dataesr/scientific-paragraphs-categorization huggingface dataset:
Unidentified and misidentified Isolates by VITEK MS A total of 23 isolates were unidentified by the VITEK MS Ver 3. 0 system. Among these species, the 11 isolates not in the database included 1 M. florentinum, 6 M. marseillense, 2 M. colombiense, and 2 M. monacense. The other 12 unidentified isolates included 1 MTBC, 3 M. intracellulare, and 2 each of M. avium, M. kansasii, M. abscessus, and M. fortuitum isolates. There were no misidentifications at the genus level when using the VITEK MS Ver 3. 0 database. At the species level, 8 isolates were misidentified. Misidentifications were observed for 4 isolates of M. gastri, which were identified as M. kansasii, 2 M. parascrofulaceum isolates were identified as M. scrofulaceum and 1 isolate each of M. timonense and M. chimaera was identified as M.
Discussion To our knowledge, this study represents the most comprehensive evaluation of the CE/IVD and FDAapproved VITEK MS V3. 0 for the identification of clinically isolated mycobacteria. The correct identification rate of Mycobacterium spp. after retesting was 93. 9%. In addition, no isolates were misidentified at the genus level through VITEK MS V3. 0. MALDI-TOF MS is widely used for routine bacterial identification in clinical laboratories. Unlike bacteria and yeasts, mycobacteria have thicker cell walls and thus These species were all identified as M. fortuitum group f These subspecies were all identified as M. abscessus in VITEK MS V3. 0 database require an additional protein extraction procedure to ensure effective identification. Although many methods have been described, and perfect inactivation effects were obtained  18, 21  , there is still a lack of uniform procedures for strain inactivation and protein extraction.
avium and M. intracellulare but absent from the VITEK MS V3. 0 database  32, 33. During the VITEK MS V3. 0 analysis, all M. colombiense and M. marseillense strains were not identified, but M. chimaera and M. timonense were misidentified as M. intracellulare. This misidentification may be due to the close phylogenetic relationships between M. intracellulare and these two species  34, 35. Mycobacterium kansasii is second in frequency to M. avium and M. intracellulare as a cause of NTM lung disease, and its response to chemotherapy is much better  5. Although the present results showed that the identification performance of M. kansasii is excellent, the major problem is that M. gastri was readily misidentified as M. kansasi. One reason for this misidentification is that incubation conditions may lead to excessive polymer production, which could greatly interfere with the spectra acquisition during MALDI-TOF MS analysis, while other explanations may be attributed to the genetic similarity between M.
kansasii and M. gastri, as well as the potential that the entire range of strain diversity is not covered in the databases. However, these two species were also easy to interchange and may still need more spectra incorporated in the database  22, 29, [36] [37] [38]. Other SGM species involved in pulmonary diseases were all correctly identified (including M. xenopi, M. lentiflavum and M. szulgai)  4, 39. As expected, one isolate of M. florentinum not included in the database was unidentified. Except for the species not included in the database, human disease-related SGM species were well identified. Mycobacterium gordonae, an SGM species that rarely causes human diseases, is a frequent clinical isolate, and all of these isolates were correctly identified  40. Other SGM species mainly isolated from the respiratory tract but rarely associated with human diseases, such as M.
parascrofulaceum, M. celatum, and M. arupense, were also included in the present study  [41] [42] [43]. These findings were also subjected to the close relationships and limited spectra included in the knowledge database; one isolate of M. scrofulaceum was not well identified, while two isolates of M. parascrofulaceum were misidentified as M. scrofulaceum  44. For the limited numbers of some species, such as M. celatum and M. arupense, 100% correct identifications were also observed. In addition to human disease-related SGM species, these rare SGM species also showed good identification performance in VITEK MS V3. 0. Evaluation of more strains of these rare species could provide useful information. The RGM are opportunistic pathogens that produce disease in a variety of clinical settings  39.
However, although the correct identification rate was perfect for M. abscessus (the unidentified two isolates are smooth-growing, one each of M. abscessus subspecies abscessus and massiliense), these subspecies could not be discriminated in the VITEK MS V3. 0 knowledge database. In prospect, these subspecies should be differentiated by the VITEK MS IVD (In Vitro Diagnosis) system, owing to the different treatment requirements. M. fortuitum group includes up to 13 species, but the VITEK MS V3. 0 knowledge database includes the seven most prominent and closely related species. Species such as M. peregrinum, M. senegalense and M. septicum, were all identified as the M. fortuitum group. Except for M. septicum species, M. peregrinum and M. senegalense were included in the database, which may be partially explained by the limited strains and spectra used for the database construction  48.
