dataesr/scientific-paragraphs-categorization huggingface dataset:
Specific SNP discrimination genotyping assay Two specific canSNPs (A02/B1-NL and A02/A) that define the Dutch A. Br. 001/002 clusters were developed into HRM assays. Two other assays, specific to the A. Br. 008/011 cluster including the heroin-associated isolates and CVI-un2 (A08/D) or to the A. Br. Vollum cluster including  CVI-23932 and CDC 684 (19)  (AVO/ A2a 0 ), were designed (Table  1 , Fig. 1 ). Three SNP specific, respectively, to strains CVI-23932, CVI-56430 or CVI-un2 were also developed into assays. These novel diagnostic assays were validated against 250 B. anthracis DNAs in collection. The two expected alternate alleles exhibited distinct melting curves and melting temperatures, allowing unambiguous discrimination of the Dutch isolates within their respective genetic sub-groups (data not shown).
Acknowledgements This work was supported by the  French National Research Agency (ANR)  and  Direction Générale de l'Armement (DGA)  (Project Number  ANR11ASTR0007 ). GG is a PhD student co-supported by  Anses  and  DGA  grants. This work has benefited from the facilities and expertise of the high throughput sequencing platform of  IMAGIF (Centre de Recherche de Gif  [http://www. imagif. cnrs. fr]).
, 2012 A. Br. 14 2824144 T to C A. Br. Aust94 Reference: Birdsell et al. , 2012 A. Br. 15 317219 A to G A. Br. Aust94 Reference: Birdsell et al. , 2012 A. Br. 26 3640599 C to T A. Br. Aust94 Reference: Khmaladze et al. , 2014 A. Br. 27 4355524 C to T A. Br. Aust94 Reference: Khmaladze et al. , 2014 Unnamed 111199 A to G A. Br. Vollum Reference: Okinaka et al. , 2011 A11/3 1975689 G to A A. Br. 011/009 branch 3 Reference: Girault et al. , 2014b a Localisation on the Ames Ancestor chromosome (GenBank Accession No. AE017334. 2).
5 mM HEPES pH 7. 5 and cells were placed in a thermostatic chamber set at 37°C. Image acquisition was performed on the imaging platform of IPMC CNRS and on workstations of the Montpellier RIO Imaging facility. Images were analyzed with the FIJI software (http://fiji. sc/Fiji). Intensity profiles were obtained with the "Plot profile" tool, or a macro developed by F. Brau for multi-channel analysis. For the t-test analysis, intensity profiles were obtained as described above. GFP and mCherry intensities of 10 consecutive pixels spanning cytoplasm, tubules or cisternae were compared using a paired Student t-test. The data were plotted using Prism. The texture parameter "Contrast" as defined by Haralick  [39]  was obtained with an ImageJ GLCM Texture plug-in modified from Julio E. Cabrera's plug-in.
The texture parameters were computed for a 10 μm 2 area in the peripheral ER region. All images were acquired with identical settings, in non-saturating conditions. Contrast is defined by Eq (1): cont ¼ X N i¼1 X N j¼1 ði À jÞ 2 Pði; jÞ where N is the number of grey levels, P(i,j) is the probability that a pixel of intensity i neighbours a pixel of intensity j. As expression level of the fluorescent proteins may vary from cell to cell, we plotted the normalized contrast defined by Eq (2): C ¼ cont m 2 where μ is the mean intensity of the analyzed area. Contrast data were plotted with the Prism software. "Position" column. Sequences of the linkers are in italic, when it applies. (DOCX).
Acknowledgments We would like to thank  Frédéric Brau  for help with imaging,  Nathalie Leroudier  for sequencing and  Patrice Dosset  for help with Fiji GLCM plugin. OMX images were acquired and analyzed by  Julio Mateos Langerak at the Montpellier RIO Imaging facility. We thank our lab members for their critical comments on this work, and especially  Stefano Vanni  for numerous and inspiring discussions. The authors wish to thank the  Montpellier RIO Imaging facility  and their financing bodies.
The humpback whale population of New Caledonia appears to display a novel migratory pattern characterized by multiple directions, long migratory paths and frequent pauses over seamounts and other shallow geographical features. Using satellite-monitored radio tags, we tracked 34 whales for between 5 and 110 days, travelling between 270 and 8540 km on their southward migration from a breeding ground in southern New Caledonia. Mean migration speed was 3. 53 ± 2. 22 km h -1 , while movements within the breeding ground averaged 2. 01 ± 1. 63 km h -1. The tag data demonstrate that seamounts play an important role as offshore habitats for this species. Whales displayed an intensive use of oceanic seamounts both in the breeding season and on migration. Seamounts probably serve multiple and important roles as breeding locations, resting areas, navigational landmarks or even supplemental feeding grounds for this species, which can be viewed as a transient component of the seamount communities.
