dataesr/scientific-paragraphs-categorization huggingface dataset:
A 578 nt alignment of our 113 cloned Ostreobium sp. rbcL sequences was generated, to allow comparison with reference sequences from type strains or clones from Red Sea massive corals, using ClustalW Multiple Alignment tool in MEGAv6 software. Phylogenetic reconstruction was carried out using the maximum likelihood algorithm, with Kimura 2-parameter distance  39  and 500 bootstraps. Sequences of rbcL from the Bryopsidale Bryopsidella neglecta (AY004766) and Halimeda discoidea (AB038488) were used as outgroup for the targeted Ostreobidineae family. Operational Taxonomic Units (OTUs) were defined by clustering sequences with a cut-off of 99% similarity. Ostreobium rbcL sequences have been deposited in Genbank under Accession Numbers MG569988 -MG570021.
Statistical analyses. All statistical analyses were performed using the software R version 3. 2. 2. The mean and standard error were calculated for the following datasets: abundance and penetration depth of microborers in the host, and vertical/horizontal extension of juveniles. The non-parametric Mann and Whitney or Kruskal-Wallis tests were used as data did not meet assumptions of normal distribution (Shapiro test) and/or homoscedasticity (Bartlett test). When Kruskal-Wallis test was significant, a pairwise post-hoc analysis of Mann and Whitney was realized using Bonferroni correction  40  and α = 0. 05.
Acknowledgements This work was supported by  UPMC IPV  (' Interface Pour le Vivant') doctoral grant  to AM and  Sorbonne-Universités 'Cycles de la Vie ' project  CORALBOUCLE  to IDC and AT. Additional support came from ISPL-LOCEAN lab  UMR7159  to AT and MCAM lab  UMR7245  to IDC. We thank the expert aquariologists from the aquaria  ATPD (Paris) and Océanopolis (Brest)  for providing access to reproducing coral colonies and facilities for experiments. The  Canet-en-Roussillon aquarium and Eilat IUI (Israël)  are thanked for providing access to adult colonies. We thank  Sylvain Santoni  from  SupAgro Montpellier  for contributing an rbcL sequence amplified from a Pocillopora sp. collected in New Caledonia as part the  MIDACOR  project funded by the  French Ministry of Ecology  (supporting fund to AT).
Introduction Patients, families and clinicians rely on published research to help inform treatment decisions. Without complete reporting of the outcomes studied, evidence-based clinical and policy decisions are limited and researchers cannot synthesise, replicate or build on existing research findings. To facilitate harmonised reporting of outcomes in published trial protocols and reports, the Instrument for reporting Planned Endpoints in Clinical Trials (InsPECT) is under development. As one of the initial steps in the development of InsPECT, a scoping review will identify and synthesise existing guidance on the reporting of trial outcomes. Methods and analysis We will apply methods based on the Joanna Briggs Institute scoping review methods manual. Documents that provide explicit guidance on trial outcome reporting will be searched for using: (1)  an electronic bibliographic database search; (2) a grey literature search; and (3) solicitation of colleagues for guidance documents using a snowballing approach.
Reference list screening will be performed for included documents. Search results will be divided between two trained reviewers who will complete title and abstract screening, full-text screening and data charting. Captured trial outcome reporting guidance will be compared with candidate InsPECT items to support, refute or refine InsPECT content and to assess the need for the development of additional items. Data analysis will explore common features of guidance and use quantitative measures (eg, frequencies) to characterise guidance and its sources. Ethics and dissemination A paper describing the review findings will be published in a peer-reviewed journal. The results will be used to inform the InsPECT development process, helping to ensure that InsPECT provides an evidence-based tool for standardising trial outcome reporting.
6 8] [9]  Key information about how trial outcomes were selected, defined, measured and analysed is often missing or poorly reported. 2 3 7 10-14 1] [12]  Notably, 40%-60% of trials have been found to have at least one primary outcome that was changed, introduced or omitted between protocol and publication. 7 ithout clear and complete reporting of trial outcomes, researchers cannot adequately appraise, consolidate or replicate findings, hindering the translation of evidence into clinical practice and policy. Despite recommendations that a change in the reporting of trial outcomes is needed,  10 15-17  there is currently no dedicated strengths and limitations of this study ► We will employ a comprehensive search strategy to identify guidance on trial outcome reporting including electronic databases, grey literature sources, expert colleagues and reference list screening published in the last 10 years.
