dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusions and Future Work The bio. tools registry allows Galaxy server maintainers to increase the visibility of their services, set in context of offerings from other providers. The ReGaTE utility is a fast and convenient solution to enhance, publish, and maintain the services provided by a Galaxy server in the registry. Furthermore, ReGaTE can prove a valuable contribution toward providing bio. tools with more comprehensive coverage of the community resources. Current work on ReGaTE is focused on migration of the core functionality and tool semantics to the Galaxy Project itself. This integration will rely on the direct annotation of Galaxy datatypes with EDAM format and data concepts (see https://github. com/ galaxyproject/galaxy/pull/2387 and https://github. com/galaxy project/galaxy/pull/2428), as well as the possibility to specify an EDAM topic (see https://github.
com/galaxyproject/galaxy/pull/ 2397) and operational concepts (see https://github. com/galaxy project/galaxy/pull/2379) directly in Galaxy tool definitions (see https://github. com/galaxyproject/galaxy/pull/3221). The use of EDAM as a standard for describing bioinformatics resources can provide a backbone to improve interoperability and guide users to connect and compose Galaxy tools  [18] , extending potentially to external components and environments that share this common vocabulary. A future priority will therefore be to exploit EDAM annotations in these ways for the benefit of Galaxy users and providers.
Results Establishment of a work flow for long time-lapse live imaging and cell lineage tracing in marine embryos and larvae Live imaging at single-cell resolution over extended time periods, and analysis of these 4D image datasets for determining cell lineages require overcoming technical barriers. In this work, we used a standard scanning confocal microscope, which allowed us to trace cells in a specific body region of the embryo. To this end, we overcame a number of specific difficulties, piecing together a complete workflow that could be applied to other marine embryos and larvae. For the immobilization of embryos and larvae, we mounted samples in a thin layer of low-melting sea-water agarose using glass-bottom dishes. After injection and a careful selection of normal developing embryos at the time of mounting, we observed normal development of all embryos and larvae in agarose.
In addition, for datasets that have low time-or image-resolution, or embryos which have significantly variable cell sizes and nuclei, segmentation and lineage-tracing algorithms available via different platforms are currently not able to carry out an automated lineage analysis with high accuracy  (Ulman et al. , 2017). Consequently, lineage tracing in such samples still largely rely on manual curation. For determining cell lineages at single-cell resolution in Platynereis dumerilii (P. dumerilii), we used a combination of labeling techniques. In addition to the conventional nuclear and membrane labeling, we also used a live-cell cycle reporter. This added the necessary information to trace lineages accurately, making it easier to predict when a cell will divide and follow daughter cells after a division, without the need to increase time resolution and thus light exposure.
Using the high-resolution timelapse video, we were able to track the pPGCs, and observed that mVenus signal persisted in pPGCs after they were born (Figure  3A -H, Figure  3 -figure supplement 1 for close-ups). Thus, in addition to differentiated cells such as ciliated cells, Pdu-FUCCI is a useful tool to trace the cells that are undifferentiated but arrested in G0/G1, such as the pPGCs. We then investigated the migration behavior of pPGCs in the same imaging dataset from the sample injected in the D quadrant with Pdu-FUCCI and EGFP-caax mix. When live imaging was started, 4d cell had already divided once giving rise to the left and right mesoblasts (ML and MR), and ML and MR had divided twice giving rise to two pPGCs each (Figure  3A -A'', Figure  3 -figure supplement 2 shows the first two divisions of ML and MR in another sample).
However, each PBC makes 'one hemisegment-worth' of mesoderm  (Gline et al. , 2011; Weisblat and Kuo, 2014). This stereotypic, anterior to posterior-oriented, asymmetric division process is termed teloblastic growth. In P. dumerilii, to determine whether the 4d lineage (after the divisions that generate pPGCs) makes the mesodermal hemisegments in the larva via the teloblastic process as in the clitellates, we followed divisions of this lineage and analyzed the origin of mesodermal cell clusters (4d lineage is summarized in Figure  4A ). If mesoderm formation in P. dumerilii follows a teloblastic process, a key expectation is the presence of clonally homogeneous mesodermal regions, each originating from one specific primary blast cell as in the clitellate annelids. To do this, we manually traced cell lineages originating from 4d blastomere in live imaging datasets using Imaris software (for details, see Materials and methods).
