dataesr/scientific-paragraphs-categorization huggingface dataset:
362 The P/B ratio for the primary producer groups was derived from satellite estimates of 363 primary production and chlorophyll a concentration in the study area during the period 1998-364 2007. The microzooplankton P/B ratio is consistent with values that can be calculated from 365 data given in  Hansen et al. (1997). For the zooplankton groups included in the sWAP food 366 web model, P/B ratios were taken from previous studies (Table  A. 1). For the fish groups, the 367 P/B ratios were obtained from the regression given in  Banse and Mosher (1980) , which 368 relates the P/B ratio to mass at maturity (Mm) as: 369 (Mm) b + a = ) B P ( log log (8) 370 where a is 0. 44 and b is -0. 23. The values of the coefficients in Eq. (  8 ) were derived from a 371 meta-analysis of fish species in temperate and tropical regions and did not include organisms 372 that inhabit cold environments.
This paper is based on a workshop held in Oslo, Norway in November 2013, in which experts discussed how to reach consensus on the healthiness of red and processed meat. Recent nutritional recommendations include reducing intake of red and processed meat to reduce cancer risk, in particular colorectal cancer (CRC). Epidemiological and mechanistic data on associations between red and processed meat intake and CRC are inconsistent and underlying mechanisms are unclear. There is a need for further studies on differences between white and red meat, between processed and whole red meat and between different types of processed meats, as potential health risks may not be the same for all products. Better biomarkers of meat intake and of cancer occurrence and updated food composition databases are required for future studies.
Improving food composition databases In addition to reliable measures of meat intake, it is also vital to have an up-to-date and accurate overview of the composition of different red meats. Most countries track the composition of their food, but often at frequencies defined by their accessibility to direct funding or indirect food industry funding; typically within ~10 years intervals. Few national authorities have the resources to keep up-to-date with all the developments and advances in the current food supply. Europe has its food compositional analysis in the EuroFIR database (http://www. eurofir. org), which contains national data from 26 countries (New Zealand and Canada being the only countries outside Europe). In order to determine how red meat or processed meat is related to health or disease risk, it is crucial to have access to updated data on the composition of the consumed meat.
However, there may be a large variability between different pieces of red meat, due to breed/genetics, trimming, animal feed processing and choices, geographic feed origin, age at slaughtering and others, but also sampling procedures and analytical differences. For comparisons it is important to use a representative part of the carcass, such as the minced beef trimming standardized to 14-16% fat: this covers a large share of the edible part of the carcass (in Norway ~40%). It is also important to know whether the samples measured are representative for the entire country. Nutritional databases currently lack information about minimum and maximum values, or standard deviations of the measurements. Regarding the components measured, there is a lack of information on some nutrients in meat that may have health implications.
Differentiation into inorganic iron and heme iron seems scarce (see http://nevo-online. rivm. nl/Default. aspx for an exception). Plant components (chlorophyll and polyphenols) or their metabolites are typically not included; neither are possible toxins produced for example during a suboptimal fermentation of harvested forage (see  Versilovskis & De Saeger, 2010 , for an example of such a discussion). It is important that levels of present and emerging compounds suggestively linked to human diseases are all quantified and included in databases. This will make it more efficient to identify causal relationships.
Replacing nitrite with phytochemicals, as currently is being explored in the PHYTOME project, is just one example of a possible improvement. Collaboration with the meat industry and public health authorities is vital for a successful implementation of research results into the food supply chain, in order to minimize the health risks of red meat consumption. Box 4 Why should we keep eating red meat? Strong media coverage and ambiguous research results could stimulate consumers to adapt a 'safety first' strategy that could result in abolishment of red meat from the diet completely. However, there are reasons to keep red meat in the diet. Red meat (beef in particular) is a nutrient dense food and typically has a better ratio of N6:N3-polyunsaturated fatty acids and significantly more vitamin A, B6 and B12, zinc and iron than white meat (compared values from the Dutch Food Composition Database 2013, raw meat).