28 formation sources and search strategy Documents that provide guidance on trial outcome reporting will be searched for through: (1)  for sources using a snowballing approach. Reference list screening will be performed for included documents. This comprehensive search approach was selected as outcome reporting guidance is found commonly in 'difficult to locate' sources such as the grey literature in addition to the published literature. 16 29 ectronic bibliographic databases The search strategy was developed with consultation with an experienced research librarian (TAW) for MEDLINE and the Cochrane Methodology Register (online supplementary appendix B). Development of the search strategy was informed by analysis of the Medical Subject Headings (MeSH) terms and text words contained in the title, abstract and keyword headings from a sample of documents that provide guidance on outcome reporting identified from the personal collections of the InsPECT Group.
5 6 10 15 29 To increase sensitivity, the search includes all synonyms for study "outcomes" identified in a recent systematic review. 10 The search strategy was finalised following iterative refinements from reviewing a sample of the search results for relevance. The search strategy was validated using the same set of papers. 5 6 10 15 29 Nevertheless, we note that the concepts of "outcome", "guidance" and "reporting" are not indexed well using MeSH terms for the purposes of identifying guidance on reporting trial outcomes, and as a result, the electronic search strategy may not capture all relevant documents. A trained team member will perform the final searches from inception to date of search, export the search results into EndNote version X8  30  and remove all duplicates. Consistent with other reporting guideline developers, we limited the electronic bibliographic database search to MEDLINE and the Cochrane Methodology Register.
31 32 e anticipate that most reporting guidance documents will be located using other search methods, as described below. A previous systematic review to identify outcome reporting guidance specific to PRO did not yield a considerable amount of guidance from an electronic bibliographic database search  27  and this experience was replicated in an environmental scan for general outcome reporting guidance. 16 ublished peer-review articles eligible for inclusion will include: original articles, reviews, commentaries, editorials, letters or other opinion pieces. Trial reports or trial protocols will be excluded as these are unlikely to contain reporting guidance. Documents meeting these criteria identified through our other search methods will similarly be included.
Open access Reference list screening Additional sources will be sought by searching the full reference lists of all included sources. source selection Initial screening Titles and abstracts of documents retrieved from the electronic bibliographic database search will be screened for potential eligibility by one of two reviewers before full texts are thoroughly examined. The two reviewers will have graduate-level epidemiological training. A training exercise will be conducted on a random sample of 100 documents to ensure high inter-rater reliability between reviewers. Additional training and reliability testing on a larger sample will be performed if needed (eg, <0. 8 kappa score obtained). The reviewers will review training results with a senior member of the team to evaluate if additional training and/or a refinement of the inclusion criteria is needed.
The reviewers will review results with a senior member of the team to evaluate if additional training is needed. The remaining search results will then be divided and independently screened by one of the two reviewers, with periodic checks performed by a senior team member. Full-text screening and reasons for exclusion will be logged using a standardised form developed using Research Electronic Data Capture (REDCap) software. 37 Included sources will move to data charting. When necessary, we will contact authors to clarify eligibility criteria.
data extraction and charting The reviewers will extract data from the sources each included following full-text review using a standardised charting form developed using REDCap software,  37  with periodic checks of the extracted data performed by a senior team member. Two coauthors (one reviewer and one author not involved in developing the full-text screening form or the charting form) will pilot at least 10 documents through full-text review and charting before training for data charting begins. A preliminary analysis will also be performed to pilot the data summary process. 38 ecommendations identified within the included sources will be compared with candidate InsPECT items to support, refute or refine InsPECT content and to assess the need for the development of additional items. To achieve these aims, the reviewer will map each recommendation to the existing InsPECT candidate items, supported by full-text extraction captured in free text boxes within the charting form.
synthesis of results Data analysis will include descriptive quantitative measures (eg, counts and frequencies) to characterise the guidance document characteristics, their recommendations and the applicability of the recommendations to the list of candidate InsPECT items. We will have a meeting between the lead author, senior author and at least three coauthors to review study results to develop and approve any new candidate InsPECT items, if identified, and/or refinement of existing candidate InsPECT items.
