dataesr/scientific-paragraphs-categorization huggingface dataset:
Background. Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods. Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples.
INTRODUCTION Salmonids are a fish group particularly interesting because, although native from the north Hemisphere, they are spread worldwide. Many species have been introduced into streams for recreational fishing  (Hasegawa & Maekawa, 2006)  and for aquaculture. Five species: Oncorhynchus mykiss, Salmo salar, Salmo trutta, Salvelinus fontinalis and Salvelinus namaycush are considered invasive and included in the Global Invasive Species Database (GISD) (http://www. issg. org/database) of the IUCN. Moreover, brown trout (S. trutta) and rainbow trout (O. mykiss) are within the One Hundred of the World's Worst Invasive Alien Species list, which includes species that cause serious negative impacts on biological diversity and/or human activities  (Lowe et al. , 2000). The five salmonids listed above have been introduced worldwide.
Salmonidae specific primers To obtain enough PCR product to perform the RFLP analysis, a nested PCR strategy was used. The method here described was based on the DNA fragment amplified with Salmonidae-specific primers described in  Zaiko et al. (2015). We designed a new primer pair to nest  Zaiko et al. (2015)  primers inside its amplification product. The 16S rRNA gene was chosen because, as a mitochondrial gene, it is more abundant than nuclear DNA in water samples  (Ficetola et al. , 2008) , it is generally well conserved within species and exhibits higher variation between species  (Maretto et al. , 2007; Zhang & Hanner, 2012). All the 16S rRNA gene sequences available for the Salmonidae species O. mykiss, S. trutta, S. salar, S. namaycush and S. fontinalis were downloaded from the NCBI database of DNA sequences, either individual 16S DNA sequences or complete mitochondrial genomes.
Polymorphisms were analyzed with the DNASP software V. 5. 10  (Rozas et al. , 2003). The different haplotypes were visualized employing the BioEdit Sequence Alignment Editor software  (Hall, 1999). Sequences were aligned with the ClustalW application included in BioEdit  (Thompson, Higgins & Gibson, 1994). The Primer Blast application included in the NCBI webpage  (Ye et al. , 2012)  was employed to design one forward 16S general primer, which amplified a fragment of 567 bp in the 16S rRNA gene using the reverse 16S-Br universal primer from  Palumbi et al. (2002). The two Salmonidae-specific primers described by  Zaiko et al. (2015)  anneal within the 567 bp amplicon obtained from the new primers pair. These Salmonidae specific primers were tested in silico with the BLAST tool in the NCBI webpage  (Altschul et al.
PCR-RFLP method development The RFLP (restriction fragment length polymorphism) protocol was designed within the DNA fragment amplified with the primers described by  Zaiko et al. (2015). To design species-specific RFLPs, all the haplotypes from the five species in study were aligned. Diagnostic single nucleotide sites (monomorphic within species and different between species) were identified for each species. The restriction enzymes recognizing those sites were selected and restriction pattern determined using the NEBcutter application  (Vincze, Posfai & Roberts, 2003). For the species S. namaycush there were not enough sequences in the database. DNA extracted from 25 samples of this species kindly provided by the Université Laval of Québec were amplified with the universal primers for the 16S RNA gene  (Palumbi et al.
Primers designed The new general forward primer was: 16S-new-F (5 -GCCTGCCCTGTGACTATGG-3 ). Together with the universal 16S-Br reverse primer  (Palumbi et al. , 2002) , they amplify a fragment of 567 nucleotides within the 16S rRNA gene, located between the sites 2046 and 2613 of the Salmo salar mitochondrion complete genome (GenBank: KF792729. 1). The Salmonidae specific primers designed in silico from the analysis of databases and new sequences of salmonids were: Forward primer: 16S-F-Salm (5 -AAGACCTGTATGAATGGCATC-3 ) Reverse primer: 16S-R-Salm (5 -TCGATAGGGACTCTGGGAGA-3 ). These primers amplify a fragment of 377 nucleotides within the 16S rRNA gene, located between the sites 2125 and 2502 of the same S. salar reference sequence used before. The assays of annealing temperatures for the PCR with Salmonidae specific primers showed that the best results were obtained at 68 • C with 2 mM MgCl 2.
