dataesr/scientific-paragraphs-categorization huggingface dataset:
When incubated at 70°C for 2 days, colonies of E. coli carrying HA-cmc-1 showed a clear hydrolysis halo after Congo red staining when grown on agar plates containing CMC (Figure  1B ). This indicated the presence of a thermophilic cellulase encoded by the fosmid insert. This fosmid contained a DNA insert derived from HA enrichment cultures, which originated from deep sea hydrothermal vents. sequencing and Bioinformatic analysis of Fosmid ha-cmc-1 In order to reveal the gene(s) carried on the cellulase activityencoding fosmid HA-cmc-1, the fosmid was sequenced using a combination of Sanger and 454-sequencing. Assembly of the obtained sequence reads resulted in a fosmid insert of 38,175 bp DNA (Genbank/EMBL/DDBJ accession no. LN850140). Sequence analysis revealed 48 putative open reading frames (ORFs) that are represented in the fosmid map on Figure  2A.
All predicted ORFs encoded proteins with highest similarity to Thermococcus species. Inspection of the predicted ORFs for the presence of glycoside hydrolase domains revealed that ORF 23 encodes a predicted glycoside hydrolase family 12 (GHF12, pfam family pf01670) protein of 566 amino acids with a predicted molecular mass of 62. 3 kDa and an isoelectric point of 4. 26. The protein showed amino acid sequence similarity to endo-1,4-β-glucanase b of Thermococcus sp. AM4 (Genbank accession no. YP_002581913. 2, 45% identity, blastp E-value of 2 × e -82 ). Analysis of the domain structure of this ORF revealed one GH12 module followed by two separated carbohydrate binding modules (CBMS) of family 2 (CBM2) (Figure  2B ). Multiple sequence alignments revealed two conserved glutamates as catalytic residues in the active site (nucleophile Glu-171 and the acid-base Glu-266).
A surprisingly low number of GHF12 proteins from hyperthermophilic archaea (Sulfolobus solfataricus P2, Pyrococcus furiosus DSM 3638, and Caldivirga maquilingensis IC-167) have been identified and characterized so far. They are all remarkably thermostable proteins with extremely high temperature optima between 80 and 100°C, while pH optima,  substrate specificities, and activities can vary substantially  (Bauer et al. , 1999; Limauro et al. , 2001; Huang et al. , 2005; Girfoglio et al. , 2012). The GHF12 (formerly known as cellulase family H) belongs to glycoside hydrolase clan C, the members of which have a β-jelly roll structure with two glutamate residues serving as catalytic nucleophile/base and catalytic proton donor in a retaining mechanism of hydrolysis. According to the CAZy database 2  (Lombard et al.
acknowledgments The authors gratefully acknowledge the support by the Faculty Graduate Center Weihenstephan of TUM Graduate School at Technische Universität München, Germany. We thank Marie Roumagnac and Nadège Bienvenu for performing growth experiments and DNA preparation from strains deposited in the UBO Culture Collection UBOCC (http://www. univ-brest. fr/ souchotheque/Collection+LM2E). This work was funded by the German Federal Ministry of Education and Research (BMBF) in the collaborative project ExpresSys within the funding measure GenoMik-Transfer. PG acknowledges EU FP7 Project MicroB3 (FP7-OCEAN. 2011 287589), PG and MJ acknowledge EU FP7 Project MAMBA (FP7-  KBBE-2008-226977). Publication of this work was supported by the German Research Foundation (DFG) and the Technische Universität München within the funding program Open Access Publishing.
Determination of adipocyte size (morphometric analysis) Subcutaneous adipose tissue was fixed with 4% buffered formalin, pH 7. 4, during 1 week at 4°C and embedded in paraffin  [35, 36]. Three 4 μm sections per rat shifted by 150 μm were cut using a microtome LEICA (Milton Keynes, UK) and the sections were mounted onto glass slides and stained in Hemalun-Eosin-Safran (H. E. S). The adipocyte areas were manually traced and analyzed using the NIS Elements software. Adipocyte diameter, area and perimeter were calculated for 5 separate photographs per tissue sections. These data were used to calculate the frequency distribution of adipocyte diameters and the mean diameter.