Here we only report data for the left mesoblast (ML) (Sample A), but confirmed in other samples (Samples B and C) that MR behaves like ML (  Figure 5-figure supplement 1, Figure 5-video 1, Figure 5-video 2). Imaris creates a temporal series of fully re-orientable 3D reconstructions of the embryo, allowing the manual tracking of cell divisions. Spots corresponding to the nucleus of each cell are generated and cell lineages can be connected via these spots across time (Figure  4 -video 1). In addition to nuclear divisions, the cell cycle reporter helped us predict when cell division was approaching, and the cell membrane rounding (visualized via the EGFP-caax construct) helped us detect without ambiguity each mitosis and the resulting daughter cells. Once a cell lineage tree is available, subsets of lineages can be highlighted to visualize where the progeny is located in the 3D reconstruction.
First, we further analyzed the dorso-ventral position of the clonal mesodermal clusters at the final time point (t = 72, or about 37. 5 hpf of development (Table  1 ) of the time lapse dataset. At this time point, chaetal sacs (ectodermal structures used as anatomical markers of larval segment formation) had already started forming with a few elongating bristles evident, and each clonal mesoderm cluster from a single PBC overlapped with a pair of chaetal sacs present in each hemisegment (Figure  4 -figure supplement 2A-B',). Then we analyzed the cross-sections of the 3D stacks with the Imaris lineage spots. We found that spots marking the mesodermal lineage lie just beneath each pair of chaetal sacs within a larval hemisegment (Figure 4-figure supplement 2C-D''), confirming that these were mesodermal cells forming the layer beneath the elongating chaetal sacs at this stage.
Mesodermal posterior growth zone originates from 8ML and 8MR At the eighth division of ML and MR, cells 8ML/R and 8ml/r are generated. As described above, 8ml/r are the founder cells of the third segmental mesoderm (Figure  4G , Figure  4 -figure supplement 1, Figure  4 -video 16). We next investigated the progeny of 8ML/MR (Figure  5 ). We compared three separate individuals (Samples A, B, C) for the 8ML and 8MR divisions and found them to be similar in all samples (Figure  5   supplement 1A''-C'' ) expanding the progeny of 8ML and 8MR to 5 cells on each side (10 total). Thus, by the last time point of our datasets (corresponding to the end of mid-trochophore stage), 8ML and 8MR had given rise to five cells each that were surrounding the four pPGCs and formed a posterior 'bridge' between the right and left mesodermal bands.
For example, Figure  3 -video 1 (used in Figures  3, 4 , 5 and 6) starts at eight hpf (stereoblastula stage), and in the final time point the sample appears towards the end of mid trochophore stage. Even though elapsed time is 12 hr of imaging (72 time points), under 18˚C incubation conditions, about 35-40 hr is required to reach this stage. Thus, we calculated each time point in the live-image dataset corresponding roughly to: T = 8 hr + (25mins x tp), where 'tp' is time point, and T is the calculated developmental time. According to this, the end calculated developmental time for Figure  3 -video 1 is: T = 8 hr + (25 mins x 72)=37 hr 35 min. (Fischer and Arendt, 2013) , and the divisions after this were not possible to observe due to the limitations of this imaging technique. We took advantage of high-resolution confocal imaging with injection of the fluorescent markers Pdu-FUCCI (nuclear) and EGFP-caax (cell membrane, making the cell size very easy to observe).
Here, we show the imaging dataset of an embryo (Sample A, same dataset as reported above) injected into its D quadrant and live-imaged from 8 hpf until larval stages when segmental mesoderm morphology started becoming obvious (Table  1 , Figure  3 -video 1). In the confocal stacks, we were able to investigate division of 4d lineage further than previously reported, and we analyzed the size asymmetry as well as cell division angle for this lineage. The first division of 4d is equal, creating two sister mesoblast cells positioned bilaterally symmetrically (ML and MR) (Figure  6A -B, Figure  3 -figure supplement 2). However, most of the rest of the divisions were unequal, as expected of teloblasts. The first two divisions of ML and MR, are the most unequal. They gave rise to large daughter cells (1ML, 1MR, 2ML, 2MR) and very small ones (1ml, 1mr, 2ml, 2mr).
