dataesr/scientific-paragraphs-categorization huggingface dataset:
Immunophenotyping of adipose tissue-derived human mesenchymal stem cells Cells (1 × 10 5 ) were seeded in 6-well plates and incubated for 24 h. Then, the cells were collected by mechanical dissociation in 10 mM EDTA solution. The immunophenotypic characterization was done by flow cytometry. Next, cells were incubated for 30 min at 4 °C with specific antibodies as described by Pesarini et al  [6]. For this purpose, surface specific/nonspecific labels (CD44, CD90, CD29, CD34, CD11b and MHC II; Pharmingen BD, USA) were utilized. Cells were analyzed by flow cytometry in the ACCURI C6 cytometer (Becton Dickinson, USA). Characterization plots were generated by capturing 10,000 events using standard equipment software (ACCURI C6 BD software, Becton Dickinson, USA).
qRT-PCR was performed in triplicate (Rotor Gene®; Qiagen). Analyzed genes are described in Table  1. We tested genes involved in the processes of apoptosis, DNA damage, and cell cycle. For the reaction, 10 μl of GoTaq® master mix, 2 pmol of each oligonucleotide, 500 ng of cDNA and ribonuclease-free water up to a total volume of 20 μl (Promega®, catalog number A6002) were utilized. qRT-PCR occurred as follows: 95 °C for 5 min, followed by 40 cycles of 95 °C for 2 s and 60 °C for 30 s. At the end, a melting curve analysis was performed to evaluate the specificity of the products formed. The housekeeping betaactin gene (ACTB) was used as an internal control, and the results were analyzed with the Rotor Gene® software (Qiagen) v2. 3. 1.
Furthermore, the activity of this gene is related to the increase in p53 gene expression  [57, 59]. However, we did not observe an increase in p53 or p21 in ADSCs treated with calcitriol and CaCl 2. In agreement with our results, Johnson et al  [60]  demonstrated that GADD45 can influence the cell cycle independently of p53 activation. The ADSCs treated with calcitriol and CaCl 2 induced cell cycle arrest in S phase. It is believed that S arrest occurs in response to single-strand breaks in DNA, culminating in a significant increase in ATM expression  [52]. Our data indicate that cell cycle progression was blocked by the GADD45 gene, thus corroborating other studies that evaluated the influence of this gene on the cell cycle  [54, 61, 62]. It is worth noting that regardless of the phase in which cell cycle arrest occurs, if there is no repair, genes that initiate the apoptosis cascade must be expressed, culminating in programmed cell death  [52, [63] [64] [65] [66].
Acknowledgements This work was supported by the  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) ,  Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia de Mato Grosso do Sul -FUNDECT  -under grant number  79/2014  ( 23/200. 225/2014 )and the  Conselho Nacional de Desenvolvimento Científico e Tecnológico -CNPq - under grant number  447205/2014-5. We thank  Sidney Paulo Miyashiro  and  Andreza Negreli  for their support.
Again, we standardized the metabolite levels and adjusted for age (at entry), sex, BMI, and lipid-lowering medication. For VUmc Alzheimer Center, we used logistic regression adjusted for age and sex. The relations with incident dementia and AD were evaluated in a second model additionally adjusting for APOE ε4 genotypes. In the discovery cohorts, we used linear regression analysis to study associations of lifestyle factors (smoking, physical activity, and fish [oil] consumption) with metabolites and cognitive function, adjusting for age, sex, BMI, and lipid-lowering medication. All analyses were performed in R (version 3. 2. 1, 2015-06-18). Summary statistics by cohort were combined with inverse variance-weighted fixed-effects meta-analysis using the "rmeta" package (version 2. 16). The association magnitudes are reported in units of standard deviation (SD) or odds ratio (OR) change per 1-SD increase in each metabolite  [38, 39]  easing comparison of effects.
Acknowledgments None of the funders had any role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; or decision to submit the manuscript for publication. This work was performed within the framework of the  BBMRI Metabolomics Consortium  funded by  BBMRI-NL , a research infrastructure financed by the  Dutch government (NWO , grant nr  184. 021. 007  and  184033111 ). This work is funded by the  European Union 's  Horizon 2020 research and innovation programme  as part of the  Common mechanisms and pathways in Stroke and Alzheimer's disease (CoST-REAM ) project (www. costream. eu,grant agreement No  667375 ); the  Netherlands Organisation for Health Research and Development (ZonMW)  as part of the  Joint Programming for Neurological Disease (JPND)  project  PERADES (Defining Genetic , Polygenic and  Environmental Risk  for Alzheimer's Disease using multiple powerful cohorts, focused Epigenetics and Stem cell metabolomics -grant number  733051021 ); the  European Union Innovative Medicine Initiative (IMI) programme  under grant agreement No  115975  as part of the  Alzheimer Disease Apolipoprotein Pathology  for Treatment Elucidation and Development (ADAPTED, https://www.