Statistical analysis Statistical analyses were realized using GraphPad Prism (GraphPad Software Inc. , San Diego, CA, USA). Group differences were analyzed by the non-parametric Kruskal-Wallis test with the Dunn's post-tests or with non-parametric Mann-Whitney test to compare the amount of C8:0 between two sections of the stomach. A two-way ANOVA (not repeated measures) was used to analyze the effect of the diet and the localization in the stomach (fundus or corpus) on the C8:0 availability, and the effect of the tricaprylin on the frequency distribution of adipocyte diameter. Body weight gain was analyzed using the two-way ANOVA with repeated measures. All Data are expressed as the mean ± SEM and for all tests, P<0. 05 was considered as statistically significant.
Acknowledgments The authors thank  N. Boulier-Monthéan  and  Dr. D. Catheline  for their technical assistance,  F. Boissel  for animal cares and lipid extractions,  X. Blanc  ( UPAE, INRA, Jouy-en-Josas, France ) for the preparation of the diets,  Dr. C. Bourlieu  for the analysis of plasma free fatty acids and  Dr. A. Fautrel  ( H2P2 ,  Fédération de Recherche, Biosit, University of Rennes 1 ) for the morphometric analysis and the immunohistochemistry.
ACKNOWLEDGMENTS This work has benefited from research funding from patients associations:  E3M  ( Entraide aux Malades de Myofasciite à Macrophages ) " Neurodélivrance des particules injectées par voie intra musculaire et sécurité des adjuvants aluminiques ,"  Association Française contre les Myopathies (AFM)  " Etude des mécanismes de la myofasciite à macrophages ," and  Dwoskin Foundation  (Nano in brain); from  Région Ile-de-France  through a program  PICRI (Partenariat Institutions-Citoyens pour la Recherche et l'Innovation) "Recherche de polymorphismes dans les gènes codant pour des facteurs inflammatoires (chimiokines) dans la myofasciite à macrophages " and from  ANSM , procédure hors appel d'offre " Biopersistence and neuromigration of aluminic adjuvants of vaccines: genetic risk factors and experimental neurotoxicity.
e. , blinding for group allocation during RCT2 continued). Outcome parameters for the current analyses were assessed at baseline and, depending on the nutrient, week 24 of RCT1, RCT2 and RCT3 and at week 24 (presented as week 48) of the OLE. The screening or baseline visit for the OLE was combined with the final visit (week 24) of RCT2. In addition, homocysteine (Hcy), vitamin E, uric acid and percentages of DHA, eicosapentaenoic acid (EPA) and docosapentaenoic acid (DPA) of total fatty acids in erythrocyte membrane also were assessed at week 6 and week 12 of RCT1. These are not statistically analyzed in the present article. However, data on percentage DHA of total fatty acids in erythrocyte membrane is shown in Fig. 1. Written informed consent was obtained from subjects and their caregivers before study participation.
For these analyses, several parameters were log-transformed to get a distribution closer to the normal distribution. Statistical analyses were performed using SAS software (SAS Enterprise Guide 4. 3 for Windows; SAS Institute, Cary, NC, USA). Data are presented as means ± standard deviation (SD) unless stated otherwise. OLE data are presented according to the intervention received during the double-blind study period of RCT2 (i. e. , controlactive and active-active). Statistical significance was set at p < 0. 05 and was not corrected for multiple testing.
Acknowledgments We sincerely thank the patients and their caregivers for their participation in the Souvenir, Souvenir II,  S-Connect  and OLE studies. Study design and planning and data analysis and interpretation were carried out in conjunction with the sponsor, Nutricia Research, on behalf of  Nutricia Advanced Medical Nutrition. The sponsor also provided the study product and funding for the research and data collection. The Souvenir II study was further supported by the  Netherlands Food & Nutrition Delta  project (FND number  10003 ).
As part of our ongoing work, we recently genotyped these subjects for the UCP3-55C>T polymorphism, finding an association between UCP3 genotype and sACE activity. Such data suggest a role for UCPs in the regulation of ACE activity, rather than the (previously recognised) converse observation. We sought to confirm the validity of the finding by performing more detailed genetic analysis in this sample of 210 type 1 diabetic study patients (≥18 years old; 117 women; mean age 45•5 ± 13•7 years; none taking RAS antagonists): the T1DM study. We then sought replication of our findings in a second completely independent dataset, comprising 250 Caucasian British healthy male army recruits (mean age 19•4 ± 2•2 years): the HMAR study. Finally, as sACE is derived from endothelial cells, we performed in vitro experimentation to confirm the co-expression of both ACE and UCP2 mRNA in human umbilical vein endothelial cells (HUVECs) before determining whether changes in UCP expression (by RNA interference) could directly alter endothelial ACE expression.
