dataesr/scientific-paragraphs-categorization huggingface dataset:
Serapias vomeracea gene expression in symbiotic and asymbiotic protocorms As the genome of S. vomeracea has not yet been sequenced, a de novo assembly of S. vomeracea transcripts was generated and contigs were annotated by BLASTX searches against the A. thaliana (TAIR) and the P. equestris  (Cai et al. , 2015)  proteomes. Although de novo assembly was highly fragmented and only included sequences derived from asymbiotic protocorms, it represented a useful tool to identify genetic functions that were then validated by RT-qPCR. A list of contigs that, based on their annotation in A. thaliana, may be related to N uptake in S. vomeracea and their level of expression in symbiotic and asymbiotic protocorms can be found in Table  2. Two contigs annotated as ammonium transporters, named, respectively, SvAMT1 and SvAMT2, showed upregulation in symbiotic protocorms, but their induction was not statistically significant in the RNA-Seq experiment (Table  2 ).
Acknowledgements We thank  Nuria Ferrol  ( CSIC ) for kindly providing the S. cerevisiae isolates for functional complementation,  Enrico Ercole ,  Stefania Daghino ,  Antonella Faccio  and  Alessandro Lopa  for technical help and  Roland Marmeisse  for critical reading of the manuscript. We also thank the anonymous reviewers for their valuable comments. V. F. was supported by a PhD fellowship from  MIUR. The research was partly supported by local funding from the  University of Turin  ( 2014-2015 ) and was performed in the frame of the  IPSP research line 'Biodiversit a in sistemi agrari e forestali: basi genetiche, epigenetiche e molecolari  ' (AG. AP04. 025 ). The LMD system up-grade was possible thanks to the financial support of the  'Compagnia di San Paolo' (Torino, Italy). RNA sequencing has been carried out at the  US Department of Energy (DOE) Joint Genome Institute  (contract no.
Reads were mapped on TOSV reference sequences to produce long consensus contigs. The criteria for read validation were Ͼ50% mapping in length and Ͼ80% identity to the selected reference sequence ISS. Phl. 3 (GenBank accession numbers NC_006318 to NC_006320) for lin-eage A TOSV-5904242804; for the other 5 lineage B strains, sequences were mapped onto TOSV-AR 2007 (GenBank accession numbers EF656361 to EF656363). The open reading frames (ORFs) of the 6 strains encoded N (254 amino acids [aa]), NSs (316 aa), Gn (527 aa), Gc (502 aa) and L (2,101 aa). The full-length sequences of each gene were aligned with homologous TOSV sequences using the CLUSTAL algorithm. Neighbor-joining analysis (Kimura 2-parameter and p-distance models) was performed by MEGA6, with 1,000 bootstrap pseudoreplications. These six TOSV strains are available for academic research purposes in the collection of the European Virus Archive (EVAg).
Nucleotide sequence accession numbers. The sequences of TOSV-9028, TOSV-4906, TOSV-11368, TOSV-5963930705, TOSV-5904242804, and TOSV-54441132704 have been deposited in GenBank under the accession numbers KU904263 to KU904265, KU922125 to KU922127, KU925897 to KU925899, KU935733 to KU935735, KU935736 to KU933538, and KX010932 to KX010934.
ACKNOWLEDGMENTS This work was supported through funds received from (i) the  EU  grant  FP7-261504  EDENext, and this paper is catalogued by the EDENext Steering Committee as EDENext455 (http://www. edenext. eu),and (ii) the  European Virus Archive goes Global (EVAg)  project in the European Union's  Horizon 2020 research and innovation programme  under grant agreement  653316  (http://global. european-virus-archive. com/). The work of R. N. C. was done under the frame of EurNegVec COST Action TD1303.
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Erosion and accretion rates Annual erosion and accretion rates were assessed using diachronic PVLs for two periods (Table  2 ). Long-term erosion and  accretion rates were computed when several decades of data (aerial photographs and satellite images) were available. Longterm rates were assessed for 7 islets over durations of 30-79 years. The long-term erosion rate ranges from 0. 39 to 4. 9 m y À 1 while the long-term accretion rate ranges from 0 to 1. 7 m y À 1. Shortterm rates, over a time span of 4-9 years, were assessed for only 18 islets due to the lack of any images of the eastern reef barrier, while the rates for 3 islets (Faux-Tabac, Bois de Fer and Baye) were impossible to assess. The short-term rates obtained are logically substantially higher than those for the long term, with a maximum of 13.
