dataesr/scientific-paragraphs-categorization huggingface dataset:
05, ## P < 0. 001). (D) Food intake at 10 th week of treatment during the light and dark cycle. Food was measured by weighing the food consumption separately during the day (from 8:00 to 20:00) and the food consumption during the night (from 20:00 to 8:00). Differences between C vs HFD (***P < 0. 001); and HFD vs HFD+ T ( ## P < 0. 01). (E) Water Intake at 10 th week of treatment. Data are expressed as mean ± SEM.
Acknowledgements This scientific paper was supported by the  Generalitat de Catalunya  ( 2014 SGR 659 ) and the  Ministerio de Economía y Competitividad  ( FIS PI13/01500 ). AF was supported by a  Doctoral fellowship  from the  CONSEJO NACIONAL DE CIENCIA Y TECNOLOGIA (CONACYT)  from  México. We want to thank  Yaiza Esteban  for technical support ( CIBERDEM) CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona ,  Spain. And Kimberly Katte  for revising the manuscript. This work was done at  Centro Esther Koplowitz ,  Barcelona Spain.
Differences between HFD vs HFD+ T ( # P < 0. 05, ## P < 0. 001). (D) Food intake at 10 th week of treatment during the light and dark cycle. Food was measured by weighing the food consumption separately during the day (from 8:00 to 20:00) and the food consumption during the night (from 20:00 to 8:00). Differences between C vs HFD (***P < 0. 001); and HFD vs HFD+ T ( ## P < 0. 01). (E) Water Intake at 10 th week of treatment. Data are expressed as mean ± SEM.
(  14 ) to hold at every moment. The drop diameter increases in time according to: 0 6 ⁄ 15 and depend on , so vary with time as well. Equation (  14 ) is solved numerically by the fourth order Runge-Kutta method. The integration time step is 0. 01. We begin calculations with 0 1. 01 as is not defined for 1 ⁄. We fix initial conditions of 0 ⁄ and 0 0. Figure  3  reports simulation results (dotted line) with ranging from 0 to 0. 325 mm (increment of 0. 005 mm) for one dataset on the reference system (a typical drop center of mass simulated motion close to the threshold is shown in supplementary material E). Drop size at the transition is well predicted but it is overestimated far from the transition. Moreover, the threshold amplitude is underestimated: in this example, the predicted value is twice lower than experimentally.
Microarray sample preparation Replicate wells (n = 3-4) of WT BMDMs were treated with LPS (1 ng/mL), SA or OA (250 μM), or BSA (125 μM) for 5 or 20 hours as indicated. Purified DNase-treated total RNA was analyzed for quality using chip-based capillary electrophoresis (Bioanalyzer, Agilent, Inc) and quantity and purity was determined with a NanoDrop spectrometer. The NuGEN Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation, and biotinlabeling of ~10 ng input RNA. The labeled cDNA was hybridized to GeneChip Mouse Gene 1. 0 ST microarrays (Affymetrix, Santa Clara, CA). Signal intensities of fluorescent images produced during GeneChip hybridizations were read by an Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).
Microarray data analysis Data were quantile normalized and median centered across samples as described  (Baccarella et al. , 2013). Differentially expressed genes were identified using Significance Analysis of Microarrays  (Tusher et al. , 2001)  using two-class unpaired comparisons with 3% false discovery rate (FDR) and 1. 5-fold change cutoffs. Clustering was performed with xcluster  (Gollub and Sherlock, 2006)  and visualized as heatmaps using Java Treeview  (Saldanha, 2004). Gene set intersections were determined using custom Perl scripts. Principal component analysis was performed in R. Functional enrichment analysis utilized DAVID  (Huang et al. , 2009). Human monocyte-derived macrophage datasets were downloaded from GEO (Accession number GSE46903) and processed identically to our mouse datasets.
In vivo luminescence imaging Male ERAI-Luc mice  (Iwawaki et al. , 2009)  fed chow or HFD (Harlan Teklad TD. 88137) starting at 4-6 weeks of age were imaged in the IVIS Spectrum (PerkinElmer) under isoflurane anesthesia 10 minutes after intraperitoneal injection of luciferin (150 mg/kg, GoldBio). Whole body radiance was quantified using Living Image software (PerkinElmer).
