dataesr/scientific-paragraphs-categorization huggingface dataset:
The HMM shows the lowest computational time (16. 78 seconds), followed by   the RF and the SVM models (22. 09 and 23. 07 seconds, respectively). Next it is the HSMM (64. 04 seconds) and finally the most expensive one is the ANN (140. 14 seconds). For the HMM and the HSMM, the computational time comprised the estimation of the probability density function parameters and Viterbi algorithm application. For the SVM, the RF and the ANN, it comprised the optimal parameter setting, as described in the Methods section. The high computational cost of the ANN could be greatly affected by the call to a graphical interface as automatically performed by the Neural Network toolbox of Matlab TM. This computational analysis should only be regarded in relative terms. Optimized implementations of these models could be expected to provide important computational gains (by a factor of 10 or more).
Real Behavioural Modes and the Relevance of Model Validation The technological and methodological advances enable access to larger amounts of data and lead to continuously elaborating and applying new flexible modelling approaches for animal movement  [73]. While following this trend, model validation and evaluation are often disregarded. [74]  discuss this issue as a challenge in the future of statistics in general. It is also a challenge in movement modelling, particularly due to the conceptual and practical difficulties for obtaining groundtruthed data on animal behaviour. Hence, when validating models with groundtruthed data, not only the models should be discussed but the data as well. In this work, we had access to a groundtruthed dataset, where behavioural modes were not chosen by us.
According to the fishermen, observed patterns for fishing and cruising are more stable. The low F1 score for searching may also be due to the time resolution of the data. As for fishing, the activity lasts ,2 hours on average. However, 30-minute searching modes between two fishing modes were also reported by on-board observers. Such short state segments result in mixed signatures at the one-hour steps of the VMS data and can hardly be analysed. Higherresolution tracking data should clearly contribute to a better identification of such searching modes, and would decrease the confusion rates with fishing and cruising; thus improve the inference accuracy of all behavioural modes. Moreover, as shown by the simulation study, HSMMs would increase their inference power if data resolution increases.
Beyond Validation: Inference in Supervised and Semisupervised Contexts In supervised contexts, inferring behavioural modes is not only useful for achieving model validation. Supervised contexts do not necessarily imply that groundtruthed data on the behavioural modes of the whole population of tracks are available. Known behavioural modes may only be available for a subset of the tracks. In the case of fishermen, for instance, there may not be enough resources for on-board observers to register activities from all fishing trips of the entire population of vessels with tracking devices. For the Peruvian anchovy fishing fleet, more than 30000 fishing trips are tracked by VMS per year, but behavioural modes of only ,300 of those trips are registered by on-board observers. Likewise, financial limitations could make possible tagging more individuals with GPS than with time-depth recorders (e.
Synthesis We have shown a pioneer evaluation and comparison of Markovian and discriminative models for inferring behavioural modes within movement tracks in a supervised framework. The surpassing performance of Markovian models over the discriminative models highlights the importance of modelling state dynamics for accurately inferring the behavioural mode sequences. HMMs have been the most common approach in movement ecology. However, semi-Markov processes represent better the behavioural mode sequences than first-order Markov processes, since they explicitly model state duration and consider transitions at a segment scale. The HSMM performance on the groundtruthed dataset is slightly better than that of the HMM. As discussed above, this result responds to the nature of these particular behavioural modes as well as to the low resolution of the data.
Acknowledgments We would like to express our gratitude to the people that facilitated access to the data, particularly  Marilu Bouchon  and other members of the  Unidad de Investigaciones en Dinamica de Poblaciones  and the  UPRSIG of IMARPE. We highly appreciated the work and dedication of  Rodrigo Tito  for typing a great amount of logbook information from on-board observers. We warmly thank  Mariano Gutierrez ,  Federico Iriarte  and  Dante Espinoza  for valuable conversations about fishermen behaviour; and  Mariano again  for facilitating the embarkation on a fishing vessel. We are also grateful to  Yann Gue  ´don for valuable discussions on hidden semi-Markov models, as well as the anonymous referees for their helpful comments on the manuscript. This work is a contribution to the cooperative agreement between the  Instituto del Mar del Peru(IMARPE) , the  Institut de Recherche pour le Developpement (IRD) , the  Agence Nationale de la Recherche (ANR)  project ' Top Predators as Indicators of Exploited Marine Ecosystem dynamics (TOPINEME ), and the  International Joint Laboratory DIS-COH.
