dataesr/scientific-paragraphs-categorization huggingface dataset:
The results presented above are based on analyses conducted with data of the rats without any signs of underlying illness. Dioxygen consumption (VO 2 ), carbon dioxide production (VCO 2 ), food and drink intakes, and daily activity of control and vitamin D-depleted rats were measured using a PhenoMaster/Lab-Master four-cage TSE System (Bad Homburg, Germany) at the end of the 9-month experimental period. Rats were housed individually in cages for indirect calorimetry. Energy expenditure was calculated using Weir's equation (31). Food and drink consumption was measured using a weight sensor. Spontaneous activity was assessed using a three-dimensional meshing of light beams. On the day of sacrifice, the remaining control (n = 7) and vitamin D-depleted (n = 9) rats were weighed and sacrificed by exsanguination under anesthesia by inhalation with a mix of isoflurane and oxygen.
Mice were weighed once every two weeks. Forearm grip strength was measured at 23 months of age, using a calibrated grip strength device (Panlab, Cornella, Spain). Body composition was measured by DEXA scan using a PIXImus imager (GE Lunar, Madison, WI). Six mice were removed during the study or showed pathologies at necropsy. The results presented below are based on the analyses conducted with data of the mice without any signs of underlying illness. At the end of the study, the remaining control (n = 10) and vitamin D-depleted (n = 9) mice were sacrificed under anesthesia by inhalation with a mix of isoflurane and oxygen, and blood was collected. Hindlimb skeletal muscles were removed, weighed, snapfrozen in liquid nitrogen, and stored at -80 °C until later analysis. Mouse experiment 2: generation of human skeletal actin-MCM-VDRfl/fl transgenic mice.
2 software (Fujifilm Corporation). Ponceau S staining was used to normalize protein loading between samples. Data are expressed as fold change vs. control group value. RNA and DNA analysis. Total RNAs and nuclear/mitochondrial DNA were extracted using Tri-Reagent (Euromedex, Mundolsheim, France) according to the manufacturer's instructions and as reported in our previous publication  35. Total RNAs and mitochondrial and genomic DNA concentrations were quantified by measuring optical density at 260 nm  15, 35. Concentrations of mRNAs corresponding to genes of interest were measured by reverse transcription followed by PCR using a Rotor-Gene Q system (Qiagen, Courtaboeuf, France). Five micrograms of total RNA was reverse-transcribed using SuperScript III reverse transcriptase and a combination of random hexamer and oligo dT primers (Invitrogen, Life Technologies, Saint-Aubin, France).
3  and 5 , and Supplementary Fig. 3. Nuclear/mitochondrial DNA was isolated using Tri-Reagent followed by back extraction with 4 M guanidine thiocyanate, 50 mM sodium citrate, and 1 M Tris, and an alcohol precipitation as described previously by us  35. Mitochondrial DNA (mtDNA) content was determined by quantitative real-time PCR analysis using a Rotor-Gene Q system (Qiagen, Courtaboeuf, France). To this end, the levels of NADH dehydrogenase subunit 1 (ND1) (mitochondrial DNA) were normalized to the levels of beta-actin (genomic DNA). Data are expressed as fold change vs. control group value. The list of the primers used for real-time PCR amplification is reported in Supplementary Table  5. Mitochondrial enzymatic assays. Fifty milligrams of frozen rat plantaris muscle, mice gastrocnemius muscle, C2C12 myotubes or human primary myotubes were homogenized with a glass-glass Potter in 9 volumes of homogenization buffer (225 mM mannitol, 75 mM sucrose, 10 mM Tris-HCl, 10 m EDTA, pH 7.
4 µg/mL, or ascorbate 3 mM and N,N,N′,N′-tetramethyl-p-phenylenediamine (TMPD) 0. 5 mM. State 3 was obtained by adding 2 mM ADP. After each respiration experiment, the fibers were dried and weighed. Activities are expressed in natom O/min/mg of fiber  38, 40. Microarray analysis. RNA profiling in rat plantaris muscle and C2C12 myotubes was performed using a Rat GE 4x44K v3 Microarray Kit and a Mouse GE 4x44K v2 Microarray Kit, respectively (Agilent Technologies, Massy, France). Briefly, 200 ng of total RNA isolated from frozen muscle samples or C2C12 cells was labeled using the Low Input Quick Amp Labeling kit (CY3) (Agilent Technologies, Massy, France), and microarrays were hybridized and scanned following the manufacturer's instructions. Data extraction was performed using Agilent Feature Extraction Software 11.
