dataesr/scientific-paragraphs-categorization huggingface dataset:
Orthology analysis To determine orthology of the transcript sequences studied in detail (Table  1 ) we searched for homologs by reciprocal BLASTp. When reciprocal blast and domain analysis (see above) gave unambiguous identities (non-multigene families), gene names were attributed directly (Sulf, Aat, Asparaginase, Amt, UCP). For certain multigenic developmental regulator families, we added our candidate sequence and the retrieved cnidarian sequences to alignments from previously published studies kindly provided by authors (see File S2 and acknowledgements). Where no existing appropriate alignments were available, sequences from a range of eumetazoan genomes (Drosophila melanogaster, Lottia giganta, Strongylocentrotus purpuratus, Xenopus laevis or Homo sapiens, H. magnipapillata and N. vectensis) were aligned using MUSCLE, the best fitting model of evolution was determined using ProtTest2.
4, and phylogenetic analysis performed using PhyML3. 0. The trees are available in File S2. In cases where clear Hydra magnipapillata orthologs were identified, further analysis was performed using the Hydra vulgaris transcript dataset (HAEP) available at http://compagen. zoologie. uni-kiel. de/blast. html) [91]. The number of matching reads recorded in each separated cell population (endoderm, ectoderm and nanos-positive cells) was normalized with respect to total read number (File S5). For cnidarian-specific sequences, WegO1, WegO2, WegIE2, WegA2, WegD2, Zpd, had no recognisable homologs in Hydra or in Nematostella genomes. For WegIE1, WegD1 we identified single orthologs in Hydra: (listed in File S5).
B) Equivalent Z-score plot mapping a transcriptome dataset for Stbm-MO early gastrula-stage embryos against the Fz1-MO dataset. Dot colors correspond to the 4 classes defined in A. There is a strong correlation between expression responses in these two conditions, especially for classes 3 and 4 (green and grey dots, ie transcripts over-expressed in Wnt3-MO embryos). C) Z-score plot mapping the Stbm-MO transcriptome dataset embryos against the Wnt3-MO dataset. This illustrates that the 4 DGE classes defined on the basis of Fz1-Mo and Wnt3-MO responses situate largely but not exclusively in the equivalent zones of the Stbm-MO vs Wnt3-Mo graph. doi:10. 1371/journal. pgen. 1004590. g007.
S1 Primary list of transcripts differentially expressed in Wnt3-MO compared to non-injected embryos identified by DGE (z-score cutoff of +/2 5. 0), with putative identities, domain analysis, z-scores calculated for three MO-injected embryo conditions, accession numbers and DGE classes assigned in relation to Wnt3-MO and Fz1-MO responses (see text). (XLS) File S2 Phylogenetic analyses (using PhyML) to determine the orthology of the Clytia sequences studied in detail in this study : Antp family (HD02, Six4/5 and Gsc) ; T-box family (Tbx, Bra1, Bra2); Pax Family (PaxA), Notum family (NotumA, NotumO); Botch Family (Botch1 and Botch2); Dkk; DMRT-E; Forkhead family (FoxA, FoxC, FoxQ2a, FoxQ2b, FoxQ2c,); Frizzled/sFRP family (sFRP-A, sFRP-B, Fz1, Fz2, Fz3, Fz4); Dan family (Dan1); Hlh family (HlhIE1; HlhIE2); Mos family (Mos1, Mos2, Mos3); Erg; Myb; Znf subfamilies for ZnfO, ZnfA and Znf845.
For bZip, Asp, Amt, Sulf, phylogenetic analysis was not performed since only one Clytia homolog was found. Hydra orthologs are provided in File S5. Note that only the Clytia genes featured in this study were included, not other related Clytia sequences. See Materials and Methods for details of the datasets used. (DOC) File S3 Secondary list of differentially expressed sequences in Wnt3-MO compared to non-injected embryos identified by DGE with z-scores outside the +/2 5. 0 cutoff but greater than +3. 3/less than 23. 3. (XLS) File S4 Expression patterns of additional selected transcripts. In situ hybridization profiles for FoxQ2c (A); NotumO (B); WegO3 (C); Goosecoı ¨d (D); sFRP-A (E) and Tbx (F). FoxQ2c shows an IEtype pattern, NotumO, WegO3 and Goosecoı ¨d show O-type patterns, sFRP-A and Tbx show A-type patterns.
