dataesr/scientific-paragraphs-categorization huggingface dataset:
M1404), 0. 5 mM colchicine (Sigma-Aldrich; catalog no. C9754), or 1 µM vincristine on a microscope stage set at 37°C with 5% CO 2 for live-cell imaging. A time-lapse movie was recorded for microtubule depolymerization events on a Nikon TIRF microscope with a 1-3-s frame interval. More than 30-min movies were acquired for nocodazole and colchicine-treated cells, and 5-15-min movies were acquired for vincristine-treated cells to observe near-complete depolymerization events of microtubules. Cells were analyzed manually for plotting the parameters of polymerization, depolymerization, dynamic instability, and severing events from the complete frames of the movies. Graphs were plotted on GraphPad Prism6 software. Cell viability assay (Trypan blue, PI, and DAPI staining; Fig. S5,  A  and B ) 1 million wild-type U2OS cells (as control) and stable U2OS cells expressing the red or the blue tyrosination sensor were diluted 1,000 times in complete McCoy's media in separate microcentrifuge tubes.
For DAPI staining, an incubation of 15 min was performed on ice. Forward and side scatter was adjusted with a blue (488 nm) laser to mark the dense population of the cells for analysis. Percentage viability was calculated by subtracting the number of dead cells (DAPI-or PI-positive cells) from the total number of cells counted in stable U2OS cells with the tyrosination sensor and comparing it with the wild-type U2OS control. Cells stained for DAPI and PI were analyzed with a violet (405 nm) and green (561 nm) laser, respectively, on a BD FACS Aria was performed using Sparky software. Backbone assignments were obtained by NMRPIPE and confirmed manually. The structural model of a1aY1 was calculated by CS-ROSETTA  (Shen et al. , 2009). The structural model of Hs_TUBA1A peptide was calculated in Xplor-NIH.
FWHM estimation Line profiles of several microtubules from 10 labeled cells were obtained and fitted with a Gaussian distribution using Fiji image processing software. For the profile, a line width of 165 nm was chosen to cover a minimum width of four pixels in SIM images. Microtubule widths in SIM stacks were measured in the z-axis section where the microtubule fluoresced most strongly. The FWHM was calculated with the following formula, where σ is the Gaussian width parameter: FWHM = 2. 355σ. Cell fixation, immunofluorescence, and imaging for VASH2_X1-GFP-2A-SVBP (Fig. S4, A-D ) and CLIP-170 staining (Fig. 6  C) HeLa cells plated on glass coverslips were transduced with lentiviruses encoding different constructs of mVash-mSVBP for 24 h and fixed according to previously described protocols  (Magiera and Janke, 2013).
Cells were washed three times with 0. 15% Triton-X-100, blocked for 1 h in 1% BSA solution prepared in PBS containing 0. 15% Tween-20. Cells were then incubated with CLIP170 antibody (1:300 dilution in blocking solution) for 2 h. Washes after primary and secondary antibodies were performed using blocking solution as described above. Images were acquired using Optigrid (Leica) with a 63× (NA 1. 40) oil-immersion objective or 100× oil-immersion objective for CLIP170 images and the ORCA-Flash4. 0 camera (Hamamatsu), operated through Leica MM AF imaging software. Images were processed using ImageJ v1. 51a (National Institutes of Health), and final figures were prepared using Adobe Photoshop and Illustrator.
All images acquired were analyzed on Fiji software (ImageJ) using the appropriate plugins. For the colormap, Fiji plugin "colocalization colormap" was used to obtain the colocalization value (index of correlation) and the colormap distribution. Pearson's correlation coefficient (R-value) calculation in Fig. 4  B was carried on z-projections of the images acquired on FV3000 confocal microscope for each enzyme overexpression. For each enzyme experiment, the confocal stacks were z-projected for TagRFP-T (561-nm laser channel), enzyme channel (488-nm laser), and SiR-tubulin channel (640nm laser channel). A 50-pixel background was subtracted from 561 (sensor) and 640 (SiR-tubulin) channels. The colocalization was calculated using ImageJ coloc-2 plugin. Pearson's R-value (no threshold) was calculated for each image, which represents the percentage overlap of the fluorescent intensity TagRFP-T over SiR-tubulin.