Method and materials The data presented in this paper have been retrieved from the Science Citation Index Expanded, accessed via Web of Science, published by Thomson Reuters. The keyword "ecology" has been used as the search term in the field of "publication name" and the time period was limited to 2003 to 2012 (ten years). 3,359 papers from Ecology were retrieved. Microsoft Office Excel and Microsoft Office Word were used to analyse the final data collected in order to generate tables, charts, and graphs.
To identify the h-index values of the prominent authors, we used the ''create citation report'' tool of the Web of Knowledge database. The information relating to the ''sum of the times cited'', "sum of times cited without self-citations", "citing articles", "citing articles without self-citations", ''average citations per item'', and ''h-index'' were noted down. VOSviewer is primarily intended to be used for analysing bibliometric networks. The program can, for instance, be used to create maps of publications, authors, or journals based on a co-citation network and also to create maps of keywords based on a co-occurrence network. VOSviewer (version 1. 5. 4) (http://www. vosviewer. com/), a freely available computer program is used for constructing distance-based maps based on co-occurrence data.
E. S. S. data format. To be able to deal with different data rates, depending on different run configurations or hardware upgrades, the trigger pace as well as the number of nodes used can be dynamically altered and adjusted accordingly. The H. E. S. S. DAQ allows the array to operate in different observation modes with different sets of telescopes at the same time using so-called SubArrays. The different modes include, but are not limited to, observation runs as well as calibration and maintenance runs. The detector configuration used during such a run is defined in a MySQL database and can be easily changed and adapted to specific needs. The flexibility of this approach allowed the commissioning of the newest telescope, CT 5, while the Phase I array (CT 1-4) was taking scientific data. To improve data taking efficiency and to reduce the possibility for human error, the H.
Acknowledgments The authors would like to acknowledge the support of their host institutions. We want to thank the whole  H. E. S. S. Collaboration  for their support. The support of the  Namibian authorities and of the University of Namibia  in facilitating the construction and operation of H. E. S. S. is gratefully acknowledged, as is the support by the  German 20th International Conference on Computing in High Energy and Nuclear Physics  ( CHEP2013 ) IOP Publishing Journal of Physics: Conference Series 513 (2014) 012003 doi: 10. 1088/1742-6596/513/1/012003Ministry  for  Education and Research (BMBF) , the  Max Planck Society , the  German Research Foundation (DFG) , the  French Ministry for Research , the  CNRS-IN2P3  and the  Astroparticle Interdisciplinary Programme of the CNRS , the  U.
To deal with multiple testings, the ANOVA p-values were then submitted to a False Discovery Rate correction. Genes with a corrected p-value ,0. 05, and more than a 2-fold change in transcript level were considered as significantly differentially expressed. BlastN analyses for the 20,885 spotted genes [2; URGI database] were performed to identify the matching gene models derived from the resequencing approaches by  Staats & van Kan [91; Broad Institute]. By this, the number of differentially expressed genes was reduced because incorrect gene models derived from discontinuous sequences were revised and furthermore previously non-matching ESTs could be mapped. The four gene lists were then pooled and cluster analyses were performed to highlight the different expression profiles encountered. For this purpose, the log2normalized intensities scaled by gene across the 16 hybridizations were clustered using Genesis tools  [102].
embnet. dkfz-heidelberg. de/) and the following protein sequences: B. cinerea LTF1 (481 aa; B0510_3555), A. nidulans NsdD (461 aa; AAB16914), and N. crassa SUB-1 (466 aa; NCU01154. 5). Amino acids that are identical in all sequences are shaded black, amino acids that are shared by B. cinerea and N. crassa or A. nidulans are shaded in gray. The nuclear localization signal (NLS) is highlighted in blue, the GATA zinc finger motif (PF00320) with the four conserved cysteine residues (indicated by asterisks) is highlighted in pink. doi:10. 1371/journal. pgen. 1004040. g001.
