dataesr/scientific-paragraphs-categorization huggingface dataset:
Pathways analysis The list of proteins exhibiting expression profile variations was submitted to IPA software using the Core Analysis function. Considering the Downstream Effect Analysis (DEA) of IPA, "Cell Death and Survival" functions resulted increased, while the "Cell Movement" and "Cell growth and proliferation" functions (Figure  4A-4C ) decreased. These data are in agreement with previous studies where it was showed that BAG3 silencing increased apoptosis in 8505C cells and in xenografts  [8]. Furthermore, the IPA/DEA results showed also that, aside the global decrease of invasiveness and growth, BAG3-silenced cells adapted to this perturbation modifying the expression levels of proteins involved in compensatory molecular mechanisms. Upstream Regulator Analysis (URA) is another tool of IPA allowing to predict the upstream molecules (transcription factor, microRNA) that could have a causal role in the observed proteome profiling.
Submitting to IPA/URA our dataset, we obtained the enrichment of 5 precursors that we can distinguish in two clusters (Figure  5A ). The first one is characterized by the predicted activation of 4 tumor suppressor miRNAs (miR-133a-3p, miR-203a-3p, miR-17-5p, miR-124-3p)  [27] [28] [29] [30]. These miRNAs are associated to the expression control of proteins already evidenced by DEA to be related to increase of cell death and decrease of invasiveness. The second is the transcription factor TP63, whose levels are predicted to be increased in a compensatory adaptation of 8505C cells to BAG3 silencing. TP63 is a member of TP53 family, whose oncogene/onco-suppressor features have been long debated  [31]. Finally, the most significant upstream factor predicted to be inhibited is the growth factor TGFβ1, confirming the relation between BAG3 silencing and tumor growth repression (Figure  5B ).
r. l. , Fisciano, SA, Italy) and anti-PAI2 rabbit polyclonal antibody H-70 (Santa Cruz Biotechnology, Texas, USA) and anti-CAV1 mouse monoclonal antibody 7C8 (Santa Cruz Biotechnology). Anti-α-Tubulin mouse monoclonal antibody (Sigma-Aldrich, Saint Louis, MO, USA) and anti-GAPDH rabbit polyclonal antibody (TREVIGEN, Gaithersburg, MD, USA) were used as loading control. Immunoreactivity was detected by incubation with horseradish peroxidase-conjugated secondary antibody (Bio-Rad) and enhanced chemiluminescence reagents (SuperSignal West Dura Extended Duration Substrate, Pierce, Thermo Fisher Scientific) following manufacturer' protocol. Bands were digitally visualized using ChemiDoc XRS+ (Bio-Rad) imager and images were captured using Image Lab TM Software (Bio-Rad).
Evaluation of apoptosis by DNA-flow cytometry Apoptosis evaluation was performed using FITC Annexin V Apoptosis Detection Kit I (Catalog No. 556547, BD Pharmigen, Sparks, Maryland, USA). Briefly, 8505C cells, transfected with specific siRNA targeting BAG3, CAV1, SERPINB2 and scrambled siRNA used as control, were harvested 48 h after transfections. According to manufacturer's instructions, cells were washed twice with cold PBS and then resuspended in 1X Binding Buffer at a concentration of 1 × 106 cells/ ml. 100 µl of the solution (1 × 10 5 cells) were incubated with 5 µl of FITC Annexin V and 5 µl of Propidium Iodide (PI) and incubated 15 min in the dark. 400 µl of 1X Binding Buffer was added to each tube. A minimum of 20 000 events for each sample was collected. Data acquisition was performed using BD FACSCanto II Flow Cytometer, and data were analyzed using BD FacsDiva 6.
Data analysis Database analysis was performed using MaxQuant (version 1. 3. 0. 5) with Swiss-Prot database (version 2015_05). Methionine oxidation and cysteine carbamidomethylation were selected as variable modifications. First search error tolerance was 20 ppm while main search error tolerance was set to 6 ppm. MS/MS search was performed with 20 ppm of error tolerance. Protein identification was performed with a False Discovery Rate (FDR) of 1%. Protein relative quantification was performed calculating the.