Implications InsPECT will provide the first evidence-informed and consensus-based standard focused on outcome reporting in clinical trials and clinical trial protocols that can be applied across diverse disease areas, populations and types of outcomes. Complete and harmonised reporting of outcomes in clinical trials could improve research efficiency and reduce bias in data synthesis in systematic reviews. 11 41 The InsPECT CONSORT and SPIRIT extensions will help reduce research waste by facilitating evidence synthesis that will help inform decision making at the bedside, ultimately improving patient and health system outcomes. Although the results of this scoping review, and InsPECT, will focus on clinical trials and clinical trial protocols, we anticipate that the findings will be generalisable to other evaluative study designs.
Acknowledgements The authors wish to thank  Tamsin Adams-Webber  for her assistance in developing the electronic bibliographic database search strategy and  Mufiza Kapadia  for developing an initial draft of the InsPECT items. Contributors NJB was responsible for study conception. NJB, EJM, and MO were responsible for the initial study design. NJB and EJM drafted the manuscript. All authors critically reviewed and provided feedback on the study design and manuscript, contributed to the development of the candidate InsPECT items, and read and approved the protocol prior to its submission. MO obtained funding for the development of InsPECT. NJB is the guarantor of the review.
Unfortunately, cN-II staining (monoclonal antibody against cN-II clone ECNII) was not successful in our study samples (data not shown). To evaluate whether modulation of gene expression similar to the gene expression variability detected in the lung tissues might affect the cytotoxic activity of gemcitabine, we performed specific experiments with siRNA gene silencing against cN-II in three NSCLC cell lines. In these experiments, we observed expression differences comparable  with those detected in the clinical samples, and cytotoxicity assays showed that down-regulation of cN-II caused a significant increase of gemcitabine sensitivity. As negativecontrol siRNA, which did not affect cN-II expression, did not alter the cell growth, these results indicate that the modulation of gemcitabine cytotoxicity was determined by the specific perturbation of the expression of cN-II.
Indeed, recent studies in lymphoblastoid cell lines with the common polymorphism rs2274341 in the cN-II had lower cN-II expression and cytarabine sensitivity  [42]  and the presence of this polymorphism in lung cancer patients treated with gemcitabine was significantly associated with a better survival  [42, 43]. We can therefore hypothesize that the presence of single nucleotide polymorphisms (SNPs) of the cN-II gene might affect also clinical response by modulating cN-II expression, and further studies on these SNPs are warranted. The expression of cN-II might be influenced by several other factors. In particular, some recent studies suggested the key role of microRNA (miRNA) in the regulation on key determinants of chemotherapeutic drugs activity  [44]. According to the miRTarBase database a total of 62 miRNAs might target cN-II, but only 6 miRNAs were validated in next-generation sequencing studies in more than two articles, as described in the Supplementary Table  1.
Quantitative-PCR analysis From 50 to 500 ng RNA was reverse-transcribed. The resulting cDNA was amplified with the 7900HT sequence detection system (Applied Biosystems, Foster City, CA, USA). Forward and reverse primers and probes were designed with Primer Express 2. 0 (Applied Biosystems) based on dCK (NM_000788), cN-II (NM_012229), and CDA (NM_001785) gene sequence obtained from the GenBank, whereas primers and probes for RRM1 (NM_001033), RRM2 (NM_001034), hENT1 (NM_004955) and ERCC1 were obtained from Applied Biosystems Assay-on-Demand products (Hs00168784, Hs0035724, Hs00191940 and Hs01012158). Validation experiments were carried out with cDNA obtained from QPCR Human Reference Total RNA (Stratagene, La Jolla, CA, USA), as described previously  [48, 49]. Specimens were amplified in triplicate with appropriate nontemplate controls, and the coefficient of variation was <2% for all replicates.
