dataesr/scientific-paragraphs-categorization huggingface dataset:
Initial and principal domain annotation was performed using the Pfam database (release 24. 0) and HMMER software (version 3. 0). Only domains satisfying the Pfam-recommended thresholds (gathering cutoffs) were retained. Overlaps were resolved heuristically by selecting the domain with a strategy based on the best E-value. Additional domains were assigned using Interproscan (v4. 3) including SUPERFAMILY, GENE3D, TIGR-FAMs, SMART, PROSITE and PRINTS domain models. Proteins were further annotated by GO terms. We created GO annotations with two levels of confidence. The first level is high confidence. Pfam domains and other domains from the previously mentioned databases are annotated by GO terms (pfam2go, smart2go and so on mappings), as well as the Interpro entries (interpro2go). The annotation of a given domain corresponds to the GO terms shared by all annotated proteins possessing this domain (or significantly over-represented for superfamily2go).
Hence, when a domain is identified in a protein, the GO annotation of this domain can be safely transferred to that protein. The second level is low confidence. Blast2GO, which is prone to 35% annotation errors, was applied with default values to transfer GO terms significantly overrepresented in the best BLASTP hits of termite's proteins against the NCBI nonredundant database. Note that based on the BLASTP results against the NCBI, we created the list of orphan genes in Z. nevadensis, if no detectable homology (E-valueo10e À 3) was obtained. The KEGG Automatic Annotation Server was used to assign proteins to KEGG orthology (KO) groups, using the recommended eukaryote set plus all other available arthropods as references. The KO system is the basis of the KEGG database, since it links annotated proteins to KEGG's metabolic pathways (PATHWAY) and functional ontology (BRITE).
nevadensis protein repertoire with those of D. melanogaster, T. castaneum, N. vitripennis, A. mellifera, C. floridanus, H. saltator, A. pisum, P. humanus and the crustacean D. pulex. Families exhibiting expansion were detected using Fisher's exact tests (pairwise comparisons of Z. nevadensis with other genomes) on protein domain architecture counts using Pfam, or Interpro for uncovered families (Supplementary Note 5. 5). In addition, the OrthoMCL procedure was run using standard parameters on these species and C. elegans to allow a finer perspective over subfamilies (Supplementary Note 3. 2). Phylogenetic analysis. We conducted phylogenetic analysis to ascertain the position of termites in the evolution of arthropods. Several data sets of orthologous proteins were tested (see below), but the procedure used for phylogenetic reconstructions was the same for each data set: (1) protein sequences were aligned with MAFFT; (2) alignments were cleaned with Gblocks; (3) protein alignments were concatenated into a unique protein superalignment; (4) the underlying DNA superalignment was deduced using only the first two nucleotides of each codon (custom scripts); and (5) four topologies were computed using the two superalignments (nucleotides and amino acids) from two perspectives: a maximum likelihood approach (morePhyML script based on PhyML) and a Bayesian approach (Phylobayes software).
4), which may probably be misinterpreted as highly derived genes and thus introduce further artefacts; (4) the high phylogenetic distance of this non-insect species from the common ancestor of termites and Paraneoptera might prevent clarification of the ancient rapid radiation of these taxa. We then searched for clear 1:1 orthologues in the expressed sequence tag (EST) data sets of the NCBI non-redundant database. We used reciprocal BLAST best hits with the termite proteins as queries and required a threshold E-value of 10e À 50 and a match covering at least 60% of the proteins. We identified three taxa, Diplura, Archaeognatha and Thysanura, offering a common set of 16 orthologous proteins. These taxa are outgroups of Neoptera and belong to the Hexapoda clade (Supplementary Fig. 4 ). The topologies resulting from this second analysis agreed with the most recently published topologies and the fourth topology had a polytomy that did not contradict the other proposed grouping (Supplementary Fig.
