bluuebunny/crossref_metadata_2025_split huggingface dataset:
The quality of midday meals eaten at school by adolescents; school lunches compared with packed lunches and their contribution to total energy and nutrient intakes
Authors: Prynne Celia J , Handford Caroline , Dunn Valerie , Bamber Diane , Goodyer Ian M , Stephen Alison M 
Published: September 2011

AbstractObjectiveTo compare food and nutrient intakes from midday meals provided by schools with those from packed lunches and to estimate the contribution from food eaten at midday to the total daily energy and nutrient intakes of teenagers.DesignDietary data were recorded in 4 d estimated diaries of which 2 d were school days. The school day data were analysed for total and midday energy and nutrient intakes. The latter were compared with the recommendations of the Caroline Walker Trust (CWT).SettingCambridgeshire, UK, 2006.SubjectsTeenagers (n 757) aged 14–15 years, from eighteen secondary schools, who reported food eaten at school.ResultsThe contribution to total daily energy intake from all lunches eaten at school was 29 % (boys) and 28 % (girls). School meals provided greater quantities of protein, starch, carotene and folate but also more saturated fats and Na than packed lunches. Intakes of energy and several nutrients fell below the CWT recommendations for both types of lunch. School meals and packed lunches provided different types of foods; greater quantities of rice, pasta and vegetables in school meals; more yoghurt, cheese, fruit and juices but also more confectionery and soft drinks in packed lunches.ConclusionsThere has been concern that schoolchildren who are not opting for lunch provided by schools are compromising the overall quality of their diet, but the present study showed small differences in nutrient content between packed and school lunches. These data were collected in 2005–2007 before the government programme of improvements reached secondary schools.
BioModels Database: curation and annotation
Authors: Schubert Michael , Ajmera Ishan , Chelliah Vijayalakshmi , Endler Lukas , Rodriguez Nicolas , Laibe Camille , Le Novère Nicolas 
Published: September 2011

AbstractThe BioModels Database is a freely accessible online resource for storing, viewing, retrieving, and analyzing published, peer-reviewed quantitative models of biological processes.In this poster we provide an overview of its capabilities, as well as the curation and annotation process with two use cases concerning blood coagulation and glucose homeostasis.
Sociability is decreased following deletion of the trpc4 gene
Authors: Rasmus Kristin , Wang Jun-Gang , Varnell Andrew , Ostertag Eric , Cooper Donald 
Published: September 2011

AbstractShyness and social anxiety are predominant features of some psychiatric disorders including autism, schizophrenia, anxiety and depression. Understanding the cellular and molecular determinants of sociability may reveal therapeutic approaches to treat individuals with these disorders and improve their quality of life. Previous experiments from our laboratory have identified selective mRNA and protein expression of a nonselective cation channel known as the canonical transient receptor potential channel 4 (TRPC4s) in brain regions implicated in emotional regulation and anxiety. TRPC4 is highly expressed in the corticolimbic regions of the mammalian brain. We hypothesized that robust corticolimbic expression of TRPC4 may regulate the brain’s response to emotion and anxiety resulting in changes in social interaction. Here we test trpc4 gene knockout rats in a model of social anxiety/interaction. We found that the Trpc4 knockout animals spent significantly less time exploring a juvenile intruder rat compared to their wild-type counterparts and Sprague-Dawley (SD) rats. Furthermore, Trpc4 wild-type (Fisher 344) rats explored the juvenile significantly less than the SD rats. These findings indicate that the trpc4 gene plays a role in modulating cellular excitability in specific regions of the brain associated sociality and/or anxiety.
MAGNETOROTATIONAL-INSTABILITY-DRIVEN ACCRETION IN PROTOPLANETARY DISKS
Authors: Bai Xue-Ning 
Published: September 2011