Acknowledgments We thank  C. Fourrage  and  A. Charlet  for their participation in some experiments, and  L. Lecle  `re,  R. Copley  and  M. Manuel  for constructive criticism of the manuscript. PL also thanks  L. & X Wang  for advice on changing graphic settings in the DEGseq Package,  L. Lecle  `re and  F. Gyoja  for providing alignments and sequences. We thank the  Observatoire de la Cote d'Azur  for use of their calculation capacity.
This study was funded by grants from the  ANR (Agence National de la Recherche)  project  DiploDevo ,  Coordinator M. Manuel  ( Paris ) # ANR-09-blan-0236-02 ,  ARC  grant  ARC1098  to TM, and core LBDV funding from the  CNRS  and  UPMC. AR obtained a PhD student fellowship from the  MRT (Ministere de Recherche et Technologie). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
File S1 Primary list of transcripts differentially expressed in Wnt3-MO compared to non-injected embryos identified by DGE (z-score cutoff of +/2 5. 0), with putative identities, domain analysis, z-scores calculated for three MO-injected embryo conditions, accession numbers and DGE classes assigned in relation to Wnt3-MO and Fz1-MO responses (see text). (XLS) File S2 Phylogenetic analyses (using PhyML) to determine the orthology of the Clytia sequences studied in detail in this study : Antp family (HD02, Six4/5 and Gsc) ; T-box family (Tbx, Bra1, Bra2); Pax Family (PaxA), Notum family (NotumA, NotumO); Botch Family (Botch1 and Botch2); Dkk; DMRT-E; Forkhead family (FoxA, FoxC, FoxQ2a, FoxQ2b, FoxQ2c,); Frizzled/sFRP family (sFRP-A, sFRP-B, Fz1, Fz2, Fz3, Fz4); Dan family (Dan1); Hlh family (HlhIE1; HlhIE2); Mos family (Mos1, Mos2, Mos3); Erg; Myb; Znf subfamilies for ZnfO, ZnfA and Znf845.
Introduction Publishing content on the Internet has become a daily task for a large number of users. People publish content on social networks, blogs, or on their own websites on a daily basis. The increasing availability of broadband connectivity has even prompted users to start hosting their websites themselves on small servers that are always on in their homes. Small inexpensive plug computers like the Raspberry Pi  [25]  allow users to set up a personal web server for as little as $30. Software solutions like FreedomBox  [15]  allow even inexperienced users to deploy their own websites on their plug computers within minutes. Traffic demands for most of these self-hosted websites may appear negligible. But experience has shown that even small websites can experience instant surges of traffic due to the accidental discovery of interesting content  [27].
62MB consisting of an average of 94 files per page, with an average size of 18KB each. The average lookup time on a DHT may significantly exceed the time required to download most of these files. Our extensive simulations on real data traces show instead that Behave can provide zero-hop lookup latency on 50% of the content indexed by an entire DHT. Moreover, mimicking the performance of a single Behave overlay with existing solutions such as FlowerCDN requires each node to participate in more than 10 gossip overlays.
org), and profiles with a small-footprint SQL Java database (http://www. h2database. com). Users can access Behave with any browser simply by configuring it to use localhost:8080 as a proxy server. This allows our implementation to handle all requests and serve them either using the behavioral cache, or by directly contacting the target server. We are also working on a Firefox-based implementation that leverages We-bRTC, as well as the browser's internal API (Mozilla's XPCOM). Despite being in an early design stage, our code is already available at https://github. com/ mgoessen/behave/. In the remainder of this section, we detail the concepts underlying the Behave architecture.
Evaluation Setting We evaluated Behave on two real-world traces provided by the Ircache-DITL 1  initiative-a web proxy farm with servers deployed at various US universities and research institutes. The first trace refers to January 9, 2007, the second to January 10 of the same year. Each records 24 hours of logs for approximately 1000 clients. After removing NAT endpoints, the traces contain, respectively, 4. 2M and 3. 8M requests from 982 and 1000 unique clients for about 2M and 1. 7M web objects with average sizes of 24. 3KB and 23. 7KB. Ircache also provides more recent datasets, but these only contain data for 150-200 clients. Due to the absence of caching information in the dataset, we assume that 46% the content is cachable, consistently with the data published by the HTTP Archive initiative  [17].
