dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analyses The effect of the origin of the soil suspensions on the enzymatic assays was determined by analysis of variance (one factor ANOVA). Quantification data from real-time PCR were compared as Log gene copy number between the two soil horizons through a Student-t test. To determine the taxonomic, metabolic and CAZyme differences between the organic and mineral metagenomes extracted from MG-RAST, one-factor (horizon origin) ANOVA at a threshold level of P = 0. 05 and a Bonferroni-Dunn test were applied on the relative distribution values after an arcsine transformation. All statistical analyses were performed using the Superanova software (Abacus Concepts, Inc. , Berkeley, CA). Taxonomic (based on the genera assigned in MG-RAST; H' T ), functional (based on the functional categories assigned in MG-RAST; H' F ) and metabolic diversity (based on the Biolog profiles; H' m ) levels per biological replicate were estimated using the Shannon index (H').
Mantel tests (10,000 permutations, Pearson correlations) were performed in XLstat2011 (Addinsoft, Paris, France) in order to test correlations between biolog, metagenomic functions and SEED genera, based on Euclidean distances dissimilarity matrices generated from scaled data. In this analysis, principal component axis 1 and 2 explain most of the variance in the data cumulatively (F1 = 37. 3% and F2 = 21. 3%). B. Analysis of the relative proportion of the major functional categories present in the metagenomic data of the organic and mineral soil horizons. In this analysis, principal component axis 1 and 2 explain most of the variance in the data cumulatively (F1 = 72% and F2 = 8. 89%). Soil metagenomes are presented as follow: red squares, biological replicates from the organic horizon; blue squares, biological replicates from the mineral horizon.
Distribution of phylogenetic groups in forest soil organic (ORG-S) and mineral (Min-S) horizons. A. RDP and SEED-bases analysis. The distribution of the reads and contigs generated in this study was performed using all the annotated reads against the SEED database and the identified 16S rRNA fragments against the RDP database. B. Community comparison. The phylogenetic heatmap presented was performed using the Bray-Curtis similarity matrices generated by MG-RAST on the organic (O1,O2 and O3) and the mineral (M1,M2 and M3) metagenomic data. doi:10. 1371/journal. pone. 0055929. g002 Table  2. Comparison of the organic (O) and mineral (M) metagenomes at the domain, phylum and class levels. drolase activities detected in the soil solutions were significantly higher in the organic soil horizon (P,0.
Taxonomic Analyses Metagenomic DNA extracted from each soil replicate was used to assess the structure and diversity of the soil microbial communities inhabiting the two soil horizons. According to the SEED database of the MG-RAST portal, the microbial communities inhabiting the two soil horizons were taxonomically similar (Figure  2A  and 2B ). This analysis also highlighted that ca. 53% of the pyrosequencing reads had a significant match in the nucleotide databases, which corresponded to a total of 1,064,196 reads from the Min-S samples and 1,134,455 from the Org-S samples. Of these, the vast majority of the matching reads (ca. 94% for each horizon) belonged to bacteria, with a significant higher proportion in the organic horizon (Table  2 ), supporting the quantitative results obtained by the real time PCR (Table  3 ).
2660. 35% for Min-S and 8. 9460. 27% for Org-S), Candidatus Koribacter (Acidobacteria; 7. 1060. 04% for Min-S and 7. 3360. 20% for Org-S), Bradyrhizobium (Proteobacteria; 3. 5560. 09% for Min-S and 3. 6360. 12% for Org-S) and Burkholderia (Proteobacteria; 3. 0160. 14% for Min-S and 3. 3760. 19% for Org-S). Although the taxonomic diversity (H' T index based on the genera identified through SEED assignment) and the rarefaction analyses were not significantly different between the two soil horizons, significant Figure 3. Functional analysis of the organic and mineral horizon metagenomes based on the MG-RAST database. The reads from the soil organic and mineral horizons of the forest experimental site of Breuil-Chenue (France) were screened for known functional subsystems. The data presented here corresponds to the hierarchy subsystem 1.
