dataesr/scientific-paragraphs-categorization huggingface dataset:
After washing, goat anti-rabbit Alexa FluorH 488 secondary antibody (1/1000) was applied on sections for 30 min at 37uC. Sections were washed and post-fixed in 4% PAF. All sections were mounted with Dako Fluorescent Mounting Medium (Dako, #S3023, Carpinteria, CA) and images were collected using a microscope (ZEISS Axiophot) coupled with a CCD camera and analyzed using ImageJH software. BrdU-stained cells were counted as SCs when located intra-laminin staining and correlated to the number of fibers (,500 fibers per muscle).
Inclusion criteria include patients undergoing cytotoxic chemotherapy for malignancy and receiving Nivestim as primary or secondary prophylaxis (NEXT and VENICE), or as treatment for ongoing FN (NEXT only). In accordance with European Union pharmacovigilance guidelines, the primary objective is to evaluate the safety of Nivestim™ by gathering data on adverse events in all system organ classes. Secondary objectives include obtaining information on patient characteristics, efficacy of Nivestim™ therapy (including chemotherapy dose intensity), patterns of use of Nivestim™, and physician knowledge regarding filgrastim prescription and the reasons for choosing Nivestim™. Data will be gathered at three visits: 1. At the initial inclusion visit, 2. At a 1-month follow-up visit, and 3. At the end of chemotherapy.
Objectives The authors present the design of two phase IV, longitudinal, observational, safety and efficacy studies that will evaluate the safety profile of biosimilar G-CSF (Nivestim™) for the prevention and treatment of FN in patients undergoing cytotoxic chemotherapy. The two observational studies are termed NEXT (Tolerance de Nivestim chez les patiEnts traités par une chimiothérapie anti-cancéreuse cytotoXique en praTique courante; NCT01574235) and VENICE (VErträglichkeit von NIvestim unter zytotoxischer Chemotherapie in der Behandlung maligner Erkrankungen; NCT01627990). The studies aim to evaluate the safety of a biosimilar G-CSF by producing evaluable long-term data on its use in a large patient population, without the constraints of a randomised controlled trial. The safety evaluation will include the recording of adverse events (AEs) in all system organ classes, as required by European Union (EU) pharmacovigilance guidelines.
Endpoints NEXT and VENICE are both gathering similar endpoints on the safety and clinical efficacy of Nivestim. The primary endpoint is the safety and tolerability of Nivestim™ evaluated by the collection of data on all AEs experienced by patients as well as the incidence of and reasons for hospitalisation. The secondary endpoints are varied and include efficacy and practice pattern data. For baseline patient characteristics, the study will record data on socio-demographics, surgical and therapeutic medical histories, the nature of the patients' malignancies (including location and stage), details of previous chemotherapy received, and clinical and laboratory parameters before treatment with Nivestim commenced. In the VENICE study only, data will be recorded on the CD34+ count at baseline.
Using a questionnaire, the studies will also collect data concerning the mode of treatment of patients with Nivestim™, including indication for treatment, dose, route of administration, treatment duration, and any delay in the initiation of Nivestim™ treatment owing to chemotherapy treatment. Timings of ANC nadir and chemotherapy adjustments will also be recorded. To understand the factors that influence prescribing behaviour for biosimilar filgrastims, both studies will collect data on physician age, sex, specialty, practice structure and job title. Additionally, their general and specific G-CSF prescribing habits will be observed.
Statistical analysis NEXT and VENICE will analyse the outcomes for all subjects and all researched study populationsall data will be described in the analyses and missing data will not be substituted. The analysis sets for the studies will comprise an all-treated set, a safety set, an efficacy set and an investigator set. The all-treated set will be made up of patients who have received Nivestim™ at least once, and whose enrolment visit was documented. The safety set will include patients from the all-treated set for whom at least one further visit has been documented. A sub population analysis of the safety set will involve stratification by age (<18, 18-65, >65 years), and stratification by tumour type (haematological versus solid). The efficacy set will include patients from the safety analysis set who fulfil all the inclusion and exclusion criteria and whose baseline ANC value and one other ANC value (ANC-nadir/ANC-value) has been documented either during the therapy or shortly afterwards.