There are not enough data for 1935-2004 to allow an in-depth analysis of surface area fluctuations linked to past extreme events. This very moderate loss of land during the past seven decades is confirmed by the close proximity of the shoreline to the beach rocks, which protect the coast from erosion. -Canard islet clearly increased in surface area from the 1930s to the 1990s, and has rapidly lost land since 2000. This has occurred despite the work carried out on the beach in the last few years to prevent erosion (sand supply, sandbag protection). -Kutomërë islet offers a spectacular example of a two-phase history, with a large and rapid increase in surface area from 1954 to 1976 (up to 28,245 m 2 ) followed after 1976 by a phase of rapid and steady decay leading to the virtual disappearance of the islet today (less than 2400 m 2 ).
Stage Intuitively, the relationship between the surface areas of the islets and those of the patch-reef would suggest that the islet area would be proportional to the patch-reef area. In fact, the data (Table  1 ) clearly show that these ratios vary considerably, from 0. 03% to 41. 12%, so that the surface area of an islet is completely uncorrelated with the patch-reef area (Fig. 20 ). A comparison of the LEI with the characteristics of the islets (Table  1 ) appears to show that there is no simple and direct correlation between the mobility or life expectancy of the islets and certain simple parameters such as their distance from the barrier reef, the distance to the nearest pass or the size of the sector directly exposed to swells. This lack of direct correlation is explained by the complexity of the interactions between processes acting on an islet segment and producing a specific change.
Acknowledgements This study was carried out as part of the  OBLIC  project ( Observatoire du littoral de Nouvelle-Calédonie ) supported by the  New Caledonia Government (DIMENC)  and by the  BRGM (French Geological Survey). Thanks to the  New Caledonia Government (DITTT, DTSI)  and the  South Province (DENV)  for providing the satellite images, orthophoto, and early aerial photographs, to the  SHOM (Service Hydrographique de la Marine)  for providing bathymetric data, and to  METEO NC  for cyclone and meteorological data. Thanks to  B. Sevin ,  S. Lesimple  and  M. Mengin  ( Geological Survey of New Caledonia ), to  Ilona Bossanyi  for improving the English, to the taxi-boat companies (" LHOOK", "Tieti Diving ") for their help during the field campaigns. Finally, we would like to thank the anonymous reviewers for their insightful comments and suggestions to improve this paper.
Two DNA genomic libraries were constructed using the Nextera sequencing kits: a paired-end library (insert size of 500 bp), and a mate-pair library, with a theoretical insert size of 8 kb. They were bidirectionally sequenced using a MiSeq sequencer with 250-bp read chemistry (Illumina). The removal of low-quality reads (Q Ͻ 30) and trimming of low-quality read ends (Q Ͻ 30), adapters, and cloning vector sequences resulted in 4,421,329 mate-pair and 2,928,198 paired-end reads, with an average length of 237 bp. To optimize the assembly, the reads corresponding to pADP-1 (GenBank accession no. U66917) were separated from the ones corresponding to the chromosome by using a homemade script. De novo assembly and scaffolding of both sets of reads were performed using Velvet 1. 2. 10 (5). They were optimized by (i) using the Velvet estimation of the insert size of the mate pairs (6,000 Ϯ 3,500 bp) and paired ends (450 Ϯ 50 bp) and by (ii) choosing the k-mer value generating the higher N 50 and the lower number of scaffolds.
To determine the genetic basis of the evolution of the atrazine degradation capacity that occurred during our evolution experiment, further studies will aim to compare this genome to the ones of the evolved populations. Nucleotide sequence accession numbers. This wholegenome shotgun project has been deposited at DDBJ/EMBL/ GenBank under the accession no. LKAX00000000. The version described in this paper is version LKAX01000000.
Recruitment and phenotyping of patients The institutional review board of the University of Lausanne, Switzerland approved this study. Participants were enrolled in the study after signing an informed consent form and being clinically assessed by their respective physicians. For the data collected through questionnaires, information was gathered retrospectively and anonymously by physicians who had ordered chromosomal microarray analyses performed for clinical purposes only. Consequently, research-based informed consent was not required by the institutional review board of the University of Lausanne, which granted an exemption for this part of the data collection. Overall cognitive functioning was assessed as published. 15 o better assess the phenotypic features associated with the 16p11. 2 220 kb BP2-BP3 rearrangements, we recruited and phenotyped 110 and 57 carriers of the 220 kb BP2-BP3 deletion (OMIM#613444) and duplication from 88 and 49 families, respectively (Supplementary Table  S1 ).
