dataesr/scientific-paragraphs-categorization huggingface dataset:
Data Processing for Proteomics Analysis and Pathway Analysis DDA data were processed with the MaxQuant software (Ver. 1. 6. 17. 0, Max-Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Munich, Germany). Database searching was performed against the human FASTA database downloaded from UniProtKB/Swiss-Prot. Interrogation of the databank was based on the following criteria: precursor mass tolerance of 7 ppm, fragment ions mass tolerance of 0. 6 Da, and 2 maximum missed cleavages with trypsin as the enzyme. Search parameters for post-translational modifications were variable modifications of N-acetylation on protein N-terminal residues, oxidation on methionine residues, and pyro-Glu modification on glutamine residues. The matching between runs was also checked.
Statistical Analysis of Transcriptomic and Proteomic Levels Differentially expressed genes were identified by one-way analysis of variance of quantile-normalized signals followed by a Scheffe test for multiple comparisons. The SPSS Statistics version 25 (IBM, Armonk, NY, USA) software was used for all statistical computations. Once this selection was made, the data in the different conditions for proteomic and transcriptomic datasets were compared with the data on the TEAD-responsive elements found in the YAP/TAZ/TEAD Chromatin Immunoprecipitation followed by Sequencing (ChIP-Seq) data  [21]  in Supplementary Table  S2. Venn diagrams were drawn by Draw Venn Diagram (http://ugent. be (accessed on 16 August 2022)).
Capillary Western Immunoassay (Jess) A total protein assay was conducted for data normalization and comparison on the Jess following the manufacturer's instructions (ProteinSimple, San Jose, CA, USA) with a 12-230 kDa separation module (SM-W004, ProteinSimple). Target proteins were detected with antibodies from Abcam HAUS6 (ab173281), BUBR1 (ab215351), DIAPH3 (ab245660) and from Cell Signaling Technology (CST), Danvers, MA, USA, BUB1 (#5421) RRID:AB_10691315, CDC20 (#14866) RRID:AB_2715567, PLK1 (#4513) RRID:AB_2167409 and CYR61 (#14479) RRID:AB_2798492. The level was normalized to the total protein for each target protein studied, and then, the inhibition rate was calculated vs. DMSO. Three independent experiments were carried out.
On the cell pellet, 200 µL of Guava Cell Cycle reagent was added to each tube and incubated for 30 min at room temperature in the dark. Quantification of the cell cycle was realized with a flow cytometer from Luminex (Guava easyCyte 6HT-2L) and analyzed by CellCycle GuavaSoft 4. 5 software. Recording excitation and emission wavelengths were 488 and 785 nm, respectively. Five thousand events were analyzed for each sample. At least three independent experiments were carried out. For data comparisons and statistical analyses, 2-way ANOVA and Tukey's multiple comparisons test were used (GraphPad Prism v8). A p value < 0. 05 was considered statistically significant.
Incucyte with Cell-by-Cell Detection NCI-H2030-CC and NCI-H1792-CC cell lines were seeded at 1500 cells/well in 96-well plates in a complete medium for 24 h. The compounds were added at different dilutions to obtain a final percentage of 0. 2% DMSO. Cells were then placed in INCUCYTE S5 (Sartorius, Göttingen, Germany). Photos were taken every 24 h at 10×. Data analysis was performed with a cell-by-cell adherent module with the IncuCyte software v. 2022A, as indicated by the supplier's recommendations.
Post Translational Modification (PTM) Scan Analysis NCI-H2030 cells were seeded in a complete medium at 200,000 cells in 500 cm 2. After 72 h, compounds were added to the dishes. After 24 h incubation, cell lysis was realized according to the PTM scan urea protocol provided by CST. This experiment was realized three times for each condition. Samples extracts were sent to CST for PTM scan studies characterized by detecting phosphorylated tyrosine, serine, and threonine. Phosphorylated tyrosine (pY) was detected via immunoprecipitation, and phosphorylated serine and threonine were detected via Immobilized Metal Affinity Chromatography (IMAC). PTM scan data were processed by CST. Log2FC was calculated for each peptide expression, comparing each treatment condition against DMSO-vehicle control.