Arp2/3 inhibitory proteins containing an A motif, PICK1 and Gadkin (also known as AP1AR and c-BAR), were detected at endocytic pits and at endosomes  10, 11. Thus, although endocytic pits and endosomes possess antagonistic activities towards the Arp2/3 complex, it was not known whether lamellipodia contain a similar Arp2/3 inhibitory protein to counteract WAVE. To identify such a protein, we performed a bioinformatics search for proteins displaying the typical A motif of human NPFs, characterized by a tryptophan residue at the antepenultimate position in an acidic context. We identified an uncharacterized protein (C15orf38) clustered with NPFs with this procedure (Fig. 1a ). This protein was named Arpin. Arpin is encoded by a single gene in metazoans and amoeba. Predictions and NMR analysis indicate that this protein of about 220 residues is structured with the exception of its highly mobile C-terminal end, which contains the putative Arp2/3-binding site (Extended Data Figs  1  and 2 ).
Indeed, Arpin binds to Arp2/3 mostly through its acidic motif (Fig. 1b  and Extended Data Figs  3  and 4 ). The molecular function of Arpin on Arp2/3 activity was assayed by spectrofluorimetry and total internal reflection fluorescence (TIRF) microscopy using purified proteins. Arpin was unable to activate the Arp2/3 complex, consistent with its lack of verprolin (V) and cofilin (C) homology motifs. However, when Arp2/3 was activated by VCA, Arpin, but not its truncated form lacking the acidic motif (ArpinDA), inhibited actin polymerization in a dose-dependent manner (Fig. 1c ). The acidic peptide was sufficient for this inhibition, although it was less effective than full-length Arpin, in line with its lower affinity for the Arp2/3 complex (Extended Data Fig. 4 ). Arpin inhibited Arp2/3 activation, because we observed by TIRF microscopy the generation of fewer actin branched junctions in the presence of Arpin (Fig.
1d  and Supplementary Video 1). Full-length Arpin and its acidic motif, but not ArpinDA, compete with VCA for Arp2/3 binding (Fig. 1e  and Extended Data Fig. 4 ). Therefore, Arpin is a new competitive inhibitor of the Arp2/3 complex. The name Arpin is a mnemonic for its activity (Arp2/ 3 inhibition). The subcellular localization of Arpin was examined by immunofluorescence in spreading mouse embryonic fibroblasts (MEFs). Arpin was detected in restricted segments of the plasma membrane, which were also stained by three lamellipodial markers-the WAVE complex, the Arp2/3 complex and cortactin (Fig. 2a  and Extended Data Fig. 5 ). Radial line scans of immunofluorescence pictures through lamellipodial outlines were generated, registered with the edge as a reference, and averaged to reveal the relative distributions of these different lamellipodial components.
For Arpin localization, MEF cells were fixed with 10% TCA, permeabilized with 0. 2% Triton X-100, and processed for immunofluorescence. To draw radial line scans, a custommade ImageJ plug-in was developed, edge was determined using 'Isodata' and 'Analyze particle', and then a custom-made VBA macro in Excel was used to align data relative to the edge. Keratocytes were isolated from scales of freshly killed brook trout (Salvelinus fontinalis) and microinjected with a Femtojet (Eppendorf). Plots were drawn with SigmaPlot (SPSS) and statistics were performed with SigmaStat (SPSS).
2% Triton X-100, and processed for immunofluorescence. To draw radial line scans, a custom made ImageJ plug-in was developed, edge was determined using 'Isodata' thresholding, then a custom-made VBA macro in Excel was used to align data relative to the edge. Lamellipodial dynamics and random migration were analysed with ImageJ using the plugins 'Kymograph' and 'MtrackJ', respectively. All imaging was done on a Axio Observer microscope (Zeiss) equipped with a Plan-Apochromat 633/1. 40 oil immersion objective, an EC Plan-Neofluar 403/1. 30 oil immersion objective and a Plan-Apochromat 203/0. 80 air objective, a Hamamatsu camera C10600 Orca-R 2 and a Pecon Zeiss incubator XL multi S1 RED LS (Heating Unit XL S, Temp module, CO 2 module, Heating Insert PS and CO 2 cover). Fish keratocytes. Keratocytes were isolated from scales of freshly killed brook trout (Salvelinus fontinalis) as previously described  35  and imaged by phase contrast on an inverted Zeiss Axioscope using 363 optics, and a halogen lamp as light source.
