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3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

Lu, Xiang-Jun; Olson, Wilma K.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/09/2003 EN
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26.79%
We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar–phosphate backbone and publication quality ‘standardized’ base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program.

Rebuilding immunity in cancer patients

Vuk-Pavlovic, Stanimir
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
27.04%
Rebuilding and maintaining immunity is paramount to the success of cancer immunotherapy and hematopoietic stem cell transplantation. If immune surveillance indeed can protect from cancer, the very manifestation of malignancy means that the disease has prevailed over immunity. Yet, often, tumor–specific T cells can be found in cancer patients irrespective of vaccination. Interestingly, patients suffering from malignancy often harbor unexpectedly high levels of immature CD14+HLA-DR− monocytes, although the abundance of CD4+ cells, CD8+ cells and CD4+CD25high cells may be normal. It is plausible that in cancer such cells suppress T cell function, analogous to CD14+HLA-DR− cells in sepsis and major trauma, in addition to their likely failure to re–present tumor-associated antigens once dendritic cells have initiated the T cell response. Recent evidence indicates that tumor–borne adenosine, lactate and hypoxia in the tumor environment may modulate tumor–specific immunity to a significant extent, but their effects on myeloid cell function is unclear. Thus, understanding and controlling these factors may appreciably impact the success of rebuilding and maintaining immunity in cancer patients.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Adams, Paul D.; Moriarty, Nigel W.; Zwart, Peter; Read, Randy J.; Turk, Dusan; Hung, Li-Wei
Fonte: International Union of Crystallography Publicador: International Union of Crystallography
Tipo: Artigo de Revista Científica
EN
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26.79%
Heterogeneity in ensembles generated by independent model rebuilding principally reflects the limitations of the data and of the model-building process rather than the diversity of structures in the crystal.

The Research of Sequential Images: Rebuilding of Gray (Position) ~ Time Function on Direction Lines and Their Applications

Lin, Qiang; Li, Wei
Fonte: Bentham Open Publicador: Bentham Open
Tipo: Artigo de Revista Científica
Publicado em 27/07/2011 EN
Relevância na Pesquisa
26.79%
Contrasted with other information carriers, such as speech and text, images contains larger amount of information, especially in sequential images, that is waiting to be exploited, in particular the dynamic information of correlation, difference, and temporal relationship between different frames. This dynamic information contributes a great deal in analysis of 4D images. This paper proposes a method for detecting dynamic information from sequential images, based on the rebuilding of their gray (position)~time function on direction lines, an approach that has been analyzed and studied extensively on the setting of various direction lines. This method is based on motion that is presented on sequential images. In particular, the method, Omni directional M-mode Echocardiography system, which we have studied extensively, will be described leading to a robust way of diagnosing heart diseases.

Benefits of Rebuilding Global Marine Fisheries Outweigh Costs

Sumaila, Ussif Rashid; Cheung, William; Dyck, Andrew; Gueye, Kamal; Huang, Ling; Lam, Vicky; Pauly, Daniel; Srinivasan, Thara; Swartz, Wilf; Watson, Reginald; Zeller, Dirk
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 13/07/2012 EN
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27.3%
Global marine fisheries are currently underperforming, largely due to overfishing. An analysis of global databases finds that resource rent net of subsidies from rebuilt world fisheries could increase from the current negative US$13 billion to positive US$54 billion per year, resulting in a net gain of US$600 to US$1,400 billion in present value over fifty years after rebuilding. To realize this gain, governments need to implement a rebuilding program at a cost of about US$203 (US$130–US$292) billion in present value. We estimate that it would take just 12 years after rebuilding begins for the benefits to surpass the cost. Even without accounting for the potential boost to recreational fisheries, and ignoring ancillary and non-market values that would likely increase, the potential benefits of rebuilding global fisheries far outweigh the costs.

Examining the 10-Year Rebuilding Dilemma for U.S. Fish Stocks

Patrick, Wesley S.; Cope, Jason
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 06/11/2014 EN
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27.38%
Worldwide, fishery managers strive to maintain fish stocks at or above levels that produce maximum sustainable yields, and to rebuild overexploited stocks that can no longer support such yields. In the United States, rebuilding overexploited stocks is a contentious issue, where most stocks are mandated to rebuild in as short a time as possible, and in a time period not to exceed 10 years. Opponents of such mandates and related guidance argue that rebuilding requirements are arbitrary, and create discontinuities in the time and fishing effort allowed for stocks to rebuild due to differences in productivity. Proponents, however, highlight how these mandates and guidance were needed to curtail the continued overexploitation of these stocks by setting firm deadlines on rebuilding. Here we evaluate the statements made by opponents and proponents of the 10-year rebuilding mandate and related guidance to determine whether such points are technically accurate using a simple population dynamics model and a database of U.S. fish stocks to parameterize the model. We also offer solutions to many of the issues surrounding this mandate and its implementation by recommending some fishing mortality based frameworks, which meet the intent of the 10-year rebuilding requirement while also providing more flexibility.