Tumor perpendicular diameters were measured twice per week with a caliper, and tumor volume (V) was calculated according to the following equation: V (mm 3 ) = (d 2 (mm 2 ) × D (mm))/2, where d is the smallest and D the largest perpendicular tumor diameters. A contrast analysis using Bonferroni-Holm correction for multiplicity following a two-way analysis of variance (ANOVA) { XE "Anova" \f Abbreviation \t "analysis of variance" } with factor treatment and day (repeated) was performed on tumor volume changes from baseline, to compare globally and at each day, all treated groups to the control group and all treated groups with the combination group. A probability of less than 5% (p < 0. 05) was considered significant. Statistical analysis was performed using EverStat6 software.
Data Availability Statement: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral. proteomexchange. org (accessed on 15 February 2023)) with the dataset identifier PXD039726 and to the jPOSTrepository (https://repository. jpostdb. org (accessed on 15 February 2023)) with the dataset identifier JPST002012. The transcriptomic data from RNA-Seq have been deposited to GEO with the dataset identifier GSE224439. These data are scheduled to be publicly available on 9 February 2023 at: https://www. ncbi. nlm. nih. gov/geo/ query/acc. cgi?acc=GSE224439 (accessed on 9 February 2023).
Introduction The Mars 2020 Perseverance rover is the first Mars mission that has been able to return acoustic data in the audible range (i. e. 20 Hz to 20 kHz) from the surface, notably from a microphone that is part of the SuperCam instrument  (Maurice et al. , 2022). Among the sounds recorded are wind and turbulence noise and various equipment operations. Most prominent among these is the sound of the Ingenuity helicopter. This paper documents the acoustic features of helicopter flights and their relation to flight parameters and ambient conditions. Because the source characteristics are somewhat known, the sounds are of potential interest as a probe of the near-surface atmosphere (e. g. Ingård, 1953; Piercy et al. , 1977). Ingenuity (Fig. 1 ) is a 1. 8 kg coaxial helicopter with two-bladed rotors that spin at nominally 2537 rpm (see e.
A summary of the relevant flight characteristics is given in Table  1 : additional data, including the start/end location referenced to a standard Jezero map projection, are provided in Appendix 1. The helicopter coordinates were derived by registering helicopter navigation camera mosaics to an orbital HiRISE basemap. The geometry of the flights is illustrated in Figs. 2 3 4 5. An important additional dataset for interpreting the acoustic data is the helicopter navigation camera images. The down-looking greyscale images are used in real-time on board the helicopter where successive images are cross-correlated to derive the velocity over the ground. A subset of these images is downlinked via the rover to the ground after the flight. These images can be mosaicked and a rather precise position history derived.
On the other hand, other experiments can be envisaged, which would comply with the >50m safety policye. g. having the vehicle hover at some altitude in a fixed location might permit probing of the winds above the ground via Doppler effects. Experiments with rotor operation in a landed configuration (e. g. with low collective pitch so as not to develop much lift) could be of interest at short ranges, yielding a comb of emitted tones with a different propagation geometry from hovering flight. Supercam microphone data may be obtained at the NASA Planetary Data system Perseverance archive (https://pds-geosciences. wustl. edu/missions/ mars2020/). Data are in the Supercam bundle, and 'Raw' (Engineering data record -EDR) and 'Calibrated' (CDR) data volumes are available: the latter are likely most appropriate for most users.
Since SuperCam's data handling system is natively set up for image data, the acoustic data are archived in Flexible Image Transport Format (FITS) files, for which readers exist in many data processing packages (e. g. R, IDL, Matlab etc. ). Dedicated freeware readers also exist, e. g. fv (https://heasarc. gsfc. nasa. gov/ftools/fv/). For the convenience of acousticians and the public, raw sound records (. wav) files are also made available. The CDR data file identifiers are shown in Table  A2. Note. Note: Flight 7 was intended to be executed on Sol 105, and this Supercam microphone observation was initially planned to observe it. However, a watchdog timer anomaly on the helicopter aborted the flight which was then deferred until Sol 107 and to avoid complexity (this was the first flight after the flight 6 anomaly) and the microphone observation was not replanned.
Acknowledgements RL is supported by the  Mars   2020 Project SuperCam investigation , via contract # 1655893  with the  Jet Propulsion Laboratory. We thank the  Mars 2020 Project  for supporting acoustic observations and helicopter operations. Bart Hibbs of Aerovironment is thanked for discussion of the high frequency noise on the Terry demonstrator. Aimee Quon  of  JPL  is thanked for confirming some details of test chamber sound recording. RCW was supported by  JPL  contract # 1681089. B. C. is supported by the  Director's Postdoctoral Fellowship  from the  Los Alamos National Laboratory , grant  20210960PRD3.
