dataesr/scientific-paragraphs-categorization huggingface dataset:
RNA-seq data analysis Three biological replicates of CSC-CON (SW620 CSC non-treated control) and CSC-CMK (SW620 CSC treated with Decanoyl-RVKR-CMK) were used for the transcriptomics analysis. HISAT2  [34]  was used to align the 151 bp paired-end RNA-seq reads for each of the samples to the human reference genome GRCh38. The Cufflinks  [35]  was used to assemble the mapped reads into possible transcripts and generate a transcriptome assembly, and the counts of aligned reads to each gene were evaluated using HTSeq  [36]. In-house software was used to merge the expression results into a single text file to be used in the downstream analysis  [37]  in Matlab (MathWorks). Quantile normalization was performed to equalize the data and the data was further stabilized through the log 2 transform of the data plus one.
Gene Ontology (GO) statistically significant enrichment analysis of DEGs The GO terms were taken from the curated collection of molecular signatures (gene set collection C5) of version 3. 0 of the Molecular Signatures Database (MSigDB)  [39]. The statistical significance of the GO terms was analyzed as previously described  [38]  using an enrichment approach based on the hypergeometric distribution to estimate the significance (p-value) of the gene set enrichment. The multitest effect influence was tackled through control of the False Discovery Rate (FDR) using the Benjamini-Hochberg method for correcting the initial p-values with significance threshold α GO = 0. 05.
Gene-coverage count track plots We sorted the alignment bam files with samtools  [40]  and produced the bed files with bedtools  [41]. We used our previously developed function in Matlab (MathWorks)  [42]  that for each gene of interest takes the exon boundary information from the basic annotation file in gtf format from Gencode (https://www. gencodegenes. org/human/) version 33, and plots the gene-coverage count track plots, preserving the same scale for the tracks of the same gene in all the samples.
(caption on next page)  D. Gerovska  et al. BBA -Molecular Cell Research 1868 (2021) 118912 Acknowledgements This study was supported by  doctoral program Euskampus. Further funding was provided by the  University of the Basque Country, Spain , Project ref. :  PPGA20/22. D. G. and M. J. A. -B. have been supported by  Grants of the Ministry of Economy and Competitiveness, Spain ,  MINECO  Grant  BFU2016-77987-P  and  Instituto de Salud Carlos III  ( AC17/00012 ) Grant co-funded by the  European Union (Eracosysmed/H2020  Grant Agreement No. 643271 ) and  European Union  ( H2020-FETOPEN, Project 899417 ). D. G. , M. J. A. -B. and I. B. have been supported by  Grants Health Department of the Basque Government (Spain) , RIS3 call, Exp. No. 2020333039  and  2020333001. This research was also funded by  SIRIC-Brio, La Ligue Contre le Cancer and Region Nouvelle Aquitaine  to AMK.
Fluorescence microscopic imaging The worms were immobilized using a 5 mM solution of levamisole in an M9 buffer and mounted on 2% agarose pads on glass slides. The images were acquired using a Lionheart Fx Automated Live Cell Imager (BioTek, VT, United States) under non-saturating exposure conditions. For each condition, 25 worms from five fields were observed and imaged. The quantification of the Green fluorescent protein (GFP) expression was analyzed using Image J software (Wayne Rasband, NIH, United States).
Acknowledgements This study was supported by the  National Key Research and Development Program of China  ( 2017YFC1702103 ),  National Natural Science Foundation of China  ( U19A2013 ), the  Science and Technology Development Plan Project of Jilin Province  ( 20190101010JH ,  202002053JC ), the  National Key Research and Development Program of China  ( 2019YFC1709900 ) and the  Administration of Traditional Chinese Medicine of Jilin Province  ( 2020172 ).
Patients and methods This cross-sectional, comparative case-controlled pilot study was performed in the home parenteral nutrition pediatric unit of a university pediatric hospital between March 2014 and June 2015. Patients. Inclusion criteria were children receiving home PN for more than 2 years for intestinal failure, which seems a sufficiently long period to evaluate the impact of PN on bone metabolism; older than 9 years of age due to technical limitations of HR-pQCT (need to have a perfectly still child), and with regular follow-up in a university HPN center. Exclusion criteria were congenital bone diseases (2 patients with McKusick syndrome) and corticosteroid use for more than one month during the 6 previous months (1 patients with rheumatologic inflammatory disease). For each assessment, the patient's anthropometric data were collected: birth term, birth height and weight, gender, weight, height, BMI, and Tanner status.