Developmental Stage-Specific Hepatocytes Induce Maturation of HepG2 Cells by Rebuilding the Regulatory Circuit

Li, Yanning; Liu, Demei; Zong, Yanhong; Qi, Jinsheng; Li, Bin; Liu, Kun; Xiao, Hui
Fonte: ScholarOne Publicador: ScholarOne
Tipo: Artigo de Revista Científica
Publicado em 14/04/2015 EN
Relevância na Pesquisa
26.79%
On the basis of their characteristics, we presume that developmental stage-specific hepatocytes should have the ability to induce maturation of hepatoma cells. A regulatory circuit formed by hepatocyte nuclear factor (HNF)-4α, HNF-1α, HNF-6 and the upstream stimulatory factor (USF-1) play a key role in the maturation of embryonic hepatocytes; however, it is unclear whether the regulatory circuit mediates the embryonic induction of hepatoma cell maturation. In this study, 12.5-d to 15.5-d mouse embryonic hepatocytes or their medium were used to coculture or treat HepG2 cells, and the induced maturation was evaluated in vitro and in vivo. In the induced HepG2 cells, the components of the regulatory circuit were detected, their cross-regulation was evaluated and HNF-4α RNA interference was performed. We found that 13.5-d to 14.5-d embryonic hepatocytes could induce HepG2 cell maturation, demonstrated by morphological changes, increased maturation markers and decreased c-Myc and α-fetoprotein (AFP) in vitro. The majority of HepG2 tumors were eliminated by 13.5-d embryonic induction in vivo. All components of the regulatory circuit were upregulated and the binding of HNF-4α, HNF-1α, HNF-6 and USF-1 to their target sites was promoted to rebuild the regulatory circuit in the induced HepG2 cells. Moreover...

Answering the bell : rebuilding New Orleans around neighborhood schools; Rebuilding New Orleans around neighborhood schools

Knudsen, Seth (Seth Cunningham)
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 91 p.
ENG
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27.49%
Schools are one of the most important and visible infrastructure elements in residential neighborhoods, given their large physical presence and the social network that they represent. A review of real estate, sociology, and urban design research suggests that neighborhoods and residents benefit in a variety of ways from proximity to a well-maintained school of good quality. Not surprisingly, New Orleans residents have identified schools as critical elements in the recovery of their neighborhoods in the myriad of post-Katrina planning processes. In this context, residential rebuilding decisions in substantially flood damaged neighborhoods may be influenced by the status of the neighborhood school. As residential redevelopment patterns begin to emerge in spring 2008, the master planning process for the public school system is underway. While the public school system was responsible for the education of nearly 66,000 students at 126 campus locations across the city prior to Katrina, private schools provided an educational option for 26,000 other students at 79 campuses citywide. Nearly seventy percent of private school students attended Catholic schools managed by the Archdiocese of New Orleans. In contrast to the public school system that has taken nearly three years to chart its course for the future...

Rebuilding less vulnerable communities : the case of Holy Cross

Pradi Bonilha, Camila
Fonte: Université de Montréal Publicador: Université de Montréal
Tipo: Thèse ou Mémoire numérique / Electronic Thesis or Dissertation
EN
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27.04%
La résilience est la capacité à s’adapter aux menaces et à atténuer ou éviter un risque, elle peut être trouvée dans des bâtiments résistant aux dangers ou dans des systèmes sociaux adaptables (Pelling, 2003). Par conséquence, ce concept peut aussi être compris comme la capacité de reconstruire un quartier avec des composants plus solides et plus viables. Presque quatre ans après l’ouragan Katrina, la Nouvelle-Orléans est considérée comme un laboratoire à ciel ouvert. Le niveau de résilience de ses communautés peut y être examiné. L’état actuel de la reconstitution de ses quartiers diffère largement des uns aux autres. L’arrondissement historique de Holy Cross est l’un des plus vieux quartiers de la ville, cette communauté vulnérable est connue pour son patrimoine culturel, apparent non seulement dans son architecture unique, mais aussi ses relations sociales. Un des principaux défi de la reconstruction du quartier de Holly Cross est de trouver une façon de concilier la préservation du patrimoine bâti et de son tissu urbain ancien avec de nouveaux plans de développement, afin de créer une communauté durable. Cette étude examine les rôles des acteurs impliqués dans le processus de reconstruction et leur efficacité sur la création d’un Holy Cross plus durable...