Argos data processing Location data were obtained from the ARGOS-CLS system. Each location incorporates a measure of error represented by the following location classes (LC) in descending order of accuracy: 3, 2, 1, 0, A, B and Z  [37]. In this study, we removed Argos locations with LC Z and filtered the remaining Argos locations using the statistical package Trip in R  [33, 41]  in order to remove locations that implied unrealistically rapid movements. Removal occurred if travel speed between two consecutive locations exceeded 12 km h -1 , based on maximum speeds reported for humpback whales  [42, 43]. Tracks were then reconstructed using these filtered positions.
Switching state-space modelling A Bayesian switching state-space model (SSSM)  [44] [45] [46]  was applied to the filtered Argos data in order to estimate whale movement parameters and behavioural states from telemetry data. Model fitting was performed using freely available software R (R Development Team, 2011) and WinBugs  [47]. The latter uses Markov Chain Monte Carlo (MCMC) methods to compute multi-dimensional integration required in Bayesian statistics to produce a posterior distribution of the parameters of interest. The model was fit to each individual dataset with a total of 40 000 MCMC samples with the first 20 000 discarded as a burn-in. The remaining 20 000 samples were reduced to 2000 by retaining one out of every 10 samples, from which the marginal posterior distribution of parameters of interest was computed.
Environmental data In order to evaluate potential differences in habitat characteristics between searching and transiting areas, we calculated depth, as well as distance to the 200 m and the 500 m isobaths for each location using the results of SSSM. Depth was obtained from the NOAA ETOPO Bathymetry (https://www. ngdc. noaa. gov/mgg/global/etopo1sources. html). Distance to isobaths was calculated using the Geographic Information System package Arc View 10. 0, and its extension Spatial Analyst, from ESRII Corporation. We conducted one-way factorial analysis of variance (ANOVA) on depth and distance to the 200 m and 500 m isobaths to identify the characteristics of each habitat.
All analyzed dinoflagellates in this study were located in the oral gastroderm epithelium, which contains by far the highest density of symbiotic cells compared to the aboral gastroderm (see Fig. S1  in the supplemental material). Data were processed using the L'IMAGE software. A smooth width of 3 pixels was applied for NanoSIMS 13 C/ 12 C and 15 N/ 14 N isotopic images, and a line width of 1 pixel was applied when illustrative line scans were defined from these smoothed images. NanoSIMS quantification of both 13 C and 15 N enrichments was carried out by defining regions of interest (ROIs), as illustrated in Fig. S2  in the supplemental material. For the whole dinoflagellates and their C reserves (i. e. , starch granules and LDs), the ROIs were obtained by drawing their contours. Quantification of the remaining cell compartments (i.
ACKNOWLEDGMENTS This work was supported by  European Research Council  advanced grant  246749  (BIOCARB),  Fonds National Suisse  grant  CR2312-141048 , and the  École Polytechnique Fédérale de Lausanne  to A. M. , CNRS grant Interface 2010 (NanoSIMS and symbiosis) to I. D. C. , and the  Faculty of Biology and Medicine of the University of Lausanne. We thank  Jean Daraspe ,  Chakib Djediat ,  Céline Loussert , and  Antonio Mucciolo  for providing help with TEM preparations. We are grateful for access to and expert help with aquarium facilities at ATPD, in particular to  Jean-Daniel Galois  and  Sylvain Joumier. Mathieu Pernice ,  Stephanie Cohen , and  Thomas Krueger  are thanked for discussions. Two anonymous reviewers are thanked for highly constructive comments and suggestions that helped improve the manuscript.
Moreover, the absence of necrosis in the Medes Islands area was also noted during regular monitoring activities on other species that were conducted during the previous decades. To search for differences in the thermal regimes between both sites, hourly temperature data were recorded from dataloggers (Water Temp pro v2, ONSET, Cape Cod, MA, USA) installed at 15 m depth (average depth were the coral colonies occur) at each location. Because warming-related necrosis in this coral occurs directly after the summer  5  , only the summer water temperature data were analyzed (June -September from 2010 to 2013).
Statistical analysis. Linear mixed effects models (nlme package for R  47  ) were used to test for differences in necrosis rates and photosynthetic efficiency between both studied populations (experiment T1) and algal-temperature synergistic effects (experiment T2). Linear mixed effects models are used to model data that can cope with repeated measures over time  47. The fixed factors in experiment T1 were location (Medes and Columbretes Islands), temperature (warming and control) and time. In experiment T2, the fixed factors were invasive alga treatment (uncovered, covered with artificial material and covered with W. setacea), temperature (warming and control) and time. In both experiments, the tank was set as a random factor, and the response variables were the percentage of tissue necrosis and photosynthetic efficiency.