All the 16S rDNA sequences obtained and employed in this work are available in GenBank with the accession numbers stated in Table  S1. In cross-amplification assays we have confirmed that the new primers only amplified from salmonids species. The sequence of the amplicons obtained for O. mykiss, S. trutta, S. salar, S. fontinalis and S. namaycush are available in GenBank with the accession numbers KU510521, KU510522, KU510523, KU510525 and KU510526 respectively. The threshold of detection for direct PCR with the two Salmonidae-specific primersand visualization in agarose gels was 0. 1 ng/ml. We observed a band of the expected size in the dilution 1 to 10,000 from the five tested samples with an initial concentration of 1 µg/ml. The detection limit for the nested PCR method (16S PCR with the new general primer designed and one universal Palumbi's primer followed by a PCR with the two Salmonidaespecific primers) was 10 pg/ml, since positive bands of the expected amplicon size were observed in agarose from the dilution 1 to 100,000 of the five samples with an initial concentration of 1 µg/ml.
The water sample from Nora River, with a known population of S. trutta, and the water sample from ''El Arenero,'' with a known population of O. mykiss, provided a clear band of 370 nucleotides with the Salmonid-specific primers (Fig. 4B ). The PCR products obtained from River Nora and ''El Arenero'' water DNA were purified, sequenced and the sequence   identified by BLAST as S. trutta and O. mykiss respectively. Both sequences are available in GenBank (Accession numbers KU510527 and KX904362). RFLP digestions confirmed the species present in water samples in all cases (Figs. 5B and 5C). Typical bands of S. trutta (205 and 172 bp) were obtained after digestion with the enzyme TaaI in Nora River sample. In the sample from the fishing reservoir ''El Arenero,'' it is possible to identify O. mykiss; the bands expected of O.
These analyzes were performed following the standard procedures commonly used in the laboratory (see details in  Schaffhauser et al. 2014  for summary). The data have been partly presented and discussed in previous works  (Prunier 2008; Pierret et al. 2014; Schaffhauser 2013; Schaffhauser et al. 2014) , which have emphasized the interest of coupling various geochemical tracers to constrain the main (bio)-geochemical processes involved in the CZ functioning. The multi-component reactive transport model KIRMAT (KInetic Reactions and MAss transport) has been also applied to constrain the main water-rock interactions controlling the chemical composition of the Strengbach and Ringelbach spring and borehole waters  (Schaffhauser 2013; Ackerer 2017). The code KIRMAT solves the geochemical reaction and transport mass balance equations in a saturated porous medium.
Acknowledgements This study was financially supported by funding from the  CPER-Alsace REALISE program , the  Equipex program CRITEX , the  CNRS SOERE RBV  and the  LABEX ''G-Eau-Thermie profonde''. It also received funding from the  French ANR Program  under grant agreement  ANR-15-CE06-0014  ( Projet CANTARE-Alsace ). Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://crea tivecommons. org/licenses/by/4. 0/),which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Material characterization The structural X-ray studies of the synthesized oxides were carried out at room temperature (RT) in the range of 10-110 degrees with CuK a radiation using a PANalytical Empyrean diffractometer. For high-temperature measurements, an Anton Paar HTK 1200N oven-chamber was installed. Measurements in pure O 2 using a flow rate of 100 cm 3 min À1 were conducted for 15 min per scan. To observe the structural changes during the long-term oxidation at a carefully chosen temperature, the sample was rapidly heated (ca. 5 min) to 250 1C. Additional measurements were conducted for the temperature increases and decreases of 10 1C in a range of 220-300 1C for the HoMnO 3+d 15MM sample. The XRD tests of the phase stability and thermal expansion in air were also carried out up to 900 1C with the data taken every 100 1C.
The GSAS/EXPGUI set of software was used for the Rietveld analysis of the data. 34, 35 canning electron microscopy (SEM) evaluation of the chemical composition and the element mapping were done for powders using JEOL JSM-7610F apparatus equipped with an EDS detector by using a magnification range of 1000-10 000. The OSCs during reduction/oxidation runs were determined by using the thermogravimetric (TG) method. All experiments were conducted on a TA Q5000 IR apparatus. For all the studies, either pure O 2 or synthetic air flow at 100 cm 3 min À1 and heating rates of 0. 1-51 min À1 were used. Prior to the studies in an oxygen atmosphere, all the investigated samples were heated up to 500 1C and cooled down to RT with a heating rate of 51 min À1 in a flow of synthetic air to remove possible surface contamination.