Third, we did not examine the identification performances of Mycobacterium species from other liquid media and thus cannot draw any conclusions regarding the performance of other isolation media. In follow-up studies, we plan to identify Mycobacterium directly from positive MGIT broth cultures to obtain a more comprehensive evaluation of MALDI-TOF MS used for Mycobacterium identification. Nevertheless, the present study had several strengths. First, the present study evaluated the performance of the identification of a large number of clinical Mycobacterium isolates using the CE/IVD and FDA-approved VITEK MS Version 3. 0 database. Second, the combined use of the VITEK MS Mycobacterium/Nocardia sample processing kit in Mycobacterium inactivation and protein extraction generated sample spectra compatible with the reference spectra provided by the manufacturer.
With the process presented here, the identification performance was slightly higher than those reported by other researchers using the VITEK MS Version 3. 0 database  28, 29. In summary, we showed that Mycobacterium spp. can be adequately identified by the VITEK MS Version 3. 0 database. The use of a commercial sample processing kit and standard protocols are likely to yield highly reliable results in the identification of Mycobacterium species. This study further confirmed that the implementation of MALDI-TOF MS in the clinical laboratory enables the highly accurate identification of Mycobacterium species.
Acknowledgements This project was supported through grants from the  National Natural Science Foundation of China  (No. 811012310  and No. 81371775 ), The Medical Guide Program of the  Shanghai Science and Technology Committee  (No. 14411970500 ), and  Shanghai Municipal Health Outstanding Youth Clinical Medical Talents Funding  (No. 201604 ). The authors would like to thank  David H. Pincus  for careful review and editing of the manuscript and  Sheldon Wei  and  Kevin Li  for their many useful suggestions and assistance. The sample processing kit used in the present study was provided by bioMérieux.
MATERIALS AND METHODS Human CRC samples and analysis The 566 transcriptomic profiles recorded in GSE39582l  (Marisa et al. , 2013)  were analyzed. Comparison of the expression levels of CDX2 between the C4 CRC subtype and the other subtypes was performed using independent twogroup t test (function t. test, stats R package). CRC subtypes means comparison was performed using Tukey post hoc test after two-way ANO VA (function TukeyHSD, stats R package). Disease-free survival was defined as the time from surgery to the first recurrence. Survival curves were obtained according to the method of Kaplan and Meier (function Surv, R package survival), and differences between survival distributions were assessed by log-rank test. Human tissue samples were obtained at the University Hospital of Strasbourg (France) according to the recommendations of the French Ethical Committee and the ethical standards of the 1964 Declaration of Helsinki.
Normalization and differential expression analysis was made with DESeq2  (Love et al. , 2014). Unless otherwise stated, genes with a log2(fold change [FC]) ≥1 and adjusted p-value (q-value) <0. 01 were considered as differentially expressed. Data analysis was performed using Ingenuity Pathway Analysis (Qiagen). The transcriptomic data have been deposited in the GEO database under accession number GSE89992.
ACKNOWLEDGMENTS We thank  Prof. M. P. Chenard  for help in pathohistology evaluation,  Prof. D. J. Winton  ( Cancer Research UK, Cambridge, England, UK ) for the AhCre ERT mice,  Dr. C. Perret  ( Inserm U1016, Institut Cochin, Paris ) for the Apc +/Δ14 mice,  Dr. C. Tomaseto  ( Inserm U1258, IGB MC, Illkirch ) for the anti-Tff1 and -Tff2 antibodies, and  Dr. A. De Reynes  ( Cartes d'Identité des Tumeurs Program, Ligue Contre le Cancer, Paris, France ) for discussions. This work was supported by the  Ligue Contre le Cancer du Haut-Rhin (France) , the  Fondation ARC pour la Recherche sur le Cancer (France ;  PGA120140200834 ), and the  Institut National du Cancer  ( INCa2014-178 ). C. Balbinot was funded by the  Ministère de l'Enseignement Supérieur et de la Recherche (France)  and the  Ligue Contre le Cancer.