In VENICE, patients from the efficacy analysis set will be stratified according to baseline CD34+ cell counts (low or high). The investigator set will include all participating physicians who have at least partially completed the Physician's Questionnaire. Endpoints with quantitative variables will be described in terms of the number of values, the number of missing values, means, medians, standard deviation, minima and maxima. Endpoints with qualitative data will be represented with percentages and frequencies. The duration of each patient's participation in the studies will be factored such that incidence rates can be extrapolated to patient-years. The level of significance for the two observational studies has been set at 0. 05; however, NEXT and VENICE have used different methods for estimating the required sample size to accurately represent the proportion of patients who will be hospitalised because of FN or infection during the study.
NEXT and VENICE come at a time regulators are seeking data from long-term observational studies in clinical practice. In many cases, regulatory agencies will approve a drug for clinical use and ask that additional data be gathered via pharmacovigilance programmes or via specifically designed phase IV clinical trials. In the UK, the Medicines and Healthcare products Regulatory Agency MHRA has been examining its approval process for medicines, and has gone as far as to suggest that certain new agents should receive an accelerated provisional approval based on registrational clinical trials, and that drugs should then be subject to close monitoring in a 'real world' setting prior to full approval  [45]. The same agency has contributed to the UK Clinical Research Collaboration report and the National Institute for Health Research's Research Capability programme, which together have demonstrated the possibility for collecting long-term data on a large scale  [46, 47].
Conclusion Owing to the duration of the studies, the large number of patients planned for enrolment in multiple centres, and the clinical practice setting of NEXT and VENICE, these studies will produce a significant amount of comprehensive, high-quality, evaluable data relating to the safety, efficacy and clinical use Nivestim™. The large cohort of patients, particularly for NEXT, will enable the objective evaluation of the safety and efficacy profiles of Nivestim™. Access to filgrastims remains limited for many patients and physicians in the EU  [25]. The NEXT and VENICE studies will provide healthcare agencies with much needed additional data, and may assist in maintaining and expanding access to biosimilar filgrastims for the treatment of CIN. Observational studies of differing designs have been conducted in chemotherapy-induced FN in the past.
Patients enrolled in a health maintenance organisation (HMO) were less likely to receive G-CSFs compared with non-HMO patients  [20]. Neither of these findings are particularly surprising; however, the study also found that 96% of patients were receiving G-CSF in clinical situations outside of label-and guidelinesmandated indications  [20]. This is a major deviation from recommended practice, the type of which could only be revealed in an observational study. These kinds of data support the notion of ASCO that there are opportunities to improve care and reduce the cost of G-CSF therapy  [23]. NEXT and VENICE are designed differently, and use label-mandated posology for the administration of G-CSF. In this way, the NEXT and VENICE trials will answer different clinical questions to existing observational studies, and thereby add to the totality of real world data on supportive care for cancer.
Microarray hybridization and data analysis Hybridizations were performed at the Genome Québec Innovation Centre (McGill University, Montréal, Canada). Raw data were corrected for background signals using the RMA algorithm and quantile normalization  [16]. Raw data were deposited to the Gene Expression Omnibus (GEO) public database (NCBI) under series entry "GSE51076". Expression levels obtained from three replicates for each condition were compared using the FlexArray 1. 3 software  [17]. Only genes showing a p-value < 0. 05 using the Empirical Bayes (Wright and Simon) algorithm were considered further. Since the RMA algorithm decreases the false positive rate and compresses the fold change, a 2-fold change cut-off value was used for the determination of differentially expressed genes. Functional classification and over-representation analyses were performed using the PseudoCAP functional classes (http://www.
