilize available transmission resources, such as power, rate, and bandwidth, while adhering to the quality of service (QoS) requirements of the licensed (primary) users of the shared spectrum band. In particular, we first consider that the cognitive (secondary) user\\'s communication is assisted by an intermediate relay that implements the decode-and-forward (DF) technique onto the secondary user\\'s relayed signal to help with communication between the corresponding source and the destination nodes. In this context, we obtain first-order statistics pertaining to the first- and second-hop transmission channels, and then, we investigate the end-to-end performance of the proposed spectrum-sharing cooperative relaying system under resource constraints defined to assure that the primary QoS is unaffected. Specifically, we investigate the overall average bit error rate (BER), ergodic capacity, and outage probability of the secondary\\'s communication subject to appropriate constraints on the interference power at the primary receivers. We then consider a general scenario where a cluster of relays is available between the secondary source and destination nodes. In this case, making use of the partial relay selection method, we generalize our results for the single-relay scheme and obtain the end-to-end performance of the cooperative spectrum-sharing system with a cluster of L available relays. Finally, we examine our theoretical results through simulations and comparisons, illustrating the overall performance of the proposed spectrum-sharing cooperative system and quantify its advantages for different operating scenarios and conditions. © 2011 IEEE.

MRI simulation: end-to-end testing for prostate radiation therapy using geometric pelvic MRI phantoms

International Nuclear Information System (INIS)

Sun, Jidi; Menk, Fred; Lambert, Jonathan; Martin, Jarad; Denham, James W; Greer, Peter B; Dowling, Jason; Rivest-Henault, David; Pichler, Peter; Parker, Joel; Arm, Jameen; Best, Leah

2015-01-01

To clinically implement MRI simulation or MRI-alone treatment planning requires comprehensive end-to-end testing to ensure an accurate process. The purpose of this study was to design and build a geometric phantom simulating a human male pelvis that is suitable for both CT and MRI scanning and use it to test geometric and dosimetric aspects of MRI simulation including treatment planning and digitally reconstructed radiograph (DRR) generation.A liquid filled pelvic shaped phantom with simulated pelvic organs was scanned in a 3T MRI simulator with dedicated radiotherapy couch-top, laser bridge and pelvic coil mounts. A second phantom with the same external shape but with an internal distortion grid was used to quantify the distortion of the MR image. Both phantoms were also CT scanned as the gold-standard for both geometry and dosimetry. Deformable image registration was used to quantify the MR distortion. Dose comparison was made using a seven-field IMRT plan developed on the CT scan with the fluences copied to the MR image and recalculated using bulk electron densities.Without correction the maximum distortion of the MR compared with the CT scan was 7.5 mm across the pelvis, while this was reduced to 2.6 and 1.7 mm by the vendor’s 2D and 3D correction algorithms, respectively. Within the locations of the internal organs of interest, the distortion was <1.5 and <1 mm with 2D and 3D correction algorithms, respectively. The dose at the prostate isocentre calculated on CT and MRI images differed by 0.01% (1.1 cGy). Positioning shifts were within 1 mm when setup was performed using MRI generated DRRs compared to setup using CT DRRs.The MRI pelvic phantom allows end-to-end testing of the MRI simulation workflow with comparison to the gold-standard CT based process. MRI simulation was found to be geometrically accurate with organ dimensions, dose distributions and DRR based setup within acceptable limits compared to CT. (paper)

jade: An End-To-End Data Transfer and Catalog Tool

Science.gov (United States)

Meade, P.

2017-10-01

The IceCube Neutrino Observatory is a cubic kilometer neutrino telescope located at the Geographic South Pole. IceCube collects 1 TB of data every day. An online filtering farm processes this data in real time and selects 10% to be sent via satellite to the main data center at the University of Wisconsin-Madison. IceCube has two year-round on-site operators. New operators are hired every year, due to the hard conditions of wintering at the South Pole. These operators are tasked with the daily operations of running a complex detector in serious isolation conditions. One of the systems they operate is the data archiving and transfer system. Due to these challenging operational conditions, the data archive and transfer system must above all be simple and robust. It must also share the limited resource of satellite bandwidth, and collect and preserve useful metadata. The original data archive and transfer software for IceCube was written in 2005. After running in production for several years, the decision was taken to fully rewrite it, in order to address a number of structural drawbacks. The new data archive and transfer software (JADE2) has been in production for several months providing improved performance and resiliency. One of the main goals for JADE2 is to provide a unified system that handles the IceCube data end-to-end: from collection at the South Pole, all the way to long-term archive and preservation in dedicated repositories at the North. In this contribution, we describe our experiences and lessons learned from developing and operating the data archive and transfer software for a particle physics experiment in extreme operational conditions like IceCube.

Apparatus for assembling and welding end plugs to nuclear fuel cladding tubes and inspecting the end plug welds on an automated basis

International Nuclear Information System (INIS)

Schoenig, F.C. Jr.; Walker, E.S.; Cueman, M.K.; Haughton, R.A.; Zuloaga, J.A. Jr.

1989-01-01

This patent describes an automated apparatus for welding a separate end plug to one open end of each of a succession of nuclear fuel cladding tubes and for inspecting each end plug weld. The apparatus comprising, in combination: a welding station; a cooldown station for cooling each end plug weld in an inert gas atmosphere; a serial number reader station for reading a serial number on each end plug; a first weld inspection station; a second weld inspection station for generating second weld inspection data; a computer system linked with the serial number reader and the first and second weld inspection stations; an input queue for holding a plurality of tubes; a tube transporter for periodically picking individual tubes from the input queque and conveying the tubes in a direction transverse to their tube axis in indexing steps to index positions respectively axially aligned with the welding, serial number reader, and first and second weld inspection stations; and a sorter positioned at an output end of the tube transporter

Life's end: Ethnographic perspectives.

Science.gov (United States)

Goodwin-Hawkins, Bryonny; Dawson, Andrew

2018-01-01

In this introduction to the special issue, Life's End: Ethnographic Perspectives, we review the field of anthropological studies of death and dying. We make the argument that, largely because of its sub-disciplining into the larger field of the anthropology of religion, ritual and symbolism, the focus of anthropological research on death has been predominantly on post- rather than pre-death events, on death's beginnings rather than life's ends. Additionally, we argue that an anthropological aversion to the study of dying may also lie in the intimacy of the discipline's principal method, ethnography. Contrastingly, we argue that this very methodological intimacy can be a source of insight, and we offer this as a rationale for the special issue as a whole, which comprises eight ethnographic studies of dying and social relations at life's end from across Africa, Australia, Europe, and North America. Each of these studies is then summarized, and a rationale for their presentation around the themes of "structures of dying," "care for the dying," "hope in dying," and "ending life" is presented.

Applying the means-end chain concept to product development

DEFF Research Database (Denmark)

Søndergaard, Helle Alsted

This paper proposes that the means-end chain (MEC) approach can influence the use of market information and inter-functional communication in new product development (NPD). The central question is whether market information represented by means-end chain data can be a vehicle for inter......-functional communication. This paper describes a PhD project - that through case studies and action research in two companies - aims at investigating the effects on communication and attitudes to communication by those involved when introducing means-end chain data as market information in NPD....

A multicentre 'end to end' dosimetry audit of motion management (4DCT-defined motion envelope) in radiotherapy.

Science.gov (United States)

Palmer, Antony L; Nash, David; Kearton, John R; Jafari, Shakardokht M; Muscat, Sarah

2017-12-01

External dosimetry audit is valuable for the assurance of radiotherapy quality. However, motion management has not been rigorously audited, despite its complexity and importance for accuracy. We describe the first end-to-end dosimetry audit for non-SABR (stereotactic ablative body radiotherapy) lung treatments, measuring dose accumulation in a moving target, and assessing adequacy of target dose coverage. A respiratory motion lung-phantom with custom-designed insert was used. Dose was measured with radiochromic film, employing triple-channel dosimetry and uncertainty reduction. The host's 4DCT scan, outlining and planning techniques were used. Measurements with the phantom static and then moving at treatment delivery separated inherent treatment uncertainties from motion effects. Calculated and measured dose distributions were compared by isodose overlay, gamma analysis, and we introduce the concept of 'dose plane histograms' for clinically relevant interpretation of film dosimetry. 12 radiotherapy centres and 19 plans were audited: conformal, IMRT (intensity modulated radiotherapy) and VMAT (volumetric modulated radiotherapy). Excellent agreement between planned and static-phantom results were seen (mean gamma pass 98.7% at 3% 2 mm). Dose blurring was evident in the moving-phantom measurements (mean gamma pass 88.2% at 3% 2 mm). Planning techniques for motion management were adequate to deliver the intended moving-target dose coverage. A novel, clinically-relevant, end-to-end dosimetry audit of motion management strategies in radiotherapy is reported. Copyright © 2017 Elsevier B.V. All rights reserved.

Fuel cell end plate structure

Science.gov (United States)

Guthrie, Robin J.; Katz, Murray; Schroll, Craig R.

1991-04-23

The end plates (16) of a fuel cell stack (12) are formed of a thin membrane. Pressure plates (20) exert compressive load through insulation layers (22, 26) to the membrane. Electrical contact between the end plates (16) and electrodes (50, 58) is maintained without deleterious making and breaking of electrical contacts during thermal transients. The thin end plate (16) under compressive load will not distort with a temperature difference across its thickness. Pressure plate (20) experiences a low thermal transient because it is insulated from the cell. The impact on the end plate of any slight deflection created in the pressure plate by temperature difference is minimized by the resilient pressure pad, in the form of insulation, therebetween.

Fukuyama's theory about the end of history end the last man

Directory of Open Access Journals (Sweden)

Nedeljković Zoran

2007-01-01

Full Text Available 'End of the History' Fukuyama wrote under strong influence of Hegel's philosophic history. Since 1806 year there is no essential political progress, according to Fukuyama, abroad principles of French bourgeois revolution there is no advance. History which appears to be progressive and directional, suggest Fukuyama, ends right there. Word is divided into historical and post historical, social balance of the first one depend of the social misbalance of the second. Professional corporation are the surrogate for family, last man will substitute family moral with professional.

