dataesr/scientific-paragraphs-categorization huggingface dataset:
No articles were identified describing FTT as an adverse event following immunisation. A search of the US Vaccine Adverse Event Reporting System (VAERS) database (performed July 2016) described 47 reports where FTT was included in adverse event descriptions. There is no uniformly accepted definition of FTT in vaccine pharmacovigilance. This represents a missed opportunity, as data comparability is crucial to enable both systematic analysis of clinical trial safety as well as meaningful surveillance and investigation of adverse events reported in existing programs. The increasing implementation of vaccination programs in pregnancy, and breadth of antenatal vaccine research in diverse healthcare settings where FTT is seen, makes the development of a definition able to be used in all of these settings urgent.
Related term(s) of Failure to Thrive Malnutrition/under-nutrition represents the most common cause of FTT globally. Differential diagnoses of FTT that may present in infancy include: genetic short stature; constitutional growth delay; ''regression to the mean" also known as ''catch down growth"; and preterm infants whose gestational age is not corrected appropriately  [14]. Formulating a case definition that reflects diagnostic certainty: Weighing specificity versus sensitivity It needs to be re-emphasised that the grading of definition levels is entirely about diagnostic certainty, not clinical severity of an event. Thus, a clinically very severe event may appropriately be classified as Level 2 or 3 rather than Level 1 if it could reasonably be of non-FTT aetiology. Detailed information about the severity of the event should additionally always be recorded, as specified by the data collection guidelines.
We postulate that a definition designed to be a suitable tool for testing causal relationships requires ascertainment of the outcome (e. g. FTT) independent from the exposure (e. g. immunisations). Therefore, to avoid selection bias, a restrictive time interval from immunisation to onset of FTT should not be an integral part of such a definition. Instead, where feasible, details of this interval should be assessed and reported as described in the data collection guidelines. Further, FTT often occurs outside the controlled setting of a clinical trial or hospital. In some settings, it may be impossible to obtain a clear timeline of the event, particularly in less developed or rural settings. In order to avoid selecting against such cases, the Brighton Collaboration case definition avoids setting arbitrary time frames.
When using weight for age use the growth chart most accurate for the infants age. The birth to 6 months age range should be used where data is available for this range only, the birth to 2 years chart should be used where data is available beyond 6 months of life. When using weight for length, use the chart for birth to 2 years. For infants born less than 37 completed weeks gestation, the Intergrowth charts for postnatal growth standards in preterm infant should be used. All infants should be plotted on their respective growth chart using their corrected age. Links to relevant growth charts can be found in Appendix A. -Infants with no weight available AND -Physical examination consistent with FTT  6 AND -MUAC  7  indicative of severe wasting.
Guidelines for data collection, analysis and presentation of failure to thrive It was the consensus of the Brighton Collaboration Failure to Thrive Working Group to recommend the following guidelines to enable meaningful and standardised collection, analysis, and presentation of information about Failure to thrive. However, implementation of all guidelines might not be possible in all settings. The availability of information may vary depending upon resources, geographical region, and whether the source of information is a prospective clinical trial, a post-marketing surveillance or epidemiological study, or an individual report of Failure to Thrive. Also, as explained in more detail in the overview paper in this volume, these guidelines have been developed by this working group for guidance only, and are not to be considered a mandatory requirement for data collection, analysis, or presentation.
Source of information/reporter For all cases and/or all study participants, as appropriate, the following information should be recorded: (1) Date of report. (2) Name and contact information of person reporting  8  and/or diagnosing the Failure to Thrive as specified by country-specific data protection law. (3) Name and contact information of the investigator responsible for the subject, as applicable. (4) Relation to the patient (e. g. , immuniser [clinician, nurse], family member [indicate relationship], other). 3. 1. 2. Vaccinee/control 3. 1. 2. 1. Demographics. For all cases and/or all study participants, as appropriate, the following information should be recorded: (5) Case/study participant identifiers (e. g. first name initial followed by last name initial) or code (or in accordance with country-specific data protection laws).
