dataesr/scientific-paragraphs-categorization huggingface dataset:
Beside the measurement technique (MT), a method also comprises suited sample preparation and data analysis procedures. The validation of methods has been established by using well-defined quality control materials (QCMs) and representative test materials (RTMs)  [2]. Systematic results on particle size measurement, obtained with practically all methods able to determine particle size (see later details), were cross-checked against values obtained by electron microscopy which was considered to be the reference method. The specific purpose of a method as used in the NanoDefine tiered approach consists of the determination of the median value of the number-based size distribution (x 50,0 ) of constituent particles of a particular material, after successful, homogeneous dispersion. The number-based particle size distribution is a list of values, defining the relative amount by numbers of particles according to their size, following ISO/TS 19590:2019  [3].
Selection of suitable MTs for identification of a potential nanomaterial usually requires expert knowledge which is not always available. Moreover, for this purpose currently no other decision support frameworks or recommendation systems are available. This manuscript gives a comprehensive introduction to the NanoDefiner e-tool as an implementation of the NanoDefiner framework, following the concepts and terms  [11]  used in the EC NM recommendation. The e-tool (https://fh. do/nanodefiner/ (access 2019-08-16))  [12]  was implemented as an expert system for material categorization and aims to support material registration processes. Therefore, it provides MT recommendations for the assessment of specific materials. Its material categorization approach is based on the NanoDefine Decision Support Flow Scheme (NanoDefine DSFS)  [13].
A single attribute a has data fields (henceforth referred to as a [<field name>] ) that incorporate a unique name a [name] , a data type a A specific MT t ∈ T and a specific type of particles p are described each by an independent set of attributes Ω. These descriptive attributes contain matchable attributes A ∈ Ω (see Tables S1-S4 in Supplementary Materials) and controlling attributes C ∈ Ω. The set of matchable attributes A does not intersect the set of controlling attributes C used exclusively for logical management on a programmatic level. Thus, for a single MT t there is a set of k matchable attributes A t = {a t 1 ,. , a t k } = Ω t \ C t (1) defined in the Measurement technique performance dictionary and assigned with values in its derived sheet of the knowledge base. For a particle type p there is a set of l matchable attributes A p = {a p 1 ,.
Also, for a powder material the VSSA obtained by the BET method  [7]  can be given. It should be noticed that a prerequisite for the calculation of the VSSA value is the knowledge of the skeleton density of the powder material. For the case that the skeleton density is unknown, this can be determined by, e. g. , Helium pycnometry as a standardized measurement method following ISO 12154:2014  [16]. In addition, manual input of the x 50,0 is possible. For these processible inputs an automated nano, non-nano, or borderline decision is determined. Other data will not be processed but may still be attached to the resulting report to support evidence. Supporting a wider variety of analysis data formats was outside the scope of the NanoDefine project; however, it can be established by adding custom implementations of analysis data importers.
Customizability, Extensibility, and Reusability The NanoDefiner e-tool allows user-individual instrumentation and laboratory settings on MT availability, analysis-related estimated cost and duration, and result measurement uncertainty. Localization and internationalization can be established by altering spreadsheet-based language files. Translations of text blocks into different languages, other than the originally provided localization in British English, can easily be added. Its knowledge base is entangled with its functionality and buildup. Changes directly affect the decision making and generation of elements and labels in the graphical user interface, for instance those of the MCS. Hence, customization and extension of the knowledge base allow direct changes in the whole e-tool without altering its source code.
New material property and MT performance criteria profiles can be added to extend the set of available QCMs, RTMs, and MTs. Further support of also proprietary analysis data formats can be established by extending the e-tool with custom analysis data importers, using the provided API. Its source code is available on GitHub (https://github. com/NanoDefiner/NanoDefiner (access 2019-08-16)) and was published under the MIT license (https://opensource. org/licenses/MIT (access 2019-08-16)).
Supplementary information on MT suitability is appended. Results of e-tool assessments obtained from independent industrial case studies confirmed its consistency with the underlying NanoDefine DSFS in all cases  [14]. In October 2017, the e-tool was released in version 1. 0. 0  [12]. Currently, it is available in version 1. 0. 2 and kept up to date in regard to security aspects, reported bugs, wording, and possible revisions of the EC NM recommendation. A publicly accessible service (https://labs. inf. fh-dortmund. de/NanoDefiner/ (access 2019-08-16)) is available for trial purpose. Installation packages and related documentation can be downloaded for local deployment. A virtual machine as well as a Docker (https://www. docker. com/ (access 2019-08-16)) container with installed software packages and default configuration are provided likewise.
