dataesr/scientific-paragraphs-categorization huggingface dataset:
This study contributes to the  French ANR   DISCOVER  project ( ANR-05-BDIV-010-01 ). V. Maire was funded by a  Ph-D  grant of French research ministry (MENRT). N. Gross was funded through a grant  FEDER, 'l'Europe s'engage en région Auvergne'. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Downloaded from Ni-filtered CuKα radiation. All data were collected in the 2θ range of 3 • -70 • , with a step scan of 0. 02 • and a counting time of 8 s per step. For each analysis, 10 mg of powdered sample was mounted into the central hole of a nominally zero-background Si-sample holder  (Li & Albe 1993). The identification of crystalline phases for each pattern was performed using crystal models reported in the commercial inorganic crystal structure database (ICSD) allowing a better fit to the observed Bragg reflection (2θ positions and relative intensities). For each crystalline compound identified, the lattice parameters, atomic positions and space groups were then used for the successive Le Bail and Rietveld refinements  (Young 1993; Le Bail 2005; Percharsky & Zavaliji 2005) , both implemented in the EXPGUI-GSAS software package  (Larson & von Dreele 1997; Toby 2001 ).
Changes in physical and mechanical properties Standard rock characterization methods were employed as a tool to assess the impact of decarbonation under the various conditions implemented in this study. While the absolute values may not be representative of the in situ values (since our physical properties were measured under ambient pressures and temperatures, since they could not be measured during the decarbonation experiments), our data aim to show the trends and relationships between the physical properties and the progression of the decarbonation under the different conditions (temperature, duration and f CO 2 ). Variations in physical and mechanical properties due to carbonate thermal decomposition have recently been reported in the literature   (Mollo et al. 2011 (Mollo et al. , 2012;; Heap et al.
oxfordjournals. org/ Downloaded from elastic moduli). The magnitude of the changes in rock physical properties at low levels of decarbonation (η dec = 0. 12) were greatly increased as temperature was increased. At 1200 • C the rock physical properties were drastically altered. Since the chemical changes at this stage are minimal, these changes can be explained by thermal microcracking, a result of the highly anisotropic thermal expansion of calcite. It is likely that thermal microcracking is more prevalent in 'tight' rocks such as SLN. As decarbonation progressed above η dec = 0. 12, up to η dec = 1. 00, further changes in rock physical properties were very modest. From these data we surmise that thermal microcracking exerts a greater influence on rock physical properties than decarbonation.
6, 1. 0, 1. 1, 1. 9, and 20 µg C-Ctx-1equiv. /kg fish, suggested that CFP by C-Ctx can be induced within a similar concentration range as P-Ctx-1  (CDC, 2009; Perez-Arellano et al. , 2005; Poli et al. , 1997). However, the above values where determined by various analytical and biochemical assays, thus making determination of a more reliable concentration range and thus threshold for the onset of CFP symptoms difficult. Above datasets all were gained from adult or juvenile intoxication cases, whereas there are only a very few limited descriptions of cases that have been associated with pregnancy. From the latter cases it was estimated that a contamination of approximately 1. 0 μg P-CTX-1equiv. /kg fish in conjunction with the consumption of 500g fish by the mother will lead to symptoms in the mother and to tumultuous movements of the unborn child.
In the current database, the amount consumed is either unknown or had to be estimated. the actual amount consumed however, can vary dramatically as in many moderate to severe intoxications patients react with immediate diarrhea or emesis and thus a major reduction of the meal consumed. As toxin concentrations, especially in crustaceans and fish, may differ substantially between different body parts/organs consumed  (lin et al. , 2004) , the analysis of meal leftovers can seriously underestimate/overestimate the amount consumed and thus the amount of toxins the patient was originally exposed to. Moreover, transport and storage conditions (frozen, cooled, uncooled) to the laboratory and type and time of storage until analysis of the meal upon preservation, the method of toxin extraction as well as the method of analysis will have major influence on the amount of toxins detected in the leftovers, leading to a poor estimate of the actual amount ingested.