For the same patient, all anthropometric measurements were performed by the same operator during follow-up appointments in a standardized manner: for height, with a wall height chart with increments of 0. 5 cm; for weight, with a calibrated scale with increments of the nearest 0. 1 kg. The Z-scores were calculated for each value according to national data references  21. Tibia length was measured, the knee flexed at 90%, from the proximal margin of the medial malleolus to the proximal border of the medial tibial condyle (manually located) with a tape measure by the same trained operator. For each patient, IF characteristics and bone complication histories were obtained from medical files: IF etiology and intestinal residual length with or without ileocecal valve, fractures and bone pain. PN was formulated according to the child's individual needs.
Statistical analysis. Statistical analyses were performed using the SPSS Software. All eligible patients were included. Comparisons between patients and controls were performed using the nonparametric Wilcoxon signed rank test since the number of patients was low. Correlations between density, microarchitectural and biological parameters were computed with the Spearman bivariate analysis. All statistical tests were performed at the two-sided 0. 05 level of significance. Data are presented as median, minimum and maximum: med [min-max].
Results Subjects characteristics. We included 11 patients and 22 controls. Anthropometric and clinical data for patients and controls are summarized in Table  1. The median age of initiating PN was 17 (0-150) months, and this nutritional support was given for a median of 10. 3 (6. 4-18. 3) years at the time of this study. All patients receiving long-term PN had intestinal failure; etiologies are indicated in Table  1. Two patients at the time of examination had withdrawn PN since 4 months and 5 months respectively. Calories in parenteral nutrition represented a median intake of 77 (40-190) % of recommended dietary allowances. All patients also had oral supplementation: 100 000 UI of vitamin D 3 each 3 months. Median vitamin D3 intake in PN was 220 (0-250) UI/day. Table  2  summarizes the main PN parameters applied to this cohort.
Data analysis In the quantitative phase, data was extracted in Microsoft Excel 2010 (Microsoft, Redmond, WA, USA) and analyzed using STATA (version 12. 1 STATA Corp. , College Station, TX, USA). Key analytic outputs were the number (proportion) of children that were clinically assessed (each criteria presented separately) and the number (proportion) that underwent smear microscopy or rapid molecular tests to establish microbiological confirmation. It was operationally decided to include sputum microscopy for the assessment of microbiological confirmation. The STROBE guideline was followed for reporting the quantitative component of the study  [33]. In the qualitative phase, transcripts obtained were compiled and discussed among investigators to become familiar with the data. Manual descriptive thematic analysis was used  [34].
Acknowledgments The authors thank the  National TB Elimination Programme and National Health Mission of Madhya Pradesh (India)  for providing support and necessary guidance. We express our gratitude for our data collection team, comprising of  Mrs. Seema Gotiwale  (Project Coordinator),  Mr. Saurabh Singh  and  Mr. Saurabh Rajak  (both Field Data Collector). Disclaimer: The contents of this paper do not necessarily reflect the views of the institutions the authors are affiliated to.
ACKNOWLEDGMENTS We thank our collaborating partners in Cambodia: Reproductive and  Child Health Alliance ,  World Food Programme  and  Institut de Recherche pour le Développement. We would also like to thank staff at  DFPTQ ,  Teuk Thla Health Center in Phnom Penh and Kamchay Mear Hospital in Prey Veng  for their generosity and openness in providing venues and assistance during the study. Most importantly, we are grateful for the participants' time, willingness and curiosity to join the study. This study was funded by the following: The  University of Copenhagen ,  Denmark; Danida ,  The Ministry of Foreign Affairs, Denmark  through the  'WinFood'  project (Grant  57-08-LIFE ); The  European Commission  through the  FP7 project  ' Sustainable Micronutrient Interventions to Control Deficiencies and Improve Nutritional Status and General Health in Asia' (SMILING-Project reference 289616 ); The  Institut de Recherche pour le Développement (IRD) , France; CSB++ was donated by the  World Food Programme, Rome, Italy.
