dataesr/scientific-paragraphs-categorization huggingface dataset:
Bacteriochlorophyll a is not synthesized. Cells are cytochrome c-oxidase positive, weakly positive for catalase as well as ureasepositive. Nitrate is not reduced  [1]. Intracellular inclusion bodies containing polyphosphate and polyhydroxyalkanoates are produced  [1]   The physiology of R. thermophilum DSM 16684 T was investigated in this study using Generation-III microplates in an OmniLog phenotyping device (BIOLOG Inc. , Hayward, CA, USA). The microplates were inoculated at 28°C and 37°C, respectively, with a cell suspension at a cell density of 95-96% turbidity and dye IF-A. Further additives were vitamin, micronutrient and sea-salt solutions. The plates were sealed with parafilm to avoid a loss of fluid. The exported measurement data were further analyzed with the opm package for R  [23, 24] , using its functionality for statistically estimating parameters from the respiration curves such as the maximum height, and automatically translating these values into negative and positive reactions.
Genome project history The genome was sequenced within the project "Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria" funded by the German Research Council (DFG). The strain was chosen for genome sequencing according the Genomic Encyclopedia of Bacteria and Archaea (GEBA) criteria  [26, 27]. Project information is stored at the Genomes On-Line Database  [12]. The Whole Genome Shotgun (WGS) sequence is deposited in Genbank and the Integrated Microbial Genomes database (IMG)  [28]. A summary of the project information is shown in Table  2.
Genome annotation Genes were identified using Prodigal  [35]  as part of the JGI genome annotation pipeline  [36]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Identification of RNA genes were carried out by using HMMER 3. 0rc1  [37]  (rRNAs) and tRNAscan-SE 1. 23  [38]  (tRNAs). Other non-coding genes were predicted using INFER-NAL 1. 0. 2 [39]  Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes -Expert Review (IMG-ER) platform  [40]. CRISPR elements were detected using CRT  [41]  and PILER-CR  [42].
Acknowledgements The authors gratefully acknowledge the assistance of  Iljana Schröder  for growing R. thermophilum DSM 16684 T cultures and  Meike Döppner  for DNA extraction and quality control (both at the DSMZ). This work was performed under the auspices of the  German Research Foundation (DFG)   Transregio-SFB 51 Roseobacter grant.
The GPS coordinates of houses surveyed and positive larval habitats of the two species were projected onto maps with ArcGis software (ArcGisH9. 2, ESRI). n inspected, number of potential containers inspected; % positive, percentage of containers infested with at least one larva or pupa of one species; Ae. aegypti only, containers containing only Ae. aegypti; Ae. albopictus only, containers containing only Ae. albopictus; mixed, containers infested with at least one larva or pupa of each species; *Container used to give drinking-water to pets. doi:10. 1371/journal. pntd. 0002590. t002 Mitochondrial DNA analysis for Ae. albopictus Sequence polymorphisms in the mitochondrial genes encoding for the nicotinamide adenine dinucleotide dehydrogenase subunit 5 (ND5) and for cytochrome oxidase I (COI) were explored in 95 individual Ae.
albopictus mosquitoes from CAR. We included in the analysis 22 specimens of Ae. albopictus from Franceville (1u379S, 13u349E) and Dienga (1u529S, 12u409E) in Gabon, collected at the larval stage in June 2013. DNA extraction and PCR amplification were done as described previously  [34]. Mosquito DNA extracts were used as templates to amplify a 400-bp fragment of ND5 and a 550-bp fragment of COI. PCR products were purified and sent to GATC Biotech (Konstanz, Germany) for sequencing. Sequences were cleaned, when necessary, with SEQSCAPE software 2. 5 (Applied Biosystems) and aligned with Clustal W  [40]. ND5 and COI sequences were numbered according to the reference sequences GeneBank ID JF309321 and JF309317, respectively. Basic sequence statistics, including the number of haplotypes per sample, the number of segregating sites (S), haplotype diversity, nucleotide diversity (p) and the average number of nucleotide differences, were computed with DnaSP 4.
albopictus specimens from two localities in Gabon. The analysis revealed the existence of only one haplotype Table  4. Immature mosquito sampling in southern Central African Republic. (H1) for each gene (Table  5 ). The sequence of the main CAR and Gabon ND5 (H1) and COI (H1) haplotypes perfectly matched the dominant haplotypes found in Cameroonian Ae. albopictus samples from a database (Table  5 ). When all the sequences were analysed as a unique sample, the Tajima D, Fu and Li F* and D*, and Fu Fs statistics for the COI gene were negative but not statistically significant so (Table  6 ). Negative values for these indexes indicate an excess of rare polymorphisms in a population and suggest either population expansion or background selection  [43].