Funding Acquisition, D. M. -R. Funding: This work was benefited from funding from the  Consejo Nacional de Ciencia y Tecnología (CONACYT)  from  Mexico  (No. 456558 ). The authors thank the " ARC Energies Auvergne-Rhône Alpes ", for their economic support through a Ph. D. grant, and the  Agence Nationale de Recherche (ANR, France)  via the project  DESPATCH  (No. ANR-16-CE05-0021 ). This work benefited from the facilities and expertise of the  OPE)N(RA characterization platform of FMNT  ( FR 2542 , fmnt. fr)supported by  CNRS, Grenoble INP , and  UGA. DMR  acknowledges funding through the  Marie Curie Actions  ( FP7/ 2007-2013 , Grant No. 631111 ). This project was financially supported by " Carnot Energies du Futur " ( ALDASH  project). This project has received funding from the  European Union 's  Horizon 2020 FETOPEN-1-2016-2017 research and innovation programme  under grant agreement  801464.
Acknowledgements The authors duly acknowledge the following funding agencies for the present work through 1. Grant agreement 692216 SUPERMAT from  European Union 's  Horizon 2020 research and innovation program 2. Grant agreement ERAMIN 2  COFUND-Research & Innovation program  on raw materials to foster circular economy-" MONAMIX"- " ANR-17-MIN2-0003-03 " 3. Part of collaboration in photonics between  University of Bordeaux and Huazhong University of Science and Technology.
Geochemical simulation using thermodynamic properties of IRTOCM One of the interests in the study of synthesis or IRTOCM is their incorporation in geochemical simulations in order to predict long-term stability of certain geological formations. Clay minerals have a wide variety of isomorphic substitutions, they occur as mixed-layer phases and have small particle size usually less than 2µm. This structural and chemical complexity makes it difficult to introduce them in such simulations. Nevertheless, several numerical approaches have been developed for the estimation of thermodynamic properties of clay minerals  (Chen, 1975; Chermak and Rimstidt, 1989; Nriagu, 1975; Sposito, 1986; Tardy and Fritz, 1981; Tardy and Garrels, 1974; Vieillard, 2000 Vieillard, , 1994) )  and introduced in different databases such as Thermoddem  (Blanc et al.
, 2012)  or LLNL  (Johnson et al. , 2000). These databases are particularly useful when applied in geochemical simulation codes such as PHREEQC  (Parkhurst and Appelo, 2013)  or Geochemist's Workbench®  (Bethke, 2007)  among others to simulate various systems. Three approaches can be distinguished for the estimation of thermodynamic properties of clay minerals. First approach, consists of the summation of respective oxyde and/or hydroxyde parameters using "polyhedral summation"  (Chermak and Rimstidt, 1989; Nriagu, 1975; Sposito, 1986; Tardy and Garrels, 1974) , "regression"  (Chen, 1975)  or "electronegativity differences of cations"  (Vieillard, 2000 (Vieillard, , 1994) )  techniques. Second approach is based on the ideal mixing of end-member clays  (Tardy and Fritz, 1981)  and the third approach uses the data of ionic species for the estimation of thermodynamic properties  (Eugster and Chou, 1973).
, 2013; Wilson et al. , 2015). The experiments performed by  Wilson et al. (2015)  estimated montmorillonite stability in contact with iron. In this study the polyhedral summation technique of clay mineral constituting oxides and hydroxides were used to obtain their thermodynamic properties  (Helgeson et al. , 1978; Holland, 1989). The study revealed that experimentally detected phases were in agreement with simulations. Another experiment of  Pignatelli et al. (2013)  used a database Thermoddem  (Blanc et al. , 2012)  (which includes the approach of  Vieillard (2000 Vieillard ( , 1994) )  on oxyde summation based on the electronegativity differences of cations). In this study  (Pignatelli et al. , 2014)  the stability field of cronstedtite was calculated and confronted with the data of their experimental observations.
Microscopy Characterization and Image Analyses The extrudates were dipped into liquid nitrogen to be frozen and fractured by a razor blade in cross-and longitudinal sections. SEM (Hitachi S4700, Hitachi, Tokyo, Japan) was utilized to investigate the cryogenic fracture surfaces. The accelerating voltage is 6. 0 kV. The dispersed PVA particles sizes were determined by ImageJ software (National Institutes of Health (NIH), Bethesda, MD, USA), and more than 300 PVA particles were measured in SEM micrographs of longitudinal fracture surfaces. Form factor (ff) is a measure of the deviation of a finite shape from circularity (=4 × π × area/perimeter 2 ), and the parameter can be a powerful evidence in determining the PVA continuity. When ff is close to 1, it tends to be a perfect circle; when ff is approaching 0, it illustrates that the perimeter is extremely tremendous and the shape is irregular.