One of our goals was to understand what the exact differences are from all points of view: time, results, and economic costs between Agisoft Photoscan and MicMac. The models of the two applications are well made, but we noticed that the model created by MicMac software is excellent, despite being an open source application. In 2017, due to the positive geomathic results during the last three seasons of our excavations on the site of Capo Don, the first Multimedial Exhibition Space (SEM) of the town Riva Ligure was inaugurated, thanks to Comune of Riva Ligure, and all research team members guided by professor Philippe Pergola. Geomatics is a powerful tool not only for preserving memories, but it is ideal for dissemination heritage on the public levels, exactly like the role of archaeology.
The archaeology of rural landscape in Liguria and Provence restored a very similar image to the Syrian territorial reality. We have fragmentary archaeological data deriving from singular researches and emergency and didactic excavations conducted by various university teams, such as the Pontifical Institute of Christian Archaeology, the University of Genova, and the University of Aix Marseille. The recent archaeological acquisitions in the field allow us to delineate with a certain precision the geography of the oldest rural ecclesiastical settlements in Liguria. Since the beginning of 2000, archaeology has highlighted important examples of Christian settlements of different types. There are the ruins of the baptismal-funeral basilica of Capo Don, Costa Balenae, near Riva Ligure (6 th century) 4 , the Pieve del Finale (5 th -7 th century)  (5)  , San Paragorio in Noli (V-VI), Santa Maria of Vezzano (5 th -6 th century)  (6)  , and San Venerio in Antonina, near Migliariana, in the territory of La Spezia  (7).
MICMAC: MODALITIES, EXPERIENCES, AND RESULTS The so-called MicMac software is developed by the French Institut National de l'Information Géographique et Forestière. It is, for the moment, the only multiplatform (Windows, Mac OS, Linux), and completely free solution for photogrammetry from tie points matching to meshing and texturing. Released under the license CeCILL-C, it is a free software as stated by the Free Software Foundation. It offers two ways to work: the first one, and the more preferable one, is the terminal, which is well designed and easily supports scripts in many languages to serialize operations; the other way is a GUI called CEREMA, which is not updated frequently with the last version dating back two years. Of course when a graphic interaction is needed, e. g. when GCPs must be specified on photos or a mask drawn, it is available as a graphic solution to interact with the program.
It is obligatory to present two more cases to get a full idea of the team's experiences and applications of the MicMac software. During the survey, the team had some difficulties because of the high movements of the trees by the strong blowing wind. Some rendering problems were met on the areas partially exposed to the sun. The total taken photos is 164 on both sides of the foundations, even on the dark side under the shadows, which is partially unreadable. The procedure is similar, as the equipment (lens Canon 18-55mm, focal length 30mm), is similar to the one used with the sarcophagus in Riva Ligure and completely automatic. The final treatment for mesh and texture was made with Meshlab (figure  3 ). As expected, the areas where the shadows were not static gave us a mesh with a big amount of noise.
This version is also distinguished by a reduced presence of artifacts and more realistic values over bodies of water. In 2015, two years before the end of reduction of my PhD, it also used STRM data (Shuttle Radar Topography Mission). It is highest-resolution  (17)  For more information about features, and utilization of STRM data: https://asterweb. jpl. nasa. gov/gdem. asp topographic data generated from NASA's Shuttle Radar Topography 18. Most voids are filled with elevation data from the ASTER GDEM2. All the steps of the present spatial analysis, could be performed in both the softwares of ArcGis and QGIS. At the conclusion of this paragraph, the reader will find a complete table of all the used commands in both software products. DEM data, before being used, should be prepared for utilization, because it often presents some empty cells without metric values (no-data pixel).
The 3D surveys could be used for the investigations and the restoration projects of the archaeological buildings. The 3D survey technologies are useful to monitor the process of physical and structural deformation and degradation of the archaeological monuments. So, geomatics could be essential to planning in a conscious way, and at the most opportune moment, any requisite interventions on things that are subject to risk of destruction in some way. Geomatics techniques must in the future contribute effectively to the implementation of specific databases related to the mapping of Cultural Heritage under a risk 21. The heritage resources of Syria, unfortunately, are largely unknown. This is a natural consequence of the lack of a comprehensive record of sites, monuments, and significant finds.