001. We compared available data on weight, height, body mass index (BMI) and HC for 77 and 39 unrelated deletion and duplication carriers, respectively (including published cases). The mean age of this group of patients was 16 years (range 0. 42-78 years, with 34 cases older than 18 years). The prevalence of the 16p11. 2 1] [42] [43] [44] [45] [46] [47] [48] [49]  The Signature Genomics cases were recently described in Jorgez et al. 50 Patients were identified through routine etiological work-ups of patients ascertained for developmental delay/intellectual disability in cytogenetic centers. The coordinates of the rearrangements' breakpoints (Supplementary Table  S2 ) were recognized by different chromosomal microarray platforms.
Lymphoblastoid cell lines and transcriptome profiling We had previously established by Epstein-Barr virus transformation lymphoblastoid cell lines (LCLs) from 16p11. 2 BP4-BP5 patients, as well as controls. The LCL transcriptome of 50 deletion and 31 duplication carriers, as well as 17 control individuals was previously profiled with Affymetrix GeneChips Human Genome U133+ PM 24 array plates (Affymetrix, Santa Clara, CA, USA). The results are deposited in the NCBI Gene Expression Omnibus under accession number GSE57802. The Robust Multi-array Average approach was used for the creation and normalization of the summarized probe set signals. We applied a nonspecific filter to discard probe sets with low variability and low signal, that is, detectable expression levels. Specifically, probe sets with both (i) signal SD4median of signal SD of all probe sets and (ii) larger signal4median of larger signal of all probe sets were retained as described in Migliavacca et al.
Quantitative reverse transcriptase-PCR For qPCR, 100 ng of high-quality total RNA was converted to cDNA using Superscript VILO (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Primers were designed using PrimerExpress 2. 0 software (Applied Biosystems, Foster City, CA, USA), with default parameters except for the primer-and minimal amplicon lengths, which were set at 17-26 and 60 bp respectively. The amplification factor of each primer pair was tested using a cDNA dilution series and only assays with amplification factors between 1. 75 and 2. 00 were retained. A representative set of samples was tested for genomic contamination. qPCR experiments were performed in triplicate using SYBR-Green (Roche, Basel, Switzerland) as reporter. The reaction mixtures were prepared in 384-well plates using a Freedom Evo robot (Tecan, Männedorf, Switzerland) and run in an ABI 7900HT sequence detection system (Applied Biosystems) using the following conditions: 50°C for 2 min, 95°C for 10 min, followed by 45 cycles of 95°C for 15 s and then 60°C for 1 min, after which dissociation curves were established.
Applicable normalization genes were included in each experiment to enable compensation for fluctuations in expression levels between experiments. Using SDS v2. 4 software (Applied Biosystems) the threshold and baseline values were adjusted when necessary to obtain raw cycle threshold (Ct) values. The Ct values were further analysed using qBase plus software (Biogazelle, Zwijnaarde, Belgium), which calculates relative expression values per sample per tested gene upon designation of the normalization genes and corrects for the amplification efficiency of the performed assay. We assessed by qPCR the RNA levels of seven DE genes belonging to the ciliopathy or PTEN pathway (BBS4 (MIM#600374), BBS7 (MIM#607590), BBS10 (MIM#610148), XPOT (MIM#603180), NUP58 (MIM#607615), PTPN11 (MIM#176876) and SMAD2 (MIM#601366)), and five others that map either to the BP4-BP5 (ALDOA (MIM#103850), KCTD13, MAPK3 (MIM#601795) and MVP (MIM#605088)) or the BP2-BP3 interval (SH2B1 (MIM#608937)) in LCLs from eight carriers of the 220 kb BP2-BP3 deletion, eight carriers of the 600 kb BP4-BP5 deletion and 10 control individuals.
The region directly surrounding the viewpoint is usually highly enriched and can show considerable experimental variation, thereby influencing overall fragment count. To minimize these effects, the viewpoint itself and the directly neighboring 'undigested' fragment were excluded during the procedure. In addition to this filtering, we modeled the data to apply a profile correction similar to the one described in Tolhuis et al. 72  using a fit with a slope -1 in a log-log scale. 73 Significantly interacting regions were detected by applying a domainogram analysis as described. 74 We selected BRICKS (Blocks of Regulators In Chromosomal Kontext) with a P-value threshold smaller than 0. 01 for both 'cis' and 'trans' interactions. To determine differentially interacting regions between the 16p11.