Two clones isolated after each transformation gave similar results. Statistics. Statistical analysis of the results was carried out with SigmaStat software (SPSS inc. , v2. 03). When data satisfied the two criteria of normality and equal variance, parametric tests were used: t-test to compare two groups; ANOVA for more than two. Where indicated, a bijective transformation was applied to the data to pass the two criteria of normality and equal variance. When data did not satisfy both criteria even after transformation, non-parametric tests were applied: Mann-Whitney to compare two groups; Kruskal-Wallis for more than two. A representative experiment is plotted and results are expressed as mean s. e. m. with respect to the number of cells (n). Differences were considered significant at confidence levels greater than 95% (two-tailed).
Three levels of statistical significance are distinguished: *P , 0. 05; **P , 0. 01; ***P , 0. 001. Extended Data Figure  1  | Prediction of secondary structure elements and disordered regions of Arpin. A multiple alignment of the Arpin orthologues was performed with MUSCLE  41  and displayed with Jalview  42. Two methods relying on multiple alignments of Arpin orthologues were used to predict secondary structures and disordered regions, Psipred  43  and Disopred  44  , respectively. The predicted secondary structure (SS) elements are indicated by green arrows for b-strands, red cylinders for a-helices, and a black line for coils; the associated confidence (conf) score is displayed below, ranging from 0 to 9 for poor and high confidence, respectively. Amino acid conservation is indicated by a 0 to 10 score, and highlighted by brown to yellow histogram bars.
Arp2/3 is displaced from its interaction with 5 mM GST N-WASP VCA immobilized on glutathione beads by the Arpin acidic peptide (304 mM and serial twofold dilutions). Extended Data Figure  5  | Specific localization of Arpin at the lamellipodium tip. a, Arpin overlaps with the Arp2/3 complex at the lamellipodium tip. b, Arpin overlaps with cortactin at the lamellipodium tip. Arpin staining is lost after short interfering RNA (siRNA)-mediated depletion. Intensity profiles along multiple line scans encompassing the cell periphery were registered to the outer edge of the staining of a lamellipodial marker. This marker was Arpin in a and cortactin in b. The multiple line scans were then averaged and displayed as an intensity plot, where the y axis represents fluorescent intensity, arbitrary units (mean 6 s.
2c ). Intensity profiles along multiple line scans encompassing the cell periphery were averaged after manual drawing of the cell edge (mean 6 s. e. m. , n 5 16). Scale bar, 20 mm. Extended Data Figure  6  | Arpin regulates cell spreading through its interaction with the Arp2/3 complex. Arpin was depleted from human RPE1 cells after transient transfection of shRNA plasmids and blasticidin-mediated selection of transfected cells. After 5 days, cells were either analysed by western blot or used for the spreading assay. Cells were serum-starved for 90 min in suspension in polyHEMA-coated dishes and then allowed to spread on collagen-I-coated coverslips for 2 h. Phalloidin staining was used to calculate cell surface area of individual cells using ImageJ. Mean 6 s. e. m. ; **P , 0. 01, ***P , 0.
Acknowledgements A. G. acknowledges his PhD supervisor  M. Arpin , the name of the here identified protein is a tribute to her mentoring. We thank  G. Romet-Lemonne ,  E. Portnoy  and  F. Marletaz  for suggestions. We acknowledge support from  Agence Nationale pour la Recherche  ( ANR-08-BLAN-0012-CSD 8  to A. G. and L. B. ,  ANR-08-PCVI-0010-03  to A. G. ,  ANR-11-BSV8-0010-02  to A. G. , J. C. and S. Z. -J. ),  Association pour la Recherche sur le Cancer  ( SFI20101201512  to A. G. , PDF20111204331 to R. G. ,  SFI20111203770  to N. B. D. ), the  Bio-Emergences IBISA facility and Fundacao para a Ciencia e a Tecnologia  ( SFRH/BPD/46451/2008  to C. S. -B. ), the  Austrian Science Fund  ( FWF P21292-B09  to J. V. S. ), the  Deutsche Forschungsgemeinschaft  ( FA 330/5-1  to J. F. ) and grant number  8066 , code  2012-1.
