bluuebunny/crossref_metadata_2025_split huggingface dataset:
A stochastic self-replicating robot capable of hierarchical assembly
Authors: Kaloutsakis Georgios , Chirikjian Gregory S. 
Published: January 2011

SUMMARYThis paper presents the development of a self-replicating mobile robot that functions by undergoing stochastic motions. The robot functions hierarchically. There are three stages in this hierarchy: (1) An initial pool of feed modules/parts together with one functional basic robot; (2) a collection of basic robots that are spontaneously formed out of these parts as a result of a chain reaction induced by stochastic motion of the initial seed robot at stage 1; (3) complex formations of joined basic robots from stage 2. In the first part of this paper we demonstrate basic stochastic self-replication in unstructured environments. A single functional robot moves around at random in a sea of stock modules and catalyzes the conversion of these modules into replicas. In the second part of the paper, the robots are upgraded with a layer that enables mechanical connections between robots. The replicas can then connect to each other and aggregate. Finally, self-reconfigurability is presented for two robotic aggregations.
Who needs theory anyway? The relationship between theory and practice of music education in a philosophical outlook
Authors: Westerlund Heidi , Väkevä Lauri 
Published: January 2011

For a practicing arts educator, the relationship between theory and practice is often unproblematic: theory is considered to be irrelevant for the good practice. Considering the matter from an academic standpoint, one faces the distinction between poietic, or productive, and contemplative, or responsive, mindsets stemming from the classical philosophical tradition. Still more confusing is the question of the relationship between theory and philosophy; one's theory seems to follow one's chosen philosophical commitment, even to a degree that advocates of different philosophical stances do not necessarily understand each others' conceptions of theory.In this article,1we examine the complex relationships between philosophy, theory and practice in music education. We shall begin with analysing different approaches to philosophy of music education. Proceeding towards more general conceptions of the relationship between theory and practice, we will examine the work of some of the well-known authors within the field of music education in order to pave way to a philosophical outlook that conceives the role of philosophy of music education as a form of cultural critique. The suggested alternative approach mediates between contemplative and poietic fields in pedagogical praxis. This guides us towards an understanding that considers theoretical concepts as philosophically loaded pragmatic tools that serve critical rationality embedded in practical action. From this standpoint there is indeed no need to cut theory apart from a good practice: both can be taken to serve the same master, philosophically informed way of living meaningfully.
Evaluating the relative effectiveness of alternative conservation interventions in influencing stated behavioural intentions: the saiga antelope in Kalmykia (Russia)
Authors: HOWE CAROLINE , MEDZHIDOV RUSLAN , MILNER-GULLAND E. J. 
Published: January 2011

SUMMARYEvaluating the relative effectiveness of different conservation interventions is difficult and rarely undertaken. Conservation of the critically endangered saiga antelope in the Republic of Kalmykia (Russia) provides a unique experimental set-up that was used to disentangle this issue. This study uses the amount pledged for conservation, adapted from contingent valuation methods, as a measure of behavioural intention to contribute to saiga conservation, to evaluate conservation effectiveness. Semi-structured interviews were undertaken with 250 individuals in eight villages exposed to traditional ‘fences-and-fines’ conservation, livelihoods enhancement (social engagement) or low-level media coverage. The intervention employed had a direct effect on amount pledged for saiga conservation. Social engagement programmes decreased protest-bidding behaviour but resulted in low amounts pledged for saiga conservation. Those exposed to media coverage pledged the greatest amounts on average, whilst those exposed to traditional conservation had both a high level of protest bidding and low pledges from those who pledged something. The primary reason given for protest bids was that the government or international community should pay for conservation. This may be a relic from the Soviet era, and may explain low pledges for conservation under social engagement. Ecological knowledge strongly affected amount pledged. The results were influenced by cultural and demographic factors, including residence time, exposure to saigas, age, wealth and knowledge regarding conservation. This study is unusual in disentangling the effect of a conservation intervention from other factors, and proposes using amount pledged for conservation as a practical tool for evaluating the effectiveness of projects aimed at increasing awareness and promoting positive behavioural intentions towards conservation. It provides support for media awareness-raising as a successful conservation intervention.
Effect of age, GV transfer and modified nucleocytoplasmic ratio on PKCα in mouse oocytes and early embryos
Authors: Cui Long-Bo , Zhao Zhen-Jun , Zhou Xue-Ying , Li Qian , Huang Xiu-Ying , Sun Fang-Zhen 
Published: January 2011