To do this, mean fluorescence intensity information was extracted for each spot from the cell lineage datasets using statistics module in Imaris and these were plotted as graphs (Figure  7A , Figure  7 -source data 1). Each spot was manually placed inside each nucleus (Figure  7A  was calculated for subsets of lineages (see Materials and methods for details). The measurement reflects the abundance of mVenus-Cdt1(aa1-147) protein, providing quantitation of the cycling of the construct. pPGCs stopped cycling after they were born (Figures  2  and 3 ; Figure  3 -figure supplement 1) and as expected, a roughly linear plot, without significant valleys and peaks was obtained for these cells (Figure  7B ). The mesoblast ML, in contrast, had clear cycling with prominent valleys and peaks (Figure  7B , Figure  7 -figure supplement 1A).
, 2012 , Rebscher et al. , 2007). Our imaging dataset is only until mid-/late-trochophore stage, thus we do not know whether all or a subset of these cells will produce the mesodermal SAZ in the later larval stages and juveniles. Thus, how these precursors go onto form the ring-like mesodermal SAZ and how they contribute to new tissues in juvenile worms remain to be determined. This study in P. dumerilii helps putting different types of development in the annelids into a phylogenetic perspective (Figure  9 ). In the leeches, the totality of a species-specific number of segments are made during embryogenesis through the activity of large embryonic teloblasts. In contrast, in most marine annelids, the majority of segments are made during post-embryonic juvenile development, through the activity of inconspicuous posterior stem cells whose characteristics are still largely unknown.
Gene cloning Pdu-cdt1 coding sequence was obtained from transcriptome databases by the Jekely and Arendt Labs (jekely-lab. tuebingen. mpg. de/blast; 4dx. embl. de/platy). An amino acid alignment against several species was carried out to confirm the sequence (MUSCLE alignment in GENEIOUS 6. 1. 8). From the full 2337 bp coding sequence, a 1946 bp part including the start site, and ending before the stop codon was amplified (Pdu-cdt1-Forward Primer: TTGTTTTCTTGTTGAGGTGGGATG; Reverse For Imaging embryonic and pre-larval stages (7-24 hpf) (5-6 hpf) (5-6 hpf)   A' ). An agarose platform (A'') with a groove large enough to contain embryos was prepared using a plastic custom-made mold. Under a dissecting scope, small incisions were made to the right side of the groove (A'''), and these incisions were used to remove embryos from the needle by sliding the needle through them.
The agarose platform was placed into a small petri dish lid and covered with filtered sea water before the embryos were transferred into the dish. In B and C, the steps of general experimental outline for live imaging samples at different stages are listed. DOI: https://doi. org/10. 7554/eLife. 30463. 050 (7-8 hpf) (0-2 hpf) ( 24 The following figure supplement is available for figure  10 : Primer: GGAGATGACGAGACAGGCAG). The PCR fragment was gel purified, cloned into TOPO-TA pCRII plasmid, and sequenced (GenBank No: MF614951).
This KOZAK-mVenus-cdt1(aa1-147) sequence was synthetized by a provider (IDTDNA gBlocks, Belgium). The synthetized fragment (200 ng) was resuspended in 20 ml nuclease-free water to a final concentration of 10 ng/ml, and it was cloned using Gibson reaction into pCS2+ expression vector which was amplified via PCR (pCS2+ vector backbone -Forward Primer: CTAGAACTATAGTGTGTTGTA TTACGT; Reverse Primer: AGAGGCCTTGAATTCGAATCG) (GenBank No: MF614950). For the Gibson reaction, Gibson assembly master mix (NEB, France, E2611S) and NEB 5-alpha Competent E. coli (NEB C2987H) were used, following the manufacturer's protocol.
Fluorescent protein production from the injected mRNA started becoming detectable around 5-6 hr after injections, thus imaging could not be carried out earlier. For the samples imaged for cell lineage analysis (Samples A, B, C in Figure  5 -figure supplement 1), 1. 13 mm step size and 60-70 mm total stack thickness was used, representing the proximal embryonic hemisphere roughly. The 4D Z-stack for Sample A has been uploaded online as a dataset and can be accessed at https://doi. org/10. 5281/zenodo. 1063531.
Image analysis and processing EdU assays, and immunostaining stacks were analyzed and exported using Fiji release of ImageJ  (Schindelin et al. , 2012). Nuclear signal counts were done manually in Fiji for Edu assays on injected samples. For live imaging datasets, 3D-projected stacks were exported as videos also using Fiji, except cell lineage tracking (see below). Time frame, and frequency of imaging is indicated for each video specifically. Annotated videos were edited using Adobe Premiere Pro CC 2017, and video encoding was adjusted to web-viewing using Hanbrake. To better represent graphically an embryo that is spherical in shape, or parts of the embryo that are laid out in a curved manner, we wrote a Fiji script called 'Onionizer'. (The onionized images appear in Figure  1 -figure supplement 2C, and Figure  4 -figure supplement 3.
