dataesr/scientific-paragraphs-categorization huggingface dataset:
Transwell® migration Migration capacity of homotypic and heterotypic cultures was measured using 6. 5 mm Transwell ® with 8. 0 μm Pore Polycarbonate Membrane Insert (Corning, Madrid, Spain). The transwells were coated with 100 µL of growth factor reduced Matrigel (10 ug/µL) and incubated for 30 minutes enabling polymerization. MDA-MB-231 or MCF7 were co-cultured with vCAF 24 hours before the assay to obtain heterotypic clusters and were maintained in serodeprivation. The day after, 5 x 10 4 cells/ Transwell ® were seeded in a 10% FBS gradient (37°C, 5% CO2) for 8 hours (MDA-MB-231) or 24 hours (MCF7). After incubation, the insert was washed with phosphate saline buffer (PBS) (BIOWEST), and the top area of the insert was scraped to remove the non-migrated cells. Migrated cells were fixed with 3% paraformaldehyde (PFA) + 1% glutaraldehyde (Sigma-Aldrich) for 15 minutes and GFP positive cells were counted using Leica DMi8 (Leica Microsystems) and the free software ImageJ Fiji (NIH Image).
Soft-agar colony formation assay Homotypic or heterotypic clusters (1 x 10 4 tumor cells/well) were resuspended in 0. 3 % (w/v) molecular grade agarose (Fisher BioReagents, Madrid, Spain) in DMEM (10% FBS, 1% P/S) inside a 6 wells plate. Cells were incubated at 37°C, 5% CO2 for 3-4 weeks to allow colonies to spawn, At the end of the experiment, colonies were fixed with 3% PFA + 1% glutaraldehyde (Sigma-Aldrich) for 15 minutes. The number and area of colonies were measured using a Leica DMi8 microscope (Leica Microsystems) and the free software ImageJ Fiji (NIH Image). Because of the small size of MDA-MB-231 colonies, a minimum size of 75 µm was established to quantify colonies from MDA-MB-231 homotypic and heterotypic clusters.
Cytokine detection assay Cytokine levels produced by homotypic and heterotypic cultures were analyzed using the Proteome Profiler TM Human Cytokine Array (ARY005B; R&D SYSTEMS) kit. MDA-MB-231 or vCAF cultures were seeded in different plates, and MDA-MB-231 + vCAF cocultures were seeded in the same plate, allowing physical interactions, or separated by 0. 4 µM pore Transwell (Corning), to study paracrine interactions. The number of cells seeded was adjusted to allow all cultures to reach 80% confluence at the same time when the FBS was retired and cells were incubated with DMEM (P/S) for 48 hours. Supernatants were retired and centrifuged at 264 xg for 5 minutes to eliminate suspension particles. Samples were processed following manufacturer instructions and incubated over membranes. These membranes were revealed at 40 seconds of exposure using a Chemidoc MP system (Bio-Rad) and cytokine expression levels were determined by densitometry using the free software ImageJ Fiji (NIH Image).
Data analysis Microscopic images from in vitro and in vivo assays were analyzed with Leica Application Suite X software (Leica Microsystems) and free ImageJ Fiji software (NIH Image). Fluorescence images from zebrafish xenografts were analyzed using the free software Quantifish (Zebrafish Image Analyser). Quantification, statistic analysis and graphic representation were performed using the GraphPad Prism 8 software (GraphPad Software). Data from functional in vitro assays, and mouse and zebrafish xenografts, when different experimental groups are compared, were statistically analyzed using the Mann-Whitney test. Zebrafish experiments, when different time points were compared in one experimental group, were analyzed using the Wilcoxon test (non-parametric test for paired samples). Regarding the correlation study in zebrafish, a linear regression analysis was performed.
Funding This work was supported by  Roche-Chus Joint Unit  ( IN853B 2018/03 ) funded by  Axencia Galega de Innovación (GAIN) ,  Consellería de Economía, Emprego e Industria. PH was funded by a  Predoctoral fellowship  ( IN606A-2018/019 ) from  Axencia Galega de Innovación  ( GAIN, Xunta de Galicia ). IM-P was funded by the  Training Program for Academic Staff fellowship  ( FPU16/01018 ), from the  Ministry of Education and Vocational Training ,  Spanish Government.