We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced 'cybertype' notion.
In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.
DNA barcode sequencing DNA extraction was conducted in the the Canadian Centre for DNA Barcoding, Guelph on complete animals or part of the leg of the specimens preserved in 96% ethanol. Standard protocols of the Canadian Centre for DNA Barcoding were used for both DNA extraction and amplification. All specimen data are stored in the Barcode of Life Data System (BOLD) online database and are available also in the dataset DS-EUPCAV (http:// dx. doi. org/10. 5883/DS-EUPCAV), where they are linked to the respective Barcode Index Numbers clusters. This dataset contains sequences from ten species: E. cavernicolus Komerički & Stoev sp. n. , E. leostygis (Verhoeff, 1899), E. obrovensis (Verhoeff, 1930), E. grossipes (CL Koch, 1847), E. gloriastygis  (Absolon, 1916) , E. nudicornis, E. litoralis, E.
kahfi, E. transsylvanicus (Latzel, 1882) and E. tridentinus. In addition, all sequences were registered in GenBank (accession numbers KF715038-KF715064, HM065042-HM065044, HQ941581-HQ941585, JN269950, JN269951, JQ350447, JQ350449), one sequence of E. fasciatus (Newport, 1845) was recovered from GenBank (accession number AY214420). Two sequences from two Lithobius species were included as outgroups: L. austriacus (Verhoeff, 1937) (MYFAB442-11) and L. crassipes L. Koch, 1962 (MYFAB443-11). The final dataset comprises 39 sequences. Molecular delimitation of species was achieved by the implementation of the Automatic Barcoding Gap Discovery (ABGD) procedure as described in Puillandre et al. (2012)  and by the reversed Statistical Parsimony (SP) approach as suggested by Hart and Sunday (2007). A Neighbor-Joining (NJ) tree was built for visualization.
The extracted cDNA was utilised for library construction with an insert size of 250 bp. Finally, the library was sequenced on the Illumina HiSeq2000 sequencing platform (Illumina, Inc. , San Diego, California, USA) at BGI-Shenzhen using a 150bp pairend strategy to generate a total of 2. 5 Gb raw reads. Illumina HCS1. 5. 15. 1 + RTA1. 13. 48. 0 were applied to generate a "bcl" file which was then downloaded to local computers. Secondly, the "bcl" file was converted to qseq format using BclConverter-1. 9. 0-11-03-08. Finally, we separated individual sample data from multiplexed machine runs based on the specific barcode primer sequences, and converted the file format to fastq.
Micro-CT scanning The micro-CT scanning of one adult female specimen was performed at Bruker microCT, Kontich, Belgium, using a SkyScan 1172 system with the following settings: 40kV, 0. 43°r otation step, acquiring 839 projection images from 360°with a pixel size of 8µm. Prior to scanning, the sample was dehydrated in graded ethanol: 50%, 70%, 90%, 100%, for 2 hours in total, and then transferred to HMDS (hexamethyldisilasane) for 2 hours, and air dried. Reconstruction was done with the SkyScan software NRecon, using a modified Feldkamp algorithm, and adjusting for beam hardening and applying ring artefact correction resulting in 3865 cross sections in. bmp format, with image size 2000x2000 pixels. The video of 3D volume renderings was created with CTVox, using the flight recorder function, and saved as an AVI (Audio Video Interface) file.
The obtained data were processed through a transfer function where the different voxels with different grey value were (or weren't) made opaque and where the color was assigned to a certain grey value. The image stack is stored in GigaDB (Stoev et al. 2013) under a Creative Commons CC0 public domain waiver. The only software used was CTVox, a viewing software, not analysis software (although you could argue that viewing the images is also a way of analyzing them).