Drosophila strains The Actin5C-GAL4, tub-GAL80 ts , Twist-GAL4, UAS-RNAi Luciferase and the w 1118 stocks were obtained from the Bloomington Stock center (BL#4414, BL#7018, BL#31603, BL#5905). The Traffic-Jam-GAL4 line and the Nos-GAL4>UAS-Dicer line were gifts of Nicola Iovino. The UAS-Tomato-Piwi line was a gift of Chantal Vaury  (19). Transgenic UAS-RNAi lines, gypsy-lacZ reporters and the GFP tagged serpent transgenic line were obtained from the Vienna Drosophila Research Center (VDRC) (accession numbers: 25218/GD; 35578/GD; 109521/KK, 313222, 313223, 318053). dLsd1 ΔN flies are described in  (13). w 1118 flies were used as wild-type control in all experiments. Flies were grown on standard Drosophila medium and maintained at 25 • C unless specified otherwise.
In order to represent the mean signal per base around the TSS, for the three datasets (input, preimmune, dLsd1), we calculated the coverage in a windows of [-1 kb; +2 kb] around the TSS position (re-fGene) corresponding to dLsd1 specific peaks nearest genes. Genes were classified according to the modENCODE RNASeq analysis in ovaries (Accession: SRX494116, SRX494041, SRX014987) on the basis of their reads per kilobase per million (rpkm). We defined them as highly expressed (rpkm > 100 ; n = 574), moderately expressed (100 < rpkm < 10, n = 3650), lowly expressed (10 < rpkm < 1, n = 2691), not expressed (rpkm < 1, n = 9620). The mean coverage per base was then normalized using the input mean signal calculated on the same [-1 kb; +2 kb] window around the TSS. To determine whether dLsd1 peaks overlap with H3K4me2, H3K9me2 and Pol2 Ser5-P, ChIP-chip data and ChIP-Seq data from ovary samples were downloaded from the GEO website (Accession: H3K4me2: GSE45524, H3K9me2: GSE45522, Pol2 Ser5-P: SRP018251) and analyzed with ComEpiTools or BedTools v2.
dLsd1 primarily binds TSS dLsd1 is essential for fertility and its depletion causes strong defects in Drosophila oogenesis  (13). To tackle the functions of dLsd1 in oogenesis, we sought to test if it might target specific genes to control their expression. To this end, we performed chromatin immuno-precipitation followed by massively parallel DNA sequencing (ChIP-Seq) in the ovary using a previously validated anti-dLsd1 antibody  (13). The analysis of dLsd1 ChIP-Seq data led to the identification of 1555 dLsd1 peaks above the background when normalized against the pre-immune serum IP (Supplementary Table  S1 ). Representative dLsd1 peaks are shown in Figure  1A  and Supplementary Figure  S1. To confirm the ChIP-Seq data, we selected a panel of genes bound by dLsd1 according to our ChIP-Seq experiments and performed independent ChIP-qPCR.
To determine where dLsd1 is bound in the genome, we analyzed the overlap of dLsd1 peaks with annotated regions. 68% of dLsd1 peaks were located at promoter regions of annotated genes (defined as the regions between 1Kb upstream and 500 bp downstream of the TSS) (Figure  1C ). Importantly, analysis of the distribution of the reads across the promoter shows that dLsd1 binds at or in close proximity to the TSS (Supplementary Figure  S2B ). We then performed a classification of dLsd1 target genes into highly, moderately, lowly and not expressed on the basis of their expression levels in the ovary according to the modENCODE datasets. These analyses suggest that dLsd1 is bound with a slightly higher affinity to expressed genes (Pearson's Chisquared test P value < 2. 2e-16) (Figure  1D ). We next performed gene ontology (GO) analysis to assess the functions of the genes bound by dLsd1.