Are marine reserves and harvest control rules substitutes or complements for rebuilding fisheries?

Yamazaki, Satoshi; Jennings, Sarah; Grafton, R. Quentin; Kompas, Tom
Fonte: Elsevier Publicador: Elsevier
Tipo: Artigo de Revista Científica Formato: 18 pages
Relevância na Pesquisa
27.2%
Harvest control rules and no-take marine reserves are two management approaches increasingly advocated as effective means of rebuilding depleted fish stocks and averting the collapse of fisheries. We incorporate the two approaches into a bioeconomic model and evaluate how they act as substitutes and/or complements when used together in fisheries stock recovery plans. Simulations ofthe model with estimated parameters from an actual fishery show that the cost of adopting a harvest strategy of slow stock rebuilding can be offset or substituted by a no-take reserve. For each of the harvest strategies explored, we find there is a range of reserve sizes that can act as a complement in a stock recovery plan such that a no-take reserve improves both the profitability of fishers and average annual harvest during stock rebuilding. We demonstrate that a stock recovery plan that incorporates both harvest control rules and no-take reserves can simultaneously contribute to conservation, economic and socio-economic objectives of fisheries management.

Operation Solar Eagle: a study examining photovoltaic (PV) solar power as an alternative for the rebuilding of the Iraqi electrical power generation infrastructure

Borja, Ralph; Austin, Curtis; Phillips, Jeffery
Fonte: Monterey, California. Naval Postgraduate School Publicador: Monterey, California. Naval Postgraduate School
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27.04%
MBA Professional Report; The purpose of this project is to examine the cost and feasibility of using photovoltaic solar power to assist in the rebuilding of the Iraqi infrastructure. The project will examine available solar equipment and technologies coupled with requirements for operation, installation and maintenance of such systems. The report begins with an analysis of the current state of the Iraqi infrastructure with special emphasis placed on identifying potential candidates for initial solar PV system installation. Next, the report addresses available commercial solar equipment and emerging technologies that enhance such systems. This section will address areas including installation, operation, maintenance, and durability. Finally, the report will conclude with a cost estimate for using solar PV systems in the rebuilding of Iraq. At the conclusion of the project, information will be available for decision makers to include as part of an operations order or to attach as an annex to an existing operations order.

Creating Jobs and Rebuilding Livelihoods in Post-Conflict Situations

Larson, Holly
Fonte: Monterey, California: Naval Postgraduate School. Publicador: Monterey, California: Naval Postgraduate School.
Tipo: Newsletter
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The Center for Stabilization and Reconstruction Studies held its fi rst economic recovery workshop, Creating Jobs and Rebuilding Livelihoods in Post-Confl ict Situations, from October 26-29, 2008, in Monterey, California. The interactive workshop, which was designed and facilitated by Dr. Nat J. Colletta and Dr. Sophal Ear, brought together 40 practitioners from the different groups of actors charged with rebuilding fragile states. Participants discussed the challenges and trade-offs of various economic recovery priorities and strategies, explored best practices and lessons learned from past initiatives, and crafted possible job creation solutions for different countries in crisis.

Implications of fisheries-induced evolution for stock rebuilding and recovery

Enberg, Katja; Jørgensen, Christian; Dunlop, Erin S; Heino, Mikko; Dieckmann, Ulf
Fonte: Blackwell Publishing Ltd Publicador: Blackwell Publishing Ltd
Tipo: Artigo de Revista Científica
Publicado em /08/2009 EN
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27.04%
Worldwide depletion of fish stocks has led fisheries managers to become increasingly concerned about rebuilding and recovery planning. To succeed, factors affecting recovery dynamics need to be understood, including the role of fisheries-induced evolution. Here we investigate a stock's response to fishing followed by a harvest moratorium by analyzing an individual-based evolutionary model parameterized for Atlantic cod Gadus morhua from its northern range, representative of long-lived, late-maturing species. The model allows evolution of life-history processes including maturation, reproduction, and growth. It also incorporates environmental variability, phenotypic plasticity, and density-dependent feedbacks. Fisheries-induced evolution affects recovery in several ways. The first decades of recovery were dominated by demographic and density-dependent processes. Biomass rebuilding was only lightly influenced by fisheries-induced evolution, whereas other stock characteristics such as maturation age, spawning stock biomass, and recruitment were substantially affected, recovering to new demographic equilibria below their preharvest levels. This is because genetic traits took thousands of years to evolve back to preharvest levels, indicating that natural selection driving recovery of these traits is weaker than fisheries-induced selection was. Our results strengthen the case for proactive management of fisheries-induced evolution...

