dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2008; Di edhiou et al. , 2010; Peay et al. , 2010; Smith et al. , 2011 Smith et al. , , 2013;; Corrales et al. , 2016; Horton et al. , 2017). Interestingly, high fungal diversity in the tropics has often been encountered in monodominant and co-dominant rainforests  (Peay et al. , 2010; Smith et al. , 2011 Smith et al. , , 2013;; Corrales et al. , 2016) , a situation which is similar to that in temperate forests in terms of abundance of ectomycorrhizal trees. Another striking finding in this study is the large proportion of OTUs, namely 95%, that lack species level matches to existing databases. If these molecular species are indeed only present in New Caledonia, this would indicate that New Caledonian ectomycorrhizal fungi display an endemism rate of 95%. Such high endemicity is consistent with the high endemism rates encountered in other taxonomic groups, particularly in vascular plants with about 74% of species being endemic to the New Caledonian archipelago  (Morat et al.
, 2012) , with endemism rates about 90% in rainforests  (Ibanez et al. , 2018). However, it cannot be excluded that the same molecular species are present in the surrounding South West Pacific region (e. g. in Australia and New Zealand) but have not been sequenced or deposited yet in international sequence databases. Further large investigations in this biogeographic region are thus needed. The long term geographic isolation and the complex geological history of New Caledonia are seen as factors that led to the exceptional New Caledonian biodiversity  (Isnard et al. , 2016). Since the re-emergence of the main island at the end of the Eocene, approximately 37 Mya, living organisms must have colonized the archipelago by long distance dispersal and multiple introductions. Adaptation or pre-adaptation (exaptation) to ultramafic substrates, founding effects, limitation of gene flow between populations, large ultramafic surfaces, habitat patchiness and interactions with host plants (e.
Conclusion The present work is the first extensive molecular study undertaken on ectomycorrhizal fungi in New Caledonia, an archipelago renowned for its exceptional plant diversity and recognized as a biodiversity hotspot. The investigation of the below-and aboveground ectomycorrhizal fungal communities in mixed and monodominant rainforests from ultramafic substrates clearly revealed, with 311 OTUs and 28 phylogenetic lineages, the existence of a remarkable fungal diversity. Comparison to international sequence databases suggests that up to 95% of the molecular species we identified are endemic to New Caledonia. The archipelago may thus represent an outlier to the hypothesized general pattern of a reversed latitudinal gradient of biodiversity in ectomycorrhizal fungi. Our data even support that monodominant plant systems can act as centres of ectomycorrhizal fungal biodiversity in the tropics.
Acknowledgements We gratefully acknowledge the field worker staff of  IAC ('Unit e SARA'): Alexandre Bouarat, Ren e Guiglion ,  Anthony Pain  and  Hyppolite Lenoir  for their substantial assistance in fieldwork. We also thank  Thomas Leborgne  for his critical review of the project. We thank the  "Plateforme du Vivant " ( Noum ea, New Caledonia ) for access to their facilities. M. G. thanks the  Labex TULIP  for support ( ANR-10-LABX-41 ,  ANR-11-IDEX-0002-02 ). This work has been founded by the  "Minist ere des Outre mer", the "Convention Biodiversit e, Vale Nouvelle-Cal  edonie" and the  IAC. Funding was granted to FC. We would like to thank  F. Brearley  and the anonymous reviewer, as well as the editor  K. G. Peay , for their useful comments on the manuscript. We are very grateful to the editor-inchief,  L.
The values of the MPT of the three concrete mixtures were actually very close (Figure  8. 12). The most significant plastic shrinkage concerned concrete with recycled sand. Because of the higher surface area of fine RCA, the bleeding water is lower than in the control mix, and the risk of plastic shrinkage related to insufficient curing increases. This study aimed at providing data to understand the evolution of the shrinkage-induced cracking sensitivity of different conventional and RCs at the early age. The concrete tensile strength was experimentally assessed 24 h after casting using the direct tensile test. The percentage of substitution of recycled gravel or sand significantly affected the mechanical properties, such as elastic modulus and tensile strength (Figure  8. 13).