5 μl of desalinated water. The solution was stirred and left for 20 min to rest. The absorbance at 620 nm was determined with a spectrophotometer (CM 3500-d, Konica Minolta Sensing Inc. , Mahwah, US-NJ). Tests were performed in triplicate for each sample using three 3-ml flasks for each storage duration because the amount of soluble amylose is known to decrease with increasing storage time due to the more pronounced organization of the retrograded AM  (Patel et al. , 2005). Calibration was performed with a blank and with a sample containing 27% pure AM (Corn starch, Argo, Best Food, CPC International Inc. , Bergen, US-NJ). The percentage of AM was calculated from the absorbance of the sample multiplied by 27 and divided by the absorbance of the reference sample (27%). Three repetitions were performed for each data point.
An inverse Laplace transformation (ILT) was applied to convert the relaxation signal into a continuous distribution of T2 relaxation times. The T2 distributions were then deconvoluted, and each "peak" was modeled using an asymmetric normal law  ( Berman et al. , 2010). The software used was developed (in part) and implemented using MATLAB © R2014a (MathWorks, Natick, US-MA).
Environmental Scanning Electronic Microscopy Images Environmental Scanning Electronic Microscopy (ESEM) is an electron microscopy technique (Philips, Leuven, Belgium) capable of producing high-resolution surface images. ESEM scans the surface of the sample to be analysed with an electron beam to obtain data at the particle scale. Different detectors that reconstruct a three-dimensional image of the surface were used to analyze these particles. The crumb samples, stored at 4°C, were fractured into sizes of approximately 1x1x0. 5 cm using a knife and a hammer before the sample was quickly transferred to the SEM chamber. The interior surface of the samples was coated with an ultrathin coating of metal (gold) or carbon. A 2D image of the sample was displayed on a computer monitor. The crumb samples were scanned by a focused electron beam in a Philips XL30-ESEM system at an accelerating potential of 8 kV at 4°C.
Participants, research assistants, and study investigators were blinded to the randomized groups. Data analysts were necessarily unblinded during the analysis due to the primary analysis. 8 ocedures Participant demographic, socioeconomic, and health information were collected by healthcare workers at delivery, and by field workers at baseline (2 weeks postnatal), midline (12 weeks postnatal), endline (24 weeks postnatal), and at 1 year (52 weeks postnatal). Using calibrated instruments and standard protocols,  15  infant anthropometric measurements (weight, length, and head circumference) were collected. Length-for-age Z scores were computed using the WHO Anthro plug-in for SPSS. Standardized tests of infant neurological and cognitive development were collected by field staff at all four time points.
Covariates and tests of interactions. A set of theoretically motivated covariates was examined to determine possible inclusion in our primary analysis. The covariates included child sex, maternal and paternal highest level of education, household wealth index, and a standardized measure of infant growth status at 2 weeks postpartum (length-for-age Z-score). At the time of preregistration,  8  and based on the cognitive findings of Fattal-Valevski et al. ,  1, [3] [4]  we estimated that we would have power (1 -β error probability) > 0. 87 to detect small to medium effect sizes with our secondary outcomes of interest with a planned sample size of n = 320, or n = 80 per treatment arm. All analyses were performed in SPSS R Version 25 (2017, IBM Corp, Armonk, NY).
Sample characteristics The trial profile is shown in Figure  S1  (online only) and the participant baseline characteristics are shown in Table  1. At baseline, 335 families were participating in the study; usable cognitive data were available for 295 and 309 infants at 24 and 52 weeks, respectively, with migration being the main reason for loss to follow up. At birth, infants' anthropometric status was typically below WHO Z-score means in terms of length-for-age, a finding that is consistent with other data collected from many LMICs. 10, 20, 21 The majority of both the women and their husbands had at least a primary education level. Reflecting the success of randomization, there were no differences among the treatment groups for all characteristics except family wealth. All central analyses initially were run controlling for family wealth, but it was dropped from our presented results because it was a nonsignificant predictor in all models.
Acknowledgments We express our deepest gratitude to the mothers and infants who participated in this study. We thank the members of the study's scientific advisory board for valuable input on the study protocol (alphabetical order):  Drs. Megan Bourassa ,  Levente Diosady ,  Lisa Houghton ,  Arnaud Laillou , and  Annie Wesley. We thank  Dr. Ken Brown  for assistance and insight during study conception,  Dr. Geraldine Richmond  for her role in early protocol development,  Dr. Robert A. Brown  for logistical support, and  Keith Porter  for early input on project feasibility and implementation. We thank the following individuals from  Helen Keller International, Cambodia :  Rem Ngik ,  Leng Sotheth ,  Um Sarith ,  Bon Voeurth ,  Lay Dara ,  Chun Sokhan ,  Non Channak ,  Chhen Sokkhov ,  Prak Sotharoth ,  Choeung Dalin , and  Sreang Sambo  for help with recruitment, field coordination, and data collection.