The parameters nu and p were estimated for each chromosome and each population. These parameters greatly varied among chromosomes and among populations, with values of nu ranging from 2 to 50, and p ranging from 0 to 0. 4. Since the population sizes are modest, part of this variation is expected to be due to statistical noise. We thus focused on comparing pooled data, either over chromosomes or over populations. Figure  4A  shows the values estimated for nu and p when pooling all chromosomes together for each population and for the pooled Dent × Dent and Flint × Flint populations. Confidence intervals for estimates of nu and p from individual populations were large as expected given the population sizes (data not shown). Statistical tests showed that differences between individual populations were not significant at the 5% threshold levelhardly any pairs of individual populations had significantly different values for nu (Additional file 12).
Array hybridization and raw data processing were performed according to manufacturer's instructions (Illumina W ). Raw data were analyzed in Illumina W 's Genome Studio software version v2011 (Illumina W ) using an improved version of the public cluster file (MaizeSNP50_B. egt, [62] ). SNP data were filtered based on the GTscore using a threshold of 0. 7. Heterozygous SNPs were set to missing values (NA) and only markers with a minor allele frequency >0. 1 per population were used for mapping. For each population, the allele of the central line was coded as the 'A' allele, and the allele of the founder line was coded as 'B' allele (Additional file 4). Raw genotyping data of parents and DH lines are available at NCBI Gene Expression Omnibus as dataset GSE50558  [63].
Effect of population structure on recombination rate Genetic map lengths tended to be longer in populations involving Flint parents, suggesting that some alleles of factors controlling recombination rate may be differentially fixed in the two pools. To use a solid and objective measure of degree of 'flintness', we estimated the probability of the 22 parental lines to belong to one of the two main groups (Dent or Flint). To do this, we estimated admixture in a combined analysis of the Dent and Flint diversity panels described earlier  [37] , which included also the lines of our study. This analysis was done with the Admixture software (version 1. 22)  [72] , using 25,237 PANZEA SNPs and 559 maize lines. We chose k = 2 for the number of groups assuming the two pools Dent and Flint, and used the probability of each of the 22 parental lines to belong to the Flint pool for a correlation analysis with recombination rates.
Acknowledgments We thank  Christine Dillmann ,  Philippe Brabant , and  Domenica Manicacci  for discussing statistical approaches, and  Christine Mézard  and  Raphaël Mercier  for helpful comments on the manuscript. We thank  Michael Seidel  for providing the physical map coordinates of SNP markers in the  B73 AGPv2  assembly, and  Hans-Jürgen Auinger ,  Christina Lehermeier , and  Valentin Wimmer  for help with R scripts. We also thank  Ruedi Fries  and  Hubert Pausch  for processing of SNP arrays and  Stefan Schwertfirm  for excellent technical assistance. Results have been achieved in the framework of the  Transnational (Germany, France, Spain) Cooperation  within the  PLANT-KBBE Initiative  Cornfed, additionally supported by the project  AMAIZING. The work was financed by grants from  Agence Nationale de la Recherche  (' ANR ') to AC, MF, MM, and PF, grants from the  Ministry of Science and Innovation (Ministerio de Ciencia e Innovación ('MICINN'))  to JMG and PR, and grants from the  Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, 'BMBF')  to TA, AEM, MO, and  CCS.
BLAST searches and Alignments We performed a BLAST search using the Universal Protein Resource (www. uniprot. org), by querying first the TCSP peptide, then the repeated region harboring the peptide. This region, referenced as Q7M3W1 (97 amino-acids), is a fragment of T. cruzi ribosomal protein 60s L19 (XP_808122; 357 amino-acids). We searched across the Swiss Prot non-redundant database sequences by using the default settings  [21].
Alkaline Phosphatase-conjugated (PARIS BIOTECH, Compiegne, France) was diluted 1/1000 in conjugate buffer, and 100ml were then added to the microplate which was incubated for a final 60 min at room temperature. At the end of the incubation period, the plates were washed three times with wash buffer. Finally 100ml of para-Nitrophenyl Phosphate (p-NPP) substrate solution (1 mg/mL) were added to each well. The plate was then incubated at room temperature for 15 min. The absorbance was measured at 405 nm using a 96-well plate reader (Labatech LT-4000 Microplate reader) and the results analyzed using analysis software (Manta, Labatech). All reported data represent the average optical density (OD) of duplicate measurements. A cut-off value of 0. 5 OD was calculated for determining seropositivity, it is determined as the mean plus 3 times the standard deviations (SD) of the tested samples OD on negative control samples.