9%). Seven patients (6. 19%) have a progression and 4 of these were recommended for surgery. Of 26 patients who abandoned the treatment, at the time of abandonment (12. 5 age), 19 cases (70. 0%) have achieved curve correction, 5 cases (19%) stabilized, and 3 cases (11%) progressed. Negrini et al. [181] , in a prospective cohort study of 73 patients, treated with the Sforzesco brace, following both the SRS and SOSORT criteria, reported 34 patients (52. 3%) improved; seven (9. 6%) worsened, of which 1 progressed beyond 45°and was fused and employing intentto-treat analysis, there were failures in 11 patients (15. 1%). Finally, Aulisa et al. [182]  following both the SRS and SOSORT criteria, studied a cohort of 102 patients treated with Lyon Brace, who were drawn from a prospective database and found the following: 69 patients had a definite outcome, 17 have abandoned treatment and 16 are still in treatment.
To the best of our knowledge, there are three more RCTs underway: (1) the UK trial Active Treatment for Idiopathic Adolescent Scoliosis (ACTIvATeS), trial registry identifier ISRCTN90480705, (2) the Swedish trial CONTRAIS: CONservative TReatment for Adolescent Idiopathic Scoliosis: a randomized controlled trial (NCT01761305), (3) the Canadian multicentre trial: Multicentre Schroth Exercise Trial for Scoliosis -MultiSETS (NCT01610908) and  (4)  the US multicentre trial Scoliosis-Specific Exercises for At-Risk AIS Curves (NCT02807545).
The search strategy for each database is presented in Additional file 1. We identified additional published, unpublished, and ongoing studies by hand- searching reference lists of relevant reviews, and abstracts from SOSORT Meetings (2003 to 2015), as well as by con- tacting topic specialists. Inclusion criteria were as follows: randomized controlled and prospective controlled cohort studies investigating the effect of exercises (any type); ef- fect of exercises during brace and surgical therapy; other conservative treatments; or sport on any scoliosis out- come, presence of an abstract, and usable numerical data. The search yielded 1760 references. After screening the titles and abstracts, 128 references were considered of interest and retrieved in full text. Of those, 7 primary studies met the inclusion criteria and were used to inform this updated guideline on PSSE to prevent scoliosis progression during growth.
, 2008; Schilt et al. , 2010; Schneider et al. , 2013). They should be displayed on the commonly-used AICC2012 gas age scale  (Bazin et al. , 2013; Veres et al. , 2013). Note that this time scale is associated with an average 1σ absolute error of ∼2 kyr between 140 and 127 ka. Atmospheric CO 2 concentration records have been measured on the EDC and TALDICE ice cores (Fig. 2 ). The EDC records from  Lourantou et al. (2010)  and  Schneider et al. (2013) , characterised by a temporal resolution of ∼0. 5 and 0. 8 kyr respectively, agree well overall. The  Schneider et al. (2013)  dataset depicts a long-term CO 2 increase starting at ∼137. 8 ka and ending at ∼128. 5 ka with a centennial-scale CO 2 rise above the subsequent LIG CO 2 values, also referred to as an "overshoot". The CO 2 overshoot is smaller in the  Schneider et al.
(2013)  dataset compared to a similar feature measured in  Lourantou et al. (2010) : while the former displays a relatively constant CO 2 concentration of ∼275 ppm between 128 and 126 ka, the latter shows a CO 2 decrease from 280 to 265 ppm between 128 and 126 ka. The offsets between CO 2 records from the same EDC core are likely related to the different air extraction techniques used in the two studies  (Schneider et al. , 2013). Consistent with the recommendation made for the PMIP4 transient simulations of the last deglaciation  (Ivanovic et al. , 2016) , we recommend the use of the EDC CO 2 record from  Schneider et al. (2013)  displayed on the AICC2012 timescale as provided by  Bereiter et al. (2015). Atmospheric CH 4 concentration records from Vostok, EDML, EDC and TALDICE agree well within the gas-age uncertainties attached to each core (Fig.
This reconstruction is still subject to debate given the limits of the datasets. For example, considerable uncertainties remain with the magnitude of the sea-level pulse during MWP-2A because some of the corals cover a wide range of paleowater depth (0 to 6 m for the pre-MWP-2A Tahiti corals, ≥20 meters for the Tahiti corals during MWP-2A, 0-25 m for the post-MWP-2A Tahiti corals and 0 to 20 m for the Aladdin's Cave corals). Despite these uncertainties in the absolute position of sea level, the relative sea-level changes for each site clearly demonstrate an ephemeral deepening during meltwater pulse MWP-2A in both cases. Glacial isostatic adjustment to the deterioration of the MIS 6 ice sheets will also differentially affect Tahiti and Huon Peninsula, which precludes a direct comparison of the magnitude of sea-level change between these sites or a direct interpretation of global mean sea-level change in the absence of modelling.
