dataesr/scientific-paragraphs-categorization huggingface dataset:
Common dolphin Common dolphins were sighted in shipboard blocks P, Q and W. Data were truncated at 2000 m perpendicular distance. The best model for detection probability included group size as well as perpendicular distance (Supplementary Appendix, Fig. A2 ). There was strong evidence of responsive movement (attraction -Supplementary Appendix, Fig. A1 , Table  A1 ). The estimated g(0) for Primary was 0. 55 (CV = 0. 17). The aerial survey analysis used estimates of detection probability for all ''patterned'' dolphins (see above). Estimated abundance of common dolphin was 56,221 (CV = 0. 234; 95% CI = 35,700-88,400); estimates for each block are given in Table  7. Highest estimated densities of common dolphin were west of Ireland (block R) and in coastal waters of SW France, Spain and Portugal (W).
Acknowledgements This work was supported financially by the  EU LIFE Nature  programme under Project  LIFE04NAT/GB/000245  and by the governments of all range states:  Belgium, Denmark, France, Germany, Ireland, Netherlands, Norway, Poland, Portugal, Spain, Sweden and UK. We thank the ship captains and crew, aircraft pilots and, especially, all the observers for their dedication and skill in ensuring that the surveys were successfully conducted. Appendix A. Supplementary material.
Pachon cavefish, which shows the most severe eye degeneration and depigmentation phenotypes is the most studied cave population and belongs to the ''old'' populations  [7]. In previous studies of the various cavefish populations, the genetic diversity was generally found to be lower in cavefish than in surface fish  [7, 19] , possibly resulting from small effective population sizes because of food and space limitations or from population bottlenecks due to sporadic environmental degradations  [20]. Obtaining large sequence datasets on Astyanax mexicanus surface fish and cave populations to assess their genetic diversity would therefore also help understand their evolutionary history. Here we have sequenced cDNA libraries from several different developmental stages of Astyanax mexicanus surface fish and Pachon cavefish.
The crucial need for long transcript sequences and the lack of a close reference genome led us to use the Sanger sequencing method. The inclusion of different developmental stages allowed scanning most of the developmental transcriptome, as well as the successive steps of eye development and degeneration in Pachon cavefish. About 200,000 clones were sequenced, providing a new resource for the Astyanax research community. These transcriptomic sequences were then used to compare the level of polymorphism in the coding sequences of the two Astyanax morphs at a larger scale than what was previously possible  [7] , and to identify fixed differences in coding sequences between surface fish and cavefish, which are candidates for being involved in some of their phenotypic differences.
Cleaning of the ESTs Sequences 198,380 Sanger ESTs (Expressed Sequence Tags) were obtained from the sequencing of the 8 libraries. The mean length of reads was 1,364 bp. 44 additional A. mexicanus mRNAs were also recovered from GenBank database (Table  S1A ). Sanger sequences were cleaned with Seqclean with the following options: i\ vector sequence pCMV_sport6, and ii\ contaminant sequences of yeast, E. coli536, and phage sequences from Genbank phage division. Then, low quality sequences at the extremities and very short sequences were removed with Prinseq  [21] , with the following parameters: window of 30, step of 5, minimal length 100 bp. A description of the libraries generated before and after cleaning is provided in Fig S1. ESTs sequences were submitted to Genbank under accession numbers FO203528 to FO393391.
Assembly and Annotation Procedure Assembly of Sanger sequences was carried out using TGICL software  [22]. This software uses the CAP3 assembler  [23]  that takes into account the quality of sequenced nucleotides into the computation of the alignment score. The choice for using TGICL software is justified by its good performance for de novo assembly of long ESTs  [24]. Moreover, TGICL generates less chimeric contigs than the more recent Newbler software  [25]. 44,145 contigs were generated, including 29,114 singlets. These contigs were annotated with the Biotoul platform pipeline, firstly performing BLAST against the following databases: i\ Reference databases: UniProtKB, RefSeq Protein and RNA, Pfam; ii\ TIGR fishes databases; iii\UniGene fishes species; iv\ Ensembl fishes Transcripts (a detailed list of databases and versions is given in Table  S1B ).