Eupolybothrus leostygis (Verhoeff, 1899) • BOLD dataset http://dx. doi. org/10. 5883/DS-EUPCAV • Plazi http://plazi. org:8080/GgSRS/html?CCEB9C62C87766E980DD858BC13468C8 • GenBank KF715047 • GenBank KF715051 • GenBank KF715053 • GenBank KF715060 • GenBank KF715055 • GenBank KF715056 • GenBank KF715057 • GenBank KF715058 • MorphBank 999021822&tsn=true Nomenclature Lithobius (Polybothrus) leostygis Verhoeff, 1899 -Verhoeff 1899: 451-452.
acherontis (Verhoeff, 1900), from Bosnia-  The 'cybertype' notion is herewith tested for the first time with the newly described taxon (Fig. 21 ), for which a rich image library has been created to allow its subsequent recognition, virtual manipulation and reuse. This image library, from which the 3D model is created, has been deposited in the GigaScience database, GigaDB, as a zip and a gzipped tar archive containing BMP images  (Stoev et al. 2013 ). The 3D model was converted into an AVI file, using the flight recorder of CTVox, and disseminated, along with the video of the living specimen (Fig. 22 ) through YouTube. According to Faulwetter et al. (  2013 ), a 'cybertype' should be linked to the original type material and be retrievable and freely accessible. We comply with these requirements by a) including a set of Darwin Core files along with the deposited volumetric data which describe the attributes and deposition of the physical type material and b) using a CCZero license and rich metadata to make the "cybertype" retrievable and reusable.
Furthermore, through the same set of Darwin Core files, the morphological data are also linked to the transcriptomic data at GigaDB, effectively extending the 'cybertype' concept and providing direct links to other data describing type material of the same species. GigaDB collects together all of the genomic and morphological data, and utilises the large computing infrastructure of the BGI and Aspera data transfer capabilities, able to host and deliver much larger and heterogeneous datasets than other repositories (Sneddon et al. 2012). Datasets are also issued with DOIs, which are discoverable through the DataCite metadata search engine and Thomson Reuters Data Citation Index, and can be integrated into a publication or independently cited. In addition to making data publicly available, it is crucial to provide rich metadata to enable data interoperability and reuse.
As there is only one transcriptome available, it is not possible to include additional 'factor' information. However, by including sequence reads, experimental design, protocols and processed data we were able to produce the maximum amount of (4*) MINSEQE compliant metadata (Brazma 2009). To maximise its interoperability, the metadata are also available from GigaDB in ISA-TAB format (Sansone et al. 2012). For volumetric data created by techniques such as micro-CT and micro-MRI, no community standards exist yet. The DICOM standard (Digital Imaging and Communications in Medicine, http://dicom. nema. org/) used by the medical community is not tailored for taxonomic purposes, thus its usefulness for this research field still has to be investigated  (Faulwetter et al. 2013 ). However, even in the absence of widely accepted standards, we provide rich metadata for the micro-CT data, based on the metadata descriptors at Morphosource (http://morphosource.
org). The same set of descriptors has been used by GigaDB, where we also applied the ISA-TAB format in order to ensure reusability and interoperability of the data (Sansone et al. 2012), describing all parameters and settings used to create the data. The data package of micro-CT deposited at GigaDB thus contain: • MicroCT image stack available in 2 different formats: • Several ZIP files, each contains 500 bmp images, the scanning log documentation file and Darwin Core type specimen data. • A single gzipped TAR archive of all 3876 bmp images, the scanning log documentation file and Darwin Core type specimen data. • Documentation of the scanning and reconstruction process through ISA-TAB metadata provided by GigaDB and the inclusion of the scanning log file with the 'cybertype'. • Specimen data in Darwin Core format and link to the location of the physical material and the transcritomic data through Darwin Core comma-separated value format (CSV) files: • Eupolybothrus_cavernicolus_sequenced_vaucher_ paratype.