0005), nucleosides and nucleotides (p = 0. 0008), protein metabolism (p = 0. 0005), regulation and cell signalling (p = 0. 0045) categories. doi:10. 1371/journal. pone. 0055929. g003 differences were measured in the relative distribution of some bacterial genera (n = 120; Data not shown). Among the most abundant, C. solibacter and Burkholderia were significantly enriched in the mineral horizon and the organic horizon, respectively (P solibacter = 0. 03; P Burkholderia = 0. 001). Similarly, Solibacter (6. 7260. 29%) and Bradyrhizobium (4. 8960. 64%) were dominant in the grassland soil metagenomes of the experimental station of Rothamsted  [26]. Notably, monogenic (16S rRNA) metagenomic studies performed on the Breuil-Chenue forest site have also showed that these bacterial genera were among the five dominant genera  [7, 35].
The prevalence of these genera was also highlighted in other soils  [4, 20, 50]. Regions of the 16S rRNA gene sequences were found in our metagenomic dataset and used for confirming the taxonomic distribution. A total of 573 and 667 reads (0. 05% of the total reads assigned to bacteria) from the Min-S and Org-S samples, respectively, had a significant match with the 16S rRNA gene sequences in the RDP database. Although the 16S rRNA-based analyses are known to provide more accurate taxonomic information, the limited number of 16S rRNA gene fragments identified here precludes relevant statistical analyses. Low proportions (0. 01 to 0. 20%) of 16S rRNA gene sequences were also reported in other shotgun studies such as in biogas fermenters  [51]. Notably, both classifications (RDP and SEED) gave similar results, with the exception that the Verrumicrobia and Plancto-mycetes were relatively more abundant in the RDP-based classification (Figure  2A ).
Notably, most of the fungal reads belonged to Ascomycota according to the MG-RAST or NCBI databases. A significant enrichment of sequences related to Sordariomycetes was observed in the organic horizon (Table  2 ). These fungi are ubiquitous and most of the members of this phylogenetic class are considered as potential pathogens, endophytes and/or saprobes involved in plant organic matter decomposition and nutrient cycling. However, in this same spruce plantation, two species diversity surveys previously showed that the number of fungal species was relatively high  [12, 31]. The gap between the eukaryotic data obtained by our shotgun metagenomic approach and the diversity observed in the same experimental site by other methods illustrates the need to use alternative approaches such as metatranscriptomics targeting polyA RNA  [55] [56]  to study the soil eukaryotic communities.
Illumina Contribution to Soil Metagenome Characterisation The mgDNA samples sequenced by 454 pyrosequencing were also sequenced using the Illumina sequencing. Although the assignment of reads with a size of approximately 75 bp was complex, both the taxonomic and functional analyses were performed using MG-RAST and the SEED database with the default parameters (Table  4 ). In contrast to the 454 sequences, only 25% of the Illumina sequences had a significant match in the databases, which corresponded to a total of 18. 5610 6 reads from the Min-S samples and 29. 2610 6 reads from the Org-S samples. Comparative analysis of the two soil horizons based on the replicates also revealed that 8 and 6 functional categories (Level 1 of MG-RAST) were significantly more abundant in the organic and in the mineral horizon (p,0.
Relationship between Metabolic Potentials, Functional and Taxonomic Diversity Our metagenomic datasets highlight a significant increase of the metabolic diversity (H' m ; O. M, P = 0. 01) and functional diversity (H' F ; O. M, P = 0. 01) in the organic horizon compared to the mineral horizon. Although some differences in the taxa distribution were observed for the bacteria, archaea or eukaryotes, the diversity indices were not significantly different, suggesting that the communities were taxonomically quite similar between the two soil horizons and with a similar diversity, but differentiated at the functional level. Notably, Will et al. [9]  and Jumpponen et al. [47]  reported that the diversity indices decreased with depth in a grassland soil, suggesting that this diversity was linked to the microbial biomass, which is known to decrease with soil depth.
Halobacteria*** *P,0. 05, **P,0. 005, ***P,0. 0005. Identity was determined using the SEED database of MG-RAST with an e-value cut-off of 1e205. The relative distributions of the sequences in the different taxonomic levels considered were analyzed by one-factor ANOVA (and a Bonferroni-Dunn test, P,0. 05). doi:10. 1371/journal. pone. 0055929. t002.
Acknowledgments The  UMR1136   INRA 'Interactions arbres microorganisms ' is supported by the  Labex 'ARBRE '. We thank  Drs J. Ranger ,  P. Frey-Klett  and  L. C. Kelly  for helpful discussions. The English language was reviewed by American Journal Experts. We would like to thank the reviewers, and especially Reviewer 1 for his assiduous implication in the improvement of our manuscript.