CONCLUSIONS Two experimental programs were connected to provide data on the influence of RCA proportion and initial water saturation on plastic shrinkage, cracking risk, and concrete properties at the early age. Several conclusions can be drawn from this comprehensive study. • Due to the relatively high porosity, RCA absorb water that can be released in cement paste. In sealed conditions or under moderate drying conditions, this provides internal curing that mitigates plastic shrinkage. However, under severe conditions, high evaporation rates are likely to trigger the drying of aggregates, which results in an increase in shrinkage magnitude. • Air entry concept can be used to investigate the influence of RCA on cracking risk of fresh concrete. Cracking time was assessed through specific testing (ASTM C1579), and experimental results actually showed a strong correlation with air entry determined from water content versus capillary pressure curves of the studied concretes.
These two-marker models have cvAUCs ranging from 91. 0% (versus 93. 4% for the full model) for a 1-year window to 94. 3% (versus 97. 1% for the full model) for a 45-day window (Table  2 ). The vibriocidal assay is more time consuming and expensive than the ELISA methods used for the other potential biomarkers that we considered. Hence, we estimated the performance of models based only on four ELISA-based assays (CTB and LPS IgA and IgG) and found that the cvAUCs were reduced by less than 10% from the full model across all time windows (Table  2 ) and ranged from 87. 0% (365-day window) to 93. 6% (45-day window). ELISA-based models fit to the dataset with IgM available had slightly better performance than models without the inclusion of anti-CTB and anti-LPS IgM (table  S4 ): The cvAUCs from these ELISA models with IgM isotypes ranged from 92.
Models perform well in external validation set of North American volunteers Although our models were able to classify recent infections within a cohort in Bangladesh, where cholera is hyperendemic, it was unclear whether they would generalize to other settings, particularly to cholera epidemics in previously naïve populations. We used data from 38 healthy North American adult volunteers challenged with V. cholerae O1 Inaba (11) who were then followed serologically for 6 months (figs. S9 to S11). Applying the vibriocidal thresholds derived from the Bangladesh cohort to the North American volunteers yielded equivalent or higher sensitivity and specificity as estimated for 45-, 100-, and 200-day infection windows in the Bangladesh dataset (table  S7 ). Thresholds for CTB antibodies derived from the Bangladesh cohort, when considered alone, had low sensitivity for identifying recent infections (69.
However, they alone were not predictive in the North American volunteers, which may be related to differences in previous exposure to the heat-labile enterotoxin of enterotoxigenic Escherichia coli, which is highly homologous with cholera toxin. Antibodies of IgM isotypes were not among the most influential predictors of recent infection in the Bangladesh cohort. However, anti-LPS IgM may be more important among primary infections, and future models tailored to settings with minimal historical exposure may consider IgM isotypes more heavily. Our random forest model performed well with training and validation datasets (external and internal). However, as new data become available, they may warrant the updating of a new single model or the development of new models for different epidemiologic settings or populations.
Study design Our research objective was to explore the potential for using crosssectional serological antibody measurements to identify recent V. cholerae O1 infections. We primarily relied on two datasets from previously published studies to train and test models: one from Dhaka, Bangladesh  (20, 21)  and an external validation dataset from North American volunteers  (11). The primary data used to characterize the post-infection immune response kinetics and to train our models composed of a cohort of confirmed cholera cases seeking care at the icddr,b Dhaka hospital (Bangladesh) and their household contacts from previously described studies  (20, 21). Patients 2 to 60 years old presenting to the icddr,b Dhaka hospital between 2006 and 2015 with severe acute watery diarrhea, a stool sample positive for V.
After consent, blood samples were collected from contacts on the day of enrollment (day 2) and on days 7 and 30 after hospitalization of the index case with rectal swabs collected daily during the first 10 days after enrollment. These individuals were used as controls in analyses to provide more data on the background antibody distribution in addition to day 0 measurements of confirmed cases. To minimize the risk of misclassification, we excluded person visits starting from any visit where individuals had more than a twofold rise in vibriocidal titer from his/her previous visit after the observed convalescent peak (in cases only). We excluded data from household contacts who had a vibriocidal titer greater than 640 at all study visits because this was suggestive of recent infection. Because of the high risk of secondary cases within households  (18) , we excluded household contact visits after they reported having acute watery diarrhea or when we detected a stool culture positive for V.