Gene ontology (GO) terms associated to each contig best hit (from TrEMBL, RefSeq or Swissprot databases) were analyzed using Blast2GO v. 2. 5. 1  [26]  to build a pie chart of their frequency distribution. The repeat sequences were detected by RepeatMasker  [27]. All those annotations were loaded into an EnsEMBL-like browser called Contigbrowser. Browsing Unigene Astyanax contigs and data mining by BioMart are available at http://genotoulcontigbrowser. toulouse. inra. fr:9099.
Polymorphism Analysis Non-singlets contigs were blasted against the zebrafish proteome (Zv9 assembly, downloaded from EnsEMBL  [28] ), the closest species with a sequenced genome, to annotate them. Only one contig per zebrafish hit was kept, to avoid artificial increase of polymorphism by counting twice the same polymorphic site detected in two different contigs. When multiple contigs blasted on the same zebrafish protein, the contig with the largest depth was selected. In total 6,431 contigs were retained. ESTs for these contigs were modified so that each nucleotide with a quality score below 20 was replaced by 'N' and they were then realigned to their respective contig by Megablast (parameters: opening gap cost 0, penalty for mismatch 22), which is a more stringent alignment algorithm than the assembling software.
This allowed regions where ESTs did not align properly to the contig to be discarded. Then in the aligned regions, ESTs were compared to the reference contig sequence (BLAST results were processed using the Bio::SearchIO module of BioPerl toolkit  [29] ). Polymorphism analysis was performed independently for cavefish and surface fish, and the minimal depth for each morph was set to be 4. With a depth of 4, two representatives of the minor allele had to be present at a given position to be considered polymorphic, and the minimal occurrence required for the minor allele increased with the depth D. Two conditions had to be fulfilled for the minor allele not to be discarded: firstly there had to be enough occurrences of this allele to eliminate the likelihood of an error; secondly it had to be present at a frequency that made sense considering the biological samples that were sequenced.
The expression pattern of the genes with radical mutations was searched for using the Zfin database  [31]. The enrichment for genes expressed in the eyes was statistically tested using Fisher's exact test. For genes with mutations which had occurred in the cavefish lineage, the presence of conserved domains was identified using the Prosite  [32]  and NCBI Conserved Domain databases  [33]. Several files containing a description of detected polymorphisms can be downloaded from the Astyanax browser. The same approach was applied to detect population-specific indels, but no such indels were found in the contig coding sequences aligned to zebrafish proteins. Orthology relationships were verified for all the cited potential candidate genes using Neighbor Joining phylogenetic analysis with Mega5  [34]  (not shown).
Results and Discussion Eight Astyanax Cavefish and Surface Fish cDNA Libraries Our aim was double: (1) to generate cDNA libraries from biologically relevant developmental stages for surface fish and cavefish as a clone resource, and (2) to generate transcriptome data for analysis of the genetic basis of cavefish evolution. Therefore, we extracted total RNA from 4 different stages of surface fish and Pachon cavefish embryos and larvae chosen according to the Astyanax mexicanus developmental staging table  [36] : (1) gastrulae to neurulae (6-16 hpf), (2) hatched larvae (24-36 hpf), (3) swimming larvae (48-60 hpf) and (  4 ) juveniles (2 weeks old). The first stage corresponds to the period in which the optic cup and lens placode are formed in surface fish and cavefish embryos. During the second stage, the cavefish but not the surface fish lens initiates apoptosis and arrests in differentiation.
Assembly and Annotation of the Sanger Sequences Approximately 19,000 clones of each non-normalized library, as well as 43,000 clones of each normalized library were sequenced by the Sanger method (Fig S1B ), and none of these libraries showed saturation (Fig S2 ), meaning that during the sequencing project when new clones were sequenced, they mostly corresponded to genes that had not been sequenced earlier in the project. After removal of the vector, polyA sequences and poorly sequenced regions, the resulting ESTs had a mean length of 624 bp. 189,933 ESTs from all libraries were used to build 44,145 contigs. The mean length of the contigs is 985 bp, and the mean depth is 6. 8. The contigs were annotated by BLAST analysis against several databases (see Methods and Table  S1B ). As a result, more than 90% of the contigs were annotated.
