dataesr/scientific-paragraphs-categorization huggingface dataset:
LTSmin LTSmin 5   [27]  has competed in the MCC since 2015. Already in the first editions, LTSmin participated in several subcategories, while since 2017 LTSmin competes in all subcategories, except for colored Petri nets, and reporting the number of fireable transitions in the marking graph. For the MCC of this year, LTSmin only competes in the StateSpace and UpperBounds categories, as the tool is now equipped with a fully parallelized symbolic saturation algorithm for computing the state space. Otherwise the tool is relatively unchanged compared to last year, so we restrict the tool to only demonstrate the new techniques. Main Features of LTSmin. LTSmin has been designed as a language independent model checker. This allowed us to reuse algorithms that were already used for other languages, such as Promela and mCRL2.
For the MCC, we only needed to implement a PNML front-end and translate the MCC formula syntax. Improvements to the model checking algorithms, like handling integers in atomic formulas, can now in principle also be used in other languages. LTSmin's main interface is called the Partitioned Interface to the Next-State function (PINS)  [27]. Each PINS language front-end needs to implement the next-state function. It must also provide the initial state, and a dependency matrix (see below). The multi-core explicit-state and multi-core symbolic model checking back-ends of LTSmin use this information to compute the state space on-the-fly, i. e. new states and atomic predicates are only computed when necessary for the algorithm. A key part of LTSmin are its dependency matrices. Dependency matrices must be precomputed statically by the front-end, and are extensively used during reachability analysis and model checking.
In the context of the MCC, we can use state space generation to answer all the questions from the StateSpace examination, that is computing the number of markings of an input net; its number of transitions; and the maximum number of tokens in a marking and in a place. The core capabilities of tedd, based on SDD, has shown competitive performances, on par with most of the symbolic tools present in the previous MCC contests. The tool can accept models in the PNML format and provides a large collection of options for selecting good variable orders. A variable order module provides a rich choice of order computing algorithms based on net traversals and the structural analysis of the net (semi-flows, flows, etc. ). In each case, a force  [1]  heuristics can be used to improve any given order. Hierarchical orders, which are a characteristic of SDD, are also available but have been seldom used so far.
There exist several methods for solving this problem, which amounts to computing the number of integer points in a convex polytope. Actually, this has been a hot topic of research in the last decade and some tools are purposely available for this task, notably LattE  [29]  and barvinok  [35]. TINA. tedd is able to interface with these tools in order to compute the number of reachable markings in a net. With some adjustments, implemented in tedd, similar techniques can also be used for computing the number of transitions. This approach, based on "geometric techniques", is extremely powerful when the number of variables -the number of places in the net -is low. (We restrict its use to nets with less than 50 places in the MCC. ) To overcome this limitation, we have recently started experiments with our own counting method, based on a recursion-solving approach, and implemented in a dedicated package called polycount.
The sequence and the loop structure are well conserved among animal species (Figures  1D  and S1H ). To explore which RNA-binding proteins (RBPs) associate with the CUIC motif, we analyzed published cross-linking immunoprecipitation (CLIP)-seq datasets in the POSTAR2 database  (Zhu et al. , 2019). In this analysis, we counted the number of CLIP clusters that overlapped with the CUIC region of RP-coding mRNAs for each RBP and normalized them to the total number of clusters on any region of the mRNAs to evaluate the specificity of RBP (legend continued on next page) binding (Figure  1E ). This revealed that components of the eIF3 complex are particularly enriched in the proteins that specifically bind to the CUIC motif of RP-coding mRNAs  (Figures 1E and 1F). CUIC Motif Is Associated with Alternative 5 0 Ends and Netrin-1-Stimulated Translation of Axonal mRNAs Our analysis of CLIP-seq data also showed that TIA1 and TIAL1 bind with high specificity to the CUIC region (Figure  1E ).
These results suggest that the alternative 5 0 end at the CUIC region can generate a 5 0 TOP-like sequence in RPcoding mRNAs (Figure  2B ). Since 5 0 TOP mRNAs are regulated by the mammalian target of rapamycin (mTOR) pathway  (Jefferies et al. , 1997) , and the mTOR pathway is required for Netrin-1-mediated local translation  (Campbell and Holt, 2001) , the CUIC motif could play a crucial role in regulated RP synthesis in the axon. To investigate the relation between Netrin-1 stimulation and CUIC-containing RP mRNAs, we analyzed a proteomics dataset of the cue-induced nascent (newly synthesized) proteome in cultured Xenopus RGC axons  (Cagnetta et al. , 2018). The analysis revealed that RPs are particularly enriched in the group of proteins whose translation is promoted by Netrin-1 (p = 0.