5. 1. 1. Data quality analysis and processing was performed with bioconductor using Agi4x44PreProcess and Limma packages (Smyth GK, 2004). Background subtraction was performed using the Normexp correction with offset = 50. Quantile normalization was then applied. Features flagged in Feature Extraction as control, non-uniform outliers, saturating or too weak were excluded. Statistical analysis was performed on 26,902 probes for plantaris muscle samples and on 30,094 probes for C2C12 samples with the Limma package. Probes selected for further analysis had a p-value < 0. 05 for plantaris muscle experiments and a Benjamini-Hochberg adjusted p-value < 0. 05 for C2C12 experiments. Functional enrichment analysis was performed with g Profiler using a list of downregulated genes differentially expressed in plantaris muscles of vitamin D-depleted old rats and upregulated genes differentially expressed in C2C12 myotubes treated with 10 nM of 1,25(OH)2 vitamin D3.
Functional enrichment results were filtered and only the top 10 annotations for Gene Ontology BP, CC, KEGG, and Reactome were kept for functional enrichment visualization using Cytoscape (v3. 8) with Enrich-mentMap and AutoAnnotate plugins  21, 41. Datasets are available from the GEO database (GSE67274 and GSE64803). Statistics and reproducibility. All data are presented as means ± SEM. For the human vitamin D supplementation study (interventional study), the sample size was calculated to detect the difference of appendicular skeletal muscle mass at 6 months (primary efficacy endpoint) between the two treatment arms with a two-sided type-I error of 0. 05 and a power of 80%. Statistical analysis for the human interventional study, the long-term vitamin D depletion rat experiment, the HSA-MCM-VDRfl/fl transgenic mice study and the cell culture studies with two conditions was performed using a two-tailed unpaired t test.
Data availability Microarray analysis data of rat plantaris muscle and C2C12 myotubes have been deposited to the Gene Expression Omnibus (GEO) database (GSE67274 and GSE64803, respectively). Any remaining information can be obtained from the corresponding author upon reasonable request. All requests will need to specify how the data will be used and will require approval by co-investigators. Uncropped and unedited blot/gel images are listed in Supplementary Fig. 4.
With an aim to afford a comparison with all previously published transient spectroscopy studies, 5,9,14-18 we Scheme 1. (a) General Photodynamical Scheme of OCP Photoactivation Mechanism a a In the dark, two sub-populations of the closed OCP O are present, a "normal" one and a red-shifted one (the size represents their contribution, Figure  S2  in Supporting Information). (b) OCP structure (reproduced from PDB ID 3MG1) comprises a fully α-helical NTD, featuring a fold that is unique to cyanobacteria, whereas the CTD has a mixed α/β architecture and belongs to the NTF-2 family. 8 His-tags can be attached to the Nterminal extension or to the C-terminal tail investigated light-induced excited-state dynamics upon excitation by either 470 or 540 nm light. Stationary irradiation experiments were also performed at the two excitation wavelengths.
The transient spectra were registered with 1 nm per pixel and by averaging 500 supercontinuum spectra with and without excitation, respectively. The entire set of the pump-probe time delay points was repeated four times to ensure data reproducibility, then the data were inspected and averaged. Moreover, to ensure that all data sets are comparable to each other, they were measured in one experimental session, in identical conditions except for varied parameters (like pump energy, explicitly given). The pump beam was depolarized to avoid anisotropy effects. The sample temperature was set to 22 °C. The stability of the sample was checked by comparing the stationary UV-vis absorption spectra measured before and after the experiments.