Acknowledgements We thank the  Secretaría General de Pesca (MAGRAMA)  and the  Columbretes Islands Marine Reserve  staff for their logistic support. Support for this work was provided by a Ramon y Cajal research contract ( RyC-2011-08134 ) to C. L. and by a  JAE-doc (FSE)  to E. C. This study was funded by the  Spanish Ministry of Economy and Innovation Smart project  ( CGL2012-32194 ). The authors are part of the  Marine Conservation research group  ( 2014 SGR 1297 ) from the  Generalitat de Catalunya.
Results Results are based on the analysis of 4,155 amphibians tested for the presence of Bd, 1,113 of which have been presented in previous publications  [13] [14] [15] [16] 32, 34. Fifty two sites across Madagascar were sampled, with the earliest sampling undertaken in 2005. Ninety-nine different sampling events were completed, with a mean sample size of 42 6 3 SE frogs across these sampling events. For this study we combined all data available to us from 2005-2014. These data are from (i) samples of the National Monitoring Plan, (ii) samples obtained in the context of a skin microbiota study of Madagascar's amphibians, and (iii) samples collected opportunistically. While the data thus do not agree with an ideal sampling design, they do cover all major biomes and elevation zones of the island, as well as both the dry and wet season, allowing for the first assessment of spatial and temporal patterns of Bd occurrence and prevalence in Madagascar (see Supplementary Table  1  for more details).
Bd lineage in Madagascar. Lineage-specific qPCR was undertaken to determine if the Bd present in Madagascar was more closely related to the BdGPL, BdCAPE or BdCH lineages. A subset of samples, that were Bd positive with the general ITS probe, were tested with lineage specific probes (Table  3 ). While not all samples showed positive amplification, the ones that amplified with the lineage specific probes all showed the presence of a BdGPL-like lineage (Table  3 ). This BdGPL-like lineage may be the true BdGPL, an endemic BdGPL-like, or a non-endemic BdGPL-like lineage. None of the tested samples showed positive amplification with the CAPE-specific or CH-specific probe (Table  3 ). Amphibian chytrid fungus infectivity. No data are so far available on the susceptibility of Malagasy frogs to chytridiomycosis.
These organisms could be a potential source for Bd introduction as crayfish can be an  alternative host for the pathogen  46. However, invasive as well as native crayfish were sampled in January and February of 2014 and no Bd was detected. This result, along with data showing that the distribution of the invasive crayfish does not overlap with the occurrences of Bd, suggests that crayfish are most likely not responsible for introducing Bd in Madagascar. Recently it has also been documented that an alien toad species (Duttaphrynus melanostictus) has locally invaded eastern Madagascar  47. If the origin of these invaders was a Bd-positive area of the world, then these amphibians could be Bdcarriers and may have subsequently introduced Bd to Madagascar; however, so far this species has never been recorded as a carrier of the pathogen  48.
Acknowledgments We are grateful to all Malagasy colleagues and authorities who helped in establishing a solid network of collaboration, facilitate chytrid research within the country and were committed to the creation and implementation of the  Chytrid National Monitoring Program. We thank the  Direction des Eaux et Forets, Ministry of the Environment, and Madagascar National Parks  for supplying research and export permits. We are grateful to numerous students, assistants and colleagues who assisted during fieldwork. In particular we thank  P. Bora ,  A. Thorel ,  J. Dawson ,  J. Lewis ,  L. Woolaver ,  R. Dolch ,  J. Noe  ¨l,  B. Iambana ,  K. Freeman ,  A. Bollen ,  M. Moore ,  L. du Preez ,  J. B. Ramanamanjato ,  J. C. Rakotoarisoa ,  A. Rakotoarison ,  T. F. Rakotonanahary ,  H. Razafindraibe ,  E.
Funding was provided by the  Saint Louis Zoo Field Conservation program  (grants: FC # 11-5 ) to F. A. , A. C. , F. R. , D. E. and C. W. ; the  Rufford Small Grants for Nature Conservation  (grant:  12931-1 ) to F. A. , A. C. , F. R. and C. W. ; The  Mohamed bin Zayed Species Conservation Fund  (grants:  10051700 ;  1025982  and  12253505 ) to F. A. , A. C. , F. R. , N. R. and C. W. ;  Andrew Sabin Family Foundation  grant to F. A. ; the  European Association of Zoos and Aquaria  grant to F. A. and C. W. ; a grant of the  Paris Zoo, France and of the Parc de Thoiry, France  to F. A. and A. C. ; a small grant from  Brother Industries (Brother earth ,  2010-2012 ) to N. R. ;  Volkswagen Foundation  and the  Deutsche Forschungsgemeinschaft  (grant  VE247/9-1 ) to M. V. , The  Mohamed bin Zayed Species Conservation Fund  (grant  13255440 ) to R.