Acknowledgments We thank  Brian Williamson  for critical reading of the manuscript,  Sabine Giesbert  for discussion,  Gianina Ramos  and  Bettina Richter  ( WWU Mu ¨nster ) for technical assistance,  Jens Heller  and  Anne Viefhues  ( WWU Mu ¨nster ) for roGFP2 analyses,  Sylvain Baulande  and  Mathilde Duthieuw  (PartnerChip, http://www. partnerchip. fr)for NimbleGen microarray hybridizations, and the URGI fungal genomic annotation platform (http://urgi. versailles. inra. fr/About-us/Team/Fungal-genomics)for bioinformatics support.
asiaticum DSM 44297 strain. Genomic DNA was extracted from mycobacteria grown on Middlebrook 7H10 agar medium at 37°C under a 5% CO 2 atmosphere. A shotgun XLϩ library and 3-kb paired-end library were pyrosequenced on a 454_Roche_Titanium platform (Roche-454 Life Sciences, Boulogne-Billancourt, France)  (10). This project was loaded on a 1/4 region for each application on picotiter plates. The 454 sequencing generated 362,293 reads assembled into contigs and scaffolds using Newbler version 2. 8 (Roche, 454 Life Sciences). Contigs obtained were combined together using Opera software v1. 2  (11)  and GapFiller v1. 10 (12) to reduce the set. Finally, some manual refinements using CLC Genomics v5 software (CLC bio, Aarhus, Denmark) improved the genome. The draft genome sequence of M. asiaticum consists of 10 scaffolds of 106 contigs containing 5,910,460 bp, with an estimated genome size including gaps of 5,935,986 bp.
Its GϩC content is 66. 03%. Noncoding genes and miscellaneous features were predicted using RNAmmer  (13) , ARAGORN  (14) , Rfam  (15) , and PFAM  (16). Open reading frames were predicted using Prodigal  (17) , and functional annotation was achieved using BLASTp against the GenBank database (18) and the Clusters of Orthologous Groups (COG) database  (19, 20). The genome was shown to encode at least 81 predicted RNAs, including 3 rRNAs in a single operon, 51 tRNAs, 1 transfer-messenger RNA, and 26 miscellaneous RNAs. A total of 5,591 genes were also identified, representing a coding capacity of 5,458,539 bp (coding percentage: 91. 9%). Among these genes, 742 (13. 27%) were found to encode putative proteins and 881 (15. 75%) were assigned as encoding hypothetical proteins. Moreover, 5,537 genes matched a least one sequence in the COG database with BLASTp default parameters.
Background: The Syrian hamster (golden hamster, Mesocricetus auratus) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species. Results: A cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our Mesocricetus auratus Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat.
We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species. Conclusions: This Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species.
For instance, this species has been widely used in the studies of circadian rhythms  [15] , cardiomyopathy  [16] , aggression  [17] , reproduction  [18] , and sensory systems  [19]. Genotyping of Mesocricetus auratus is currently under way at the Broad Institute (NCBI-BioProject accession: PRJNA77669) but not yet published. So far, only 860 cDNA sequences from the Syrian hamster are available in the NCBI-dbEST database  [20] , where 728 sequences have been collected in the context of testis organs  [21]  and 125 sequences have been collected in the context of embryonic cells  [22]. More recently, while Schmucki et al. analyzed the liver transcriptome of the Syrian hamster with a focus on lipid metabolism  [23]  the data is not publicly available as of this writing. Drafts of the genome and transcriptome of Chinese hamster ovary (CHO) cells have recently been published  [24, 25] , although it should be noted that CHO cells represent cells in an immortalized condition and therefore will likely contain genetic mutations not present in natural conditions.
