dataesr/scientific-paragraphs-categorization huggingface dataset:
Bioinformatic analysis of protein sequences Using the peptides identified from the proteomic survey described above, partial or, in most cases, full length coding sequences were isolated by standard or RACE polymerase chain reaction (PCR) as described in  [31]. In some cases, Illumina transcriptome data (see below) were used to clarify the putative complete mRNA. Open reading frames were translated with the Ex-PASy translate tool  [32]. Protein sequences were searched for signal sequences with SignalP 4. 1  [33]. The theoretical pI, amino acid composition, and number of amino acids were determined using the ExPasy ProtParam tool  [34]. Tandem repeats were identified with the T-REKS tool  [35]. Sequence similarities searches were performed with the Basic Local Alignment Search Tool (BLAST) algorithm  [36]  with tBLASTx against nr and dbEST and BLASTx against SwissProt.
Domain searches were performed with CD search  [37]. Molecular function was predicted with In-terProScan  [38]. GalNAc O-glycosylation sites were predicted using the NetOGlyc 4. 0 Server  [39]. Scaled schematics of protein se-quences were generated using Gene Structure Draw  [40]. Intronexon boundaries were mapped to a draft genome of L. stagnalis originally reported in  [41]  using Splign  [42]. Similar transcripts were retrieved from the assembled transcriptomes of mantle zones 1-5 combined, mantle zone 5 alone, cephalic tentacle, cephalic lobe, central nervous system (CNS), foot, buccal mass, and larval stages 42 hours post first cleavage (hpfc), 52 hpfc, and 67 hpfc using BLASTn searches (see below for NGS details). All transcripts with complete open reading frames were considered. Only candidates yielding an mRNA coverage of >98% and an overall identity of >98% are documented.
5), and IDBA-tran. The resulting assemblies were then merged and filtered for redundancy using our pipeline  [44]. Mantle transcriptome assemblies and cDNA and protein translations of the 34 shell-forming genes are available in the GigaScience Database, GigaDB  [45]. In addition, transcriptomes from five adult tissues (cephalic tentacle, cephalic lobe, CNS, foot, and buccal mass) and three larval stages (42 hpfc, 52 hpfc, and 67 hpfc) were sequenced and assembled as described above. These transcriptomes were used to assess the tissue-specific alternative splicing characteristics of all shell-forming genes. All raw NGS data has been deposited in the Sequence Read Archive (SRA) with BioSample accession numbers SAMN08117214, SAMN08117215, SAMN08709370, SAMN08709371, SAMN08709372, SAMN08709373, SAMN08709374, SAMN08709375, SAMN08709376, and SAMN08709377.
Proteomic analysis of the biomineralized matrix of L. stagnalis shells More than 1,230 peptides were analyzed by High-performance Liquid Chromatography (HPLC)-MS and subsequently used for protein identification using Mascot against our translated mantle transcriptomes. Of these 1,230 peptides, 329 returned significant matches. From these 329 matches, a total of 40 shellforming candidate transcripts were identified (see Additional file 1). Of these 40 gene products, 31 (78%) could be cloned and exhibit in situ hybridization signals compatible with a role in shell formation (either in larval stages and/or in the adult mantle tissue). Seven of these 40 candidates (18%) could be cloned from L. stagnalis cDNA but did not produce a positive or consistent in situ signal in any tissue. Three of the 40 candidate genes (8%) could not be amplified by gene-specific PCR or RACE PCR.
This modular L. stagnalis ). Transparent red lines connect proteins with the lowest quartile of similarity (with a threshold of 10e -6 ) and green lines with the highest quartile of similarity. The percentage of each shell proteome that shared similarity with the L. stagnalis proteome is indicated. The table provides further information for those candidates that share sequence similarity with another species. Abbreviations: CD: conserved domain database; NR: GenBank non-redundant protein database; SP: SwissProt database. nature of the molluscan mantle is not unique to Lymnaea  [82] [83] [84]. Although the precise functions of these zones (and of the individual gene products that define them) await the development of targeted genome editing methods, it is clear that they must act in a coordinated way to deposit the shell.