III. STRAIN REDISTRIBUTION MODELING The principle of the fabrication for the strain concentration  [2] ,  [27] ,  [28]  in crossbeam  [29]  is reminded in the Fig. 2. A Ge layer on top of SiO 2 on Si is used as initial layer stack  [30]  (Fig. 2a ). For GeOI layer stack, which gives the maximum reported strain in the literature, up to date  [3] ,  [15] ,  [31] , the residual strain has been evaluated at around ∼0. 16% coming from typical values for Ge grown on Si  [32] -  [36]  at the beginning of the GeOI processing  [30]. The Ge layer is then patterned by dry etching (Fig. 2b ) and finally under etched using vapor HF  [15]  (Fig. 2c ). At the end, the strain is thus concentrated in the central area of the device by suspending the patterned Ge layer. To evaluate the strain distribution at room temperature, we used a 2D linear elastic model  [15] ,  [37] -  [39]  with COMSOL multi-physics software, taking into account the anisotropic germanium stiffness matrix, for calculating ε xx , ε yy and ε xy  [38].
The dust concern in ITER fusion facility calls for improvement of the knowledge of their fundamental properties because important safety issues are associated with them; including radiological hazard, toxicity as well as chemical reactivity in terms of explosion risks. Additional risk related to the particle class of nanometric size has to be futhermore consider due to their impact on biological environment since their production in fusion facility has been put in evidence. Specifically, although no data has been acquired on beryllium nanoparticles (NPs) and their reactivity within tritium, the aim of this present paper is to establish a first comprehensive picture of beryllium -hydrogen based nanoparticles. The structural and electronic properties of Be n and Be n H m NPs of "medium" sizes are investigated using Density Functional Theory calculations.
For small nanoclusters ( n ≤ 9 ), the lowest energy geometry has linear or polymeric form while for larger nanoclusters, calculations confirm that ring structures are energetically more favorable. In addition to the binding energies of the structures Koukaras et al. report on polymerization energies, Be -H bond energies with respect to coordination details, hydrogen desorption energies of saturated and oversaturated species. In the present study, structural and cohesive characteristics (geometries, binding energies and desorption energies) of nanostructured Be n and Be n H m have been examined with suitable DFT calculations, focusing on the reactivity of hydrogen within Be nanoparticles (NPs) of "medium" sizes ( ≈ 2 nm). All obtained structural and energetic data can be used in the future to establish a dataset able to extend the existing beryllium -hydrogen interatomic potential (for molecular dynamic codes) to study the nanoparticles.
005 Ha. Secondly, single point calculations were performed using the TURBOMOLE program  [31]  , for all the optimized structures. The functional was again PBE, while the basis set was def-SV(P)  [32]  , since it has been found that they offer good agreement when compared to results from higher level of theory on similar type of NPs of smaller sizes  [21, 27]. The convergence criterion was set to 10 -6 and the DIIS to 10. Also thermodynamic temperature broadening  [31]  was used to help convergence. Two approaches have been used for the construction of the Be n NP structures ( Fig. 1  ). The first nanoparticle shape is obtained by performing a spherical cut into bulk beryllium crystal whereas the second one is based on equilibrium shape of NP using the Wulff construction  [33]. Regarding the latter, the NP input structure files are computed within the support of MPinterface python package  [34]  , whereas the energies of any beryllium bare surfaces are taken from Ref.
Results indicate that desorption energy remains positive even at full coverage due to negative adsorption energy as well as weak hydrogen -hydrogen interaction. All these DFT data with respect to the hydrogen behaviour onto and into NP will be used in future works as energy dataset for optimization of a beryllium -hydrogen interatomic potential. This improvement would facilitate molecular dynamics simulations in a wide range of cases related to hydrogen reactivity with beryllium nanoparticle, as for example the desorption temperature of hydrogen isotopes or their agglomeration and adhesion mechanisms. Molecular dynamics simulations will permit also the investigation of more representative (realistic) sizes of nanoparticles up to ≈ 10 nm.
B) using the Platinum Taq DNA Polymerase (Invitrogen) and the Nextera XT Index Kit V2 (Illumina, San Diego, California). DNA sequencing with a 15% PhiX spike-in was performed using the MiSeq System and the MiSeq Reagent Kit v2 (Illumina). Reads were trimmed to meet a quality score of Q20. Then, pair-ended reads were assembled using PANDAseq  (Masella et al. , 2012)  at a sequence length between 410 and 500 bp and an overlap length between 20 and 100 bp, using the rdp_mle algorithm. Each of the DNA sequences was annotated to the genus level using the Ribosome Data Project (RDP) database and the RDP Bayesian classifier using an assignment confidence cut-off of 0. 6  (Wang et al. , 2007). Obtained sequencing depths are plotted in Supplementary Figure  S6A. Contaminant sequences from blanks and non-template controls were removed using the decontam package in R  (Davis et al.