Intoxication timetable: In many cases a detailed description of when the meal was consumed, the timing of the onset of first symptoms and a detailed description of the clinical progression and intensity of symptoms and adverse effects is missing. A detailed description of the latter would help to understand differences in patients as to onset and progression of adverse effects. Patient description: the present epidemiological and case datasets do not provide for a detailed individual patient descrip-consequence, none of the regulatory authorities in Asia-Pacific, USA, Canada, or europe declare themselves capable of estimating a tolerable daily intake (tDI) or a provisional tolerable weekly intake (PtWI). However, in view of the strong recurrent adverse reactions as reported (e. g. , by ciguatoxin patients, or the DA exposure associated temporal lobe epilepsy in a patient nearly a year after poisoning and after all symptoms had disappeared) the establishment of systematic long-term studies, preferably employing in vitro systems with human cells or artificial organs would be advisable.
Such a chain of custody was recently exemplified by a ciguatoxin intoxication of Germans exposed to contaminated fish from India (German Federal Institute for Risk Assessment, 2013). Simultaneously, medical primary care providers should be trained and provided with a national intoxication center where they can report intoxications as well as receive advice on treatment options. Database: From an epidemiological point of view and for risk assessors the establishment of a detailed database on toxicity of different marine biotoxins and their analogues is a prerequisite for any reasonable hazard identification and risk assessment. this database should provide information on the range of adverse effects, on immediate and long-term effects, on treatment and on dose-effect relationships as well as on patient specific traits (body weight, ethnicity, predispositions, etc.
Consumption: there are some attempts to collect data on consumption habits involving surveys and questionnaires, but still the amount and quality of this type of information is insufficient. The uniformity and accuracy of questionnaires and surveys are important qualifiers in the establishment of robust datasets. Moreover, some parameters of current questionnaires and surveys have to be reconsidered, e. g. , a survey per meal or per day would make more sense than the consumption patterns over several days, as the initial signs and symptoms of marine biotoxin poisoning occur within minutes to hours, when the concentration of toxin(s) is sufficiently high. Notably, most of the surveys and questionnaires do not aim to gain information on the meal size, the species consumed, or the processing status of the organisms used to make the meal.
It is noteworthy that based on the available data from oral dose toxicity studies, humans appear to be several fold more sensitive to the DA excitotoxic effects than rodent model species (lefebvre and Robertson, 2010). It is primarily for this reason that an incidence of ASP outbreak in Canada in 1987 was employed for risk calculations by eFSA  (eFSA, 2009c). the dose of DA leading to the symptoms was estimated from 9 poisoning cases (6 with mild gastrointestinal symptoms, 4 with dizziness, 1 with memory loss). the range of exposure was estimated from 0. 9 to 4. 2 mg DA/kg b. w. , therefore the eFSA CONtAM panel suggested 0. 9 mg DA/kg b. w. as lOAel for ASP toxin exposure  (eFSA, 2009c). A safety factor of 3 to derive a NOAel from the reported lOAel was employed, plus an additional factor of 10 to account for human variability, thereby establishing an ARfD of 30 µg DA/kg b.
w. Because DA can be converted to epi-DA during storage, the ARfD applies to the sum of DA and epi-DA. eFSA recommends a safety threshold of 4. 5 µg DA/g shellfish in order not to exceed the acute reference dose (AR-fD), which is lower than the maximum tolerated residue level of 20 µg DA/g f. w. (20 mg DA/kg f. w. ) effective in Canada, USA and the eU. the eFSA recommendation is based on an assumed consumption of a 400 g portion of shellfish, the ARfD of 30 µg DA/kg b. w, and a 60 kg adult person. Obviously, the calculation of the ARfD as well as the calculations based on the con-dependent on the relevant toxicological database, which in the case of marine biotoxins is primarily related to acute intoxications of a very few well documented human cases and a high number of surrogate animal tests with yet questionable relevance to humans (see above).
4 μg AZA per 60 kg person that would result in symptoms  (FSAI, 2006). As the latter risk estimate assumed equal potencies for all AZA analogues, the eFSA risk assessment on AZA (eFSA, 2008a) employed toxicity equivalent factors (TEF) that were based on very few mouse experiments using i. p. injection, suggesting teF as AZA1 = 1. 0, AZA2 = 1. 8, AZA3 = 1. 4, AZA4 = 0. 4, AZA5 = 0. 2 (see Fig. 1  for structures), whereby AZA1, 2, and 3 were considered to be the most prevalent AZAs found in mussels. the latter estimation was carried out as a provisional measure only, thus emphasizing that a better toxicity database is required in order to provide a more reliable risk assessment. Similarly, lack or extremely limited data on the chronic toxicity of AZA prevented the establishment of a tDI, again emphasizing the need for an improved and validated database for risk assessment.