XAS data were obtained at T B 350 K in order to reduce the charging problem in these insulating oxides. The experimental energy resolution for the XAS data was set to B100 meV at hn B 600 eV. All the XAS spectra were normalized to the incident photon flux. Magnetization measurements were performed using a Magnetic Property Measurement System (Quantum Design). Temperature dependence of magnetization was measured in a magnetic field H = 1 kOe in the temperature range of 2-395 K, initially in a ''zero field cooling'' mode (cooling the sample to T = 2 K in a zero magnetic field, switching a magnetic field on, and measuring upon warming), then in a ''field cooling'' mode (measuring upon cooling in a magnetic field) and finally the remanent magnetization was measured upon warming in the zero magnetic field after switching the magnetic field off at T = 2 K.
The final XRD data created by adding up all the 24 measurements at respective temperatures for the single-phase phases Hex0 at 300 1C and Hex1 at 220 1C are presented in Fig. 4 , together with the Rietveld refinements using the P6 3 cm and R3c space groups, respectively. The structural parameters are listed in Table  1. Changes in the oxygen stoichiometry with temperature for the HoMnO 3+d 15MM sample were investigated using the thermogravimetric technique and compared with the structural data. The results of the temperature swing processes carried out consecutively at different heating rates (51 min À1 , 11 min À1 , and then 0. 11 min À1 ) are presented in Fig. 5a. For comparison, the data for the initial HoMnO 3+d 0MM sample are shown in Fig. 5b. Based on these measurements, the oxygen storagerelated properties of the studied samples have been derived and are presented in Table  2.
Acknowledgements This project was funded by the  National Science Centre, Poland , on the basis of the decision number  UMO-2015/19/B/ ST8/00871. The work at the CUK was supported by the  Korean National Research Foundation (NRF)  under the contract number (No. 2016R1D1A1B03932391 ). A synchrotron radiation spectroscopy experiment was supported by the  PAL (Pohang Accelerator Laboratory)  and  MSIP in Korea.
Phylogenetic Relationships and Population Structure Phylogenetic relationships among individuals were inferred based on the concatenated sequences of individuals using variable and invariant sites as recommended  (Leache et al. 2015)  and UIPAC codes for polymorphic sites. All polymorphic positions present in at least 24 individuals were used. A Maximum Likelihood (ML) tree was generated using the GTR model with a Gamma distribution parameter allowing rate variation across sites (C ¼ 0. 02). We performed 700 rapid heuristic bootstrap followed by a thorough ML search implemented in the program RAxML v. 8  (Stamatakis 2014 ). The number of bootstrap replicates was determined using the automatic BS convergence criterion  (Pattengale et al. 2010). In order to detect population genetic structure, we first performed a Discriminant Analysis of Principal Components  (Jombart et al.
Genetic Diversity and Geographical Differentiation Genetic diversity by individual (individual heterozygosity: observed heterozygosity), within each sampled locality (population genetic diversity: expected heterozygosity), and between all population pairs was assessed using GENEPOP4. 7 software  (Raymond and Rousset 1995). F IS and F ST were estimated according to  Weir and Cockerham (1984). Genetic variation partitioning among and within populations and geographical groups was tested in hierarchical analyses of molecular variance (AMOVA) using nonparametric permutational procedures (1,023 iterations) as implemented in Arlequin 3. 5  (Excoffier et al. 2005). We first tested for the effect of the three sampling regions (Benin/Guyane/Antilles) on genetic diversity. We then focused on the Caribbean populations to test for genetic continuity between Guyane and Antilles, and for genetic similarities among the four islands of the Antilles.
In order to assess the respective roles of geographical distance and the presence of sea in population genetic differentiation of Ae. aegypti, multiple correlations between genetic (F ST /[1ÀF ST ]), straight-line geographic distance (square-root transformed), and distance based on the presence/absence of sea (coded as 0/1) were tested by performing a multiple regression on distance matrix (MRM in the R package ecodist, Goslee and Urban 2007) using permutation tests of significance (999 permutations) for regression coefficients and Rsquared.