This work was funded by the '' Lorraine Region Council '', the  INRA (Institut National de la Recherche Agronomique) Center of Nancy , the  French National Research Agency (ANR   Metasoil , Project  ANR-08-GENM-025 ) and the  European project 'ECOFINDER'. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Aim: The objective of this study was to describe the French practice of hypothermia treatment (HT) in full-term newborns with hypoxic-ischemic encephalopathy (HIE) and to analyze the deviations from the guidelines of the French Society of Neonatology. Materials and Methods: From May 2010 to March 2012 we recorded all cases of HIE treated by HT in a French national database. The population was divided into three groups, "optimal HT" (OHT), ''late HT'' (LHT) and ''non-indicated'' HT (NIHT), according to the guidelines. Results: Of the 311 newborns registered in the database and having HT, 65% were classified in the OHT group, 22% and 13% in the LHT and NIHT groups respectively. The severity of asphyxia and HIE were comparable between newborns with OHT and LHT, apart from EEG. HT was initiated at a mean time of 12 hours of life in the LHT group.
Over the last fifteen years, several randomized trials on the neuroprotective effect of hypothermia (HT) have been published  [12] [13] [14] [15] [16] [17] [18]. The results are summarized in four meta-analyzes, which show a reduction of 25% in the combined risk of death and major neuro-developmental disability at 18 months (RR = 0. 76 [0. 65 to 0. 89])  [18] [19] [20] [21]. Currently, HT is the standard treatment for HIE, and in 2009, the French Society of Neonatology (SFN) published guidelines on both the indications for HT and how it should be performed  [22]. The role of HT on the medium and long term prognosis of these children remains unclear. Databases set up in England and the USA (Toby Cooling Register and Vermont Oxford Register) could help provide answers to this question  [9, 23, 24].
In France, in May 2010, the SFN set up a database with similar objectives. It is intended to register all HIE cases admitted to neonatal intensive care units (NICU), whether treated or not with HT, and to ensure their subsequent follow-up. To our knowledge, few studies have been published on the evaluation of the practice of HT in the various countries where this treatment is recommended. This is necessary before any assessment of the long term impact of this new treatment can be made. The aim of this study was to describe the practice in France for full-term newborns with HIE treated by HT, and to analyze deviations from the SFN guidelines and the reasons for these.
Materials and Methods Since May 2010, the full-term neonate HIE database records newborns of gestational age (GA) $ 36 weeks, weighing $ 1800g and presenting with HIE (mild, moderate or severe), regardless of the treatment (HT or standard care). All French Level III NICU (including overseas territories) have secure access and reporting of cases is declarative, without control of completeness. During the study period, 33 level III NICUs among 57 nationwide included newborns in the database, with a mean number of infants reported per center of 9. 2 (+ / -8. 2). As of  March 22, 2012 , the database contained 465 cases registered in 23 months. Not all French Level III NICU participated, so the number of newborns included is not exhaustive.
Ethics statement Data collection was approved by the French authority entitled ''Commission Nationale de l'Informatique et des Libertes'' (National Data Protection Authority, Ref: AT/FLR/DI103637, Authorization Nu1426721, 2010-266). This data collection was initiated in 2010 to study the newborns with HIE and to assess the implementation of the hypothermia treatment in France. No written consent from the parents was required by this French authority. According to their guidelines for an observational study, we advised clinicians to provide a parent information leaflet about data collection. If parents express a disagreement with this survey, none data collection on their child was performed but we did not collect this information from each centers. The main finality of this data base, specified by the approving of the Commission Nationale de l'Informatique et des Libertes, is to use the data for statistical and epidemiological analysis on order to ameliorate the management of newborns with HIE.
Selection of the study population and variables studied Our study included all newborns reported in the database between May 2010 and March 2012 except newborns with missing data concerning at least one of the criteria for the indication of HT (n = 40) and those with HIE but not treated by HT (n = 114) (Figure  1 ). According to our definition, a lack of clinical indications was observed for 58 newborns (50. 9%) among 114. Among the remaining 56 untreated cases, the main reasons reported by neonatologists were the lack of electrophysiological anomalies or clinical indications for HT (n = 16), the presence of contraindications (n = 15), late admission to the NICU (n = 13) and the restriction of neonatal care for critically ill neonates (n = 11). The variables recorded in the database and analyzed were: - Due to missing data (46% of the data base population), criterion 4 concerning EEG was not taken into account.