The spatial expression of a peroxidase in the adult mantle allows a model of shell formation to be developed In agreement with Timmermans histochemical study of peroxidase activity  [59] , the expression of Lstag-sfc-5, a shell-forming candidate with an "animal heme-dependent peroxidase" domain (Pfam PF03098; Additional file 41B) is localized to zones 1 and 2. Peroxidases may be involved in periostracum formation by cross-linking fibrous proteins rich in reactive quinones to form water insoluble, protease-resistant polymers  [85] [86] [87]. This process, also referred to as tanning or sclerotization, can also be catalyzed by tyrosinase (also known as catechol oxidase, catecholase, polyphenoloxidase, phenoloxidase, and phenolase). Within the molluscan biomineralization literature, sclerotization by tyrosinase appears to be the more commonly assumed mechanism, rather than by peroxidase.
Broad sequence similarity comparisons of metazoan biomineralizing proteomes The crossed-lamellar microstructure is fabricated by phylogenetically diverse molluscan taxa and is by far the most commonly employed shell design of the Conchifera  [21, 22, 28]. While much attention has been dedicated to the characterization of nacre-forming bivalve shell proteomes, technical advances in nucleic acid sequencing and proteome-scale surveys have seen a rapid growth in the number and diversity of molluscan shell-forming proteomes and allow broad comparisons of these datasets to be performed. These comparisons can provide insight into the degree of evolutionary conservation that exists across shell-forming proteomes  [50]. In general, molluscan shell-forming proteomes are markedly different, with some deeply conserved elements such as alkaline phosphatases, peroxidases, and carbonic anhydrases  [28, 57, 105, 106].
The significant diversity of molluscan shell ultrastructures, crystal textures, colors, and materials properties therefore cannot be explained by the use of the same genes in different ways. Rather, each lineage has uniquely evolved a large fraction of its shellforming proteome  [14-16, 100, 107]. To expand on this comparative theme, we collected 879 biomineralizing proteins validated by proteomics from 10 molluscs, 1 brachiopod, 1 sea urchin, and 1 coral and performed sequence similarity comparisons against our L. stagnalis dataset. Two of the 10 molluscs, Cepaea nemoralis and Mya truncata  [51, 108] , construct shells that contain crossedlamellar texture. Interestingly, our comparative analyses show that L. stagnalis and M. truncata have only three proteins that share relatively low degrees of sequence similarity, while L.
nemoralis. Conversely, L. stagnalis shellforming candidates expressed asymmetrically on the right side in larvae were not present in any other biomineralizing proteomes. Some L. stagnalis shell-forming proteins contain domains found in a number of the biomineralizing proteins present in the dataset we assembled or are known to play a role in processes other than biomineralization such as the Sushi domain, the von Willebrand factor A domain, the immunoglobulin domain, and the filament protein domain  [14, 109]. The Pif-like protein is prevalent in both bivalve and gastropod nacreous shell proteomes and is known to bind aragonite crystals and to regulate nacre formation  [110]. However, limpets, which construct crossed-lamellar structures, also contain Pif in their shells  [15, 110, 111]. Our results further demonstrate that Pif is not limited to nacreous matrices and that it is likely to be a deeply conserved element of the molluscan biomineralizing proteome.
Availability of supporting data All raw NGS data has been deposited with the SRA with BioSample accession numbers SAMN08117214, SAMN08117215, SAMN08709370, SAMN08709371, SAMN08709372, SAMN08709373, SAMN08709374, SAMN08709375, SAMN08709376, and SAMN08709377. Individual image files for the in situ hybridization gene expression patterns and the sense strand cDNA sequences used to generate the in situ hybridization riboprobes can be accessed from the associated GigaDB repository  [45]. The mantle transcriptome assemblies are also available via GigaDB  [45]  (file names: C2844 CLC idba Trinity for annotation. fasta and C2845 CLC idba Trinity for annotation. fasta). All MS data have been deposited with the ProteomeXchange Consortium with the dataset identifiers PXD008547 and 10. 6019/PXD008547. Other supporting data are available from additional files, also including an extended description of the in situ hybridization results (see additional file 47).
Question marks indicate expression patterns that could not be categorized according to our scheme. An "x" indicates no expression was detected. A "?" indicates that the expression pattern could not be categorized according to our scheme. The names of enzymes and other molecular features indicated in zones 1-5 on the schematic of the adult mantle are summarized from [59]  and [3]. Sequence similarity and conserved domains in the final column of the table are summarized from a number of BLAST searches against SwissProt, the non-redundant National Center for Biotechnology Information database, and the Conserved Domain database. See Additional files 40-42 for the results of all BLAST and domain searches. The lineages of the top BLAST hits are listed in Additional file 43. A version of this figure that includes a more complete summary of the molecular features of each gene is provided in Additional file 36.
