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BMC Structural Biology - Latest Articles   [more] [xml]
 2014-07-19T00:00:00Z A simple method for finding a protein¿s ligand-binding pockets
Background: This paper provides a simple and rapid method for a protein-clustering strategy. The basic idea implemented here is to use computational geometry methods to predict and characterize ligand-binding pockets of a given protein structure. In addition to geometrical characteristics of the protein structure, we consider some simple biochemical properties that help recognize the best candidates for pockets in a protein’s active site. Results: Our results are shown to produce good agreement with known empirical results. Conclusions: The method presented in this paper is a low-cost rapid computational method that could be used to classify proteins and other biomolecules, and furthermore could be useful in reducing the cost and time of drug discovery.


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BMC Bioinformatics - Latest Articles   [more] [xml]
 2014-08-23T00:00:00Z A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems
Background: Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is relation extraction, which aims to identify designated relations among biological entities reported in literature. A relation extraction system achieving high performance is expensive to develop because of the substantial time and effort required for its design and implementation. Here, we report a novel framework to facilitate the development of a pattern-based biomedical relation extraction system. It has several unique design features: (1) leveraging syntactic variations possible in a language and automatically generating extraction patterns in a systematic manner, (2) applying sentence simplification to improve the coverage of extraction patterns, and (3) identifying referential relations between a syntactic argument of a predicate and the actual target expected in the relation extraction task. Results: A relation extraction system derived using the proposed framework achieved overall F-scores of 72.66% for the Simple events and 55.57% for the Binding events on the BioNLP-ST 2011 GE test set, comparing favorably with the top performing systems that participated in the BioNLP-ST 2011 GE task. We obtained similar results on the BioNLP-ST 2013 GE test set (80.07% and 60.58%, respectively). We conducted additional experiments on the training and development sets to provide a more detailed analysis of the system and its individual modules. This analysis indicates that without increasing the number of patterns, simplification and referential relation linking play a key role in the effective extraction of biomedical relations. Conclusions: In this paper, we present a novel framework for fast development of relation extraction systems. The framework requires only a list of triggers as input, and does not need information from an annotated corpus. Thus, we reduce the involvement of domain experts, who would otherwise have to provide manual annotations and help with the design of hand crafted patterns. We demonstrate how our framework is used to develop a system which achieves state-of-the-art performance on a public benchmark corpus.


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BMC Genomics - Latest Articles   [more] [xml]
 2014-08-23T00:00:00Z Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly
Background: In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly. Results: Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome. Conclusions: A high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-08-09T00:00:00Z Comparative analysis of diosgenin in Dioscorea species and related medicinal plants by UPLC-DAD-MS
Background: Dioscorea is a genus of flowering plants, and some Dioscorea species are known and used as a source for the steroidal sapogenin diosgenin. To screen potential resource from Dioscorea species and related medicinal plants for diosgenin extraction, a rapid method to compare the contents of diosgenin in various plants is crucial. Results: An ultra-performance liquid chromatography (UPLC) coupled with diode array detection (DAD) and electrospray ionization mass spectrometry (ESI-MS) method was developed for identification and determination of diosgenin in various plants. A comprehensive validation of the developed method was conducted. Twenty-four batches of plant samples from four Dioscorea species, one Smilax species and two Heterosmilax species were analyzed by using the developed method.The present method presented good sensitivity, precision and accuracy. Diosgenin was found in three Dioscorea species and one Heterosmilax species, namely D. zingiberensis, D. septemloba, D. collettii and H. yunnanensis. Conclusion: The method is suitable for the screening of diosgenin resources from plants. D. zingiberensis is an important resource for diosgenin harvesting.


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Nature   [more] [xml]
 2005-01-19 Einstein is dead
Until its next revolution, much of the glory of physics will be in engineering. It is a shame that the physicists who do so much of it keep so quiet about it.

Einstein is dead

Nature 433, 179 (2005). doi:10.1038/433179a

Until its next revolution, much of the glory of physics will be in engineering. It is a shame that the physicists who do so much of it keep so quiet about it.