, 2017)  and genera that had less than 10 sequences annotated in the ensemble of samples were removed. Then, genus richness, evenness and diversity were calculated using the vegan package in R  (Oksanen et al. , 2019). In addition, genus relative abundances were calculated and the average abundance of the 24 most abundant genera was compared between sites. A NMDS analysis based on Bray-Curtis distances was performed using the vegan package in R.
Metagenomic Sequencing and Analysis DNA was quantified using the Qubit High Sensitivity dsDNA Kit (Invitrogen). Metagenomic libraries were prepared from <1 ng of DNA using the Nextera XT Library Pep Kit and Indexes (Illumina), as detailed in Illumina's "Nextera XT DNA Library Prep Kit" reference guide (15,031,942 v03). DNA sequencing with a 1% PhiX spike-in was performed using the MiSeq System and the MiSeq Reagent Kit v2 (Illumina). Sequencing depths are plotted on Supplementary Figure  S6B. Short reads were submitted to an ARG screening. Firstly, reads were trimmed using the Fastq Quality Trimmer tool of the FASTX-Toolkit. Nucleotides that did not meet a minimum quality score of Q20 were trimmed from the sequences, and sequences shorter than 100 nucleotides after trimming were removed. Then, reads from R1 and R2 were concatenated and blasted against the CARD antibiotic gene database  (Alcock et al.
, 2020)  using Diamond  (Buchfink et al. , 2015). The obtained results were filtered at a minimum identity of 60%, a minimum length of 33 amino acids and an e-value of 10e -5 , and the best hit was chosen. Singletons and ARGs present in blanks were removed. Then, ARG copies were normalized per liter of melted snow or per number of copies of the 16S rRNA gene. Both ARG reads normalized by liter of melted snow and normalized by 16S rRNA gene copies were grouped by antibiotic class and their average abundance was compared between sites. In addition, a NMDS analysis was performed on ARG abundances per liter of snow using the vegan package in R. Finally, statistical differences in ARG abundance between sites were found using the DESeq2 package in R  (Love et al. , 2014). Log2FoldChange values were adjusted using the Approximate Posterior Estimation for generalized linear model or apeglm.
Statistical Analyses Statistical analyses were performed for all the numerical parameters evaluated in this study: NDVI, pH, conductivity, concentration of trace elements, sequencing depth, 16S rRNA gene copies per L of melted snow, bacterial richness, evenness and diversity, ARG copies per L of melted snow, ARG copies per 16S rRNA gene copies. Data normality was checked for each parameter using the Shapiro-Wilk test. Statistical differences between sites were evaluated using ANOVA tests and pairwise t-student tests for data that showed a normal distribution and Kruskal-Wallis and pairwise Wilcoxon signedrank tests for data that showed a non-normal distribution. All statistical analyses were done using the ggpubr package in R  (Kassambara, 2020). In addition, statistical differences in genus and ARG abundance between sites were found using the DESeq2 package in R  (Love et al.
FUNDING This work was partially funded by the  NAWA PHC   Polonium 2020 program  of the  French-Polish Hubert Curien partnership  [project number  PPN/BFR/2019/1/00052/U/00001  (PL) and 45023QL (FR) in 2020]. Partial funding was received from the  ANRT  ( Association Nationale de la Recherche et de la Technologie ) and  Promega Corporation , as part of the CIFRE PhD grant  2017/0486. BL and AN were also supported by the  Institute of Geophysics, Polish Academy of Sciences  within statutory activities no. 3841/E-41/S/2020  of the  Ministry of Science and Higher Education of Poland.
The isotropy of the a-Sb 2 S 3 dielectric function was proven by imaging polarimetry, as the Mueller Matrix measured on different a-Sb 2 S 3 films revealed the identity matrix, typical of isotropic materials, as shown in Figure S1  (Gutierrez et al. , 2022). The a-Sb 2 S 3 index of refraction (n) and extinction coefficient (k) are compared with literature data in Figure  3D. The different amplitude of the curves can be explained by the different contribution of voids resulting from a large number of Sb-atoms electrons lone-pair  (Xu et al. , 2021) , depending on the stoichiometry of the deposited amorphous samples. Furthermore, more voids mean larger Peierls-like distortions, therefore, emphasizing the role of those distortions on the a-Sb 2 S 3 dielectric function. Specifically, the strength of an optical transition and, hence, the maximum of ε 2 , decreases with increasing Peierls distortion, i.