ABSTRACT
Non-ideal MHD effects play an important role in the gas dynamics in protoplanetary disks (PPDs). This paper addresses the influence of non-ideal MHD effects on the magnetorotational instability (MRI) and angular momentum transport in PPDs using the most up-to-date results from numerical simulations. We perform chemistry calculations using a complex reaction network with standard prescriptions for X-ray and cosmic-ray ionizations. We first show that whether or not grains are included, the recombination time is at least one order of magnitude less than the orbital time within five disk scale heights, justifying the validity of local ionization equilibrium and strong coupling limit in PPDs. The full conductivity tensor at different disk radii and heights is evaluated, with the MRI active region determined by requiring that (1) the Ohmic Elsasser number Λ be greater than 1 and (2) the ratio of gas to magnetic pressure β be greater than βmin(Am) as identified in the recent study by Bai & Stone, where Am is the Elsasser number for ambipolar diffusion. With full flexibility as to the magnetic field strength, we provide a general framework for estimating the MRI-driven accretion rate

and the magnetic field strength in the MRI active layer. We find that the MRI active layer always exists at any disk radius as long as the magnetic field in PPDs is sufficiently weak. However, the optimistically predicted

in the inner disk (r = 1–10 AU) appears insufficient to account for the observed range of accretion rates in PPDs (around 10−8
M
☉ yr−1) even in the grain-free calculation, and the presence of solar abundance sub-micron grains further reduces

by one to two orders of magnitude. Moreover, we find that the predicted

increases with radius in the inner disk where accretion is layered, which would lead to runaway mass accumulation if disk accretion is solely driven by the MRI. Our results suggest that stronger sources of ionization and/or additional mechanisms such as magnetized wind are needed to explain the observed accretion rates in PPDs. In contrast, our predicted

is on the order of 10−9
M
☉ yr−1 in the outer disk, consistent with the observed accretion rates in transitional disks.
The Economics of a Blender's Tax Credit versus a Tax Exemption: The Case of U.S. “Splash and Dash” Biodiesel Exports to the European Union
Authors: de Gorter Harry , Drabik Dusan , Just David R. 
Published: September 2011

AbstractA conceptual framework is advanced that determines world biodiesel prices, the policy parameters in the country establishing the price, and the binding mandate or tax exemption. The effect of a tax credit differs with international trade compared to traditional closed economy analysis. The U.S. “splash & dash” program, with its $1/gallon tax credit, had minimal impacts on European Union (EU) biodiesel producer profits. Reduced world oil prices and EU tax exemptions, as well as increased rapeseed oil prices, are shown to have reduced the profitability of EU biodiesel production. EU imports from the United States can be beneficial for EU taxpayers, fuel consumers, and U.S. biodiesel producers.
wapRNA: a web-based application for the processing of RNA sequences
Authors: Zhao Wenming , Liu Wanfei , Tian Dongmei , Tang Bixia , Wang Yanqing , Yu Caixia , Li Rujiao , Ling Yunchao , Wu Jiayan , Song Shuhui , Hu Songnian 
Published: September 2011

Abstract
Summary: mRNA/miRNA-seq technology is becoming the leading technology to globally profile gene expression and elucidate the transcriptional regulation mechanisms in living cells. Although there are many tools available for analyzing RNA-seq data, few of them are available as easy accessible online web tools for processing both mRNA and miRNA data for the RNA-seq based user community. As such, we have developed a comprehensive web application tool for processing mRNA-seq and miRNA-seq data. Our web tool wapRNA includes four different modules: mRNA-seq and miRNA-seq sequenced from SOLiD or Solexa platform and all the modules were tested on previously published experimental data. We accept raw sequence data with an optional reads filter, followed by mapping and gene annotation or miRNA prediction. wapRNA also integrates downstream functional analyses such as Gene Ontology, KEGG pathway, miRNA targets prediction and comparison of gene's or miRNA's different expression in different samples. Moreover, we provide the executable packages for installation on user's local server.
Availability: wapRNA is freely available for use at http://waprna.big.ac.cn. The executable packages and the instruction for installation can be downloaded from our web site.
Contact: husn@big.ac.cn; songshh@big.ac.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Robust relative compression of genomes with random access
Authors: Deorowicz Sebastian , Grabowski Szymon 
Published: September 2011

Abstract
Motivation: Storing, transferring and maintaining genomic databases becomes a major challenge because of the rapid technology progress in DNA sequencing and correspondingly growing pace at which the sequencing data are being produced. Efficient compression, with support for extraction of arbitrary snippets of any sequence, is the key to maintaining those huge amounts of data.
Results: We present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over an order of magnitude greater. In particular, 69 differentially encoded human genomes are compressed over 400 times at fast compression, or even 1000 times at slower compression (the reference genome itself needs much more space). Adding fast random access to text snippets decreases the ratio to ~300.
Availability: GDC is available at http://sun.aei.polsl.pl/gdc.
Contact: sebastian.deorowicz@polsl.pl
Supplementary Information: Supplementary data are available at Bioinformatics online.
SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Authors: Wu Jie , Akerman Martin , Sun Shuying , McCombie W. Richard , Krainer Adrian R. , Zhang Michael Q. 
Published: September 2011