QLG2-CT-2002-01254 );  FP7  project  EUROHEADPAIN  (nr 602633), the  Internationale Stichting Alzheimer Onderzoek (ISAO) ; the  Hersenstichting Nederland (HSN). Metabolomics measurements of ERF have been funded by  Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)-NL  ( 184. 021. 007 ). A. D. is supported by a  Veni grant  ( 2015 ) from  ZonMw. The ERF-follow up study is funded by  Cardio-Vasculair Onderzoek Nederland  ( CVON 2012-03 ). We are grateful to all study participants and their relatives, general practitioners, and neurologists for their contributions and to  P. Veraart  for her help in genealogy,  J. Vergeer  for the supervision of the laboratory work, both S. J. v. d. L. and  A. van der Spek  for collection of the follow-up data, and  P. Snijders, M. D. , for his help in data collection of both baseline and follow-up data.
The  Rotterdam Study  is supported by the  Erasmus MC University Medical Center and Erasmus University Rotterdam ; The  Netherlands Organisation for Scientific Research (NWO) ; The  Netherlands Organisation for Health Research and Development (ZonMw) ; the  Research Institute for Diseases in the Elderly (RIDE) ; The  Netherlands Genomics Initiative (NGI) ; the  Ministry of Education, Culture and Science ; the  Ministry of Health , Welfare and Sports; the  European Commission (DG XII) ; and the  Municipality of Rotterdam. The contribution of inhabitants, general practitioners, and pharmacists of the Ommoord district to the  Rotterdam Study  is gratefully acknowledged. Metabolomics measurements were funded by  Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)-NL  ( 184. 021.
007 ). The  Whitehall II study  is supported by the  Medical Research Council  ( K013351 ), the  British Heart Foundation , and the  National Institute on Aging  ( R01 AG013196 ). Netherlands Twin Register (NTR): Funding was obtained from the  Netherlands Organization for Scientific Research (NWO)  and  MagW/ZonMW  grants  904-61-090 ,  985-10-002 ,  904-61-193 , 480-04-004 ,  400-05-717 ,  Addiction-31160008 ,  Middelgroot-911-09-032 ,  Spinozapremie 56-464-14192 ,  Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-NL ,  184. 021. 007 ); VU University's Institute for Health and Care Research  ( EMGO1 ) and  Neuroscience Campus Amsterdam (NCA) ; the  European Community 's  Seventh Framework Program  (FP7/2007-2013),  ENGAGE  ( HEALTH-F4-2007-201413 ); and the  European Science Council (ERC Advanced ,  230374 ),  Rutgers University Cell and DNA Repository  ( NIMH U24 MH068457-06 ), the  Avera Institute ,  Sioux Falls ,  South Dakota (USA) , and the  National Institutes of Health (NIH ,  R01D0042157-01A ,  MH081802 ,  Grand Opportunity  grants  1RC2 MH089951 ).
Part of the genotyping and analyses were funded by the  Genetic Association Information Network (GAIN) of the Foundation for the National Institutes of Health. Computing was supported by  BiG Grid , the  Dutch e-Science Grid , which is financially supported by  NWO. FINRISK 1997 has been mainly funded by the budgetary funds of the  National Institute for Health and Welfare. Important additional funding has been obtained from the  Academy of Finland ,  Finnish Foundation for Cardiovascular Research  and other domestic foundations. The NMR metabolomics determinations were funded by a grant from the  Academy of Finland  (# 139635  to V. S. ). DILGOM 2007 baseline survey was funded by the  Academy of Finland  (grant #  136895  and  263836 ). V. S. was.
Dietary sequences were included in the model as a fixed effect and the block as a random effect. ANOVA were performed using the MIXED procedure of SAS  (Statistical Analysis System Institute Inc. , 2003)  after the normality of the variables had been checked using the Shapiro-Wilk test. Orthogonal contrasts with linear (Lin) and quadratic (Qua) effects were used in the grower phase (C v. M v. L) and for the overall experiment to study the extent of the depletion in dietary nPP and Ca levels (CC v. MM v. LL), the impact of the depletion duration (ML v. LL), and the effect of the levels of dietary nPP and Ca during the finisher phase (CC v. LC v. LM). Linear regression between tibia, toe and whole-body criteria was conducted within each phase. Differences were considered significant at P < 0.