Similarly, we assume that all clients negotiate content in the same language. Even if the dataset does not contain such information, this is probably close to reality as the dataset records web accesses from US Universities. Finally, we assume that every client remains online during the entire experiment. Default parameters. Due to the large size of the datasets, we implemented a simulated version of Behave, which we configured as follows. We set the sizes of the RPS and clustering views respectively to v rps = 12 and v cluster = 25. We used a gossip period p g = 10min for both protocols and a profile-update period p u = 1min with a threshold of t = 5%. Finally, we set the profile size to 5000 elements and the cache size to 2300 with bloom filters that use respectively 20 and 12 bits per element.
Each point represents the hit rate in the previous hour of simulated time. Clearly, the DHT-based solution (indicated as Squirrel) constantly achieves a higher hit rate, but Behave still manages to offer a large fraction of the content available through the DHT. Moreover, its Behavioral cache index provides this content with zero lookup latency. Squirrel, on the other hand, serves a pointer to the content, or notifies of its absence, with a significantly higher lookup delay. The plot also shows the hit-rate obtained by the gossip-based overlay in Flow-erCDN (labeled as Flower-clusters) for different maximum numbers of clusters. The data shows that Behave's hit-rate is between that achieved by FlowerCDN's gossip overlays with a maximum of 10 and 20 clusters. However, the cost associated with Behave's gossip exchanges roughly equals that of FlowerCDN with four clusters (Behave nodes exchange profiles and cache indexes both in the clustering and RPS protocols).
This shows that a behavioral cache like Behave can be effective both as a complement and as an alternative to DHT-based solutions. tribution of Squirrel nodes on the other hand is a lot more spread out. A large number of nodes receive thousands of requests: more than 80% receive more than 10000 requests (data for FlowerCDN would likely be similar). To explain this behavior, we observe that in DHT-based approaches, each piece of content is managed by one or a few nodes. With power-law content distributions such as the web, this inevitably overloads nodes that are responsible for very popular content. Behave, on the other hand, naturally replicates content according to its popularity.
We adopt a similar signature-based approach in Behave. FlowerCDN  [10]  combines a DHT with gossip-based communities of nodes that focus on specific content. Unlike our approach, they form these communities on a per-site and per-location basis. This means that the communities associated with two websites remain uncorrelated even if they may contain common nodes. This prevents FlowerCDN from exploiting semantic links between websites. Maygh  [29]  takes advantage of the recent WebRTC and RTMP technologies to build a decentralized CDN without installing new software on clients. However, its approach requires intervention from website owners who must modify their websites in order to employ Maygh's technology. Moreover Maygh's archi-tecture relies on coordinator nodes that must be deployed by each participating website.
Acknowledgments This work was partially funded by the  ERC SG GOSS- PLE  project (204742) (http://gossple. fr), the  EIT/ICT-Labs AllYours project  ( CLD 13 021 ), and by the  French National Research Agency (ANR)  project  SocioPlug  ( ANR-13-INFR-0003 ) (http://socioplug. univ-nantes. fr). We would like to thank the  Ircache  project (National Science Foundation grants  NCR-9616602  and  NCR-9521745 ), and the  National Laboratory for Applied Network Research  for providing traces used in our evaluation. Finally, we are grateful to  Mohammed Alaggan ,  Stephane Bortzmeyer ,  Arnaud Jegou ,  Julien Stainer  and the  Firefox "Necko" networking team , for useful comments and discussions.
Bactrocera minax is a major citrus pest distributed in China, Bhutan and India. The long pupal diapause duration of this fly is a major bottleneck for artificial rearing and underlying mechanisms remain unknown. Genetic information on B. minax transcriptome and gene expression profiles are needed to understand its pupal diapause. High-throughput RNA-seq technology was used to characterize the B. minax transcriptome and to identify differentially expressed genes during pupal diapause development. A total number of 52,519,948 reads were generated and assembled into 47,217 unigenes. 26,843 unigenes matched to proteins in the NCBI database using the BLAST search. Four digital gene expression (DGE) libraries were constructed for pupae at early diapause, late diapause, post-diapause and diapause terminated developmental status.