Acknowledgments We thank  Hui Wang  and the  Gladstone Institutes Genomics and Bioinformatics Cores  for technical assistance,  Dr. Joachim Schultze  and his laboratory for making available their human macrophage array data, and the laboratory of  David Ron ,  University of Cambridge , for reagents and advice. This work was supported by  NIH  grants  5K08DK080174  and  R01DK103175  (to S. K. K. ), an  NSF   Graduate Research Fellowship  (to M. M. R. ), The  UCSF Diabetes Research Center (DRC) , and The  UCSF Nutrition and Obesity Research Center (NORC).
We performed further costaining of Tailor and Dis3L2 variants but these all showed similar patterns with no combination that was more notably colocalized (data not shown). However, we note that TailorΔDUF exhibited a more cortical pattern, which may relate to its poor association with Dis3L2 (Fig. 2B ). We assessed the accumulation of Tailor and Dis3L2 in cells depleted of the reciprocal factor. For these tests, we analyzed endogenous Tailor but used transfected Dis3L2 owing to lack of availability of Dis3L2 antibodies. Western blotting showed that either Tailor-CDS or 3 ′ UTR dsRNAs could effectively deplete endogenous Tailor, and that Dis3L2 dsRNA effectively suppressed the accumulation of transfected HA-Dis3L2 (Fig. 2C ). Under these conditions, loss of Dis3L2 did not substantially affect Tailor accumulation, while loss of Tailor did not affect the accumulation of transfected Dis3L2.
Transcriptome analysis We isolated total RNA from 5-d-old flies using TRIzol. We made two independent dissections to generate biologically replicate RNA samples, whose quality was assessed by a Bioanalyzer. We used the Illumina Truseq Total RNA library Prep Kit LT to make RNA-seq libraries from 650 ng of total RNA. Manufacturer's protocol was followed except for using eight cycles of PCR to amplify the final library instead of the recommended 15 cycles, to minimize artifacts caused by PCR amplification. All samples were pooled together, using the barcoded adapters provided by the manufacturer, over two flow cells of a HiSeq2500 and sequenced using PE50 at the New York Genome Center. The raw sequencing data have been deposited to the NCBI Gene Expression Omnibus (GEO) under accession GSE92305.
We mapped total RNA-seq reads from four data sets to the UCSC Drosophila melanogaster (dm6) genome assembly. We normalized RNA-seq by the trimmed mean of M-values (TMM) normalization method in the edgeR/Limma Bioconductor library  (Oshlack et al. 2010). We used the voom method of Limma  (Smyth 2005)  to correct for the Poisson noise due to the discrete counts of RNA-seq. The gene annotation (R6. 12) was from the flybase FB2016_04 release. Differentially expressed mRNA and IncRNA loci between Tailor/ Dis3L2 mutants versus wild type were identified by a moderated ttest, and FDR (Benjamini-Hochberg) was estimated, using the Limma library  (Smyth 2005)  in Bioconductor. The genes with FDR ≤0. 1 and FC greater than or equal to twofold were considered to be differentially expressed. Transcript per million (TPM) was calculated to give gene expression per gene.
ACKNOWLEDGMENTS We thank  Stefan Ameres  for Tailor mutants and antibody, and the  Bloomington Stock Center, Vienna Drosophila RNAi Center, Drosophila Genomics Resource Center , and the  Developmental Studies Hybridoma Bank  for other fly stocks, cells, and antibodies. Work in E. C. L. 's group was supported by the  National Institutes of Health  ( R01-GM083300 ) and Memorial Sloan Kettering Core Grant  P30-CA008748  ( National Cancer Institute ). Received October 7, 2016; accepted December 7, 2016.
Acknowledgements. We thank the  EURODELTA III modelling community , especially INERIS, TNO and  ECMWF , for providing various model input data. Calculations of land use data were performed at the  Swiss National Supercomputing Centre (CSCS). We thank  D. Oderbolz  for developing the CAMxRunner framework to ensure reproducibility and data quality among the simulations and sensitivity tests,  M. Tinguely  for the visualization software and RAMBOLL ENVIRON for their valuable support. This study was financially supported by the  Swiss Federal Office of Environment (FOEN). The research leading to these results received funding from the  European Community 's  Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement no. 290605  ( PSI-FELLOW ), from the  Competence Center Environment and Sustainability (CCES)  (project  OPTIWARES ) and from the  Swiss National Science Foundation  ( WOOSHI grant   140590 ).