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Science: Current Issue   [more] [xml]
 2014-08-22 [Editorial] A swan in the making
Reproducibility is the ugly duckling of science. It provokes distress, denial, and passionate calls for action. With $1.5 trillion spent globally each year on R&D,* the idea that 80% of it is irreproducible† can cause downright dread. It threatens the foundations and credibility of the scientific enterprise. But look past the surface, and reproducibility may well be a swan in the making. Author: Timothy Gardner
 2014-08-22 [In Brief] This Week's Section
A roundup of weekly science policy and related news.
 2014-08-22 [In Depth] Study exposes Chinese censors' deepest fears
The power of the masses proves most unnerving. Author: Mara Hvistendahl
 2014-08-22 [In Depth] Is Atlantic holding Earth's missing heat?
New leads in the hunt to explain the global warming hiatus. Author: Eli Kintisch
 2014-08-22 [In Depth] A one-two punch against polio
The once-sidelined injected vaccine could boost eradication. Author: Leslie Roberts
 2014-08-22 [In Depth] Wheels when you need them
Can special algorithms help keep shared bicycles rolling?. Author: Chelsea Wald
 2014-08-22 [In Depth] Wolves cooperate but dogs submit, study suggests
Breeding for dependence, not cooperation, may have driven initial dog domestication. Author: Virginia Morell
 2014-08-22 [Feature] The cancer drug that almost wasn't
After years in drug development limbo, a compound that interrupts cell division has revitalized a troubled area of cancer research. Author: Ken Garber
 2014-08-22 [Perspective] Imprint of an ancient conflagration
Evidence is found for the massive stars that populated the early universe [Also see Report by Aoki et al.] Author: Volker Bromm
 2014-08-22 [Perspective] Carbon cycling in the Arctic
Sunlight drives the emission of carbon from arctic waters [Also see Report by Cory et al.] Author: Lars Tranvik
 2014-08-22 [Perspective] A photon steers a photon with an atom
Nonlinear optics with single quanta of light and matter becomes reality [Also see Report by Shomroni et al.] Author: Gerhard Rempe
 2014-08-22 [Perspective] Glacier retreat crosses a line
Mountain glacier loss since the 1970s has mostly been caused by human influences on climate change [Also see Report by Marzeion et al.] Author: Shawn Marshall
 2014-08-22 [Policy Forum] Boosting GDP growth by accounting for the environment
Including air pollution and greenhouse gas damages increases estimated U.S. growth Author: Nicholas Z. Muller
 2014-08-22 [Perspective] Making phloem—a near-death experience
How to get rid of the phloem cell nucleus to make a root-to-shoot tip transport system [Also see Report by Furuta et al.] Author: Niko Geldner
 2014-08-22 [Perspective] Riboswitch regulates RNA
Nutrient metabolism in bacteria is controlled by a circuit in which RNA is regulated by RNA [Also see Reports by DebRoy et al. and Mellin et al.] Authors: Jiandong Chen, Susan Gottesman
 2014-08-22 [Perspective] Sensing nectar's sweetness
A taste receptor evolves to sense sugar in adapting to the diet of some birds [Also see Report by Baldwin et al.] Authors: Peihua Jiang, Gary K. Beauchamp
 2014-08-22 [Perspective] How do coral reefs recover?
Experiments on juvenile coral and fish behavior may have implications for reef restoration efforts [Also see Research Article by Dixson et al.] Author: John F. Bruno
 2014-08-22 [Perspective] Joep Lange (1954–2014)
A leader in developing therapy for AIDS is tragically killed Author: Jaap Goudsmit
 2014-08-22 [Book Review] Morality for skeptics?
Author: Les Beldo
 2014-08-22 [Book Review] Innovation: myths and prospects
Author: Davide Consoli
 2014-08-22 [Books et al.] Books Received
A listing of books received at Science during the week ending 15 August 2014.