The Mitotracker probe was used to cross check the images recorded by labeling aconitase: both sets of images qualitatively agreed and, since the latter were of better quality than the former, only wells in which aconitase was detected were analyzed in details. Several fields were recorded for each slide and quantitative analysis with the Image J (imagej. nih. gov) and Volocity (Improvision, Perkin-Elmer, Courtaboeuf, France) computer programs was carried out on all of them as follows. In a first step, tophat filtering was applied to the images recorded with the mitochondrial channel (aconitase fluorescence) in Image J to remove noise and to obtain a precise definition of the mitochondrial morphology. The filtered images were then analyzed with the Volocity software which provides morphological parameters like perimeter, area, skeletal length and diameter for each identified object.
Respiration Rates The oxygen consumption rates of INS-1 cells were measured with a temperature-controlled Hansatech oxygraph equipped with a Clark electrode and monitored with the oxygraph software. For measurements with glucose stimulation, harvested cells were suspended in Krebs-Ringer Bicarbonate HEPES buffer (KRBH: NaCl 125 mM, CaCl 2 1 mM, MgSO 4 1. 2 mM, KCl 4. 74 mM, NaHCO 3 5 mM, BSA 0. 1%, pH 7. 4) with 2. 8 or 16. 7 mM of glucose at ca. 4 × 10 6 cells/mL. These glucose concentrations were chosen at the lower and higher ends of the sigmoid response of β-cells to glucose. Cellular respiration was measured and, when required, 1 µg/mL oligomycin was added. The fraction of O 2 consumption used for producing ATP was calculated as Equation (  2 ). fraction of O 2 consumption = (basaloligomycin)/basal (2).
Oxygen Consumption of INS-1 Cells after Long Term Exposure to Moderate Levels of Cadmium As above for nucleotide measurements, the respiration rates were first recorded for intact cells in the complete growth medium. The basal respiration rate was compared with that of the same cells in the presence of oligomycin that inhibits the proton channel of the F 0 F 1 complex V. From these data it is possible to calculate the fraction of oxygen consumption used to produce mitochondrial ATP (see Section 2. 5). The plot of the results in Figure  6a  shows that this fraction did not vary with the cadmium treatment below concentrations triggering cell death. Accordingly, the level of oxidative species within similarly treated cells did not change as a function of the cadmium dose as determined by reaction with dihydroethidium (see Section 2.
The French CF registry had data for children <18 years old but no data for the group 2-12 years old. The national median BMI z-score for <18 years in 2010 was -0. 35, and in our center for the same age group was -0. 5 [5]. Our multidisciplinary team chose to address the nutritional status of 2-12 year-old CF patients as our results for this age group showed a very large variation in BMI z-score with a mean value of -0. 49 (range: -3. 5 z-score to +1. 8 zscore). This significant variability in our values for this group of children thus left room for improvement. All children aged 2-12 years (34 patients) followed-up at our center were included in the program. Our aim was to attain an average BMI z-score = 0 by end of 2014. We also expected an impact on FEV1 for patients (> 5 years old) at the end of the program in 12/2014.
Methods A quality team comprising a pediatrician, a dietitian, an adult patient, a social worker, a physiotherapist, a nurse coordinator and a study-coordinator was established. The team participated in 4 training sessions organized by the National training-team for CF centers participating in PHARE-M pilot phase. The pediatrician also had the opportunity to participate in a similar Learning and Leadership Collaborative face-to-face meeting in the USA organized by the CF Foundation in Anaheim (2011). Following these training sessions, our team evaluated nutritional indicators in our center based on annual data and analysis of patient records: BMI z-score, number of clinic and dietitian visits/year, number of stool fat analysis/ year, number of nutritional supplements prescribed. We used a tool, the Ishikawa fishbone cause and effect diagram  [6] , to determine positive and negative factors influencing nutritional status among our patients.
Bibliometric Study Searches in the Web of Science Core Collection databases (WoS) and Google Scholar (GS) web have been done between 1985 and June 2017 using different keywords and combination of them in the title of the articles. The terms edible, vegetable, or olive have been used to characterize oils while the synonyms vitamin K 1 and phylloquinone have been employed to restrict the study only to the compound of interest. This research also focused on PH quantification methods based on Gas Chromatography (GC) and High Pressure Liquid Chromatography (HPLC). Searches in WoS database have been performed for TOPIC ("edible oil Ã " or "vegetable oil Ã " or "olive oil Ã ") AND TOPIC ("vitamin K1" or phylloquinone) AND TOPIC (HPLC or GC). A similar search was realized with GS tool by also performing an advanced search for the exact expression in quotation marks throughout the entire document.