After 24 hours, the cells were treated with gemcitabine (0. 01-500 nM) for 48 hours, while RNA was extracted from parallel wells, using the TRI REAGENT LS (Sigma-Aldrich). At the end of drug treatment, the cell growth inhibitory effect of gemcitabine was studied by direct cell count using the trypan blue. Growth inhibition was expressed as the percentage of gemcitabine-untreated controls (untransfected and negative-control siRNAtreated cells), and the 50% inhibitory concentration of cell growth (IC50) was calculated by non-linear least squares curve fitting (GraphPad PRISM, Intuitive Software for Science, San Diego, CA, USA). Additional pharmacological studies were performed with the cN-II inhibitor diethylpyrocarbonate (DEPC). Cells were plated in 96-well plates, and treated with gemcitabine for 72 hours alone or in combination with 10 μM DEPC.
Normality was tested using the Shapiro-Wilk test. Univariate and multivariate logistic regressions were carried out to determine the association between gene expression and therapy responsiveness, calculating the crude and adjusted odds ratio (OR) with 95% confidence intervals (CI) using the first, second and third quartiles of the gene expression distributions. Lower quartiles were used as reference category. The level of significance was set at 5%, all test were two-sided. The Kaplan-Meier method was used to plot overall survival, and the log-rank test was used to compare curves in univariate analysis. Data were analyzed using SAS 9. 2 (Cary, NC, USA) and STATA/SE 11. 1 (StataCorp. , TX, USA). All in vitro experiments were performed in triplicate and were repeated at least three times. Data were expressed www.
Data collection Qualitative concept elicitation interviews were conducted with caregivers and healthcare professionals, to elicit spontaneous reports about their experience of DS. All interviews were conducted by telephone in French by trained native language researchers following the semi-structured interview guide, using open-ended questioning designed to elicit spontaneous information from participants. This ensured that participants discussed concepts most important to their experience. Participants were then asked more focused questioning designed to probe issues not previously mentioned. For example, if participants had not spontaneously mentioned key symptoms or child and caregiver impacts. All interviews lasted up to an hour, were digitally recorded and transcribed verbatim. Scientific terms of key concepts (for example, anorexia and somnolence) were not used during the interviews, unless participants used these terms spontaneously.
Analysis Interview transcripts were translated into English prior to qualitative analysis, whereby quotes were sorted into concepts using methods derived from thematic analysis  [23]. Analysis was performed using Atlas. ti computerized software, which facilitates the breakdown of qualitative data into groups  [24]. An inductive analysis approach was adopted whereby all themes identified were driven by data rather than defined a-priori. A coding tree was developed prior to analysis of any interviews to structure how concepts and subconcepts would be coded. The coding tree was used consistently to guide coding of all interviews (Fig. 1 ). A team of experienced qualitative researchers coded the transcripts in parallel using a constant comparative method to ensure that codes were consistently applied  [25].
It is possible that a larger number of concepts could have been included in the final core set, for example by including patients in the Delphi panel. However, the final outcome measure would be considerably longer, more burdensome for caregivers to complete, and compliance in completing the measures would likely be reduced. This would result in a large number of missing data and therefore, jeopardizing the reliability of the results obtained from The results from both the qualitative interviews with caregivers and healthcare professionals and the Delphi consensus panel of clinical experts confirm the content validity of the patient-and caregiverrelevant concepts. Six validated instruments were identified for assessment of these concepts (and endpoints). Each provided good conceptual coverage and was thus considered appropriate to comprehensively assess DS, from both the patient and caregiver perspectives.
Acknowledgments The Delphi consensus panel was administered online in which the following clinical experts participated:  Professors Rima Nabbout ,  Catherine Chiron ,  Stephane Auvin  (France, respectively),  Renzo Guerrini  (Italy),  Elizabeth Thiele  ( United States of America ),  Ingrid Scheffer  (Australia), and  Sameer Zuberi  and  Helen Cross  (UK, respectively).
cruzi clade, using T. lewisi and T. microti as outgroup taxa; d) HSP70 sequences from trypanosomes of the T. cruzi clade in isolation, or combined with V7-V8 SSU rRNA and gGAPDH sequences. All sequences determined in this study were submitted to GenBank (Accession numbers given in Supplementary Table  1 ). Phylogenies were inferred using maximum likelihood (ML), parsimony (P) and Bayesian inferences (BI) analyses. Parsimony and bootstrap analyses were performed using PAUP  (Swofford, 2002)  with 500 replicates of random addition sequences followed by branch swapping (RAS-TBR). The ML analyses were performed using RAxML  (Stamatakis, 2006)  with tree searches performed using a GTR model with gammadistributed rate variation across sites and proportion of invariable sites (GTRGAMMA model), and 500 maximum parsimony-starting trees; model parameters were estimated in RAxML for the duration of the tree search.