When blasted against the zebrafish proteome, they corresponded to parts of 11,197 different proteins (among the 41,693 EnsEMBL zebrafish proteins). These proteins are encoded by 10,058 different genes (among the 32,469 EnsEMBL zebrafish genes). If the numbers of genes and proteins are similar in zebrafish and Astyanax, these contigs would then represent more than a quarter of the Astyanax proteome and a third of its genes (Table  S2 ). Moreover, 17,152 contigs were annotated for gene ontologies, and these gene ontologies are varied, thus the contigs appear to be representative of the Astyanax embryonic/larval transcriptome (Fig. 1BC ). The Astyanax transcriptomic sequences are available through the web browser http://genotoul-contigbrowser. toulouse. inra. fr:9099. They were also submitted to Genbank under accession numbers FO203528 to FO393391.
Polymorphism Analysis To further exploit the Astyanax sequence resource, we performed polymorphism analysis (Fig. 2 ). We blasted the 15,031 non-singlets contigs against the zebrafish proteome and selected one contig per zebrafish hit. Accordingly, 6,431contigs were subsequently analyzed (see Methods). As expected, polymorphic contigs were built with a relatively high number of ESTs from non-normalized libraries: 65. 8% of the ESTs belonging to polymorphic contigs were derived from nonnormalized libraries, whereas non-normalized libraries provided only 54. 6% of the total number of sequenced ESTs. Polymorphism was found to be approximately twice as high in surface fish compared to cavefish (Fig. 2A ). This result confirms and extends with a large dataset the findings of previous studies based on a few microsatellites  [7].
It is thus possible that the 3 proteins mutated in CF and annotated with this GO term (pgls, eno3 and chia. 3) participate in this change of metabolism. Finally, the expression patterns of the 79 transcripts with radical substitutions between surface fish and cavefish were investigated in Zfin, the zebrafish reference database  [31]. Fifty-four of these transcripts had available expression patterns in Zfin. The analysis showed that 11 of the 21 ( = 52. 4%) transcripts with expression annotation and carrying a mutation in cavefish are expressed in the zebrafish eye, while only 1 of the 14 ( = 7. 1%) genes mutated in the surface fish lineage is expressed in this structure (Table  1 ). This difference is statistically significant (p = 0. 00972; Fisher's exact test). These 11 transcripts are: bcas2, fkbp3, mycbp, ndufv2, rpl13, rrp36, rrs1, eno3, capsla, sec13 and selt1a.
Conclusions We present here de novo Sanger sequencing of the embryonic and larval transcriptomes of Astyanax mexicanus surface fish and cavefish. This is the first large scale sequence resource available for the Astyanax research community, which will increase the usefulness of this model species in evodevo research. We also describe genetic variations within and between the two morphs. Polymorphism in cavefish seems to be much lower than in surface fish, and we describe 940 fixed differences between surface fish and cavefish coding sequences, some of them being potentially involved in adaptation to cave life. Among the proteins showing radical substitutions in cavefish, a third are potentially expressed in the eye, based on their expression patterns in the zebrafish in situ hybridization database.
The NW Mediterranean region experiences every year heavy rainfall and flash floods that occasionally produce catastrophic damages. Less frequent are floods that affect large regions. Although a large number of databases devoted exclusively to floods or considering all kind of natural hazards do exist, usually they only record catastrophic flood events. This paper deals with the new flood database that is being developed within the framework of HYMEX project. Results are focused on four regions representative of the NW sector of Mediterranean Europe: Catalonia, Spain; the Balearic Islands, Spain; Calabria, Italy; and Languedoc-Roussillon, Midi-Pyrénées and PACA, France. The common available 30-yr period starts in 1981 and ends in 2010. The paper shows the database structure and criteria, the comparison with other flood databases, some statistics on spatial and temporal distribution, and an identification of the most important events.