5 times larger for the N-tagged OCP). This difference in OCP R yield could stem either from different excited-state dynamics, leading to different P 1 formation quantum yield, or from changes in the yield of subsequent ground-state species forming in the ns-ms time scale (Scheme 1, carotenoid translocation and domain separation dynamics). 9, 11, 12 To split a difference between the two hypotheses, a more detailed analysis of the early stages of the photoinduced processes is needed. The ultrafast photodynamics of N-tagged OCP was studied upon 470 and 540 nm excitation wavelengths. The excitation pulse energy was initially set to 0. 4 μJ at 470 nm and to 0. 8 μJ at 540 nm, which ensures being in the linear photoexcitation range (Figure  4 ), while getting enough S/N to characterize P 1 and keeping the data free of additional signals arising when higher energy is used (detailed discussion in the next section).
Global Analysis of Transient Absorption Data in the Linear and Nonlinear Excitation Regime For the 540 nm data sets, four exponential components convoluted with a Gaussian-shaped pulse of 110 fs (FWHM) and an offset for long-lived photoproducts (>10 ns) are required to obtain a quality fit of all kinetic traces. These components provide four characteristic time constants that can be used to describe the behavior of the different excited states (S 2 , ICT, S 1 , and S*) and the long-lived photoproduct P 1 , populated in the end of our time window (1 ns). As already mentioned, for 470 nm excitation, one additional component is needed, which is denoted as S ∼ (see Figure  S8 ). For all data sets, the first component around 100 fs is associated with the S 2 state, and also includes the growth of S 1 , ICT, and S*, overlapped with artefacts such as stimulated Raman and eventually any ultrafast intramolecular vibrational relaxation.
Study design The current study is embedded within the Energy for life after ColoRectal cancer (EnCoRe) study. This is a multi-center prospective cohort study initiated in 2012, in which patients diagnosed with stage I-III CRC at three hospitals in the south-eastern region of the Netherlands (Maastricht University Medical Centre+, VieCuri Medical Centre, and Zuyderland Medical Centre) are included. Eligible for participation were men and women above the age of 18, diagnosed with stage I, II, or III CRC. Exclusion criteria were stage IV CRC, inability to understand and speak Dutch, residence outside of the Netherlands, or the presence of comorbidities hindering successful participation (e. g. Alzheimer and visibility/hearing disorder)  [24]. Data available up to July 16th 2018 were used for the present analyses, including data from participants included at diagnosis (n = 459) and followed up with repeated measurements at 6 weeks (n = 396), 6 months (n = 348), 12 months (n = 287), and 24 months post-treatment (n = 208).
96) in healthy individuals  [26]. Prolonged sedentary time (hours/day) is derived by summing total daily time accrued in sedentary bouts with a duration of at least 30 minutes  [27, 28]. Although the device also measures total physical activity (all activities with an energy expenditure > 1. 5 METs), the monitor unfortunately has limited reproducibility to distinguish between light and moderate-to-vigorous physical activity  [26]. Therefore, LPA and MVPA were measured by means of a validated questionnaire, as described below. Accelerometer data were deemed valid with ≥ 10 hours of waking wear time per day; only participants with ≥ 4 valid days were included in analyses. Self-reported time spent in LPA and MVPA was measured at all timepoints (including at diagnosis) using the Short QUestionnaire to ASsess Healthenhancing physical activity (SQUASH)  [20].
Fatigue Data on fatigue were self-assessed using the well-validated and reliable European Organization for Research and Treatment of Cancer Quality of Life Questionnaire C30 (EORTC QLQ-C30) version 3. 0  [37] , as well as the validated comprehensive multidimensional Checklist Individual Strength (CIS)  [38, 39]. The fatigue symptom scale from the EORTC QLQ-C30 was linearly transformed to a 0-100 scale. The CIS is a 20-item questionnaire, with each item being scored on a 7-point Likert scale and consisting of four subscales: subjective fatigue (range in score: 8-56), concentration problems , reduced motivation (4-28), and activity-related fatigue  (3) (4) (5) (6) (7) (8) (9) (10) (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) (21). The total fatigue score (range: 20-140) was obtained by summing all item scores.
Lifestyle, clinical, sociodemographic factors Age, sex, and clinical information (i. e. cancer stage, surgery/chemotherapy/radiotherapy treatment, and tumour site) were retrieved from medical records. Self-reported data were collected on other factors, including current smoking status at all time points and highest attained education level at diagnosis. Comorbidities were assessed with the Self-Administered Comorbidity Questionnaire at all post-treatment time points  [40]. Total dietary energy intake was measured through 7-day food diaries collected at each post-treatment time point  [41].