53BP1 foci size comparison Foci area measurement offers an insight into the extent of the damage, has been previously used to study the impact of radiation quality of DNA DSB damage  (Ward et al 2003 , Marková et al 2007) , and has been shown to reasonably correlate to the LET of the ions  (Costes et al 2006). 53BP1 foci area measurements were done using the particle counter function of the Image J image Analysis program  (Schindelin et al 2012 , Rueden et al 2017). Briefly, the length in pixels on an image was calibrated in micrometres by using the scale function in Image J and option 'global' was checked so that same setting could be applied to all images. Images with 53BP1 foci (FITC channel only) were threshold-adjusted so that only the foci were visible in the image. After adjusting the threshold, the 'Analyze particles' options was used to check each focus.
The total number of foci analysed was at least 100 for each dataset. We then compared the 53BP1 foci area measurements in the cells exposed to laserdriven carbon ions and 225 kVp x-rays. 2. 6. Relative foci induction RBE, which is defined as the biological effectiveness of any particular type of radiation relative to reference radiation such as gamma or x-rays, has been shown to be a very useful parameter for optimizing ion beam radiotherapy  (Carabe et al 2013 , Jones et al 2018). While the cell-killing RBE is mainly utilized in such studies, here, we have used an alternative quantity named relative foci induction (RFI), which is simply the ratio of the values of carbon ions-induced 53BP1 foci to the x-rays induced foci at any given time after irradiation. This provides a comparative overview of the repair of DSB damage induced by x-rays and carbon ions.
Funding and acknowledgments The authors acknowledge the funding received from the  Engineering and Physical Sciences Research Council (EPSRC) , through Grants  EP/K022415/1 ,  EPJ500094/1  and  EP/P010059/1. This work has also been partly supported by project  18HLT04   UHD pulse , which has received funding from the  EMPIR  programme cofinanced by the Participating States and from the  European Union 's  Horizon 2020 Research and Innovation Programme. KMP acknowledges support from  Brainwaves NI, Northern Ireland. Aaron McMurray  acknowledges the funding support provided by  Department for the Economy, Northern Ireland. Authors are also grateful to  Prof Anthony J Chalmers ,  University of Glasgow  and  Prof Colin Watts ,  University of Birmingham , for providing the E2 cells. We further acknowledge the Biolab access and support provided by  Dr.
Statistical tests Data were reported as the mean ± SEM of at least three experiments. Statistical significance (p <0. 05 or less) was determined using Student's t test or analysis of variance (ANOVA) as appropriate and performed with GraphPad Prism software (GraphPad Software, San Diego, CA, USA). Values of p are indicated as follows: *p <0. 05; **p <0. 01; ***p <0. 001; ****p <0. 0001; n. s. , nonsignificant.
Given that those murine tumours were found to be transcriptionally close to human mesenchymal HBs,  12  we were prompted to explore fascin-1 expression in human HBs. Fascin-1 is a marker of embryonal contingent in human HB To analyse fascin-1 expression in human HBs, we first resorted to public datasets. 3, 6, 21 Doing so, we found that fascin-1 mRNA is specifically expressed in the C2-subtype of HBs that corresponds to poor-prognosis tumours, with no obvious difference between C2A and C2B subtypes (Fig. 6A ). As observed in mice, fascin-1 mRNA expression correlated negatively with markers of differentiated hepatocytes such as HNF4a, APOC3, GJB1, and CLDN1 (Fig. S8A ). Moreover, in the cohort used by Sumazin et al. 21 to classify HBs in three risk-stratifying molecular subtypes, we found that fascin-1 is significantly more expressed in high-risk and intermediate-risk tumours than in low-risk tumours, indicating that high-fascin expression is associated with poor-prognosis subgroups (Fig.
Acknowledgements We thank  Dr D. Vignjevic  ( Curie Institute, Paris, France ) for Fascin-1 DNA constructs. We thank the plateforme  GenomEast of Strasbourg (Strasbourg, France ). Microscopy was done in the  Bordeaux Imaging Center , a service unit of the  CNRS-INSERM and Bordeaux University , member of the national infrastructure  France Bio Imaging , with the help of  Dr Philippe Legros  for STED analysis. We thank  Anne-Aurélie Raymond  ( INSERM U1053, Bordeaux, France ) for her help in transcriptomic data analysis. We thank the  department of Pathology  and the  Centre de Ressources Biologiques of the University Bordeaux Hospital  for human HB sample stains. The graphical abstract was created with  BioRender. com.