Analysis may also include other characteristics like qualitative patterns of criteria defining the event. (35)  The distribution of data (as numerator and denominator data) could be analysed in predefined increments (e. g. measured values, times), where applicable. Increments specified above should be used. When only a small number of cases is presented, the respective values or time course can be presented individually. (36) Data on Failure to Thrive obtained from subjects receiving a vaccine should be compared with those obtained from an appropriately selected and documented control group(s) to assess background rates of hypersensitivity in non-exposed populations, and should be analysed by study arm and dose where possible, e. g. in prospective clinical trials.
g. population served, mode of report solicitation); The search strategy in surveillance databases; Comparison group(s), if used for analysis; The instrument of data collection (e. g. standardised questionnaire, diary card, report form); Whether the day of immunisation was considered ''day one" or ''day zero" in the analysis; Whether the date of onset 8 and/or the date of first observation 9 and/or the date of diagnosis 10 was used for analysis; and Use of this case definition for Failure to Thrive, in the abstract or methods section of a publication 17,18. finding of a necessary criterion (necessary condition) for diagnosis. Such an event should be rejected and classified as ''Not a case of Failure to Thrive". 18 Use of this document should preferably be referenced by referring to the respective link on the Brighton Collaboration website (http://www.
The XPS spectra were processed using Spectral Data Processor v2. 3 (SDP) software. The colloidal properties of the Ca 10-x Zn x (PO 4 ) 6 (OH) 2 with 0. 01≤ x Zn ≤0. 05 nanocomposites were investigated by Dynamic Light Scattering (DLS) and zeta potential using dynamic light scattering (SZ-100 Nanoparticle Analyzer, HORIBA, Ltd. , Kyoto, Japan) at 25 ± 1 • C. All the samples were diluted in distilled water before analysis. Before measuring of zeta potential, all samples were sonicated for 15 min. The pH of Zn:HAp suspension was equal to 7. For each sample analyzed, three determinations were recorded. The final value was determined by averaging the three measurements. The textural characteristics of synthesized nanocomposites were investigated by low temperature N 2 adsorption desorption using a Micromeritics ASAP 2020 Physisorption Analyzer (Micromeritics Instrument Corp.
Acknowledgments: This work was supported by  PN II 259/2014  project. The authors would like to thank  Cristina Liana Popa  for her participation in the samples synthesis and  Catalin Constantin Negrila  for performing the XPS measurements. Author Contributions:  Daniela Predoi  and  Isabelle Michaud-Soret  conceived and designed the experiments;  Aurélien Deniaud  and  Mireille Chevallet  performed the in vitro antibacterial experiments;  Aurélien Deniaud ,  Mireille Chevallet  and  Isabelle Michaud-Soret  analyzed the results of the in vitro antibacterial experiments;  Nicolas Buton  performed the colloidal characterization of the materials;  Simona Liliana Iconaru  performed the FTIR, SEM and EDX studies; Alina Mihaela Prodan performed the HepG2 cell viability assays and analyzed the data; and  Daniela Predoi  wrote the paper.
Selected cohorts and the study population Details on the design of both studies have been reported before  [23, 24]. GCS was launched in 2004 in Golestan province, Northeast of Iran and recruited 50,045 adults aged between 40 and 87 years from Gonbad city and 326 rural villages (20% urban, 80% rural). Five years after recruitment, a random sample of about 12,000 participants were invited to participate in a re-measurement study. The same questionnaires were filled and all participants were asked to give 30 ml of blood for biomarker measurements including fasting plasma glucose (FPG) and hemoglobin A1c (HbA1c). We used data from the remeasurement sub-sample in this analysis. Tehran Lipid and Glucose Study (TLGS) enrolled 15,005 participants who were 3 years of age or older residing in the 13th district of Tehran, between 1999 and 2001.