e. , shortening Sb-S bonds. Therefore, tailoring Peierls-like distortion in the a-Sb 2 S 3 could be a way to increase the optical contrast between the amorphous and crystalline phases. (D) Refractive index, n, and extinction coefficient, k, of a-Sb 2 S 3 also compared with the data in literature  (Delaney et al. , 2020; Dong et al. , 2019; Hassam et al. , 2021). The surface topographical images recorded by SEM and AFM in various laboratories for a-Sb 2 S 3 films with thicknesses of z150 nm, shown in Figure  3B , confirms the presence of voids, with films characterized by a grainy-like morphology. The measured grain size and roughness (root-mean-square roughness, RMS) are statistically as 30 G 5 and À3. 5 G 0. 5 nm, respectively. The irregular shapes of the grains stem from the fact that at room temperature during deposition, the kinetic energy is not enough to induce the coalescence of the grains  (Tigau, 2007).
Sb 2 S 3 amorphous-to-crystalline phase change by thermal annealing and laser crystallization Here we address the interplay between structure and optical properties induced by both thermal and laser crystallization. Figure  4  shows the representative optical, SEM, and AFM images of crystallized Sb 2 S 3 upon thermal annealing. The annealing was run under various conditions in different laboratories (see STAR Methods). Noteworthy, data from the various laboratories could be grouped in two different kinds of structures/morphologies independently of the annealing in vacuum, argon, and air, revealing the role mainly of the annealing temperature (T = 250-300 C and 300-350 C) on the evolution of structure upon thermal crystallization. Specifically, Type-I crystallized c-Sb 2 S 3 , with an almost unchanged S/Sb ratio of 1.
Similar behavior, although with lower signals, can be seen in both CD and   2  (consistently with the bending scheme in Figure  S4 ), leading to an optical contrast during the amorphous-to-crystalline transition of Dn $ 0. 2 in the spectral region <1. 5 eV. The spectra of the refractive index, n, and extinction coefficient, k, are compared with data from literature in Figures  7C  and 7D , whereas the values of absorption edge are compared with literature data in Table  1. Laser crystallization has also been investigated using green CW lasers (514 and 532 nm) with wavelengths above the absorption edge of both c-Sb 2 S 3 and a-Sb 2 S 3 , operated at different power. Raman spectra taken after laser irradiation at increasing power are shown in Figure  8. Comparing the Raman spectrum for the lower power of 2.
Polarimetry Polarimetric measurements were performed with an adapted microscope set-up (Nikon Eclipse LV-N). The microscope base structure includes a monochromatic unpolarized light source (CoolLED pE-100, 633 nm), a polarizer (P1) before de sample holder, objectives (5x, 20x and 50x with NA of 0. 15, 0. 4 and 0. 6 respectively) and an analyzer (P2) before the CCD camera (The Imaging Source DMK 33UX174). To achieve the measurement of the Mueller Matrix (MM) with the microscope two l/4 waveplate retarders (R1 and R2) with controllable angular orientation of the fast axes were included. One after P1 and another before P2. Both retarders are identical (Thorlabs WPH05M-633) and are mounted onto motorized rotation stations (Thorlabs PRM1/MZ8) controlled by an ordinary laptop. We worked out a MATLAB routine that controls the angular position of R1 and R2 fast axis synchronously with the acquisition process of the camera.
The routine consisted in measuring N images, with angular increments in the fast axis orientation of 180 /N for R1 and 900 /N for R2 (5:1 speed ratio) between each image acquisition. As a result, in each pixel of the camera we measured a full Fourier measurement cycle that was processed to obtain the corresponding MM of a given part of the sample. As a result, a polarimetric image is obtained, i. e. , an image that describes with spatial resolution what changes are produced in the light polarization by a sample. The full process (data acquisition plus post processing) took less than 20 minutes. A differential analysis of the Mueller matrices using the Mueller Matrix Differential Decomposition (MMDD) was performed  (Arteaga and Kahr, 2013). The differential matrix m relates the Mueller matrix M as dM dz = mM (Equation  2 ) If the differential matrix, m does not depend on z, i.
The chloride channel dysfunction caused by deleterious cystic fibrosis transmembrane conductance regulator ( CFTR) variants generally correlates with severity of cystic fibrosis (CF). However, 3 adults bearing the common severe variant p. Phe508del (legacy: F508del) and a deletion variant in an ivacaftor binding region of CFTR (p. Phe312del; legacy: F312del) manifested only elevated sweat chloride concentration (sw[Cl -]; 87-105 mEq/L). A database review of 25 individuals with F312del and a CF-causing variant revealed elevated sw[Cl -] (75-123 mEq/L) and variable CF features. F312del occurs at a higher-than-expected frequency in the general population, confirming that individuals with F312del and a CF-causing variant do not consistently develop overt CF features. In primary nasal cells, CFTR bearing F312del and F508del generated substantial chloride transport (66.