Plasmid Construction To construct Venus reporter plasmids used in FRAP and single molecule translation imaging, Venus cDNA and 5 0 / 3 0 UTR of mouse Rps4x/eS4 (NM_009094) were integrated into BamHI-XbaI sites of pCS2+ (University of Michigan, Ann Arbor, Mich. ). 8 nucleotides (CTCTTTCC) in the 5 0 UTR were deleted in the ''Del-motif'' construct. To generate Rps4x-Venus fusion constructs, Venus and X. laevis Rps4x. S sequences were inserted into the BamHI-RcoRI sites of pCS2+. In these constructs, a CMV promoter drives the expression of 5 0 UTR(Rps4x. S)-Venus-linker (Gly-Gly-Ser-Gly-Gly-Gly-Ser-Gly)-CDS (Rps4x. S, NM_001097003. 1)-3 0 UTR(Rps4x. S). Because frog 5 0 UTR sequences of Rps4x. S in public databases could be truncated, we used a sequence of actually transcribed mRNA in frog embryos, which is obtained from a previously published RNA-seq data (GSM1948717) mapped to genome Xla.
0 V2 CMOS camera (Hamamatsu) using Volocity software (PerkinElmer). Photobleaching was performed using an UltraVIEW PhotoKinesis device (PerkinElmer). Photobleaching was performed at 85%-90% laser power (488 nm laser line) with 20-30 bleach cycles. For the FRAP experiment imaging axons expressing Rps4x UTR-containing Venus constructs or the Venus-only construct indicated in Figures  2F  and S2F , axons of the 24h retinal cultures were severed from the eye and 600ng/ml Netrin-1 was added into the culture. A randomly selected fluorescent growth cone of a severed axon then proceeded to the photobleaching step using 488 nm laser line, immediately after pre-photobleaching fluorescent and phase contrast images were acquired. The photobleached area was manually defined so that growth cones and > 50 mm of the axon shaft were bleached (thus reducing likelihood of fluorescence recovery resulting from Venus diffusion from unbleached areas of the axon shaft).
1 Da respectively. The false discovery rate (FDR) was set at < 1% with two peptide matches to proteins considered as reliable. For the analysis of SILAC labeled proteins, we used Maxquant in addition to Proteome Discoverer since it is the most commonly used software for SILAC analysis. Raw data were processed using Maxquant (version 1. 6. 1. 0) (Cox and Mann, 2008)  with default settings. MS/MS spectra were searched against the X. laevis protein sequences from Xenbase (xlaevisProtein. fasta). Enzyme specificity was set to trypsin/P, allowing a maximum of two missed cleavages. The minimal peptide length allowed was set to seven amino acids. Global false discovery rates for peptide and protein identification were set to 1%. The match-between runs and re-quantify options were enabled. To avoid false positives, we analyzed only those RPs where more than two labeled peptides were detected by the software or if the MS spectrum of the detected labeled peptides showed clear peaks at the expected m/z value.
Bioinformatics Analysis We analyzed the developmental change of level of all mRNAs translated in the mouse RGC axons in dataset (GSE79352). The sequence reads were mapped to the mouse genome (mm10) using TopHat 2 version 2. 0. 12 with default settings, except for the ''-read-realign-edit-dist 0'' option. Transcript assembly and estimation of FPKM (Fragments Per Kilobase of transcript per Million fragments sequenced) values were performed using Cufflinks version 2. 2. 1. For RNA-seq analysis of frog RGC axons, the sequence reads were mapped to the X. laevis v9. 2 genome (Xenbase) using HISAT2 2. 1. 0 with default settings. Transcript assembly and estimation of FPKM (Fragments Per Kilobase of transcript per Million fragments sequenced) values were performed using Cufflinks version 2. 1. 1. For the GO enrichment analysis, we only analyzed genes showing FPKM > 1 in both of two replicates.
