dataesr/scientific-paragraphs-categorization huggingface dataset:
Origin of the Research Teams Involved in the Publications If we refer to Figure  4 , we can notice that the main contributors to the knowledge of L. lactis come from France, The Netherlands and the USA. But, this figure hides three facts: • Firstly, for the analysis, we only kept the first affiliation mentioned in the databases. If this choice is not problematic for the years between 1991 and 2004-2006, we slowly observed thereafter the implication of an increasing number of research teams in many articles, especially from The Netherlands and France. As a consequence, the first affiliation can appear reductive in many cases.
lactis after its taxonomic re-affiliation. To our knowledge, such work has never been conducted in this specific scientific field. The methodology we followed was based on the exploration of the SCOPUS database, followed by the specific examination of each individual article. This is probably the main limitation to our work. Other works published on similar subjects chose the PubMed database  [7]  ( Falagas et al. , 2006  [11]  ) which is perhaps more exhaustive. Indeed, we observed that some articles (at that time, no more than five) were not present in the SCOPUS base. As these documents were found fortuitously, we have no idea of the real number of articles which have not been included in the database. But if we consider the number of citations obtained on "Lactococcus lactis" (2535), it is difficult to imagine that the missing number of articles would fundamentally change our observations.
Transcriptome resequencing for SNP discovery Pyrosequencing and de novo transcript assembly of RNA from seedling tissues of two contrasting faba bean lines -NV643-4, a partly inbred line derived from the white flowered, white hilum Polish variety 'Albus' and NV648-1, a derivative of the ICARDA Bean Pure Line 'BPL10 0 , a coloured flower, black hilum inbred line yielded 17 397 and 16 041 contigs >200 bp in length for NV643-4 and NV648-1, respectively. From amongst these 5562 and 5534 contigs of NV643-4 and NV648-1, respectively, aligned to contigs from the other V. faba line as well as to at least one putative gene of M. truncatula. These transcript assemblies are available from the GenBank Transcript Sequence Assembly (TSA) repository under the accession names GARZ00000000 (NV643-4) and GASA00000000 (NV648-1).
Discussion Emergence of V. faba from 'orphan legume' status In the space of just over 1 year, faba bean entries in GenBank have gone from 5000 EST reads  (Ray and Georges, 2010)  to multiple transcriptomes  (Kaur et al. , 2014a,b; this study). Like pigeon pea, groundnut, lentil and other legumes, there is now a linkage map available with a density of marker coverage appropriate to most currently available RIL mapping populations. Legume crop species now enjoying low-medium density SNP coverage of their genomes include cowpea  (Muchero et al. , 2009) , common bean (Cort es et al. , 2011), chickpea  (Hiremath et al. , 2012) , lentil  (Sharpe et al. , 2013) , pea  (Deulvot et al. , 2010)  and faba bean (this work). outcrossing rate, which suggests that these markers will be broadly useable in each of the main recognized seed size based gene pools  ('major', 'equina' and 'minor').
, 2013; Khazaei et al. , 2015)  and a novel anthocyanin pigmentation locus, ssp1  (Khazaei et al. , 2014b). Similarly, SNP markers from this study used to generate the linkage map for population 4 (Table  4 ) have been found linked to a novel dwarfing locus, Dwf1 (K. Khamassi, K. Gostkiewicz, and D. M. O'Sullivan, Unpublished data) and associated with frost tolerance  (Sallam, 2014). Furthermore, to facilitate redesign of individual markers to suit existing laboratory set-ups and locations not easily served by KASP chemistry and commercial genotyping services, an interactive database-driven website (O'Sullivan and Green, 2012) has been set up to allow users to click from a marker name/location through to a choice of viewing or downloading the original sequence alignment on which the SNP assay design was based as well as accessing clustering profiles, genotype scores and links to any associated references.
RNA library preparation and sequencing RNA was extracted from complete 7-day-old seedlings of part inbred line NV643-4 (Albus) and inbred line NV648-1 (BPL10) using the Qiagen RNeasy Plant Mini Kit, and sequenced using Roche 454 GS-FLX Titanium chemistry. Raw reads were assembled in gsAssembler, based on Newbler v2. 3, available free from Roche Life Sciences at http://454. com/products/analysis-software/ index. asp (Anonymous, 2010). CDS, whole transcript and protein sequences from M. truncatula were obtained online from the M. truncatula Genome Sequencing Project, led by the International Medicago Genome Annotation Group (IMGAG). Version Mt3. 5 (Data freeze: 12/31/ 2009, Assembly release date: 02/10/2010, annotation release date: 05/27/2010) of the annotated genome of M. truncatula, consisting of 8 chromosomes and some unanchored BACs was downloaded from http://www.