Statistical Analyses All statistical analyses were conducted in R version 3. 1. 2 (R Core Team, 2014). Data were checked for approximate normal distribution by graphical visualizing of residuals. The effects of the different factors (pea cultivar, aphid lineage, expressed gene) were tested and the simplest model explaining the data was used. Analyses of survival rates (Figures  2A  and 3A ) and fecundity counts (Figure  3B ) were performed by classical linear regressions using generalized linear models (GLM) with binomial and Poisson distributions, respectively. Both tests were followed by multiple comparisons of means by the Tukey contrast method implemented in the package "multcomp"  (Hothorn et al. , 2008). The influence of pea cultivars and aphid lineage on aphid biomass (Figure  2B ) was analyzed by a two-way ANOVA.
ACKNOWLEDGMENTS Authors acknowledge to  Gaëtan Denis  and  Jean-François Le Gallic  for experimental support,  Drs Marie-Laure Pilet-Nayel  and  Alain Baranger  and their team for providing pea seeds,  Anne Moussart  for providing alfalfa seeds,  Dr. George P. Lomonossoff  for providing pEAQ vectors,  Prof. Tsuyoshi Nakagawa  for providing pGWB vectors and  Mathew Smoker  for Agrobacterium strains. This project was supported by the  French Agence Nationale de la Recherche  grant ( 13-JSV7-0012-01-Bugspit ) to AS and by  Procope German-French collaboration program  funded by the  German Academic Exchange Service (DAAD)  and  Campus France  to GK ( 57049694 ) and  J-CS  ( 30753SE ). Ph. D. grant to HB is funded by  INRA SPE and Région Bretagne.
SEM, histology and quantitative analyzes of cystogenesis For SEM the cilia were imaged at the Schepens Eye Research Institute (MEEI, Boston, MA). Mouse kidneys were fixed for 48 h in 1/2 strength Karnovsky's fixative (2% paraformaldehyde þ 2. 5% glutaraldehyde in phosphate buffer, pH 7. 4). Tissue samples were then rinsed three times in PBS, dehydrated in a graded series of Ethanol baths (35%, 50%, 70%, 95% and 2X 100% for 30 min each) and critical point dried in a Tousimis Samdri-795 Critical Point Dryer (Tousimis, Rockville, MD). Finally, kidney samples were mounted on aluminum stubs and coated with a 150A Chromium layer in a GATAN Ion Beam Coater 610. Cilia were viewed on a JEOL Field Emission Scanning Electron Microscope FESEM 7401F (JEOL, Peabody, MA). Cilia length was quantified with MetaMorph Imaging SeriesV R software (Molecular Devices Corp, Dowington, PA).
Cilia length distribution was calculated by measuring cilia in 20 random fields per sample. Total number of cilia measured in each group were 400. Statistical analysis was performed using GraphPad prism software (GraphPad Software, San Diego, CA). To determine whether these values differed significantly between experimental groups, P values were obtained using an unpaired parametric t-test. For histological analysis, kidneys were cut 4 lm thick from both sagital and transversal sections and stained with hematoxylin and eosin using a Tissue TekV R 2000 processor (Sakura-Finetek, Torrance, CA). Slides were digitized with a Nanozoomer digital slide scanner (Hamamatsu, Bridgewater, NJ) and processed with the Metamorph Software (Molecular Devices Corp). Cystic volume was measured as percentage of cystic area to a total section area normalized by body weight.
IF images were acquired on a Leica DM5500B microscope fitted with x40 objectives using Leica Application Suite Advance Fluorescence software (Leica Microsystems). Cell culture, siRNA transfection and primary cilium staining Wild type, jck and jck;Cdk5 cKO cell lines were established and maintained as described previously  (42, 60). Jck cells were cultured on collagen I coated glass slides (BD biosciences, SanJose, CA) and transiently transfected with negative control siRNAs, CDK2, CDK5, CDK7 or CRMP2 siRNA (Life Technologies, Carslbad, CA) using lipofectamine RNAiMAX as recommended by the manufacturer (Life Technologies). After transfection, cells were cultured for 48 h in complete culture medium and for an additional 48 h in serum-free medium. To study the role of R-roscovitine, cells were cultured for 48 h on collagen I-coated glass slides in complete culture medium followed by an additional 48 h in serum-free medium containing 20 lM R-roscovitine.
Background: Cost-effectiveness analysis has been recognized as an important tool to determine the efficiency of healthcare interventions and services. There is a need for evaluating the reporting of methods and results of costeffectiveness analyses and establishing their validity. We describe and examine reporting characteristics of methods and results of cost-effectiveness analyses conducted in Spain during more than two decades. Methods: A methodological systematic review was conducted with the information obtained through an updated literature review in PubMed and complementary databases (e. g. Scopus, ISI Web of Science, National Health Service Economic Evaluation Database (NHS EED) and Health Technology Assessment (HTA) databases from Centre for Reviews and Dissemination (CRD), Índice Médico Español (IME) Índice Bibliográfico Español en Ciencias de la Salud (IBECS)).