Acknowledgements We should like to thank the staff and recruits of  ATR Bassingbourn  for their help and support in providing samples for analysis of DNA and sACE activity. The authors declare no conflict of interest. This work was supported by The  British Heart Foundation , which provides core funding to  UCL Centre for Cardiovascular Genetics , and we express our thanks to them. H. M. was supported by the  National Institute for Health Research University College London Hospitals Biomedical Research Centre.
Data collection Baseline data At baseline, socio-demographic and anthropometric characteristics, medical history, clinical data, and biological data will be collected: in addition to the blood film and hemoglobin concentration performed at screening, capillary blood will be collected from a finger prick, and a few drops will be placed on filter paper to perform PCR genotyping (all children) and to measure Anti-AMA1 IgG (sub-study restricted to children enrolled in Mali).
Statistical considerations Study data will be double entered using REDCap electronic data capture tools hosted at Epicentre  [33]  then data management and analysis will be performed with STATA 12, StataCorp®, College Station, TX, according to written data entry procedures and data management plan. A flowchart will present the following information: number of patients screened, number of patients infected with P. falciparum malaria, number of patients infected by other Plasmodium species, number of patients excluded (and reasons why they were not eligible), number of patients enrolled and analyzable in each group of SAM and non-SAM children. For all enrolled children, baseline characteristics will be presented for each group (SAM versus non-SAM).
Antimalarial efficacy Clinical and parasitological efficacy outcomes will be presented for SAM and non-SAM children: number of ETF, LCF, LPF, ACPR, re-infection, recrudescence, mixed infection, by day 28 and day 42. Two methods will be used to estimate the therapeutic efficacy in each group: The Kaplan-Meier survival analysis will be used to calculate estimates of survival without subsequent infection in both intent-to-treat and per-protocol populations. This analysis will allow accounting for censored data  [15, 34]. Logistic regression analysis will be used to compare at day 28 (and then day 42) the proportion of ACPR in patients for which the endpoint has been determined, excluding those lost to follow-up or with missing endpoint. After univariate analyses, multivariate analyses using survival models (time to recurrence) and logistic regression (proportion of ACPR) will be performed where the therapeutic success will be explained by the degree of malnutrition and other cofactors, including lumefantrine PK profile.
Ethical considerations A French version of the protocol and informed consent form has been approved by the Ethics Committee of the Faculty of Medicine and Odonto-Stomatologie and the Faculty of Pharmacy in Bamako, Mali and Niger National Ethics Committee of the Ministry of Health. An English version has been approved by MSF Ethical Review Board. Any amendment to the protocol that may affect the rights, safety and / or welfare of the participants or the conduct of research will be submitted again to Ethics Committees before being implemented. Individual data will not be disclosed to anyone outside the research team, unless it is necessary for the proper medical management of children (useful data can then be shared with the physician, in respect of medical confidentiality). The database will not contain any personally identifiable information; patients are only identified by their inclusion number.
Acknowledgements We acknowledge the contribution of  Doctors Without Borders, Paris and Barcelona , to the conception of the research, and the  International Innovative Fund  for funding the study. We thank the study participants already enrolled and their parents, the community leaders, the managing boards of health facilities where the study is conducted, and the study staff in both sites. We are grateful to all those in the  Department of Clinical Pharmacology of Cape Town  who will perform lumefantrine concentration assays:  Jennifer Norman  and colleagues. We are also grateful to the  WWARN  for expert opinion in PK and parasite clearance sampling schemes. We would like to thank the monitoring team ( Agence Africaine de Recherche en Santé, AARSH ):  Haoua Amadou  and  Veronique Mazarin-Diop.
Description of volunteers 24 volunteers were recruited in two nursing homes in the Dijon area (France). Two volunteers with a GIR dependency score less than 3 were maintained in the study as they were deemed capable of participating in the evaluation. Three volunteers were removed during the study because of a sporadic digestive disorder which they ascribed to eating the compote, and thus the rules set out in ''Data analysis'' were applied to the data for those subjects. The 24 volunteers maintained in the analysis were aged on average 83. 7 ± 6. 2 years (min 70. 0, max 93. 0) and 62. 5 % of them were women. Of the volunteers, 25. 0 % were overweight and 20. 8 % obese. Two (8. 3 %) had an AGGIR score of 2, 12 (50. 0 %) of 3, 7 (29. 2 %) of 4 and 3 (12. 5 %) of 5. Their fatigue evaluated on the Pichot scale ranging from 0 (no fatigue) to 32 (extreme fatigue) was 12.