Zigzag Codes: MDS Array Codes with Optimal Rebuilding

Tamo, Itzhak; Wang, Zhiying; Bruck, Jehoshua
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 01/12/2011
Relevância na Pesquisa
27.38%
MDS array codes are widely used in storage systems to protect data against erasures. We address the \emph{rebuilding ratio} problem, namely, in the case of erasures, what is the fraction of the remaining information that needs to be accessed in order to rebuild \emph{exactly} the lost information? It is clear that when the number of erasures equals the maximum number of erasures that an MDS code can correct then the rebuilding ratio is 1 (access all the remaining information). However, the interesting and more practical case is when the number of erasures is smaller than the erasure correcting capability of the code. For example, consider an MDS code that can correct two erasures: What is the smallest amount of information that one needs to access in order to correct a single erasure? Previous work showed that the rebuilding ratio is bounded between 1/2 and 3/4, however, the exact value was left as an open problem. In this paper, we solve this open problem and prove that for the case of a single erasure with a 2-erasure correcting code, the rebuilding ratio is 1/2. In general, we construct a new family of $r$-erasure correcting MDS array codes that has optimal rebuilding ratio of $\frac{e}{r}$ in the case of $e$ erasures, $1 \le e \le r$. Our array codes have efficient encoding and decoding algorithms (for the case $r=2$ they use a finite field of size 3) and an optimal update property.; Comment: 23 pages...

On Codes for Optimal Rebuilding Access

Wang, Zhiying; Tamo, Itzhak; Bruck, Jehoshua
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 08/07/2011
Relevância na Pesquisa
27.49%
MDS (maximum distance separable) array codes are widely used in storage systems due to their computationally efficient encoding and decoding procedures. An MDS code with r redundancy nodes can correct any r erasures by accessing (reading) all the remaining information in both the systematic nodes and the parity (redundancy) nodes. However, in practice, a single erasure is the most likely failure event; hence, a natural question is how much information do we need to access in order to rebuild a single storage node? We define the rebuilding ratio as the fraction of remaining information accessed during the rebuilding of a single erasure. In our previous work we showed that the optimal rebuilding ratio of 1/r is achievable (using our newly constructed array codes) for the rebuilding of any systematic node, however, all the information needs to be accessed for the rebuilding of the parity nodes. Namely, constructing array codes with a rebuilding ratio of 1/r was left as an open problem. In this paper, we solve this open problem and present array codes that achieve the lower bound of 1/r for rebuilding any single systematic or parity node.; Comment: Submitted to Allerton 2011

MDS Array Codes with Optimal Rebuilding

Tamo, Itzhak; Wang, Zhiying; Bruck, Jehoshua
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 18/03/2011
Relevância na Pesquisa
27.38%
MDS array codes are widely used in storage systems to protect data against erasures. We address the \emph{rebuilding ratio} problem, namely, in the case of erasures, what is the the fraction of the remaining information that needs to be accessed in order to rebuild \emph{exactly} the lost information? It is clear that when the number of erasures equals the maximum number of erasures that an MDS code can correct then the rebuilding ratio is 1 (access all the remaining information). However, the interesting (and more practical) case is when the number of erasures is smaller than the erasure correcting capability of the code. For example, consider an MDS code that can correct two erasures: What is the smallest amount of information that one needs to access in order to correct a single erasure? Previous work showed that the rebuilding ratio is bounded between 1/2 and 3/4, however, the exact value was left as an open problem. In this paper, we solve this open problem and prove that for the case of a single erasure with a 2-erasure correcting code, the rebuilding ratio is 1/2. In general, we construct a new family of $r$-erasure correcting MDS array codes that has optimal rebuilding ratio of $\frac{1}{r}$ in the case of a single erasure. Our array codes have efficient encoding and decoding algorithms (for the case $r=2$ they use a finite field of size 3) and an optimal update property.; Comment: 14 pages...