The current release of the CHO cell draft genome is composed of 109,152 scaffolds and 265,786 contigs representing a total length of 2,318,115,958 nucleotides. Preliminary gene annotation of the CHO cell genome was performed using vertebrate experimental data and crossspecies comparisons. The current release of the CHO cell transcriptome comprises 121,636 transcript fragments representing a total length of 179,731,611 nucleotides. More recently, Lewis et al. compared the genome of CHO cells and the genome of the Chinese hamster obtained from tissues, and they showed a significant proximity between these different conditions  [26]. Further efforts will be continued regarding the update of the CHO and Chinese hamster genomes and transcriptomes. The aims of our study were: (i) to provide to the scientific community a large panel of annotated mRNA sequences from the Mesocricetus auratus transcriptome; (ii) to provide new biological insights and knowledge about the Mesocricetus auratus species; and (iii) to use this data to allow the design of a future gene expression microarray.
Here we sequenced a normalized 39 mRNA fragment primed cDNA library produced from pooled RNA isolated from the major organs of adult female Syrian hamsters following strategies in common-use described elsewhere  [27, 28]. We reasoned that pooling a large variety of different organs of animals will provide a large pool of mRNA fragments to sequence and annotate. Sequencing reads were de novo assembled into contigs. The combined contig and unassembled read (singleton) dataset, designated as the Syrian hamster transcriptome, was annotated based on the mouse and rat transcriptomes. We identified the most highly covered and the most highly expressed transcripts in our Syrian hamster transcriptome and performed a functional enrichment analysis to identify which canonical pathways and biological functions were most significantly represented.
Library assembly Quality-filtered reads were assembled into contigs. Resulting contigs and unassembled reads (singletons) were quality filtered and contigs or singletons shorter than 50 bases were discarded. Among the 1,212,395 reads, 62,482 contigs and 111,796 singletons were generated. Figure  1B  shows the length distributions of the 174,278 combined contig/singleton dataset. The lengths of the singletons ranged from 50 to 614, with a median length of 187. 50 bases. The lengths of the contigs ranged from 50 to 4,054, with a median length of 473. 50 bases. We observed that most of the reads ranging between 75 and 400 nucleotides were assembled. Short reads are subject to noise and have low quality scores, making them more difficult to assemble. On the other hand, larger reads are difficult to assemble in this context because our library was targeted against 39 mRNA priming.
With respect to the mouse transcriptome reference, 4,314 fragments of our Syrian hamster transcriptome (10. 36%) aligned to 59 UTRs, while 6,493 fragments of our dataset (15. 59%) aligned to coding regions. In addition, 26,764 fragments of the Syrian hamster transcriptome (64. 26%) aligned to 39 UTRs (Figure  2A ). A further 4,080 fragments of the Syrian hamster transcriptome (9. 80%) aligned between 59 UTRs, coding regions, and 39 UTRs of the mouse transcriptome. Based on the rat transcriptome reference, 521 fragments of the Syrian hamster transcriptome (1. 98%) aligned to 59 UTRs while, 5,568 fragments of the Syrian hamster transcriptome (21. 20%) aligned to coding regions. In addition, 13,371 fragments of the Syrian hamster transcriptome (50. 92%) aligned to 39 UTRs (Figure  2B ). Finally, a total of 6,798 fragments of the Syrian hamster transcriptome (25.
89%) aligned between 59 UTRs, coding regions, and 39 UTRs of the rat transcriptome. As expected from the experimental design of our library, the majority of our Syrian hamster transcriptome sequences aligned to 39 UTRs of mouse and rat annotated transcripts. Regarding the publicly available mouse and rat genome datasets, 45,804 of our Syrian hamster transcriptome fragments aligned to either the mouse or rat transcriptomes, and 22,105 of these same sequences aligned to both transcriptomes simultaneously, suggesting commonly occurring transcripts. Our Syrian hamster transcriptome dataset was 65. 10% similar to the mouse transcriptome and 64. 46% similar to the rat transcriptome. These similarities increased to 74. 48% and 74. 26% for the mouse and rat respectively, when comparisons were restricted to coding regionsonly within those two reference genomes.