SummaryProtein kinase C (PKC) is a family of Ser/Thr protein kinases that can be activated by Ca2+, phospholipid and diacylglycerol. There is evidence that PKC plays key roles in the meiotic maturation and activation of mammalian oocytes. The present study aimed to monitor the effect of age, germinal vesicle (GV) transfer and modified nucleoplasmic ratio on the subcellular distribution profile of PKCα, an important isozyme of PKC, in mouse oocytes undergoing meiotic maturation and following egg activation. Germinal vesicle oocytes were collected from 6–8-week-old and 12-month-old mice. Germinal vesicle-reconstructed oocytes and GV oocytes with one-half or one-third of the original oocyte volume were created using micromanipulation and electrofusion. The subcellular localization of PKCα was detected by immunocytochemistry and laser confocal microscopy. Our study showed that PKCα had a similar location pattern in oocytes and early embryos from young and old mice. PKCα was localized evenly in ooplasm, with weak staining in GV at the GV stage, and present in the entire meiosis II (MII) spindle at the MII stage. In pronuclear and 2-cell embryos, PKCα was concentrated in the nucleus except for the nucleolus. After the GV oocytes were reconstructed, the resultant MII oocytes and embryos showed a similar distribution of PKCα between reconstructed and unreconstructed controls. After one-half or two-thirds of the cytoplasm was removed from the GV oocytes, PKCα still had a similar location pattern in MII oocytes and early embryos from the GV oocytes with modified nucleoplasmic ratio. Our study showed that age, GV transfer and modified nucleocytoplasmic ratio does not affect distribution of PKCα during mouse oocyte maturation, activation, and early embryonic mitosis.
Nuclear Fusion Award 2010 speech
Authors: John Rice  
Published: January 2011

Following the suggestion of Earl Marmar in 1995, I installed a compact von Hamos type x-ray spectrometer (originally built with Elisabeth Rachlew and Jan Kallne) on a tangentially viewing port on the Alcator C-Mod tokamak. The spectrometer views the plasma through a 2 cm diameter hole, and is tuned to H-like argon, suitable for passive measurement of the core toroidal rotation velocity from the Doppler shift. It soon became evident that the rotation in Ohmic L-mode discharges, while for the most part directed counter-current, depends in a very complicated fashion on plasma parameters, notably the electron density, current and magnetic configuration. The rotation can even flip sign for almost no apparent reason! In Ohmic and ion cyclotron range of frequencies (ICRF) heated H-mode plasmas the rotation is in the co-current direction and has a relatively simple dependence on plasma parameters, proportional to the stored energy normalized to the current. Rotation velocities as high as 130 km s-1 have been observed without external momentum input. In dimensionless terms this intrinsic (or spontaneous rotation) depends on the normalized plasma pressure. The association of toroidal rotation with plasma pressure in ICRF H-modes was first observed by Lars-Goran Eriksson in JET discharges. Similar results were subsequently reported for Tore Supra enhanced confinement plasmas.
In the early 2000s concerns began to surface about the lack of substantial neutral beam driven rotation in ITER, and intrinsic rotation became a topic of interest in the ITPA Transport Group. Through that connection, similar observations from DIII-D, TCV and JT-60U were added to the growing list. A database of intrinsic rotation observations was assembled with the goal of extrapolating to the expected values for ITER. Both dimensional and dimensionless scalings were developed and formed the backbone of the 2007 Nuclear Fusion paper. I gratefully acknowledge the important contributions to this paper from Alex Ince-Cushman, John deGrassie, Lars-Goran Eriksson, Yoshiteru Sakamoto, Andrea Scarabosio and Yuri Podpaly, as well as the other coauthors. I would like to express my sincere appreciation to Earl Marmar, Martin Greenwald and Miklos Porkolab at MIT for continued support of this work, as well as to the entire C-Mod team.
This award was made possible due to the insight of Mitsuru Kikuchi and the support of the IAEA through Werner Burkhart, and I am truly grateful to both of them. Many thanks as well to the outstanding staff at Nuclear Fusion. It is a distinct honor to be included in the group of previous winners: Tim Luce, Clemente Angioni, Todd Evans and Steve Sabbagh. It is also a great honor to be considered alongside the 2010 nominees: Phil Snyder, Sibylle Guenter, Maiko Yoshida, Hajime Urano, Fulvio Zonca, Erik Garcia, Costanza Maggi, Hartmut Zohm, Thierry Loarer and Bruce Lipschultz.
Finally, I would like to thank the readers of Nuclear Fusion for the many citations.
John Rice
2010 Nuclear Fusion Award winner
Plasma Science and Fusion Center, MIT, Cambridge, MA, USA
ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration
Authors: Bottolo Leonardo , Chadeau-Hyam Marc , Hastie David I. , Langley Sarah R. , Petretto Enrico , Tiret Laurence , Tregouet David , Richardson Sylvia 
Published: January 2011