Thirteen balloon soundings were conducted from Sodankylä during 17 January-6 February, involving CFH and FLASH-B hygrometers flown together with the COBALD backscatter sonde. The measurements of water vapour, obtained using two independent techniques, are in excellent agreement, which allows for using FLASH-B and CFH profiles as consistent and interchangeable data sets. The balloon measurements taken on 17 January capture freshly formed layers of ice PSC and concurrent uptake of water from the gas phase in great detail, providing an unprecedented highresolution "snapshot" of the process of ice PSC formation. Possible formation pathways of the observed PSC are discussed in the companion paper by  Engel et al. (2013b). Furthermore, balloon soundings provided evidence of irreversible dehydration by showing a permanent layer of reduced water mixing ratio between 19.
Acknowledgements. We thank the personnel of the  FMI-ARC  and RECONCILE coordination teams and the  Myasischev Design Bureau. Through the same contract, the aircraft campaign in Kiruna and  I. Engel  and  F. Wienhold , were partially funded by the  EC  as part of the  FP7  project  RECONCILE  ( 226365-FP7-ENV-2008-1 ). The balloon campaign in Sodankylä was partly funded by the  Lapland Atmosphere-Biosphere Facility (LAPBIAT). Stratospheric water vapour research in the FMI was supported by  Finnish Academy  under grant no. 140408. The work was partly funded by the  Russian Foundation for Basic Research  grants  12-05-31384 -Mol-a and  11-05-00475 -a. Work at the  Jet Propulsion Laboratory, California Institute of Technology , was done under contract with the  National Aeronautics and Space Administration.
Bioinformatics workflow Sanger trace reads from SSH libraries clones were processed in batch for base-calling using Phred  [44]  (kindly provided by Phil Green, University of Washington) under default parameters and trimming all sequence regions with a Phred quality score lower than 20. For the 454-FLX sequencing of SSH libraries, trace files (*. SFF) were first separated according to their MID adapters, and base-calling was performed by means of script packages sfffile and sffinfo, included in the Newbler software (454 Life Sciences). Sanger reads were deposited into dbEST-NCBI database (Genbank accessions JZ199499 to JZ200027), and the 454-FLX reads were uploaded through the European Nucleotide Archive Study ERP002162 (ENA/SRA-NCBI accessions ERX199134 and ERX199135). A hybrid assembly was conducted including the reads obtained from clone sequencing by Sanger and amplicon libraries from 454-FLX sequencing using the Newbler GS de novo Assembler ver.
2. 6 (454 Life Sciences), with the cDNA mode option, a minimum overlap of 30 bases and 90% similarity, and with the rest of the computational parameters set to default values. The final dataset of isotigs (putative distinct transcripts; an equivalent term to the widely used ''contig'' given by Newbler software) and singletons (single reads that were not included into isotigs after assembling) were annotated using the Blast2GO tool, a platform-independent suite for BLAST-search description annotation, gene ontology (GO) mapping and data management  [45]. BLASTX searches were conducted through the NCBI server, considering an E-value cutoff of 1610 23 , after the release of the annotated protein sequences of Crassostrea gigas genome sequencing project (NCBI BioProject PRHNA70283;  [46]  into the Genbank-NCBI non-redundant database.
GO mapping was done after the blastx search, and it included a final integration of the relational GO categories with the Annex option. The uniqueness of sequences per library was obtained from the final assembly using a program written in Perl that identifies isotigs resulting from sequences in both libraries. An enrichment analysis of ontology terms was performed for the isotigs and singletons that were represented in each library, according to a Fisher-exact test in the Blast2GO software. Transcripts from the maturing testis library were extracted from the total pool of transcripts, searching the descriptions and GO terms with the purpose of summarizing genes by the following functional categories: meiosis, spermatogenesis, sex-and transposon-related.
