dataesr/scientific-paragraphs-categorization huggingface dataset:
70°N, 6. 15°W); this colony had an estimated population of 100-150 females. In contrast to these seminatural colonies, the fourth population is found in a large natural Mediterranean mixed oak forest in "Los Alcornocales Natural Park" (ANP) around 100-150 km southeast of Seville (36. 31°N, 5. 44°W) and has an estimated size of several thousand individuals that were sampled at different localities. Samples consisted of wing punch biopsies (Worthington Wilmer and Barratt 1996) stored in 70% ethanol. We analyzed 84 samples from MLP, 52 from ANP and 32 individuals from ZJF. A total of 47 individuals were sampled from the newly forming colony in DNP. This data set was split into: (1) the Doñana "original" colonizing group (D O ; N = 23), consisting of samples collected between  2003 and 2005; and  (2) the Doñana "recolonization" group (D R ; N = 24), sampled after the yet unexplained three-year breakdown  (2007) (2008) (2009) , during the subsequent recolonization process from 2010 to 2013.
Microsatellites All microsatellite loci were tested for genotyping errors  using MICROCHECKER v. 2. 2. 3 (Van Oosterhout et al. 2004). Linkage disequilibrium among markers was assessed using FSTAT v. 2. 8. 3. 2  (Goudet 2001). Identification of loci under selection was performed using the software ARLEQUIN v. 3. 5. 1. 2. Calculations of allele frequencies (including null alleles) across colonies, observed (H o ) and expected (H e ) heterozygosities, as well as deviations from Hardy-Weinberg equilibrium (HWE) were performed in CERVUS v. 3. 0. 6 (Kalinowski et al. 2007). Allelic richness was assessed using the R package "hierfstat"  (Goudet 2005). Given the recent developments and ongoing debate about the various existing population differentiation measures and their appropriate use  (Hedrick 1999; Jost 2008; Heller and Siegismund 2009; Meirmans and Hedrick 2011) , we opted to estimate both D EST and F ST , the former for a more robust analysis and as a reference for future studies, the latter to facilitate comparison with results from previous studies.
Genetic relatedness Pairwise and mean relatedness values (R), both among colonies and for matrilines (between individuals with shared mitochondrial haplotypes), were estimated using ML-Relate  (Kalinowski et al. 2006 ). This software implements a corrected maximum-likelihood approach that allows loci with null alleles to be incorporated into the analysis  (Wagner et al. 2006). Mother-daughter pairs were identified, allowing not only to determine the number and proportion of close kin (r > 0. 25) and of mother-daughter pairs within our data set, but also to examine the distribution of these dyads across colonies. Assignments inconsistent with mitochondrial haplotypes were excluded. For each colony, we estimated the proportion of close associations out of all possible pairs of individuals (% r > 0.
Regional kin structure We estimated relationships among individuals based on shared nuclear alleles and analyzed the distribution of close kin (r > 0. 25) and mother-daughter pairs across the region. The number of females with at least one close relative in the same colony was unexpectedly high for some sites, particularly for the colony in the city park of Seville (MLP). However, it is the number of parental associations found within our complete data set and encompassing the whole area studied that stands out the most with 57. 1% of parental associations found to be intracolonial. The complementary 42. 9% of these involved females from separate colonies, suggesting still, relatively frequent movements and thus significant gene flow between the colonies. A recent study revealed a negative correlation between wing loading, migration tendency, and the magnitude of genetic differentiation among bat populations  (Burns and Broders 2014).
Acknowledgments J. Nogueras  and  C. Ruiz  helped collecting bat samples. We particularly thank  J. L. Garc ıa-Mudarra  and  J. M. Arroyos-Salas  for valuable advice and their technical insight, and  M. Tavares-Queiroga  for her creativity in producing the map. We also acknowledge the staff of the  Servicio de Parques y Jardines de Sevilla , the  Zoo-Bot anico of Jerez de la Frontera ,  La Almoraima SA , and  Los Alcornocales Natural Park  for their help and continuous support of our research. Logistical support was provided by the  Laboratorio de Ecolog ıa Molecular, Estaci on Biol ogica de Doñana, CSIC (LEM-EBD). The regional government of Andalusia and  Doñana National Park  provided permits for collecting samples and handling of bats. This study was partially funded by the  Spanish MICINN   CGL 2009-12393 , the  PPNN 021/2002  and  1981/2010 , and the  EBD-Severo Ochoa  ( SEV-2012-443 0262 ) projects.