Current debates on end-of-life sedation: an international expert elicitation study.

Science.gov (United States)

Papavasiliou, Evangelia Evie; Payne, Sheila; Brearley, Sarah

2014-08-01

End-of-life sedation, though increasingly prevalent and widespread internationally, remains one of the most highly debated medical practices in the context of palliative medicine. This qualitative study aims to elicit and record the perspectives of leading international palliative care experts on current debates. Twenty-one professionals from diverse backgrounds, sharing field-specific knowledge/expertise defined by significant scholarly contribution on end-of-life sedation, were recruited. Open-ended, semi-structured interviews, following a topic-oriented structure reflecting on current debates, were conducted. Results were analysed using thematic content analysis. Three main aspects of sedation were identified and discussed as potentially problematic: (a) continuous deep sedation as an extreme facet of end-of-life sedation, (b) psycho-existential suffering as an ambivalent indication for sedation and (c) withdrawal or withholding of artificial nutrition and hydration as potentially life-shortening. On these grounds, concerns were reported over end-of-life sedation being morally equivalent to euthanasia. Considerable emphasis was placed on intentions as the distinguishing factor between end-of-life acts, and protective safeguards were introduced to distance sedation from euthanasia. This study shows that, despite the safeguards introduced, certain aspects of sedation, including the intentions associated with the practice, are still under question, parallels being drawn between end-of-life sedation and euthanasia. This reaffirms the existence of a grey area surrounding the two practices, already evidenced in countries where euthanasia is legalized. More clarity over the issues that generate this grey area, with their causes being uncovered and eliminated, is imperative to resolve current debates and effectively inform research, policy and practice of end-of-life sedation.

ATLAS electromagnetic end-cap detector

CERN Multimedia

Maximilien Brice

2003-01-01

After the insertion of the first end-cap into this cryostat, the team proceed to the wiring operations. Millions of wires are connected to the electromagnetic calorimeter on this end-cap, whch must be carefully fed out from the detector so that data can be read out. The energy of photons, electrons and positrons will be measured as they pass through the end-cap having been created along the line of the beams in the proton-proton collisions.

SU-E-T-282: Dose Measurements with An End-To-End Audit Phantom for Stereotactic Radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Jones, R; Artschan, R [Calvary Mater Newcastle, Newcastle, NSW (Australia); Thwaites, D [University of Sydney, Sydney, NSW (Australia); Lehmann, J [Calvary Mater Newcastle, Newcastle, NSW (Australia); University of Sydney, Sydney, NSW (Australia)

2015-06-15

Purpose: Report on dose measurements as part of an end-to-end test for stereotactic radiotherapy, using a new audit tool, which allows audits to be performed efficiently either by an onsite team or as a postal audit. Methods: Film measurements have been performed with a new Stereotactic Cube Phantom. The phantom has been designed to perform Winston Lutz type position verification measurements and dose measurements in one setup. It comprises a plastic cube with a high density ball in its centre (used for MV imaging with film or EPID) and low density markers in the periphery (used for Cone Beam Computed Tomography, CBCT imaging). It also features strategically placed gold markers near the posterior and right surfaces, which can be used to calculate phantom rotations on MV images. Slit-like openings allow insertion of film or other detectors.The phantom was scanned and small field treatment plans were created. The fields do not traverse any inhomogeneities of the phantom on their paths to the measurement location. The phantom was setup at the delivery system using CBCT imaging. The calculated treatment fields were delivered, each with a piece of radiochromic film (EBT3) placed in the anterior film holder of the phantom. MU had been selected in planning to achieve similar exposures on all films. Calibration films were exposed in solid water for dose levels around the expected doses. Films were scanned and analysed following established procedures. Results: Setup of the cube showed excellent suitability for CBCT 3D alignment. MV imaging with EPID allowed for clear identification of all markers. Film based dose measurements showed good agreement for MLC created fields down to 0.5 mm × 0.5 mm. Conclusion: An end-to-end audit phantom for stereotactic radiotherapy has been developed and tested.

Challenges in end-of-life communication.

Science.gov (United States)

Galushko, Maren; Romotzky, Vanessa; Voltz, Raymond

2012-09-01

The purpose of this review is to give an overview of challenges that have been addressed in recent research in end-of-life communication. Diversity of difficulties that may occur in communication about end-of-life issues has been showed. The emotional quality of this communication requires special skills from professionals involved. Studies showed that physicians and medical students are often overstrained and avoid end-of-life discussions. Health professionals and patients are often ambivalent about end-of-life discussions. Nevertheless, professionals are expected to initiate these in an honest, needs-oriented way. Patient preferences are difficult to infer and have to be assessed explicitly and regularly. Studies showed that the emotional impact of end-of-life discussions can lead to a high burden or avoidance of professionals. Interdisciplinary, multi-professional work can support health professionals in end-of-life care but often structural barriers obstruct possible benefits. Health professionals need to initiate end-of-life communication in a sensitive way. Specific demands for health professionals in end-of-life communication are to differentiate own emotions and life events from those of patients and to deal with both adequately. Moreover, structural aspects can lead to difficulties between different specialties, professions and sectors, which can have a negative impact on adequate care for patient and relatives. Special efforts for improvement are needed.

A 3-hydroxy β-end group in xanthophylls is preferentially oxidized to a 3-oxo ε-end group in mammals[S

Science.gov (United States)

Nagao, Akihiko; Maoka, Takashi; Ono, Hiroshi; Kotake-Nara, Eiichi; Kobayashi, Miyuki; Tomita, Mie

2015-01-01

We previously found that mice fed lutein accumulated its oxidative metabolites (3′-hydroxy-ε,ε-caroten-3-one and ε,ε-carotene-3,3′-dione) as major carotenoids, suggesting that mammals can convert xanthophylls to keto-carotenoids by the oxidation of hydroxyl groups. Here we elucidated the metabolic activities of mouse liver for several xanthophylls. When lutein was incubated with liver postmitochondrial fraction in the presence of NAD+, (3′R,6′R)-3′-hydroxy-β,ε-caroten-3-one and (6RS,3′R,6′R)-3′-hydroxy-ε,ε-caroten-3-one were produced as major oxidation products. The former accumulated only at the early stage and was assumed to be an intermediate, followed by isomerization to the latter. The configuration at the C3′ and C6′ of the ε-end group in lutein was retained in the two oxidation products. These results indicate that the 3-hydroxy β-end group in lutein was preferentially oxidized to a 3-oxo ε-end group via a 3-oxo β-end group. Other xanthophylls such as β-cryptoxanthin and zeaxanthin, which have a 3-hydroxy β-end group, were also oxidized in the same manner as lutein. These keto-carotenoids, derived from dietary xanthophylls, were confirmed to be present in plasma of normal human subjects, and β,ε-caroten-3′-one was significantly increased by the ingestion of β-cryptoxanthin. Thus, humans as well as mice have oxidative activity to convert the 3-hydroxy β-end group of xanthophylls to a 3-oxo ε-end group. PMID:25502844

A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5′ End or within the Genome of Feline Parvovirus and Can Modify Virus Replication

Science.gov (United States)

Wang, Dai; Parrish, Colin R.

1999-01-01

Phage display of cDNA clones prepared from feline cells was used to identify host cell proteins that bound to DNA-containing feline panleukopenia virus (FPV) capsids but not to empty capsids. One gene found in several clones encoded a heterogeneous nuclear ribonucleoprotein (hnRNP)-related protein (DBP40) that was very similar in sequence to the A/B-type hnRNP proteins. DBP40 bound specifically to oligonucleotides representing a sequence near the 5′ end of the genome which is exposed on the outside of the full capsid but did not bind most other terminal sequences. Adding purified DBP40 to an in vitro fill-in reaction using viral DNA as a template inhibited the production of the second strand after nucleotide (nt) 289 but prior to nt 469. DBP40 bound to various regions of the viral genome, including a region between nt 295 and 330 of the viral genome which has been associated with transcriptional attenuation of the parvovirus minute virus of mice, which is mediated by a stem-loop structure of the DNA and cellular proteins. Overexpression of the protein in feline cells from a plasmid vector made them largely resistant to FPV infection. Mutagenesis of the protein binding site within the 5′ end viral genome did not affect replication of the virus. PMID:10438866

End-of-Life Nursing Care and Education: End-of-Life Nursing Education: Past and Present.

Science.gov (United States)

DʼAntonio, Jocelyn

The dying experience is forever carried in the life story of those for whom the nurse cares. A goal of end-of-life nursing education is to produce nurses who are comfortable with death and dying and who have had the opportunity to reflect on their thoughts and feelings about end-of-life care. This article reviews the history, development, and teaching methods of end-of-life care, offering recommendations for future education.

An alternate end design for SSC dipoles

International Nuclear Information System (INIS)

Peters, C.; Caspi, S.; Taylor, C.

1989-02-01

Experience in the SSC dipole program has shown that fabrication of cylindrical coil ends is difficult. Cable stiffness requires large forces to maintain the proper position of the conductors in the end during winding. After winding, the coil ends remain distorted nd significant motion of the need conductors is required to force the coil end into the molding cavity. Local mechanical stresses are high during this process and extra pieces of insulation are required to prevent turn-to-turn shorts from developing during the winding and molding steps. Prior to assembly the coil end is compressed in a mold cavity and injected with a filler material to correct surface irregularities and fill voids in the end. LBL has developed an alternate design which permits the conductors to be wound over the end using minimal force and technician coerosion. The conductors are placed on a conical surface where the largest diameter over the outer layer conductors is 10 cm. No coil end spaces or insulation pieces between turns are required. The conductor geometry was analytically optimized to meet SSC multipole requirements for the ends. The first 1-m dipole utilizing this end geometry has been constructed and successfully tested. Design and construction data are presented. Also model test results, including training and multipole measurements of the end are given. 1 ref., 12 figs., 3 tabs

Interoperable End-to-End Remote Patient Monitoring Platform Based on IEEE 11073 PHD and ZigBee Health Care Profile.