However, its underlying molecular mechanism remains poorly understood. Although B. minax is a biologically interesting and economically important pest, genomic sequence information has not been widely documented. Up to April 18th, 2014, there have been about 20,255 Nucleotide sequences including 186 ESTs deposited in NCBI (http://www. ncbi. nlm. nih. gov/) for Bactrocera genus. The lack of genomic resources still remains a barrier for further study of this fly species. Next-generation DNA sequencing technologies are currently dramatically improving the efficiency of genetic and biological research  [30] , and will facilitate the study of important biological processes by means of mass expression profile analyses for non-model tephritids that lack genome database  [31] [32] [33]. In the present study, we have performed de novo transcriptome analysis using short read sequencing technology.
A library pool containing all of the developmental stages, i. e. , eggs, larvae, pupae and adult flies, was established and sequenced. More than 52 million reads with 4. 7 billion nucleotides (nt) were assembled into 47,217 unigenes. Using the transcriptome background, we selected and analysed pupae collected in November (early diapause, ED), January (late diapause, LD), April (post-diapause, PD) and diapause pupae treated with 20-hydroxyecdysone (diapause terminated, DT) for gene expression to evaluate global differences in transcript abundance across different stages. Large amounts of differentially expressed gene sets in the six pairwise comparisons of samples were analysed. Here we have presented comprehensive transcriptome and digital gene expression (DGE) expression profile data that provide sequences of 47,217 unigenes and yield novel insight into the molecular regulation mechanisms on pupal diapause development of an economically important agricultural pest, the Chinese citrus fly.
Preparation of materials To obtain an overview of B. minax genetic data, a mixed cDNA sample from different developmental stages was prepared and sequenced using the Illumina sequencing platform, including eggs, larvae, pupae and adults (Additional File 1: Table  S1 ). Samples were field-collected periodically at Sandouping (Latitude: 30. 821, Longitude: 111. 051) in Yichang, Hubei province, China. Adults were reared on sucrose and brewer's yeast at ~25ºC with a long photoperiod of 14L:10D  [34]. As opposed to the facultative diapause species (e. g. S. crassipalpis)  [35] , pupal diapause in B. minax is obligatory and cannot be terminated if directly exposed to high temperature or if organic chemicals are topically applied  [20]. However, diapause individuals can be rescued from developmental arrest with a topical application of 20-hydroxyecdysone, an endocrine trigger known to terminate insect diapause  [36] , and discriminated from diapause destined individuals by comparing the metabolic rate using a flow-through respirometry system with Expadata data logging software (Sable Systems International Inc.
Illumina sequencing and bioinformatics analysis The cDNA library was sequenced on Illumina HiSeq TM 2000 using paired-end technology in a single run (2×91bp). The raw reads from the images were generated by Illumina GA Pipeline v 1. 6. After filtering raw reads, transcriptome de novo assembly was performed with the transcriptome assembly software Trinity  [37]. After assembly, we then aligned those unigenes to database NR, Swiss-Prot, KEGG, and COG using BLASTX (E-value < 0. 00001). We performed GO annotation using Blast2GO program, a universal tool for annotation and analysis in functional genomics research  [38]. To further study genes' biological functions, KEGG annotation was also conducted  [39].
Analysis and mapping of DGE tags The tags were obtained after removing 3' adaptor sequence, empty tags (no tag sequence detected except 3' adaptor), low quality tags (tag sequence containing unknown nucleotide 'N'), and over-long/short tags and tags with only one copy number (perhaps generated by sequencing errors) from the raw data. All tags with CTAG and 17 bp tag sequence were mapped to our transcriptome reference database with no nucleotide mismatch. The unambiguous tags were annotated and calculated for the number of copies which were normalized to TPM (Transcript Per Million tags) following the normalization methods in AC't Hoen P et al. [41].
Illumina sequencing and data processing A total number of 58,334,980 raw reads was generated from the cDNA library (Table  1 ). The raw trancriptome data were deposited in the GenBank Sequence Read Archive (Accession: SRR1238396). After filtering raw reads, a total of 52,519,948 reads were assembled into 100,498 contigs with an average length of 363 bp. The contigs were then assembled into 47,217 unigenes including 8,981 distinct clusters and 38,236 distinct singletons after paired-end reads and realignment which showed an average length of 815 bp. This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GBIT00000000. The version described in this paper is the first version, GBIT01000000. To check the quality of sequencing data, we selected 14 unigenes and amplified their partial sequences by PCR using 14 pairs of primers.