MDS Array Codes with Optimal Rebuilding

Tamo, Itzhak; Wang, Zhiying; Bruck, Jehoshua
Fonte: California Institute of Technology Publicador: California Institute of Technology
Tipo: Report or Paper; PeerReviewed Formato: application/pdf
Publicado em 18/03/2011
Relevância na Pesquisa
27.38%
MDS array codes are widely used in storage systems to protect data against erasures. We address the rebuilding ratio problem, namely, in the case of erasures, what is the the fraction of the remaining information that needs to be accessed in order to rebuild exactly the lost information? It is clear that when the number of erasures equals the maximum number of erasures that an MDS code can correct then the rebuilding ratio is 1 (access all the remaining information). However, the interesting (and more practical) case is when the number of erasures is smaller than the erasure correcting capability of the code. For example, consider an MDS code that can correct two erasures: What is the smallest amount of information that one needs to access in order to correct a single erasure? Previous work showed that the rebuilding ratio is bounded between 1/2 and 3/4 , however, the exact value was left as an open problem. In this paper, we solve this open problem and prove that for the case of a single erasure with a 2-erasure correcting code, the rebuilding ratio is 1/2 . In general, we construct a new family of r-erasure correcting MDS array codes that has optimal rebuilding ratio of 1/r in the case of a single erasure. Our array codes have efficient encoding and decoding algorithms (for the case r = 2 they use a finite field of size 3) and an optimal update property.

On Codes for Optimal Rebuilding Access

Wang, Zhiying; Tamo, Itzhak; Bruck, Jehoshua
Fonte: California Institute of Technology Publicador: California Institute of Technology
Tipo: Report or Paper; PeerReviewed Formato: application/pdf
Publicado em 08/07/2011
Relevância na Pesquisa
27.49%
MDS (maximum distance separable) array codes are widely used in storage systems due to their computationally efficient encoding and decoding procedures. An MDS code with r redundancy nodes can correct any r erasures by accessing (reading) all the remaining information in both the systematic nodes and the parity (redundancy) nodes. However, in practice, a single erasure is the most likely failure event; hence, a natural question is how much information do we need to access in order to rebuild a single storage node? We define the rebuilding ratio as the fraction of remaining information accessed during the rebuilding of a single erasure. In our previous work we showed that the optimal rebuilding ratio of 1/r is achievable (using our newly constructed array codes) for the rebuilding of any systematic node, however, all the information needs to be accessed for the rebuilding of the parity nodes. Namely, constructing array codes with a rebuilding ratio of 1/r was left as an open problem. In this paper, we solve this open problem and present array codes that achieve the lower bound of 1/r for rebuilding any single systematic or parity node.

Rebuilding St. Georges Hundred

Jicha, III., Hubert F.; Bensinger, Trish
Fonte: Universidade de Delaware Publicador: Universidade de Delaware
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
27.2%
The twenty-eight sites included in the thematic nomination, "Rebuilding St. Georges Hundred, 1850 - 1880", are representative of a broad pattern of historically documented architectural, agricultural, and social change that swept through southern New Castle County, Delaware, in the second and third quarters of the 19th century. The selected sites all document one of three major areas of change in domestic architecture as it relates to rebuilding cycles: the improvement of standing buildings, the replacement of standing structures , and the development of new sites (often at the cost of abandoning earlier settings). Also associated with these dwellings and the social processes they represent and articulate are a number of agricultural buildings reflecting the new design options for work space developed in the course of the rebuilding.

Book review: Coming home to New Orleans: neighborhood rebuilding after Katrina

Martin, Richard
Fonte: Blog post from London School of Economics & Political Science Publicador: Blog post from London School of Economics & Political Science
Tipo: Website; NonPeerReviewed Formato: application/pdf
Publicado em 31/08/2013 EN; EN
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27.2%
"Coming Home to New Orleans: Neighborhood Rebuilding after Katrina." Karl F. Seidman. Oxford University Press. April 2013. --- Coming Home to New Orleans documents grassroots rebuilding efforts in New Orleans neighbourhoods after hurricane Katrina, and draws lessons on their contribution to the post-disaster recovery of cities. With chapters on rebuilding narratives, socio-economic factors, and volunteer initiatives, this rigorous book demonstrates the fascinating range of cultures that continue to shape this unique city, concludes Richard Martin.