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12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era Nature Precedings
Rafał Wóycicki; Justyna Witkowicz; Magdalena Pawełkowicz; Ewa Siedlecka; Wojciech Gutman; Wojciech Pląder; Anna Seroczyńska; Mieczysław Śmiech; Katarzyna Niemirowicz-Szczytt; Stanisław Karpiński; Stefan Malepszy; Zbigniew Przybecki.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects. 
We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length...
Tipo: Poster Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5466/version/1
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21 Tesla Micro-MRI of Rat Skin Nature Precedings
Rakesh Sharma; Suniket Fulzele; Kiran Shetty; Mandeep Sachdeva; Bruce R. Locke.
*Aim:* A rapid ultra high resolution ex vivo MRI imaging method was evaluated to visualize rat skin structure. The main objectives were:1.qualitative assessment of viable epidermis, hair, oil and fat-rich skin features by multi-contrast approach;2.achievement of spatial resolution up to 15 microns; 3.comparison of skin histology with MRI skin features obtained by 21 Tesla magnetic resonance imaging (MRI) imager. 

*Introduction:* The ultrawide bore 900 MHz magnet has high resolution NMR magnet has a central field of 21.1 T. The high resolution MRI technique has potential for both quantitative and non-invasive morphological evaluation at micrometer level. The MRI signal was sensitive to water protons and glycolipid...
Tipo: Poster Palavras-chave: Biotechnology.
Ano: 2008 URL: http://precedings.nature.com/documents/2639/version/1
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21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound Nanoparticles Nature Precedings
Rakesh Sharma.
Superparamagnetic iron-oxide bound antimyoglobin (SPIOM) characteristics were analyzed at different pH. After injecting SPIOM in heart, ex vivo magnetic resonance microimaging (MRM) technique was used to visualize microvasculature of rat heart including cardiac arteries, veins, cordate tendons attached with valves. The measurement accuracy of ventricles, aorta, vasculature and dimensions of cordate tendons were close to coregistered histology measurements.
Tipo: Poster Palavras-chave: Biotechnology.
Ano: 2008 URL: http://precedings.nature.com/documents/2643/version/1
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21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound Nanoparticles Nature Precedings
Rakesh Sharma.
Superparamagnetic iron-oxide bound antimyoglobin (SPIOM) characteristics were analyzed at different pH. After injecting SPIOM in heart, ex vivo magnetic resonance microimaging (MRM) technique was used to visualize microvasculature of rat heart including cardiac arteries, veins, cordate tendons attached with valves. The measurement accuracy of ventricles, aorta, vasculature and dimensions of cordate tendons were close to coregistered histology measurements.
Tipo: Poster Palavras-chave: Biotechnology.
Ano: 2009 URL: http://precedings.nature.com/documents/2643/version/2
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A global assessment of deep-sea basalt sites for carbon sequestration Nature Precedings
David Goldberg; Angela L. Slagle.
In recent years, the debate over the most effective means to stabilize greenhouse gas concentrations in the atmosphere has endorsed multiple approaches and a variety of technologies. Assuring secure storage of anthropogenic carbon dioxide is one of our most pressing global scientific challenges that may contribute to achieving a stable solution over the next several decades. Geological sequestration by injection into deep-sea basalt formations provides unique and significant advantages over other potential storage options, including: (a) vast reservoir capacities with high porosity and permeability, sufficient to accommodate centuries-long U.S. production of fossil fuel CO~2~ at locations within a few hundreds of kilometers of populated areas; (b) chemical...
Tipo: Poster Palavras-chave: Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2640/version/1
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A hydrometric analysis of the Moose Jaw River near Burdick (05JE006): Temporal trends and frequency analyses for mean, minimum, and maximum flows Nature Precedings
Sierra Rayne; Kaya Forest.
A hydrometric analysis over the available historical record (1973-2010) was conducted for the Moose Jaw River station near Burdick in south-central Saskatchewan, Canada. Frequency analyses on mean monthly, average annual, monthly minimum/maximum, and annual minimum flows generally yielded poor fits, and problems with negative flow predictions for mid- to long-term return periods regardless of distribution type. The annual maximum streamflow time series is reasonably well-described by linear and log Pearson Type III distributions, although both distribution types underestimate extreme maximum flows. Mann-Kendall linear time series analysis on mean monthly and annual streamflows reveals no trend in annual water yields, nor in mean monthly flows between March...
Tipo: Poster Palavras-chave: Earth & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/6697/version/1
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A Linked Data Approach to Help Identify Therapeutic Targets for Cancer Nature Precedings
Helena Deus.
Cancer is still one of the leading causes of death in the developed world. To address this problem, the US National Institutes of Health (NIH) has launched The Cancer Genome Atlas (TCGA), a large scale systematic approach to characterize tumor samples from 20 cancer types and approximately 10,000 donor patients by using multiple high-throughput approaches. 