Additional information Accession Codes: The Whole Genome Shotgun project for the dampwood termite Z. nevadensis has been deposited in the GenBank nucleotide core database under the accession code AUST00000000. RNA sequencing data have been deposited in the GenBank sequence read archive (SRA) under the accession code SRP022929. Supplementary Information accompanies this paper at http://www. nature. com/ naturecommunications Competing financial interests: The authors declare no competing financial interests. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3. 0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material.
From 1966 to 1974, the mandatory notification of cases resulted in an average reported incidence of 4. 3 cases per 100,000 inhabitants per year. From 1975 to 1985, when two sources of data were available, the average incidence varied from 7. 5 to 13 cases per 100,000 inhabitants. For 1982 only, the incidence varied from 7. 4 to 21. 3 cases per 100,000 inhabitants. From 1987 to 1997, no data were available from the literature, the regional health agency reports or the NRC reports. From 1998 to the early 2000s, as the number of strains sent to the NRC was increasing, two studies were conducted to assess the burden of leptospirosis: a descriptive study in 2002 and a case control study in 2003 to precisely identify the determinants of leptospirosis on the island  [28, 29]. In the case control study, two analyses were conducted.
The forms were then transmitted to the Cire OI for the data to be analyzed. A medical form providing information concerning the patient, clinical symptoms, outcome, and biological diagnosis was completed by the practitioner following admittance of the patient. Practitioners who sent an incomplete form were contacted by the CVAGS for data completion. Cases were classified on the basis of case definitions that included clinical and/or biological data. Two types of cases were considered: confirmed cases (positive cultures, positive PCR from blood or urine, or positive MAT on a single serum with titer >1/400) and possible cases (clinical manifestations compatible with leptospirosis (fever >38. 5 °C with arthralgia and myalgia) and positive ELISA IgM). Cases that did not fit the definition (lack of biological proof, isolated positive ELISA IgM) and non-hospitalized cases were excluded.
Analysis The study analyzed data from the 2004-2012 period. Data from the medical and environmental forms were recorded using EPIData 3. 1 ® and analyzed with Stata 11 ® statistical software using the chi-squared test for observed frequencies and the t-test for quantitative data. A multiple correspondence analysis was conducted to describe the population of the hospitalized cases according to their identified exposures to leptospirosis. Then, an agglomerative clustering made on variable modalities was performed to describe specific high-risk groups of people. Demographic data from the French Institute of Statistic and Economic Studies (INSEE) were used to calculate the incidence rates by year, as well as within different periods of study on the island and in the 24 communal districts. Using the regional database PMSI (Programme Medicalise des Systemes d'Informations), an estimation of the annual hospital cost of leptospirosis was made using the related cost of the GHS (homogeneous group of stays) including leptospirosis and the mean per day cost of an intensive care unit (ICU) stay.
Data from the French NRC for leptospirosis were used to estimate the infecting serogroup on Reunion Island. The NRC receives serum samples from mainland France and French overseas territories (approximately 4,500 samples each year) to perform the serological diagnosis of leptospirosis by MAT and ELISA IgM. The NRC also collects the diagnosis data from other laboratories. For Reunion Island, the diagnostic data include the PCR data from the university hospital Félix Guyon (Saint-Denis Réunion) and the PCR and MAT data from the university hospitals of Groupe Hospitalier Sud Réunion (Saint Pierre), as well as, to a lesser extent, the private French laboratories. Annual reports from the NRC can be found in the NRC and Pasteur Institute websites  [14, 30].
Identification of Leptospira Serogroups Involved in Human Leptospirosis Infections on Reunion Island From 2004 to 2012, the NRC received serum samples or collected diagnosis data for 629 leptospirosis cases on the island, including 267 cases that were diagnosed by PCR. MAT analyses were available for 338 cases, and the serogroup Icterohaemorrhagiae was found in 194 (57. 4%) cases. Other samples included primarily serum taken very early in the disease, which showed a high degree of cross-reactivity between different serogroups as previously described in acute-phase samples  [32].
