dataesr/scientific-paragraphs-categorization huggingface dataset:
Discussion and open issues Looking ahead, we see a wide range of possible research directions in both short-and longterm bond to the human mobility routine analysis. Mobility from different nature. Even if we have presented mobility analysis from both CDRand GPS-based trajectories (refer to Section 5), we envision other possibilities. Services such as Foursquare and Instagram provide large-scale human data collection, which often contains geolocalized information. Similar to a CDR record, user positioning is only available when he performs an activity, which in this context indicates his presence (e. g. , check-in on Foursquare) at a certain location. This comprises a whole area of research called Participatory Sensing Networks  [40, 41]. As with a CDR, a sequence of check-ins represent a user trajectory, e.
g. , temporally concatenating them, or by inference  [42]. Human mobility and routine analysis from this source is still unexplored, to the best of our knowledge. Therefore, we claim the same analysis herein presented could be performed with different natures of datasets, such as, check-ins. Concluding results could be of extreme value to this still not-well-exploited mobility source. Dataset collection. Analysis presented in our paper rely on the precision in the mobility information given by the dataset. For instance, more precise the geolocalized information is, more we can understand and better analysis/models can be inferred from user's mobility. As a vast spectrum of work can take advantage of dataset analysis in the area of human mobility and network, experiments aiming to collect rich information from users are of enormous value for the research community.
Information regarding the user, his device, and surrounding scenario, e. g. , fine-grained mobility, battery level, running applications, access points, bluetooth devices, network traffic usage can contribute to a deeper understanding on how we interact with the network and with the environment around. Examples of research projects in this direction are the European MACACO  [43]  and the French Priva'Mov  [44]  projects. In general, there is a trade-off between the number of participants in the collected data and the amount of private information collected from them. Due to privacy concerns users are less inclined to participate in projects that collect private information regarding their behavior. Therefore, the limitated availability of valuable datasets is still an impacting factor in the mobility research field.
Routine-based data prefetching. Prefetching has been shown to effectively reduce user perceived latency. An interesting approach might be to merge trajectory information provided by mobility datasets, as the ones used in this work, with datasets or models describing demanded content in urban scenarios. Analysis results could be then used in the design of smart data prefetching approaches. Based on the routine of a user, the prefetching service could store static content of often visited web pages in more adapted locations visited by the user. This content could be downloaded using access points present in the locations he routinely visits. For instance, an application for mobile phones could download content in advance at home using WiFi and this would be later presented along with content downloaded using the mobile cellular network in real time.
Conclusions In this paper, we have made an extensive analysis of human mobility on several categories of datasets describing mobility in several large metropolitan areas, in order to unveil common aspects present in human mobility. We firstly presented our system model, which unifies different datasets into a common representation of urban scenario. Then, we presented analyses on the visiting patterns to PIs. Results unveiled a clear repetitivity on people's visiting behavior. Additionally, we have proposed a metric to measure the repetitiveness of people's visits to PIs. Next, we have evaluated displacement in their trajectories. The main conclusions are two: people have a tendency to use shortest-path when moving around, and their mobility is confined, i. e. , displacement is generally limited to 10 km.
A method of worst case data imputation was used to address missing values. The patients lost to follow-up or with missing data at 12 months were imputed as non-responders. The primary lead safety endpoints: rate of freedom from acute and rate of freedom from chronic lead complications were compared with 91%  19  and 94%  20  pre-specified values, respectively, using a onesided exact test of one binomial proportion at an alpha level of 0. 025. The safety analyses were performed on the safety population which included all patients successfully implanted with SonRtip lead and patients with SonRtip lead fracture, insulation breach or perforation occurring during the implant procedure, regardless successful implantation. If all statistical tests were passed, the secondary CRT efficacy endpoints, rate of clinically worsened patients, and the rate of composite of all-cause mortality or HF hospitalization were tested using a À10.
0% absolute non-inferiority margin. The pre-specified long-term ancillary time-to-event analyses were conducted using Kaplan-Meier statistics on all follow-up data available at the time of the 12 month database lock. The log-rank test and hazard ratios with 95% confidence intervals (CIs) were estimated from the Cox proportional hazard model. Echocardiographic parameters were assessed on patients with data at implant and at 1 year follow-up. Mean intra-patient changes from baseline to 12 months in LV ejection fraction and LV end-systolic volume were tested in each group using a paired t-test or Wilcoxon test. Mean changes were compared between groups using one-sided noninferiority test, with an alpha level of 0. 025 and a pre-defined absolute non-inferiority margin of À2. 5% in LV ejection fraction and 15 mL in LV end-systolic volume, respectively.