Enrichment analyses Gene annotation was obtained through BioScript (http://gdv. epfl. ch/bs). Protein interaction networks for the genes selected by BRICKS calling and from the list of interacting regions affected by the rearrangements were determined using STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) v9. 1 (http://string-db. org/). 76 We exploited Bioscript for Gene Ontology analysis (topGO) (http://gdv. epfl. ch/bs), DAVID GO and KEGG, OMIM Disease and KEGG coupled with Enrichr to assess if the chromatin-contacted genes were enriched in specific pathways and genes associated with Mendelian diseases  [77] [78] [79] [80]  (http://www. omim. org/down loads). The OMIM gene-set library was obtained directly from the NCBI's OMIM Morbid Map. 81 We exploited the SFARI Gene lists and scores (https:// sfari.
43 and 1. 24 μm, respectively; Wilcoxon rank-sum test, P = 1. 45e -17 ) (Figure  3c , Supplementary Figure  S4 ). We also examined published Hi-C (genome-wide conformation capture) and high-resolution Hi-C data from LCLs. Although they cannot confirm our chromatin connections given their limited resolution, they support a preferential three-dimensional proximity of these two regions  73, 75  (Figure  3b ). Concordant results were found in both human IMR90 fibroblasts and embryonic stem cells  26, 101  and mouse cortex and embryonic stem cells, suggesting the conservation of the structure of this topological-associated domain across species and tissues,  101  as recently shown for the topological-associated domain spanning the WNT6/IHH/EPHA4/PAX3 (MIM#604663; #600726; #602188; #606597) locus.
ACKNOWLEDGMENTS We thank the members of the  Lausanne Genomic Technologies Facility  and  Jacqueline Chrast  for technical help and  Catia Attanasio  for comments on the manuscript. NG is a grantee of the  Marie Heim Vögtlin  and the  Pro-Women  programs of the SNSF and the  Faculty of Biology and Medicine, University of Lausanne , respectively. KM was awarded a fellowship from the  Swiss Scientific Exchange NMS Program. IvdW was recipient of scholarships from the  Nora Baart Foundation and Erasmus European Union  Lifelong Learning Programme. AAA was awarded a scholarship from the  Saudi Arabian National Guard Health Affairs. SMW was supported by  SNSF  ( Swiss National Science Foundation )( P2ELP3_155365 ) and  EMBO  ( ALTF 755-2014 ) fellowships. SJ is recipient of a  SNSF Bursary Professor fellowship.
The contigs were annotated by a BlastX and BlastN comparison with GenBank. A single large scaffold was reconstructed for each genomic segment, integrating data from a total of 53,694 reads (71. 1% of the total reads). For a few segments, the 5= and 3= ends were determined using a Rapid Amplification of cDNA Ends (RACE) strategy, according to the kit manufacturer's instructions (TaKaRa Bio Europe/Clontech, France). The genome of MRDV, coding for 13 viral proteins, is composed of 29,145 nucleotides (nt), 1 nt longer than the recently reported complete genomic sequence of an Italian MRDV isolate collected in 2008 (accession numbers HQ637550 to HQ637559)  (5). For each segment, the conserved extreme 5=-(5=-AAGTTT TTT) and 3=-(CAGCT[A/G][A/T][T/C]GTC-3=) end sequences were retrieved and are similar to those reported, not only for MRDV isolates, but also for the other group 2 fijiviruses  (6).
At the nucleotide sequence level, the 10 genome segments of the French isolate show identity levels ranging from 94. 5% to 99. 2% with the corresponding segments of the Italian MRDV isolate, and from 95. 4% to 98. 8% with the partial sequences for segments S1 to S9 and the full sequence of segment S10 of the Spanish MRDV isolate LSP collected in 1999 (accession numbers LK392325 and LK392331 to LK392343)  (7). Furthermore, a comparison performed on the segment S10 sequences from six additional Spanish MRDV isolates collected from 2005 to 2010 (accession numbers JQ975001 and LK392326 to LK392330)  (7)  shows a within-group nucleotide identity ranging from 97. 6% to 99. 9%, which is in the same range of the nucleotide identity found between French isolate and MRDV LSP S10 sequences (98%). Focusing on the encoded proteins, all but three (P4, P7-2, and P8) show a very high level of amino acid identity (Ͼ98.