Caenorhabditis elegans infection model Experimental procedures and data analysis were performed as previously described  [11]. Briefly, C. elegans wild-type Bristol strain N2 worms were grown at 22°C on nematode growth medium (NGM) agar plates using E. coli OP50 as the nutrient. Bacteria were grown as described above in M9G broth overnight and harvested, and 10 9 bacteria were spread onto NGM solidified agar plates and incubated at 37°C overnight. The lawn that covered the NGM agar plates was homogeneous and visually similar for each strain tested. The plates were cooled to room temperature for 4 h, and 20 to 30 L4synchronized worms were placed on the plates and incubated at 22°C. Worm survival was scored daily for 12 days using an Axiovert S100 optical microscope (Zeiss, Oberkochen, Germany) equipped with a digital camera (DXM 1200F; Nikon Instruments, Melville, NY).
positively regulated by SigX under the given condition), while 154 were upregulated. Twenty four genes that were differentially expressed between the wildtype H103 and the sigX mutant strain were selected for validation using qRT-PCR (Table  1 ), including sigX and oprF, a previously confirmed SigX gene target  [6, 7]. The comparison of expression data from microarrays and qRT-PCR demonstrated a very good correlation between the two datasets with a Pearson correlation coefficient of 0. 98 (data not shown). These data further confirmed that SigX regulates the expression of its own gene, a common feature of stressresponsive ECF sigma factors  [26] , as well as that of two major outer membrane protein encoding genes, oprF, as previously determined, and oprD. Based on PseudoCAP analysis  [18] , most dysregulated genes belong to six functional classes, which represented more than 10% of the total genes in each of these classes (Figure  1 ).
aeruginosa virulence  [55]  may support the link between SigX and biofilm formation and virulence. The Anr and Dnr proteins are two global transcriptional regulators homologous to Fnr (fumarate nitrate reductase regulator), and involved in anaerobiosis  [56]  and response to nitrogen oxides  [57] , respectively. Here we observed that anr was moderately up-regulated (1. 6 fold) while dnr was strongly up-regulated (3. 8 to 5. 8 fold) in the sigX mutant (Table  2 ). Consistently, several Anr/Dnr-regulated genes were upregulated (see Table  2 , Anr-regulated genes). Thus it seems likely that Anr and Dnr are more active in the sigX mutant than in the wildtype strain. Overall, since our mutant was grown under largely aerobic conditions, rather than the anaerobic conditions normally required to activate the Anr and Dnr regulators, these data may suggest a role for SigX in suppressing the production of genes required for the anaerobic lifestyle.
This work was supported by the  French government and Région Haute Normandie, France  (part of the doctoral fellowship to  G. Gicquel ), the  Grand Evreux Agglomération  (financial support of O. Maillot), the  European FEDER  funds number  32789  for the LMSM (post doctoral fellowships to  E. Bouffartigues  and  V. Oxaran ) and by  Canadian Institutes for Health Research (CIHR)  grants to ED and REWH. REWH was further supported by a  Cystic Fibrosis Canada  grant. ED holds a tier 2 Canada Research Chair and REWH holds a tier 1  Canada Research Chair. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
All of these data indicate that the Sabin3-like CVB3 IRES mutant was more handicapped than the Sabin 3 in PV1 (M) and the attenuated Sabin 3 strain  [16]. The poor translation efficiency of the Sabin3-like IRES mutant could be explicated by its inability to correctly bind some essential non-canonical translation factors during the initiation of translation. In order to test this hypothesis, formation of ribosomal complexes 48S and 80S was analyzed for both CVB3 IRESes (wild-type and Sabin3-like). The identity of ribosomal initiation complexes was confirmed by using stage-specific translation inhibitors. Small molecule inhibitors of bacterial protein synthesis have served as powerful tools in the elucidation of the function of the prokaryotic ribosome. Among the known inhibitors of eukaryotic translation is cycloheximide (CHX)  [47].
Acknowledgments We gratefully acknowledge all members of the  Laboratory UMR 8015: "Biological Cristallography and RMN ";  Faculty of Pharmacy; University Paris-Descartes (France)  for the scientific help. The work was supported by research grants from  DGRS/CNRS :  Direction Générale de la Recherche Scientifique, Tunisie et Centre National de la Recherche Scientifique, France.