, 2013; Briggs et al. , 2014 ) (Section 4), are provided in the associated data repository. They include the evolution of the ice-mask, as well as surface and bedrock elevations. Kageyama et al. (2017)  provide guidelines for computing land fraction, land-ice fraction and orography from the ice-sheet reconstruction datasets. The details of these forcings and the approach taken to compute them will ultimately depend on each model resolution and restrictions. The large glacial ice-sheets of MIS 6 impacted sea level and the land-sea mask. It would be best to modify the land-sea mask resulting from ice-sheet changes. Depending on the resolution of the model, this might not be a crucial parameter, except for some bathymetry and land-sea mask features, which have particular importance for ocean circulation.
Tables  3  and 4  also detail the timing of the major changes (and associated uncertainties) as recorded in each timeseries. These major changes are identified using the RAMPFIT or BREAKFIT software programs  (Mudelsee, 2000 (Mudelsee, , 2009)). Age uncertainties (1σ) reported in Tables  3  and 4  include i) the "internal" error of the event given by RAMPFIT or BREAKFIT, ii) the relative error related to the climatic alignment method for marine sediment and Ioannina records and iii) the absolute dating error of the reference time scale. Note that the selected ice-and sediment-based records are all displayed on AICC2012 or on a timescale coherent to this ice-core age scale, while terrestrial records are displayed on their own independent chronology. Among these paleoclimatic time series, several isotopic records are presented here and we strongly encourage transient simulations to be performed with oxygen and/or carbon isotope-enabled models to allow direct quantitative comparison between simulated and measured isotopic time series.
■ ACKNOWLEDGMENTS The authors are grateful to  Dr. Watanabe  for her assistance on SEM analyses at the  Center of Advanced Instrumental Analysis, Kyushu University. This study is partially supported by  JST Initiatives for Atomic Energy Basic and Generic Strategic Research  and by a  Grant-in-Aid for Scientific Research (KAKENHI)  from the  Japan Society for the Promotion of Science  (grant nos. 16K12585 ,  16H04634 , and  JP26257402 ). S. U. is also supported by  The Mitsubishi Foundation/Research Grants  in the Natural Sciences and by  ESPEC Foundation for Global Environment Research and Technology (Charitable Trust) (ESPEC Prize for the Encouragement of Environmental Studies). G. T. W. L and  W. R. B acknowledge RCUK  funding (grant nos. NE/M014088/1  and  ST/N002474/1 ). The findings and conclusions of the authors of this paper do not necessarily state or reflect those of the JST.
48 ± 0. 02, with 200 µm core diameter and 230 µm cladding diameter. The output power detected from both MMF arms are then transmitted to a dedicated computer via a 14-bit 2-MHz Agilent data acquisition system (DAQ) for further processing. The MMF sensing region is realized by thermally removing a certain length of the fiber cladding (as shown in the inset of Fig. 1 ), followed by a simple procedure of cleaning the fiber core using acetone and isopropanol solutions. Although the buffer still contains some filaments of the coating material, both the core and cladding sections are smooth (i. e. continous) and undamaged, and hence will not influence or affect the propagation of the launched lightwaves within the sensing region. Three different sensing lengths of 1 cm, 2. 5 cm, and 4 cm of stripped fiber cladding have been prepared.
2012). Most unmapped reads corresponded to E. coli sequences, which were in variable quantity depending on the sample (most in the 2-10% range and in a few cases. 50%). The mapped sequences were analyzed using Stacks 1. 30 with the ref_map routine (with parameter n = 1, else default parameters) and a mysql database. All individuals could not be analyzed at the same time because of memory limitations, so groups of individuals were first analyzed with the Stacks populations script per location, and in Orsay per years, and the results exported as a vcf file. vcftoools was then used to filter out genomic sites with data for ,70% of the individuals in the population and with mostly "heterozygous" as called variants (mismapping/ duplications/PCR errors). Each individual was assigned to a haplotype or labeled as a putative heterozygote.