cholerae O1 or O139. After applying these exclusion criteria, this "uninfected" group of contacts included potentially both uninfected and recent but asymptomatic infections. To assess the external validity of our models, we used data from a cohort of 38 North American volunteers challenged with cholera as part of the placebo arm of a vaccine clinical trial  (11). These adult volunteers ranged in age from 19 to 44 years (median age, 30. 5 years) and had no known history of cholera. They were challenged with virulent V. cholerae O1 El Tor Inaba N16961 and had blood collected on days 0, 10, 28, 90, and 170 after challenge. Vibriocidal antibodies and anti-CTB antibodies (IgA, IgM, and IgG) were assessed using the same methods as the samples from Bangladesh.
Single-marker thresholds First, we explored the performance of different single-marker thresholds for identifying individuals infected over different time frames. We assessed performance by estimating the 20-fold cvAUC, dividing individuals, rather than individual observations, into 1 of the 20 different folds. Inference on cvAUCs, which accounted for repeated observations per person, was performed using influence curve methods as implemented in the cvAUC package in R  (23). We also explored the exact titer thresholds that led to maximization of the sensitivity and specificity combined  [Youden index (24) ]. First, for each exposure time window and antibody, we identified the anti-body titer threshold that maximized the sensitivity and specificity of most of the 1000 training sets (made up of 70% of participants), with a single observation (time point) selected for each person.
Random forest classification models We used random forest models to identify recently infected individuals based on cross-sectional antibody titers and, in some models, blood type and demographic data. We built a series of models with a binary outcome of recent infection, considering different time windows (as described above). In each model, those infected inside the time window were considered "recently infected" and those cases infected outside the time window (or never), including "uninfected controls," were considered "not recently infected. " We then fit the models using the randomForest R package with 1000 trees. We assessed model performance by estimating the 20-fold cvAUC. We estimated the 95% CIs for the AUCs with influence curves accounting for within-person correlation with cvAUC  (23).
We assessed variable importance within these different models using a permutation test-based metric, mean decrease in accuracy  (25). Given the correlated nature of our data within individuals, we also explored estimating AUCs using a subsampling cross-validation approach. We sampled a single observation per individual and then divided the observations between a training set (70%) used to fit the model and a testing set (30%) used to estimate the AUC. Repeating this procedure 500 times, we found that AUC estimates were almost identical to those found using full data from each individual and that the 2. 5th and 97. 5th percentiles of the AUC distributions were similar to the estimated 95% CIs of cvAUCs.
Statistical analysis We explored the distributions of antibody titers at different times using Gaussian kernel density estimation methods using the ggplot2 package in R  (26). We compared differences in baseline titer for the different antibodies by sex, age group, and blood group using Mann-Whitney tests and applied a Bonferroni correction to account for the multiple tests being conducted (by antibody). To better characterize the bimodal distribution of contact titers, we constructed a two-component Gaussian mixture model of the log of the vibriocidal titers (maximum of Inaba and Ogawa) with JAGS (version 4. 3. 0_2) and implemented in R with runjags. Observations were treated as interval censored with the two Gaussian distributions assumed to share a common variance. We assigned a Gamma(0.
Acknowledgments: We thank all the staff at icddr,b who have collected these data and the participants in both the Bangladesh and the North American studies. Funding: A. S. A. , J. L. , T. R. B. , A. I. K. , F. C. , A. K. , J. B. H. , D. T. L. , and F. Q. 's work was funded by grants from the  Bill and Melinda Gates Foundation  ( OPP1171700  to A. S. A. and J. L. and  OPP1191944  to A. S. A. , J. L. , T. R. B. , A. I. K. , F. C. , A. K. , J. B. H. , D. T. L. , and F. Q. ) and the  NIH  grants  R01 AI135115  (to D. T. L. , A. S. A. , and F. Q. ),  R01 AI106878  (to E. T. R. and F. Q. ),  R01 AI103055  (to J. B. H. and F. Q. ),  R01AI130378  (to D. T. L. , T. R. B. , and F. Q. ),  D43 TW005572  (to T. R. B. ),  K08AI123494  (to A. A. W. ),  K08AI100923  (to D. T. L. ), and  K43TW010362  (to T.