) This is essentially a tool that allows in silico flattening of the embryo at various tissue depths. Concretely, the script extracts the intersection of the 3D stacks and a series of near spherical surfaces located at increasing depth from the tissue surface. The intersections are then 2D projected as if successive 'onion layers' of the sample were flattened. The stack (x; y; z) is replaced by a (x; y; ol) stack where 'ol' represent onion layers of increasing depth. This allows flattening of ectodermal tissues for low 'ol' values and mesodermal for higher 'ol' values. The FIJI script is available on FigShare. com (https://figshare. com/ s/1c0dcd120d13deb888ba). All the cell lineage and cell cycle analyses were done using Bitplane Imaris (Version 8. 2). Three different samples from two independent injection batches were used for lineage analysis, and these are letter coded throughout the manuscript: Sample A, Sample B, and Sample C.
Imaris -cell cycle Spots (each sphere marking a cell in Imaris dataset) can be used for measuring fluorescence intensity for the pixels that fall into that spot's volume. We used this feature for obtaining a quantitation of the cell cycle construct. To do this, spot size and position were manually adjusted so that each spot was slightly smaller than the nucleus signal, and was positioned to be completely inside the nucleus. Fluorescence intensity mean calculation for the mVenus channel was extracted for different cell lineages. During mitosis (when cell nucleus disappeared) the spot was positioned roughly to contain chromosomes. Criteria for choosing lineages to compare was as follows: we picked always the larger of the two sister cells after a division, and if the division was equal, we picked the one more posterior/closer to the Mesoblast.
30463. 011 Figure supplement 2. The first two divisions of ML and MR. DOI: https://doi. org/10. 7554/eLife. 30463. 012 Figure 3-video 1. Original 3D-projected time-lapse dataset with annotations (for Sample A). DOI: https://doi. org/10. 7554/eLife. 30463. 013 Figure 3-video 2. Video of stack showing the same individual from Figure 3-video 1 imaged next day. DOI: https://doi. org/10. 7554/eLife. 30463. 014 Figure 3-video 3. pPGC migration traced in Imaris, posterior view. DOI: https://doi. org/10. 7554/eLife. 30463. 015 Figure 3-video 4. pPGC migration traced in Imaris, lateral view Figure 3 continued on next page.
Note that the initial divisions are highly asymmetric in size (E, G, J, L, S) while the division that creates 7ml and 7ML appears symmetric (O). In V, the division axes for all primary blast cells are shown together. See Figure3-video 1 for the time-lapse dataset, the snapshots are derived from (Sample A). Arrowheads in (U, U'): pPGCs. Time is shown as elapsed imaging time (Table1). DOI: https://doi. org/10. 7554/eLife. 30463. 043.
Acknowledgements We thank the  Balavoine Lab Members, Vervoort Lab Members , and  Ryan Null  for helpful discussions and feedback on the manuscript. We thank  Solene Song  for help with the 'onionization' code. We acknowledge the  Company of Biologists  for the travel award to BDO, which enabled a trip to  Florian Raible's laboratory (MFPL, Vienna, Austria)  for learning injections. We thank  Karim Vadiwala  ( Raible Lab ) for his assistance during this training period. We acknowledge the  ImagoSeine facility  (member of the  France BioImaging infrastructure  supported by the  French National Research Agency ,  ANR-10-INSB-04 , ' Investments of the future ') and its experienced staff for their assistance in imaging and image analysis. We also thank  Caren Norden Lab (MPI-CBG, Dresden, Germany)  for providing the plasmids for the construction of EGFP-caax and HistoneH2A-mCherry vectors.
(A''-H'') Lateral view of the same Imaris dataset, posterior to the right, dorsal up (Figure 3-video 4). Yellow arrow shows the approximate path of pPGCs as they migrate. Note that they travel on the surface (until E''), then start assuming an internal position (indicated with the dashed yellow line) with the onset of epiboly. For the original video showing all time points and full-projection of stacks see Figure 3-video 1. For close-ups see Figure 3-figure supplement 1. (In the rest of the manuscript, this sample is analyzed for other developmental processes and is referred to as Sample A. Information from additional samples (Samples B and C) is provided in figure supplements. ). DOI: https://doi. org/10. 7554/eLife. 30463. 010 The following video and figure supplements are available for figure 3: Figure supplement 1.