SNP discovery and validation Assembled contigs from NV643-4 and NV648-1 were aligned to each other and to transcript sequences of M. truncatula using BLASTn. All contigs which gave unique reciprocal best hits over at least 100 bases at a BLASTn cut-off of E À30 in the respective faba bean transcriptome assemblies and to a single predicted M. truncatula gene over more than 100 bases were selected for further analysis. The complete contigs of each NV643-4:NV648-1 pair were aligned using ClustalW  (Chenna et al. , 2003)  and alignments containing SNPs more than 50 bp from either end of a contig were flagged for marker development. For each SNP, a consensus sequence with the target SNP and at least 50 bp either side of it was then searched against the database of M. truncatula pseudomolecules v.
SNP-marker quality filtering Clustering of alternate homozygous SNP alleles and heterozygous genotypes was manually inspected using LGC Genomics SNP viewer. Each SNP assay was scored on a I-IV scale according to tightness of clustering and the number of missing data calls. As an additional criterion on which to rank assays, gene diversity, often referred to as expected heterozygosity, a measure of how informative individual assays are, was calculated as 2pq where p is the frequency of the first allele and q (the frequency of the alternate allele). Lines or markers with more than 6% no-calls were excluded in an iterative process. Markers were regarded as very skewed and removed, if either one of the homozygous parental alleles was absent or the homozygous to heterozygous ratio was >2. 1 or <0.
Acknowledgements We would like to acknowledge funding from the  Defra Pulse Crop Genetic Improvement Network and Technology Strategy Board  grant  TS/I001301  to DOS and JET. We are grateful to  Peter Smith  of  Wherry & Sons Ltd. for access to mapping populations and to  Melanie Febrer  and  Jane Rogers  of  The Genome Analysis Centre (TGAC), Norwich  for generating the NV643 and NV648 transcriptome sequence data sets.
1. A Measurement of a linear polarizer To evaluate the overall system performance we measured the Mueller matrix of a linear polarizer (a commercial grid polarizer) rotated at various orientations respect to the plane of incidence. The polarizer was placed after the PSG. Since the Mueller ellipsometer was set in the reflection mode, a gold mirror was placed on the sample-holder. The Mueller matrix of the polarizer was obtained multiplying the matrix of the system polarizer-mirror by the inverse of the matrix of the mirror measured without the polarizer. The results corresponding to a wavenumber of 1500 cm -1 are shown in Fig. 6. Spectra was recorded with 16 cm -1 resolution and 32 integrations. In those conditions, according to data in Fig. 5  and Fig. 6  the uncertainty due to random noise in Mueller matrix elements is expected to be approximately 0.
Acknowledgements The authors wish to express their acknowledgment to  Dr. Y. Bonnassieux , and  Dr. P. Bradu  for their help in finding funds and providing part of the components. Moreover, the authors wish to express their gratitude to  Mr. D. Clément ,  Mr. C. Jadaud  and  Mr. F. Farci  for their help in designing and building the nonstandard opto-mechanical pieces used. The development of the broadband Mueller ellipsometer was a project included in the Master's  Program at Ecole Polytechnique. The authors, wish to thank  Mr. R. Landon , supervisor of one the programs, for his help in communication and integration of students in the project.
Epidemiological and clinical observations The two areas studied have dissimilar histories in terms of Chagas disease transmission intensity. Vector-borne T. cruzi transmission in Goias and its surrounding states (where samples were collected-Table  1 ) was interrupted approximately 20 years before the sampling detailed in this study  [26, 27]. In the sub-Andean semi-arid valleys of Cochabamba and its environs, however, vector-borne domestic transmission is still a likely source of new infections, albeit at a reduced rate since intensive spraying campaigns in the mid 2000s  [28]. Clinical data collected in this study were categorised simply into symptomatic and asymptomatic classes for statistical tests in view of samples sizes. Sub-categories within symptoms were defined as 1) Cardiopathy (including any electrocardiographic and/ or echocardiographic abnormalities, X-ray with cardiac enlargement.