N. H. and M. C. B. , the  Chester Zoo Conservation  and  Research Grant  to R. N. H. and M. C. B. ,  National Science Foundation  grant  1136602  to  R. N. H. ,  Naturevolution Association Environnementale  (grant: MakayNature) to E. C. and C. R. , and the  National Science Foundation  (grant:  DEB 0641023 ) to C. R. , and a grant from the  ERANET BiodivERsA  project  RACE (Risk Assessment of Chytridiomycosis  to European amphibian biodiversity  2008-29014-62678-16 ) to E. A. C. , M. C. F. and D. S. S. G. M. R. holds a doctoral scholarship from the  Fundaça ˜o para a Ciencia e a Tecnologia (FCT)  ( SFRH/BD/69194/ 2010 ); A. C. was supported by a postdoctoral grant from  FCT  ( SFRH/BPD/96982/2013 ) under the  Programa Operacional Potencial Humano -Quadro de Referencia Estrategico Nacional  funds from the  European Social Fund and Portuguese Ministerio da Educaça  ˜o e.
N6L is composed of a short template, rich in lysine residues on which six pseudotripeptide Lysψ(CH 2 N)-Pro-Arg is covalently anchored  [12]. N6L specifically targets cancer cells, exhibiting anti-tumor activity in various human tumor cell lines derived from mammary, colorectal carcinoma, melanoma and glioblastoma (GB)  [12]. This therapeutic peptide is currently in phase I/IIa clinical trials (NCT01711398). Since mature brain expresses important levels of NCL during the differentiation of neural cells, it is reasonable to suggest that NCL has a fundamental role in mediating signals by extracellular matrix molecules, and furthermore contributes to the differentiation and maintenance of neural tissue  [13]. Our previous data showed that in gliomas, surface NCL localization increased with the malignancy grade suggesting that NCL could be considered as a histopathological marker for glioma grading  [14] , a tumor difficult to be early diagnosed due to the faint appearance of clear symptoms  [15].
Cell viability assay Cells were seeded (2500 cells/well) in a 96 wells plate in presence or absence of treatment (every treatment was performed in triplicate) and incubated for indicated time in the figure. At expiration of incubation period cell viability was determined using Cell Titer One Solution Cell Proliferation Assay (Promega, Lyon, France) reading the absorbance at 492 nm, in a spectrophotometric microplate reader Infinite F200 (Tecan, Männedorf, Swiss). The results are expressed as ratio between the absorbance of treated cells compared to absorbance of control untreated cells. GI 50 was calculated fitting the experimental data using the software Grafit 5. 0 (Erithacus Software, UK).
Statistical analysis For statistical analysis samples were processed by SPSS software. Statistical analysis of two population means was performed by the unpaired Student's t test, while statistical differences comparing multiple means were analyzed by the analysis of variance (ANOVA) followed by Scheffe's post hoc test" analysis. *P < 0. 05; **P < 0. 005, **P < 0. 0005. Data were expressed as mean ± SE of 4 separate experiments.
ACKNOWLEDGMENTS AND FUNDING The Authors thank the  Human Health Foundation  for the support. Many of the experiments have been performed in the  Research Center for Molecular Diagnostics  and  Advanced Therapies  granted by the  Abruzzo Earthquacke Relief Fund (AERF). This work has been supported by  RIA  funds ( Prof Cimini ,  Ippoliti and Benedetti)  and by grants from the  French charitable organisation "Ligue National contre le Cancer" , the " ANR-14-LE16-OO23-NORMATHER " and Immupharma.
Sphere forming assay Sphere forming assay was used to enrich mammary stem cells (mammospheres) as previously described by Dontu  [24]. We slightly modified that protocol and co-cultured mammospheres with GFP + ECs at 1:10 ratio under nonadherent condition to obtain mammo-angiospheres. Mammo-angiospheres were therefore composed of both tumor and GFP + endothelial colonies mingling together. Spheres were grown in a so-called "3D media" as described by Dontu and colleagues by using DMEM-F12 (HyClone, USA) supplemented with 2% B27, 20 ng/mL basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF), and 5 μg/mL insulin. In order to prevent the formation of cellular aggregates, a highly viscose 3D media was prepared by addition of 0. 2% methylcellulose (Sigma, USA). Stem cell enrichment was evaluated by measuring the perimeter of mammospheres or angiospheres with NIH ImageJ 64 software or by quantifying the number of spheres.