Also, as a pilot project, we annotate all currently valid Eupolybothrus (Schizopolybothrus) species with their original descriptions that were extracted from the original publications through applying optical character recognition (OCR) and additionally tagged by using Golden Gate software  (Sautter et al. 2007 ). All species treatments are deposited at Plazi. This represents part of a more ambitious project aiming at digitization of all species descriptions and important taxonomic treatments of Eupolybothrus species that is currently being carried out in the framework of the pro-iBiosphere project (http://www. proibiosphere. eu). To create reliable links between the published sequence IDs and BOLD, an online dataset DS-EUPCAV was generated in the BOLD system, through which the respective Barcode Index Numbers (BINs) of the specimens barcoded for this study may be tracked (for the BIN concept see Ratnasingham and Hebert 2013).
Several different kinds of data belonging to the "cybertype" concept are treated in this study, from free text to sequence data, and from images to volumetric data. Questions have to be addressed such as whether a cybertype should only be restricted to morphological data, what data can be used to constitute a cybertype and whether a cybertype can be composite (i. e. consisting of several data types) or even distributed (different parts of the data residing on different physical servers). Further problems to be addressed are the lack of appropriate mechanisms for cross-linking molecular and morphological data, as well as the absence of global metadata standards and reliable data repositories for micro-CT image libraries. The metadata descriptors for micro-CT files used by the Morphosource and GigaDB repositories are a good starting point for that, as is the use of ISA-TAB to integrate everything together.
Whatever the answers to these questions, there is one mandatory requirement for data that we can already identify: discoverability and accessibility. With complex taxon descriptions such as the present one, we are entering new dimensions of data volumes that have to be managed properly to realise their true value. The deposition of large data pools in appropriate repositories is not yet straightforward, and such initiatives have started to emerge only recently. It is our task to ensure from the beginning that they do not develop into isolated data worlds but that they support community standards, describing the datasets in a way that they can be retrieved and cross-linked. Currently, even in modern taxon descriptions, different pieces of data are only linked through a central locus: the published article.
In a future, data-centric world of taxonomy, articles published through next generation journal workflows will become an even more important node in a linked network of data elements describing the taxon. These data elements have to be defined and made accessible through persistent identifiers -not unlike the traditional practice for physical specimens that are accessible through their museum accession number. In combination with rich metadata standards, taxonomy will thus open itself up to the semantic Web with its possibilities for intelligent, complex queries. In this study, we have taken a first step towards that direction. All data have been deposited in publicly accessible repositories, such as GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.
GigaDB in this example provides direct links between the genomic and micro-CT data, through a Darwin Core CSV dataset describing the type specimens, as well as capturing all of the metadata in the interoperable ISA-TAB format. Molecular data and images are annotated with rich metadata to ensure discoverability and reuse. Techniques such as micro-CT are, however, still in their infancy, and no standardised metadata schemas exist yet -a gap that needs urgently to be addressed by the community if we are to avoid a proliferation of isolated datasets. Taxonomy is at a turning point in its history. New technologies allow for creation of new types of information at high speed and in gigantic volumes, but without clear rules for communication standards, we will not be able to exploit their full potential.
g. , Penev et al. 2011, Costello et al. 2013, Drew et al. 2013) and following the recent developments in open access data publishing (Smith et al. 2013) we also propose a novel workflow in the Biodiversity Data Journal of producing, storing, evaluating, publishing and disseminating complex data sets. The large-scale data handling, management and storage was provided by the GigaScience GigaDB database (see Stoev et al. 2013), with transcriptomic and annotation data made publicly available to the most stringent metadata standards in INSDC (NCBI/EMBL/DDBJ) databases, GigaDB and the relevant datatype specific repositories.
Nature Genetics 44 (2): 121-126. DOI: 10. 1038/ng. 1054 • Sautter G, Agosti D, Böhm K (2007) Semi-Automated XML Markup of Biosystematics Legacy Literature with the GoldenGATE Editor. Proceedings of PSB, Wailea, HI, USA, 2007. 1-12 pp. URL: http://psb. stanford. edu/psb-online/proceedings/psb07/sautter. pdf • Smith V, Georgiev T, Stoev P, Biserkov J, Miller J, Livermore L, Baker E, Mietchen D, Couvreur TP, Mueller G, Dikow T, Helgen K, Frank J, Agosti D, Roberts D, Penev L (2013) Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal. Biodiversity Data Journal 1: e995. DOI: 10. 3897/BDJ. 1. e995 • Sneddon TP, Li P, Edmunds SC (2012) GigaDB: announcing the GigaScience database. GigaScience 1 (1): 11. DOI: 10. 1186/2047-217X-1-11 • Spelda J, Reip H, Oliveira-Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda -a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda).