Primary analyses: Longitudinal associations We applied linear mixed model regression to analyze longitudinal associations of sedentary behavior, standing, LPA, and MVPA with anthropometric measures, using data collected between 6 weeks and 24 months post-treatment. Each of the exposure variables of interest, i. e. total sedentary time (per 2 hours/day), prolonged sedentary time (per 2 hours/day), standing (per hour/day), LPA (per 8 hours/day), and MVPA (per 150 min/week) were analyzed in separate models as a continuous exposure variables and separate models were run for each of the anthropometric measures as continuous outcomes (BMI, waist circumference, body fat percentage, MUAMC, and handgrip strength). A random intercept for each subject was added to all models. The use of random slopes was tested with a likelihood-ratio test; when the model t improved statistically signi cantly random slopes were added.
First, the path from total sedentary time and MVPA to fatigue, independent of body composition (i. e. the direct association). Second, the path from total sedentary time and MVPA to fatigue that passes through potential mediating variables of body composition (both BMI and handgrip strength), which is referred to as the speci c indirect association. The sum of the speci c indirect association through BMI and the speci c indirect association through handgrip strength is referred to as the total indirect association. The sum of the direct and total indirect associations is referred to as the total association. Model 4 of the PROCESS macro version 3. 5 for SPSS was used to assess speci c indirect, total indirect, direct, and total associations of total sedentary time and MVPA with fatigue. A 95% percentile bootstrap con dence interval for the indirect effect using 10,000 bootstrap samples was generated.
Nevertheless, the monitor enabled us to investigate the separate association of standing with body composition outcomes. For LPA and MVPA, questionnaire data were used resulting in potential reporting bias. For example, large differences can be seen when comparing the amount of self-reported LPA in this study to previous accelerometer-based research in cancer survivors  [17]. In addition, the limited response rate at diagnosis (45%) might have resulted in selection bias. Participants with worse body composition and lower levels of physical activity and higher levels of sedentary behavior may have been less likely to participate, potentially having led to an attenuation of associations. Finally, we cannot rule out the possibility of false positive hypothesis tests due to the large number of tests performed.
Acknowledgments We would like to thank all participants of the EnCoRe study and the health professionals in the three hospitals involved in the recruitment of study participants:  Maastricht University Medical Centre+, VieCuri Medical Center and Zuyderland Medical Centre. We would also like to thank the MEMIC center for data and information management for facilitating the logistic processes and data management of our study. Finally, we would like to thank the research dieticians and research assistant who were mainly responsible for patient inclusion and performing home visits, as well as data collection and processing.
Plasmaspheric QP Observations Over the course of the nearly 2-year mission, there were at least 45 episodes of quasi-periodic emissions detected by the BBR. QP emissions were identified as episodes of clear unambiguous periodic events (i. e. , broadband bursts or updrift tones) detected by both the electric antenna and search coil magnetic antenna in the survey data. The survey data has a temporal resolution of 30 s, so the QP episodes presented herein typically had events with periodicities greater than 1 min. We note that the DSX detection rate of QP episodes is less than that reported by  Němec et al. (2018)  using the Van Allen Probes. However, our selection criteria of having both an unambiguous E and B signal together may be a more constraining limit. Of the 45 episodes, about 66% of the these occurred in a frequency range between 1 and 4 kHz in the band described previously by  Němec et al.
Acknowledgments We are very grateful from the support of the DSX project team and especially the operations team that kept the complex spacecraft flying successfully for 2 years. This work was supported by the  Air Force Research Laboratory , and we want to also gratefully acknowledge the  AFRL  management team that provided resources for the mission and its extensions. The openness and sharing between the WPIx consortium partners, encouraged by its leadership team, has benefited the overall project and continues to be greatly appreciated. We also want to thank the BBR instrument development team for building such a robust and low noise flight system.