Amplicon sequence data analysis De-multiplexed paired-end sequences were submitted to quality control and trimming in Sickle  [32]  and mate pairs trimmed in FASTX Toolkit (http://hannonlab. cshl. edu/fastx_toolkit/). ND5, TcGP63 and contaminating sequences were then sorted against a reference using BOW-TIE2  [33]. Individual paired reads were found to be overlapping in only a minority of cases. Thus we chose to proceed with analysis of a sequence fragment with a truncated central section for both targets. Further sequence manipulations were undertaken using FASTX Toolkit and custom awk scripts to parse files and concatenate each mate pair into a single sequence for downstream analysis. MUSCLE  [30]  was used for alignment of amplicon sequences in each patient sample. Next, analysis was undertaken in the Mothur software package  [34]  for the elimination of putative PCR chimeras and individual sequence clustering.
The Shannon index of diversity was calculated at the intra-patient level based on sequence types (STs) defined at 97% and 99% identity in Mothur  [34]. Comparisons of Shannon diversity were made between patients in each cohort (Bolivia chronic, Bolivia congenital, Goias chronic) via analyses of covariance and linear regression in the R package (http://CRAN. R-project. org). TcGP63I sequence datasets for patients from each cohort were then merged and analyses conducted using 97% and 99% STs defined with UPARSE  [35]  across patients. Weighted UniFrac distances between TcGP63I STs among samples were generated and subsequently clustered via a principal coordinates analysis in QIIME  [36]. Significance of association between UniFrac clustering, disease status and age was tested in the vegan package in R  [37].
Sequence yields and discrete typing unit (DTU) designations After quality filtering, trimming, decontamination and removal of unpaired reads, 6,736,749 reads were assigned to the ND5 mitochondrial marker and 871,855 to TcGP63I marker across the 92 clinical samples, perhaps reflecting higher copy number in the former than the latter. After trimming, the overlap between individual mate pairs was marginally too short to be assembled into a single read. Thus paired reads were first aligned against a full-length reference fragment and the central portion excised to remove any gaps and ensure correct alignment. Sequence depth thresholds per sample for inclusion were set for each dataset (Goias-ND5 & TcGP63-10,000; Cochabamba-ND5: 30,000; TcGP63 10,000; see Fig. 1 ). Reads from samples in excess of this threshold were discarded and samples with read counts below this threshold excluded.
TcGP63I ST distributions among clinical and congenital CD patients Individual sample sequence datasets within each of the different study cohorts (Cochabamba congenital, Cochabamba non-congenital and Goias) were merged to facilitate analysis of the distribution of antigen 99% STs among individuals (i. e. beta-diversity comparisons). Pairwise weighted Unifrac distances were calculated within cohorts of chronic cases from Cochabamba and Goias to examine whether the sequence diversity of the TcGP63I antigenic repertoire present in each patient could be associated with disease outcome. Principal coordinate analyses of the resulting matrices are displayed in Fig. 4. Among cases from Goias, repertoires varied considerably among cases, with several outliers. However, repertoires from symptomatic and asymptomatic cases were broadly overlapping in terms of sequence identity, and no clustering was noted among different symptom classes either (Fig.
Thus, if patients from different sites share dissimilar histories in the intensity and diversity of exposure to T. cruzi clones, comparisons between them are difficult to make. Secondly, the relationship between MOI and age is not necessarily linear. If a degree of cross-genotype immunity accumulates with exposure, one might expect a slower increase in intra-host antigenic diversity in older age groups. However, this was not the case in our dataset and neither a linear, nor a unimodal relationship could be established. Amplicon sequencing approaches to the study of transmission patterns in human parasites have so far been restricted to those species that replicate and reach high parasitemias in peripheral blood (i. e. T. brucei  [56]  and P. falciparum  [13, 15] ). T. cruzi trypomastigote circulating parasitemias, as measured by qPCR, are thought to vary considerably between acute (400 parasites/ml), newborn (150-12000 parasites/ml) and chronic (3-16 parasites/ml) cases  [25, 57].
Instead we elected to enrich for parasite DNA via culture-in Goias without further repassage, but in Bolivia with at least one repassage before cryopreservation. Low circulating parasitemia in Chagas patients also means it is possible that amplicon-sequencing strategies might rapidly 'bottom out,' if few parasites are present within a sample. In our dataset, for example, at the ND5 locus, minority DTUs at 97% divergence can be present as a proportion of < 1 in 1000 (Fig. 1 ), with the implication that several thousand parasites must be present in the sample. In both Goias and Bolivia matched instances occurred in congenital cases where TcI exists in mother and infant as the minor DTU at similar relative abundance (i. e. 1 in 1000, Fig. 1 ). It is highly unlikely that these data directly reflect chronic CD parasitemia levels.