Abstract
Motivation: Alternative splicing (AS) is a pre-mRNA maturation process leading to the expression of multiple mRNA variants from the same primary transcript. More than 90% of human genes are expressed via AS. Therefore, quantifying the inclusion level of every exon is crucial for generating accurate transcriptomic maps and studying the regulation of AS.
Results: Here we introduce SpliceTrap, a method to quantify exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus on full-length transcript isoforms, SpliceTrap approaches the expression-level estimation of each exon as an independent Bayesian inference problem. In addition, SpliceTrap can identify major classes of alternative splicing events under a single cellular condition, without requiring a background set of reads to estimate relative splicing changes. We tested SpliceTrap both by simulation and real data analysis, and compared it to state-of-the-art tools for transcript quantification. SpliceTrap demonstrated improved accuracy, robustness and reliability in quantifying exon-inclusion ratios.
Conclusions: SpliceTrap is a useful tool to study alternative splicing regulation, especially for accurate quantification of local exon-inclusion ratios from RNA-seq data.
Availability and Implementation: SpliceTrap can be implemented online through the CSH Galaxy server http://cancan.cshl.edu/splicetrap and is also available for download and installation at http://rulai.cshl.edu/splicetrap/.
Contact: michael.zhang@utdallas.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Clinical characteristics and major comorbidities in heart failure patients more than 85 years of age compared with younger age groups
Authors: Mogensen Ulrik Madvig , Ersbøll Mads , Andersen Mads , Andersson Charlotte , Hassager Christian , Torp‐Pedersen Christian , Gustafsson Finn , Køber Lars 
Published: September 2011

AimsHeart failure (HF) is increasingly prevalent among the growing number of elderly people, but not well studied. We sought to evaluate disease pattern and importance of prognostic factors among very elderly patients with HF.Methods and resultsAmong 8507 patients screened for entry into two studies on HF, we analysed the clinical characteristics, major comorbidities and prognostic factors in 825 patients older than 85 years (very elderly) compared with younger age groups. Adjusted hazard ratios [HR (95% confidence intervals)] of long‐term mortality were calculated using Cox models. The very elderly were more often female (60 vs. 26%) and had a higher prevalence of preserved ejection fraction (53 vs. 36%) compared with patients younger than 65 years (P< 0.001). The prevalence of cardiovascular comorbidities increased with advancing age only until the seventh decade and then declined, resulting in the lowest prevalence of diabetes (12 vs. 16%, P< 0.001), hypertension (20 vs. 26%, P< 0.001), ischaemic heart disease (42 vs. 53%, P< 0.001), and peripheral artery disease (4 vs. 6%, P= 0.017) among the very elderly compared with patients aged <85 years. Non‐cardiovascular comorbidities generally increased linearly with age. Long‐term mortality was associated with atrial fibrillation [HR = 1.30 (1.06–1.60), P= 0.013] with greater prognostic importance in the very elderly, while ejection fraction, diabetes [HR = 1.31 (1.01–1.61), P= 0.04], and renal insufficiency [HR = 1.36 (1.13–0.63), P< 0.0001] had less prognostic importance than in younger patients (P for interactions <0.003).ConclusionThe prevalence of cardiovascular comorbidities is lower in very elderly HF patients and has different prognostic importance.
First Report of Group 16SrXII Phytoplasma Associated with Papaya Yellows in Taiwan
Authors: Bau H. J. , Hung S. C. , Chang W. C. , Chen Y. K. 
Published: September 2011