 2014-08-22 [Letter] Fauna in decline: Plight of the pangolin
Authors: Yuning Liu, Qiang Weng
 2014-08-22 [Letter] Fauna in decline: First do no harm
Authors: Anthony Ricciardi, Daniel Simberloff
 2014-08-22 [Letter] Fauna in decline: Global assessments
Authors: Harold Mooney, Heather Tallis
 2014-08-22 [Letter] Ailing academia needs culture change
Authors: Viviane Callier, Nathan L. Vanderford
 2014-08-22 [Letter] Let minority-serving institutions lead
Authors: Fatimah Jackson, Clarence M. Lee, Sherese Taylor
 2014-08-22 This Week in Science
How huge early stars enriched the universe | Corals and reef fish choose nice homes | Routing one photon with a few others | The makings of a powerful sweet tooth | An inhibitor breaks RANK | Two vaccines together are better than one alone | Deep-sea warming slows down global warming | How immune cells fight TB and show it | Opening and closing blood enhancers | Putting the heat on Mother Nature | Challenges for stem cell–based therapies | Censorship of social media in China | Removing the nucleus in sieve elements | A dual-action RNA switch for expression | Watching platinum nanocube growth | Detailed structure of a gold nanoparticle | X-raying superfluid helium droplets | The genomic origins of rape oilseed | Illuminating the pathway to destruction
 2014-08-22 Editors' Choice
Tissue mimics brain's cortical layers | How to boost cancer immunotherapy | Students produce assessment materials | How much methane from landfills? | Counting human intestinal stem cells | Bacteria scrimp and save themselves | Giants in the outer halo of the Milky Way | Bat calls shaped by sexual selection
 2014-08-22 [Review] Use of differentiated pluripotent stem cells as replacement therapy for treating disease
Pluripotent stem cells (PSCs) directed to various cell fates holds promise as source material for treating numerous disorders. The availability of precisely differentiated PSC-derived cells will dramatically affect blood component and hematopoietic stem cell therapies and should facilitate treatment of diabetes, some forms of liver disease and neurologic disorders, retinal diseases, and possibly heart disease. Although an unlimited supply of specific cell types is needed, other barriers must be overcome. This review of the state of cell therapies highlights important challenges. Successful cell transplantation will require optimizing the best cell type and site for engraftment, overcoming limitations to cell migration and tissue integration, and occasionally needing to control immunologic reactivity, as well as a number of other challenges. Collaboration among scientists, clinicians, and industry is critical for generating new stem cell–based therapies. Authors: Ira J. Fox, George Q. Daley, Steven A. Goldman, Johnny Huard, Timothy J. Kamp, Massimo Trucco
 2014-08-22 [Research Article] Reverse-engineering censorship in China: Randomized experimentation and participant observation
China censors online posts that advocate collective action. Authors: Gary King, Jennifer Pan, Margaret E. Roberts
 2014-08-22 [Research Article] Chemically mediated behavior of recruiting corals and fishes: A tipping point that may limit reef recovery
Juvenile corals and reef fish are attracted by chemical signals of healthy reefs, preventing settlement in degraded areas. [Also see Perspective by Bruno] Authors: Danielle L Dixson, David Abrego, Mark E Hay
 2014-08-22 [Research Article] Varying planetary heat sink led to global-warming slowdown and acceleration
The slowdown in global warming over the beginning of the 21st century has resulted from heat transport into the deep ocean. Authors: Xianyao Chen, Ka-Kit Tung