Additionally, dietary information was gathered before diabetes diagnosis in both studies. Thus, any measurement error in white rice intake would be non-differential. Although we have previously shown a notable agreement between self-reported diabetes and diabetes as defined by measurements of blood glucose  [34] , the self-reported nature of diabetes assessment at baseline in Golestan could have led to overestimation of diabetes incidence in this population. Third, the relatively small sample size in TLGS affected the reliability of some of the estimates from the stratified analyses (i. e. , physical activity). Finally, the possibility of residual confounding by unmeasured confounders or measurement error in measured confounders cannot be ruled out. Some of the strengths of this study include its large sample size, accurate outcome assessment (FPG in both studies, HbA1c in GCS and 2-h plasma glucose in TLGS) and available data on many potential confounders as well as the opportunity to assess the association between white rice intake and diabetes in urban and rural populations in the Middle East.
Ongoing studies Two large cardiovascular outcome studies of the effects of omega-3 fatty acids are currently being performed in subjects with hypertriglyceridemia and mixed dyslipidemia  [5]. In the REDUCE-IT (NCT01492361), EPA ethyl ester (Vascepa R ) is evaluated in combination with statin therapy against statin alone, whereas the STRENGTH (NCT02104817) study evaluates a combination of statin treatment with either carboxylic acids with a DHA-to-EPA ratio of 1:2. 75 (Epanova R ) or corn oil. It should be noted that the omega-3 doses used in the latter two studies (4 g/day) are higher compared with previous trials (1-1. 8 g/day;  [17] [18] [19] [20] ).
RNA-sequencing The analysis of RNA-seq data was performed as described previously  [43]. In brief, RNA-seq data was subjected to an in-house quality control workflow. Read quality was assessed using FastQC (http://www. bioinformatics. babraham. ac. uk/projects/fastqc/) (v0. 10. 1) to identify sequencing cycles with low average quality, adapter contamination, or repetitive sequences from PCR amplification. Alignment quality was analyzed using samtools flagstat  [58]  (v0. 1. 18) with default parameters. RNA-seq data was aligned to the genome using gapped alignment as RNA transcripts are subject to splicing and reads might therefore span two distant exons. Reads were aligned to the whole Mus musculus mm10 genome using STAR aligner  [23]  (2. 3. 0e_r291) with default options, generating mapping files (BAM format).
Read counts for all genes and all exons (Ensembl annotation v72) were obtained using FeaturesCount (http:// bioinf. wehi. edu. au/featureCounts/). For data visualisation, BAM files were converted into WIG and BigWig files using the MEDIPS 'MEDIPS. exportWIG' function with a window of 50bp and RPM normalization. For the differential expression analysis, read counts that were generated with FeaturesCount were compared between groups using DESeq2  [64]. Genes with a >0. 5 logFC cut off and FDR-adjusted p-value smaller or equal to 0. 05 were considered to be differentially expressed.
Deregulated expression and activation of Calpains in sCJD Increase in intracellular Ca 2+ concentration leads to the activation of the Ca 2+ -dependent non-lysosomal cysteine proteases Calpains, which are over activated in several pathological conditions including neurodegenerative diseases  [26, 47]. Thus, Calpain expression and activation state was analysed in sCJD. At mRNA expression level, Calpain 2 (CAPN2) was overexpressed in the frontal cortex and cerebellum of sCJD MM1 and VV2 subtypes. (CAPN1) levels in the cerebellum of sCJD MM1 cases, no major alterations were detected for Calpain 1 (Fig. 2a ) and for the small regulatory Calpain subunit 4 (CAPN4/ CAPSN1) (Additional file 4: Figure  S3A ). Analysis at protein level matched data obtained at mRNA level. In addition, the presence of autolytic Calpain 2 bands was found in sCJD cases as an indirect observation of increased Calpain activity (Fig.
Cathepsin S activation in sCJD The demonstration of neuronal lysosomal disruption in sCJD made us speculate that release of lysosomal content, especially Cathepsins, could be a key determinant on the neurotoxicity linked to prion diseases through the so-called Calpain-Cathepsin hypothesis observed in some neurological and neurodegenerative conditions  [88, 103]. We profiled the complete Cathepsin family signature in the cortex of the tg340-PRNP129MM sCJD mice from the RNA-seq dataset at clinical stages. Eight members of the Cathepsin family as well as their endogenous inhibitor Cystatin C appeared overexpressed compared to controls (Fig. 6a ). Among upregulated Cathepsins, Cathepsin S retaining proteolytic activity at neutral pH  [53] , and Cathepsin D, associated with increased risk of variant CJD  [10]  and with enhanced immunoreactivity in sCJD  [56] , were initially explored.