Close-ups of time-lapse video of pPGCs. DOI: https://doi. org/10. 7554/eLife. 30463. 011 Figure supplement 2. The first two divisions of ML and MR. DOI: https://doi. org/10. 7554/eLife. 30463. 012 Figure 3-video 1. Original 3D-projected time-lapse dataset with annotations (for Sample A). DOI: https://doi. org/10. 7554/eLife. 30463. 013 Figure 3-video 2. Video of stack showing the same individual from Figure 3-video 1 imaged next day. DOI: https://doi. org/10. 7554/eLife. 30463. 014 Figure 3-video 3. pPGC migration traced in Imaris, posterior view. DOI: https://doi. org/10. 7554/eLife. 30463. 015 Figure 3-video 4. pPGC migration traced in Imaris, lateral view Figure 3 continued on next page.
(Dorresteijn et al. , 1993)yos were obtained from lab cultures at the Institut Jacques Monod. Cultures are reared based on previous protocols(Dorresteijn et al. , 1993)(available in English by Fischer and Dorresteijn on www. platynereis. de). Embryos and larvae are staged afterFischer et al. ,   2010. All staging is made at 18 ˚C unless otherwise stated. For live time-lapse imaging, the imaging temperatures were typically higher (estimated 26-28 ˚C). We provide a table with calculated developmental times and stages corresponding to each time point (Table Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Strain, strain background Wild Type Institut Jacques (P. dumerilii) Monod cultures Recombinant DNA reagent pCS2+ mVenus-cdt1 this paper GenBank No: (aa1-147) MF614950 Recombinant DNA reagent pEXPTol2-H2A-mCherry Other Plasmid was not specifically produced for this paper, and has been published before.
2) Software, algorithm Onionizer https://figshare. com/s/ 1c0dcd120d13deb888ba Animal cultures and staging Reagent type (species) or resource Designation Source or reference Identifiers Additional information Gene (Platynereis dumerilii) Pdu-cdt1 NA GenBank No: From the full 2337 bp coding sequence, MF614951 a 1946 bp part including the start site, and ending before the stop codon was amplified Continued on next page.
Ghilas et al. (2013)  investigate the opportunity of making use of available public transport as a part of the freight journey of logistics service providers, which operates according to predetermined routes and schedules. An arc-based mixed integer program is presented and it is amenable to solve by CPLEX. The numerical analysis shows significant reductions in operating cost and carbon dioxide emission, and the potential for mitigating traffic congestion. Along the same vein,  Shen et al. (2015)  conduct a case study on the Yuantong Express, one of the major national logistics enterprises in China, to explore the feasibility of the proposed public transit-based freight system using the existing bus network in Zhenjiang City in China. Such an integrated system results in a significant reduction in the fleet size required for good delivery service.
Acknowledgements This research is partially funded by Dinalog, the  Dutch Institute for Advanced Logistics , as part of the  R&D  project  CargoHitching. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://creativecommons. 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.
The benchmark included 151 structures from 32 RNA families (with a total of 1734 pairwise superpositions). The accuracy of superpositions was assessed by comparing structure-based sequence alignments to the reference alignments from the Rfam database. SupeRNAlign and SupeRNAlign-Coffee achieved significantly higher scores than most of the benchmarked methods: SupeRNAlign generated the most accurate sequence alignments among the structure superposition methods, and SupeRNAlign-Coffee performed best among the sequence alignment methods.
INTRODUCTION Comparison is the most fundamental research technique in biology. Knowledge of similarity between biomolecules enables clustering them, grouping them into families, inferring their evolutionary history, detecting functional motifs and thus predicting the mechanism of their action  (1). Comparison of protein structures has led to the development of commonly used databases and hierarchical structural classifications, such as SCOP  (2)  and CATH  (3). To assess the similarities between two three-dimensional structures, they typically need to be superimposed in space--that is, one of them positioned over the other, so that the best fit is obtained. Superposition of homologous (evolutionarily related) structures reveals correspondence between evolutionarily conserved residues and motifs that may be indicative of common biological functions.