Multidisciplinary projects such as TCGA and related projects across Europe aim at identifying cancer “driver” mutations to be used as therapeutic targets or diagnostic tests. Extracting and aggregating the knowledge necessary to identify such mutations remains a challenge primarily due to the need to reliably integrate the experimental datasets...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6169/version/1
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A Long-Term Analysis of the Moose Jaw Climate Station (4015322/4015320): Temporal Trends and Frequency Analyses for Temperatures, Precipitation, and Wind Speed Nature Precedings
Sierra Rayne; Kaya Forest.
A long-term analysis of temporal trends and frequency analyses for temperatures (1913-2010), precipitation (1909-2010), and wind speed (1954-1996) was conducted on the Moose Jaw climate station in south-central Saskatchewan, Canada. Average annual and springtime temperatures are increasing over time, as are daily mean temperatures during March. Mean daily maximum temperatures are increasing on an annual basis and during the spring period, whereas mean daily minimum temperatures are increasing during February, March, August, and September, as well as on an annual basis and during spring and summer. There are significant positive time trends for growing degree days base 8C (GDD~8~) and 10C (GDD~10~). Rainfall has been increasing during March as well as...
Tipo: Poster Palavras-chave: Earth & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/6703/version/1
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A memoryless, stochastic mechanism of timing of phases of behavior by a neural network controller Nature Precedings
Saaniya Contractor; Nataliya Kozlova; Vladimir Brezina.
For a sensorimotor network to generate adaptive behavior in the environment, the phases of the behavior must be appropriately timed. When the behavior is driven simply by the sensory stimuli from the environment, these can supply the timing. But when the behavior is driven by an internal "goal" that ignores and perhaps even opposes the immediate sensory stimuli, the timing must be generated internally by the network. We have modeled a realistic behavioral scenario that requires such internal timing.

When the sea slug Aplysia feeds, it incrementally ingests long strips of seaweed, driven by ingestive stimuli emanating from the seaweed. But if, having ingested a strip, the animal fails to break the...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/2817/version/1
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A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0 Nature Precedings
Michael T. Cooling.
In the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to transforming mathematical models from esoteric to informative resources. 

We have developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend), BIBO (Bibliographic...
Tipo: Poster Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6391/version/1
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A neural model for the visual tuning properties of action-selective neurons Nature Precedings
Martin A. Giese; Vittorio Caggiano; Falk Fleischer.
SUMMARY: The recognition of actions of conspecifics is crucial for survival and social interaction. Most current models on the recognition of transitive (goal-directed) actions rely on the hypothesized role of internal motor simulations for action recognition. However, these models do not specify how visual information can be processed by cortical mechanisms in order to be compared with such motor representations. This raises the question how such visual processing might be accomplished, and in how far motor processing is critical in order to account for the visual properties of action-selective neurons.
We present a neural model for the visual processing of transient actions that is consistent with physiological data and that accomplishes...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/5862/version/1
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A new approach to generating research-quality data through citizen science: The USA National Phenology Monitoring System Nature Precedings
Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Lisa Benton; Theresa M. Crimmins; Mark Losleben; Andrew D. Richardson; Alyssa Rosemartin; Mark D. Schwartz; Kathryn A. Thomas; Jake F. Weltzin; Bruce E. Wilson.
Phenology is one of the most sensitive biological responses to climate change, and recent changes in phenology have the potential to shake up ecosystems. In some cases, it appears they already are. Thus, for ecological reasons it is critical that we improve our understanding of species’ phenologies and how these phenologies are responding to recent, rapid climate change. Phenological events like flowering and bird migrations are easy to observe, culturally important, and, at a fundamental level, naturally inspire human curiosity— thus providing an excellent opportunity to engage citizen scientists. The USA National Phenology Network has recently initiated a national effort to encourage people at different levels of...
Tipo: Poster Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/3695/version/1
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A new approach to generating research-quality phenology data: The USA National Phenology Monitoring System Nature Precedings
Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Bruce E. Wilson; Jake F. Weltzin; the rest of the USA-NPN Protocol Development Team.
The USA National Phenology Network (www.usanpn.org) has recently initiated a national effort to encourage people at different levels of expertise—from backyard naturalists to professional scientists—to observe phenology and contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology and associated phenological responses to climate change. Many phenological observation protocols identify specific single dates at which individual phenological events are observed, but the scientific usefulness of long-term phenological observations can be improved with a more carefully structured protocol. At the USA-NPN we have developed a new approach that...
Tipo: Poster Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/3695/version/2
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A new functional role for lateral inhibition in the striatum: Pavlovian conditioning Nature Precedings
Patrick Connor; Thomas Trappenberg.
The striatum has long been implicated in reinforcement learning and has been suggested by several neurophysiological studies as the substrate for encoding the reward value of stimuli. Reward prediction error (RPE) has been used in several basal ganglia models as the underlying learning signal, which leads to Pavlovian conditioning abilities that can be simulated by the Rescorla-Wagner model.