Acknowledgements This project was developed in collaboration between several research institutions and driven by  Pensoft Publishers ,  BGI-Shenzhen and GigaScience. We would like to thank  Philippe Rocca-Serra  and the  ISA-Team  for help in producing the ISA-TAB metadata. We are very grateful to Biodiversity Data Journal editor  Bob Mesibov  ( Queen Victoria Museum and Art Gallery, Tasmania, Australia ), and the referee  Greg Edgecombe  ( NHM, London ) for their constructive comments and useful suggestions that greatly improved the manuscript. Special thanks to Henrik Enghoff who facilitated AK and PS' respective visits to the  Natural History Museum of Denmark , financially supported by the  European Commission 's ( FP 6) Integrated Infrastructure Program SYNTHESYS (DK-TAF ). All specimens were collected during cave fauna research projects conducted by the  Croatian Biospeleological Society  and funded by The  Krka National Park.
AK thanks all colleagues from the  CBSS  who assisted her in collecting the specimens. Stylianos Simaiakis  ( Natural History Museum of Crete ) kindly provided material from the type locality of E. litoralis for DNA barcoding. Pensoft has received financial support by the  EU   FP7 projects ViBRANT  ( Virtual Biodiversity Research  and  Access Network for Taxonomy , www. vbrant. eu,Contract no. RI-261532 ) and pro-iBiosphere ( Coordination & Policy Development in Preparation for a European Open Biodiversity Knowledge Management System, Addressing Acquisition, Curation, Synthesis, Interoperability & Dissemination , Contract no. RI-312848 , www. pro-StoevP et al. • Zimmermann D,  Randolf S, Metscher B, Aspöck  U (2011) The function and phylogenetic implications of the tentorium in adult Neuroptera (Insecta).
Description Description of holotype: Body length: approx. 30 mm (measured from anterior margin of cephalic plate to posterior margin of telson); leg 15 -22. 6 mm long, or 75% length of body. • SRA project accession http://www. ebi. ac. uk/ena/data/view/ERP003841 verbatimLatitude: 44°00'01. 1''N; verbatimLongitude: 16°00'58. 5''E; samplingProtocol: • ArrayExpress accession http://www. ebi. ac. uk/arrayexpress/experiments/E-MTAB-1859 hand collected; eventDate: 4 May 2010; individualCount: 1; sex: female; lifeStage: subadult; recordedBy: A. Kirin; institutionCode: CBSS; collectionCode: CHP420 • GigaDB http://dx. doi. org/10. 5524/100063 g. country: Croatia; stateProvince: Knin; verbatimLocality: NP Krka, village Kistanje, cave • GenBank KF715043 Miljacka IV (= Špilja kod mlina na Miljacki); verbatimElevation: 115 m; verbatimLatitude: • GenBank KF715049 44°00'12.
8''N; verbatimLongitude: 16°01'08. 8''E; samplingProtocol: hand collected; • GenBank KF715050 eventDate: 4 May 2010; individualCount: 1; sex: damaged female; lifeStage: subadult; • GenBank KF715059 recordedBy: A. Komerički; institutionCode: CBSS; collectionCode: CHP416 • BOLD dataset http://dx. doi. org/10. 5883/DS-EUPCAV h. country: Croatia; stateProvince: Knin; verbatimLocality: NP Krka, village Kistanje, • MorphBank 999021821&tsn=true Hydroelectric power plant Miljacka, cave Miljacka II; verbatimElevation: 115 m; • MorphoSource http://morphosource. org/index. php/Detail/SpecimenDetail/Show/ verbatimLatitude: 44°00'01. 1''N; verbatimLongitude: 16°00'58. 5''E; samplingProtocol: specimen_id/514 hand collected; eventDate: 21 October 2012; individualCount: 1; sex: damaged male; lifeStage: adult; recordedBy: A.