All individuals of a given main haplotype were reanalyzed as a group for polymorphisms. 2b-RAD sequencing produces sequences on opposite strands derived from fragments ligated in opposite directions. PCR errors may appear in reads in one direction, but not the other. We used the fact that Stacks returns the +1 position on the minus strand (of the reference genome) to verify genotypes on both strands in the vcf file, and then eliminate the minus strand entries. The web display of the Stacks mysql database was used to filter dubious sites. Representatives of all haplotypes of all locations were finally analyzed as a group. We used 7760 fragments of 36 bp in the C. elegans reference genome (distributed along each chromosome at an average of every 13 kb). We did not utilize polymorphisms of presence versus absence of the fragments nor small insertions or deletions.
Thus, we used 30 bp of information for each fragment. Given the low level of polymorphisms (nucleotide diversity 10 23 /bp) in C. elegans, we could expect an average of 30 3 7760 3 10 23 = 233 polymorphic sites between two random worldwide isolates, likely higher than average local diversity. When the same RAD locus (36 bp) contained two SNPs that were fully in phase in our dataset (17 occurrences), only the first SNP was retained. If the SNPs were not in phase, both were retained. After stringent filtering, we kept 275 informative sites. Based on these 275 loci, the mean divergence among haplotypes is 4. 44 3 10 24 substitutions per nucleotide in Orsay and 3. 22 3 10 24 in Santeuil. Because of the stringent filtering and the collapsing of fully linked variants in the same RAD locus (Table  S3 ), these numbers underestimate absolute nucleotide diversity at the whole genome level.
Experimental validation of genotypes The data were further tested experimentally by genotyping SNPs using pyrosequencing (Table  S4 ). Individuals that were putative heterozygotes at many sites were rescreened by genotyping one or a few SNPs. Apart from the three confirmed cases that were heterozygous at nearly all polymorphic sites between two main haplotypes, we did not confirm any other putative heterozygous loci. The partial heterozygosity likely corresponds to low quality and partial PCR contamination in the RAD sequencing test. Several cases of multiple genotypes per sample were also checked, focusing on the most dubious and unexpected cases. All RAD results of mixing of genotypes within a sample were confirmed, except for the inversion of S135. 3 and S151. 1 in the RAD data compared to the original frozen tube.
Population genetic analyses STRUCTURE and principal component analysis were performed using SNiPlay (http://sniplay. southgreen. fr/cgi-bin/ home. cgi) (Dereeper et al. 2011). Haplotype networks were built using SplitsTree4  (Huson and Bryant 2006). Comparison with a worldwide dataset was made using April 2016 data on hundreds of 152 worldwide haplotypes  (Cook et al. 2016)  downloaded from https://elegansvariation. org. Hierarchical Fst estimations were performed using the hierfstat package in R  (Goudet and Jombart 2015). To plot the spatial structure in Santeuil in Figure  3 , a single spatial coordinate was estimated by projection of the sample position onto the main axis of the sampling (approximately north-south axis, Figure  S7 ). The origin (0 m) is at the north end.
Number of colonizing individuals We selected all samples that corresponded to cases where two genotypes were present at distances of ,1 m (excluding leaf litter, soil, rotting grass, moss, and snail samples). We found that 60% (n = 10) of the stem or fruit samples carried these two haplotypes when at least six individuals were genotyped, and 50% when at least two individuals were genotyped (n = 18) (Figure  5 ). As the number of genotyped individuals is low in some instances (e. g. , two), these proportions are underestimates of the true proportion. We used R version 3. 2. 1 (R Core Team 2015) to estimate the maximum likelihood of the proportion of samples with more than one genotype if the data were not limited by the number of genotyped individuals. Using the 18 samples, we assumed a given frequency of the two alleles in each sample drawn from a random uniform distribution, and computed the probability of the observed data on the samples with a single genotype if they in fact had contained two genotypes.
Dauers in synthetic pheromone plates were identified morphologically (dark intestines and radially constricted bodies). More than 30 dauers were collected from the synthetic pheromone plates in M9 buffer using a glass capillary (Chase) and placed on a microdirt chip. After 10-30 min, when most dauers move actively, the fraction of nictating dauers among moving dauers was measured. The nictation ratio was calculated from the independent biological replicates of multiple nictation assays. Quiescent dauers were not scored. We tested representatives of 11 Orsay genotypes (Figure  6 ). All strains were tested on eight different assay blocks (days) (one assay of JU1581 and JU1511 failed). An ANOVA analysis was conducted in R on arcsine-transformed data using strains nested in haplotype and day of assay: nic = haplotype(strain) + day.