Qualitative variables are described by frequencies and percentage; quantitative variables by means and standard deviations. Percentage comparisons over the course of the various follow-up visits were made using McNemar tests for paired variables; by Wilcoxon rank tests on repeated series for multimodal qualitative variables; and by analysis of variance on repeated series for quantitative variables. The data were recorded on Capture system software and the statistical analyses conducted using SAS version 9. 2 software.
This review focuses on the developmental expression and function of various classes of efflux transporters. These include the multispecific transporters of the ATP-binding cassette transporter families ABCB, ABCC, ABCG, the organic anion and cation transporters of the solute carrier families SLC21/SLCO and SLC22, and the peptide transporters of the SLC15 family. These transporters play a key role in preventing brain entry of blood-borne molecules such as drugs, environmental toxicants, and endogenous metabolites, or else in increasing the clearance of potentially harmful organic ions from the brain. The limited data available for laboratory animals and human highlight transporter-specific developmental patterns of expression and function, which differ between blood-brain interfaces. The BCSFB achieves an adult phenotype earlier than BBB.
, 2011). With the reservation that substrate specificities for Abcb1 are not absolute, in particular for digoxin which can be recognized by other transporters such as Slco1a4/oatp2, overall, these partial data suggest that ABCB1 functional activity parallels gene expression levels, both increasing from prenatal to pre-adult stages in various animal species, including non-human primates. The amount of ABCB1 protein in rat and human choroid plexus is low by comparison to the levels measured in brain microvessels  (Gazzin et al. , 2008) , and its cellular and subcellular localization within the choroidal tissue is subject to conflictual results. Its implication in the regulation of exchanges across the BCSFB is likely limited. In contrast to the BBB, Abcb1a mRNAs are not detected by RT-PCR in the BCSFB.
Developmental localization, expression and activity of SLC22 and SLCO efflux transporters at blood-brain interfaces Data on the developmental expression of efflux transporters that belong to the SLC22 and SLCO gene families are scarce and obtained only from rat and mouse studies. Transcriptomic analysis of endothelial cells isolated from adult vs. postnatal mouse brains suggests that developmental profiles are heterogeneous among genes  (Daneman et al. , 2010a). While mRNA levels for Slc22a5 (octn2) and Slco1a4 were 2-to 5-fold lower in endothelial cells from developing animals compared to adults, Slc22a8 expression was similar at both stages. Slc22a17 and Slco2b1, whose precise functions are currently unknown at brain barriers, did not display developmental changes either. Of note in this study, the mRNA levels of Slco2a1, the prostaglandin transporter with an unknown directionality of transport, were much higher at the BBB from developing vs.
Mineralization Osteoblasts seeded in 12-well plates were cultured for 21 days in minimal medium containing 50 µg/mL ascorbic acid and 10 mM β-glycerophosphate to investigate bone nodule formation. Extracellular matrix calcium deposits were stained using Alizarin red dye, as previously described  [58]. Osteoblasts were fixed with ice-cold 70% (v/v) ethanol and then stained with Alizarin Red S (40 mM) (Sigma-Aldrich, St. Louis, MO, USA) for 30 min. Mineralization was evaluated by the light microscopy and image processing software ImageJ (National Institutes of Health, Bethesda, MD, USA).
Bone Mineral Density (BMD) Analysis Bone morphological analysis was performed using an eXplore CT 120 scanner (GE Healthcare, Little Chalfont, United Kingdom). After the removal of soft tissues, the left femurs were placed in PBS buffer with 10% formaldehyde at 4 ˝C for one week and scanned. Acquisition consisted of 360 views acquired in 1 soft tissues, the left femurs were placed in PBS buffer with 1 millisecond exposure/view and X-ray tube settings of 100 kV and 50 mA. CT images were reconstructed using a modified conebeam algorithm with an isotropic voxel of 0. 045 x 0. 045 x 0. 045 mm 3. CT scans were analysed using MicroViewH version 2. 3 software (General Electric Healthcare Bio-Sciences, Pittsburgh, PA, USA). A hydroxyapatite calibration phantom (SB3, Gamex RMI, WI, USA) was used to convert grey-scale levels to hydroxyapatite density values.