Phytoplasmas have been reported to cause various disorders in papaya (Carica papaya L.), including dieback, mosaic, and yellow crinkle in Australia, Nivun Haamir dieback in Israel, and bunchy top-like disease in Cuba (1). Papaya is an economically important crop in Taiwan, and therefore, is monitored for viral infections. In 2005, papaya plants showing chlorosis, yellows and shriveling of leaves, dieback and lateral growth of branches, bending of apical branches, latexosis of fruits, and brown necrosis in phloem tissues were observed in southern Taiwan. Examination by an electron microscope revealed the presence of pleomorphic phytoplasma cells in sieve tubes of the phloem of petioles and leaf veins of diseased plants. Total DNA was extracted individually from at least three diseased plants at each location with a commercial DNA preparation kit (Axygen Scientific, Union City, CA) and used for amplification of the phytoplasma 16S rRNA gene in PCR with universal primer pairs P1 and Tint (3). The full-length 16S rRNA gene has been amplified and cloned. Sequence analysis revealed that the fragment was 1,581 bp long (GenBank Accession No. AJ919994) and shared 99.6% sequence identity with that of the ‘Candidatus Phytoplasma solani’ reference strain (GenBank Accession No. AF248959). A virtual restriction fragment length polymorphism analysis of the 16S rDNA sequence amplified from the R16F2n/R16R2 primers (2) was performed with iPhyClassifier (4) and pDRAW32. In silico restriction analysis identified the studied papaya phytoplasma as a subgroup 16SrXII-A strain. The sequence had 97 to 98% sequence identity with papaya phytoplasmas of the 16SrXII group in Australia (GenBank Accession No. Y10095), Israel (GenBank Accession No. AY903951), and Cuba (GenBank Accession No. AY725234). The disease incidence was 30 to 35% during the 2006 to 2010 growing seasons, and field surveys indicated that the disease has spread to central Taiwan with sporadic occurrence in recent years. To our knowledge, this is the first report of phytoplasma associated with papaya yellows in Taiwan. References: (1) Y. Arocha et al. Int. J. Syst. Evol. Microbiol. 55:2451, 2005. (2) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Chromosomes Carrying Meiotic Avoidance Loci in Three Apomictic Eudicot Hieracium Subgenus Pilosella Species Share Structural Features with Two Monocot Apomicts
Authors: Okada Takashi , Ito Kanae , Johnson Susan D. , Oelkers Karsten , Suzuki Go , Houben Andreas , Mukai Yasuhiko , Koltunow Anna M. 
Published: September 2011

Abstract
The LOSS OF APOMEIOSIS (LOA) locus is one of two dominant loci known to control apomixis in the eudicot Hieracium praealtum. LOA stimulates the differentiation of somatic aposporous initial cells after the initiation of meiosis in ovules. Aposporous initial cells undergo nuclear proliferation close to sexual megaspores, forming unreduced aposporous embryo sacs, and the sexual program ceases. LOA-linked genetic markers were used to isolate 1.2 Mb of LOA-associated DNAs from H. praealtum. Physical mapping defined the genomic region essential for LOA function between two markers, flanking 400 kb of identified sequence and central unknown sequences. Cytogenetic and sequence analyses revealed that the LOA locus is located on a single chromosome near the tip of the long arm and surrounded by extensive, abundant complex repeat and transposon sequences. Chromosomal features and LOA-linked markers are conserved in aposporous Hieracium caespitosum and Hieracium piloselloides but absent in sexual Hieracium pilosella. Their absence in apomictic Hieracium aurantiacum suggests that meiotic avoidance may have evolved independently in aposporous subgenus Pilosella species. The structure of the hemizygous chromosomal region containing the LOA locus in the three Hieracium subgenus Pilosella species resembles that of the hemizygous apospory-specific genomic regions in monocot Pennisetum squamulatum and Cenchrus ciliaris. Analyses of partial DNA sequences at these loci show no obvious conservation, indicating that they are unlikely to share a common ancestral origin. This suggests convergent evolution of repeat-rich hemizygous chromosomal regions containing apospory loci in these monocot and eudicot species, which may be required for the function and maintenance of the trait.
A Wheat Homolog of MOTHER OF FT AND TFL1 Acts in the Regulation of Germination
Authors: Nakamura Shingo , Abe Fumitaka , Kawahigashi Hiroyuki , Nakazono Kou , Tagiri Akemi , Matsumoto Takashi , Utsugi Shigeko , Ogawa Taiichi , Handa Hirokazu , Ishida Hiroki , Mori Masahiko , Kawaura Kanako , Ogihara Yasunari , Miura Hideho 
Published: September 2011