Science.gov (United States)

Clarke, Malcolm; de Folter, Joost; Verma, Vivek; Gokalp, Hulya

2018-05-01

This paper describes the implementation of an end-to-end remote monitoring platform based on the IEEE 11073 standards for personal health devices (PHD). It provides an overview of the concepts and approaches and describes how the standard has been optimized for small devices with limited resources of processor, memory, and power that use short-range wireless technology. It explains aspects of IEEE 11073, including the domain information model, state model, and nomenclature, and how these support its plug-and-play architecture. It shows how these aspects underpin a much larger ecosystem of interoperable devices and systems that include IHE PCD-01, HL7, and BlueTooth LE medical devices, and the relationship to the Continua Guidelines, advocating the adoption of data standards and nomenclature to support semantic interoperability between health and ambient assisted living in future platforms. The paper further describes the adaptions that have been made in order to implement the standard on the ZigBee Health Care Profile and the experiences of implementing an end-to-end platform that has been deployed to frail elderly patients with chronic disease(s) and patients with diabetes.

SSC collider dipole magnet end mechanical design

International Nuclear Information System (INIS)

Delchamps, S.W.; Bossert, R.C.; Carson, J.; Ewald, K.; Fulton, H.; Kerby, J.; Koska, W.; Strait, J.; Wake, M.; Leung, K.K.

1991-01-01

This paper describes the mechanical design of the ends of Superconducting Super Collider dipole magnets to be constructed and tested at Fermilab. Coil end clamps, end yoke configuration, and end plate design are discussed. Loading of the end plate by axial Lorentz forces is discussed. Relevant data from 40 mm and 50 mm aperture model dipole magnets built and tested at Fermilab are presented. In particular, the apparent influence of end clamp design on the quench behavior of model SSC dipoles is described

End-to-End Assessment of a Large Aperture Segmented Ultraviolet Optical Infrared (UVOIR) Telescope Architecture

Science.gov (United States)

Feinberg, Lee; Rioux, Norman; Bolcar, Matthew; Liu, Alice; Guyon, Oliver; Stark, Chris; Arenberg, Jon

2016-01-01

Key challenges of a future large aperture, segmented Ultraviolet Optical Infrared (UVOIR) Telescope capable of performing a spectroscopic survey of hundreds of Exoplanets will be sufficient stability to achieve 10^-10 contrast measurements and sufficient throughput and sensitivity for high yield Exo-Earth spectroscopic detection. Our team has collectively assessed an optimized end to end architecture including a high throughput coronagraph capable of working with a segmented telescope, a cost-effective and heritage based stable segmented telescope, a control architecture that minimizes the amount of new technologies, and an Exo-Earth yield assessment to evaluate potential performance. These efforts are combined through integrated modeling, coronagraph evaluations, and Exo-Earth yield calculations to assess the potential performance of the selected architecture. In addition, we discusses the scalability of this architecture to larger apertures and the technological tall poles to enabling it.

INTERACTIONS OF REALM BOUNDARIES AND END-TO-ENG NETWORK APPLICATIONS

Energy Technology Data Exchange (ETDEWEB)

M. FISK; W. FENG

2000-08-01

One of the design principles of the Internet is that the network is made more flexible, and therefore useful, by placing functionality in end applications rather than in network infrastructure. Network gateways that violate this principle are considered harmful. This paper demonstrates that such upper-level gateways exist because of realm-specific performance, security, and protocol needs of certain portions of the Internet. Placing this functionality in end hosts is, conversely, harmful to the flexibility of using the Internet to link disparate networks. Requirements are developed for a protocol to allow end-hosts and gateways to negotiate the functionality of these gateways in terms of the needs of both end applications and network realms.

First Demonstration of Real-Time End-to-End 40 Gb/s PAM-4 System using 10-G Transmitter for Next Generation Access Applications

DEFF Research Database (Denmark)

Wei, Jinlong; Eiselt, Nicklas; Griesser, Helmut

We demonstrate the first known experiment of a real-time end-to-end 40-Gb/s PAM-4 system for next generation access applications using 10G class transmitters only. Up to 25-dB upstream link budget for 20 km SMF is achieved.......We demonstrate the first known experiment of a real-time end-to-end 40-Gb/s PAM-4 system for next generation access applications using 10G class transmitters only. Up to 25-dB upstream link budget for 20 km SMF is achieved....

Analysis of fuel end-temperature peaking

Energy Technology Data Exchange (ETDEWEB)

Xu, Z.; Jiang, Q.; Lai, L.; Shams, M. [CANDU Energy Inc., Fuel Engineering Dept., Mississauga, Ontario (Canada)

2013-07-01

During normal operation and refuelling of CANDU® fuel, fuel temperatures near bundle ends will increase due to a phenomenon called end flux peaking. Similar phenomenon would also be expected to occur during a postulated large break LOCA event. The end flux peaking in a CANDU fuel element is due to the fact that neutron flux is higher near a bundle end, in contact with a neighbouring bundle or close to heavy water coolant, than in the bundle mid-plane, because of less absorption of thermal neutrons by Zircaloy or heavy water than by the UO{sub 2} material. This paper describes Candu Energy experience in analysing behaviour of bundle due to end flux peaking using fuel codes FEAT, ELESTRES and ELOCA. (author)

SSC collider dipole magnet end mechanical design

International Nuclear Information System (INIS)

Delchamps, S.W.; Bossert, R.C.; Carson, J.; Ewald, K.; Fulton, H.; Kerby, J.; Koska, W.; Strait, J.; Wake, S.M.; Leung, K.K.

1991-05-01

This paper describes the mechanical design of the ends of Superconducting Super Collider dipole magnets to be constructed and tested at Fermilab. Coil end clamps, end yoke configuration, and end plate design are discussed. Loading of the end plate by axial Lorentz forces is discussed. Relevant data from 40 mm and 50 mm aperture model dipole magnets built and tested at Fermilab are presented. In particular, the apparent influence of end clamp design on the quench behavior of model SSC dipoles is described. 8 refs., 3 figs

End-User Development of Information Visualization

DEFF Research Database (Denmark)

Pantazos, Kostas; Lauesen, Søren; Vatrapu, Ravi

2013-01-01

such as data manipulation, but no formal training in programming. 18 visualization tools were surveyed from an enduser developer perspective. The results of this survey study show that end-user developers need better tools to create and modify custom visualizations. A closer collaboration between End......This paper investigates End-User Development of Information Visualization. More specifically, we investigated how existing visualization tools allow end-user developers to construct visualizations. End-user developers have some developing or scripting skills to perform relatively advanced tasks......-User Development and Information Visualization researchers could contribute towards the development of better tools to support custom visualizations. In addition, as empirical evaluations of these tools are lacking both research communities should focus more on this aspect. The study serves as a starting point...

Nerve endings in the heart of teleosts.

Science.gov (United States)

Kumar, S

1979-01-01

The nerve endings in the heart of fishes were studied using silver impregnation techniques. The heart chambers are profusely innervated by the sympathetic, parasympathetic (vagal) and postganglionic fibers of the intracardiac ganglia situated at the sinuatrial and the atrioventricular junctions. The plexuses are composed of medullated and nonmedullated fibers. The nerve fibers generally end freely and are slightly branched or unbranched terminations of myelinated and unmyelinated fibers. Moreover, a few nerve fibers end redundant in the form of end-rings, bulb-like, bush-like, club-shaped end end-coil like structures. The complex unencapsulated types of endings are also found in the myocardium of the atrium and the ventricle. The encapsulated endings (Vater-Pacinian; Krause end-bulb) could not be observed.

Increasing gas producer profitability with virtual well visibility via an end-to-end, wireless Internet gas monitoring system

Energy Technology Data Exchange (ETDEWEB)

McDougall, M.; Coleman, K.; Beck, R.; Lyon, R.; Potts, R. [Northrock Resources Ltd., Calgary, AB (Canada); Benterud, K. [Zed.i solutions, Calgary, AB (Canada)

2003-07-01

Most gas producing companies still use 100-year old technology to measure gas volumes because of the prohibitive costs of implementing corporate wide electronic information systems to replace circular mechanical chart technology. This paper describes how Northrock Resources Ltd. increased profitability using Smart-Alek{sup TM} while avoiding high implementation costs. Smart-Alek is a new type of fully integrated end-to-end electronic gas flow measurement (GFM) system based on Field Intelligence Network and End User Interference (FINE). Smart-Alek can analyze gas production through public wireless communications and a web-browser delivery system. The system has enabled Northrock to increase gas volumes with more accurate measurement and reduced downtime. In addition, operating costs were also decreased because the frequency of well visits was reduced and the administrative procedures of data collection was more efficient. The real-time well visibility of the tool has proven to be very effective in optimizing business profitability. 9 refs., 1 tab., 9 figs.

Analysis of effect of different construction methods of piles on the end effect on skin friction of piles

Institute of Scientific and Technical Information of China (English)

ZHOU Hongbo; CHEN Zhuchang

2007-01-01

Based on the comparative analysis of end effect on skin friction of displacement-pile (driven pile),the end effect on skin friction of bored pile is studied.The end effect on skin friction between driven pile and bored pile is different and the end effect on skin friction of bored pile is reduce of skin friction in the soil layer adjacent to the pile end.The degradation degree of skin friction is deduced with the increase of the distance from pile end.The concept of additional mud cake formed by the effect of cushion at the bottom of borehole during pouring concrete is introduced to explain the mechanism of end effect on skin friction of the bored pile.The test results of post-grouting piles indicate that the post-grouting technique is an effective way to improve the end effect on skin friction of bored pile.