Taqman Low Density Arrays (TLDA) For each experimental group, four sets of extractions were performed with two tibias pooled in each. Frozen bones were ground in liquid nitrogen to obtain a fine powder. Then, total RNA was extracted according to the manufacturer's instructions from either bone powder for the in vivo experiment or cell culture, using Trizol reagent (Invitrogen, Life Technologies, Saint Aubin, France). RNA was converted to cDNA using the high capacity cDNA reverse transcription (RT) kit (Applied Biosystems). The resulting cDNA was used for TaqMan low-density arrays (TLDAs) (Applied Biosystems 7900HT real-time PCR system). Relative expression values were calculated using the comparative threshold cycle (2 ´∆∆ CT) according to the Data Assist software (Applied Biosystems, Life Technologies, Saint Aubin, France).
Statistical Analysis Results are expressed in the form of mean with standard error (SEM). All the data were analysed using XLSTAT Pro software  [63]  (Addinsoft, 40 rue Damrémont, Paris, France). In vitro data were analysed using a two-way analysis of variance (ANOVA) to test for differences among groups. If the result was found to be significant (p < 0. 05), the fisher multiple comparison test was then performed to determine the specific difference between means. TLDA data and in vivo data were analysed using non-parametric Kruskal-Wallis one-way analysis of variance, which allows testing for differences among groups. If the result was found to be significant (p < 0. 05), the Mann-Whitney U test was performed to determine the specific difference between means.
Effect of PGPE on ALP Activity and Mineralization of MC3T3-E1 Cells The kinetic measurement of ALP activity in cells treated with mice serum raised in either Control or PGPE conditions on days 2, 7 and 14 was first assessed to investigate the effect of the tested diets on osteoblast differentiation. With regard to the Control condition (FBS), as expected, the osteoblasts treated with optimized medium (C+) exhibited higher ALP activity compared to osteoblasts exposed to a minimal medium (C´), as of day 2 (+72%), day 7 (+374%; p < 0. 01) and day 14 (+139%) (data not shown). The cells that had been exposed to PGPE mice serum exhibited higher values compared to the Control condition (+46% at day 7 and +16% at day 14; p < 0. 05). (Figure  2B ). Nutrients 2015, 7 7, page-page 7 and as expected, the osteoblasts treated with PGPE mouse serum were able to produce many more calcium nodules after 21 days of culture than osteoblasts treated with Control mouse serum (Figure  2D ).
Effect of PGPE on Transcriptional Activity of RAW264. 7 Cells To further investigate the effect of PGPE on bone resorption, the expression levels of specific differentiation markers and transcription factors were assessed. A TLDA analysis was therefore performed on mRNA extracted from RAW264. 7 cells treated with mouse serum (Control or PGPE) under the differentiated condition (C+) after three days of culture. The expression of the most relevant targets is shown in Figure  3C. The exposure to serum from PGPE mice was compared to the results of Control treated cells (Fold increase value = 1). The TLDA data indicate that the exposure of RAW264. 7 differentiated cells to serum from PGPE mice was associated with a slight, but significant (p < 0. 05), decrease in the mRNA levels of many crucial osteoclast-specific markers, such as calmodulin (CaM) (0.
Pomegranate Intake Was Associated with an Improved Expression Profile of Specific Bone Markers To elucidate the possible molecular mechanisms involved in this effect on bone morphology and to confirm the in vitro findings, we performed a transcriptomic analysis on bone tissue samples using Taqman Low Density Arrays (TLDA, Applied Biosystems, Life Technologies, Saint Aubin, France). Because of the large number of genes modulated, only the most important bone markers are presented. Data on the OVX PGPE group were compared to the data measured for the OVX Control group. The TLDA data on osteoclasts are shown in Figure  5A. Accordingly, PGPE consumption significantly (p < 0. 05) down-regulated the mRNA levels of some of the major osteoclast-specific markers: define (0. 39 fold) and integrin β3 (ITG b3: 0.
Nutrients 2015, 7 7, page-page 12 osteoblast-specific markers, the TLDA data presented in Figure  5A  show that PGPE consumption by ovariectomized mice was able to significantly improve the expression of a co-receptor implied in Wnt/β-catenin signalling in the osteoblast, LRP5 (1. 62 fold; p < 0. 05), in comparison with the OVX Control group. However, the other osteoblast markers investigated were not significantly modulated by dietary PGPE. To obtain further conclusions regarding the potent bone-sparing effect of pomegranate consumption, we investigated the expression of major inflammation and oxidation markers, which are known to exacerbate bone resorption. We therefore analysed the transcription of some inflammatory and oxidation markers in bone tissue samples using Taqman Low Density Arrays (TLDA).