Methods FG participants were recruited among the staff of Charles Foix geriatric hospital (Assistance Publique -Hôpitaux de Paris, France). The evaluation protocol was made of three steps: (i) a short tutorial to present the study context, the description of guidelinebased decision support modalities, and the introduction of the dashboard-with-gauge visualization on a simulated patient case, (ii) semi-structured discussion to question four dimensions: "Assessment of the dashboard", "Assessment of gauges", "Assessment of recommendations' display", and "Assessment of the global user interface", (iii) qualitative user assessment of usefulness, ease of use, ease of learning, and satisfaction through a short USE-derived questionnaire  [3]. Discussions between participants were audio-recorded. Data were analyzed using the six steps of the thematic analysis  [4] : familiarization with the data, generating initial codes, searching for themes, reviewing themes, defining and naming themes, and producing the report.
Data Availability Statement: Not applicable. Acknowledgments: This work was performed by using the resources of the USFQ's High Performance Computing System (HPC-USFQ). Computational resources and services were also provided by the Shared ICT Services Centre funded by the Vrije Universiteit Brussel, the Flemish Supercomputer Center (VSC) and FWO. FT wishes to acknowledge the VUB for support, among other through a Strategic Research Program awarded to his group.
Electrophysiology Whole-cell patch-clamp recordings in voltage-clamp configuration were performed using Axopatch 200 amplifier (Molecular Devices). Data were sampled at 20 kHz and filtered at 10 kHz (-3 dB) using PCLAMP8. 2. 0. 235 software (Molecular Devices). Recording pipettes (2-4 MΩ) were filled with internal solution (in mM): 134 CsCl, 10 EGTA, 1 EDTA, 10 HEPES and 4 MgATP (pH 7. 2 with CsOH). Leak current was subtracted online using a P/-4 protocol. External solution was perfused (flow rate ∼1 ml/min) by gravity and contained (in mM): 140 choline chloride, 10 HEPES, 1 MgCl 2. 6H 2 O and 2 CaCl 2. 2H 2 O (pH 7. 3-7. 4 with CsOH). Recordings were obtained at RT.
ACKNOWLEDGMENTS We would like to thank to  Silvia Rodriguez  for her technical assistance and  P. Nicolás De Francesco  and  Cambria Chou-Freed  for carefully reading our manuscript. All Ca V subunits were generously provided by  D. Lipscombe  ( Brown University, Providence, RI, United States ), GHSR clone was provided by  J. Marie  ( Université de Montpellier, Montpellier, France ) and D2R was donated by  Marcelo Rubinstein  ( INGEBI, Buenos Aires, Argentina ). We also would like to thank  MinCyT-ECOS-Sud program  ( A13B01 ) for collaborative work between the Argentine and French research teams.
The HCQ-AZ group includes patients that received at least a 3-day course of HCQ-AZ. The other regimens comprise shorter course of HCQ-AZ, AZ alone, HCQ alone, or none of these molecules. The assessment of plasmatic zinc level was performed by inductively coupled plasmamass spectrometry (ICP-MS) using a Nexion ICP MS (Perki-nElmer, Waltham, Massachusetts, USA). We performed Student t-test and ManneWhitney U test, where applicable, using GraphPad Prism 7. 0 (GraphPad Software, La Jolla, USA) while we performed the Chi-square test using the OpenEpi Platform (www. openepi. com). Logistic regression was performed using XLStat 2016 (Addinsoft, Paris, France). Data from patients were protected according to the European General Data Protection Regulation and follow the MR004 processing registered under N MR 5010010520.