 2014-08-22 [Report] All-optical routing of single photons by a one-atom switch controlled by a single photon
An all-optical scheme for routing single photons by single photons is demonstrated. [Also see Perspective by Rempe] Authors: Itay Shomroni, Serge Rosenblum, Yulia Lovsky, Orel Bechler, Gabriel Guendelman, Barak Dayan
 2014-08-22 [Report] Shapes and vorticities of superfluid helium nanodroplets
Vortex lattices inside individual helium droplets are imaged using x-ray diffraction. Authors: Luis F. Gomez, Ken R. Ferguson, James P. Cryan, Camila Bacellar, Rico Mayro P. Tanyag, Curtis Jones, Sebastian Schorb, Denis Anielski, Ali Belkacem, Charles Bernando, Rebecca Boll, John Bozek, Sebastian Carron, Gang Chen, Tjark Delmas, Lars Englert, Sascha W. Epp, Benjamin Erk, Lutz Foucar, Robert Hartmann, Alexander Hexemer, Martin Huth, Justin Kwok, Stephen R. Leone, Jonathan H. S. Ma, Filipe R. N. C. Maia, Erik Malmerberg, Stefano Marchesini, Daniel M. Neumark, Billy Poon, James Prell, Daniel Rolles, Benedikt Rudek, Artem Rudenko, Martin Seifrid, Katrin R. Siefermann, Felix P. Sturm, Michele Swiggers, Joachim Ullrich, Fabian Weise, Petrus Zwart, Christoph Bostedt, Oliver Gessner, Andrey F. Vilesov
 2014-08-22 [Report] Electron microscopy of gold nanoparticles at atomic resolution
The atomic structure of a 68–gold atom nanoparticle is determined without prior structural knowledge or model fitting. Authors: Maia Azubel, Jaakko Koivisto, Sami Malola, David Bushnell, Greg L. Hura, Ai Leen Koh, Hironori Tsunoyama, Tatsuya Tsukuda, Mika Pettersson, Hannu Häkkinen, Roger D. Kornberg
 2014-08-22 [Report] A chemical signature of first-generation very massive stars
Elemental abundances in a metal-poor star suggest enrichment by a supernova involving a progenitor heavier than 100 solar masses. [Also see Perspective by Bromm] Authors: W. Aoki, N. Tominaga, T. C. Beers, S. Honda, Y. S. Lee
 2014-08-22 [Report] Facet development during platinum nanocube growth
Observation of atomic facet development during platinum nanocube growth reveals shape control. Authors: Hong-Gang Liao, Danylo Zherebetskyy, Huolin Xin, Cory Czarnik, Peter Ercius, Hans Elmlund, Ming Pan, Lin-Wang Wang, Haimei Zheng
 2014-08-22 [Report] Attribution of global glacier mass loss to anthropogenic and natural causes
Human influence is now responsible for more glacial mass loss than are natural causes. [Also see Perspective by Marshall] Authors: Ben Marzeion, J. Graham Cogley, Kristin Richter, David Parkes
 2014-08-22 [Report] Efficacy of inactivated poliovirus vaccine in India
Controversy over vaccine choice for polio eradication can be reconciled by effective combined use. Authors: Hamid Jafari, Jagadish M. Deshpande, Roland W. Sutter, Sunil Bahl, Harish Verma, Mohammad Ahmad, Abhishek Kunwar, Rakesh Vishwakarma, Ashutosh Agarwal, Shilpi Jain, Concepcion Estivariz, Raman Sethi, Natalie A. Molodecky, Nicholas C. Grassly, Mark A. Pallansch, Arani Chatterjee, R. Bruce Aylward
 2014-08-22 [Report] Sunlight controls water column processing of carbon in arctic fresh waters
Photochemical reactions cause most of the breakdown of carbon released from permafrost into arctic inland waters. [Also see Perspective by Tranvik] Authors: Rose M. Cory, Collin P. Ward, Byron C. Crump, George W. Kling
 2014-08-22 [Report] Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor
The ancestral savory receptor has been converted for sweet reception in hummingbirds. [Also see Perspective by Jiang and Beauchamp] Authors: Maude W. Baldwin, Yasuka Toda, Tomoya Nakagita, Mary J. O'Connell, Kirk C. Klasing, Takumi Misaka, Scott V. Edwards, Stephen D. Liberles