1519_1521delATC (p. Ile507del; legacy: [delta]I507 or I507del); c. 3011_3019delCTATAGCAG (p. Ala1004_Ala1006del; legacy: 3141del9 or 3143del9); and c. 3067_3072delATAGTG (p. Ile1023_Val1024del; legacy: 3199del6) (https:// cftr2. org) (2). Like F508del  (3) (4) (5) , these variants are associated with a classic presentation of CF, as the loss of an amino acid typically disrupts CFTR folding and transports to the apical surface of the epithelium, and significantly impairs its function. Consequently, the mild CF phenotype associated with the in-frame deletion c. 935_937delTCT (p. Phe312del; legacy: [delta]F311 or F312del) in the CFTR2 database (https:// cftr2. org) seemed incongruous. Although the F312del variant was originally reported in association with classic CF  (6) , it was later also identified in patients with milder disease (pancreatic sufficiency)  (7, 8)  and The chloride channel dysfunction caused by deleterious cystic fibrosis transmembrane conductance regulator (CFTR) variants generally correlates with severity of cystic fibrosis (CF).
However, 3 adults bearing the common severe variant p. Phe508del (legacy: F508del) and a deletion variant in an ivacaftor binding region of CFTR (p. Phe312del; legacy: F312del) manifested only elevated sweat chloride concentration (sw[Cl -]; 87-105 mEq/L). A database review of 25 individuals with F312del and a CF-causing variant revealed elevated sw[Cl -] (75-123 mEq/L) and variable CF features. F312del occurs at a higher-than-expected frequency in the general population, confirming that individuals with F312del and a CF-causing variant do not consistently develop overt CF features. In primary nasal cells, CFTR bearing F312del and F508del generated substantial chloride transport (66. 0% ± 4. 5% of WT-CFTR) but did not respond to ivacaftor. Single-channel analysis demonstrated that F312del did not affect current flow through CFTR, minimally altered gating, and ablated the ivacaftor response.
Second, 25 individuals in CF databases reported to have F312del as a presumed pathogenic variant had consistently elevated sweat chloride, yet highly variable lung and pancreas features. Third, the frequency of F312del in the healthy population (https://gnomad. broadinstitute. org/) is higher than predicted compared with the worldwide CF population in the CFTR2 database. Fourth, the 312 position is involved in the binding of 2 CFTR potentiators: ivacaftor and GLPG1837  (9) (10) (11). Thus, in-depth evaluation of the clinical and functional effects of F312del would likely inform understanding of the relationship between CFTR structure and function.
Individuals bearing F312del who are enrolled in CF databases consistently have elevated sweat chloride concentrations but other features of CF are highly variable. Two subjects from the EPIC Observational Study  (12)  were found to carry F312del. Subject C (F312del and F508del) was evaluated at age 7 months due to failure to thrive and malnutrition. She had an elevated sweat chloride concentration and was treated with pancreatic enzymes. Her FEV 1 at age 18 was 80% predicted (Table  1 ). Subject D was identified following an abnormal newborn screening (NBS) result and elevated sweat chloride concentration and was found to be homozygous JCI Insight 2022;7(6):e148841 https://doi. org/10. 1172/jci. insight. 148841 for F312del and the intron 9 variant c. 1210-7_1210-6delTT (legacy: 5T;TG11). Lung and pancreatic disease, Pseudomonas aeruginosa infection, and CF-related diabetes were absent at 12 years old (Table  1 ).
broadinstitute. org/variant/7-117180210-CCTT-C?dataset=gnomad_r2_1) than estimated by its frequency in the CFTR2 population (details available in Supplemental Material). The gnomAD population, composed of individuals with "normal" phenotypes  (13) , also included 1 F312del-homozygous individual. The higher-than-expected frequency of F312del in the healthy population is consistent with the observation that only a fraction of individuals with F312del develops overt symptoms of CF. F312del is a recurrent variant existing on at least 2 genetic backgrounds. While ascertaining the complete CFTR genotype associated with F312del, we noted that it occurred with 3 different versions of the polythymidine (polyT) and TG repeat tracts in intron 9  (14). Five individuals compound heterozygous for F312del and a CF-causing variant had CFTR intron 9 polyT or polyT;TG typing reported (Table  1 ).