Abstract
Summary: ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the ‘large p, small n’ case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements.
Availability: C++ source code and documentation including compilation instructions are available under GNU licence at http://bgx.org.uk/software/ESS.html.
Contact: l.bottolo@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
X-MATE: a flexible system for mapping short read data
Authors: Wood David L. A. , Xu Qinying , Pearson John V. , Cloonan Nicole , Grimmond Sean M. 
Published: January 2011

Abstract
Summary: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file formats, we now present X-MATE, an updated version of RNA-MATE, capable of mapping both RNA-Seq and DNA datasets and with improved performance, output file formats, configuration files, and flexibility in core mapping software.
Availability: Executables, source code, junction libraries, test data and results and the user manual are available from http://grimmond.imb.uq.edu.au/X-MATE/.
Contact: n.cloonan@uq.edu.au; s.grimmond@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics Online.
HiSpOD: probe design for functional DNA microarrays
Authors: Dugat-Bony Eric , Missaoui Mohieddine , Peyretaillade Eric , Biderre-Petit Corinne , Bouzid Ourdia , Gouinaud Christophe , Hill David , Peyret Pierre 
Published: January 2011

Abstract
Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays.
Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contaminated environmental sample proved the specificity and the sensitivity of probes designed with the HiSpOD program.
Availability: http://fc.isima.fr/~g2im/hispod/.
Contact: pierre.peyret@univ-bpclermont.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
Authors: Abyzov Alexej , Gerstein Mark 
Published: January 2011

Abstract
Motivation: Defining the precise location of structural variations (SVs) at single-nucleotide breakpoint resolution is an important problem, as it is a prerequisite for classifying SVs, evaluating their functional impact and reconstructing personal genome sequences. Given approximate breakpoint locations and a bridging assembly or split read, the problem essentially reduces to finding a correct sequence alignment. Classical algorithms for alignment and their generalizations guarantee finding the optimal (in terms of scoring) global or local alignment of two sequences. However, they cannot generally be applied to finding the biologically correct alignment of genomic sequences containing SVs because of the need to simultaneously span the SV (e.g. make a large gap) and perform precise local alignments at the flanking ends.
Results: Here, we formulate the computations involved in this problem and describe a dynamic-programming algorithm for its solution. Specifically, our algorithm, called AGE for Alignment with Gap Excision, finds the optimal solution by simultaneously aligning the 5′ and 3′ ends of two given sequences and introducing a ‘large-gap jump’ between the local end alignments to maximize the total alignment score. We also describe extensions allowing the application of AGE to tandem duplications, inversions and complex events involving two large gaps. We develop a memory-efficient implementation of AGE (allowing application to long contigs) and make it available as a downloadable software package. Finally, we applied AGE for breakpoint determination and standardization in the 1000 Genomes Project by aligning locally assembled contigs to the human genome.
Availability and Implementation: AGE is freely available at http://sv.gersteinlab.org/age.
Contact: pi@gersteinlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
The Physiome Model Repository 2
Authors: Yu Tommy , Lloyd Catherine M. , Nickerson David P. , Cooling Michael T. , Miller Andrew K. , Garny Alan , Terkildsen Jonna R. , Lawson James , Britten Randall D. , Hunter Peter J. , Nielsen Poul M. F. 
Published: January 2011

Abstract
Motivation: The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model.
Availability: PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.
Contact: tommy.yu@auckland.ac.nz
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies
Authors: Ong Rick Twee-Hee , Liu Xuanyao , Poh Wan-Ting , Sim Xueling , Chia Kee-Seng , Teo Yik-Ying 
Published: January 2011