Statistical analysis Descriptive statistics are presented as frequencies (percentages) for categorical variables and as means (SD) for continuous variables. The Mann Whitney U test was used to compare age between sexes and Fisher's Exact test was used to test equality of the proportion of males and females in the TcCRA positive group (Table  2 ). To investigate the equality of viral serology of other viruses and TcCRA status, the null-hypothesis that the proportion of discordant test results equals zero is tested using a single proportion test (Table  3 ). All statistical analyses were performed using SPSS software (SPSS version 17. 0).
Discussion We have discovered novel antibodies, called TcCRA, observed in around 45% of French blood donors though detected with an antigen derived from a Latin American parasite. French individuals are virtually not exposed to T. cruzi. We however observed at a high frequency binding reactions in the ELISA tests performed on French blood samples. This strong TcCRA cross-reactivity with T. cruzi was further evidenced by the specific reaction obtained between affinity-purified TcCRA and T. Cruzi epimastigotes in immunofluorescence assays used for routine serodiagnosis. This led us to search for characteristics of the trigger immunogen through different approaches. We estimated seroprevalence in different groups of individuals. Our data show a steady increase of seroprevalence from early childhood to an approximate level of 47%.
The type strain is deposited in the German Collection of Microorganisms and Cell Culture (DSMZ) as DSM 20714. The ST1464 strain exhibited a 99% nucleotide sequence similarity with the Staphylococcus aureus 16S rRNA gene (Genbank accession number D83357. 1) (Figure  2 ). Matrix-assisted laser desorption/ionization timeof-flight mass spectrometry (MALDI-TOF-MS) (Brüker Daltonics, Bremen, Germany) was used as previously described  [27]. Briefly, a pipette tip was used to pick one S. aureus subsp. anaerobius colony from a 5% blood agar plate and to spread it on a MTP 384 MALDI-TOF target plate (Brüker Daltonics). Smears were overlaid with 1. 5 μL of matrix solution (saturated solution of alphacyano-4-hydroxycinnamic acid) in 50% acetonitrile, 2. 5% tri-fluoracetic-acid and allowed to dry. MALDI-TOF without bacteria was used as a negative control and the positive control consisted of 1.
Genome annotation The prodigal program was used to predict open reading frames (ORFs) from the 100 large contigs  [28]. tRNAs were predicted using the Aragorn program  [29]  and rRNAs were predicted using RNAmmer. The predicted genes were Blasted against the non-redundant database. The functional annotation of predicted ORFs was performed using RPS-BLAST  [30]  against the cluster of orthologous groups (COG) database  [31]  and Pfam database  [32]. TMHMM program was used for gene prediction with transmembrane helices  [33]  and signalP program was used for prediction of genes with peptide signals  [34]. PHAST software was used for bacteriophage detection  [35]. To estimate the similarity at the genome level between S. aureus subsp. anaerobius strain ST1464 and S. aureus, BLASTP was performed for genes with query coverage ≥70% and identity ≥30%.
Quantification of Myelination For each coverslip, 30 randomly located images were taken of MBP and NF staining (using either a 106 objective, with a field of view of 843 mm6636 mm, or a 206 objective, with a field of view of 709 mm6530 mm). Within each image, myelination was quantified by counting the number of myelinating MBP-positive oligodendrocytes (Figure  1B, C ) as a percentage of the total number of MBP-positive oligodendrocytes  [8]. The density of axons was expressed as the percentage of the same area occupied by NF (calculated from a binarised NF image using ImageJ software, version 1. 34s). There was no correlation between oligodendrocyte density and axon density. The fraction of myelinating cells was plotted against the axon density for the different images, and fitted assuming a linear dependence  [8]  of fraction of oligodendrocytes myelinating (F) on axon density (D), F ~A: D{K ð Þ, ð1Þ where K is a free constant and the slope A is the measure of myelination plotted in Figure  2 , Figure  S2A , Figure  S3A , and Figure  7.
Immunoreactive proteins were visualised with enhanced chemiluminescence (GE Healthcare). When phosphorylated and total amounts of the same protein were measured, this was done by first probing with the antibody to the phosphorylated protein, then stripping the membranes to remove the antibody, and reprobing with antibody recognizing both phosphorylated and unphosphorylated forms. Stripping membranes was performed with 50 mM dithiothreitol, 50 mM Tris (pH 6. 8), and 2% SDS at 70uC for 30 min and washing three times in PBS-T before blocking and incubating with the primary antibody. Densitometric analysis was conducted using ImageJ gel analysis software (version 1. 43u). For each sample, pAkt, pERK, pNR2B, and pNR2C signals were normalised to the total levels of their respective proteins present.