Locus-Specific Departure from Neutrality To search for loci more differentiated than expected under the neutrality assumption, we used the hierarchical Bayesian BayeScan package v2. 1  (Foll and Gaggiotti 2008) , which incorporates the uncertainty in allele frequencies due to small population sample sizes. Selection is introduced by decomposing each locus F ST into a population-specific component, shared by all loci, and a locus-specific component (a) shared by all the populations using a logistic regression. Departure from neutrality at a locus is assumed when the locus-specific component is necessary to explain the observed pattern of diversity (a significantly different from 0). The estimation of model parameters was automatically tuned on the basis of short pilot runs (ten pilot runs, length 2,000).
Environmental Variables and Genome-Environment Association Tests For each sampled locality, we extracted all the 19 bioclimatic variables averaged on 30 years  from the WorldClim database (http://www. worldclim. org; Hijmans et al. 2005 ) and we used a principal component analysis (PCA) to reduce these variables to two uncorrelated climatic variables: mean temperature and total precipitation (supplementary fig. S1 , Supplementary Material online). In addition, two human-induced local pressure proxies were considered: human density and resistance to deltamethrin. Human density (inhabitants per km 2 ) from the 2014 census was extracted from the INSEE database (https://www. insee. fr). Resistance to deltamethrin, the main insecticide currently used against adult mosquitoes, was used as a proxy for the local insecticide selective pressure  (Marcombe et al.
2012 (Marcombe et al. , 2013;; Faucon et al. 2015; Goindin et al. 2017 ) (table  1 ). These two anthropogenic variables are not correlated (Pearson's R ¼ 0. 25, P ¼ 0. 36). In order to determine which environmental (climatic or anthropogenic) variables have the most important impact on genetic variation in Ae. aegypti populations, we used two different correlative methods: redundancy analysis (RDA,  Legendre and Legendre 1998) , and latent factor mixed models (LFMM,  Frichot et al. 2013). RDA is a constrained version of principal component analysis that summarizes the component of genetic variation explained by a set of environmental variables. We used RDA as implemented in the R package vegan  (Oksanen et al. 2017). To remove the effect of geography on genetic variation, we used a combination of each sampled locality coordinates (latitude þ longitude) as a conditional factor in the RDA  (Nadeau et al.
The latent factor models were run with K ¼ 6 factors, following the results of population structure analyses. We evaluated association between each SNP and each environmental variable by running 30 independent replicates of LFMM. Assuming a Gaussian distribution under the null hypothesis, Z-scores from all runs were combined using the Stouffer method and the P values were adjusted by using a genomic inflation factor correction  (Frichot and Franc¸ois 2015; Franc¸ois et al. 2016 ). The Storey-Tibshirani FDR control algorithm was applied to detect the most interesting loci with an expected FDR level of 10%  (Storey and Tibshirani 2003). RDA and LFMM tests were applied on a subset of the SNP data set without missing genotypes (578 SNPs), and we extrapolated the level of resistance to deltamethrin in the island La Desirade (DES) to the average level observed in Guadeloupe.
Demographic History of Populations The SFS computed from the imputed SNP data set revealed an excess of common variants compared with the neutral expectations (fig. 4A ). The stairway plot method used to infer demographic events revealed a strong decrease in effective population size that occurred $300 years ago (fig. 4B ). In addition, the stairway curve exhibited a strong decrease in population size (down to near extinction) $100 years ago, followed by a rapid recovery and population expansion during the latest century. The population-specific F ST coefficients ranged from 0. 04 in St-Pierre (Martinique) up to 0. 25 in CAY (Guyane) (table 2). As expected for populations undergoing genetic drift effect, populations with high specific F ST also had low genetic diversity (Pearson's R¼ À0. 74, P < 0.
Acknowledgments We thank  Sebastien Marcombe  for collecting all samples from  Martinique  and for providing the SBE strain, and  Isabelle Dusfour  ( Institut Pasteur Guyane ) for providing the samples from Guyane. We thank  Julien Renaud  for help with the bioclimatic variables analyses. This work was funded by  Centre National de la Recherche Scientifique ,  Universite Grenoble Alpes and Institut Pasteur Guadeloupe.