Patients A total of 1039 patients were assessed for eligibility from 125 sites in 12 countries in Europe, Australia, and North America, from 13 January 2012 through 29 October 2014. Of these patients, 670 were randomly assigned to SonR and 328 to Echo (Figure  2 ). One patient was lost to follow-up. Nineteen patients were excluded from the analysis before unblinding due to violations of Good Clinical Practice guidelines at two sites, making the data unreliable. Mean follow-up (of up to 12 months) was 358. 1 6 61. 3 days (range, 7. 0-543. 0). The patients' baseline characteristics were generally well matched between groups (Table  1 ). Mean age was 67. 0 6 10. 2 years and 68. 8% were men; 96. 2% of patients were in NYHA class III; mean LV ejection   S1. Successful implantation of the SonRtip lead was achieved in 1027/1029 (99.
Long-term follow-up When using all adjudicated data available in the database at the time of the primary analysis, the overall mean follow-up was 548. 2 6 190. 3 days (range, 0. 0-867. 0). The composite of death or HF hospitalization (pre-specified ancillary analysis) showed no significant difference in freedom from event between SonR and Echo over time (hazard ratio, 0. 79; 95% CI, 0. 60-1. 06; log-rank P ¼ 0. 12, two-sided) (Figure  3 ). A 35% risk reduction in HF hospitalization was associated with SonR (hazard ratio, 0. 65; 95% CI, 0. 46-0. 92; log-rank P ¼ 0. 01, two sided) (Figure  4 ).
Examination of the CA1 area was performed using digitalized slices using a Nanozoomer virtual microscopy system (Hamamatsu, Massy, France). CA1 measurement and pyramidal cell counts were processed using a 40 × objective using ImageJ software (NIH). Data were expressed as mean number of viable cells per mm, from at least four slices × 3 CA1 fields × 2 hemispheres for each group, according to the previously reported method  12. For immunohistochemical labeling of the vesicular acetylcholine transporter (VAChT), sections were incubated overnight at 4 °C with Rabbit monoclonal anti-VAChT (SOSV00002G, Thermofisher). Then, sections were incubated with Rabbit biotinylated secondary antibody (B8895, Sigma-Aldrich) and incubated for 1 h in avidin-biotin complex (ABC Vector laboratory). Signal was detected with the diaminobenzidine kit (Vector, Laboratories).
In vivo bioluminescence imaging Images were acquired using the IVIS spectrum system (Perkin Elmer) as previously described  [16]. In brief, mice were anesthetized using a constant flow of 2. 5% isoflurane mixed with oxygen using an XGI-8 gas anesthesia system (Xenogen Corporation). 100 μl D-luciferin in PBS (33. 3 mg/ml) was injected intra-peritoneally 10 min prior to photon detection. Data acquisition and quantification was performed using Living Image software version 3. 1 (Xenogen Corporation). Quantification of photons per second was performed on defined regions of interest from the chest area.
i. Thus conidial phagocytosis was more rapid in the "Re-Inf" group than in the"L" group. Furthermore, the type of phagocytes involved in this process differed among the two groups. At 24 h in the "L" group, 73% of macrophages phagocytosed conidia while, at 48 h, 67% of neutrophils internalized the majority of conidia. In contrast, in the "Re-Inf" group neutrophils represented 75% of the cells that engulfed conidia at 24 h time point. This changed to 29% at 48 h with conidia primarily found in macrophages (71%) at this time point (Fig  4B ). These data suggest that neutrophils conidial phagocytosis occurs more quickly and completely in the "Re-Inf" compared to the "L" group. In the next experiments, we determined ROS and MPO production by neutrophils at various time points. Both neutrophil activity markers were significantly higher at 24 and 48 h in the "Re-Inf" group (Fig  4C ).