3 ± 4. 5 [mean ± 95%CI]; slope = 1. 15 ± 0. 17; R 2 = 0. 89). The concrete is covered with epoxy-resin to prevent its CO 2 absorption. Each macrocosm was designed as an open flow gas exchange system. A multiplexer allowed for the CO 2 concentrations at the inlet and outlet of each dome to be measured every 12 min (LI-7000 CO2/ H2O analysers, LI-COR Biosciences, Lincoln, NE, USA). These data combined with the measurement of the air mass flow through each dome allowed for the calculation of canopy carbon assimilation (A c ). Transpiration (mass loss of the lysimeter) was monitored continuously by four CMI-C3 shear beam load cells (Precia-Molen, Privas, France) providing 3 measurements per minute. We ensured only canopy carbon (A c ) and water (E c ) balances were measured by covering the ground with a dark plastic cover that prevented flux mixing.
Statistical analyses. Transpiration was calculated from the slope of the linear regression between lysimeter weight and time every 3 hours successive periods. Statistical analyses of temporal patterns were then conducted with Generalized Additive Mixed Model (GAMM) fitting with automated smoothness selection  33  in the R software environment (mgcv library in R 3. 0. 2, The R Foundation for Statistical Computing, Vienna, Austria), including macrocosms as a random factor, and without including outliers (values above 95% quantile during day or night). This approach was chosen because it makes no a priori assumption about the functional relationship between variables. We accounted for temporal autocorrelation in the residuals by adding a first-order autoregressive process structure (nlme library  34  ).
Acknowledgement This study benefited from the  CNRS  human and technical resources allocated to the  ECOTRONS Research Infrastructures as well as from the state allocation 'Investissement d' Avenir '  ANR-11-INBS-0001 , ExpeER  FP7 Transnational Access program ,  Ramón y Cajal fellowships  ( RYC-2012-10970  to VRD and  RYC-2008-02050  to JPF), the  Erasmus Mundus Master Course Mediterranean Forestry and Natural Resources Management (MEDfOR)  and internal grants from  UWS-HIE  to VRD and ZALF to AG. We remain indebted to  E. Gerardeau ,  D. Dessauw ,  J. Jean ,  P. Prudent  ( Aïda CIRAD ),  C. Pernot  ( Eco&Sol INRA ),  B. Buatois ,  A. Rocheteau  ( CEFE CNRS ),  S. Devidal ,  C. Piel ,  O. Ravel  and the full Ecotron team,  J. del Castillo ,  P. Martín ,  A. Mokhtar ,  A. Pra ,  S. Salekin ,  J.
The collection localities were near either livestock or a forest. To catch the specimens, we used UV CDC miniature light traps. PNOC sequence of donkeys (Equus asinus) was sequenced and submitted because it was missing in GenBank. Our findings emphasize that the PNOC marker is not suitable to separate closely related Equid species such as horses and donkeys. The Cyt b marker was able to identify 204 more samples when compared to PNOC (99. 55% of specimens). Cyt b appears to be better able to detect the origin of blood meals from females with digested blood in their abdomens. We conclude that Cyt b is a good marker as it increases the accuracy of blood meal identification of engorged females containing digested blood in their abdomens. The host opportunist behavior of Culicoides, especially that of C.
To date, there is no study to compare these molecular markers, except that of Slama et al. (17)  during which the authors showed that in the PNOC-PCR sequencing methods, the sensitivity of host DNA detection was lower than found by Cyt b PCR method. Here, to compare and to test the ability to identify the origin of blood meals taken from vertebrate hosts of both molecular markers, i. e. , PNOC and Cyt b, we carried out our study on 565 wild-caught females of Culicoides spp trapped near livestock and forest in two localities in France. Determination of the blood meal origin was carried out through simple sequencing and Blast of the sequences in GenBank. We also compared the ability of each marker to provide interpreted sequences depending on blood digestion stage. The capacity of each marker to amplify bird DNA and to separate related animal species was also checked.
Sequencing and Data Analyses Sequences of at least 200 bp for PNOC and 300 bp for Cyt b were compared to homologous sequences deposited in Gen-Bank using BLAST. Blood meals were considered as identified to the species level if their sequence showed ≥98% homology with a sequence deposited into GenBank. Sequence editing and analyses were performed using BioEdit Sequence Alignment Editor V7. 2. 3 software.