Acknowledgements We are grateful to  Wolfgang Dr  öse for assistance and advice with in situ sectioning,  Isabelle Zanella-Cleon  from  IBCP (Lyon ) for MS analysis, and  Jennifer Hohagen  and  Dorothea Hause-Reitner  who generated SEM images. Illumina sequencing was performed by  Markus B. Schilhabel  and his team at the  Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel. This work was funded by  DFG  ( JA 2108/2-1  and  JA 2108/6-1 ) and VolkswagenStiftung (92075) grants to D. J. J.
A Bruker D8 Advance diffractometer (Bruker Corporation, Billerica, USA), equipped with a HI-STAR area detector, operating at 30 kV and 25 mA, using filtered iron radiation and polycapillary focusing optics was used. The corresponding orientation distribution functions (ODFs) were calculated using the JTEX software (Universite de Lorraine, Metz, France)  [43].
15 µm and were post-processed utilizing the HKL Channel 5 software (Oxford Instruments plc, Abington, Great Britain). The TEM specimens were analyzed using a JEOL JEM 2000 FX II analytical TEM (JEOL Ltd. , Akishima, Japan) operated at 200 kV. In order to characterize the crystallographic textures, X-ray pole figure measurements were performed by acquiring three incomplete (0-85 • ) pole figures {111}, {200}, and {220}. A Bruker D8 Advance diffractometer (Bruker Corporation, Billerica, USA), equipped with a HI-STAR area detector, operating at 30 kV and 25 mA, using filtered iron radiation and polycapillary focusing optics was used. The corresponding orientation distribution functions (ODFs) were calculated using the JTEX software (Universite de Lorraine, Metz, France)  [43].
Acknowledgments:  Christian Haase  and  Dmitri A. Molodov  acknowledge gratefully the financial support of the  Deutsche Forschungsgemeinschaft (DFG)  within the  Collaborative Research Center (SFB)   761  " Steel-ab initio; quantum mechanics guided design of new Fe based materials ". Laszlo S. Toth  and  Robert Allen  would like to acknowledge the support from the  French State  through the program "Investment in the future" operated by the  National Research Agency (ANR)  and referenced by  ANR-11-LABX-0008-01  ( LabEx DAMAS ).
As for the PLA thin disk, a washer was placed between the clamps to prevent sliding. The load vs. displacement curves were recorded by the software WinTest (TA Instruments, New Castle, DE, USA). All the tests were performed with a loading rate of 0. 005 mm/s. The sample placement on the Bose device is sketched in Figure  2b. A preliminary evaluation of the possibility to perform successful pull-out tests led to the observation of two ineffective outcomes of the test: either the fibers broke before the interface failed or, less frequently, the fiber tip and/or the matrix thin disk slid between the grips. The experimental results were classed as regular or non-regular depending not only on the global shape of the curve recorded during the pull-out test, but also on the aspect of the fiber tip after extraction from the matrix and the aspect of the hole left behind.
6 MPa. Fuentes et al. [38]  performed fiber pull-out tests on technical bamboo fibers embedded in poly(vinylidene fluoride) (PVDF) and polypropylene (PP). The diameter of the fibers was not given, but their perimeter was estimated by the Wilhelmy equation applied to dynamic contact-angle measurements. They considered different Lemb (0. 6 to 5 mm) and fit the experimental data with Greszczuk's model  [35] , Tokoro et al. [20]  used short bamboo fiber bundles (diameter 39. 2 µm and length 215 µm before fabrication) to obtain PLA composites by injection molding. They performed micro-droplet tests to evaluate τ app according to Equation (2) and found an average value of about 4. 3 MPa (estimating that processing reduced both the diameter and the length to 21. 3 µm and 86. 3 µm respectively), but no statistical variations were given about these values.
A clear comparison is difficult to make, because the samples used for this study have larger D f (200-480 µm) and L emb (423-790 µm) and the results obtained for regular samples spread over a range going from 2. 1 to 13. 6 MPa. Fuentes et al. [38]  performed fiber pull-out tests on technical bamboo fibers embedded in poly(vinylidene fluoride) (PVDF) and polypropylene (PP). The diameter of the fibers was not given, but their perimeter was estimated by the Wilhelmy equation applied to dynamic contact-angle measurements. They considered different L emb (0. 6 to 5 mm) and fit the experimental data with Greszczuk's model  [35] , finding a value of ultimate interfacial shear strength of about 7. 5 MPa for PVDF (polar) and 3. 4 MPa for PP (non polar). As a comparison, the value obtained here is quite close to the value obtained for PVDF, which is consistent considering that PLA is a fairly polar polymer.