Acknowledgments We greatly thank  A. Iserentant ,  A. Lannoye ,  P. Populaire ,  F. Van Hoye ,  W. Nguefack  for their contribution on the soil characterization,  C. Siebert ,  R. Guicharnaud ,  B. Sigfusson ,  P. Savage ,  S. Gislason  for their help in the field in Iceland,  S. Hammond  for ICP-MS analyses, and  W. Debouge  for Zn isotope chemistry and  J. De Jong  for the MC-ICP-MS maintenance. The manuscript benefited from discussions with  H. Titeux  and  O. Pourret. We thank the Associate Editor and three anonymous reviewers for their constructive comments to improve the manuscript. S. Opfergelt is funded by the  "Fonds de la Recherche Scientifique" (FNRS, Belgium ,  FC69480 ) and acknowledges a funding from  FSR  ( Fonds Special de Recherche 2008 ,  ADRE86C5 ,  UCL, Belgium ). Funding for Zn isotope analyses was provided by a grant from  FNRS  to  N.
ERI-ICP aims at disseminating "official" (but ameliorable) methods and protocols applicable to the exploration of cellular pathologies. ERI-ICP also emerges as an organizing platform for international conferences and participates in efforts of data integration and distribution. As a consequence, to provide a platform for exchanging data and ideas in the cellular pathology field, ERI-ICP now launches a new journal, Cell Stress. This open-access, online-only journal covers all areas from basic research to therapy development and evaluation. Cell Stress intends to provide a platform for unraveling the link between failure to maintain homeostasis, cellular aberration and organismal pathologies. In addition, Cell Stress will promote the quest for diagnostic markers, as well as therapeutic interventions against a manifold of pathologies, tying basic to translational research and clinical application.
Articles may also feature the use of integrative systems biology, which implements the application of "holistic" data (e. g. metabolomics, genomics, transcriptomics) as well as trans-species approaches to link ephemeral sources of stress to disease etiology and progression. Cell Stress meets the challenge of handling this broad thematic diversity by a publication strategy built on several pillars. The journal uses the experience and reputation of its sister journal, Microbial Cell, and the dynamic technological platform of Shared Science Publishers, a young publishing house devoted to the dissemination of scientific data and knowledge as a universal public good and not a restricted pay-per-view source. Importantly, Cell Stress is a journal with its policies designed and its content curated by scientists, who have a broad experience in the publishing field, but who are primarily active researchers rather than specialists only committed to the publishing process itself.
This is clearly mirrored at several levels, from the uncomplicated submission system to the attempt to untighten formal rigidness. In fact, Cell Stress implements a high degree of formal flexibility to facilitate the inclusion of all kinds of key observations in an accurate manner. Therefore, the article types offered by the journal are diverse and range from primary research articles and reports to different types of review and commentary articles, most of which are not subjected to limits in terms of word count, number of figures or references. This policy relieves the authors from the formal pressure that otherwise might force scientists to omit crucial explanations, data and references. While this policy aims at breaking restrictions, the Cell Stress peer review and editorial handling guidelines do also demand scientific precision in the manuscripts.
Thus, referees and editors will ensure that the language of the article is clear and concise, that the figures reflect only results essential for the conclusions of the article, and that the references reflect a correct and balanced picture of the literature. Of note, Cell Stress is committed to the principles of open-access publishing, making all articles freely available on the World Wide Web to be read, downloaded, stored, printed, copied, and distributed by any scientist or interested individual around the globe. To finance this policy, Cell Stress charges authors or research sponsors for each article published with article processing charges (APCs). This follows the concept that publishing a research work and thus relevant data and/or stimulating thoughts is an elemental part of doing research.