Motif Analysis All sequences of mouse cDNAs were retrieved from BioMart at Ensembl (GRCm38, ensemble Genes 91). De novo motif analysis was performed using HOMER version 3. 0 with custom FASTA files containing all 5 0 UTR sequences of mouse RP-coding cDNAs. For the analysis of CUIC-containing genes, we selected all genes whose mRNA contains the 8-mer nucleotides (T/C)(T/C)(T/C)(T/C)TT(T/C)C located less than 100nt upstream of the initiation codon. The secondary structure analysis of UTRs was performed using performed using RNAfold in the ViennaRNA package version 2. 4. 3 with default settings. The conservation among species of all CUIC-containing RP mRNAs was calculated from phastCons60way. UCSC. mm10. For the analysis of proteins binding the CUIC region, we used Human RBP binding sites data downloaded from the POSTAR2 database  (Zhu et al.
FRAP analysis Quantification of fluorescence intensity was performed using Volocity software (PerkinElmer). At each time point, the outline of the growth cone was traced using phase contrast images. Mean gray values from the 488-channel were subsequently calculated as mean pixel intensity per unit area within the specified region of interest (ROI). This ROI was then placed in an adjacent area clear of cellular material to record the background fluorescent intensity. This reading was subtracted from the growth cone reading, yielding the background-corrected intensity. Unhealthy axons exhibiting signs of photo-toxicity after FRAP (characterized by blebbing, growth cone collapse and/or retraction) were excluded from analysis. In addition, only growth cones of axons extending more than 100 mm from the eye explant were quantified to reduce effects of somal diffusion.
Branching Analysis A filopodium was defined as a protrusion with length < 5 mm while a branch was defined as a protrusion with length > 5 mm  (Drinjakovic et al. , 2010; Ho ¨rnberg et al. , 2013; Kalous et al. , 2014; Wong et al. , 2017). Data were analyzed in PRISM 7 (GraphPad). 'n' represents the number of axons. *p < 0. 05, **p < 0. 01, ***p < 0. 001, #p < 0. 05, ##p < 0. 01, ###p < 0. 001. Details of statistic results such as p values, degree of freedom, and t/F values are presented in the figure legends. For axon arbor analysis, 3D projection of axon arbors acquired at 40X were semi-automatically traced through the z axis using the Simple Neurite Tracer plugin  (Longair et al. , 2011)  in Fiji. The resulting traces were then analyzed for the number and the length of axon branches as well as the Axon Complexity Index (ACI)  (Marshak et al.
DATA AND SOFTWARE AVAILABILITY The accession numbers for the mass spectrometry proteomics data reported in this paper are PRIDE: PXD011032 and PRIDE: PXD015574. The accession number for the RNA-seq data reported in this paper is GEO: GSE135502. %"of"Targets" p5value" 0'''''''''''''20''''''''''''40''''''''''''60''''''''''''80' 0''''''''''''''5'''''''''''''10''''''''''''15''''''''''''20' E17. 5""""""""P0. 5""""""""""P7. 5""""""""""Adult"""" G C C A A C U U C C G U A C C G G C G G U U U U A G C U U C G C U G G A A A C C G U G A U G G A G G U U U C U U C C G G A A G C C U G C C C C U C U C U C A G U G A C C U C A G A G A U A C A C U U C C G G A A G A C G G A A G U G A C C C G U C C G C C C G C C C C U U C C G C C U C U C U C U U U C C G G U G G A G G A G U C U G G A G A C G A C G A U C A G A A Rps14& Rpl5& C A G C C A C U C U U U C U C A C G U C G C U U G C G U G C U G G U G G U G C U A C A U A C U G C G C A U G C GUA C G U G A C U C C G G U C U U U U U C C C C C U U A G C G C G G C C G A C U C U G C A G G U C U G C G U G G A G C C G C G G U U G C G G G U C U C U A U U C C G C A G G A A G C U C A U G G G A A U U G G G C U G G G C C A U C C U U U U C A G C C A A G Rpl23a& C G G C C G C A A A C U G C A G C G C C U C U CCG G C U U G G C U G A G C G C G G A A C G U G C C C G U A A C G G G C A A CU CU C G C G A G A A C G C G G G C U C U A U U U G A G C G C A U G C G C A A A G C G C U C U G C C U U C U U U C C G G U U U C C G C G G C A G C C G C A G C C Rpl10a& 0.