Utilization of the Data Obtained from the Environmental Forms Environmental data were available for 405 hospitalized cases (385 confirmed cases and 20 possible cases) and 32 non-hospitalized cases (26 confirmed cases and six possible cases). 437 infections occurred in men (384 hospitalized and 27 non-hospitalized) and 26 in women (21 hospitalized and 5 non-hospitalized). The environmental investigations were conducted for 350 cases: 319 hospitalized cases (309 confirmed cases and 10 possible cases) and 31 non-hospitalized cases (30 confirmed cases and one possible case). The total number of investigations that were not conducted was 88 (77 confirmed cases and 11 possible cases). The primary reason investigations were not conducted was the refusal of the patients or their families. The distribution of leptospirosis cases by age and sex is presented in Figure  4.
Nevertheless, for 41% of cases, the place of infection could not be determined due to the accumulation of residential and non-residential exposures. A multiple correspondence analysis was performed (data not shown). However, the two main axes of analysis could explain less than 20% of the observed variability but distinguished between people belonging to a high-risk profession and showed a possible correlation between young age and the practices of bathing, fishing and hunting. In addition, agglomerative clustering permitted different groups of individuals to be identified. The first group (women and people over 60 years of age) included populations that were not significantly affected by leptospirosis. Meanwhile, this clustering highlighted the following groups at higher risk: People belonging to a high-risk profession, people under 20 years of age that participate in aquatic activities, people between 20 and 30 years of age that fish and people between 50 and 60 years of age that garden at home.
Discussion From 2004 to 2012, there was an increase in the number of reported leptospirosis cases to the regional surveillance system. This phenomenon occurred in part due to improvements in the system compared to the reports of the French NRC for leptospirosis  [14]. The discrepancy between the surveillance and the NRC data occurred mainly during the first few years following implementation of the surveillance system. Since 2008, the data from both sources have been similar. While the surveillance system may underestimate the incidence of leptospirosis resulting in hospitalization, the trends in this disease over the years are well estimated and the findings of the regional surveillance are now reliable. Nevertheless, the surveillance system is focused on hospitalized cases and is most likely underestimating the number of ambulatory cases.
In contrast to Wennberg, 2010, we either recorded ECOG, which has a consistent location relative to the grey matter imposed by physical constraints, or from bipolar transcortical SEEG, which must be locally generated given the amplitudes that we observed. Nir et al. , who recorded SEEG relative to a largely inactive reference (linked earlobes), found KCs in ventromedial temporal limbic structures associated with decreased unit firing, supporting local generation  [20]. Together with our observations, these data suggest that ventral temporal structures also generate KCs. Nir et al. also found that slow waves in the medial temporal lobe limbic cortex systematically followed those in medial frontal cortex by about 180 ms  [20]. This difference from our results could reflect the fact that their observations were mainly of SOs, or that they were between cortical and limbic areas rather than between neocortical locations.
Intracortical exploration of temporal neocortical areas and of the medial pulvinar nucleus was possible using a single multicontact electrode, so that thalamic exploration did not increase the risk of the procedure by requiring an additional electrode track. All patients were fully informed of the aim of this investigation and gave their written consent for the implantation and recording procedure, which was approved by the local ethics committee. The data were sampled at 256 Hz and a 0. 33-128 Hz band pass filter was applied. Spontaneous KCs were recorded during NREM sleep. EEG recording was obtained in one 23 year-old female subject during a full night recording. The subject was free of any neurological disorders, was not taking medication, and did not have caffeine or alcohol on the recording day.
g. 100 for PY neurons). Population specific measures of conductance, current, calcium levels, and inactivation and activation states were measured for PY, TC, and RE neurons. For PY neurons, these measures were: average axosomal I Na(p) ; average dendritic I Na(p) ; average I K(Ca) ; average I KL ; and level of calcium. For TC neurons, these were: average g h conductance; average I h ; average I T ; average I KL ; I T inactivation and activation states; sum of PY to TC total currents; and level of calcium. For RE neurons, these were: average I T ; average I K current; I T inactivation and activation states; and sum of PY to RE total currents. Spindle and High Gamma Power were calculated using Morlet wavelets or the Hilbert transform with customized Matlab routines incorporating the publicly available FieldTrip toolbox  [89].