Acknowledgements. Giulia Zazzeri  would like to thank  Royal Holloway, University of London  for the provision of a Crossland scholarship and a contribution from the  Department of Earth Sciences  from 2011 to 2014. The analysis of samples from Poland was funded through the  European Community 's  Seventh Framework Programme  (FP7/2007-2013) in the  InGOS  project under grant agreement no. 284274. Sampling in Australia was possible due to a grant from the  Cotton Research and Development Corporation. Edited by: M. Heimann Reviewed by:  I. Levin  and one anonymous referee.
Methods A database comprising all patients seen at a tertiary referral sleep centre undergoing MSLT between October 2007 and July 2013 (n = 551) was cross-examined. 'Diagnosis of narcolepsy' on the referral letter was defined as patients given a diagnosis of 'narcolepsy', patients labelled with 'probable narcolepsy' (with/without treatment) and patients deemed as 'possibly' having narcolepsy provided they had received treatment with stimulant medication prior to referral. All patient referrals came from regional centres that did not have expertise in non-respiratory sleep medicine. Most patients had received little to no assessment or testing for narcolepsy before presenting at the sleep clinic (very few had a limited study or PSG, but none had an MSLT). The ICSD-2  [9]  was used to determine criteria for the narcolepsy and cataplexy diagnosis.
g. OSAHS). [3] Arand et al. [15]  recommend improving the reliability of the MSLT by combining it with the results from a PSG and obtaining a suitable history of the patient. The sleep specialists reviewed the referrals in addition to obtaining detailed history directly from the patient and acquiring information from objective test results from actigraphy over 2 weeks, PSG followed by MSLT, a urine drug screen, as well as a subjective 2week sleep diary. Difficult cases were discussed at multidisciplinary meetings and diagnosis was achieved by consensus and further review. Investigation and scoring of sleep data were conducted in a blinded manner; technicians who scored the data were not involved with history taking nor allowed to review the patient files to prevent any bias in scoring. Specific ethical approval was not considered necessary, as the Ethics Advisory Committee in Edinburgh does not require approval for case series.
(d,e) sB2M-9 was detected in the secretion of (d) A549 and (e) HBEC upon IL-1β (1 ng/ml), SA (1. 2 × 10 4 cfu/ml), and KP (1. 2 × 10 4 cfu/ml) treatment. mass of each individual peak was determined by using a golden chip/SELDI-TOF MS. Among them, peak 15, 17, and 20 containing the equivalent masses as those determined by CM10 protein chip with SELDI-TOF were collected and their N-terminal amino acid sequences were determined by automatic sequencing using Edman degradation. By searching through protein database (NCBI: http://www. ncbi. nih. gov and Swiss-Prot: www. ebi. ac. uk/swissport), it reveals that peak 15, 17 and 20 match precisely with the molecular N-terminal sequences of NAP3, B2M, and CXCL5, respectively (Supplementary Table  S1 ). The mature form of B2M with a molecular mass of 11729 Da did not fit at all with the detected present mass of 8910 Da.
It clearly shows that B2M-derived molecules in extract 1 could bind the surface of SA clumps (Fig. 5d , upper panel). This phenomenon was neither observed by treatment of extract 0 or extract 2, nor by native B2M alone. Here, we rule out the immunostaining from cross reaction by normal IgG (Fig. 5d , lower panel). Together, these data support that sB2M-9 with higher pI value binds the surface of SA and is responsible for antibacterial potential of REC. Effect of sB2M-9 on THP-1 migration. Given that sB2M-9 could be also detected in the culture medium of SA-infected A549, we suspected, as a result of sB2M-9 binding on the surface of SA clumps, that monocytes might be recruited to the SA clumps. To determine whether the presence of sB2M-9 is correlated with monocyte recruitment, chemotaxis assay was performed to compare the effect of extract 1 with extract 2 on THP-1 migration.
Peptides eluted from capillary columns were directed into the nanospray needle by a 20 μ m i. d. and 90 μ m o. d. fused-silica capillary. A voltage of 3. 2 kV was applied to the nanosource. The mass spectrometer was operated in positive ion mode and TOF analyzer was set in the V-mode. MS/MS spectra were obtained in a data-dependent acquisition mode in which the two major multiple-charged (+ 2 and + 3) peaks with the three most abundant ions were selected for collision-induced dissociation (CID). The scan range of precursor and fragment ions was m/z 400-3,000 and m/z 100-3,000, respectively. MS/MS spectra acquired for each of the parent ions was processed by MassLynx 4. 0 software (Manchester, UK). Peptide sequences were identified by searching against protein database.