Single-plane microscopy imaging for microtubule dynamics, growth rate (EB3 experiments), motor movement, and druginduced microtubule depolymerization experiments was performed on a Nikon Ti2 H-TIRF microscope with a 100× oil objective (1. 49 NA) connected with four solid-state lasers lines (405, 488, 561, and 640 nm) under total internal reflection mode. The images were acquired using an appropriate filter set using the s-CMOS camera (Hamamatsu; Orca Flash 4. 0) controlled by Nikon NIS-elements software. All the images were analyzed on Fiji (ImageJ) software to construct movies and kymographs to measure the velocities/processivity (run length) of motors and EB3 comets. For measuring the number of comets per square micrometer per minute, a single-cell image from the TIRF movies was extracted by cropping the area around cell boundary and making the intensity outside the cell as zero, using Fiji software.
Total five cells were considered each for control and TagRFP-T_A1aY1 expressing cells transfected with EB3-GFP. All the images were thresholded for all 20 frames (3-s interval, 1 min total movie) to completely remove the background from the image. The binary image obtained was analyzed to count the number of comets in all 20 frames, which was further divided with the area of the cell to plot the graph in Fig. S5 H. All live-cell experiments using U2OS cells were performed in McCoy's 5A complete media (with 10% FBS and antibiotics) on a 37°C preheated microscopy stage in a moist-air chamber regulated with 5% CO 2. 6, B, D , and E for EB3-GFP comet, K560, and Kif1a motor velocities and processivity and Fig. S5  D were plotted for histograms/distributions and Gaussian fit on Origin laboratory software.
For microtubule growth and depolymerization rate measurements, manual tracking of individual microtubules was performed using Fiji software by drawing a segmented line over the microtubule undergoing such events. The distributions of the growth and depolymerization rates were plotted on origin laboratory software to calculate mean ratio and SD (Fig. S5 D ). Catastrophe frequency was calculated by considering continuous catastrophe events over time (total; per minute) and the length of the microtubule (per micrometer) undergoing depolymerization. The values were plotted on GraphPad Prism6 software (Fig. S5 G ). All the kymographs displayed are analyzed on Fiji software. Statistical analysis performed for mean ratio, SD, SEM, and n value are mentioned in respective figure legends.
Acknowledgments The authors acknowledge the  NMR facility of Biophysics Core  and the  Central Imaging and Flow Facility at NCBS/inStem/ Centre for Cellular and Molecular Platforms campus. The authors thank  V. Henriot  ( Institut Curie, Paris, France ) for technical assistance and  A. Akhmanova  ( University of Utrecht, Utrecht, Netherlands ) for kindly providing essential reagents. S. Kesarwani  and  P. Lama  are supported by the  inStem Graduate Program. A. Chandra  is a  Wellcome Trust Department of Biotechnology (DBT) India Alliance   Early Career Fellow  ( IA/E/ 15/1/502339 ). C. Janke is supported by the  Institut Curie ,  Agence Nationale de la Recherche  award  ANR-17-CE13-0021 ,  Institut National du Cancer  grant  2014-PL BIO-11-ICR-1 , and the  Fondation pour la Recherche Medicale  grant  DEQ20170336756.
Statistical analyses Isotopic signatures of fish, preys and baselines were compared using MANOVA analysis with site, vegetation and site/vegetation interaction as factors. Fish diet partitioning was achieved using Bayesian mixing model performed with package MixSIAR 3. 1. 10 (Stock and Semmens, 2013)  in R 3. 6. 1 (R Core Team, 2020) with two tracers: δ 13 C and δ 15 N. As a first step, models were built for each fish species with POM, MPB and terrestrial vegetation as potential sources. We used baseline sources rather than potential preys as we were interested in studying the effect of terrestrial vegetation changes in the overall contribution of salt-marsh components. For species with a significant effect of vegetation changes, we built models with potential preys (inferred from stomach contents).
(2012)  following  Selleslagh et al. (2015). Two sets of values were used according to fish species trophic guilds. Values for predators (D. labrax and P. microps) were: 2 ± 0. 6% and 5. 6 ± 1. 5% for δ 13 C and δ 15 N respectively. Values for grazers (C. ramada) were: 1 ± 0. 6% and 3. 4 ± 1. 5% for δ 13 C and δ 15 N respectively  (Carpentier et al. , 2014; Como et al. , 2018). The fish trophic position was estimated using a two sources Bayesian model. The two sources included were the ones contributing most to the fish diet according to previous mixing models. Estimation was performed using the tRophicPosition 0. 7. 7 package  (Quezada-Romegialli et al. , 2019). Input values for each model were the raw isotopic values for fish and sources. The grouping variable was vegetation type. The isotopic niche of fish was approximated through standard ellipse area derived from δ 13 C and δ 15 N values using the Bayesian framework developed by  Jackson et al.