Statistical and principal component analysis The statistical tests were performed using the software Minitab 17. The data normality was analyzed by Shapiro-Wilk test and homoscedasticity by Brown-Forsythe test. Significant differences among antioxidant activities of isolated flavonol and commercial flavonols were evaluated by Tukey post hoc, with the decision level at P b. 05 (Zar, 2010). Principal component analysis (PCA) was performed using a matrix calculated with the average values of the antioxidant assays (variables) obtained from each isolated compound. The analysis was carried out using a correlation matrix in STATISTICA 13®.
Acknowledgments We are thankful to  CAPES (Finance Code 001, Brazil)  and  CNPq  for the scholarships conceded to PN and PBT, and to  FAPESP  ( 2013/ 07543-0 ) for financial support. DYACS and MJPF are supported by a  CNPq research  fellowship. We are also thankful to  Mourisa M. de Souza Ferreira  and  Dr. Aline Cruz Bertinatto  for laboratory assistance, and to  Dr. Claudia M. Furlan  for the reagents used in the antioxidant assays.
The GridPix detector A gaseous X-ray detector is used to detect the photons focused by the XRT. This detector and its performance during the data taking are described in detail in  [12] , while here is given only a brief summary. The basis of the detector is a GridPix, which is a combination of a Timepix ASIC  [20]  and a Micromegas gas amplification stage. The readout chip features 256×256 pixels with a pitch of 55×55 µm 2. The Micromegas stage was produced directly on top of the chip by photolithographic postprocessing techniques, which allow for small feature sizes and precise alignment. In this way each grid hole of the mesh was be placed directly above one pixel. A single electron liberated by the X-ray photon interaction is guided into one hole, where an avalanche multiplication increases the charge by a gain of G ≈ 2500.
X-ray energy [keV] Prior to the data taking campaigns in 2014 and 2015, the detector response to Xray photons of different energies was characterized with a variable X-ray generator  [23]. A stable operation, good energy linearity and energy resolution were demonstrated. Also, a data sample of signals of pure X-ray photons, important for a likelihood based background suppression were collected. The operation of the GridPix detector at CAST lasted over six months split in a short test run in October and November 2014 and a long run from June to November 2015. In total 254 h of solar tracking and 4785 h of background data were recorded. The detector worked reliably and no detector related downtime occurred. A daily calibration run with an 55 Fe source showed variations of only a few percent in the gas gain, which is expected because of the changing environmental conditions, in particular of the ambient temperature.
From the measurements at a variable X-ray generator  [23]  reference distributions of these variables for eight energy ranges in the regime up to 10 keV were obtained. These are used here to compute a likelihood value for each reconstructed event based on the reference distributions of the corresponding energy range. This provides a measure of the probability (likelihood) for an X-ray, of given energy, to look like the observed event. By only keeping those events passing a certain threshold for the likelihood value, the vast majority of non-X-ray events is removed from the data set resulting in a suppression of non-X-ray-like background events. To find the optimal likelihood threshold for each energy range the same method is applied to pure X-ray calibration datasets yielding the likelihood distribution for X-ray events of each energy range.
Acknowledgments We thank  CERN  for hosting the experiment and for technical support to operate the magnet and cryogenics. We acknowledge support from  NSERC (Canada) ,  MSE (Croatia)  and  Croatian Science Foundation  under the project  IP-2014-09-3720 ,  CEA (France) ,  BMBF (Germany)  under the grant numbers  05 CC2EEA/9  and  05 CC1RD1/0  and  DFG (Germany)  under grant numbers  HO 1400/7-1  and  EXC-153 ,  GSRT (Greece) ,  NSRF: Heracleitus II, RFFR (Russia) , the  Spanish Ministry of Economy and Competitiveness (MINECO)  under Grants No. FPA2011-24058  and No. FPA2013-41085-P (grants partially funded by the  European Regional Development Fund, ERDF/FEDER) , the  European Research Council (ERC)  under grant  ERC-2009-StG-240054 (T-REX ),  Turkish Atomic Energy Authority (TAEK) ,  NSF (USA)  under Award No.