Comparison with the Chinese hamster species In order to contribute to the annotation efforts for the Chinese hamster (Cricetulus griseus) species, we aligned our Syrian hamster transcriptome to the current draft versions of the CHO cell genome and its transcriptome (Table  1 ). We found that 7,845 fragments in our Syrian hamster transcriptome aligned to the CHO cell transcriptome (Table  1 ) and 85,652 aligned to the CHO cell genome (Table  S2 ). On the other hand, 4,390 transcript fragments from the CHO cell dataset mapped to the Syrian hamster transcriptome (Table  1 ). Our aligned Syrian hamster transcriptome showed 85. 14% similarity with the CHO cell transcriptome, an expectedly higher value than what we saw for the same comparison with the mouse and rat transcriptomes.
Cross-species comparison In order to obtain further insights about the genomic evolution of the Syrian hamster we aligned our Syrian hamster transcriptome to 14 other transcriptomes, all of which are publicly available on the Ensembl database  [30]  (Table  1 ). This compendium of transcriptome references included the human (Homo sapiens), chimpanzee (Pan Troglodytes), gorilla (Gorilla gorilla gorilla), macaque (Macaca mulatta), and orangutan (Pongo abelii) sequences, as well as the ferret (Mustela putorius furo), guinea pig sequences (Cavia porcellus), and pig (Sus scrofa). As expected, the greatest number of aligned sequences occurred with the mouse and rat species transcriptomes (Table  1 ). The human and the non-human primate species also showed high numbers of aligned sequences, possibly due to the current high quality assembly and annotation of those genomes.
The CHO, ferret, pig, rabbit (Oryctolagues cuniculus), and squirrel (Ictidomys tridecemlineatus) species showed intermediary numbers of aligned sequences, while the guinea pig, kangaroo rat (Dipodomys ordii), pika (Ochotona princeps), shrew (Sorex araneus) and tree shrew (Tupaia belangeri) had the lowest numbers of aligned sequences. Of 174,278 Syrian hamster transcriptome fragments 50,433 aligned to at least one transcript reference while 61 fragments from our dataset aligned in common across all of these transcriptome references. Importantly, 76,175 of our Syrian hamster transcriptome fragments did not align to any of the 17 transcriptomes tested, nor to the CHO cell genome. It is important to note that some of the variability seen in our transcriptome comparisons may be due to differences in genome quality, assembly and annotation for the reference genomes tested.
The aim of this study For each of the top 50 expressed genes in the library, based on the mouse annotations, the Ensembl mouse gene identified, the associated gene name, description, and the number of count (number of time that the genes have been mapped by the reads) are indicated. doi:10. 1371/journal. pone. 0112617. t002 was to collect and annotate a large panel of transcripts regardless of tissue origin. These observations suggest that we have generated a representative transcriptome of the Syrian hamster. Therefore this transcriptome data could be used to generate a biologically meaningful first-generation expression DNA microarray for analysis of Syrian hamster response to disease, including those infectious agents known to alter immune and pro-inflammatory responses. Mechanisms of transcriptome regulation in the Syrian hamster, by way of these important pathways can now be monitored and analyzed further.
CHO cells have been used in a variety of genetic, cell biology, and pharmacology studies. They also are the mammalian cell line of choice for producing large quantities of recombinant proteins in large amounts or in or industrial laboratory settings. Although Chinese and Syrian hamsters are phylogenetically distinct within the rodent subfamily Cricetinae  [34, 35] , our data confirm that they are more closely related to one another as compared to other muroid rodents. Through our work, we have increased the number of contig sequences available in the public domain for the Syrian hamster from 860 to 174,278, where 50,433 (28. 93% of the Syrian hamster transcriptome) aligns to at least one transcriptome reference. Moreover, 85,652 (49. 14% of the Syrian hamster transcriptome) fragments have aligned to the draft CHO genome, leading to an overall total of 98,103 (56.