Funding: This work was partly supported by the  European Commission  within the  Erasmus Mundus Joint Doctoral program International Doctoral School in Functional Materials for Energy, Information Technology , and  Health  (ids-funmat), the  French-German University  ( UFA Doctoral College in Functional Materials for Energy and Information Technology ) and was carried out within the framework of  EMMI  (European Multifunctional  Material Institute ). Further support was received from the  European Commission  under the  FP7 project  " Novel Composite Oxides by Combinatorial Material Synthesis for Next Generation All-Oxide-Photovoltaics ," project number  309018.
For the first time, in this study, a complete characterization of the Ti 40 Zr 10 Cu 36 Pd 14 alloy was therefore performed on one unique batch of material. Moreover, the overall fabrication (including machining and sandblasting, for example) of dental implants and the realization of ISO standard mechanical tests on implant-abutment assemblies made of metallic glasses have never been done to date, which is a crucial step to open the way to industrialization of this BMG as a dental material. Mechanical tests on real-sized dental and abutment assemblies were thus also performed following the ISO 14801-2008 standard and compared to medical-grade Ti-6Al-4V ELI alloy (ISO5832-3). They include both load to failure and fatigue tests. In summary, the aim of this study was to establish a complete multifunctional characterization of the Ti 40 Zr 10 Cu 36 Pd 14 alloy's behavior using the same batch, regarding especially mechanical tests on real-sized dental implants, cytocompatibility and resistance against sterilization, in order to complete the set of data available in the literature to assess the potential of this Ti-based BMG as a future biomaterial.
Diffractograms were recorded either during continuous heating every 5 • or every 7 min during isothermal annealing at 420 • C. Grazing incident X-rays were used with a Goeble mirror to investigate a potential crystallization at the surface of the machined pieces. The 2θ angles range was 20 • -80 • with an incidence angle of 5 • , an increment of 0. 05 and a step size of 15 s. The calculated penetration depth, using the measured density of the alloy and the AbsorbX software, was approximately 1. 4 µm. The XRD pattern obtained in grazing incidence was compared with the same spectra acquired in the Bragg-Brentano configuration (penetration depth at 2θ = 80 • of 9 µm). Comparison of both diffractograms, acquired in grazing incidence or in the Bragg-Brentano configuration, will indicate localization of the crystallization initiation, either throughout the material or only at its top surface.
The Hamamatsu X-ray source was operated at a voltage of 160 kV and a current of 100 µA with a 0. 1-mm copper filter. The detector was a Hamamatsu 2300 × 2300 pixels flat panel. All the cone-beam X-ray computed Tomography (XCT) data were reconstructed by a filtered back projection Feldkamp algorithm, processed and visualized with the Image J software  [68, 69].
Acknowledgments: The authors would like to thank the  Agence National de la Recherche (ANR)  and its funding within the framework of the  ANR-14-LAB5-006  and the  Labcom 'LEAD'. The joint Laboratory Elyt Lab  is also gratefully acknowledged. A part of this research is financially supported by the  International Collaboration Center, Institute for Materials Research (ICC-IMR) ,  Tohoku University. The assistance of  Jerôme Cavoret  with optical interferometry measurements is gratefully acknowledged.
Acknowledgements The project is supported by  Aquitaine regional  grant " SMOLED " ( 2014-1R60306 ). The work in Berlin was supported by the  DFG  ( SFB951  and  AM 419/1-1 ). A. Ablat thanks the financial support of  China Scholarship Council (CSC). Authors are thankful to the  ANR  as part of the  "Investissements d'avenir" program  (reference:  ANR-10-EQPX-28-01/Equipex ELORPrintTec ) and technical support of  Dr. Roland Lefevre  in XPS measurement.
The initial guess contained the literature values of scattering lengths and densities and nominal thickness of iron oxide layer; then the densities and thicknesses of ε-Fe 2 O 3 and interface layer were allowed to vary freely in the fitting routine. All PNR datasets were fitted simultaneously with the same structural parameters and varying magnetizations of the main and interface layers corresponding to different temperature and field conditions and resolution functions corresponding to the D17 and SHARAKU instruments. The minimum found by the fitting algorithm (goodness of the fit χ 2 = 1. 42) corresponds to the model containing interface layer with thickness of d i = 37 ± 3 Å and roughness σ i = 24 ± 10 Å between iron oxide and GaN buffer. The obtained density of ε-Fe 2 O 3 layer is reduced by 5% and GaN density is reduced by 1.
This behavior resembles the loops shown in Fig. 2  that demonstrate a pronounced two-step magnetization switching: a wide hysteretic magnetization rotation between -2 T and 2 T, representing the averaged switching of 3 columnar domains, and a narrow zero-remanence magnetization switching with saturation of ≈0. 25M s. However, the contribution of the interface layer to the total magnetization is only 0. 08 M s as found from our PNR data. This suggests that another soft magnetic phase is likely present in the sample though cannot be distinguished in the PNR experiment. The most plausible candidates for the soft-magnetic phase are minor γ-Fe 2 O 3 and Fe 3 O 4 fractions homogeneously distributed within the sample plane  5, 20, 23  although not pronounced in X-ray diffraction and X-ray spectroscopy data  15.