Acknowledgements This work was supported partly by grants from  Kaohsiung Medical University, Taiwan  ( KMU-M104017 ,  M110004  and  M100005 ) and partly by  BNP Paribas, Paris  (business gift, 2009 and 2010). We thank  Drs. J. d' Alayer ,  D. Pidard  and  M. Si-Tahar , at  Pasteur Institute (Paris)  for helpful suggestions and discussion.
Briefly, peptides were dissolved in 4 μL of 10% ACN-0. 1% FA. Peptides were loaded and washed on a C 18 reverse phase pre-column (3 μm particle size, 100 Å pore size, 150 μm i. d. , 1 cm length). The loading buffer contained 98% H 2 O, 2% ACN and 0. 1% TFA. Peptides were then separated on a C 18 reverse phase resin (2 μm particle size, 100 Å pore size, 75 μm i. d. , 15 cm length) with a 1 hour gradient from 100% A (0. 1% FA and 100% H 2 O) to 50% B (80% ACN, 0. 085% FA and 20% H 2 O). The Linear Trap Quadrupole Orbitrap mass spectrometer acquired data throughout the elution process and operated in a data dependent scheme with full MS scans acquired with the Orbitrap, followed by up to 20 LTQ MS/MS CID spectra on the most abundant ions detected in the MS scan. Mass spectrometer settings were: full MS (AGC: 1 Ã 10 6 , resolution: 6 Ã 10 4 , m/z range 400-2000, maximum ion injection time: 500 ms); MS/MS (AGC: 5 Ã 10 3 , maximum injection time: 20 ms, minimum signal threshold: 500, isolation width: 2 Da, dynamic exclusion time setting: 30 s).
The fragmentation was permitted of precursor with a charge state of 2, 3, 4 and up. For the spectral processing, the software used to generate. mgf files is Proteome discoverer 1. 3. The threshold of Signal to Noise for extraction values is 3. Database searches were carried out using Mascot version 2. 4 and 2. 5 (MatrixScience, London, UK) on 'Other Metazoa' proteins (2,282,777 sequences) and on 'Other Eukaryota' proteins (1,030,911 sequences) from NCBInr databank containing 67,337,701 residues (May 2015) (www. ncbi. nlm. nih. gov/). A fusion database merging a homemade shell proteins databank (762 sequences containing 220545 residues) and three additional databases (Dreissena Expressed Sequence Tags (ESTs) extracted from NCBI; the translated Bathymodiolus azoricus, Pecten maximus and Laternula elliptica transcriptomes) described in an earlier publication  [57]  was also checked.
Two specific proteins databank-one from the sea urchin Paracentrotus lividus with restricted access (see http://octopus. obs-vlfr. fr/), constructed and provided by Laboratoire de Biologie du Développement, UMR CNRS 7009, Villefranche sur Mer-and the second one-from the genus Crassostrea (62,050 sequences)-were also included in the in silico analysis. The search parameters were as follows: carbamidomethylation as a variable modification for cysteins and oxidation as a variable modification for methionines. Up to 3 missed tryptic cleavages were tolerated and mass accuracy tolerance of 10 ppm for precursors and 0. 45 Da for fragments were used for all tryptic mass searches. The protein score should be above 50 for 'Other Metazoa' and 'Other Eukaryota' databases and 40 for the other databases while the individual ions score was above 20 for all databases.
MS-MS analysis The results of the MS-MS analysis are shown on Table  6. The search was performed on 'Other Metazoa' and 'Other Eukaryota', on a fusion database, the content of which is described in 'Material and methods' § 'MS/MS', and finally, on the databases of the genus Crassostrea and of Paracentrotus lividus. A limited number of about forty hits were obtained with the different databases. For ASM analysis, the in-gel digestion generated more hits than the in-solution digestion. This indicates that the purification of the matrix via in-gel short migration could improve the protein MS/MS identification. Nevertheless, the different digestion modalities generate not the same list of peptide sequences. Among the monospecific/monogeneric databases, that of Pecten maximus has identified more proteins, while no hit was found with the database of Laternula elliptica.
Acknowledgments This research was financially supported by the  INSU-INTERRVIE program  (Comité Thématique 4) from  CNRS , for the year 2013. Complementary support was provided by the recurrent yearly CNRS/uB budget allocated to F. I. and F. M. in 2013 and 2014. B. C. contributed to the work via a training period during his studies at the  University Technical Institute. The authors thank  Sébastien Motreuil  ( UMR 6282 Biogéosciences ) for help with sampling of D. polymorpha,  Pascal Taubaty  ( UMR 6282 Biogéosciences ) for the inclusion of the shell samples in Epoxy resin and  Jérome Thomas  ( UMR 6282 Biogéosciences ) for his contribution to the macro-photo of Fig 2. The authors would like to thank the anonymous reviewers for their constructive comments.