Gene expression analyses for meiotic transcripts Relative quantification of gene expression was performed on identified meiosis-related genes by qPCR on undifferentiated gonads, testis and ovary gonads, including both early and late maturation stages (Fig. 1 ). For each of these stages, six individual tissues were selected. Samples of individual tissues were processed in parallel for RNA isolation, DNAse treatment and cDNA synthesis, as detailed in  [2]. For qPCR analysis of gene expression, primer pairs were designed for each gene (Table  S1 ). The two reference genes used were chosen according to their stability assessed in a previous study on the same samples used in this work: ribosomal protein L8 (Genbank access JN034908. 1), and ribosomal RNA 18s subunit (  [2] ). qPCR reactions were done in duplicate on a 96-well thermal cycler (CFX-96, Bio Rad, Hercules CA) using a master mix containing 2.
Relative quantities for each, target and reference genes, were estimated with the equation RQ = (1+E) (Cq mean -Cq). Relative expression values (RE) were calculated from the ratio of relative quantity (RQ) of each individual sample with the equation RE = RQ t / RQ nf (t = target gene and nf = normalization factor = geometric mean of reference genes). Cq values above 35 were considered as no amplification. Statistical analyses were performed by one-way ANOVA after transforming RE to natural logarithms. Means were compared using Fisher's post-hoc test, using Statistica version 7 software (StatSoft; Tulsa, OK). Results are presented transformed back from the natural logarithms.
Microsatellite identification Microsatellites -single sequence repeats (SSR) -were screened in silico within the original unassembled reads using QDD2 software  [49]. It is implemented in Perl language and uses ClustalW2  [50]  and blast+  [51]  to align the reads in flanking regions and thus reducing redundancy of potential microsatellites, and Primer3 v1. 1. 4 [52]  was used for designing the best pair of primers for each microsatellite locus in the flanking regions. The minimum number of repetitions allowed was five for di-, tri-, tetra-, penta-and hexanucleotide repeats. This software was also used to determine those SSR that were polymorphic based on the variations observed on the single reads. Microsatellites with flanking regions, with the repeated motif masked out, were screened by blastn against the nr database of Genbank.
Subtractive library sequencing, assembly and annotation Combining Sanger and 454-FLX sequences, we obtained a total of 34,276 valid reads of at least 50 bp with a quality score over Q20. The number of Sanger reads meeting these quality criteria were 352 and 177 from the maturing testis gonad and inactive gonad libraries, respectively. With 454-FLX sequencing we obtained 19,876 and 13,857 reads, respectively. A hybrid assembly of all reads with the Newbler software resulted in 3,727 isotigs and 8,279 singletons. The N50 isotig size was 429 bp. We found 2,037 sequences (isotigs or singletons) with at least one significant blastx hit corresponding to 16. 9%; and within those, 51% of the top-blast hits were against proteins of Crassostrea gigas, a bivalve mollusk species with a recently sequenced genome  [46].
Functional annotation Subtraction efficiency was evidenced by finding that only 91 isotigs (from a total of 3,727) were built from both libraries. From those, 48 had at least one blastx hit and at least one significantly associated GO-term, and 3 had a blastx hit but no known annotation. Among the transcripts with annotation, there were different ribosomal proteins (n = 13), cytochrome synthase (n = 4), ATP synthases (n = 3), and NADH dehydrogenases (n = 2), among others. The low relative abundance of these highly and generally expressed genes further supports the success of the subtraction process. The remaining 43 transcripts had no blastx hit or annotation. Further proof of the subtraction efficiency for identifying genes specific to the biological conditions being compared was obtained with an enrichment analysis of ontology terms.
Identified microsatellites We identified 507 sequences with potential microsatellite loci, and successfully designed PCR primers for 310 of them. From these, a total of 272 pure and 38 compound microsatellites were found. A table of the microsatellite sequences, designed primers and the best-hit on Genbank is presented in Table  S5. One microsatellite found in a singleton sequence (ENA accession ERR224474. 16682) perfectly matched with the NsubA1B12 microsatellite from Genbank (accession no. FJ986341. 1).