AbstractSeed dormancy is an adaptive mechanism and an important agronomic trait. Temperature during seed development strongly affects seed dormancy in wheat (Triticum aestivum) with lower temperatures producing higher levels of seed dormancy. To identify genes important for seed dormancy, we used a wheat microarray to analyze gene expression in embryos from mature seeds grown at lower and higher temperatures. We found that a wheat homolog of MOTHER OF FT AND TFL1 (MFT) was upregulated after physiological maturity in dormant seeds grown at the lower temperature. In situ hybridization analysis indicated that MFT was exclusively expressed in the scutellum and coleorhiza. Mapping analysis showed that MFT on chromosome 3A (MFT-3A) colocalized with the seed dormancy quantitative trait locus (QTL) QPhs.ocs-3A.1. MFT-3A expression levels in a dormant cultivar used for the detection of the QTL were higher after physiological maturity; this increased expression correlated with a single nucleotide polymorphism in the promoter region. In a complementation analysis, high levels of MFT expression were correlated with a low germination index in T1 seeds. Furthermore, precocious germination of isolated immature embryos was suppressed by transient introduction of MFT driven by the maize (Zea mays) ubiquitin promoter. Taken together, these results suggest that MFT plays an important role in the regulation of germination in wheat.
Characterization of the time-dependentL-asparagine monohydrate crystal phase transition
Authors: de Menezes A. S. , Ardito F. M. , dos Santos A. O. , Moreno A. J. D. , Lima R. J. C. , Hayashi M. A. , Cardoso L. P. 
Published: September 2011

The high-temperature phase transition of single crystals of L-asparagine monohydrate was investigated by X-ray diffraction in association with Rietveld refinement and dilatometer measurements as a function of annealing time. The X-ray results showed that, for samples annealed at 343 K (or even 333 K) for 5 h, the expected anhydrous L-asparagine phase has been formed, monoclinic system (space groupP21), with lattice parametersa= 5.0677 (2),b= 6.7657 (2),c = 8.0742 (3) Å and β = 91.276 (4)°. The results obtained from measurements as a function of annealing time confirmed that the phase transition associated with loss of the water molecule is time dependent.
Brief exposures of human body lice to sublethal amounts of ivermectin over‐transcribes detoxification genes involved in tolerance
Authors: Yoon K. S. , Strycharz J. P. , Baek J. H. , Sun W. , Kim J. H. , Kang J. S. , Pittendrigh B. R. , Lee S. H. , Clark J. M. 
Published: September 2011

AbstractTranscriptional profiling results, using our non‐invasive induction assay {short exposure intervals (2–5 h) to sublethal amounts of insecticides [<lethal concentration 3% (LC3) at 24 h] administered by stress‐reducing means (contact vs. immersion screen) and with induction assessed in a time frame when tolerance is still present [∼lethal concentration 90% (LC90) in 2–4 h]}, showed that ivermectin‐induced detoxification genes from body lice are identified by quantitative real‐time PCR analyses. Of the cytochrome P450 monooxygenase and ATP binding cassette transporter genes induced by ivermectin, CYP6CJ1, CYP9AG1, CYP9AG2 and PhABCC4 were respectively most significantly over‐expressed, had high basal expression levels and were most closely related to genes from other organisms that metabolized insecticides, including ivermectin. Injection of double‐stranded RNAs (dsRNAs) against either CYP9AG2 or PhABCC4 into non‐induced female lice reduced their respective transcript level and resulted in increased sensitivity to ivermectin, indicating that these two genes are involved in the xenobiotic metabolism of ivermectin and in the production of tolerance.
Influence of hormone response elements (HREs) on ecdysteroid receptor concentration
Authors: Schauer S. , Azoitei A. , Braun S. , Spindler‐Barth M. 
Published: September 2011

AbstractTranscriptional activity of nuclear receptors is the result of transactivation capability and receptor protein concentration. The concentration of ecdysteroid receptor (EcR) constitutively expressed in vertebrate cells varies depending on the isoforms. Besides ligand binding and heterodimerization with ultraspiracle (USP), which stabilizes receptor protein concentration, degradation is regulated by interaction of the receptor complex with different ecdysteroid response elements (EcREs). Coexpression of EcREs significantly reduces ecdysteroid receptor concentration depending on the type of EcRE. Transcriptional activity and interaction with hormone response elements (HREs) as determined by Electrophoretic Mobility Shift Assay (EMSA) are often inversely related to receptor protein concentration. The complex regulation of receptor protein concentration offers an additional opportunity to regulate transcriptional activity in an isoform‐ and target cell‐specific manner and allows the temporal limitation of hormone action.