Literature search The results from a previous review that examined collaborative patterns of scientific production in a cohort of cost-effectiveness analyses conducted in Spain within the period 1989-2011  [23]  were updated with the studies published until December 2014 and subsequently analysed. A systematic search was performed in PubMed/ MEDLINE and other databases such as Scopus, ISI Web of Science, National Health Service Economic Evaluation Database (NHS EED) and Health Technology Assessment (HTA) databases of the Centre for Reviews and Dissemination (CRD) at the University of York, UK, as well as Índice Médico Español (IME) and Índice Bibliográfico Español en Ciencias de la Salud (IBECS). The search included a broad range of terms related to economic evaluations of healthcare interventions, costeffectiveness analyses and the geographical area "Spain".
For the section of geographical area, the search was based on a previously validated filter by Valderas  [26]  to minimize bias regarding the indexing of geographical items. This filter is constructed around three complementary approaches: (a) the term "Spain" and its variants in various languages; (b) related mainly to region and province place names and (c) acronyms for regional health services. PubMed/MEDLINE and the above mentioned complementary databases were searched from January 1, 2011 to December 31, 2014; the PubMed/ MEDLINE search strategy is provided in an online supplement to this review (see Additional file 1: Table  S1 ). Furthermore, manual searches were made for publicly available reports from the Health Technology Agencies and publications in specialized Spanish journals.
Data collection Two reviewers (with expertise in health economics and evidence synthesis) extracted data from each retrieved paper independently. Data were collected using a selfdeveloped item data collection form designed to assess reporting details of the studies. The process of data extraction was piloted in 20 records. A final data extraction form was then agreed. To enable description of the characteristics and the quality of reporting of costeffectiveness analyses in each report, we gathered the following information from all studies: year and journal of publication, impact factor (according to 2014 Journal Citation Report), country of first author, mention of a protocol, study objective, study design (e. g. randomized trial, observational study, simulation model), intervention targeted (e.
An important element in assessing research conduct and reporting is the study protocol. As showed in this review, only 4 % of studies reported working from a protocol. Study protocols play an essential role in planning, conduct, interpretation, and external review of primary studies, but also in evidence synthesis of primary research. For example, the preparation and publication of a well-written protocol may reduce arbitrariness in decision-making when extracting and using data from primary research for populating health economic models. When clearly reported protocols are made available, they enable readers to identify deviations from planned methods and whether they bias the interpretation of results and conclusions  [28, 29]. International registries (such as ClinicalTrials. gov for clinical trials and PROSPERO for systematic reviews and metaanalysis) are now a reality.
Acknowledgements This study received no specific funding. FC-L and RT-S are partially funded by  Generalitat Valenciana  ( PROMETEOII/2015/021 ),  INCLIVA  and  Institute of Health Carlos III/CIBERSAM. MR, EB-D and SP are partially funded by the  Spanish Health Services Research on Chronic Patients Network (REDISSEC). BH is supported by a  New Investigator Award  from the  Canadian Institutes of Health Research and the Drug Safety and Effectiveness Network. The authors are pleased to acknowledge  Dr. Oliver Rivero-Arias  ( University of Oxford, Oxford, UK ), who provided valuable feedback and advice throughout the study. We would like to acknowledge the editor,  Dr. Ian Shemilt , and the peer reviewers,  Dr. Andrew Booth  and  Dr Raúl Palacio-Rodríguez , for their helpful comments on our submitted manuscript.
Western Blot Whole cell lysates from human G3361 melanoma cells were run in duplicate on SDS polyacrylamide gel and transferred to a polyvinylidene difluoride membrane (GE Healthcare). The membranes were incubated with primary antibodies, i. e. anti-Hexokinase I (clone C35C4), anti-Hexokinase II (clone C64G5), anti-PKM1/2 (clone C103A3), anti-PFKP (clone D4B2), anti-Pyruvate Dehydrogenase (Clone C54G1), anti-GAPDH (clone D16H11), anti-HIF-1α (clone D2U3T), or anti-β-Actin (clone 8H10D10) (Cell Signaling Technology), and subsequently incubated with peroxidase-linked secondary antibody. The reactive bands were detected by using chemiluminescent substrate (Thermo Scientific). Quantitative Western Blot signal intensity analysis was performed using Image StudioTM Lite Software (LI-COR Biosciences).