This work was funded by  NIH   R01 MH099645 ,  R01 EB009282  (http://www. nih. gov/), ONR (MURI)   N000141310672  (http://www. onr. navy. mil/),NSF GRFP (http://www. nsfgrfp. org/)and Chateaubriand Fellowship (http://www. chateaubriand-fellowship. org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Most applications of this model are related to the study of irrigated areas, for the effective planning and use of irrigation water. In recent years, sustained scientific activity based on the interpretation of remotely sensed data has made it possible to develop various methodologies for the characterization of the spatio-temporal variability of continental surface parameters (vegetation characteristics and soil moisture), on both local and global scales. In the case of vegetation cover, various indices based on the use of optical data have been proposed for the retrieval of vegetation characteristics (e. g. , leaf area index, vegetation fraction, NDVI (Normalized Difference Vegetation Index), etc. ). The NDVI is the most commonly used index, and is expressed by the ratio: NDVI = (RNIR -RRED)/(RNIR + RRED), where RNIR is the near-infrared (NIR) reflectance and RRED is the red reflectance.
In this context, the aim of the present study is to illustrate the ability of the FAO-56 dual approach to estimate evapotranspiration at regional scales, without making use of complex physical surface models requiring large quantities of input data. In an initial step, the effectiveness of the FAO-56 dual approach, which is commonly used for irrigation management  [9, 10] , is evaluated. Then, the combination of this model with data generated by remote sensing is considered, not only for the study of vegetation as proposed in other studies  [9] [10] [11] [12] 14] , but also for the purposes of soil moisture analysis. Under such conditions, the spatio-temporal variations of these two fundamental parameters can be taken into account in the transpiration and evaporation estimations. In Section 2, the studied site and the remotely sensed and ground databases are presented.
Precipitation Data Precipitation estimations were based on a network of 30 rain gauges, distributed over the entire site (Figure  1 ). The Inverse Distance Weighting (IDW) interpolation algorithm was used to derive daily precipitation maps. This algorithm estimates values at non-sampled points, by computing the weighted average of data observed at nearby points  [49, 50]. The landscape is mainly flat in the validation areas, and there is no mountainous terrain able to influence the spatial distribution of rainfall. The precipitation time series and the NDVI data set are thus available with a spatial resolution of 1 km.
Meteorological Data Meteorological data, including air temperature, humidity, wind speed, net radiation and rainfall measurements, have been recorded over the last 20 years by an automatic weather station located in the Kairouan Plain. Daily averaged climatic parameters were computed in order to determine the daily reference evapotranspiration ET 0 (mm/day), in accordance with the FAO-56 Penman-Monteith parameterization  [51]. The global radiation was determined from Mé té osat data  [52]  retrieved from the SoDa server (Solar radiation Databases for environment  [53] ), established by the Mines ParisTech graduate school. In this database, global radiation data is available from January 1985 to December 2005, at temporal intervals of one day and a spatial resolution of 20 km.
Analysis of the ISBA-A-gs Soil Moisture Output In Figure  3 , the ERS/WSC soil moistures, validated by Amri et al. [43]  over the studied site and described in Section 2. 2, are compared with the output generated by the ISBA model, and are plotted together with the precipitation time series. Three statistical parameters: RMSE (the root mean square error), R 2 (the coefficient of determination), and the bias are used to compare the ERS and ISBA datasets. The satellite data products are compared with two ISBA-A-gs outputs; the modeled top layer (the first five centimeters of soil) and the soil moisture profiles (down to a depth of 100 cm), for the 16-year period from 1991-2007. It should be noted that the ERS measurements and the corresponding remotely sensed moisture products are not available for the period from 2001-2003.