We also analyzed IL-17 production in lung and BAL in the different infection settings. In mice from the "SL" and "L" groups, IL-17 was only present at low levels during the time course of infection (Fig  5C ). In contrast, the IL-17 profile dramatically differed in the "Re-Inf" group (Fig 5C ), in which IL-17 was secreted in highest amounts in the BAL peaking at 18 and 48 h pi. This observation suggested an important role of IL-17 in the protection process. To test this hypothesis, we evaluated the survival of IL-17 receptor A knock-out (IL-17RA -/-) mice. IL-17RA -/-mice still have the ability to produce IL-17A, but signaling through its receptor IL-17RA is abrogated  [18]. Our data showed that IL-17RA -/-mice were partially susceptible to the sublethal dose of conidia with 71% survival. Following reinfection, only 30% survival was observed compared with 100% of the parental C57BL/6 mice (S3 Fig).
Clinical study design In this single site, investigator-blinded, active-controlled, parallel-group comparison study, subjects were randomised 1 : 1 to receive either 12-week treatment of amorolfine 5% NL alone or amorolfine 5% NL plus a cosmetic nail varnish applied 24 h later (ClinicalTrials. gov identifier: NCT02321098). A randomisation list was generated using the Ranuni routine of the statistical analysis system and a kit number was assigned. To maintain blinding, the person dispensing the study drug and the subject were instructed not to discuss the study treatments with the evaluating investigator. The study was conducted in accordance with the Declaration of Helsinki, the International Conference on Harmonisation-Good Clinical Practice principles and in compliance with local regulatory requirements.
Statistical analyses As the purpose of the clinical study was to compare the antifungal activity between the two groups by descriptive analyses, no sample size was calculated. At 12 weeks, antifungal activity and mycological culture results were analysed by Cochran Mantel Haenszel test after ridit transformation. SAS version 9. 3 (SAS Institute, Cary, NC, USA) was used for all analyses. Each test was two-sided with significance declared at the 0. 050 level. All continuous data were summarised at each visit using usual statistics: number of values, mean, median, standard deviation, minimum and maximum, and by frequency distribution (n, %) for qualitative data. For ordinal data, both frequency distribution and usual statistics were presented. For the in vitro assays, all statistical analyses were performed using SPSS software (ver.
Histology scoring Kidneys were bisected and examined at 4 mm, and the cortex and medulla were individually assessed for the presence of neutrophils (acute inflammation) and lymphocytes/plasma cells (chronic inflammation) and scored as follows: score 0 = no inflammation; score 1 = ,3 foci of inflammation; score 2 = 4-6 foci of inflammation; score 3 =. 6 foci of inflammation, but less than 25% of the kidney affected; score 4 =. 25% of the kidney affected. Each individual focus was subsequently assessed to determine the area of inflammation (in square micrometers) using cellSens Software (Olympus Corporation, Tokyo, Japan), and the total percentage of the affected kidney was determined using the cumulative area of inflammation/ total area of the kidney section. Scoring was performed by a pathologist blinded to the experimental groups.
albicans cells. To confirm this observation, C. albicans and C. parapsilosis were labeled with Rhodamine Green-X, WT BMDMs were stimulated with the labeled Candida spp. for 1 h, and Candida cells per infected BMDM were counted. In agreement with previous findings  (52) , we observed that on a per cell basis, infected BMDMs ingested more C. parapsilosis cells than C. albicans cells (Fig. 2I, 2J ). These data indicate that TLR7 and NOD2 colocalize in response to Candida spp. in a manner similar to TLR9 and NOD2 colocalization.
Acknowledgments We thank  Donna MacCallum  ( University of Aberdeen, Aberdeen, U. K. ) for providing Candida spp. ;  Giorgio Trinchieri  ( National Institutes of Health, Bethesda, MD ) and  Daniel McVicar  ( National Cancer Institute-Frederick, Frederick, MD ) for providing bone marrow from  Myd88 2/2  ,  Tlr9 2/2  ,  Ifnar1 2/2  ,  Stat1 2/2  , and  Stat2 2/2  mice;  Caetano Reis e Sousa (Cancer Research UK)  for providing bones from  Tlr7 2/2  mice;  Laura Quigley ,  Pani Tourlomousis ,  Neil Rogers ,  Barbara Bodendorfer , and  Simone Lipinski  for preparing bones/bone marrow from the  Tlr2 2/2  ,  Tlr4 2/2  ,  Tlr2/4 2/2  ,  Card9 2/2  ,  Tlr7 2/2  ,  Myd88 2/2  ,  Tlr9 2/2  ,  Ifnar1 2/2  ,  Stat1 2/2  ,  Stat2 2/2  ,  Clec4e 2/2  ,  Fcre1g 2/2  , and  Nod2 2/2  mice used in this study;  Geraint Millar  and  Kathy Allsopp  for histology preparations; and  Scott Durum  for critically reviewing this manuscript.