, 2008) , research for historical information  (Grimalt and Rosselló, 2011)  and the building of databases as sources of information  (Llasat et al. , 2010b (Llasat et al. , , 2011c)). The implementation of databases requires an enormous effort not always recognised. The initial problem lies in the 1200 million C (830 million for the Department of Gard, Languedoc-Roussillon) and 25 casualties. In Calabria, one of the severest events occurred in 1951, causing 101 victims and leaving 4500 homeless: road interruptions were so numerous that communications between coastal villages were possible only by sea. More recently, in September 2000, a local flood event with debris flow affected a campsite located in Soverato, leaving 13 casualties. In the Balearic Islands, the 6 September 1989 flash flood affecting the eastern coast of Mallorca produced 3 casualties and damage to tourist infrastructures, private houses, streets, roads and bridges; a total economic valuation of thousands of millions of pesetas in damage was made and the area received official help following its declaration as catastrophe zone.
Selected regions for building the preliminary floods database of HYMEX Figure  1  shows the regions selected for this study, while some of their main geographic and climatic features are showed in Table  1. The selected regions are Catalonia and the Balearic Islands in Spain, Languedoc-Roussillon, Midi-Pyrénées and Provence-Alpes Côte d'Azur in France, and Calabria in Italy. These regions were selected because they constitute a representative example of the NW Mediterranean region, and the authors of this paper have direct access to the information that has been introduced in the database, a factor that favours future homogenization of criteria and discussions, quality controls, and so on. There are two regions that are representatives of Mediterranean Spain, the third region is in the south of Italy and the last three are representative of the south of France, where flash-floods are frequent.
Comparison between different criteria and existing flood databases The first step when a new database on flood events is built is to define the criteria to select the events and data that will be included, as well as which could constitute added value of this effort in the light of the databases already existing. Nowadays, most of the studies focusing on the economic and societal impact in a region are based on global databases (Table  2 ), usually the Natural Hazards Assessment Network (NATHAN) of the reinsurance firm Munich Re, or the Emergency Events Database (EM-DAT) from the Centre for Research on the Epidemiology of Disasters of the Université Catholique de Louvain  (Barredo, 2009). These databases are also used to identify major events, drawing up comparative statistics and writing official reports that can be determinant in policymakers' decisions.
One reason is the large area covered by the databases, but the second one lies in the difficulty of obtaining data about damage and recovery from national and private insurance companies and national and local administrations. These databases provide very useful information about catastrophic events, but for regional or local studies it is necessary to consider it with caution because, usually, they have a built-in bias towards indirect sources or consider only the information provided by some insurance companies that do not cover the entire affected regions. A second question lies in the lack of unanimity of criteria for selecting events that can be due to various reasons, such as disagreement over the evaluation of damage from different points of view, the difficulty of obtaining quantitative information and the agenda.
Another possibility involves working with national or regional flood databases, such as those included in Table  3. The PRIM-NET database  (MEDDTL, 2011)  refers to all natural disasters in France and only includes catastrophic events; for this analysis only data for Languedoc-Roussillon Midi-Pyrénées and PACA have been considered. The Spanish floods database of the Civil Protection agency contains the major floods recorded in Spain from 1995 to 2010, but due to restrictive economic conditions it had not been updated at the moment for some regions, including Catalonia. In this case there are no specific criteria for deciding whether or not an event should be included in the database, though generally all the main events are recorded. The "Consorcio de Compensación de Seguros", a Spanish national reinsurance company  (Barredo et al.