The statistics of the compared data are good: RMSE equal to 0. 03 m 3 •m -3 , R 2 = 0. 5, and a low bias equal to 0. 008. A change in behavior can be observed in 1997: before this date, less than one data point (determined using the ERS1 scatterometer only) was available per week, from which the algorithm could be developed. After 1997, the ERS1 and ERS2 scatterometers were both able to provide a combined two to three data points per week, for use in the SWI estimations, and there is thus a difference in the product's accuracy between these two periods. Although the SWI itself is not used in the evaporation estimation, comparisons made with this product are used to validate the ISBA-A-gs model over the studied site.
Inter-Comparison between ISBA-A-gs and FAO-56 Approaches Figure  4  compares the ISBA and FAO model evapotranspiration simulations over the studied area, for a single ISBA pixel with a spatial resolution corresponding to 0. 5° in latitude and 0. 5° in longitude, for the periods between 1998 and 2000 and between 2004 and 2005. These two products are compared only on dates for which ERS/WSC-based determinations of the K e evaporation parameter are available. The two products are found to be in good agreement, and the statistical parameters derived from the FAO simulation are reasonable: RMSE = 0. 36 mm/day, with a correlation R 2 = 0. 55. The discrepancies observed at some points in this figure are related, in particular, to the soil evaporation component, and to the occurrence (or not) of a precipitation event: all of the data points characterized by a strong discrepancy between the two models involve a precipitation event, which was taken into account by one of the models, but not the other.
Acknowledgments This study was funded by two sources: the  French national MISTRALS program , and the  ANR   AMETHYST -ANR-12-TMED-0006-01‖. The authors extend their thanks to VITO for kindly providing them with its SPOT-VEGETATION NDVI products, and to the  ISIS program  for providing them with the SPOT images used in this study. They would also like to thank the  Tunisian Ministry of Agriculture  for providing the precipitation data used in this study, as well as the technical teams of the  IRD, INAT, CTV-Chebika and INGC  for their strong collaboration and support with the implementation of ground-truth measurements.
Adult medulloblastoma (B. Atalar) Medulloblastoma is a common malignancy in the pediatric patients with malignancies affecting the central nervous system. However, it accounts for only 1% of all adult brain tumors and the data for adults is generally reported in very small series. Thus, there is little consensus in the literature as to the optimal treatment of adult patients. 3 Due to paucity of data because of the relative infrequency of adult medulloblastoma, treatments are typically performed according to pediatric protocols. We aimed to report the outcomes, prognostic factors and the best treatment strategy of a large group of adult patients by the participation of our colleagues from RCN. This project began in late 2011 and until now we have collected the data of more than 100 patients from 8 centers.
Glomus tumors (Y. Lassen-Ramshad) Paraganglioma of the head and neck region are rare, mostly benign, neuroendocrine tumors. 4 For this retrospective study, patient-, tumor-, radiotherapy-and outcome data about 75 paraganglioma, treated with irradiation, were submitted for analysis from 12 institutions of the Rare Cancer Network. Survival, local control and late toxicity data are being analyzed. Preliminary analysis indicates that the overall survival is good and that the treatment is in general well tolerated, sometimes late recurrences can occur.
Also, case control studies including case patients that are irradiated and control patients that are not may be useful to limit selection biases and provide even higher level of evidence for the role of radiation therapy in rare diseases, adding to the major contributions of the RCN to radiation therapy. The role of irradiation will also be regarded with respect to technological advances. The rapidly decreasing costs of genomic characterization promises a new opportunity for rare tumor research that may allow for characterization of potential chemotherapeutic targets for novel agents utilizing relatively small sample sizes. Genomic profiling raises the possibility of every tumor type becoming rare through its unique genetic makeup. 16 dditionally, advances in electronic medical records and analytics may permit large population based studies with more discrete endpoints than have been possible in the past with resources such as the SEER database.