This work was supported by a  Sir Henry Dale Fellowship jointly  funded by the  Wellcome Trust  and the  Royal Society  (Grant  099953/Z/12/Z ) (to S. J. O. ) and an  Arthritis Research UK  Fellowship (Ref. 20305) (to G. W. J. ). P. R. was supported by  Deutsche Forschungsgemeinschaft Cluster of Excellence Inflammation at Interfaces and Deutsche Forschungsgemeinschaft  Grant  SFB 877 ,  TP B9 ; P. R. T. is supported by  Medical Research Council UK  Grants  MR/J002151/1  and MR/K02003X/1; R. L. is supported by  Deutsche Forschungsgemeinschaft  Grant  SFB 796 ,  TP B6 ; C. E. B. is supported by  Biotechnology and Biological Sciences Research Council  Grant  BB/ K006436/1 ; and I. R. H. is supported by a  Wellcome Trust Senior Research Fellowship in Basic Biomedical Sciences  ( Ref. 098026 ).
e. the rapid fixation of non-native alleles in the genome of native species, for example between the non-native Barred Tiger salamanders and the native California one  (Fitzpatrick et al. 2010). In this context, we consider two newly reclassified although strongly differentiated species in the genus Ciona. These two species were considered as cryptic species of the Ciona intestinalis species complex and formerly named C. intestinalis type A and C. intestinalis type B  (Nydam & Harrison 2007; Zhan et al. 2010). Following recent taxonomic revision, they are now accepted as two distinct species (WoRMS database) and respectively named C. robusta and C. intestinalis  (Brunetti et al. 2015). They display a divergence estimated at ca. 4 Mya  (Roux et al. 2013). Currently, the two species, and particularly C.
Roux et al. (2013)  adjusted a secondary contact model to a population transcriptomic dataset and inferred, under this model of a single contact, that introgression lasted for 15,000 years (95% CI: 4,300 -56,800) during which ca. 20% of loci presumably crossed the species barriers in both direction. Most probably the two taxa repeatedly came into contacts both in past-and present time. This situation is prone to the misinterpretation of contemporary admixture when few loci are used. Among the samples studied by  Bouchemousse et al. (2016b) , what appear to be a few individuals with hetero-specific alleles could indeed be a consequence of a low genome-wide level of past introgression (e. g. only 1 to 4% of the genome of present-day non-African humans derived from gene flow between Neanderthals and modern humans  (Green et al.
Loci selection and genotyping An Illumina BeadXpress® with Veracode TM technology (GoldenGate® Genotyping Assay) was used to genotype 384 single nucleotide polymorphisms (SNPs) selected from a SNP dataset detected in the full transcriptomes of 10 individuals of C. robusta and 10 individuals of C. intestinalis (details in  Roux et al. (2013) ). The loci were first chosen to maximize their genotyping success: Because we used transcriptome data, we identified exon borders by aligning our data with C. robusta genome (vKH. 71 from Ensembl; note that the genome name is misleading as it is labelled "C. intestinalis" although it is from C. robusta following the recent taxonomic revision  (Brunetti et al. 2015) ). Polymorphic sites closer than 20bp from exon border were automatically excluded. Polymorphic positions were selected within exons to produce an individual sequence for each given SNP compatible with the Assay Design Tool (ADT) software available on Illumina webpage.
Thus, we expanded the SNP panel with polymorphic loci showing less divergence and shared between the two species. In addition, the 384 SNPs were selected to be spread over most of the chromosomes of the published genome of C. robusta  (Dehal et al. 2002)  and 25 of them were localized in introgression hotspots identified by  Roux et al. (2013). At the end, we enriched the panel with sf (101) and ss (47) SNPs and equalized the number of sxA (109) and sxB (127) SNPs as C. intestinalis is more polymorphic than C. robusta. A subset of 70 SNPs that strictly reflect the genome wide site frequency spectrum (i. e. randomly selected) was included in the SNP panel. Genotyping was performed using Genome Studio software (Illumina Inc. ). Out of the 384 SNPs, 324 SNPs amplified successfully and 310 SNPs were retained for further statistical analyses.