Data. Patients. A total of 845 CD patients were recruited from six paediatric and adult gastroenterology tertiary centres. The diagnosis of IBD was based on Lennard-Jones criteria  [22]. Patients were included between April 2002 and October 2003 if the diagnosis of CD was done at least one year before inclusion and if the patients had a continuous follow-up in the reference centres. Patients affected by a disease treated by chemotherapy or radiotherapy were excluded. The study received an ethical agreement of the French national ethic committee "Comité de Protection des Personnes" from Hôpital Saint Louis, Paris, France. All participants signed a written informed consent for their information to be stored in the hospital database and used for research. Recorded phenotypic criteria. Clinical, endoscopic and radiologic data were retrospectively collected and phenotypic items were validated by the referent expert gastroenterologist of the patients  [2].
g. , high call rate. Population information. On the initial data set with 845 individuals self-reported information was available regarding the continental origin (Europe, Asia and Africa ) of individuals and of their parents. Subjects were assigned to admixed origin if continental origin of father and mother differed. The majority of individuals, namely 677 (80. 12%) were of European origin (see Table  1 ). The rest of the sample consisted of six admixed individuals (0. 71%), six African individuals (0. 71%), five Asian (0. 59%) and 151 individuals (17. 87%) with missing information (see Table  1 ). For the subset of 450 individuals, who were genotyped on the panel of 30 ancestry informative markers, self-reported population or missing population information was replaced by population information obtained from the ancestry informative markers.
This ancestry marker-based population information was derived from a PAM cluster analysis combining the 450 individuals with a HapMap 3 reference panel consisting of individuals with European, Sub-Saharan Africa or East Asian population background. The cluster analysis was performed using Euclidean distance on the 30 ancestry markers for the combined data set. All HapMap 3 individuals, who had the same population, agreed also in their PAM cluster assignment. The decision that one of the 450 individuals belonged to a given population, that is Europe, Sub-Saharan Africa or East Asia, was then based on the assigned PAM cluster. For each individual its silhouette width was determined which provides a measure of how well the individual fits into its attributed population. Within the sample of 450 individuals, 430 subjects (95.
Latent Class Analysis. A latent class analysis was performed on the 51 CD associated SNPs within CD cases. Latent class analysis was applied using Latent GOLD Version 4. 5 assuming binomial count variables. Missing data was handled by using the available information for each subject in the parameter estimation for the latent class model assuming that data is missing at random  [23]. The number of latent classes K was determined using a bootstrap procedure and likelihood ratio (LR) testing of the null hypothesis that the population is best explained by N classes versus the alternative hypothesis with N + 1 classes. Per latent class model, 500 bootstrap samples were generated. Individuals were assigned into their class based on the highest membership probability obtained from the latent class analysis.
Influential SNPs for a given class within the final latent class model were assessed via Z-scores as provided by the Latent GOLD software. All formal testing was performed at a nominal significance level of 0. 05. Principal component analysis. The available panel of 30 ancestry informative markers were submitted to a principal components analysis in the R-package snpStats version 1. 8. 1 and R-version 2. 15. 3  [24]. Prior to the principal component computation, the matrix G=(g ij ) i=1,. ,n,j=1,. ,m containing the genotypes g ij (=0, 1 or 2) for an individual i (i=1,. , n) at marker j (j=1,. , m) was standardised. Standardisation was obtained by subtracting the column mean 2p j from each column in G and by dividing each column by its standard deviation 2p j 1 -p j , where p j is the estimated minor allele frequency of marker j  [25].
A strong increase in the agglomeration criterion indicates that two dissimilar clusters are being joined and that the agglomeration can be stopped at this step. The strength of increase was evaluated by studying the percentage change in agglomeration criterion when going from N + 1 clusters to N clusters. For reasons of parsimony, we studied the percentage change in the agglomeration criterion over the last ten agglomeration steps. Both functions pamk and hclust were able to handle missing data by considering only available data per individual. When SNPs were excluded in the calculation of the pairwise distance between two subjects, the distance was scaled up proportionally to the number of SNPs used. Furthermore, we applied the PAM clustering algorithm and hierarchical cluster analysis directly on the population unadjusted SNP variables of the 450 individuals to enable a more direct comparison between the results on the adjusted and non-adjusted SNP data by using similar methodology.