Acknowledgements We would like to thank the Programme Seine aval which financed this study included in the  DEFHFIS program. We also thank the  Agence de l'eau Loire-Bretagne  ( PEPPS  project) and the  Région Bretagne (SAD)  for supporting D. Lafage. We also want to thank the  Plateforme de Spectrométrie isotopique of the LIENSs laboratory of La Rochelle  for the isotopic analyses. Appendix C: Probability of trophic position of a fish foraging in a given vegetation type and site to be inferior or equal to another one. SE: Seine Estuary, MSMB:  Mont-Saint-Michel Bay.
Our first source of information for locating potential geosites was pre-existing databases, historical maps and photographs, and oral discussions with local experts. We also compiled a simplified urban geomorphological map, which allowed us to have an overview of the city's main geomorphological features and its geodiversity, and helped identify areas with potential geosites (geodiversity hotspots). Finally, a thorough, highly-detailed, street-by-street survey of the A -A DEM (CRAIG 2013) view from southeast, indicating the extension of built-up areas as well (OSM 2020). B -the view of the city from its highest point, the Plateau of Côtes du Clermont. The Plateau of Gergovie in the background is an inverted relief feature as well, but outside the city limits. whole city was the major way we obtained our information.
From the fieldwork, more than 50 sites were recorded and assessed, following the database format and semi-quantitative assessment method by  de Wever et al. (2015). Underground elements, in particular the caves dug into the Clermont tuff ring, under the medieval city centre, were omitted to respect privacy, and we also omitted a detailed assessment of the heritage stone potential of the city. However, considering the flexibility of the inventory, these elements could be included in a future phase. In the discussion, we underline the importance of site-specific management strategies in an urban environment through the example of selected geosites and geodiversity sites. The educational and geotouristic potential of these sites is illustrated through the proposal of geotouristic routes. We consider the possibilities for future development and look at issues such as the involvement of citizens in geoconservation (e.
In some cases, these documents provide evidence of ancient outcrops or quarries that have now been destroyed or converted into housing complexes or commercial centres. After the initial bibliographic study, we created the simplified geomorphological map of Clermont-Ferrand. As demonstrated by del  Monte et al. (2013)  in Rome, the identification of the main landforms and geomorphological processes on geomorphological maps that are often covered by an urban fabric could help in the location of potential geoheritage areas. Besides giving a general overview of the geodiversity of the whole area, certain geodiversity hotspots could be highlighted by a higher density of different phenomena. These could help in the field identification of geosites (Fig. 3 ). The map covering the whole administrative area is based on the 5 m resolution LiDAR dataset of Clermont Communauté DEM (CRAIG 2013), also using for comparison the digitized, local sheets of the Geological Map of France at 1:50,000 (BRGM 2019), and the topographic maps of  IGN (2019).
Inventory and assessment Field data was recorded with the open-source framework of ODk (Open Data kit) Collect and Aggregate application  (Vereb et al. 2018A)  and then converted to a Microsoft Access database. The inventory database closely followed the structure of the French National Inventory and its central database, the iGéotope (de  Wever et al. 2015) , the background and structure of which is described below. The Inventaire National de Patrimoine Géologique (INPG), which we followed, is the comprehensive framework that controls and guides the assessment of geoheritage, as well as the collection, processing and publication of geoheritage data in France. The conceptual background and the description of the methodology was first published by  de Wever et al. (2006) , and updated later as Géopatrimoine en France (de  Wever et al.
The number of geoheritage interest stars is also used as a fourth criterion. Values for each criterion are summed without a weighting, with 12 points being the maximum score. By closely following the framework of the INPG, it means that the selected geosites at a local level can easily be incorporated into the national inventory in the future, if the representativity justifies it. A slight modification we made was the addition of some descriptive fields (e. g. , identification of canton and cadastral number inside the city), which could be of administrative help in the city municipality where the database is to be integrated. The identification number of geosites has also been adapted to the local context using the following naming standard: CFxxyy, where xx is the official number of the city canton, while yy is the individual number of the site.