Intra-specific analysis In order to compare sympatric and allopatric populations, genetic studies were carried out for both C. robusta and C. intestinalis. Only loci that were polymorphic in the targeted species were used. For the few SNPs chosen in the same contig, only one SNP was selected, the one showing the maximum value of the minor allele frequency. Totals of 111 and 150 polymorphic loci were retained for C. robusta and C. intestinalis, respectively. Genetic diversity. At the intra-specific level, for each population, the number of polymorphic loci and the expected heterozygosity (He) were estimated using GENETIX v. 4. 05 software  (Belkhir et al. 2004). Fixation index (FIS) was estimated and departures from Hardy-Weinberg equilibrium were tested in each population using GENEPOP v4 with default parameters for tests.
P-values resulting of multiple tests were adjusted using the R package v. 3. 1. 3 (R Development Core Team 2014) QVALUE  (Storey 2002). Genetic structure. Genetic structure between populations was analyzed by estimating the fixation index FST  (Wright 1951)  using GENEPOP. Exact G test for population differentiation were carried out using 10,000 random permutations. To visualize the genetic structure between populations, a Discriminant Analysis of Principal Components (DAPC;  (Jombart et al. 2010 )) was computed for each species separately using the R package ADEGENET v. 1. 4 (Jombart & Ahmed 2011).
Genome and population admixture analysis between the two species To identify putative F1-or recently introgressed individuals (product of several generations of backcrosses within the sympatric range), a Bayesian clustering method implemented in NEWHYBRID software v. 1. 1 was used  (Anderson & Thompson 2002)  using the global dataset of 310 loci, the dataset of 58 random SNPs, as well as a dataset of the 105 most differentiated loci. Briefly, this method computes posterior probability for assigning a given individual to different hybrid categories (i. e. F1, F2-hybrids and backcrosses with parental C. robusta or C. intestinalis individuals) or parental species, using Markov chain Monte Carlo algorithms (MCMC). Here, we considered allopatric populations as representative of the parental species.
We ran five independent analyses (each using a different random starting value) with 500,000 MCMC after a period of 500,000 burn-in cycles using the Jeffreyslike prior. To examine inter-specific gene flow at the genome level, we used the R package INTROGRESS  (Gompert & Buerkle 2010). As the ancestral allelic state has to be defined (based on the minor allele frequency in each species), we selected 105 loci that were the most differentiated loci according to FST values (FST > 0. 9) computed between the two species using allopatric populations (Figure  S2 ). Such a selection is common practice in hybridization studies (e. g. between Mytilus species  (Saarman & Pogson 2015)  or Gryllus crickets  (Larson et al. 2013 (Larson et al. , 2014)) ). For each individual, the maximum likelihood value of hybrid index was estimated.
The hybrid index (h) is defined as the proportion of C. intestinalis alleles over all loci (h = 0 for individuals with C. robusta alleles only and h = 1 for individuals with C. intestinalis alleles only). To visualize and compare the genomic architecture of interspecific admixture at the individual level, the mk. image function implemented in INTROGRESS was used. NEWHYBRIDS and INTROGRESS analyses were also done using a small dataset made of the three nuclear markers used in previous studies as putatively species-diagnostic (i. e. Hox5, vAChTP and CesA, see "Loci selection and genotyping" section above). The inter-specific admixture rate was investigated on the total dataset (i. e. 310 loci) using a Bayesian clustering method implemented in STRUCTURE v. 2. 3  (Pritchard et al. 2000)  and a Principal Component Analysis (PCA) using the R package ADEGENET v.
1. 4 (Jombart & Ahmed 2011). The method implemented in STRUCTURE method used MCMC to generate posterior probabilities of assignment of each individual genotype to a number of clusters (K). Ten replicates of 500,000 MCMC after a period of 500,000 burn-in cycles were ran for K values ranging from 1 to 4; K = 2 is corresponding to the two species clusters. Results were summarized across all replicate runs using CLUMPP v. 1. 1. 2 (Jakobsson & Rosenberg 2007)  and visualized with DISTRUCT v1. 1  (Rosenberg 2004 ). To check for the absence of biases due to marker selection, we also ran STRUCTURE for K = 2 using additional dataset: 1) a subset of 58 loci selected to represent a random sampling of the genome, 2) a subset of 105 loci selected for the INTROGRESS analysis, 3) 245 SNPs corresponding to all the SNPs except those differentially fixed between the two species, 4) only those SNPs that were polymorphic in the two species (42 SNPs).