Mechanical properties. Tensile response and elastic modulus. Two types of measurements were done to determine the elastic modulus depending on the shaping. The tensile properties of dry 2D films were measured using a uniaxial tensile testing machine (Instron 3745) equipped with a 10 N load cell and a crosshead speed of 10 mm/min under standard room conditions. Samples of 20 mm × 4 mm (length × width) were mounted onto pneumatic grips and stretched to failure. Force versus elongation data were recorded and the stress-strain plots were generated. Values of the stress and elongation at break were calculated as the average of 5 independent measurements (n = 4). Ageing of the material, i. e. the evolution of the implants mechanical properties under simulated physiological conditions, was assessed.
Platelet adhesion. Static platelet adhesion was measured in vitro using washed platelet suspensions. Blood was harvested from healthy volunteers into vacuum blood-collection tubes (Vacutainer ® system, Beckton Dickinson) containing trisodium citrate acid-citric-dextrose. Washed platelet suspensions were prepared by centrifugation of the blood and analysed as previously reported  14. In brief, platelets were suspended at a final concentration of 2 × 10 8 platelets/mL. PVA and PVA-gelatin films were placed in contact with the platelets suspension at room temperature under rotation for 1 h. Adherent platelets were quantified by assessing the endogenous phosphatase activity using a pNPP buffer (0. 1 M citrate, pH 5. 4, 0. 1% Triton X-100, 5 mm paranitrophenylphosphate). After addition of 25 μl of 1 N NaOH to stop the reaction, supernatants were harvested and absorbance was measured at 405 nm and data contrasted with a calibration curve.
Acknowledgements Inserm,  Universities Paris Diderot  and  Paris 13 ,  Mines-ParisTech  and  ESPCI Paris  supported this study. The authors would like to thank  F. Nadaud  ( UTC Compiègne, France ) for SEM images,  Matthieu Roche  ( Laboratoire de physique des solides ). Funding from  department of Essone  is acknowledged for the dynamic tensile apparatus (ASTRE 2012).
Airyscan super-resolution imaging Images were collected on an LSM880 Airyscan (Carl Zeiss) system with a 63 × DIC M27 objective (PlanApo NA: 1. 4, oil immersion, Carl Zeiss) using the operating software ZEN blue 2. 3. DAPI and Alexa Fluor® 647 were excited with a 405 nm diode laser and a HeNe 633 nm laser, respectively. The filter sets BP 555-620 + LP645 for Alexa Fluor® 647 and BP 420-480 + BP 495-550 for DAPI were used in conjunction with the Airyscan detector in the super-resolution mode. Thirty z-slices were taken with a z-interval of 0. 25 µm. A 3D deconvolution step followed by a Wiener filter was carried out postacquisition. Orthogonal slices of the z-stack were made in Volocity 6. 3. 0 (Perking Elmer). A time-lapse movie was made on one focal plane with an imaging frequency of 1 min for a total duration of 30 minutes.
Acknowledgements K. B. acknowledges financial support from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No  648124 ) and from the  Ghent University Special Research Fund  ( 01B04912 ) with gratitude. J. L. gratefully acknowledges the financial support from the  China Scholarship Council (CSC)  (201506750012) and the  Special Research Fund from Ghent University  ( 01SC1416 ). R. X. gratefully acknowledges the financial support from the  China Scholarship Council (CSC)  (2010634103). H. B. acknowledges funding from the  Research Foundation Flanders (Fonds Wetenschappelijk Onderzoek, FWO)  for a doctoral fellowship ( 11ZB115N ). E. T. acknowledges funding from the  Agency for Innovation by Science and Technology (IWT).
S. S. and R. B. acknowledge financial support from the  Centre National de la Recherche Scientifique (CNRS) , the  University of Lille , the  Hauts-de-France region , the  CPER "Photonics for Society" , and the  EU union  through  FLAG-ERA JTC 2015-Graphtivity  and the  Marie Sklodowska-Curie action  ( H2020-MSCA-RISE-2015 ,  PANG-690836 ). M. A. acknowledges the support by the  FWO Research Community  " Scanning and Wide Field Microscopy of (Bio)-organic Systems " and the  Province of Limburg (Belgium)  for the financial support within the tUL  IMPULS FASE II program , allowing for the upgrade of the laser source used in this work. We would thank the  VIB BioImaging Core  for the use of the microscopy equipment.
m A P [t] 0 ZF ZF- R at T = 2 K m + S Fig. 2. Zero-field µ + SR time spectra of as-grown and cycled Na 0. 7 CoO 2 samples. (a-b) ZF-µ + SR spectra before electrochemical reaction (as-grown sample, filled blue dots) and after electrochemical reaction (filled green dots). The red solid curve represents a fit of the data using a static Gaussian Kubo-Toyabe function  [19]  for the as-grown sample and Eq. (  1 ) for the cycled one. All spectra were recorded at T = 2 K.