Acknowledgements We thank  V. Kocsis  and  N. D. Khanh  for technical assistance,  K. Kakurai  for useful discussions and ILL and J-PARC facilities for provided neutron beamtime. The authors wish to acknowledge  V. V. Lundin  for providing GaN/Al 2 O 3 wafers. This work has been supported by  RSF  (project no. 17-12-01508 ) in part related to development of epsilon ferrite growth technology and by  RFBR  (project no. 18-02-00789 ) in part related to film characterization. TEM studies have been performed on the equipment of " Material science and characterization in advanced technology "  Federal Joint Research Center  supported by the  Ministry of Education and Science of the Russian Federation  (id  RFMEFI62117X0018 ).
Optical characterizations Refractive indices of bulk samples in visible and near-IR were determined by prism coupling technique (Metricon-2010 instrument). A laser beam at several wavelengths (λ = 633, 825, 1064, 1311 and 1551 nm) and a rutile prism were used. Variable angle spectroscopic ellipsometer with rotating compensator (IR-VASE, J. A. Woollam Co. , Inc. , Lincoln, NE, USA) was employed for the optical characterization of studied materials in ~1. 7-15 µm spectral range measuring 50 scans, 15 spectra per revolution at angles of incidence of 50°, 60°, and 70°. To extract optical parameters from VASE data in the 1. 7-15 µm spectral region, suitable MIR refractive index spectral dependence function is necessary. In this work, Sellmeier equation in the form n 2 (λ) = A + (Bλ 2 /(λ 2 -C)) + (Dλ 2 /(λ 2 -E)) , where λ is wavelength, A, B, C, D, and E are empirical coefficients, was exploited setting extinction coefficient in first approximation to zero  [26].
Context. Landing on the surface of small bodies is particularly challenging, as the physical properties of the surface material are not well known and the mechanical response of this material in a low-gravity environment is not well understood. Aims. In order to improve our understanding of low-speed impact processes on granular media and their outcome in low-gravity environments, we consider the landing of the package MASCOT, to be released by the JAXA asteroid sample return mission Hayabusa2 on (162173) Ryugu in October 2018. Beyond addressing the theoretical aspects of the mechanical response of granular media in low gravity, this study also supports both engineering and scientific teams of Hayabusa2 in the search for the lander and in the determination of Ryugu's surface properties. Methods.
A campaign of hundreds of numerical simulations using the soft-sphere discrete element method implemented in the N-body code pkdgrav were performed to study the interaction between the lander and the low-gravity surface of the asteroid made of a granular medium representing the regolith. Assuming a broad range of regolith properties, and the lander's trajectory and motion, we analyzed the outcomes of the landing (distance traveled by the lander, penetration depth, and shape of the traces left in the regolith surface) to determine the influence of the many parameters defining the properties of MASCOT and of the grains, and the ingoing motion of the lander. Results. We identify well-marked trends for the fate of the lander and the traces left in the granular material. Distances traveled by the lander are greater and penetrations are shallower for gravel-like media than for less frictional material.
However, our results can provide standard coefficients of restitution (MASCOT's outgoing-to-incoming speed ratio, for example) and traveled distances that can serve as a reference for other software to study the whole evolution of MASCOT. We analyzed the traces left by MASCOT on Ryugu's surface after the first impact. We find that the signature left by MAS-COT is very different for the two considered types of regolith. We also find that there is a relation between the traces left by MASCOT (crater shape and ejecta deposits), and the resulting travel distance and direction after the first impact. The instruments on board Hayabusa2 may be able to observe these impact traces, and in that case, the data will be extremely useful to give insight on both the nature of the regolith in terms of friction properties and the location of MASCOT on Ryugu's surface.
Acknowledgements. F. T. is supported by a PhD fellowship of the  University of Nice-Sophia. P. M. and F. T. acknowledge funding support from the  French space Agency CNES  ( BCU66 ), as well as from  Academies of Excellence: Complex systems and Space , environment, risk, and resilience, part of the IDEX JEDI of the  Université Côte d'Azur  in connexion with its Center for Planetary. Simulations were performed at Mésocentre SIGAMM hosted at the  Observatoire de la Côte d'Azur  and on the Deepthought2 HPC cluster at the  University of Maryland. E. T. and S. S. acknowledge support from the  Japan Society for the Promotion of Science (JSPS)  Core-to- Core program  " International Network of Planetary Sciences ".