Individual, isolated sites include the Petrified Source of Saint-Alyre (CF-1401), the outcrop of the sedimentary infill of Maar de la Gantière (CF1221), and the national level geosites of Puy de Crouël (CF1101 in the Clermont-Ferrand inventory, AUV0093 in the national inventory), Puy de la Poix (CF1001 -AUV0094) and the quarry of Gandaillat (CF1102 -AUV0097). These latter sites have not been divided into smaller units according to their microforms, because they have limited spatial extent. Most of the other geosites are small outcrops compared to the city scale, therefore they have been recorded as point type features as well. Some sites that should also be considered as geomorphosites  (Reynard et al. 2009 ) have been marked as points according to the database structure of INPG, although they cover larger areas that could be specified in additional maps and included as annexes to the inventory, like the plateau of Puy de Var (CF1003) or the park of Montjuzet (CF1404).
g. , outcrop in the garden), asking for help with sustainable geoconservation (e. g. , stabilization of slopes with less destructive and less invasive solutions) from the city authorities. Finally, a fourth phase might include the detailed inventorying of heritage stones, requiring close coordination with cultural heritage experts and possibly a different database and assessment format. The principal role of urban geoheritage inventories is to record those elements of geodiversity that form islands in urbanized areas. This context calls for a different approach. Thus, sites in natural areas that are considered insignificant can acquire value in the urban context, as they represent the few remaining exposures of a geological feature, a habitat for wildlife or an organic element of the cityscape.
This study received the approval of the ethics committee of the University of Rostock(Nr. A 2017-0072). Data was analysed using SPSS, Version 24. 0 (SPSS Inc. , Chicago, USA). Comparisons between the groups utilized the Kruskal-Wallis test, followed by a pairwise comparison. The Shapiro-Wilk-test was used to test for normal distribution. Results: BV/TV (%;M±SD) for CS: 25. 45±2. 30; TS:18. 13±1. 38; LS:16. 25±0. 60. Regarding BV/TV (pb 0. 001), Tb. Th. (p=0.
Statistical considerations Descriptive analyses were presented using proportions for categorical variables and mean together with standard deviation (SD) or median together with the interquartile range (IQTR) for the continuous variables. Comparisons of the categorical variables were done using the Pearson's chi-square test. An ordered logistic regression model was used to assess the effect of multiple applications on the pain levels of the patients during thermal ablation treatment. Because of the scarcity of data in some the cells of the pain level-number of application crosstabulation, the true proportions in these cells were then estimated from the regression model. Cure rates were estimated only for the women showing CIN 1 or worse (CIN 1+) lesions on baseline histopathology. The data was analyzed using the STATA software, version 14.
Acknowledgments We are grateful to  Dr. Tapas Majhi , Ex-Director of  Chittaranjan National Cancer Institute  for his support and encouragement. We acknowledge the contribution of the project staff  Rakiba Begum ,  Sudipta Dutta ,  Monalisa Chitrakar ,  Masmooda Khatun  and  Kabita Dey. We thank  Dr. Rolando Herrero ,  Head of Early Detection and Prevention Section of IARC  for reviewing the manuscript.
PanC Sequence Typing To allocate the B. thuringiensis isolates tested in this study to phylogenetic groups, sequencing of a 485 bp fragment of the pantothenate synthetase gene (panC;  [27] ) was applied (Eurofins Genomics Germany GmbH, Ebersberg, Bavaria, Germany). Sequences were aligned using CLUSTAL Ω  [28]. Further cluster analysis was carried out using SplitsTree software (version 4, Eberhard Karls University Tübingen, Tübingen, Baden-Württemberg, Germany )  [29]. The sequences of the following reference strains were added to the analysis: type I: B. pseudomycoides 219,298 (CP007626. maltose in bacto nutrient broth (Oxoid, Wesel, Northrhine-Westphalia, Germany); pH 7. 6) were inoculated with 0. 5% overnight culture (see Section 2. 1) and incubated for three days at 32 • C and 200 rpm. Sporulation was monitored via bright-field microscopy.
Germination For assessing germination of B. thuringiensis spores, media were inoculated to OD 600 = 1. Two biological with three technical replicates for each strain were incubated in 96-well plates at 37 • C for one hour. As described before  [14] , OD 620 was measured every three minutes in a Tecan photometer using Ridawin software. Germination is shown as the decrease of OD 620 (in %) per time. Germination was compared in CGY and cRPMI medium, as well as with and without prior heat activation for 10 min at 80 • C.