, 2012 ) also has a database, but it is not for public distribution. For Italy, the national database of landslides and floods that occurred in the 20th century, named AVI, was available; data essentially came from newspapers, and historically affected areas were mapped at 1 : 100 000 scale  (Guzzetti et al. , 1994). The sources for building these databases were very heterogeneous, including press news, insurance data, reports from different companies or university groups and so on. Finally, it is also possible to find local or regional databases (Table  4 ). These have been usually developed within the framework of regional administration orders, or supported by public projects plus non-financed work (i. e. INUNGAMA), or, as for ASICAL, within the framework of collaborations between public research institutions (i.
e. CNR-IRPI and the University of Calabria). The advantage of these databases lies in the possibility of having more detailed information obtained from detailed surveys undertaken at regional or sub-regional scale. Table  5  shows an example of the most usual procedure followed for building local/regional databases: it is a long and hard process that is usually only evaluated in its complexity by those that have participated in similar processes. The ASICAL (Italian acronym for historically flooded areas in Calabria) floods and landslides database contains events since the 19th century  (Petrucci and Pasqua, 2008, 2009)  in the Calabria region (southern Italy). Data came from various sources such as newspapers, archives of national and regional agencies, scientific and technical reports, and so on.
For more recent cases, on-site survey reports drawn up during the event emergency management by the staff of either CNR-IRPI or regional agencies such as Civil Protection and River Basins Authority are also available, as well as information collected by interviewing the people involved and local administrators. This database has been continuously updated by both the results of local historical research  (Petrucci et al. , 2012)  and data coming from the daily survey of regional newspapers; currently it contains about 2300 records of floods that occurred in the most intensely studied period, between 1880 and 2011. In fact, even if flood damage data are available for oldest epochs, the historical research is usually focused on the period for which hydrological data also started to be available; for the majority of Calabria rain gauges this coincides with the end of 19th century/beginning of 20th century  (Polemio and Petrucci, 2012).
On the other hand, data on river flows are almost absent, mainly because of the torrential regimen of Calabrian water courses, locally known as "fiumare" and widely diffused throughout the entire Mediterranean basin. The INUNGAMA floods database refers to Catalonia (Northeast Spain) and was created in 2007  (Barnolas and Llasat, 2007a). This database also includes floods for the three main rivers in Catalonia, since the 14th century  (Barnolas and Llasat, 2007b) , and recently it has been updated to complete the present study. This database considers all the events that have produced any minor or major societal impact. The main source of information for the last 30 yr has been the press, because for non-permanent torrential rivers, the ones most frequently affected by floods, systematic river flow data are unavailable.
However, some scientific reports and hydrometeorological data have also been used to complete the information. Usually, insurances companies do not provide detailed information for each event, and only for some specific cases was it possible to recover it. Overall, for the period 1900-2010, this database contains 365 flood and flash-flood events, which are included in a GIS support. The University of Balearic Islands floods database contains heavy rainfall and flash flood events recorded between 1403 and 2011 for the islands of Majorca, Menorca, Ibiza and Formentera. It is updated yearly if information about events exist. The selection criteria were the existence of information about a flood event. The dates of the events and the affected basins and catchments were located using sources such as regional newspapers, local weekly papers, and regional and local administration reports and theses (i.
The common database The period 1981-2010 has been selected as reference in order to have a minimum period of 30 yr in length that could be considered as a climatic period. This restriction has allowed filling each local database with more information in order to achieve a "homogeneous" period in the sense that any heterogeneity would have been introduced as a consequence of non-systematic research. Taking as a departure point the databases presented previously for Catalonia (INUNGAMA) and the Balearic Islands (the UIB Database), Languedoc-Roussillon, Midi-Pyrénées and PACA (PRIM-NET) and Calabria (ASICAL) (Fig. 1 ), and after a completion process, a common database has been built. The final idea is to define a methodology that could be applied to other regions in order to obtain a homogeneous and complete Mediterranean flood database (the HYMEX Societal Impact database, FLOODHYMEX).
A common database called FLOODHYMEX has been built using EXCEL. For each event information about the following items were sought: -Date; it contains the first and last day of the entire event, i. e. from the initial day of heavy rainfalls to the day of the last floods. -Information about the event localization: -country, -region -administrative region affected by the event (i. e. Department of Midi-Pyrénées); -main areas affected by the event -using the internal administrative boundaries of each region in each country (county, municipality, etc. ); -overflowed river catchment, when known. -Kind of event: floods (FL), flash floods (FF), landslides (LS). Usually the identification of flash flood is furnished by the data provider; on the other hand, all the events that last one day or less are considered as flash flood.