Another approach to gain insight into the function of shellforming genes is to characterize their spatial expression patterns in situ. We previously adopted this approach in the tropical abalone Haliotis asinina with a Sanger Expressed Sequence Tag (EST) dataset and characterized the spatial expression patterns of more than 20 putative shell-forming genes in juvenile snails  [16]. While a spatial expression pattern in the mantle is not direct evidence of a functional role in calcification, we were able to assign putative functions to genes involved in shell pigmentation  [16]  and ecological and mineralogical transitions  [20]. Here, we have combined an next-generation sequencing (NGS) transcriptome analysis of adult mantle tissue with a proteomic survey of the adult shell of the freshwater pulmonate gastropod Lymnaea stagnalis in order to both compare the resulting data with other similar datasets and to generate the first in situvalidated ontogenetic transcriptome-scale dataset for a species that forms the most common molluscan shell microstructure, crossed lamellar  [21] [22] [23].
A striking result of our analyses in the adult mantle tissue is the degree of spatial modularity displayed by distinct sets of genes. This general observation may contribute to an explanation of why the molluscan shell is apparently so evolvable. With the availability of a draft L. stagnalis genome and transcriptome data from a variety of adult tissues, we have also investigated the genetic architectures of our biomineralization candidates and explored to what extent alternative splicing plays a role in shell formation in L. stagnalis. These genes can also be compared with similar datasets from distantly related molluscs that build shells with alternative polymorphs of calcium carbonate (calcite vs. aragonite) and textures (prismatic vs. nacreous vs. crossed lamellae). Such comparisons can generate testable hypotheses regarding which components of the shell-forming toolkit contribute to these differences and which components are required for more fundamental aspects of shell formation.
Peptide fractionation and data acquisition Mass spectrometry (MS) was performed using a Q-Star XL nanospray quadrupole/time-of-flight tandem mass spectrometer, nanospray-Qq-TOF-MS/MS (Applied Biosystems, Villebon-sur-Yvette, France) coupled to an online nanoLC system (Ultimate Famos Switchos from Dionex, Amsterdam, The Netherlands). One microliter of each sample was loaded onto a trap column (PepMap100 C18; 5 μm; 100 Å; 300 μM x 5 mm; Dionex), washed for 3 minutes at 25 μL/min with 0. 05% trifluoroacetic acid/2% acetonitrile, then eluted onto a C18 reverse phase column (PepMap100 C18; 3 μm; 100 Å; 75 μM x 150 mm; Dionex). Peptides were separated at a flow rate of 0. 300 μL/min with a linear gradient of 5-80% acetonitrile in 0. 1% formic acid over 120 minutes. MS data were acquired automatically using ANALYST QS 1.
1 software (Applied Biosystems). Following an MS survey scan over m/z 400-1600 range, MS/MS spectra were sequentially and dynamically acquired for the three most intense ions over m/z 65-2000 range. The collision energy was set by the software according to the charge and mass of the precursor ion. MS and MS/MS data were recalibrated using internal reference ions from a trypsin autolysis peptide at m/z 842. 51 [M + H] + and m/z 421. 76 [M + 2H] 2+.
Mass spectrometry data analysis Protein identification was performed using the MASCOT search engine (version 2. 1; Matrix Science, London, UK) against translations in all six frames of our mantle transcriptomes, which possessed Benchmarking Universal Single-Copy Orthologs completeness scores of >98% (see below). Liquid chromatography (LC)-MS/MS data were searched using carbamido-methylation as a fixed modification and methionine oxidation as a variable modification. The peptide mass and fragment ion tolerances were set to 0. 5 Da. The peptide hits (protein score >50; false discovery rate <0. 05; 1 missed cleavage allowed) were manually confirmed by the observation of the raw LC-MS/MS spectra with ANALYST QS software (version 1. 1). Quality criteria were the peptide MS value, the assignment of major peaks to uninterrupted y-and b-ion series of at least three to four consecutive amino acids, and the match with the de novo interpretations proposed by the software.
All MS data has been deposited with the ProteomeXchange Consortium via PRIDE  [30]  with the dataset identifiers PXD008547 and 10. 6019/PXD008547. Shell-forming candidates Lstag-sfc-7, Lstag-sfc-8, and Lstag-sfc-9 were bioinformatically selected for analysis based on the presence of a signal peptide and their glycine-rich sequences (i. e. , they were not detected using the proteomic methods described above).