Bacterial growth was estimated by counting the number of colony-forming units (CFUs) in the first isolation plates and classified according to the standard laboratory operating procedures of the laboratory performing the analysis. Specifically, bacterial growth was considered as low (1-10 CFU/10 µL), moderate (11-30 CFU/10 µL),), or high (≥31 CFU/10 µL). Macroscopic observation of colonies, Gram stain, cellular morphology, growth on selective medium, catalase, oxidase, mobility tests, and coagulase tube test were used for the identification of the bacterial genera. Bacterial species identification was carried out via MALDI-TOF MS: Microflex LT instrument (MALDI Biotyper, Bruker Daltonics, Billerica, MA, USA) using the FlexControl software (version 3. 3, Bruker Daltonics, Billerica, MA, USA).
Data Analysis The analysis, including classification of the sequences in OTUs (Operational Taxonomic Unit) with 97% similarity and taxonomy assignment, was performed in Qiime2  [29] , following the Qiime2 standard operating procedure for MiSeq data. Specifically, paired-end reads were assembled and assigned to their original sample based on the barcode. Primer sequences and barcodes were then removed. For the denoising procedure, the Deblur method implemented in Qiime2 was used. Alpha diversity and Beta diversity were measured using Qiime2, as well as all the core metrics. Taxonomy was retrieved using BLASTn rRNA typestrains; a 16S ribosomal RNA database and sample bacterial population was assessed using hand-made R procedures. Data analyses were further conducted using R ver. 4. 2. 2 (Vienna, Austria).
Methods Animals and study design. In an initial cohort (cohort 1), male C57BL/6J mice were implanted with PA-C10 and HDX-11 radiotelemetry devices (Data Sciences International [DSI]) a week before any dietary manipulations commenced, during which they were individually caged. A 4-factor cosine curve was fitted to the repeating pattern of BP  (73, 74)  as detailed in Supplemental Methods. To limit potential probe malfunctions during mouse handling, this group followed the dietary interventions, but their blood/urine was not sampled. Diets were prepared from powdered rodent diet (Teklad Diet, TD. 08251, Envigo) -being nominally K + , Na + , and Cl -free -with ionic compounds (Sigma-Aldrich) added back to generate modified diets. Twelve-week-old mice were fed a control diet of KCl (1. 05% K + ) and NaCl (0.
HCTZ and amiloride were prepared from solid by dilution in DMSO and then further diluted in sterile physiological saline before injection. Tail cuff plethysmography. In a second cohort of mice (cohort 2), conscious BP was recorded from the tail using an occlusion cuff and volume-pressure recording (VPR) sensor (Coda equipment, Kent Scientific), as detailed in Supplemental Methods. LC-MS/MS and bioinformatics. LC-MS/MS and bioinformatics were performed as described  (75)  and in detailed in Supplemental Methods. The MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD035354. Statistics. Statistical information is detailed in Supplemental Methods, with relevant statistical tests described in figure legends. Study approval.
Acknowledgments We thank  Tina Myhre Pedersen ,  Inger-Merete Paulsen ,  Christian Westberg  (all from the  Department of Biomedicine, Aarhus University ) and  Ingrid van den Berg  ( Erasmus Medical Center, the Netherlands ) for technical support. We thank  Cristina Esteva Font  ( Department of Biomedicine, Aarhus University ) for slide scanning. The project was funded by the  Leducq Foundation  ( 17CVD05 ), the  Novo Nordisk Foundation  ( NNF21OC0067647 ,  NNF17OC0029724 ,  NNF19OC0058439 ), and the  Independent Research Fund Denmark. Address correspondence to:  Robert A. Fenton , Aarhus University, Institute for Biomedicine, Wilhelm Meyers Allé 3, Building 1233, DK-8000 Aarhus C, Denmark. Phone: 45. 28992149; Email: robert. a. fenton@ biomed. au. dk.
| TE contents in mafic and ultramafic rocks Here, we considered the nickel, chromium, copper and zinc contents of basalts from seven large igneous provinces (LIP) with at least a partly continental occurrence. Their geographical extent makes them the most probable rock sources for ERW, and the availability of large geochemical datasets on these LIP allows for robust estimations of each TE central tendency and dispersion. The total elemental contents (parts per million) in these mafic rocks were obtained using the Geochemistry of Rocks of the Oceans and Continents (GEOROC) database from the Max Planck Institute recently migrated to Göttingen University (https://georoc. eu/georoc/). Basalts from the following prominent LIP across the globe were included: Central Atlantic magmatic province (CAMP), Paran a-Etendeka traps, Karoo-Ferrar LIP, North-Atlantic igneous province (NAIP), Deccan traps, Siberian traps and Emeishan traps (Figure  1 ).