Statistical analysis Statistical analyses were carried out using R  (R Core Team, Vienna, Austria, 2018). Normality and homogeneity of variance were analyzed by Levene tests. Comparisons of results from different conditions (treatment, age or both) were assessed using independentsamples Student's t-test, a one-way analysis of variance (ANOVA) followed by Duncan's test, or a two-way ANOVA, as described in the figure legends. Heat-map representations were obtained using the PHEATMAP package in R 1. 0. 12 after unidimensional hierarchical clustering by Pearson's correlation of mean-centered values of metabolites for different ages and treatments. To fit experimental data, parameters of non-linear regressions (logistic) were obtained using the non-linear least square function combined with Self-Starting Nls Logistic Model (SSlogis) function, both from R- STAT 3.
ACKNOWLEDGEMENTS TP benefited from a cotutelle PhD ( University of Bordeaux and University of the Basque Country ) and thanks the  University of the Basque Country (UPV/EHU, Spain)  for his PhD grant during the execution of this work. This research was financially supported by the  Basque Government  ( IT-932-16 ) and the  Spanish Government  ( BIO2017-84035 -R co-funded by  Fondo Europeo para el Desarrollo Regional [FEDER ]). Analytics were supported by  MetaboHUB  ( ANR-11-INBS-0010 ) and  PHENOME  ( ANR-11-INBS-0012 ) projects. Technical support was provided by  Cedric Cassan ,  Ana Renovales  and  Mandy Bordas. The authors also thank  SGIker (UPV/EHU ,  FEDER ,  EU ) for the technical and human support provided.
The proposed approach in the paper is dedicated to enrichment of CAD models storage in PLM (Product Lifecycle Management) systems or archive databases. The paper considers low level CAD models (i. e. frozen geometry and without CAD model tree) based on standards such as STL, IGES and STEP AP203 first edition where the CAD model tree is absent. The paper also highlights the differences in semantic richness between these standards and their degrees of industrial implementation. STEP AP242 standard is considered as a high level representation for CAD files. The paper aims to review the literature that addresses the methods for semantic enrichment of CAD models by using ontologies. The future challenges and one possible research direction are then discussed. A first application called VAQUERO for CAD enrichment using an ontology based on STEP AP242 standard is proposed.
galia. com/). • An senior expert specialised in CAD/PLM integration of the Inetum company (https://gfi. world/fr-fr/) The exchanges were formulated through direct interviews by conference call and e-mail exchanges. Questions were formulated to determine what formats they use in primary review, and what are their expectations regarding the usage of CAD models. Their answers indicated that there are mainly five major expectations: • Query and retrieval of CAD models: access to CAD models is essential in order to use it or to perform engineering activities. Accessing to CAD models is made through PLM systems (primary view) or CAD database. • Change, revision and annotation of CAD models: To save time when making changes or extracting information contained on an existing design regardless of the used CAD formats, CAD models must be properly annotated by containing any expert information; • Visualisation in secondary view of CAD models: The user should be able to view the CAD model and the CAD model tree related to its design; • Technical interoperability (sharing) of the information con- tained in the CAD models: Any semantic information in primary view related to the design such as a product's features, constraints, and parametric information must be shareable; • Archival CAD models by using CAD catalogues or CAD archives by indexing rules.
3D PDF 3D PDF is the name of the PDF file format, which also provides native support for 3D data  (Kahl et al. , 2017). Published as the international standard ISO 24517-1 (PDF/E), it uses U3D  (Nan et al. , 2018)  and PRC (http://3dpdfconsortium. org/) to store CAD geometry representations. However, this file format is not yet implemented in all CAD systems. In December 2017, the STEP and PDF ISO working groups formed a joint ad-hoc committee that proposed modifying the PDF standard to add STEP AP242 as a 3D stream.
STEP Standards such as ISO 10303, known as the Standard for Exchange of Product model data (STEP), deal with product structure, geometry and parts-related information  (Pratt, 2005). In STEP's modular approach, information models form modules and integrated resources, from which specific content standards (application protocols or APs) such as AP203 (Configuration controlled 3D design of mechanical parts and assemblies) and AP214 (Core data for automotive mechanical design processes) are developed. They are still evolving to meet the needs of modern CAD with AP242 ed2, CAE with AP209 ed2, CAM with AP238 and PDM with AP239 ed3. These pairings represent the implementable data specification of STEP. An extension of STEP, called STEP AP242: "Managed Model-based 3D Engineering", is motivated by the necessity for the long term archiving of 3D data.