5%) between the French and Italian MRDV isolates. Remarkably, P4 and P7-2, which show only 97. 6% and 93% amino acid (aa) identity, respectively, with the Italian MRDV sequences, display 99. 4% and 99. 6% aa identity, respectively, with the proteins of the LSP Spanish isolate, which might indicate the existence of pseudorecombination events between MRDV isolates. In conclusion, the European MRDV isolates collected over a period of 10 years in three different countries appear to show a high level of homology, suggesting a low temporal and geographical variability of this poorly characterized virus. Nucleotide sequence accession numbers. The complete genomic sequence of MRDV reported here has been deposited in GenBank under accession numbers KU984966 to KU984975, corresponding to genomics segments 1 to 10, respectively.
To examine the possibility that the tegmina of Permotettigonia could display a leaf-mimicking camouflage, we compared it with morphometric descriptors distinctive of the modern leafmimicking katydids. As such morphometric descriptors were not already available; we performed a comprehensive morphological analysis of the tegmina of modern katydids (data set in Supplementary Table  1 ). Pterochrozinae is the only tettigoniid subfamily including only leaf-mimicking species  17, 18  , which are considered the most perfectly camouflaged katydids. This subfamily was therefore used to epitomize leaf-mimicking species. We carried out morphometric analyses in a set of representative modern tettigoniids, including Pterochrozinae and other subfamilies with univariate (non-linear regression and curve-fitting), bivariate (correlation between variables) and multivariate (Principal Component Analysis or PCA) approaches, based on size-independent measures (ratios) to focus on shape analysis.
Methods Preparation, observation and description. The specimen was prepared using sharp spines. Photographs were taken with a Nikon D800 digital camera with AF-MicroNikkor 60 mm 2. 8, with dry specimens and line drawings were prepared using a camera lucida on an Olympus SZX-9 stereomicroscope. Original photographs were processed using the image-editing software Adobe Photoshop CS6. Standard wing venation nomenclature is followed for Orthoptera  9. The diagnoses given in the main text are the same for the familial, generic and specific levels because all are presently monospecific. Morphometric analyses. Our approach is based on a data set based on 253 tettigoniid species that are representative of morphological disparity of macropterous forms. We also added the Cenozoic leaf-mimetic genus Archepseudophylla.
The structure of a morphospace is also determined by the choice of the characters to include, by the way these characters are coded, and by the method of visualization/construction of the space  36. The PCA ordination method  38  is a widely used multivariate statistics method which creates a low-dimension ordination that maximizes the variation between measured specimens  17, 19  , and creates a visualization by a projection (two or three axes, or 3D outputs). The PCA was performed using R software, package ADE4 (refs 39-41) and RStudio  42. Graphic displays have been modified in Adobe Illustrator CS6. The PCA was performed using R software, package ADE4 (ref. 41). Nomenclatural acts. This published work and the nomenclatural acts it contains have been registered in ZooBank, the proposed online registration system for the International Code of Zoological Nomenclature (ICZN).
Acknowledgements This work was supported by a grant from  Agence Nationale de la Recherche  under the LabEx  ANR-10-LABX-0003-BCDiv ,  in the program 'Investissements d'avenir'   ANR-11-IDEX-0004-02  ( Labex BCDiv 'DiversiteBiologique et Culturelle ') and by the  ATM 'Blanc ' MNHN 2015-2016. Many thanks to  C. Garrouste  for the reconstruction of Permotettigonia gallica and to  S. Fouche ( Musee de Lodeve ) for the photograph of the plant Taeniopteris sp. from Lodeve. Many thanks to  B. Warren  ( University of Zurich ) for judicious and important comments on the preliminary version of the paper. We also thank the  'Musee Zoologique de la Ville et de l'Universitede Strasbourg'  for giving access to their collections and  J. L. Rodeau  for discussions on non-linear regression.
Analysis To evaluate the performance of a telescope layout, analysis tools similar to the ones used in the current IACT experiments are employed. Results presented here use methods based on the MAGIC Analysis and Reconstruction Software (MARS)  [7] , the software package used by the MAGIC collaboration. The analysis performs the following steps: • Trace integration: Pixel charge and the time of arrival are extracted from sim_telarray output for each triggered event. This is performed in a 2-step process, in which a fit to the photon arrival times for the most significant pixels is subsequently used to search for dimmer signals in a reduced time window. • Image cleaning and parameterization: A traditional Hillas-like parameterization of the images is then performed. • Stereo reconstruction: Using the information gathered by all triggered telescopes observing an event, a stereoscopic reconstruction is performed that measures the energy and direction of the primary gamma ray.