The TE contents of three major ultramafic rocks (lherzolite, dunite and harzburgite) were also extracted from the GEOROC database and were used for the sake of comparison. For each TE and rock source, values beyond 1. 5 times the interquartile range were discarded as outliers  (Tukey, 1977). Mean values for each LIP and the overall mean for basalts and ultramafic rocks were calculated for each TE (Table  S1 ).
, 2015; Beerling et al. , 2018). Our results suggest that copper may be particularly problematic. For all investigated scenarios, copper is F I G U R E 2 Nickel, copper, chromium and zinc content in basalts from several prominent continental large igneous provinces extracted from the GEOROC database (https://georoc. eu/georoc/) and represented as density plots. For each element, the mean content for basalts of each province is represented as a vertical black line and the overall basalt mean is represented as a dashed blue line. For comparison, the overall mean trace element content for common ultramafic rocks (lherzolite, dunite and harzburgite) extracted from the GEOROC database are given in red. CAMP, Central Atlantic Magmatic Province; NAIP, North Atlantic Igneous Province. indeed the first element exceeding regulatory limits.
ACKNOWLEDGEMENTS The authors would like to thank  Andrew Gray  for the English editing,  Dr. Diana Dmitrieva  from  Saint-Petersburg Mining University  and  Dr. David Zakharov  from  Western Michigan University  for their precious help with Russian regulations as well as  Dr. Qing Chen  from  China Agricultural University  and  Dr. Yansong Yin  from the  Chinese Embassy in Switzerland  for their help in the regulatory exploration of Chinese regulations. Open access funding provided by the  University of Lausanne. Open access funding provided by the  University of Lausanne.
as most of the flights in ECLIF3-2 were performed in ice-subsaturated conditions either designed as pure emission flights or in sublimating contrails, for which a quantitative data analysis of ice particles remains challenging. The first ever built Airbus A350-941 (registration: F-WXWB) equipped with two Rolls-Royce Trent XWB-84 engines and operated by Airbus served as the emission source aircraft. Fuel was supplied selectively from the two wing fuel tanks containing a reference fuel and 100% HEFA-SPK, respectively. This allowed for in-flight switching between two fuels for each engine and the operation of both engines on a single fuel using cross-feed valves. The DLR Dassault Falcon 20-E5 research aircraft followed the emission source aircraft to measure exhaust gases, volatile and non-volatile aerosol particles, and contrail ice particles.
Instrumentation and data evaluation The DLR Falcon research aircraft is a Dassault Falcon 20E5 twin-engine business jet class aircraft, which has been highly modified to accommodate a multitude of atmospheric measurements. The airframe is built sufficiently robust to enable measurements in the high-turbulence regime behind large passenger aircraft. An extensive onboard instrumentation provides highly resolved aircraft position and dynamics data, as well as data on ambient meteorological conditions  (Bögel and Baumann, 1991; Krautstrunk and Giez, 2012; Giez et al. , 2017 Giez et al. , , 2020 Giez et al. , , 2021 Giez et al. , , 2023)). These meteorological parameters such as temperature and pressure serve as input values for several calculated quantities discussed in this work. Horizontal aircraft distances were determined as the great circle distances based on WGS84 GPS latitude and longitude of both aircraft while vertical distances were determined as the difference between the WGS84 GPS altitudes of the two aircraft, resulting in a triangulated total distance.
The CoCiP model CoCiP is a Lagrangian model that traces individual contrail segments forming along given flight routes  (Schumann, 2012). For the present application, CoCiP prescribes the ambient atmosphere using numerical weather analysis data of the Integral Forecasting System (IFS) of the European Center for Medium-Range Weather Forecasts (ECMWF) with 0. 125 • spatial and 1 h temporal resolution, on model levels with about 300 m vertical resolution at the given levels. The model simulates the contrail as forming behind the Airbus aircraft for given flight route, speed, fuel consumption, and fuel hydrogen content, resulting in a soot emission index computed for the given engine type as in  Teoh et al. (2022a). In this application, CoCiP uses the Falcon-measured relative humidity changed by the difference in relative humidity in the IFS values at the contrail position and at the Falcon position (RHi at Falcon position as measured plus RHi at contrail position as derived from IFS data minus RHi at Falcon position as derived from IFS data).