Abstract
Motivation: Methods for detecting positive selection relied on finding evidence of long haplotypes to identify candidate regions under selection. However, these methods generally do not identify the length and form of the selected haplotype.
Results: We present HapFinder, a method which can find the common longest haplotype under three different settings from a database, which is relevant in the analysis of positive selection in population genetics and also in medical genetics for finding the likely haplotype form carrying the causal allele at the functional polymorphism.
Availability: A java program, implementing the methods described in HapFinder, together with R scripts and datasets for producing the figures presented in this article are publicly available at http://www.nus-cme.org.sg/sgvp/software/hapfinder.html. The site also hosts an online browser for finding haplotypes from the International HapMap Project and the Singapore Genome Variation Project.
Contact: g0801900@nus.edu.sg; statyy@nus.edu.sg
Sources of variability in prevalence and distribution of bitter crab disease in snow crab (Chionoecetes opilio) along the northeast coast of Newfoundland
Authors: Mullowney Darrell R. , Dawe Earl G. , Morado J. Frank , Cawthorn Richard J. 
Published: January 2011

AbstractMullowney, D. R., Dawe, E. G., Morado, J. F., and Cawthorn, R. J. 2011. Sources of variability in prevalence and distribution of bitter crab disease in snow crab (Chionoecetes opilio) along the northeast coast of Newfoundland. – ICES Journal of Marine Science, 68: . Bitter crab disease (BCD), caused by a parasitic dinoflagellate of the genus Hematodinium, is a source of mortality in Newfoundland and Labrador snow crab (Chionoecetes opilio). Prevalence and distribution patterns have been spatially and temporally variable since the discovery of BCD in 1990, and controlling factors are poorly understood. Data from a long-term trap survey in two bays along the northeast coast of Newfoundland are analysed, investigating the influences and interactions of various biotic and abiotic factors over BCD. Factors examined include host size and density, temperature, salinity, and depth. The density of small to medium-sized snow crabs was directly related to prevalence and distribution of BCD, whereas all other factors had either an indirect or no effect. Further, much of the spatio-temporal variability in disease expression is a function of variability in host productivity, growth, and movement. The study also considers the impacts BCD can exert on the commercial fishery, and the potential for predicting intermediate to long-term recruitment potential based on BCD prevalence levels.
The Folylpolyglutamate Synthetase Plastidial Isoform Is Required for Postembryonic Root Development in Arabidopsis
Authors: Srivastava Avinash C. , Ramos-Parra Perla A. , Bedair Mohamed , Robledo-Hernández Ana L. , Tang Yuhong , Sumner Lloyd W. , Díaz de la Garza Rocío I. , Blancaflor Elison B. 
Published: January 2011

AbstractA recessive Arabidopsis (Arabidopsis thaliana) mutant with short primary roots and root hairs was identified from a forward genetic screen. The disrupted gene in the mutant encoded the plastidial isoform of folylpolyglutamate synthetase (FPGS), previously designated as AtDFB, an enzyme that catalyzes the addition of glutamate residues to the folate molecule to form folylpolyglutamates. The short primary root of atdfb was associated with a disorganized quiescent center, dissipated auxin gradient in the root cap, bundled actin cytoskeleton, and reduced cell division and expansion. The accumulation of monoglutamylated forms of some folate classes in atdfb was consistent with impaired FPGS function. The observed cellular defects in roots of atdfb underscore the essential role of folylpolyglutamates in the highly compartmentalized one-carbon transfer reactions (C1 metabolism) that lead to the biosynthesis of compounds required for metabolically active cells found in the growing root apex. Indeed, metabolic profiling uncovered a depletion of several amino acids and nucleotides in atdfb indicative of broad alterations in metabolism. Methionine and purines, which are synthesized de novo in plastids via C1 enzymatic reactions, were particularly depleted. The root growth and quiescent center defects of atdfb were rescued by exogenous application of 5-formyl-tetrahydrofolate, a stable folate that was readily converted to metabolically active folates. Collectively, our results indicate that AtDFB is the predominant FPGS isoform that generates polyglutamylated folate cofactors to support C1 metabolism required for meristem maintenance and cell expansion during postembryonic root development in Arabidopsis.