Acknowledgements We thank the different people who contributed to the collection and characterisation of patients:  Jean-Frédéric Colombel ,  Marc Lemann ,  Laurent Beaugerie ,  Matthieu Allez ,  Jacques Cosnes ,  Jean-Marc Gornet ,  Jean-Pierre Gendre ,  Jean-Pierre Cezard ,  Frank M. Ruemmele ,  Dominique Turck ,  Habib Zouali ,  Philippe Dieudé ,  Nadem Soufir  and  Gilles Thomas. The authors would like to thank  Isabelle Cleynen  for interesting and valuable discussions.
acknowledge research opportunities offered by the  Belgian Network DYSCO  (funded by the  Interuniversity Attraction Poles Programme  and initiated by the  Belgian State, Science Policy Office. Their work was also in part supported by the  IST Programme of the European Community , under the  PASCAL2 Network of Excellence  ( Pattern Analysis ,  Statistical Modelling  and  Computational Learning ), IST-2007-216886, and by the  FNRS PDR Convention no 2. 4609. 11(1906648 ). Kristel Van Steen also acknowledges support by  Alma in Silico , funded by the  European Commission and Walloon Region  through the  Interreg IV Program. Emmanuelle Génin acknowledges funding by the grant ANR GENOPATH 2009 -CROHN MODEL. This work was financially supported by the  Ministère de la Santé (PHRC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
3 Figure  1. H-1PV and VPA synergize to induce cell death, oxidative stress and DNA damage in cervical and pancreatic derived cancer cell lines. Source data is available for this figure in the Supporting Information. A. Analysis of cell lysis. Cancer cell lines were seeded into 96-well plates and infected with H-1PV at the indicated MOI (pfu/cell) in combination or not with VPA (1 mM). The maximum viral dose tested is shown in grey. Cell lysis was measured after 72 h by means of the LDH assay, as described under Materials and Methods Section. Columns show average cell lysis values with standard deviation bars. Results from a typical experiment performed in quadruplicate are shown. Ã p<0. 05; ÃÃ p<0. 01; ÃÃÃ p<0. 001 as calculated by two sample Welch t-test and adjustment for multiple tests with the Bonferroni method.
Detection of apoptosis HeLa-NS1 and HeLa cells were plated onto coverslips and grown overnight before being treated or not with dox (HeLa-NS1) or H-1PV (HeLa) in the presence or absence of VPA (1 mM). 24 h post-treatment, the cells were loaded with 5 mM CellEvent™ Caspase-3/7 Green Detection Reagent (Invitrogen) for 30 min, followed by 4' ,6-diamidino-2-phenylindole (DAPI) staining. Positive cells were analysed on a fluorescence microscope (KEYENCE BZ-9000E, Japan) with the BZ-II Analyzer software.
GAPDH was chosen as internal control among 19 human reference genes (RealTime ready Human Reference Gene Panel, Roche Diagnostic) because its expression was stable after virus infection (data not shown). The threshold cycle of fluorescence (Ct) for each sample was determined by real-time PCR using the Mastercycler® ep realplex system (Eppendorf, Hamburg, Germany). Relative quantification of gene expression between the groups was performed applying the 2-DDCt method  (Livak & Schmittgen, 2001).
1% formic acid and solvent B contained 99. 9% ACN and 0. 1% formic acid. The nanoAcquity UPLC system was coupled online to an LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Bremen, Germany). Data were acquired by scan cycles of one FTMS scan with a resolution of 60,000 at a m/z ratio of 400 and a range from 300 to 2000 m/z in parallel with six MS/MS scans in the ion trap of the most abundant precursor ions. Instrument control, data acquisition and peak integration were performed with the Xcalibur software 2. 1 (Thermo Scientific). Database searches were performed against the NCBInr database (release 120608) with the MASCOT search engine (Matrix Science, London, UK; version 2. 1). The selected taxonomy was viruses. The peptide mass tolerance for database searches was set at 6 ppm, and fragment mass tolerance at 0.