Statistical Analyses Data were statistically validated using the column statistics program of GraphPad Prism version 5. 00 for Windows (GraphPad Software, San Diego, CA USA). Unpaired t-tests were applied with two-tailed p-values and 95% confidence interval. Significant differences were marked with * (p-value ≤ 0. 05). Furthermore, Spearman correlation tests were performed with two-tailed p-values and 95% confidence interval to determine correlations between data sets. Significant correlation was marked with * (p-value ≤ 0. 05).
Only strain MHI 3241 exhibited no haemolytic activity on sheep blood agar. Extension of the haemolytic zone varied strain-specifically, with isolates MHI 271, MHI 2873 and MHI 3370 showing the discontinuous haemolysis zone phenomenon  [13, 47, 48]. Furthermore, data obtained from EIAs and WST-1 bioassays were statistically analysed. Spearman correlation tests revealed that NheB, Hbl L2 and cytotoxicity titres of all tested B. thuringiensis isolates generally tended to increase together, but weakly and in a non-significant manner (Table  3A ). accordingly enhanced when the strains were grown in CGY medium (Figure  5A ). Data from WST-1 bioassays were supported by haemolysis (Figure  5B ). Only strain MHI 3241 exhibited no haemolytic activity on sheep blood agar. Extension of the haemolytic zone varied strain-specifically, with isolates MHI 271, MHI 2873 and MHI 3370 showing the discontinuous haemolysis zone phenomenon  [13, 47, 48].
Furthermore, data obtained from EIAs and WST-1 bioassays were statistically analysed. Spearman correlation tests revealed that NheB, Hbl L2 and cytotoxicity titres of all tested B. thuringiensis isolates generally tended to increase together, but weakly and in a non-significant manner (Table  3A ). Nearly all B. thuringiensis isolates tested in this study secreted sufficient amounts of enterotoxins under simulated intestinal conditions to harm human colon cells in a B. cereus-like magnitude. Thus, the antimicrobial activity of essential oils (EOs) was assessed as a preventive measure against putatively enteropathogenic B. thuringiensis. Initially, inhibition zones in disk diffusion assays were investigated. Except thyme, each EO was able to inhibit growth of all tested B. thuringiensis strains (Figure  6A  and Figure  S1 ).
Exome Sequencing and Variant Analysis ES was performed by the University of Washington Center for Mendelian Genomics as described previously. 24 In brief, data were annotated with the Variant Effect Predictor v89  25  and analyzed using GEMINI 0. 20. 2. 26 Variants unlikely to impact protein-coding sequence (for which GEMINI impact_severity = LOW), variants flagged by the Genome Analysis Toolkit (GATK) as low quality, and variants with an alternative allele frequency > 0. 005 in any super-population in EVS/ESP6500, 1000 Genomes (phase 3 release), or the gnomAD Browser (v. 2. 0. 1) were excluded. Variants that were frequent (alternative allele frequency >0. 5) in an internal database of >7,500 individuals (Geno2MP v1. 7 release) were excluded. Candidate genes were identified by filtering under these parameters for variants matching the predicted pattern of inheritance (i.
0657) and who was homozygous for the same variant as found in the siblings in Family A. The proband of Family B, last examined at 6 years of age, also had similar clinical findings to the siblings in Family A including a small mouth, micrognathia, scoliosis, contractures of the hands and wrists, and severe right clubfoot that was recalcitrant to treatment, ultimately leading to amputation of the lower leg. Pathological exam of the foot revealed complete absence of skeletal muscle that was confirmed histologically (Figure  1 ). In both families, we identified homozygosity for a variant (c. 470G>T) in a single gene, myosin light chain, phosphorylatable fast skeletal muscle (MYLPF [MIM 617378; Refseq accession number NM_013292. 4]) (Table  1 ; Figure  2 ). This variant is predicted to result in p.
Sangersequencing validated homozygosity of the c. 470G>T variant in all affected persons and that the parents in Family A were heterozygous carriers. These results suggested that homozygosity for c. 470G>T in MYLPF resulted in a pattern of multiple congenital contractures virtually indistinguishable from that observed in persons with DA, specifically DA1. In an effort to find additional families with a pathogenic variant in MYLPF and clinical characteristics of DA1, we submitted genetic data and phenotypic information to the MatchMaker Exchange (MME) via the MyGene2 node and identified two additional families (E and F) that had been submitted to the GeneMatcher node. Simultaneously, we queried commercial genetic testing companies and colleagues about families in which MYLPF had been identified as a candidate gene.