Quantitative analysis of these results using Image StudioTM Lite Software (LI-COR Biosciences) hereby revealed that compared to the corresponding isotype mAb treatment controls, and controlled for relative expression of beta-actin, the inhibition of ABCB5 in G3361 cells with 25 μg/ml anti-ABCB5 mAb resulted in a 32% decrease in PFKP expression, and with 50 μg/ml anti-ABCB5 mAb in a 84% decrease in PFKP expression, in a dose-dependent fashion. This finding, along with the result that expression of other enzymes upstream of PFKP in the glycolysis pathway remained unaffected by ABCB5 blockade, suggests that ABCB5 regulates the glycolysis pathway at the level of PFKP, thereby explaining the observed reduced levels of the glycolytic by-products pyruvate and lactate in ABCB5-KD melanoma cells. We have recently demonstrated regulation of an IL-1β/IL8/CXCR1 cytokine signaling circuit by ABCB5  [2].
Therefore, in the present study, the hens were maybe too old, and consequently the egg internal quality too bad, to allow significant difference in egg freshness between groups. According to USDA-Agricultural Marketing Service guidelines, below 60 HU, egg freshness is considered as poor. HU should have been measured before 28 d of storage in order to see the influence of the melon concentrate here. While melon concentrate influence was not shown in egg freshness here, the supplementation exerted beneficial effects in egg characteristics. Thus, the weight of eggs was higher (by 6%) in the MC group, compared to untreated hens, without any modification of feed intake (data not shown). Other authors have shown similar results using some antioxidants  (Al-Harthi, 2014; Hammershoj and Steefeldt, 2012; Pan et al.
ACKNOWLEDGMENTS The authors appreciate the expert technical assistance of the veterinarian  Hervé Banon  ( SELARL de Vétérinaires ABIOPOLE, Arzacq-Arraziquet, France ). The authors are grateful to  Frédérique Chaucheyras-Durand  ( Minhos, INRA, Clermont-Ferrand, France ) for very helpful corrections. This work was supported by European fund for regional development, French public bank for invest, French fund and the following territorial communities:  Languedoc Roussillon  and  Provence Alpes Cote D'Azur regions, Vaucluse general council and great Avignon community.
Study Population Infant and neonatal mortality rates were computed as the ratio of total number of cases to total number of births summed over the two time periods,  2002-2005 and 2006-2009 , for each census block in the three MAs and for the city of Paris. Infant death data were collected from death certificates recorded in the City Halls of each metropolitan area. All cases were geocoded to the census block of the birth address. We obtained permission from the French National Commission for Digitalized Information and Liberty (CNIL; 911149) to geocode and analyze the health data. Birth addresses were matched to the corresponding census blocks using map databases (Correspondence Address-Urban Areas, 2004)-software issued by INSEE. The annual number of births by census block is available from the INSEE institute.
Census blocks without any births (for example, those containing only industrial buildings, or a park) were excluded from the analysis. We also excluded 24 census blocks (4. 5%) in Lille, 12 census blocks in Lyon (2. 3%) and 50 census blocks in Marseille (7. 9%) for which no NO2 measures were available, which represent 2. 7%, 2. 8% and 4. 3% of deaths excluded respectively. None of the census blocks in the city of Paris were excluded. The final dataset included 472, 492, 565 and 935 census blocks for Lille, Lyon, Marseille MAs and the city of Paris, respectively. The same number of census blocks was analyzed for both time periods.
Deprivation Index The potential social spatial risk factor of interest is a contextual deprivation index to characterize socioeconomic neighborhood level. We constructed a composite neighborhood deprivation index at census block level that measures area level deprivation. Socioeconomic and demographic data estimated from the 1999 (for the first period 2002-2005) and 2006 (for the second period 2006-2009) national censuses were selected to construct the deprivation index for each period and each metropolitan area separately. The domains covered by the index are: family, immigration status and mobility, employment and income, and education and housing. Successive principal-component analyses were used to synthesize this information. The inertia of the first component was maximized by deleting all variables only weakly correlated with this first component and variables with a below-average contribution (more details available in the article by Based on the data reflecting a decline followed by a plateau in infant mortality, the study period was stratified by two periods of 4 years  (2002-2005 and 2006-2009)  within the three large French MAs and the city of Paris.