Proportional counter end effects eliminator

International Nuclear Information System (INIS)

Meekins, J.F.

1976-01-01

An improved gas-filled proportional counter which includes a resistor network connected between the anode and cathode at the ends of the counter in order to eliminate ''end effects'' is described. 3 Claims, 2 Drawing Figures

A fully automatic end-to-end method for content-based image retrieval of CT scans with similar liver lesion annotations.

Science.gov (United States)

Spanier, A B; Caplan, N; Sosna, J; Acar, B; Joskowicz, L

2018-01-01

The goal of medical content-based image retrieval (M-CBIR) is to assist radiologists in the decision-making process by retrieving medical cases similar to a given image. One of the key interests of radiologists is lesions and their annotations, since the patient treatment depends on the lesion diagnosis. Therefore, a key feature of M-CBIR systems is the retrieval of scans with the most similar lesion annotations. To be of value, M-CBIR systems should be fully automatic to handle large case databases. We present a fully automatic end-to-end method for the retrieval of CT scans with similar liver lesion annotations. The input is a database of abdominal CT scans labeled with liver lesions, a query CT scan, and optionally one radiologist-specified lesion annotation of interest. The output is an ordered list of the database CT scans with the most similar liver lesion annotations. The method starts by automatically segmenting the liver in the scan. It then extracts a histogram-based features vector from the segmented region, learns the features' relative importance, and ranks the database scans according to the relative importance measure. The main advantages of our method are that it fully automates the end-to-end querying process, that it uses simple and efficient techniques that are scalable to large datasets, and that it produces quality retrieval results using an unannotated CT scan. Our experimental results on 9 CT queries on a dataset of 41 volumetric CT scans from the 2014 Image CLEF Liver Annotation Task yield an average retrieval accuracy (Normalized Discounted Cumulative Gain index) of 0.77 and 0.84 without/with annotation, respectively. Fully automatic end-to-end retrieval of similar cases based on image information alone, rather that on disease diagnosis, may help radiologists to better diagnose liver lesions.

Practical End-to-End Performance Testing Tool for High Speed 3G-Based Networks

Science.gov (United States)

Shinbo, Hiroyuki; Tagami, Atsushi; Ano, Shigehiro; Hasegawa, Toru; Suzuki, Kenji

High speed IP communication is a killer application for 3rd generation (3G) mobile systems. Thus 3G network operators should perform extensive tests to check whether expected end-to-end performances are provided to customers under various environments. An important objective of such tests is to check whether network nodes fulfill requirements to durations of processing packets because a long duration of such processing causes performance degradation. This requires testers (persons who do tests) to precisely know how long a packet is hold by various network nodes. Without any tool's help, this task is time-consuming and error prone. Thus we propose a multi-point packet header analysis tool which extracts and records packet headers with synchronized timestamps at multiple observation points. Such recorded packet headers enable testers to calculate such holding durations. The notable feature of this tool is that it is implemented on off-the shelf hardware platforms, i.e., lap-top personal computers. The key challenges of the implementation are precise clock synchronization without any special hardware and a sophisticated header extraction algorithm without any drop.

Chinese Medical Question Answer Matching Using End-to-End Character-Level Multi-Scale CNNs

Directory of Open Access Journals (Sweden)

Sheng Zhang

2017-07-01

Full Text Available This paper focuses mainly on the problem of Chinese medical question answer matching, which is arguably more challenging than open-domain question answer matching in English due to the combination of its domain-restricted nature and the language-specific features of Chinese. We present an end-to-end character-level multi-scale convolutional neural framework in which character embeddings instead of word embeddings are used to avoid Chinese word segmentation in text preprocessing, and multi-scale convolutional neural networks (CNNs are then introduced to extract contextual information from either question or answer sentences over different scales. The proposed framework can be trained with minimal human supervision and does not require any handcrafted features, rule-based patterns, or external resources. To validate our framework, we create a new text corpus, named cMedQA, by harvesting questions and answers from an online Chinese health and wellness community. The experimental results on the cMedQA dataset show that our framework significantly outperforms several strong baselines, and achieves an improvement of top-1 accuracy by up to 19%.

Internet end-to-end performance monitoring for the High Energy Nuclear and Particle Physics community

International Nuclear Information System (INIS)

Matthews, W.

2000-01-01

Modern High Energy Nuclear and Particle Physics (HENP) experiments at Laboratories around the world present a significant challenge to wide area networks. Petabytes (1015) or exabytes (1018) of data will be generated during the lifetime of the experiment. Much of this data will be distributed via the Internet to the experiment's collaborators at Universities and Institutes throughout the world for analysis. In order to assess the feasibility of the computing goals of these and future experiments, the HENP networking community is actively monitoring performance across a large part of the Internet used by its collaborators. Since 1995, the pingER project has been collecting data on ping packet loss and round trip times. In January 2000, there are 28 monitoring sites in 15 countries gathering data on over 2,000 end-to-end pairs. HENP labs such as SLAC, Fermi Lab and CERN are using Advanced Network's Surveyor project and monitoring performance from one-way delay of UDP packets. More recently several HENP sites have become involved with NLANR's active measurement program (AMP). In addition SLAC and CERN are part of the RIPE test-traffic project and SLAC is home for a NIMI machine. The large End-to-end performance monitoring infrastructure allows the HENP networking community to chart long term trends and closely examine short term glitches across a wide range of networks and connections. The different methodologies provide opportunities to compare results based on different protocols and statistical samples. Understanding agreement and discrepancies between results provides particular insight into the nature of the network. This paper will highlight the practical side of monitoring by reviewing the special needs of High Energy Nuclear and Particle Physics experiments and provide an overview of the experience of measuring performance across a large number of interconnected networks throughout the world with various methodologies. In particular, results from each project

Internet end-to-end performance monitoring for the High Energy Nuclear and Particle Physics community

Energy Technology Data Exchange (ETDEWEB)

Matthews, W.

2000-02-22

Modern High Energy Nuclear and Particle Physics (HENP) experiments at Laboratories around the world present a significant challenge to wide area networks. Petabytes (1015) or exabytes (1018) of data will be generated during the lifetime of the experiment. Much of this data will be distributed via the Internet to the experiment's collaborators at Universities and Institutes throughout the world for analysis. In order to assess the feasibility of the computing goals of these and future experiments, the HENP networking community is actively monitoring performance across a large part of the Internet used by its collaborators. Since 1995, the pingER project has been collecting data on ping packet loss and round trip times. In January 2000, there are 28 monitoring sites in 15 countries gathering data on over 2,000 end-to-end pairs. HENP labs such as SLAC, Fermi Lab and CERN are using Advanced Network's Surveyor project and monitoring performance from one-way delay of UDP packets. More recently several HENP sites have become involved with NLANR's active measurement program (AMP). In addition SLAC and CERN are part of the RIPE test-traffic project and SLAC is home for a NIMI machine. The large End-to-end performance monitoring infrastructure allows the HENP networking community to chart long term trends and closely examine short term glitches across a wide range of networks and connections. The different methodologies provide opportunities to compare results based on different protocols and statistical samples. Understanding agreement and discrepancies between results provides particular insight into the nature of the network. This paper will highlight the practical side of monitoring by reviewing the special needs of High Energy Nuclear and Particle Physics experiments and provide an overview of the experience of measuring performance across a large number of interconnected networks throughout the world with various methodologies. In particular, results

End-of-Life Conversation Game Increases Confidence for Having End-of-Life Conversations for Chaplains-in-Training.

Science.gov (United States)

Van Scoy, Lauren Jodi; Watson-Martin, Elizabeth; Bohr, Tiffany A; Levi, Benjamin H; Green, Michael J

2018-04-01

Discussing end-of-life issues with patients is an essential role for chaplains. Few tools are available to help chaplains-in-training develop end-of-life communication skills. This study aimed to determine whether playing an end-of-life conversation game increases the confidence for chaplain-in-trainings to discuss end-of-life issues with patients. We used a convergent mixed methods design. Chaplains-in-training played the end-of-life conversation game twice over 2 weeks. For each game, pre- and postgame questionnaires measured confidence discussing end-of-life issues with patients and emotional affect. Between games, chaplains-in-training discussed end-of-life issues with an inpatient. One week after game 2, chaplains-in-training were individually interviewed. Quantitative data were analyzed using descriptive statistics and Wilcoxon rank-sum t tests. Content analysis identified interview themes. Quantitative and qualitative data sets were then integrated using a joint display. Twenty-three chaplains-in-training (52% female; 87% Caucasian; 70% were in year 1 of training) completed the study. Confidence scores (scale: 15-75; 75 = very confident) increased significantly after each game, increasing by 10.0 points from pregame 1 to postgame 2 ( P game, and shyness subscale scores decreased significantly after each game. Content analysis found that chaplains-in-training found the game to be a positive, useful experience and reported that playing twice was beneficial (not redundant). Mixed methods analysis suggest that an end-of-life conversation game is a useful tool that can increase chaplain-in-trainings' confidence for initiating end-of-life discussions with patients. A larger sample size is needed to confirm these findings.

Large Scale Metric Learning for Distance-Based Image Classification on Open Ended Data Sets

NARCIS (Netherlands)

Mensink, T.; Verbeek, J.; Perronnin, F.; Csurka, G.; Farinella, G.M.; Battiato, S.; Cipolla, R,

2013-01-01

Many real-life large-scale datasets are open-ended and dynamic: new images are continuously added to existing classes, new classes appear over time, and the semantics of existing classes might evolve too. Therefore, we study large-scale image classification methods that can incorporate new classes

Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy.

Science.gov (United States)

Meroni, Alice; Lazzaro, Federico; Muzi-Falconi, Marco; Podestà, Alessandro

2018-01-01

We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.