Lateral inhibition between striatal projection neurons was once thought to have a winner-take-all function, useful in selecting between possible actions. However, it has been noted that the necessary reciprocal connections for this interpretation are too few, and the relative strength of these synaptic connections is weak. Still,...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/5986/version/1
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A new gene controlling resistance to Fusarium oxysporum f. sp. melonis races 0 and 2 in melon National Institute of Agronomic Research
Oumouloud, A.; González Torres, R.; Arnedo Andrés, M.S.; Alvarez, J.M..
‘Tortuga’ is a cantalupensis accession of Spanish origin which has proven to be resistant to Fusarium oxysporum f.sp. melonis races 0 and 2. In this work we report the results of an allellism test to assess the inheritance of this resistance. Resistance in ‘Tortuga’ seems to be controlled by two genes, one of them is the already described Fom-1, and the other is either a dominant one linked to Fom-1, or an independent recessive factor. Further work will be needed to clarify the nature of this resistance.
Tipo: Poster Palavras-chave: Mediterranean country; Cucumis melo; Fusarium wilt; Physiological races; Allelism test; Disease resistance; Cantaloup.
Ano: 2008 URL: http://hdl.handle.net/2174/242
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A normalization technique for next generation sequencing experiments Nature Precedings
Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4710/version/2
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A normalization technique for next generation sequencing experiments Nature Precedings
Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4710/version/1
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A periodic pattern of SNPs in the human genome Nature Precedings
Bo Eskerod Madsen; Palle Villesen; Carsten Wiuf.
By surveying all validated SNPs in the human genome we have found that SNPs positioned 1, 2, 4, 6 or 8 bp apart are more frequent than SNPs 3, 5, 7 or 9 bp apart. This holds even when we correct for nucleotide frequencies and site dependencies in nucleotide usage in the genome. The observed pattern is not restricted to any of the genomic regions that might give sequencing or alignment errors; i.e. transposable elements (SINE, LINE and LTR), tandem repeats and large duplicated regions. However we can define periodic DNA, which virtually capture the entire pattern. Periodic DNA is defined as small DNA sequences (16.9 bp average length) with a high degree of periodicity in nucleotide usage. Periodic DNA is widely distributed in the genome, underrepresented in...
Tipo: Poster Palavras-chave: Genetics & Genomics.
Ano: 2007 URL: http://precedings.nature.com/documents/435/version/1
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A probabilistic model of plasmid replication regulation by a combination of handcuffing, iteron number and dimerization of RepA protein. Nature Precedings
Milind Watve; Gauri Tendulkar; Ketaki Ghate.
Plasmids are small circular DNA molecules in bacteria which replicate sharing the replication machinery with the bacterial chromosome. Since plasmids are much smaller than the chromosome, unless their replication is tightly regulated, their copy numbers can escalate quickly. A number of mechanisms of plasmid replication regulation are known in P1 plasmid of E. coli. Mechanisms such as autorepression of the replication initiator protein (RepA) and its dimerization are unable to explain copy number regulation by themselves. The number of RepA binding sites (iterons) is inversely related to copy numbers. Handcuffing of plasmids by RepA dimer is believed to be the main mechanism of arresting replication. We show here with a probabilistic model that for the...
Tipo: Poster Palavras-chave: Molecular Cell Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5421/version/1
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A recessive gene conferring ethylene insensitivity and androecy in Cucurbita pepo National Institute of Agronomic Research
Manzano, S.; Dominguez, V.J.; Garrido, D.; Gómez, P.; Jamilena, M..
The genetic and physiological analysis performed in the ‘Vegetable spaghetti’ (Veg) inbred line of Cucurbita pepo subsp. pepo has indicated that its androecious phenotype is determined by a single recessive gene conferring ethylene insensitivity. The production of female flowers in the androecious line starts much later than in normal varieties, and is lower than 30 %, with some of the plants producing less than 5 % female flowers. The androecious trait segregates as a single recessive gene in F2 generation, and cosegregates with a weak ethylene insensitive phenotype in seedlings. In fact, etiolated seedlings of the ‘Veg’ line and the most androecious plants in the F2 generation produce more ethylene than the contrasting line, but are less sensitive to...
Tipo: Poster Palavras-chave: Inheritance; Ethylene production; Sex expression; Cucurbita pepo; Androecy.
Ano: 2008 URL: http://hdl.handle.net/2174/280
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