Alexa Fluor® 647 fluorescence was obtained with a 650 nm red laser and 660/20 nm emission, while Alexa Fluor® 633 was obtained with 633 nm red laser and 647 nm emission. The figures display the median of fluorescence intensity (MFI) relative to controls. Doublets were excluded by FSC-W × FSC-H and SSC-W × SSC-H analysis, and single stained channels were used to compensate. Fluorescent minus one was used for gating. 10,000-30,000 events were acquired per sample. Finally, data were processed with FACSDiva 6. 3 software (BD Biosciences) or Summit 4. 3 (Dako). For sorting GFP + ECs, GFP fluorescence was acquired using 488 nm blue laser and 510/50 nm emission and sorting was done using purity masks  [13]. For sorting BCCs, cancer cells were stained with a PE-conjugated dye called PKH26 (Sigma, USA) prior to co-culture and PE fluorescent was acquired using 496/566 nm blue laser and 576 nm emission to separate them from GFP + ECs.
Wound healing assay GFP + ECs and PKH26 + BCCs were co-cultured under starvation for 3-5 days, and then the cells were sorted as described in the previous section. Sorted ECs or cancer cells were immediately plated and grown at 100% confluence in complete medium to recover overnight. Next, they were continued to culture under complete starvation for 6 hours to impede cellular growth before a wound healing assay was initiated  [25]. Finally, the migration capability of cells to close the wound (scratch) was evaluated after 48 hours using NIH ImageJ 64 software.
RNA extraction & microarray analysis RNA was isolated as explained above. Two quality control measures were carried out: (1) a spectrophotometric analysis and (2) a size fractionation procedure using a microfluidics instrument (Agilent Technologies). Total RNA (200 ng) was analyzed on Affymetrix GeneChip Human Genome U133 Plus 2. 0 Array. Data were analyzed using Partek Software (V6. 09. 1110-6; Affimetrix), Venny online software (BioinfoGP; CNB-CSIC) and Ingenuity Pathway analysis (Ingenuity Systems, Redwood City, CA). Class comparisons between ECs Norm and ECs Mes (three biological replicates of each) were performed to identify gene expression changes with significant expression differences (p < 0. 05) and two-fold increase or decrease in expression.
Ingenuity pathway analysis We used Ingenuity Pathway Analysis software (IPA) (Ingenuity Systems, Redwood City, CA) for network analysis of EC genes that were differentially regulated upon co-culture. A global gene list was defined representing IPA keywords: "Metastasis", "Proliferation of cell lines" and "Cell death of tumor cell line". All edges are supported by at least one reference from the literature, textbooks, or canonical information stored in the Ingenuity Pathways knowledge database. P-values for enrichment of biological functions were generated based on hypergeometric distribution and calculated with the right-tailed Fisher's exact for 2 × 2 contingency tables as implemented in Ingenuity.
Statistical analysis All quantitative data are expressed as mean ± standard error of the mean (SEM). Statistical analysis and graphical presentation were performed using SigmaPlot 12 (Systat Software Inc. , Chicago, IL) or Excel (Microsoft Corporation). A Shapiro-Wilk normality test, with a p = 0. 05 rejection value, was used to test normal distribution of data prior to further analysis. All pairwise multiple comparisons were performed using one-way ANOVA followed by Holm-Sidak posthoc tests for data with normal distribution or, in case of a failed normality test, by Kruskal-Wallis analysis of variance on ranks followed by Tukey posthoc tests. Paired comparisons were performed using Student's t-tests or Mann-Whitney rank sum tests in case of unequal variance or failed normality test. Statistical significance was accepted for p < 0.
(*** p < 0. 001, **p < 0. 01, *p < 0. 05, mean ± SEM, n = 3). D) Heat map demonstrating differential gene expression in ECs Mes (sorted from MDA-231cells) as compared to normal ECs (left). Functions treemap (right): rectangles represent ECs Mes differential functions as compared to ECs Norm based on literature data. Functions are grouped together into large clusters such as cellular growth and proliferation, cell cycle, cell movement etc. Rectangles are colored based on the z-score which is proportional to number of genes that are affected in any particular functional class with orange showing activation of that function and blue representing the inhibition of that function. In our dataset of ECs Mes , some functional groups showed consistent changes among all subgroups (shaded rectangles).