 2014-08-22 [Report] Arabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation
Cellular remodeling to develop phloem cells orchestrates degradation of the cell’s nucleus. [Also see Perspective by Geldner] Authors: Kaori Miyashima Furuta, Shri Ram Yadav, Satu Lehesranta, Ilya Belevich, Shunsuke Miyashima, Jung-ok Heo, Anne Vatén, Ove Lindgren, Bert De Rybel, Gert Van Isterdael, Panu Somervuo, Raffael Lichtenberger, Raquel Rocha, Siripong Thitamadee, Sari Tähtiharju, Petri Auvinen, Tom Beeckman, Eija Jokitalo, Ykä Helariutta
 2014-08-22 [Report] A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator
A riboswitch is both part of, and regulates the activity of, a small noncoding regulatory RNA. [Also see Perspective by Chen and Gottesman] Authors: Sruti DebRoy, Margo Gebbie, Arati Ramesh, Jonathan R. Goodson, Melissa R. Cruz, Ambro van Hoof, Wade C. Winkler, Danielle A. Garsin
 2014-08-22 [Report] Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA
A riboswitch is both part of, and regulates the activity of, a small noncoding regulatory RNA. [Also see Perspective by Chen and Gottesman] Authors: J. R. Mellin, Mikael Koutero, Daniel Dar, Marie-Anne Nahori, Rotem Sorek, Pascale Cossart
 2014-08-22 [Report] Chromatin state dynamics during blood formation
A chromatin precipitation technique identifies changes during the differentiation of blood cells. Authors: David Lara-Astiaso, Assaf Weiner, Erika Lorenzo-Vivas, Irina Zaretsky, Diego Adhemar Jaitin, Eyal David, Hadas Keren-Shaul, Alexander Mildner, Deborah Winter, Steffen Jung, Nir Friedman, Ido Amit
 2014-08-22 [Report] Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
The polyploid genome of oilseed rape exhibits evolution through homologous gene conversion. Authors: Boulos Chalhoub, France Denoeud, Shengyi Liu, Isobel A. P. Parkin, Haibao Tang, Xiyin Wang, Julien Chiquet, Harry Belcram, Chaobo Tong, Birgit Samans, Margot Corréa, Corinne Da Silva, Jérémy Just, Cyril Falentin, Chu Shin Koh, Isabelle Le Clainche, Maria Bernard, Pascal Bento, Benjamin Noel, Karine Labadie, Adriana Alberti, Mathieu Charles, Dominique Arnaud, Hui Guo, Christian Daviaud, Salman Alamery, Kamel Jabbari, Meixia Zhao, Patrick P. Edger, Houda Chelaifa, David Tack, Gilles Lassalle, Imen Mestiri, Nicolas Schnel, Marie-Christine Le Paslier, Guangyi Fan, Victor Renault, Philippe E. Bayer, Agnieszka A. Golicz, Sahana Manoli, Tae-Ho Lee, Vinh Ha Dinh Thi, Smahane Chalabi, Qiong Hu, Chuchuan Fan, Reece Tollenaere, Yunhai Lu, Christophe Battail, Jinxiong Shen, Christine H. D. Sidebottom, Xinfa Wang, Aurélie Canaguier, Aurélie Chauveau, Aurélie Bérard, Gwenaëlle Deniot, Mei Guan, Zhongsong Liu, Fengming Sun, Yong Pyo Lim, Eric Lyons, Christopher D. Town, Ian Bancroft, Xiaowu Wang, Jinling Meng, Jianxin Ma, J. Chris Pires, Graham J. King, Dominique Brunel, Régine Delourme, Michel Renard, Jean-Marc Aury, Keith L. Adams, Jacqueline Batley, Rod J. Snowdon, Jorg Tost, David Edwards, Yongming Zhou, Wei Hua, Andrew G. Sharpe, Andrew H. Paterson, Chunyun Guan, Patrick Wincker
 2014-08-22 [New Products] New Products
A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.
 2014-08-22 [Podcast] Science Podcast: 22 August Show
On this week's show: Reverse engineering internet censorship in China and a news roundup.
 2014-08-22 [Business Office Feature] Techniques for RNA detection: Where are we headed?
Martin J. Stoddart
 2014-08-22 [Business Office Feature] The transferrable postdoc
Kendall Powell
 2014-08-22 [Working Life] Playing a new tune
Author: Jim Austin

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