The methodology of this bibliometric study and the results of the search strings used in the two sources of information were synthetized on a graphical representation (Figure  1 ). The first remark was that all of these researches showed that the results were very different from one database to another. Bibliographic references were more numerous with GS tool because it provided broader coverage for most disciplines. It was criticized that its coverage was heterogeneous and poorly informed, including low quality "publications" such as blogs or magazine articles mixing academic and non-academic sources. Moreover, GS engine found a large number of duplicate papers. The typology of publications did not follow the same logic for WoS model which used a selection of papers and multidisciplinarity, thereby restraining its coverage.
Nevertheless, the olive oil data extracted from these 20 publications were often repetitions of some particular studies. It was the case of Booth  et al. publications in 1993, 1998, and 2012  [3, 7, 8]  and the review of Eitenmiller et al. [5]  Furthermore, Booth and Ferland were coauthors as well as Piironen and Koivu. 6] [37] [38] [39]  This bibliometric approach Websites: Google Scholar (GS); Web of Science (WoS) Topics: EO: "edible oil*"; OO: "olive oil*"; PH: phylloquinone; VO: "vegetable oil*"; VK: "vitamin K"; VK1: "vitamin K1" GS WoS EO & VK1 & PH 34 2 OO & VK1 & PH 289 2 VO & VK1 & PH 179 4 GS WoS EO & VK1 & HPLC 39 1 OO & VK1 & HPLC 241 1 VO & VK1 & HPLC 162 1 GS WoS EO & PH & HPLC 49 3 OO & PH & HPLC 355 4 VO & PH & HPLC 207 6 GS WoS EO & VK1 & PH & HPLC 16 1 OO & VK1 & PH & HPLC 118 1 VO & VK1 & PH & HPLC 87 1 GS WoS EO & VK1 & GC 29 1 OO & VK1 & GC 188 1 VO & VK1 & GC 101 1 GS WoS EO & PH & GC 39 1 OO & PH & GC 251 1 VO & PH & GC 125 2 GS WoS EO & VK1 & PH & GC 14 1 OO & VK1 & PH & GC 85 1 VO & VK1 & PH & GC 51 1 Figure 1.
Graphical representation of bibliometric search (articles number) on the determination of PH content in vegetable oils. Websites: GS, Google Scholar; WoS, Web of Science. Topics: EO, "edible oil Ã "; OO, "olive oil Ã "; PH, phylloquinone; VO, "vegetable oil Ã "; VK, "vitamin K"; VK1, "vitamin K1". showed that the search using title or keywords converged with difficulty toward the target because the choice of keywords did not always reflect the publications content. So, among the 119 keywords highlighted from the 78 papers, the terms "phylloquinone" and "vitamin K" were used most often (23 times), "vitamin(s)" for five times, "fat soluble vitamin (s)" for four times, "HPLC" for 10 times, "vegetable oil(s)" for four times against two times for "olive oil. " Often, data for edible oils have been found in publications used general words as "food," "food composition," or "food analysis" and "fat soluble vitamins" as keywords.
). Cl 2 þ 800 mL CH 3 OH þ 5 mL (2 M ZnCl 2 þ 1 M CH 3 COOH þ 1 M CH 3 COONa)/ 1 L; perhaps. Only, Woollard et al. [29]  quantified E and Z isomers in olive oils and found that E isomer was 86. 3% of the sum of the two isomers. PH content of the other vegetable oils reported in the literature was a function of varietal origin of oils. Vegetable oils data were reported in function of their commercial importance: corn, rapeseed (canola), soybean, and sunflower oils are the most studied. To compare them, the PH extreme values of all oil samples (extracted from Table  2  and 3 ) were reported in the Figure  4. Despite of the different analytical techniques used to quantify phylloquinone, two oil groups appeared: one describing oils having a maximum PH content superior at 60 μg/100 g (avocado, cottonseed, olive, pumpkin, rapeseed, and soybean) and one other closing the oils with a maximum value inferior to 20 μg/100 g.
Outcome Measures The questionnaire was sent by email to at least one doctor or breastfeeding counsellor from each unit from June 2015 to June 2016. Reminders were sent out every four months for one year as long as there was no answer. The answers were collected by e-mail and by post. The questionnaire was written in French and translated into English for this publication (Figure  S1 ). The questionnaire consisted of four parts. In the first part, general data on the neonatal unit were collected. In the second part, the current clinical practices of each service were requested. The information was related to the use of breast milk (frozen, pasteurised, raw mother milk, or donation of breast milk), the promotion of breastfeeding, and the access to a human milk bank. The third part concerned the conditions of use of raw breast milk (maternal CMV status, infants' term or weight) and the barriers to its use (mainly infectious risks).