Statistical Analysis Several hypotheses were retained to deal with missing data. As "need for assisted ventilation at 10 minutes of life" (criteria 2) was not mentioned as such in the database, newborns requiring intubation and/or non-invasive ventilation with an Apgar score ,10 at 10 min of life were considered to present this criterion. When data concerning the time to initiation of HT was missing (n = 16), the time between birth and admission to the NICU was used. Considering that this choice may underestimate this delay, a sensitivity analysis was performed: the alternative solution consisting in adding the mean time from admission to initiation of HT observed among babies with complete data was considered. The distribution of OHT, NIHT and LHT, and the factors associated with the practice of HT were reassessed according to this scenario.
As all French level III centers did not participate, main characteristics of participating and non-participating NICUs were compared. Newborns were classed into three groups, OHT, LHT and NIHT, as defined above. We compared the organizational factors at birth, the newborns clinical and paraclinical characteristics, and the conditions in which HT was performed. The Chi 2 test (or Fisher exact test if insufficient numbers) and Student's t test or an analysis of variance were used to analyze the qualitative and quantitative variables respectively. The threshold of type 1 risk was set at 5%. Statistical analysis was performed using STATA software (Stata / IC 10. 0 for Windows).
Results Among the 68 NICU in France, 33 (49%) participated. These NICUs were more likely to be teaching Hospitals (75. 8% versus 38. 2%, p,10 22 ), but did not differ for the size of the maternity unit, the size of the neonatal unit or the type of intensive care (pediatric and neonatal intensive care, or exclusively neonatal intensive care) (data not shown). For the whole study population, the main characteristics are presented in Table  1. The breakdown by severity of HIE into grade of I, II, III was 2%, 64% and 34%, respectively. Information regarding the intrapartum context associated with HIE was missing in 35% (n = 108) of cases. When details were recorded, the main complications were funicular pathologies (prolapse, circular loop) for 25% of cases, and dystocia during delivery for 19% of cases.
Difficulties in performing and obtaining an interpretation of a standard EEG, especially during the night may partly explain this result. Greater dissemination of amplitude integrated EEG, which is simpler to implement and interpret, should make it easier to obtain an electrophysiological assessment before treatment  [32]. Furthermore, the sensitivity and specificity in assessing the prognosis is between 70 and 100% depending on the study  [33, 34]. For 35% of our population, no perinatal circumstances that could explain the intrapartum asphyxia are mentioned in the database. This has already been observed in another French study for 19% of newborns with stage II or III encephalopathy  [5]. In the randomized trial of Shankaran et al, a complication during delivery was only noted in 68 cases among the 102 newborns treated with HT  [35].
This raises the question of the anoxicischemic character of encephalopathy for some cases in our series. Moreover, the designation ''HIE'' is debated in the literature, some authors preferring to use the term ''neonatal encephalopathy'' in view of the difficulty in proving an anoxic-ischemic cause of neonatal neurological distress. A major limitation of our study is the declarative nature of the database. It is likely that the population of newborns treated for HIE is selected and not completely representative, but the aspects influencing the selection and thus how they influenced our results are undocumented. Therefore the SFN database does not necessarily reflect the general practice of HT in France, as the registration of all cases is still not achieved. To maximize the number of reported cases, we contacted all the centers in December 2011.
Conclusions This is the first multicenter French study to look at the practice of HT nationally. Although the results should be treated with caution since our database is only declarative, it reveals noncompliance with the guidelines in 35% of cases. These correspond to excess treatments. Our results attest to the difficulty of implementing the guidelines in clinical practice. This initial study should prompt a better organization of perinatal care, in particular to reduce the transportation time of newborns with HIE, as well as the diffusion of mobile equipment allowing the early initiation of HT in safe conditions. We also suggest that more systematic use of amplitude EEG examinations in neonatal units could improve the rate of electrophysiological assessment before HT treatment. Finally this audit of daily practice might prompt the widespread use of this recent neuro-protective strategy, and improve the awareness of HT among neonatologists.