ACKNOWLEDGMENTS We thank  J. K. Mooslehner  for technical assistance. We also thank  Mike Deery  for invaluable expertise and the MS/MS analysis and  Jeroen Krijgsveld  and  Christian Frese  for helpful discussions. We are grateful to  Simone Pellegrino  and  Julie Aspden  for useful PyMOL software discussions,  Caia Duncan  for assistance with polysome fractionations, and  Erin Schuman 's group for helpful discussions on ribosome purification. This work was supported by  Wellcome Trust  grants  085314/Z/08/Z  and  203249/Z/16/Z  to C. E. H. and  100329/Z/12/Z  to W. A. H. ;  European Research Council   Advanced Grant  ( 322817 ) to C. E. H. ;  Champalimaud Vision Award  to C. E. H. ; and the  Netherlands Organization for Scientific Research  ( NWO Rubicon 019. 161LW. 033 ) to M. K. C. F. K.
acknowledges funding from the  UK Engineering and Physical Sciences Research Council (EPSRC)  (grants  EP/L015889/1  and  EP/H018301/1 ); the  Wellcome Trust  (grants  3-3249/Z/16/Z  and  089703/Z/09/Z ); the  UK Medical Research Council (MRC)  (grants  MR/K015850/1  and  MR/K02292X/1 ); and  Infinitus (China).
Conclusions The working group recommended a galactocentric aberration constant A G derived only from geodetic VLBI data analysis in order to be consistent with geodetic VLBI solutions (and specifically for the ICRF3 solution) rather than averaging geodetic solution estimates and estimates based on Galactic astronomy measurements. The ICRF3 solution was to be derived using data from 1979 to May 2018, which is two years more data than any of the previous VLBI solutions given in Table  1. For this reason, the working group ran a new solution using the ICRF3 data set to determine the aberration constant to be used in the final ICRF3 solution. The recommended aberation constant value of 5. 8 µas yr -1 of the component of the aberration vector in the direction of the Galactic center is reasonably close to estimates derived from Galactic astronomy measurements.
Acknowledgements. D. S. MacMillan ,  J. M. Gipson , and  D. Gordon  acknowledge support from  NASA  contracts  NNG12HP00C  and  NNG17HS00C. C. S. Jacobs acknowledges support for work done at  Jet Propulsion Laboratory, California Institute of Technology  under contract with  NASA. H. Krásná  is supported by the  Austrian Science Fund (FWF) :  T697-N29. The work of Z. Malkin was partly supported by the  Russian Government Program of Competitive Growth of Kazan Federal University. Figures were produced using the Generic Mapping Tools package (Wessel et al. 2013). Results in this paper were based on data from the IVS and its international member organizations.
Computer aided-design (CAD) tools should be able to assist the former exploration that leads the entire design process. However, current software often calls an immediate actualization of geometrical intentions by forcing the user with pre-set intentional clusters -geometric primitives, textural resources, design procedures etc. -often uncompromising, with poor intuitive feedback and generally restraining imagination spreadout: most CAD software act like over-equipped handdrafting assistants, assuming the maturity of the designer as much as the maturity of the project itself. What we aim to achieve is a computer-assisted generation process of architectural and urban plausible geometries. These self-generated objects are intended to act like "imagination enhancers" serving conceptual exploration of architectural design or providing credible 3D environments in given historical context.
Next, this "pr-object" could not only be the ponderated completion of a pluridisciplinaric integration process but, in an autonomous evolution Darwinian paradigm, the actualization of the most performant genotype, or like Celestino Soddu says, a generative project is a concept software that works producing three-dimensional unique events as possible and manifold expressions of the generating idea identified by the designer as a subjective proposal of a possible world. Some of the research tasks depicted hereby take advantage of some generative methods developed within the MAP aria research team. They are able to quickly produce architectural and urban geometric simulations for contextual or historical restitutions. In the case of the Portus project, which required 3D modelling and rendering of the Ostia harbour complex at different times, generative design quickly established itself as a solution for dealing with the heterogeneity of the available scientific hypotheses.
INTRODUCTION Computer-aided design tools have been used in architecture and design offices for more than 30 years. It must be said that, from the beginning, they have behaved more like over-equipped drawing tools than as true supports for the creative process. However, in recent years, additional modules (plugins or dedicated libraries) make it possible to enrich the software environments already implemented in creative agencies: whether in the field of design, urban planning or architecture, these tools can generate and optimise on demand an infinite number of formal or conceptual solutions whose feasibility or effectiveness in terms of input constraints will be evaluated, for example, by bioinspired processes. In the field of heritage, ancient monumental political or religious groups have often come to us.