Histology Histological analysis was performed as previously described  (17). Sections (4 µm) were dewaxed and treated in boiling citrate buffer (10 mM, pH 6. 0) for 6 min. Cooled sections were rinsed and then permeabilized in PBS 0. 2% triton X-100 at room temperature for 20 min. Sections were saturated in the same buffer containing 3% BSA for 30 min, incubated with perilipin antibody (#RDI-PROGP29, Research Diagnostic Inc. , Flanders, NJ) for 1 h, and TRITC-coupled anti-guinea pig antibody for 45 min. Nuclear staining was performed with DAPI. UCP1 immunohistochemistry was performed following manufacturer's instructions (LSAB+ system-HRP, Dako, Les Ulis, France) and using goat anti-UCP1 (clone C-17, Santa Cruz, Tebubio, Le Perray-en-Yvelines, France). Visualization was performed with an Axiovert microscope and pictures were captured with Ax-ioVision software (Carl Zeiss, Jena, Germany).
3 µM EPA. A: Expression of adipocyte markers was determined by RT-qPCR and is expressed as fold increase relative to "brite" group values. B: Basal, ATP synthase uncoupled respiration (% of residual respiration after addition of ATP synthase inhibitor oligomycin), and maximal respiration (obtained after addition of the chemical uncoupling agent FCCP) were assessed at the end of treatment to determine the oxygen consumption rate (OCR) of mitochondria. The spare respiratory capacity represents a measure for the full respiratory potential of mitochondria and is calculated as the difference between maximal and basal respiration. Data are mean ± SEM of three (A) or six (B) independent experiments. a, P < 0. 01 versus brite; b, P < 0. 01 versus brite + ARA. expression of the major enzymes involved in PGF2 synthesis.
Despite the various reported ␤-1,3-D-glucan phosphorylase activities, LBP sequences are the only ␤-1,3-D-glucan phosphorylases that have been successfully cloned to date; they have been classified as members of glycoside hydrolase family GH94 in the CAZy database (www. cazy. org) 3 (31). However, the eukaryote phosphorylases have not, to date, been classified due to the lack of sequence information, which compromises further biochemical and structural studies of this fascinating group of enzymes. The physiological role of eukaryotic ␤-1,3-D-glucan phosphorylases remains inconclusive. In contrast, the biological function of the bacterial phosphorylases can be predicted from the identity of other genes with which they are clustered within the genome. LBP from Paenibacillus sp. strain YM-1 was hypothesized to be involved in degradation of laminaribiose, based on the position of the LBP genetic locus next to ABC sugar transporter components  (26).
From a total of 253 proteins with unique peptide counts Ͼ3 and 100% protein identification probability, 240 were identified in the translated transcriptome database of E. gracilis  (14)  using Mascot (Matrix Science, Boston MA). Putative functions of these proteins were assigned by comparison with protein sequences with annotated functions in the non-redundant database NCBI by BLASTP pairwise alignment (File S1). One protein (m. 14570_dark) showed similarity to a deposited sequence, which was annotated by the depositor as a laminaridextrin phosphorylase-like protein from E. gracilis (BAV19384. 1, E-value ϭ 0, percentage identity ϭ 53). The predicted molecular mass of m. 14570_dark is 130 kDa, which is similar to what has been reported for the partially purified Euglena laminaribiose phosphorylase  (24).
Identification and characterization of a bacterial ortholog of EgP1 A proprietary metagenome database was interrogated with tBLASTN using EgP1 as a query. 4 The search identified a putative ortholog, designated Pro_7066, with 45% sequence identity to EgP1 (E-value ϭ 0). To investigate whether Pro_7066 has activity similar to that of EgP1, a recombinant form of Pro_7066 was produced in E. coli in the same manner as EgP1 (Fig. 4A  and Fig. S6 ). Characterization of Pro_7066 was performed as described previously for EgP1, which showed that the enzyme was also active as a ␤-1,3-D-glucan phosphorylase (Fig. 4 (B  and C ) and Fig. S7 (A  and B )), generating oligosaccharide detectable by MALDI-TOF up to DP 11 (Fig. S7C  and Table  S3 ). Pro_7066 showed similar pH and temperature preferences to EgP1 (Fig.