End-to-end Structural Restriction of α-Synuclein and Its Influence on Amyloid Fibril Formation

International Nuclear Information System (INIS)

Hong, Chul Suk; Park, Jae Hyung; Choe, Young Jun; Paik, Seung R.

2014-01-01

Relationship between molecular freedom of amyloidogenic protein and its self-assembly into amyloid fibrils has been evaluated with α-synuclein, an intrinsically unfolded protein related to Parkinson's disease, by restricting its structural plasticity through an end-to-end disulfide bond formation between two newly introduced cysteine residues on the N- and C-termini. Although the resulting circular form of α-synuclein exhibited an impaired fibrillation propensity, the restriction did not completely block the protein's interactive core since co-incubation with wild-type α-synuclein dramatically facilitated the fibrillation by producing distinctive forms of amyloid fibrils. The suppressed fibrillation propensity was instantly restored as the structural restriction was unleashed with β-mercaptoethanol. Conformational flexibility of the accreting amyloidogenic protein to pre-existing seeds has been demonstrated to be critical for fibrillar extension process by exerting structural adjustment to a complementary structure for the assembly

End-to-end Structural Restriction of α-Synuclein and Its Influence on Amyloid Fibril Formation

Energy Technology Data Exchange (ETDEWEB)

Hong, Chul Suk; Park, Jae Hyung; Choe, Young Jun; Paik, Seung R. [Seoul National University, Seoul (Korea, Republic of)

2014-09-15

Relationship between molecular freedom of amyloidogenic protein and its self-assembly into amyloid fibrils has been evaluated with α-synuclein, an intrinsically unfolded protein related to Parkinson's disease, by restricting its structural plasticity through an end-to-end disulfide bond formation between two newly introduced cysteine residues on the N- and C-termini. Although the resulting circular form of α-synuclein exhibited an impaired fibrillation propensity, the restriction did not completely block the protein's interactive core since co-incubation with wild-type α-synuclein dramatically facilitated the fibrillation by producing distinctive forms of amyloid fibrils. The suppressed fibrillation propensity was instantly restored as the structural restriction was unleashed with β-mercaptoethanol. Conformational flexibility of the accreting amyloidogenic protein to pre-existing seeds has been demonstrated to be critical for fibrillar extension process by exerting structural adjustment to a complementary structure for the assembly.

Programmer's guide to FFE: a fast front-end data-acquisition program

International Nuclear Information System (INIS)

Million, D.L.

1983-05-01

The Large Coil Test Facility project of the Fusion Energy Division has a data acquisition system which includes a large host computer and several small, peripheral front-end computers. The front-end processors handle details of data acquisition under the control of the host and pass data back to the host for storage. Some of the front ends are known as fast front ends and are required to collect a maximum of 64,000 samples each second. This speed and other hardware constraints resulted in a need for a stand-alone, assembly language task which could be downline loaded from the host system into the fast front ends. FFE (Fast Front End) was written to satisfy this need. It was written in the PDP-11 MACRO-11 assembly language for an LSI-11/23 processor. After the host loads the task into the front end, it controls the data acquisition process with a series of commands and parameters. This Programmer's Guide describes the structure and operation of FFE in detail from a programming point of view. A companion User's guide provides more information on the use of the program from the host system

Longitudinal forces acting at side-to-end and end-to-side anastomoses when a knitted polyester arterial prosthesis is implanted in the dog.

Science.gov (United States)

Dadgar, L; Downs, A R; Deng, X; Marois, Y; King, M W; Martin, L; Guidoin, R

1995-01-01

In a previous study, which investigated the tensions at the proximal and distal end-to-end anastomoses of a vascular prosthesis, no significant differences were found in the longitudinal forces between the two anastomotic sites after different periods of implantation. The present follow-up study was devised to study the longitudinal forces at a proximal side-to-end and a distal end-to-side anastomosis using a warp knitted polyester prosthesis implanted as a canine thorocoabdominal bypass. The external surface of the prosthesis contained a specially printed "tension indicator" design, which enabled changes in length to be assessed photographically at the two anastomoses at the time of implantation and at sacrifice. The longitudinal force at each site was then calculated using a relationship obtained experimentally between the total longitudinal force and the changes in length of the virgin graft in vitro. The in vitro measurements on the prosthesis were performed using a computer-controlled laser calibration system. Although the results showed a tendency toward a gradual loss in longitudinal force at both anastomoses over 7 months in situ, statistical analysis showed no significant difference in the longitudinal force at the two anastomotic sites after any period of implantation. Histopathological and textile analysis also showed that the characteristics of the prostheses were similar at both anastomotic sites. This does not mean, however, that the intramural stress concentrations experienced by the two sites were the same. While comparing the level of the longitudinal forces measured in this study with those observed in the previous thoracic aorta study using end-to-end anastomoses, no significant differences were observed due to the different types of anastomoses. It would appear that the longitudinal force is not one of the main etiological factors that cause the formation and localization of anastomotic failure.

West Coast fish, mammal, bird life history and abunance parameters - Developing end-to-end models of the California Current Large Marine Ecosystem

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web...

High-end encroachment patterns of new products

NARCIS (Netherlands)

Rhee, van der B.; Schmidt, G.; Orden, van J.

2012-01-01

Previous research describes two key ways in which a new product may encroach on an existing market. In high-end encroachment, the new product first sells to high-end customers and then diffuses down-market; in low-end encroachment, the new product enters at the low end and encroaches up-market. This

Novel characteristics of CtIP at damage-induced foci following the initiation of DNA end resection

International Nuclear Information System (INIS)

Fujisawa, Hiroshi; Fujimori, Akira; Okayasu, Ryuichi; Uesaka, Mitsuru; Yajima, Hirohiko

2015-01-01

Highlights: • CtIP becomes hyperphosphorylated and forms foci following cell irradiation. • CtIP accumulates in foci subsequent to the peak of hyperphosphorylation. • CtIP is maintained in a hypophosphorylated state at later times. • CtIP is continuously recruited to DNA double strand breaks downstream of resection. • CtIP presumably have a distinct role following the initiation of resection. - Abstract: Homologous recombination (HR) is a major repair pathway for DNA double strand breaks (DSBs), and end resection, which generates a 3′-single strand DNA tail at the DSB, is an early step in the process. Resection is initiated by the Mre11 nuclease together with CtIP. Here, we describe novel characteristics of CtIP at DSBs. At early times following exposure of human cells to ionizing radiation, CtIP localized to the DSB, became hyperphosphorylated and formed foci in an ATM-dependent manner. At later times, when the initiation of resection had occurred, CtIP foci persist but CtIP is maintained in a hypophosphorylated state, which is dependent on ATM and ATR. Exposure to cycloheximide revealed that CtIP turns over at DSB sites downstream of resection. Our findings provide strong evidence that CtIP is continuously recruited to DSBs downstream of both the initiation and extension step of resection, strongly suggesting that CtIP has functions in addition to promoting the initiation of resection during HR

Gulf of California species and catch spatial distributions and historical time series - Developing end-to-end models of the Gulf of California

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to develop spatially discrete end-to-end models of the northern Gulf of California, linking oceanography, biogeochemistry, food web...

End points for adjuvant therapy trials: has the time come to accept disease-free survival as a surrogate end point for overall survival?

Science.gov (United States)

Gill, Sharlene; Sargent, Daniel

2006-06-01

The intent of adjuvant therapy is to eradicate micro-metastatic residual disease following curative resection with the goal of preventing or delaying recurrence. The time-honored standard for demonstrating efficacy of new adjuvant therapies is an improvement in overall survival (OS). This typically requires phase III trials of large sample size with lengthy follow-up. With the intent of reducing the cost and time of completing such trials, there is considerable interest in developing alternative or surrogate end points. A surrogate end point may be employed as a substitute to directly assess the effects of an intervention on an already accepted clinical end point such as mortality. When used judiciously, surrogate end points can accelerate the evaluation of new therapies, resulting in the more timely dissemination of effective therapies to patients. The current review provides a perspective on the suitability and validity of disease-free survival (DFS) as an alternative end point for OS. Criteria for establishing surrogacy and the advantages and limitations associated with the use of DFS as a primary end point in adjuvant clinical trials and as the basis for approval of new adjuvant therapies are discussed.

Mere end marionetdukker

DEFF Research Database (Denmark)

Lehmann-Jacobsen, Emilie Tinne

2016-01-01

Pressefrihed er en mangelvare i flere sydøstasiatiske lande, og journalisterne beskrives sjældent som andet end viljeløse marionetdukker for de siddende magthavere. Det er dog langt fra den fulde fortælling. Men myten lever videre til frustration for de fagligt stolte journalister og med konsekve......Pressefrihed er en mangelvare i flere sydøstasiatiske lande, og journalisterne beskrives sjældent som andet end viljeløse marionetdukker for de siddende magthavere. Det er dog langt fra den fulde fortælling. Men myten lever videre til frustration for de fagligt stolte journalister og med...

Role of Double-Strand Break End-Tethering during Gene Conversion in Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Suvi Jain

2016-04-01

Full Text Available Correct repair of DNA double-strand breaks (DSBs is critical for maintaining genome stability. Whereas gene conversion (GC-mediated repair is mostly error-free, repair by break-induced replication (BIR is associated with non-reciprocal translocations and loss of heterozygosity. We have previously shown that a Recombination Execution Checkpoint (REC mediates this competition by preventing the BIR pathway from acting on DSBs that can be repaired by GC. Here, we asked if the REC can also determine whether the ends that are engaged in a GC-compatible configuration belong to the same break, since repair involving ends from different breaks will produce potentially deleterious translocations. We report that the kinetics of repair are markedly delayed when the two DSB ends that participate in GC belong to different DSBs (termed Trans compared to the case when both DSB ends come from the same break (Cis. However, repair in Trans still occurs by GC rather than BIR, and the overall efficiency of repair is comparable. Hence, the REC is not sensitive to the "origin" of the DSB ends. When the homologous ends for GC are in Trans, the delay in repair appears to reflect their tethering to sequences on the other side of the DSB that themselves recombine with other genomic locations with which they share sequence homology. These data support previous observations that the two ends of a DSB are usually tethered to each other and that this tethering facilitates both ends encountering the same donor sequence. We also found that the presence of homeologous/repetitive sequences in the vicinity of a DSB can distract the DSB end from finding its bona fide homologous donor, and that inhibition of GC by such homeologous sequences is markedly increased upon deleting Sgs1 but not Msh6.