Acknowledgments We thank  Dr Alison Foote  ( Grenoble Clinical Research Centre ) for translating the manuscript. We thank all the participating neonatologists, for their contribution to the data base :  G. Krim  (Amiens),  S. Le Bouedec  (Angers),  G Thiriez  ( Besancon ),  J. Sizun  (Brest),  B Guillois  (Caen), ? M Deiber  (Chambery),  V Zupan  (Clamart),  B Boeuf  ( Clermont Ferrand ),  L Desfrere  (Colombes),  F Decobert  ( Creteil ),  C Chantegret  (Dijon), ? M Moktari  ( Le Kremlin Bicetre ),  H Bruel  ( Le Havre ),  C Morisot  (Lens), ? A Bedu  (Limoges),  O Claris  (Lyon),  L Colettto  and  JC Picaud (Lyon) , ? V Millet  (Marseille),  I Rayet  ( St Etienne ),  G Cambonie  (Montpellier), ? P Daoud  (Montreuil), C Flamant (Nantes),  JB Mariette (Nimes), PH Jarreau (Paris), S Soudee (Paris), V Meau-Petit (Paris), JF Magny (Paris) , ? A Beuchee  (Rennes),  S Marret  ( Rouen) ,  P Bolot  ( St Denis ),  RP Dupuy  ( St Brieuc ),  P Kuhn  and  D Astruc  (Strasbourg),  MO Marcoux  (Toulouse), ? E Saliba  (Tours),  F Lapeyre  (Valenciennes).
SUBJECTS, APPARATUS, AND EXPERIMENTAL PROTOCOL Six right handed subjects (4 males and 2 females, between 22 and 47 years old) gave their written informed consent to participate in the study, which conformed with the Declaration of Helsinki and had been approved by the Ethical Review Board of the Santa Lucia Foundation. These subjects are a subset of the 14 subjects included in our previous report focusing on task performance and wrist kinematics  (Cesqui et al. , 2012)  for which EMG data was also available. Both the experimental apparatus and protocol have been described in detail previously  (Cesqui et al. , 2012). Briefly, subjects were asked to catch with the right hand a lightweight (20 g) ball (diameter 7 cm, size similar to that of a cricket or tennis ball) projected in space with different initial velocities by a launching system, built specifically for these experiments (d  'Avella et al.
DATA ACQUISITION The spatial position of the ball (covered with retro-reflective tape, Scotchlite, 3M, Pioltello, Milan, Italy) was measured together with the spatial position of 8 optical retro-reflective markers placed on the subject's trunk and arm close to the following anatomical landmarks: seventh cervical vertebra (C7), clavicle (CL), sternum (SRN), right acromion (RSHO), right epicondylus lateralis (RELB), right forearm (RFRA), right wrist ulnoid styloid (RWRU), right wrist radial styloid (RWRR). Marker positions in space were recorded with a sampling frequency of 100 Hz using a motion capture system (9-camera Vicon-612 system, Vicon, Oxford, UK). A very large tracking volume (6 × 3 × 3 m 3 ) was required for capturing the motion of both the ball and the subject upper limb. The marker reconstruction residual, averaged over the nine cameras, obtained in such volume with the Vicon calibration procedure ranged across subjects between 0.
Each electrode consisted of two parallel silver bars (10 mm spacing) and a differential preamplifier (gain, 10; rms noise, 1. 2 μV; common mode rejection ratio, > 80 dB) housed in a compact case (41 × 20 × 5 mm). Electrodes were taped on the muscle belly and connected to an amplifier (Bagnoli-16, Delsys) where the EMG signal was band-pass filtered (20-450 Hz), amplified (total gain 1000) and digitized at 1 KHz by a A/D board in the Vicon system, synchronized with the kinematic data acquisition. For each muscle, correct electrode placement was tested by asking the subject to perform a number of maneuvers involving both free movements and isometric contractions and monitoring the resulting activation patterns on a computer screen.
DATA ANALYSIS All analyses were performed with custom software written in Matlab (Mathworks, Natick, MA). We considered trials in which the subjects either intercepted but did not catch the ball or caught the ball thus excluding trials in which the subjects missed the ball (0. 9% of the total number of trials on average). Motion capture and EMG data were analyzed between 200 ms before ball launch and 100 ms after the interception. The time of ball launch was obtained by detecting the instant at which the ball passed through the hole on the screen using a photo-sensor (E3T-S112, Omron Electronics S. p. A. , Milan, Italy) mounted on the edge of the hole. The time of interception was obtained by computing the instant at which the distance between the ball trajectory (spatial coordinates as a function of time) and the plane passing through the wrist (RWRU, RWRR) and forearm (RFRA) marker positions reached its minimum  (Cesqui et al.