ESTLHLVLR. L Sol. azoricus gi|40643022 Crassostrea sp. Ribosomal protein L40, partial 41(1) 10879 K. ESTLHLVLR. L Contig13991 Paracentrotus 41(1) K. ESTLHLVLR. L Ribosomal protein L40, partial 1554:1940 lividus [Drosophila_melanogaster] sp|P18101| Contig34594 Pecten maximus 41(1) 94849 K. LNSCLCPQLSR. I Zinc finger homeobox protein 3 gi|405959418|gb| [Crassostrea gigas] EKC25460. 1| gi|566017401 Phytophthora Hypothetical protein F443_14276 50(1) 17370 K. NQKLLLQR. V No homology parasitica P1569 gi|397610729 Thalassiosira Hypothetical protein 93(1) 50510 R. ACPEGADR. A No homology oceanica THAOC_18587 AIM or ASM Gel indicate MSMS identified protein from unfractionated bulk matrices digested in-gel, AIM or ASM Sol. indicate in-solution one. a) Accession number according to those in homemade fusion database.
b) Species name derived from homemade fusion database. c) Protein name derived from homemade fusion database. d) MASCOT score for the entire protein. In brackets the number of unique identified peptides by MSMS MASCOT research. e) Molecular weight of the identified protein derived from homemade fusion database. f) Sequence of identified peptide. g) Protein identification using BLAST homology. h) Function domain determined using the NCBI database. doi:10. 1371/journal. pone. 0154264. t006.
Soil sampling SOC stocks were assessed in June 2011, prior to trial installation  (Dlamini et al. , 2014) , as a means to increase the level of confidence in the results on grassland management impact on soil C, such as suggested by  Sanderman and Baldock (2010). Three data points were randomly selected at each intensity of grassland degradation (ND, D1, D2, HD), resulting in 12 data points per grassland management. At each of the 12 points, three replicate topsoil (0-0. 05 m) samples were collected 1-m apart in a radial basis sampling strategy, resulting in 36 soil samples per grassland management. At each of the 36 pits, two soil samples were collected using a 0. 075 m diameter metallic cylinder, for the determination of SOC content and soil bulk density  (Blake and Hartge, 1986). Identical sampling was performed in July 2013, i.
Statistical analysis T-test was applied to the data to test the level of significance between the management treatments under study. The data were also subjected to an analysis of variance using the PROC MIXED procedure of SAS software  (SAS Institute, 2003). These variables were considered as fixed effects, whereas degradation intensities, year and grassland treatments were considered as random effects. Differences between means were tested with the DIFF option of LSMEANS statement with a significance level of P b 0. 05. Because the treatments were not truly replicated, statistical tests could not be in theory directly used to infer the results to other unstudied plots, unless we assume the mechanisms leading to the changes in soil carbon stocks are generalizable, a hypothesis we retained.
Acknowledgements This research has been performed in the framework of a French-South African cooperation between the  Institut de Recherche pour le Développement (IRD)  and the  University of KwaZulu-Natal (UKZN)  ( Protea Project DOC-SA ). Authors are grateful to the  Water Research Commission (WRC)  for funding this research (project number  K5 2266 ). Special thanks the  Soil Fertility and Analytical Services (Cedara) of the Department of Agriculture and Environmental Affairs (DAEA)  for analyzing the soil samples and to the  Potshini community  for giving us permission to carry out the study in their land. Final thanks to the two anonymous reviewers for their very valuable comments.
Clonal SA Analysis Labeled hearts were analyzed with an Axiozoom V16 macroscope (Carl Zeiss). For the analysis of fluorescent protein expression, a z stack was realized in each channel. The algorithm extended depth of focus of Zen Blue software (Carl Zeiss) was used to produce two-dimensional (2D) images, and the data were then merged. The SA covered by each cluster of a clone was measured using ImageJ software  (Schindelin et al. , 2012).
Clonal Volume Analysis For whole-mount confocal microscopy, hearts were cleared with ScaleCUBIC-1 and ScaleCUBIC-2 solutions as described in  Susaki et al. (2014). Hearts were incubated overnight at room temperature (RT) in ScaleCUBIC-1 solution and incubated at RT in ScaleCUBIC-2 solution for at least 2 days before their analysis. The whole-mount acquisitions were acquired with a biphoton confocal microscope (LSM780; Carl Zeiss). SA and volume occupied by a single Mesp1-expressing cells were analyzed with ImageJ software  (Schindelin et al. , 2012).