Function Annotation and classification of assembled transcripts For the unigene annotation, we aligned the transcript sequences using BLASTX against the non-redundant (nr) NCBI protein database with a cut-off E-value of 10 -5. A total of 26,843 (56. 85% of all unigenes) sequences provided a BLASTX result (Additional File 4: Table  S4 ). The E-value, similarity and species distribution of the best hits in NR database are shown in Additional File 13: Figure  S1. More than 50% mapped sequences have strong homology with E-value less than 1. 0×10 -50 whereas the remaining homological sequences ranged from 1. 0×10 -5 to 1. 0× 10 -50 (Figure  S1A ). The percentage of high similarity sequences i. e. , higher than 80% is 18. 39% while the other matched sequences (81. 61%) showed a similarity ranging from 17% to 80% (Figure  S1B ).
Unigene metabolic pathway analysis To further understand the gene functions on the biological pathways involved, the assembled unigenes were subjected to the canonical pathways referenced in the Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway analysis. Based on the comparison with the KEGG database using BLASTX with an E-value cut-off of <10 -5 , a total of 18,711 unigenes with pathway annotation were assembled into 240 KEGG pathways. The majority of unigenes were clustered in the 'Metabolic pathways' (2,929, 15. 65%) followed by 'Pathways in cancer' (746, 3. 99%) and 'Regulation of actin cytoskeleton' (666, 3. 56%) (Additional File 6: Table  S6 ). Several unigenes identified belonged to prothoracicotropic hormone (PTTH) receptor signalling transduction  [45]  and steroid hormone biosynthesis pathways (Table  2 )  [46] , as well as circadian rhythm  [47].
Digital gene expression (DGE) libraries sequencing Four DGE libraries were sequenced and generated approximately 6 million raw tags in each library. Four raw DGE data (ED, LD, PD and DT) were deposited in GenBank Sequence Read Archive (Accession: SRR1238397). After removing low quantity tags, the number of tags for each sample ranged from 5. 78 to 6. 02 million (Additional File 13: Figure  S3  and Additional File 7: Table  S7 ). Among those tags, the total number of all tags mapped to genes distributed from 4. 87 million to 5. 34 million, and the proportion of these tags ranged from 83. 27% to 88. 60% in libraries. The distribution of total tags and distinct tags with different abundance categories, i. e. , different count numbers, were analysed to evaluate DGE data (Additional File 13: Figure  S4 ).
Discussion Transcriptome data analysis and genes identified in diapause related pathway From Illumina sequencing, we obtained 58,334,980 reads and assembled into 47,217 unigenes in B. minax. Among them, 56. 85% (26,843) unigenes were found homologous to functional genes encoding specific proteins in GenBank. As a member of Diptera, B. minax showed a close relationship with Drosophila, a model Diptera species whose genomic data is well documented  [53]. A similar distribution was found in another Tephritidae fruit fly B. dorsalis  [31]. From our research results, only 11 unigene sequences were annotated with recorded sequences of B. minax in Gen-Bank, which suggested that the transcriptome sequences provided a meaningful contribution to genetic data on B. minax. Many genes linked to insect diapause regulation were identified in reported pathways.
Conclusions In the present study, a transcriptome database has been produced on a large scale for B. minax using Illumina sequencing. Through our results, we have gained new insights into the genomics of this univoltine fruit fly and they can be used as a reference to provide comparative studies within the tephritids. Based on the transcriptome background, DGE analysis has contributed significantly to speedy disclosure diapause-specific candidate genes/pathways for this organism without complete genome sequences or other genetic tools/resources. It provides valuable data with regard to further investigation on molecular mechanism underlying the pupal diapause termination in B. minax. In addition, our data provides a substantial contribution to many other meaningful biological processes in molecular research on B.
Acknowledgements We are grateful to  Professor Xiaoguang Ma  ( Institute of Health Quarantine, Chinese Academy of Inspection and Quarantine ) for his assistance in measuring pupal respiration rate. We also thank the technical support for Illumina sequencing and initial data from  Beijing Genome Institute (BGI) at Shenzhen, China. This study was funded by the  National Natural Science Foundation of China  ( 31371945  and  31071690 ), Crop disease and insect pest monitoring and control program (2014),  Hubei Research and Development Funds  ( 2012IHA01302 ), and  International Atomic Energy Agency  (via Research Contract No. 17153  and  CRP 18269 ).