GATA motifs are enriched at dLsd1 peaks Human LSD1 does not bind DNA directly  (31) (32) (33) ; rather, it is tethered to DNA through binding to specific co-factors, including CoREST. However, CoREST binding to DNA is weak and unspecific and transcription factors are needed to strengthen the association and provide specificity  (34). In Drosophila, very little is known about the transcription factors that influence dLsd1 recruitment to specific sets of genes. With the goal of identifying potential new partners of dLsd1, we used MEME suite program and motifmatchR to find transcription factors binding motifs or de novo motifs that are significantly enriched at dLsd1 peaks proximal to the TSS. We obtained a list of 13 enriched motifs (Supplementary Table  S5 ). The top 2 motifs enriched at dLsd1 ChIP-Seq peaks are GATA motifs (Figure  2A ), recognized by the GATA family of transcription factors.
dLsd1 binding to a set of Serpent motif-containing genes is Serpent-dependent We selected genes bound by dLsd1 according to our ChIP-Seq dataset and containing a GATA motif in their promoter region to ask whether Serpent or dGATAd binding might influence dLsd1 recruitment. As a first step to assess whether dLsd1 binding to the GATA motif containing targets is dependent on Srp or dGATAd, we depleted either factor using dsRNAs in S2 cells and monitored dLsd1 binding. We chose to start the analysis using S2 cells because srp and dGATAd depletion was efficient and did not affect dLsd1 mRNA levels (Supplementary Figure  S3A  and B ). Depletion of srp in S2 cell resulted in a reduction in dLsd1 binding in genes containing a GATA motif (ush, fu2, SMC1, RpS28b and Src64B) but not in Pnt, a dLsd1 target devoid of the GATA motif (Figure  2B ).
This analysis revealed a small enrichment of the dLsd1 signal at a subset of simple repeats (FDR<0. 05) (Supplementary Figure  S7B ). In par-allel, we performed ChIP-qPCR assays in the ovary, and found that the TSS of Gypsy was significantly bound by dLsd1, while we did not detect a significant enrichment at the other TEs tested (Figure  6A ). We then verified whether dLsd1 was directly regulating the main known regulator of transposons silencing  (47). We found dLsd1 peaks only in five of the 41 annotated regulators of transposons silencing (minotaur, asterix, tud, CG13741 and tej). However, the expression of these genes was not altered upon dLsd1 depletion in the ovary, according to the microarray dataset and to RT-qPCR (Supplementary Figure  S7C ), suggesting that dLsd1 does not affect transposon expression indirectly, by regulating the expression of components of the piRNA pathways.
Here, we show that Serpent depletion results in multiple oogenesis defects, opening the road to a more detailed analysis of its function in this developmental context. Comparing the transcriptional profile dataset of dLsd1 depleted ovaries to the ChIP-Seq dataset revealed direct dLsd1 targets. These targets include genes involved in cell cycle, transcription, recombination and repair. Some of these genes have already been implicated in oogenesis, including the RNA binding protein Sex-lethal (Sxl), which has been implicated in cystoblast differentiation  (51) , or the transcription factor midline (mid), which together with longitudinal lacking (lola), has been shown to play a role in gonad formation  (52, 53). Also src64, which encodes for a tyrosin kinase implicated in actin dynamics in oogenesis  (54) , is bound by dLsd1 and down-regulated upon dLsd1 deple- tion.
Their de-regulation could partially explain some of the phenotypes observed in dLsd1 mutant ovaries. Others targets have not been previously identified as being important for oogenesis and could thus be tested for their biological role in this tissue. These datasets therefore provide an important resource for elucidating novel oogenesis regulatory mechanisms. As reported previously in mammalian cells, dLsd1 depletion in the ovary results both in down-regulation and upregulation of target gene expression, indicating the dLsd1 acts both as a co-repressor and as a co-activator. Aside from direct targets, we found that 1847 mis-regulated transcripts were not bound by dLsd1 according to our ChIP-Seq dataset. This could be due to the fact that the transcriptional changes observed upon dLsd1 depletion in the ovary are associated with an aberrant developmental program or that dLsd1 control the expression of these targets from distal enhancers.
Mining these datasets, we found dLsd1 among the factors identified by Czeck et al  (56) , while dLsd1 depletion did not affect transposon silencing in the screen published by Handler et al  (57). These results are contradictory and no detailed analysis of dLsd1 role in TE silencing has previously been reported. In a recent study, the Hannon team identified Panoramix as a critical regulator of transposons and showed that dLsd1 depletion impaired Panoramix-dependent repression of a reporter line  (58) , hinting at a role for dLsd1 in the suppression of transposons. This hypothesis was very recently confirmed by Yang et al, who reports de-repression of a subset of TEs upon dLsd1 germline-specific knockdown  (59). Our data support and reinforce the evidence of an important role for dLsd1 in TE silencing not only in the germline, but also in somatic cells.