Acknowlegements This experimental work was performed at the  Swiss Muon Source (SµS) ,  Paul Scherrer Institute (PSI), Villigen, Switzerland. The research was supported by a  Marie Sk lodowska Curie Action ,  International Career Grant  through the  European Union and Swedish Research Council (VR) , Grant No. INCA-2014-6426 , as well as the  Wenner Gren Foundation. Further, we also acknowledge funding provided by the  Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan,KAKENHI  Grant No. 23108003 , and  Japan Society for the Promotion Science (JSPS) KAKENHI  Grant No. 26286084. D. A. acknowledges partial financial support from  Romanian UEFISCDI  Project No. PN-III-P4-IDPCE-2016-0534/2017.
Details on the experimental setup of DUBBLE beamline are described in  [7]. The Athena, Artemis, and Atoms software packages were used to process and simulate EXAFS data  [8]. The linear combination fitting (LCF) option of Athena was applied to estimate compositions of these composites and the ratios of various compounds in their structure. A number of the experimental references were used for LCF. To simulate the local structures around Fe and Ce atoms, Feff. inp files were generated using the crystallographic information of several relevant reference compounds  [3, 4]  shown in the literature and found in the database of the software developers, available online.
Speciation of aluminium (Al) by NMR and XPS 27 Al NMR spectra are shown in  [5]. It was determined that the main Al species in ASG, HTP and AFSG had octahedral geometry. For commercial Mg-Al LDHs (ASG), it was the only Al species in its structure. HTP had small concentration of tetrahedral geometry AlO 4 in addition to the main species, AlO 6. AFSG contained more Al species than the other two samples. Except for major species, AlO 6 , it also had some AlO 4 and AlO 5. Speciation of Al on the surface was estimated from Al 2p XPS spectra (Fig. 2 ). The data on Al speciation by NMR and XPS correlated well with each other. As shown in Fig. 2 , commercial LDHs (ASG) had strictly one species of Al on its surface. In HTP, Al was dominated by one species as well, however small portion of different species was also measured.
As anion exchangers these materials remove aqueous anions primarily via exchange of their surface OH -whose abundance on the Fe/Ce-based material surface was reflected by backscattering oscillations from both oxygen (O) and iron (Fe). Fe outer shells of the best adsorbents were simulated with both Fe-O and Fe-Fe paths chosen from Feff. inp files obtained using crystallography data of the relevant references. Extended local structure around Fe in the best 80 • C-sample (Fe2Ce1-80) was rich in backscattering oscillations from both Fe and O to Feabsorber in its outer shells, Fig. 4. However, disappearance of these extended structures after thermal treatment at 300 • C (Fe2Ce1-300) correlated with a decrease in adsorptive removal of F -and H 2 AsO - 4 (Fig. 3B ) which most probably indicated a loss of active adsorptive sites, OH -.
Acknowledgments An extensive research data used for this paper preparation were funded by  King Abdullah University of Science and Technology (KAUST)  (award  N°KUK-C1-017-12 ) and  Netherlands Organization for Scientific Research (NWO)  for EXAFS/XANES studies at  Dutch-Belgian Beamline (DUBBLE)  at the  European Synchrotron-Radiation Facilities (ESRF).
Application test: three-point bending The algorithm was implemented through a VBA subroutine in CAD software. The bio-inspired algorithm was tested on a 2. 5D beam in static three-point bending case. The beam dimensions were set as:  = 150 mm,  = 15 mm,  = 30 mm and the distance between bending supports was taken equals to 130 mm. In section §2. 1. 3, a maximal threshold equals to 50 % of porosity was determined to ensure the continuity of the material. This porosity value may induce high stress concentration. A full analytical analysis of the effect of two porosities in an anisotropic medium was proposed by Berveiller et al. [27]. Indeed, to limit stress concentrations in a medium is necessary to ensure that the minimal distance between two porosities (noted e) is greater than the porosity size (Eq.