Influence of physicians' life stances on attitudes to end-of-life decisions and actual end-of-life decision-making in six countries

DEFF Research Database (Denmark)

Cohen, J; van Delden, J; Mortier, F

2008-01-01

AIM: To examine how physicians' life stances affect their attitudes to end-of-life decisions and their actual end-of-life decision-making. METHODS: Practising physicians from various specialties involved in the care of dying patients in Belgium, Denmark, The Netherlands, Sweden, Switzerland......) and Protestants (up to 20.4% in The Netherlands) reported ever having made such a decision. DISCUSSION: The results suggest that religious teachings influence to some extent end-of-life decision-making, but are certainly not blankly accepted by physicians, especially when dealing with real patients...... large life-stance groups in each country. RESULTS: Only small differences in life stance were found in all countries in general attitudes and intended and actual behaviour with regard to various end-of-life decisions. However, with regard to the administration of drugs explicitly intended to hasten...

The microorganisms in chronically infected end-stage and non-end-stage cystic fibrosis patients

DEFF Research Database (Denmark)

Rudkjøbing, Vibeke B; Thomsen, Trine R; Alhede, Morten

2011-01-01

Patients suffering from cystic fibrosis (CF) develop chronic lung infections because of highly viscous mucus, where bacteria can form biofilms. In this study, we investigated the microorganisms present in the lungs of end-stage and non-end-stage patients using standard culturing techniques and mo...

On cryptographic security of end-to-end encrypted connections in WhatsApp and Telegram messengers

Directory of Open Access Journals (Sweden)

Sergey V. Zapechnikov

2017-11-01

Full Text Available The aim of this work is to analyze the available possibilities for improving secure messaging with end-to-end connections under conditions of external violator actions and distrusted service provider. We made a comparative analysis of cryptographic security mechanisms for two widely used messengers: Telegram and WhatsApp. It was found that Telegram is based on MTProto protocol, while WhatsApp is based on the alternative Signal protocol. We examine the specific features of messengers implementation associated with random number generation on the most popular Android mobile platform. It was shown that Signal has better security properties. It is used in several other popular messengers such as TextSecure, RedPhone, GoogleAllo, FacebookMessenger, Signal along with WhatsApp. A number of possible attacks on both messengers were analyzed in details. In particular, we demonstrate that the metadata are poorly protected in both messengers. Metadata security may be one of the goals for further studies.

Investigation of vertebral ''end plate sclerosis''

International Nuclear Information System (INIS)

Lee, S.W.; Mathie, A.G.; Jackson, J.E.; Hughes, S.P.F.

2001-01-01

To evaluate the association between vertebral ''end plate sclerosis'' and neck pain. A retrospective study was carried out of lateral cervical spine radiographs with a Picture Archive and Communication System (PACS). Two hundred patients' files were randomly assessed, comprising four equal groups, A to D. The mean ages of the patients were 62±7.4 years, 61±7.5 years, 40±5.6 years and 23±5.6 years respectively. In group A, all patients had symptoms of neck pain and a radiographic diagnosis of ''end plate sclerosis'' of the cervical spine. In groups B to D, asymptomatic patients were recruited and their age groups were 50-69, 30-49 and 10-29 years respectively. Using the PACS, the radiographic density and the sagittal diameter, thickness and area of the end plates at the C5 level were measured. Results and conclusions: No significant differences were found in the radiographic density of the end plates either between the symptomatic and asymptomatic groups (groups A and B), or between different age groups (groups B, C and D). A significant increase in end plate area and thickness was found, however, in both group B (P<0.005) and group C (P<0.01) in comparison with group D. This indicates that the extent of end plate sclerosis increases with age. Our results suggest that the radiographic density of cervical vertebral end plates correlates neither with neck pain nor with increasing age. The radiological sign of ''end plate sclerosis'' may be over-reported, further limiting its value in the assessment of patients with cervical spondylosis. (orig.)

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites.

Directory of Open Access Journals (Sweden)

Luis Gutierrez-Heredia

Full Text Available Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters, but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon and freeware (123D Catch, Meshmixer and Netfabb, allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis.

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites.

Science.gov (United States)

Gutierrez-Heredia, Luis; Benzoni, Francesca; Murphy, Emma; Reynaud, Emmanuel G

2016-01-01

Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis.

Availability and End-to-end Reliability in Low Duty Cycle Multihop Wireless Sensor Networks.

Science.gov (United States)

Suhonen, Jukka; Hämäläinen, Timo D; Hännikäinen, Marko

2009-01-01

A wireless sensor network (WSN) is an ad-hoc technology that may even consist of thousands of nodes, which necessitates autonomic, self-organizing and multihop operations. A typical WSN node is battery powered, which makes the network lifetime the primary concern. The highest energy efficiency is achieved with low duty cycle operation, however, this alone is not enough. WSNs are deployed for different uses, each requiring acceptable Quality of Service (QoS). Due to the unique characteristics of WSNs, such as dynamic wireless multihop routing and resource constraints, the legacy QoS metrics are not feasible as such. We give a new definition to measure and implement QoS in low duty cycle WSNs, namely availability and reliability. Then, we analyze the effect of duty cycling for reaching the availability and reliability. The results are obtained by simulations with ZigBee and proprietary TUTWSN protocols. Based on the results, we also propose a data forwarding algorithm suitable for resource constrained WSNs that guarantees end-to-end reliability while adding a small overhead that is relative to the packet error rate (PER). The forwarding algorithm guarantees reliability up to 30% PER.

Availability and End-to-end Reliability in Low Duty Cycle MultihopWireless Sensor Networks

Directory of Open Access Journals (Sweden)

Timo D. Hämäläinen

2009-03-01

Full Text Available A wireless sensor network (WSN is an ad-hoc technology that may even consist of thousands of nodes, which necessitates autonomic, self-organizing and multihop operations. A typical WSN node is battery powered, which makes the network lifetime the primary concern. The highest energy efficiency is achieved with low duty cycle operation, however, this alone is not enough. WSNs are deployed for different uses, each requiring acceptable Quality of Service (QoS. Due to the unique characteristics of WSNs, such as dynamic wireless multihop routing and resource constraints, the legacy QoS metrics are not feasible as such. We give a new definition to measure and implement QoS in low duty cycle WSNs, namely availability and reliability. Then, we analyze the effect of duty cycling for reaching the availability and reliability. The results are obtained by simulations with ZigBee and proprietary TUTWSN protocols. Based on the results, we also propose a data forwarding algorithm suitable for resource constrained WSNs that guarantees end-to-end reliability while adding a small overhead that is relative to the packet error rate (PER. The forwarding algorithm guarantees reliability up to 30% PER.

Both movement-end and task-end are critical for error feedback in visuomotor adaptation: a behavioral experiment.

Directory of Open Access Journals (Sweden)

Takumi Ishikawa

Full Text Available An important issue in motor learning/adaptation research is how the brain accepts the error information necessary for maintaining and improving task performance in a changing environment. The present study focuses on the effect of timing of error feedback. Previous research has demonstrated that adaptation to displacement of the visual field by prisms in a manual reaching task is significantly slowed by delayed visual feedback of the endpoint, suggesting that error feedback is most effective when given at the end of a movement. To further elucidate the brain mechanism by which error information is accepted in visuomotor adaptation, we tested whether error acceptance is linked to the end of a given task or to the end of an executed movement. We conducted a behavioral experiment using a virtual shooting task in which subjects controlled their wrist movements to meet a target with a cursor as accurately as possible. We manipulated the timing of visual feedback of the impact position so that it occurred either ahead of or behind the true time of impact. In another condition, the impact timing was explicitly indicated by an additional cue. The magnitude of the aftereffect significantly varied depending on the timing of feedback (p < 0.05, Friedman's Test. Interestingly, two distinct peaks of aftereffect were observed around movement-end and around task-end, irrespective of the existence of the timing cue. However, the peak around task-end was sharper when the timing cue was given. Our results demonstrate that the brain efficiently accepts error information at both movement-end and task-end, suggesting that two different learning mechanisms may underlie visuomotor transformation.

Electronic Nicotine Delivery Systems (ENDS): What Nurses Need to Know.

Science.gov (United States)

Essenmacher, Carol; Naegle, Madeline; Baird, Carolyn; Vest, Bridgette; Spielmann, Rene; Smith-East, Marie; Powers, Leigh

Efforts to decrease adverse effects of tobacco use are affected by emergence of new nicotine delivery products. Advertising, product promotion, and social media promote use of these products, yet a lack of evidence regarding safety leaves nurses unprepared to counsel patients. To critically evaluate current research, reviews of literature, expert opinion, and stakeholder policy proposals on use and safety of electronic nicotine delivery systems (ENDS). A targeted examination of literature generated by key stakeholders and subject matter experts was conducted using key words, modified by risk factors, and limited to the past 8 years. Current knowledge gaps in research literature and practice implications of the literature are discussed. The safety of ENDS is questionable and unclear. There are clear health risks of nicotine exposure to developing brains. Potential health risks of ENDS secondhand emissions exposure exist. Using ENDS to facilitate total tobacco cessation is not proven.

7 CFR 51.1240 - Paper ends.

Science.gov (United States)

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Paper ends. 51.1240 Section 51.1240 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Cleaned Virginia Type Peanuts in the Shell Definitions § 51.1240 Paper ends. Paper ends means...