0239812 ,  NASA  under the grant number  NAG5-10842 , the  University of Rijeka  under grant number  13. 12. 2. 2. 09 , and  IBS (Korea)  with code IBS-R017-D1-2017-a00. Part of this work was performed under the auspices of the  U. S. Department of Energy  by  Lawrence Livermore National Laboratory  under Contract No. DE-AC52-07NA27344.
Climate and Fire-Related Scenarios In this study, climate data were downloaded from the platform Medcordex. eu for both historical  (1986) (1987) (1988) (1989) (1990) (1991) (1992) (1993) (1994) (1995) (1996) (1997) (1998) (1999) (2000) (2001) (2002) (2003) (2004) (2005)  and future (2041-2060) periods. Only the intermediate Representative Concentration Pathway (RCP) 4. 5 climate emission scenario  [50]  was used because differences between RCP scenarios by 2050 were very small. The Regional Climate Model (RCM) ALADIN was chosen in the Mediterranean Agricultural Soils Conservation under global Change (MASCC) project; it was considered as a valid climate model in the comparison of RCM by  Fantini et al. (2018)   [51]. A statistical downscaling based on a quantile mapping approach was applied on the daily time rainfall series for bias correction, and a temporal downscaling based on an analog approach was then applied to transform the daily rainfall time series into five minutes' time series.
Thus, the 5-min time series have a real temporal structure as a direct result of the observations. Burnt area scenarios were calculated from climate scenarios according to Sousa et al. (  2015 )  [21]. To this end, the annual burnt area in the region surrounding Macieira (the Águeda river basin) between 1990-2016 was calculated from Portuguese historical databases  [13] , and a multiple linear regression was calculated with monthly rainfall anomalies, extreme fire weather (days with daily severity rating (DSR) above the 90th percentile [52]) and fire history in the preceding years. Meteorological data was taken from the ECMWF Re-Analysis  [53]. While the agreement with observations was not very high (r 2 = 0. 50), it was sufficient to provide a "best guess" of how much and when the burned area would change for the climate scenarios.
Data Analysis The impact of fire frequency, mulch application and changes in climate and land use and management on runoff and erosion were analyzed by comparing the LANDSOIL simulations outputs with R studio software Version 1. 0. 136. In this paper, three levels of fire frequency were tested (i. e. , 0, 1 and 2 fires every 20 years); two levels of mulch application (with or without application); two levels of climate change (with or without) and five scenarios of land use and management (S0 to S4). The simulation of the combinations of factors described in Tables  3  and 4  permitted to evaluate the distinct and combined impacts of these factors for the 2041-2060 period compared to the 1986-2005 period. A period of 3 post-fire years was also used to analyze the direct impact of fire and related contribution over 20 years.
Funding: This work benefits from the financial support of the  MASCC  project through  ARIMNET2 , an  ERA-NET  funded by the  European Union  s  Seventh Framework Program  for research, technological development and demonstration under grant agreement no. 618127. APV was funded by the  MASCC  project described above. This work was further funded by the " Fundação para a Ciência e a Tecnologia ", with personal grants attributed to  J. P. Nunes  ( IF/00586/2015 ) and  J. J. Keizer  ( IF/01465/2015 ), and funding for data collection in Macieira within project  ERLAND  ( FCOMP-01-0124-FEDER-008534 ). J. Baartman  visited the site with funding from an STSM mission within the  Connecteur COST Action   ES1306. M. Koopmans was partly funded by ERASMUS+.
Analysis of these diet data was undertaken using Dietplan-6 (version 6. 70. 43, 2013; Forestfield Software, Horsham, UK). The specific analysis methods are described in detail elsewhere  [7]. We also objectively assessed diet using discriminative metabolite signatures, an approach described in detail elsewhere  [20]. Briefly, each participant's serum metabolite profile was obtained using a targeted metabolomics assay (AbsoluteIDQ p180 Kit; BIOCRATES Life Sciences, Innsbruck, Austria), which simultaneously quantifies 188 metabolites. In a previously published diet intervention study  [20] , serum samples had been collected in 19 participants who had undergone a metabolic ward-based supervised diet intervention. We assayed these blood samples using the BIOCRATES AbsoluteIDQ p180 Kit and derived diet-discriminatory metabolomic signatures, using previously described methods  [20].