Blood Meals Analyses From the 565 Culicoides identified as blood-fed, at least 11 different species were found to have fed on horses (73. 92% for Cyt b and 95. 28% for PNOC), 5 different species on donkeys (Equus asinus), 4 different species on cattle, only 1 on a cat (Felis silvestris), and 1 on a chicken (Gallus gallus). Finally, Cyt b analyses show that 19. 20% of Culicoides fed on humans (Homo sapiens) vs. 4. 81%, the result established with PNOC (Table  3 ). Analyses from Cyt b show that all C. punctatus, which were caught in Boult-aux-Bois (forest) (n = 13) (Table  3 ), are the main species that took blood meals from donkeys. Further, we observed in GenBank two haplotypes of horse sequences with a PNOC gene differing by a single base (e. g. , sequences under the accession numbers XM_001493120 and AY011855) (Figure  2 ).
We noted that the sequence of donkeys was missing. Consequently, we provided it from donkey blood following the protocol previously described (GenBank accession number KM521860). We compared the donkey blood and found it to be identical to the first haplotype of Equus caballus (accession number XM_001493120). This led us to the conclusion that the PNOC gene is unable to distinguish E. caballus sequences from those of E. asinus (99% homology) whereas Cyt b is able to distinguish both species. Equally, no sequences were reported from PNOC using the Mallard DNA as opposed to the successful amplification that was reported using Cyt b. Evidence of mixed blood meals was not observed in the present study. In our study, analyses from PNOC and Cyt b genes detected blood meals of all 220 fully engorged females, 184 (83.
In the present study, our degenerate primers discriminated E. caballus and E. asinus, two closely related species from the same genus (Equus). In the study of Pettersson et al. (12) , in order to increase the opportunity for host identification, the authors added a second widely studied gene COI for blood meal analysis for samples that did not produce results with Cyt b primers. Consequently, identification of Culicoides blood meals using the Cyt b gene coupled with COI gene for vertebrates is a logical application since the COI and Cyt b DNA barcoding regions from more species are being sequenced and submitted to public databases. The capacity for identification of blood meals via both markers will become more and more precise. In the present study, our sampling strategy was to use light traps close to livestock as suggested by Garros et al.
Acknowledgments This work is funded by the  CPER  project " Culichamp " and by  ANSES. The authors thank  Stavana Strutz  for proofreading this manuscript. TM was supported in part by " STEP -Status and Trends of European Pollinators " ( EC FP7  grant no. 244090 ) and by  SUPER-B COST   ACTION FA 1305. The study was also funded by an internal  Applied-Oriented Research Grant  from  Naturalis Biodiversity Center. We are grateful to  Modeste De Meulemeester  and  Véronique Dubois  for help in donkey blood acquisition. The authors would like to thank the reviewers for their constructive comments which helped to improve the manuscript.
Phylogenetic analysis (supplementary material Fig. S1 ) suggests the existence of at least one Nodal ligand in P. flava. Querying the recently released P. flava transcriptome database (http://molas. iis. sinica. edu. tw/hemichordate/; Chen et al. , 2014)  further supports the existence of only one Nodal in P. flava but needs to be confirmed once the P. flava genome  (Freeman et al. , 2012)  will be released. The earliest expression of Pf-nodal was detected at the blastula (Fig. 3H ) stage, in a ring of cells surrounding the future blastopore. During gastrula stages, blastoporal expression is no longer detected, however, Pf-nodal transcripts are refined to an ectodermal domain (Fig. 3L ). At the late gastrula stage, just prior to hatching, Pf-nodal expression is detected in an ectodermal apicoventral domain (Fig.
Smad1/5 and Erk1/2 signaling are activated in dorsal territories In order to visualize activity of Nodal signaling, we performed IHC using 8 different commercial antibodies made against mouse phospho-Smad2 /Smad3. However, none of these reagents allowed us to detect a clear localization/activation of Pf-Smad2/3 despite attempts to optimize fixation, blocking, and antibody dilutions (data not shown). Bmp2/4 is a transcriptional target of Nodal signaling in echinoderm larvae  (Duboc et al. , 2004)  and required to determine dorsal fates in echinoderm  (Angerer et al. , 2000; Duboc et al. , 2004)  and hemichordate  (Lowe et al. , 2006)  embryos. Therefore, we analyzed the localization of pSmad1/5 using a monoclonal antibody against the phosphorylated form of Smad1/5. This reagent allowed us to detect a localized signal as early as the late cleavage and early blastula stages (Fig.