ACKNOWLEDGMENTS We would like to thank  J. -M. Vanderwinden  for his help with confocal microscopy. We are grateful to members of the  C. B. lab  for their comments on the manuscript. S. C. and N. M. are supported by a fellowship from the  FRS/ FRIA. F. L. has been supported by a  EMBO Long-Term Fellowship. B. D. S. and S. R. are supported by  Wellcome Trust  (grant number  098357/Z/12/Z ). C. B. is an investigator of WELBIO. This work was supported by the  FNRS , the  ULB Foundation , the  European Research Council (ERC) , and the  Bettencourt Schueller Foundation  (C. B. and F. L. ).
Our work has sought the treatment with bortezomib start date, if chemotherapy and/or radiotherapy were associated, adverse events of chemotherapy, toxicities grades and the treatment stop date. The statistical study was realized with statistical software STATA 13. 1. The results of quantitative variables were expressed as median and standard deviation. Follow up time was calculated as the interval between the date of diagnosis and last follow-up or death. For OS, defined as the time from the entry into the study and death, we used Kruskal-Wallis test (median comparison test); uni-and multivariate analysis for prognostic factors, hazard ratios and confidence intervals were calculated with a Cox regression model. For these tests, p<0. 05 was considered to be statistically significant.
Glucose assay Treatment of cells for hepatocyte glucose production was carried out essentially as described previously, using primary mouse hepatocytes with modifications  [1, 22]. Glucose production was determined after a 12-h incubation period in glucose-free DMEM with or without HBAs, other drugs or 2 mM metformin. At the end of the incubation period, medium was collected and glucose concentration determined by fluorescence measurement in the Amplex Red glucose assay (Invitrogen) for experiments including hydroxybenzoic acid or GAGO assay (Sigma) for other experiments. Each bar of a graph consists of data from at least three separate measurements, each from a separate dish of cells.
Acknowledgements We thank  Dr. Craig Beall  (Exeter) for assistance on Seahorse experiments. GR gratefully acknowledges support from  MRC  ( MR/K012924/ 1 ), the  Cunningham Trust , and the  Diabetes UK   RW & JM Collins studentship  ( 12/0004625 ), which is supporting CF. SB was supported by a Ph. D. studentship from the  Rank Prize Funds , with additional support provided by the  University of Dundee. KP was supported by a  Wellcome Trust Clinical Ph. D. studentship. The research was also supported by  Tenovus Scotland (GR) , by the  UK Medical Research Council  (KS and GR), by the  Région Ile de France-CORDDIM (MF) , and by the  Société Francophone du Diabète (MF). DS and GMcD acknowledge funding from The  Scottish Government's Rural and Environment Science and Analytical Services Division.
4%). There was no difference between the type of mutations (eg. , missense vs deletion) in malignant/ borderline PTs vs FAs/benign PTs (p = 0,14) (chi square test, data not shown) In order to determine whether MED12 exon 1 and 2 mutations are somatic mutations in PTs, we evaluated MED12 status on 10 samples with non-neoplastic tissue from the 41 lesions harboring a MED12 mutation. None of these non-neoplastic tissue samples harbored mutations, indicating the somatic nature of the MED12 mutations in PTs. We correlated MED12 mutations with follow-up (available for all 83 PTs). Fourteen patients presented a second event (13 recurrences and 1 metastasis). Second events occurred in 4/24 benign, 7/30 borderline and 3/29 malignant PTs. One of the 7 borderline PTs presented a malignant skin nodule on the chest wall and a pelvic subcutaneous metastasis.
Determination of copy number alterations For 53 PTs [borderline (n = 30) and malignant (n = 23)], 700 ng of tumor DNA were analyzed with Human CNV370 BeadChip (Illumina Inc. , San Diego, CA), containing 370,000 SNP markers, with a mean spacing of 7. 9 kb, as previously described  [25]. Hybridizations were performed by IntegraGen (Evry, France), according to instructions provided by Illumina. Fluorescence signals were imported into BeadStudio software (Illumina) and normalized. Gains, amplifications, and losses were defined using the Illumina SNP/CNV analysis pipeline software developed in INSERM U900 at Institut Curie. VAMP software was used to visualize and analyze copy number alterations. To determine the overall profiles of defined sets of tumors for each probe, the fraction of tumors with gains and losses over the dataset was computed and displayed in the FrAGL (Frequency of Amplicons, Gains and Losses) view.