Finally, the last gene annotated as involved in sex differentiation was fkbp52 (peptidyl-prolyl cis-trans isomerase), which codes for a co-chaperone for HSP90, and is known to be critical for proper development and differentiation of male reproductive organs in mammals  [97]. In the hermaphrodite nematode C. elegans, testis-specific transcriptomic profiles have been established in comparison to the soma  [98]. Testis-specific genes can be expressed by testisspecific promoters  [99, 100]  or by sex-specific splicing  [101]. The set of testis-specific genes discovered in N. subnodosus (Table  2 ) includes some of the genes that are expressed specifically in the testis in other species. For example, Kelch-like protein 10 was found expressed in mouse spermatids by in situ hybridization, and a search in the UniGene database indicated that most of the reported ESTs  (45 of 46)  for this gene were obtained from testis libraries  [102].
SSR in coding sequences Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. EST-SSRs have the advantage of being higher conservation across species than anonymous genomic SSRs, and hence are more transferable across taxonomic boundaries for genome mapping and comparative structural genomics  [122, 123]. Indeed, two of the EST-SSR identified in this work produced hits with two microsatellites described for other pectinid species, Argopecten purpuratus microsatellite B119 (Genbank accession JN799265. 1) and Chlamys farreri microsatellite clone CFFD148 (Genbank accession EF148946. 1) (Table  S5 ). Besides mapping, polymorphic SSRs in coding genes are of interest in a physiological context and hence considered as non-neutral for selection, since altered promoter expression and altered 3' stability, and slippage of transcription, might be affected by changes in repeat numbers  [122, 124].
Some of the microsatellites for which an annotation of the nucleotide sequence was obtained were found to be located in the 3' UTR of mRNAs, as a tri-repeat of TAT with a flanking region similar to the troponin I of Patinopecten yessoensis cDNA (Genbank accession AB008006. 1). Expansions or contractions of SSRs located in the coding region can lead to frame-shift mutations, premature stop codons and changes of amino acid sequences, although the most common repeat in the coding region of mRNAs is the trinucleotide (or their multiples). The region with the highest densities of trinucleotide repeats is the 5' UTR  [125]. The microsatellites identified in this study increase the panel of polymorphic microsatellites previously reported by  [126]  and  [127]  for the species, and could help to refine the genetic map in which 22 linkage groups were obtained in the consensus map  [72] , while the haploid chromosome number is 19  [128].
Acknowledgments We thank the technical assistance provided by  JoseL. Ramı ´rez ,  Susana A ´vila , and  Julio Hernandez Gonza  ´lez; and  Carmen Rodrı ´guez Jaramillo  and  Eulalia Meza Cha  ´vez for their technical support in histological processing. We also thank  Dr. Eduardo Romero-Vivas  for his advice on bioinformatics tools and server access, and  Dr. Gracia Gomez-Anduro  for providing with some facilities during libraries production. We gratefully acknowledge the reviewers ( Dr. Carlos Saavedra  and anonymous reviewer) for their important suggestions to improve the manuscript.
This work was funded by  CIBNOR  (grant  AC0. 16 ) and  CONACYT-CB-2011-1  (grant  166573 ). The first author is a Ph. D. student, financially supported by a  CONACyT  fellowship (number  204031 ). CAG wishes to thank  CONACyT  for a young investigator grant (number  133388 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
For Classical T Tauri Stars (CTTSs), the resonance doublets of N v, Si iv, and C iv, as well as the He ii 1640 Å line, trace hot gas flows and act as diagnostics of the accretion process. In this paper we assemble a large high-resolution, high-sensitivity dataset of these lines in CTTSs and Weak T Tauri Stars (WTTSs). The sample comprises 35 stars: one Herbig Ae star, 28 CTTSs, and 6 WTTSs. We find that the C iv, Si iv, and N v lines in CTTSs all have similar shapes. We decompose the C iv and He ii lines into broad and narrow Gaussian components (BC & NC). The most common (50 %) C iv line morphology in CTTSs is that of a low-velocity NC together with a redshifted BC. For CTTSs, a strong BC is the result of the accretion process. The contribution fraction of the NC to the C iv line flux in CTTSs increases with accretion rate, from ∼20% to up to ∼80%.