Kinetic approach to plasma end loss from linear devices

International Nuclear Information System (INIS)

Dreicer, H.

1976-01-01

A first step in the direction of a kinetic approach to end loss has been presented. This approach brings to light some fundamental processes not uncovered by the magnetohydrodynamic or guiding center approach. Attention was focused on the basically transient phenomenon in a way that describes the quite different behavior of collision dominated and collisionless ions, but ignores the magnetic nozzle effects near the ends of the system. The treatment illuminates some of the roles played by the parameter l/sub ii//L, and suggests the direction for more detailed investigations. End loss from linear systems is a very many faceted problem. Kinetic effects, magnetic effects, heat flow, etc. are all intermixed, and it will require a strong long term experimental and theoretical program to unravel all of its mysteries

Surrogate end points in clinical research: hazardous to your health.

Science.gov (United States)

Grimes, David A; Schulz, Kenneth F

2005-05-01

Surrogate end points in clinical research pose real danger. A surrogate end point is an outcome measure, commonly a laboratory test, that substitutes for a clinical event of true importance. Resistance to activated protein C, for example, has been used as a surrogate for venous thrombosis in women using oral contraceptives. Other examples of inappropriate surrogate end points in contraception include the postcoital test instead of pregnancy to evaluate new spermicides, breakage and slippage instead of pregnancy to evaluate condoms, and bone mineral density instead of fracture to assess the safety of depo-medroxyprogesterone acetate. None of these markers captures the effect of the treatment on the true outcome. A valid surrogate end point must both correlate with and accurately predict the outcome of interest. Although many surrogate markers correlate with an outcome, few have been shown to capture the effect of a treatment (for example, oral contraceptives) on the outcome (venous thrombosis). As a result, thousands of useless and misleading reports on surrogate end points litter the medical literature. New drugs have been shown to benefit a surrogate marker, but, paradoxically, triple the risk of death. Thousands of patients have died needlessly because of reliance on invalid surrogate markers. Researchers should avoid surrogate end points unless they have been validated; that requires at least one well done trial using both the surrogate and true outcome. The clinical maxim that "a difference to be a difference must make a difference" applies to research as well. Clinical research should focus on outcomes that matter.

The end of truth?

OpenAIRE

C. W. du Toit

1997-01-01

As we are approaching the end of the century, many ideas, systems, and certainties, previously taken for granted, seem to be questioned, altered and rejected. One of these is the notion of truth, which pervades the very fibre of Western thinking. Rejecting the relevant critique as simply a postmodem fad, this article proceeds to give attention to the questions regarding the end of religious, scientific, and metaphysical truth. Truth and power are dealt with, as well as the narrative nature of...

A gastrocnemius heterotopical transplant model with end-to-side neurorraphy.

Science.gov (United States)

Jaeger, Marcos Ricardo de Oliveira; Silva, Jefferson Luis Braga; Bain, James; Ely, Pedro Bins; Pires, Jefferson André; Ferreira, Lydia Masako

2014-01-01

To present an animal model to assess the effects of end-to-side innervation in the heterotopically transplanted model with reduced chances of neural contamination. The medial portion of the gastrocnemius muscle in wistar male rats was isolated and its pedicle dissected and performed a flap in the abdominal portion. To prevent neural contamination in the abdominal region, the muscle was wrapped with a Goretex(r) sheet. The specimens were divided into 2 groups (G). In G1 was performed an end-to-end suture between tibial nerve of the gastrocnemius and femoral motor nerve and between the saphenous sensory nerve and the motor nerve. In G2 was performed a end-to-side suture between the tibial nerve and the motor femoral and between the tibial nerve and saphenous motor nerve. The specimens were evaluated 60 days later to check the structure of the neurorraphy. Sections were obtained proximal and distal to the coaptation site. The medial gastrocnemius muscle had the advantage of maintaining visible mass after 60 days. No disruption of the coaptation site was found. No major injury to the donor nerve was seen in group 2. The proposed model is simple, reproduciple and prevent the neural contamination in the flap in end-to-side suture.

Online Help to End-Users in a Networked Environment.

Science.gov (United States)

Meyer, Paul

1991-01-01

Discusses the need for online help for end-users based on experiences with an online public access catalog (OPAC) at the University of Cape Town libraries. The concept of end users is examined, the role of search intermediaries in information systems is explained, and online help and systems design is discussed. (LRW)

Where to place the saving obligation: Energy end-users or suppliers?

International Nuclear Information System (INIS)

Bertoldi, Paolo; Labanca, Nicola; Rezessy, Silvia; Steuwer, Sibyl; Oikonomou, Vlasis

2013-01-01

Obligations to save energy differentiate, among other features, by obliged parties. These are obligations on energy suppliers and energy end-users. Supplier obligations have been introduced in North America, Europe and Australia. Under supplier obligations energy suppliers have to comply with mandatory energy saving targets and thus they implement (directly or via third parties) energy efficiency projects on their clients’ premises, or they decide to trade certified project savings if this option is envisaged by their obligation scheme. In several emerging schemes such as the UK Carbon Reduction Commitment (CRC) Energy Efficiency Scheme, the Tokyo Emission Trading Scheme or the Perform Achieve and Trade (PAT) Scheme in India, the obligation to reduce energy consumption is placed on large end-users directly and end-users are allowed to trade emissions allowances or energy saving certificates. The paper starts with presenting these two conceptually different ways for introducing energy saving obligations. Then it analyses advantages and disadvantages of end-users obligations compared to suppliers obligations. The preliminary conclusion of the paper is that supplier obligations seem to be well-suited for the residential sector, but end-user saving obligations may offer advantages when it comes to the industrial and commercial sectors. - Highlights: • We present different ways for introducing energy saving obligations. • We analyse energy end-users obligations vs. supplier obligations. • Supplier obligations seem to be well-suited for the residential sector. • End-user obligations offer advantages in the industrial and commercial sectors

Wear of micro end mills

DEFF Research Database (Denmark)

Bissacco, Giuliano; Hansen, Hans Nørgaard; De Chiffre, Leonardo

2005-01-01

This paper addresses the important issue of wear on micro end mills considering relevant metrological tools for its characterization and quantification. Investigation of wear on micro end mills is particularly difficult and no data are available in the literature. Small worn volumes cause large...... part. For this investigation 200 microns end mills are considered. Visual inspection of the micro tools requires high magnification and depth of focus. 3D reconstruction based on scanning electron microscope (SEM) images and stereo-pair technique is foreseen as a possible method for quantification...

Relative contribution of homologous recombination and non-homologous end-joining to DNA double-strand break repair after oxidative stress in Saccharomyces cerevisiae.

Science.gov (United States)

Letavayová, Lucia; Marková, Eva; Hermanská, Katarína; Vlcková, Viera; Vlasáková, Danusa; Chovanec, Miroslav; Brozmanová, Jela

2006-05-10

Oxidative damage to DNA seems to be an important factor in developing many human diseases including cancer. It involves base and sugar damage, base-free sites, DNA-protein cross-links and DNA single-strand (SSB) and double-strand (DSB) breaks. Oxidative DSB can be formed in various ways such as their direct induction by the drug or their generation either through attempted and aborted repair of primary DNA lesions or through DNA replication-dependent conversion of SSB. In general, two main pathways are responsible for repairing DSB, homologous recombination (HR) and non-homologous end-joining (NHEJ), with both of them being potential candidates for the repair of oxidative DSB. We have examined relative contribution of HR and NHEJ to cellular response after oxidative stress in Saccharomyces cerevisiae. Therefore, cell survival, mutagenesis and DSB induction and repair in the rad52, yku70 and rad52 yku70 mutants after hydrogen peroxide (H(2)O(2)), menadione (MD) or bleomycin (BLM) exposure were compared to those obtained for the corresponding wild type. We show that MD exposure does not lead to observable DSB induction in yeast, suggesting that the toxic effects of this agent are mediated by other types of DNA damage. Although H(2)O(2) treatment generates some DSB, their yield is relatively low and hence DSB may only partially be responsible for toxicity of H(2)O(2), particularly at high doses of the agent. On the other hand, the basis of the BLM toxicity resides primarily in DSB induction. Both HR and NHEJ act on BLM-induced DSB, although their relative participation in the process is not equal. Based on our results we suggest that the complexity and/or the quality of the BLM-induced DSB might represent an obstacle for the NHEJ pathway.

Long span DNA paired-end-tag (DNA-PET sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

Directory of Open Access Journals (Sweden)

Fei Yao

Full Text Available Structural variations (SVs contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10-20 kb and compared their characteristics with short insert (1 kb libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.

Status report of the end-to-end ASKAP software system: towards early science operations

Science.gov (United States)

Guzman, Juan Carlos; Chapman, Jessica; Marquarding, Malte; Whiting, Matthew

2016-08-01

300 MHz bandwidth for Array Release 1; followed by the deployment of the real-time data processing components. In addition to the Central Processor, the first production release of the CSIRO ASKAP Science Data Archive (CASDA) has also been deployed in one of the Pawsey Supercomputing Centre facilities and it is integrated to the end-to-end ASKAP data flow system. This paper describes the current status of the "end-to-end" data flow software system from preparing observations to data acquisition, processing and archiving; and the challenges of integrating an HPC facility as a key part of the instrument. It also shares some lessons learned since the start of integration activities and the challenges ahead in preparation for the start of the Early Science program.

Chromosome End Repair and Genome Stability in Plasmodium falciparum.