The clinical study was carried out in two stages. The first phase allowing the characterization of the metabolites present in human serum after consumption of the ALE and determines the time frame of their absorption peak. A second phase dedicated to collect both naïve and enriched sera, before ingestion and at the absorption peak, respectively. Then, we determined the influence of sera enriched in metabolites of interest resulting from the consumption of the ALE on the behavior of human hepatocyte, adipocyte and chondrocyte cultures. Changes in cellular activity demonstrated that ALE protects hepatocytes from lipotoxic stress, prevents adipocytes differentiation and hyperplasia and exerts chondroprotective properties in an inflammatory context. These data validate the beneficial health properties of the ALE at the clinical level and provide a better understanding of the mechanisms involved in mediating the hepatoprotective, metabolic and osteo-articular effects carried by an artichoke extract.
The first step of the study aimed at determining the polyphenol absorption peak. Three healthy volunteers who fasted for 12 h were given at once 8 g of an artichoke leaf extract (ALE). The dose was set according to validated preclinical and clinical data  [5, 11, [14] [15] [16] [17]. The ALE extract was given dissolved in 200 mL of water. Approximately 6 mL of venous blood was collected from the cubital vein before and every 20 min after the ingestion for a total period of 240 min. Serum was prepared from venous blood samples and stored at -80 • C until analysis. Polyphenol absorption profiles were evaluated by NMR spectroscopy and the total antioxidant capacity of the serum samples (Figure  S1 ). Once the absorption peak was determined, volunteers were called back for the collection of the enriched serum fraction.
Compound addition to serum. A total of 400 µL of a defrosted basal serum sample was vortexed and mixed with 100 µL of phosphate buffer prepared above, vortexed again and transferred to a 5 mm NMR tube. After NMR analysis, the sample was removed from the NMR tube. A total of 0. 5 mg of quinic acid and 50 µL of phosphate buffer were added, the obtained sample was vortexed again and transferred to a 5 mm NMR tube. Following the same procedure, 0. 5 mg of caffeic acid was added to the sample. NMR Spectroscopy. All NMR experiments were performed at 300 K on a Bruker Avance III 600 MHz spectrometer equipped with a cryogenically cooled probe CPTXI. Samples were locked and shimmed automatically using IconNMR software (Bruker Biospin, Wissembourg, France), and randomly analyzed. Samples were analyzed by proton nuclear magnetic resonance ( 1 H NMR).
The spectra were collected with offset frequency in the middle of the spectrum coinciding with the water resonance, which was suppressed by prior saturation using continuous irradiation during relaxation delay. Two complementary experiments were recorded: one-dimensional 1 H Nuclear Overhauser Effect spectroscopY NOESY1D (NOESY1dgppr sequence)  [18]  and Carr-Purcell-Meiboom-Gill CPMG (CPMGpr sequence)  [19]. NOESY1D and CPMG were acquired with 128 scans, a recycle delay of 5. 0 s, a spectral width of 12,019. 230 Hz and 64 k data points. NOESY1D was acquired with a mixing time of 100 ms. Both 90 • duration pulse and offset of the transmitter frequency were optimized automatically before each experiment using IconNMR software (Bruker Biospin, Wissembourg, France). Spectra were manually phased, baseline corrected and referenced to TSP at 0.
Regarding the type of fats accumulated, we checked for intracellular TG and cholesterol contents. Consistently with red oil staining, the presence of palmitate increased intracellular TG similarly in both types of serum (FCS +278%; naïve human serum +289%). In the presence of serum containing ALE metabolites, TG accumulation tends to be reduced (-27%) compared to the lipotoxic control condition (Figure  6A, B ), but data were not significant (p = 0. 116). The same trends were observed for cholesterol, with a palmitate-induced rise of intracellular cholesterol reaching +226% with FCS and +733% with naïve human serum. Compared to the lipotoxic control condition, the presence of serum containing ALE metabolites induced an abrogation of this rise by a magnitude close to the one observed for TG (-36%).
Human Serum Containing Metabolites from ALE Counter Adipocyte Differentiation Primary human pre-adipocytes were committed to full differentiation using a commercially available differentiation kit (Lonza, Materials and Methods 2. 6. 2). As shown in Figure  8 , when stimulated by the differentiation cocktail in the control FCS condition, red oil staining appears quite strong (+55%) when compared to FCS only. Regarding the type of fats accumulated, we checked for intracellular TG and cholesterol contents. Consistently with red oil staining, the presence of palmitate increased intracellular TG similarly in both types of serum (FCS +278%; naïve human serum +289%). In the presence of serum containing ALE metabolites, TG accumulation tends to be reduced (-27%) compared to the lipotoxic control condition (Figure  6A, B ), but data were not significant (p = 0.