Statistical analysis Based on the preliminary assessment of the NMIBC patients (data not shown), 100 patients were calculated to be sufficient to observe at least 25% decrease in pain level after flexible CS, assuming alpha 0. 05 and power of 0. 80. The numerical results are presented as mean ± standard deviation. Group comparison was analysed with Mann-Whitney test. The paired observations, pre-and post-CSs, were compared using Wilcoxon signed-rank test. The variations of frequencies were tested using χ 2. The correlations were assessed with Spearman or gamma correlation. The r s values of 0. 20-0. 39 were considered weak, 0. 40-0. 59 moderate, and >0. 60 strong associations. γ of 0. 25-0. 49 was considered a weak, 0. 50-0. 74 a moderate, and >0. 75 a strong relationship. The Bonferroni correction for multiple testing was applied when appropriate, and the adjusted p values are shown in the paper.
Anxiety and depression It has been proved that oncological patients have increased anxiety and depression levels compared to general population  [22]. It has also been shown that a large proportion of patients with BC undergoing radical cystectomy experience psychological distress during the perioperative period  [35]. Our observations confirm the hypothesis that HADS scores are also higher in NMIBC patients' population. The reported anxiety level was related to depression symptoms with no independent influence of patients' age. There are no available data on anxiety and depression levels measured by HADS scale in general Polish population. In somehow similar German population, the mean scores for anxiety and depression in males are 4. 4 and 4. 8. Using the cutoff 8+, the percentages of elevated anxiety and depression in the total sample are 21 and 23%, respectively  [36].
Flow cytometry Cell cycle analysis was performed by propidium iodide staining. Cells were trypsinized, centrifuged at 700 g and suspended in cold 70% ethanol and 30% PBS buffer before storage at -20 °C for at least 2 h or for weeks. Before staining, cells were incubated for 1 h at 37 °C with RNase A (14. 4 ng/ml in PBS, Sigma-Aldrich) and then at least 20 min in 10 µg/ml propidium iodide diluted in PBS (Invitrogen). Flow cytometry analysis was performed using a MoFlo® high-speed cell sorter (Beckman Coulter, Fort Collins, CO, USA) equipped with a blue solid-state laser operating at 488 nm and 100 mW. Propidium iodide fluorescence emission was collected with a band-pass filter 630/30 nm. Samples were pre-analysed with the Summit 4. 3 software (Beckman Coulter). Cell cycle analysis was finally done using the MultiCycle AV software (Phoenix Flow systems, San Diego, CA, USA).
Imaging Fluorescence imaging on cells was done using a Zeiss Axiovert 200 Microscope (Carl Zeiss S. A. S) and a Zeiss Camera AxioCam MRm (Carl Zeiss S. A. S) controlled by the Axiovision software (Axiovision Rel. 4. 6. 3; Carl Zeiss Imaging Solutions, GmbH, 2007). For each point, six images per well and per labelling were acquired randomly on 3 wells and quantitative analysis was done using Image J 1. 44p (NIH USA). Pax7 cell, BrdU incorporation and differentiation indexes are defined as Pax7 positive, BrdU positive and sarcomeric myosin positive nuclei over total nuclei (DAPI positive nuclei), respectively. Pax7, BrdU and sarcomeric myosin positive nuclei were colocalized with the DAPI signal using the Colocalization Stack available on the Image J website (stack authored by Pierre Bourdoncle, Institut Jacques Monod, Paris, France).
Acknowledgements We wish to thank the  INRA PHASE division (Animal Physiology and Livestock Systems , http://www. phase. inra. fr/)for its financial support, and the  INRA experimental unit UE 1295 PEAT (Nouzilly, France)  for providing the chickens used in this study. We also address special thanks to  Gilles Carnac  ( INSERM U1046 ,  Université Monpellier , Montpellier, France) for his helpful scientific advices.
Binding of AF647-CXCL14 or AF647-muCCL1 (50 nM) was performed in FACS buffer for 30 min at 4°C in a step before Ab staining. Sample acquisition was performed by using a FACS Canto II instrument (BD Biosciences). Cell aggregates were excluded according to light scatter properties. Data were analyzed by using FlowJo software (ver. 10. 04; TreeStar, Ashland, OR, USA).
Sensorgrams were corrected for signals obtained in reference flow channels (sensorchips that contained immobilized LVPs obtained from CXCR4-negative HEK293T cells or no LVPs). Sensorchip regeneration involved washing with 5 mM HCl. All steps were performed by using system robotics. Sensorgrams were recorded in real time and expressed in relative units. Sensorgrams were used to calculate (simple 1-site interaction model with Biaevaluation 4. 1 software; Biacore) kinetic parameters.