Consequently, the costs generated from publication should be considered as one of the basic expenses to be covered by research grants or by the authors' institutions. The last decade has witnessed this concept being embraced and translated into institutional policies as reflected in the so far almost 600 signatories of the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities. This policy echoes our conviction that the free exchange of ideas is one of the most valuable cornerstone and accelerator of scientific advancement, on the one hand, and public knowledge, on the other hand. For scientists publishing with Cell Stress, this open access policy maximizes the visibility of their works, promoting the quick and unrestricted use of their published data by other researchers.
This should be taken into account for nutritional databases and when experimental balanced diets have to be formulated. The supramolecular structure of lipids also differs from a food to another. Examples of native structures from animal or vegetal origins are presented in Figure  2. Complex supramolecular organizations are found for instance in egg yolk, milk fat globules or oilseed as oleosomes. Common characteristics are a TAG core surrounded by an interface or a membrane varying in composition, organization and complexity. In raw milk, the lipid globule is stabilized by a complex trilayer membrane made of phospho-and sphingo-lipids, cholesterol and proteins  (Lopez, 2011; Raynal-Ljutovac et al. , 2011). In egg yolk, the TAG core is stabilized by a monolayer interface containing phospholipids, proteins and cholesterol.
Participants and Data Collection We carried out the current study in a sample of students who already participated to a research project: the i-Share project (internet-based Students Health Research Enterprise). This project (www. i-share. fr) is an ongoing prospective e-cohort study of French-speaking students which started to recruit in February 2013. It is supported by three main French universities: the Universities of Bordeaux, Versailles, and Nice. In these partner universities, students are contacted via their email, by communication in the classes, or on the campuses. However, students not belonging to the three partner universities can also participate in the study by filling the i-Share baseline questionnaire online. To participate in i-Share, volunteers had to be registered at a university or higher education institute and understand French.
We asked them to fill out a first questionnaire about e-cigarette use, and they were then invited to answer follow-up questionnaires every 6 months for 18 months. Our current analysis was conducted on data collected by the first e-cigarette questionnaire. They then received a recall by email once a week for three weeks if they did not fill it in. Overall, 2875 students completed the first questionnaire about e-cigarette use between February and April 2016 (response rate: 34. 1%) and 2720 of them were retained for this analysis (Figure  1 ). We excluded from the analysis 136 subjects who were no longer students and 19 who did not specify their student status. Participants included and excluded are shown in Supplementary Materials (Tables  S1  and S2 ). All subjects gave their informed consent for inclusion before they participated in the i-Share project and its ancillary studies.
Tobacco-Smoking Regarding tobacco-smoking, we distinguished three groups: (1) current smokers were those smoking daily or occasionally (less than once a day); (2) former smokers had previously smoked tobacco but were no longer doing so; and (3) never smokers had never tried tobacco. If they wanted, current and former smokers specified their age (in years) when they tried smoking. When data were available, we calculated the number of years between trying e-cigarettes and trying tobacco. We categorized this continuous variable in three groups: (1) e-cigarette before tobacco; (2) e-cigarette and tobacco the same year; and (3) e-cigarette after tobacco. Current smokers filled in additional questions about their nicotine dependence, number of attempts to quit smoking, and desire to stop tobacco.
Former smokers were those who did not smoke at time of study; 2 n = 14 (data missing on smoking status); 3 Electronic cigarette use: never e-cigarette users were those who had never tried it. Current users comprised those regularly using e-cigarettes at time of survey, daily, or occasionally (less of once a day). Former users were those who were not current smokers among experimenters, as opposed to current users; 4 n = 378 (data missing on age, in years, at which students tried tobacco and/or e-cigarettes); 5 Test sequence of tobacco and e-cigarette: explored in smokers and former smokers. Chi-2 test about difference between smokers and former smokers; 6 Nicotine in cartridges: this question was asked only to current users of e-cigarette (n = 98). AOR: adjusted odds ratios. OR: odds ratios.