Science.gov (United States)

Calhoun, Susannah F; Reed, Jake; Alexander, Noah; Mason, Christopher E; Deitsch, Kirk W; Kirkman, Laura A

2017-08-08

The human malaria parasite Plasmodium falciparum replicates within circulating red blood cells, where it is subjected to conditions that frequently cause DNA damage. The repair of DNA double-stranded breaks (DSBs) is thought to rely almost exclusively on homologous recombination (HR), due to a lack of efficient nonhomologous end joining. However, given that the parasite is haploid during this stage of its life cycle, the mechanisms involved in maintaining genome stability are poorly understood. Of particular interest are the subtelomeric regions of the chromosomes, which contain the majority of the multicopy variant antigen-encoding genes responsible for virulence and disease severity. Here, we show that parasites utilize a competitive balance between de novo telomere addition, also called "telomere healing," and HR to stabilize chromosome ends. Products of both repair pathways were observed in response to DSBs that occurred spontaneously during routine in vitro culture or resulted from experimentally induced DSBs, demonstrating that both pathways are active in repairing DSBs within subtelomeric regions and that the pathway utilized was determined by the DNA sequences immediately surrounding the break. In combination, these two repair pathways enable parasites to efficiently maintain chromosome stability while also contributing to the generation of genetic diversity. IMPORTANCE Malaria is a major global health threat, causing approximately 430,000 deaths annually. This mosquito-transmitted disease is caused by Plasmodium parasites, with infection with the species Plasmodium falciparum being the most lethal. Mechanisms underlying DNA repair and maintenance of genome integrity in P. falciparum are not well understood and represent a gap in our understanding of how parasites survive the hostile environment of their vertebrate and insect hosts. Our work examines DNA repair in real time by using single-molecule real-time (SMRT) sequencing focused on the subtelomeric

End-to-End Trajectory for Conjunction Class Mars Missions Using Hybrid Solar-Electric/Chemical Transportation System

Science.gov (United States)

Chai, Patrick R.; Merrill, Raymond G.; Qu, Min

2016-01-01

NASA's Human Spaceflight Architecture Team is developing a reusable hybrid transportation architecture in which both chemical and solar-electric propulsion systems are used to deliver crew and cargo to exploration destinations. By combining chemical and solar-electric propulsion into a single spacecraft and applying each where it is most effective, the hybrid architecture enables a series of Mars trajectories that are more fuel efficient than an all chemical propulsion architecture without significant increases to trip time. The architecture calls for the aggregation of exploration assets in cislunar space prior to departure for Mars and utilizes high energy lunar-distant high Earth orbits for the final staging prior to departure. This paper presents the detailed analysis of various cislunar operations for the EMC Hybrid architecture as well as the result of the higher fidelity end-to-end trajectory analysis to understand the implications of the design choices on the Mars exploration campaign.

End-to-End Trade-space Analysis for Designing Constellation Missions

Science.gov (United States)

LeMoigne, J.; Dabney, P.; Foreman, V.; Grogan, P.; Hache, S.; Holland, M. P.; Hughes, S. P.; Nag, S.; Siddiqi, A.

2017-12-01

cost model represents an aggregate model consisting of Cost Estimating Relationships (CERs) from widely accepted models. The current GUI automatically generates graphics representing metrics such as average revisit time or coverage as a function of cost. The end-to-end system will be demonstrated as part of the presentation.

Environmental Education Research: To What Ends?

Science.gov (United States)

Jickling, Bob

2009-01-01

This paper engages questions about ends in environmental education research. In doing so, I argue that such questions are essentially normative, and that normative questions are underrepresented in this field. After cautioning about perils of prescribing research agendas, I gently suggest that in environmental education key normative questions…

A novel end-to-end classifier using domain transferred deep convolutional neural networks for biomedical images.

Science.gov (United States)

Pang, Shuchao; Yu, Zhezhou; Orgun, Mehmet A

2017-03-01

Highly accurate classification of biomedical images is an essential task in the clinical diagnosis of numerous medical diseases identified from those images. Traditional image classification methods combined with hand-crafted image feature descriptors and various classifiers are not able to effectively improve the accuracy rate and meet the high requirements of classification of biomedical images. The same also holds true for artificial neural network models directly trained with limited biomedical images used as training data or directly used as a black box to extract the deep features based on another distant dataset. In this study, we propose a highly reliable and accurate end-to-end classifier for all kinds of biomedical images via deep learning and transfer learning. We first apply domain transferred deep convolutional neural network for building a deep model; and then develop an overall deep learning architecture based on the raw pixels of original biomedical images using supervised training. In our model, we do not need the manual design of the feature space, seek an effective feature vector classifier or segment specific detection object and image patches, which are the main technological difficulties in the adoption of traditional image classification methods. Moreover, we do not need to be concerned with whether there are large training sets of annotated biomedical images, affordable parallel computing resources featuring GPUs or long times to wait for training a perfect deep model, which are the main problems to train deep neural networks for biomedical image classification as observed in recent works. With the utilization of a simple data augmentation method and fast convergence speed, our algorithm can achieve the best accuracy rate and outstanding classification ability for biomedical images. We have evaluated our classifier on several well-known public biomedical datasets and compared it with several state-of-the-art approaches. We propose a robust

Cheating at the end to avoid regret.

Science.gov (United States)

Effron, Daniel A; Bryan, Christopher J; Murnighan, J Keith

2015-09-01

How do people behave when they face a finite series of opportunities to cheat with little or no risk of detection? In 4 experiments and a small meta-analysis, we analyzed over 25,000 cheating opportunities faced by over 2,500 people. The results suggested that the odds of cheating are almost 3 times higher at the end of a series than earlier. Participants could cheat in 1 of 2 ways: They could lie about the outcome of a private coin flip to get a payoff that they would otherwise not receive (Studies 1-3) or they could overbill for their work (Study 4). We manipulated the number of cheating opportunities they expected but held the actual number of opportunities constant. The data showed that the likelihood of cheating and the extent of dishonesty were both greater when people believed that they were facing a last choice. Mediation analyses suggested that anticipatory regret about passing up a chance to enrich oneself drove this cheat-at-the-end effect. We found no support for alternative explanations based on the possibility that multiple cheating opportunities depleted people's self-control, eroded their moral standards, or made them feel that they had earned the right to cheat. The data also suggested that the cheat-at-the-end effect may be limited to relatively short series of cheating opportunities (i.e., n < 20). Our discussion addresses the psychological and behavioral dynamics of repeated ethical choices. (c) 2015 APA, all rights reserved).

Pharmacotherapy at the end-of-life.

LENUS (Irish Health Repository)

O'Mahony, Denis

2011-07-01

Older people reaching end-of-life status are particularly at risk from inter-related adverse effects of pharmacotherapy, including polypharmacy, inappropriate medications and adverse drug events. These adverse effects of pharmacotherapy may be highly detrimental, as well as highly expensive. End-of-life pharmacotherapy is sometimes perceived to be complex and challenging, probably unnecessarily. This relates in part to the poorly developed evidence base and lack of high-quality research in this area. In this article, we deal with some of the key issues relating to pharmacotherapy in end-of-life patients, namely (i) the guiding principles of drug selection, (ii) the main drugs and drug classes that are best avoided, (iii) the benefits of \\'oligopharmacy\\' (i.e. deliberate avoidance of polypharmacy) in end-of-life patients.

Secondary link adaptation in cognitive radio networks: End-to-end performance with cross-layer design

KAUST Repository

Ma, Hao

2012-04-01

Under spectrum-sharing constraints, we consider the secondary link exploiting cross-layer combining of adaptive modulation and coding (AMC) at the physical layer with truncated automatic repeat request (T-ARQ) at the data link layer in cognitive radio networks. Both, basic AMC and aggressive AMC, are adopted to optimize the overall average spectral efficiency, subject to the interference constraints imposed by the primary user of the shared spectrum band and a target packet loss rate. We achieve the optimal boundary points in closed form to choose the AMC transmission modes by taking into account the channel state information from the secondary transmitter to both the primary receiver and the secondary receiver. Moreover, numerical results substantiate that, without any cost in the transmitter/receiver design nor the end-to-end delay, the scheme with aggressive AMC outperforms that with conventional AMC. The main reason is that, with aggressive AMC, different transmission modes utilized in the initial packet transmission and the following retransmissions match the time-varying channel conditions better than the basic pattern. © 2012 IEEE.

Reconstruction after ureteral resection during HIPEC surgery: Re-implantation with uretero-neocystostomy seems safer than end-to-end anastomosis.

Science.gov (United States)

Pinar, U; Tremblay, J-F; Passot, G; Dazza, M; Glehen, O; Tuech, J-J; Pocard, M

2017-09-01

Resection of the pelvic ureter may be necessary in cytoreductive surgery for peritoneal carcinomatosis in combination with hyperthermic intraperitoneal chemotherapy (HIPEC). As the morbidity for cytoreductive surgery with HIPEC has decreased, expert teams have begun to perform increasingly complex surgical procedures associated with HIPEC, including pelvic reconstructions. After ureteral resection, two types of reconstruction are possible: uretero-ureteral end-to-end anastomosis and uretero-vesical re-implantation or uretero-neocystostomy (the so-called psoas hitch technique). By compiling the experience of three surgical teams that perform HIPEC surgeries, we have tried to compare the effectiveness of these two techniques. A retrospective comparative case-matched multicenter study was conducted for patients undergoing operation between 2005 and 2014. Patients included had undergone resection of the pelvic ureter during cytoreductive surgery with HIPEC for peritoneal carcinomatomosis; ureteral reconstruction was by either end-to-end anastomosis (EEA group) or re-implantation uretero-neocystostomy (RUC group). The primary endpoint was the occurrence of urinary fistula in postoperative follow-up. There were 14 patients in the EEA group and 14 in the RUC group. The groups were comparable for age, extent of carcinomatosis (PCI index) and operative duration. Four urinary fistulas occurred in the EEA group (28.5%) versus zero fistulas in the RUC group (0%) (P=0.0308). Re-implantation with uretero-neocystostomy during cytoreductive surgery with HIPEC is the preferred technique for reconstruction after ureteral resection in case of renal conservation. Copyright © 2017. Published by Elsevier Masson SAS.