Genes retrieved from trypanosome genomes for multilocus phylogenetic analysis Searches of 11 single-copy genes previously employed for multilocus analysis of T. cruzi DTUs  (Flores-López & Machado, 2011; Lima et al. , 2015b)  were performed using BLAST against genomes freely available in TriTrypDB and/or NCBI databanks of T. cruzi (Esmeraldo and CL Brener), T. c. marinkellei B7, T. rangeli SC58 and T. b. brucei 427, and against unpublished draft genomes generated by our group to facilitate multilocus phylogenetic analyses, and analyses of particular genes and gene families  (Lima et al. , 2012b; Caballero et al. , 2015). Draft genomes of T. cruzi clade trypanosomes (cryopreserved at the TCC collection) were used for gene surveys: T. cruzi G, T. c. marinkellei 344, T. dionisii, T. erneyi, T.
Spliced leader (SL) RNA sequences: amplification, sequencing, and data analysis. Entire SL RNA gene repeats were amplified and sequenced at both strands of 3-5 clones of each trypanosome, and the secondary structures of SL transcripts were obtained using the RNAdraw program with default settings (Maia da  Silva et al. , 2007; Lima et al. , 2013 Lima et al. , , 2015a)). The alignment of exon and intron sequences was manually refined. Network analysis of SL RNA genes was inferred by SplitsTree v4. 11. 3 using the neighbour-net method  (Huson & Bryant, 2006). Internode supports were estimated by performing 100 bootstrap replicates using the same parameters optimized for network inferences.
The joint analyses of all these data are crucial to hypothesize on better supported evolutionary scenarios for the whole T. cruzi clade. colombiensis, R. pallescens and R. prolixus suggests a degree of co-evolution between parasites and vectors. Acta  Trop. 120, 59-66. Vallejo, G. A. , Guhl, F. , Schaub, G. A. , 2009. Triatominae-Trypanosoma cruzi/T. rangeli: Vector-parasite interactions. Acta Trop. 110, 137-147. Weinman, D. , 1977. Trypanosomiasis of man and macaques in South Asia. In: Kreier, I. J. P. (Ed. ), Parasitic Protozoa. Academic Press, pp. 329-355.
Acknowledgments This study was supported by grants awarded to MMGT and EPC from  CNPq  (PROAFRICA, PROSUL and UNIVERSAL),  CAPES (PNIPB)  and  FAPESP  (process number  2016/07487-0 ) Brazilian agencies. Genome sequencing was greatly supported by the  ATOL (Assembling the Tree of Life ) Project from  National Science Foundation  (GAB,  NSF   DEB-0830056 ). OEA received PhD fellowships from  CNPq (PROTAX)  and  COLCIENCIAS (Colombia) ; PAO is a postdoctoral fellow of CAPES (PNPD); LL and AGCM are supported by a postdoctoral fellowship from  CAPES (PROTAX). We are thankful to  Cristina Schwarz  from the  Biodiversity Institute of Guinea Bissau  for collaboration with the  PROAFRICA Program , to the direction of the  Parque Nacional das Lagoas de Cufada , the warders for logistic support, and to people from Buba for their warm hospitality.
Signal processing The force and EMG signals were sampled simultaneously at 1 kHz using Biopac MP150 (Biopac System Inc. , Santa Barbara, CA), and stored on a personal computer after A/D conversion. The signals were processed off-line using AcqKnowledge 4. 3 Software (Biopac Systems Inc. , Aero Camino, Goleta, CA, USA). The force signal was smoothed using a digital zero-phase-lag finite impulse response low-pass filter with cut-off frequency of 20 Hz. The fullwave EMG signal was filtered using a digital filter with bandwidths of 10-500 Hz. All subsequent analyses were completed on the filtered signals. Force and EMG onsets during each MVC were identified using an automated method and checked visually by the same experienced investigator. For each muscle, the onset of EMG activity was determined as the first point of the signal exceeding the 95% confidence interval for baseline activity with minimum duration of 20 ms  (Di Fabio, 1987; Inglis et al.