Digital Generative Tools for Restitution and Mediation for Cultural Heritage Renato Saleri Whether for the restoration of the ancient city of Vienne (France), to show the inhabited slopes of the Fourvière hill during the time of Lugdunum or the historic urban fabric of the "Vieux Lyon" district (Figure  1 ), the generative tools are based on current knowledge of the architectural, constructive or stylistic constants of the time and are aligned with the road or masonry routes that have survived: they thus make it possible to quickly produce plausible 3D images of squares, streets or buildings during the period of interest  (Saleri 2004 ). As part of the exhibition "Claude, un empereur au destin particulier", presented at the Musée des beaux arts de Lyon, the laboratory had the opportunity to exploit the software tools developed so far by putting them at the service of a major project: the 3D restitution of the Ostia harbour complex at the time of Trajan as well as the successive transformations brought by the Emperor Claude during his lifetime.
On the other hand, we can move upstream towards web-based environments or open source formats and guarantee as much as possible in the workflows developed an automation of interoperable processes: this is how, during the first architecture biennial of the City of Lyon, in 2017, we were able to reuse the generative tools developed in 2002-2003 by using the same software classes and using the same data structures (Figure  2 ). With such a tool, we could partly put aside the books of the Babel library by J. L. Borges: the very modest installation set up by the laboratory during the Lyon Architecture Biennale of 2017 generated nearly 300,000 architectones -most of them anonymous and erased from the memory of the computer as soon as another took its place -24 hours a day, during the 5 days of the event.
The software core is developed in JAVA and uses the findContours class implemented in the openCV library under Processing. It interprets the data from an appended text file that lists all the parameters used when detecting contours and creating architectural geometries. The MEL flow generated by the application is then sent via the localhost to Maya® which interprets the received data and invokes the shaders and textures assigned on the fly to the generated shapes (Figure  5 ). The island stand parameters allow a street width of between 4 and 6 m and a building depth of between 5 and 10 meters. The 8 meters wide quotient (distance between buildings) finally allows a slight overlap of the built elements in order to break the excessive regularity that could result from an overly rigorous layout.
It is likely that the origin of the CPSC cell type underlies the emergence of coloniality in some ascidian lineages. However, the function and presence of such CPSCs in solitary species are unclear. Therefore, investigating the ancestral character state of hemoblasts in a solitary species may provide insights into the events giving rise to CPSCs and coloniality. The characterization of hemocytes in ascidians has historically lacked a uniform nomenclature due to distinct identification protocols or personal biases in selecting the most important characters for identification  [5, 16, 22]. In Styelidae, coloniality has evolved at least twice  [21]  and hemocytes of colonial species in this family have been previously described  [23] [24] [25]. Therefore, we focus this study on the solitary Styela plicata as an outgroup species to approximate the ancestral character state of hemoblast populations in the styelid ascidians.
Sample acquisition was performed with an imaging flow cytometer (FlowSight, Amnis-Merck Millipore) from the Central de Aquisição de Imagens e Microscopia of the Instituto de Biociências (CAIMI-IB). Acquisition speed was set to low and photos were captured at the highest resolution. About 20,000 cells were acquired based on area and the aspect ratio, defined as the value of minor axis divided by major cell axis on channel 1. The focused cells were gated using root mean squared gradient (RMS gradient) based on channel 1. Channels 1, 2, and 6 were used to analyze brightfield, ALDEFLUOR TM -labeling, and side scatter (SS) parameters, respectively, using the IDEAS software (Amnis-Merck Millipore). Cell doublets and debris were excluded from the single cells used in the analyses based on area and aspect ratio features (Additional file 1: Figure  S1 ).
ALDH + cells and subpopulations of hemocytes were determined based on channel 2 (green) and channel 6 intensities. No autofluorescence was detected in S. plicata hemocytes (Additional file 1: Figure  S1 ). Data acquisition was performed using the IDEAS package (Amnis, Seattle, USA). To detect significant increases in ALDH + event abundances using the ALDEFLUOR TM test, we performed Wilcoxon matchedpairs signed rank tests between tests and controls (as defined by the ALDH inhibitor DEAB).
We included sections without the primary antibody incubation as negative controls. We found no nonspecific labeling in the controls. We analyzed 10 randomly selected images from histological sections of two animals (n = 2). Percentages of positive nuclei were obtained independently for each intestinal layer, i. e. , mucosa, submucosa, and serosa. Percentages were then compared using Student's t test. Results were expressed as the mean ± standard error, and differences were considered statistically significant at p < 0. 05 (*). The analyses were done using GraphPad Prism version 6. 00 (GraphPad Software, Inc. ).