Together these results suggest the existence of a chromatinbased transposon silencing mechanism dependent on the interaction between dLsd1 and Piwi and open the road to the study of the interplay between LSD1 and Piwi in vertebrates. The majority of transposons are located in pericentric or telomeric heterochromatin  (48) , and it had been previously shown that dLsd1 is a strong suppressor of variegation and promotes heterochromatin formation at the boundary between heterochromatin and euchromatin  (13, 41, 42). It is possible that the effect of dLsd1 on the expression of the transposons located in heterochromatin might be indirectly due to dLsd1 role in the control of heterochromatin structure. This hypothesis could explain the lack of enriched dLsd1 peaks at TEs in our dataset. In alternative, dLsd1 might bind TEs at low levels or transiently.
(D) dLsd1 ChIP-Seq read density around the TSS of genes classified as highly expressed, moderately expressed, lowly expressed and inactive (very low or no expression) according to the modENCODE RNA-Seq dataset in the ovary. Expression levels were estimated as reads per kilobase per million, rpkm. (E-G) Venn diagrams showing the number of common peaks between dLsd1 ChIP-Seq and H3K4me2 ChIP on chip (E), H3K9me2 ChIP on chip (F) and Polymerase 2 phosphorylated Serine 5 (Pol2 Ser5-P) ChIP-Seq (G) peaks in the ovary.
ACKNOWLEDGEMENTS The authors would like to thank  Didier Trouche ,  Alain Vincent ,  Malek Djabali ,  Thomas Clouaire ,  David Cribbs ,  Nicholas Dyson ,  Ana Guarner-Peralta ,  Christian Mosimann ,  Olivier Cuvier  and members of the  Di Stefano and of the Haenlin team  for helpful discussions and comments on the manuscript. We would also like to thank  N. Iovino ,  C. Vaury  and  C. Antoniewski  for providing reagents and the platform  GET-Biopuces at the Génopole in Toulouse  for the microarray experiments and the associated statistical analysis. Author contributions: L. D. S, J. M. J. L. and C. I. designed and performed the experiments. Bioinformatic and statistic analysis was done by  E. G, M. A , C. M. V. R under the supervision of M. P. and L. D. S. The experiments related to GATA factors were done in collaboration with L.
FUNDING Fondation pour la Recherche Médicale (FRM)  [AJE201109];  Agence Nationale de la Recherche (ANR)  [ 2012-CHEX-0002-01 ];  Marie Curie Career Integration Grant  [ PCIG13-GA-2013-618272 ];  Région Midi-Pyrénées  [13051317]; INSERM [ EPIG201405  to L. D. S. ];  ANR  [ ANR-13-BSV-008  to L. W. ]; J. M. J. L. was supported by a postdoctoral fellowship from the  Association de la Recherche sur le Cancer ; C. I. was supported by a postdoctoral fellowship from the Ligue contre le cancer. Funding for open access charge:  ANR.
Thereafter, few authors experimented the integration of a road traffic noise model into a GIS. Thus, Li et al. [44]  proposed a GIS based traffic noise system implemented in the commercial GIS software ArcView (renamed latter ArcGIS) including a few extensions and designed for noise prediction in China. Unfortunately, the model was implemented by using a proprietary high-level algorithmic language (AVENUE), which does not allow the portability of the application to other GIS systems. Pamanikabud and Tansatcha  [45]  developed two traffic noise prediction models based on the UK's standard CoRTN  [46]  and on the US's standard FHWA  [47]  that were also integrated in the previously mentioned commercial GIS system with the same programming language, implying the same inconvenience as the preceding development.
Similarly, Gulliver et al. [48]  developed an open-source tool for road traffic noise modelling that is integrated in ArcGIS too. One can also cite the works by Reed et al. [49]  who proposed an open-source application, named SPreAD-GIS, dedicated to the modelling of anthropogenic noise propagation in natural ecosystems. The application was implemented in Python as a toolbox in the ArcGIS software, and is based on the System for the Prediction of Acoustic Detectability (SPreAD) developed by the US Forest Service (USFS) and Environmental Protection Agency (EPA). Therefore, no full open-source framework currently exists for the purpose of noise mapping at the territory scale. Moreover, further improvements are necessary to make large scale noise maps, at an agglomeration scale for instance, within the END framework.