dataesr/scientific-paragraphs-categorization huggingface dataset:
e. , we assumed a dosage effect of the CNVs: gene_i ~b0 + b1CNV CNV = -1,0,1. Gene Ontology (GO) analysis was performed using the library topGO v2. 14. 0. Gene Set Enrichment Analysis (GSEA) was conducted using the Broad Institute algorithm v2. 1. 0 [75, 76]. We used pre-ranked gene lists defined according to the LIMMA results based on the dosage model, and we utilized MSigDB C2 (c2. all. v4. 0. symbols. gmt) to collect curated gene sets from online pathways, and publications in PubMed. The data are accessible through the NCBI's Gene Expression Omnibus with the GEO Series accession number GSE66468.
Statistical analysis We assessed statistical significance using Sigma Plot software (Sigma). All acquired behavioral data were analysed using one-way or two-way ANOVA with repeated measures followed by Student's t-test or Tukey's post-hoc test as appropriate. Otherwise, the non-parametric Kruskal-Wallis analysis and Mann-Whitney U-test were used. Student's t-tests were used to compare recognition index values to the chance level (50%). A Pearson's chi-square test was used to evaluate mutant allele transmission. The data are represented as the mean ± standard error of the mean (s. e. m. ) and the significance threshold was P < 0. 05 unless otherwise indicated. In electrophysiological experiments, input-output relationships were compared initially by mixed model repeated-measures ANOVA and the Bonferroni post hoc test implemented in Prism 5 (GraphPad Software, Inc.
, San Diego, CA, USA) using individual slice data as independent observations. Because several slices were recorded routinely from every mouse, the fEPSPmax, PPF and LTP values between wt and mutant mice were also compared using a two-way nested ANOVA design with genotype (group) and mice (sub-group) as factors (STATISTICA v. 10, StatSoft, Inc. , Tulsa, OK, USA). To compare data obtained from Del/+, Dup/+ and Del/Dup mice to their litter-matched wt counterparts, we used post hoc Dunnett's Multiple Comparison test on data from individual slices. Statistical effects were considered significant if P < 0. 05. Graph plots and normalization were performed using OriginPro 8. 5 software (OriginLab, Northampton, MA, USA). Throughout the text, the electrophysiological data are presented as the mean ± s.
This work has been supported by the  National Centre for Scientific Research (CNRS) , the  French National Institute of Health and Medical Research (INSERM) , the  University of Strasbourg (UDS) , the  "Centre Européen de Recherche en Biologie et en Médecine" , the  European commission  ( AnEUploidy  project to YH,  LSHG-CT-2006-037627 ) with a fellowship from the  "Fondation pour la Recherche Médicale " to TA ( FDT20130928080 ). This study also received support from  French state funds through the "Agence Nationale de la Recherche " under the frame programmes " Investissements d'Avenir"  labelled  ANR-10-IDEX-0002-02 ,  ANR-10-LABX-0030-INRT ,  ANR-10-INBS-07  PHENOMIN as well as by grants from the  Simons Foundation  ( SFARI274424 ), the  Swiss National Science Foundation  ( 31003A_160203  and  CRSII33-133044 ) to AR, the  EU   FP7 large-scale integrated  project  GENCODYS  ( FP7-COLLABORATION PROJECT-2009-2.
Science at the heart of the digital transition The digital transition is marked by an explosion in the quantity of data that are available and accessible at any time and any place in the world. This age of Big Data is characterised by: the absence of borders and the globalisation of information; The absence of borders 7 The Internet is the flagship tool of the digital transition. This global network is notable for the absence of physical borders and entry visas, being instead characterised by cross-border flows and exchanges through the world of information. 8 Thanks to the IP protocol and the interconnection between the various operators, the Internet constitutes a seamless end-to-end network. 9 Despite flaws and inequalities such as the digital divide or equipment with differential flow rates according to a country's public policies, this global network provides everyone with access to globalised information.
Digital STI: A tool for exploration and analysis STI is primarily seen by researchers as a working instrument to which they must have access, which they can share, exchange, reuse or reprocess for the needs of their research subject. As a raw material, STI is part of the scientific process. Human and social sciences Access to publications: "In the human and social sciences, with regard to recent scientific publications, while more and more French-language journals offer free access immediately or after a few years (mainly through HumaNum, BSN or OpenEdition), English-language journals are often confined to rather expensive platforms. " Access to numerical data or the data produced by research: "Platforms for exchanging numerical data … have also been established (Quetelet Network, DIMESHS, etc.
The most important of these (PubMed) is managed by the US National Institutes of Health (NIH). " PubMed also provides access to an unformatted version of any article published commercially describing work funded by the NIH. Access to research data: "Many publishers, including Nature, also make publication of an article conditional on the depositing of mass data associated with a publication on a platform that is accessible to all, free of charge. " Access to material: "It should be noted that this requirement goes beyond digital data and also concerns material produced within the framework of a publication. " Physics Access to research data: "Free access to raw data is not yet very widespread. " "Many digital libraries have been formed and made freely accessible by groups of researchers. ".
Posting data online and sharing data should be taken into account as part of the assessment of researchers. On this point, the CNRS Ethics Committee recommends that: "The contribution to the work of data sharing must be recognised in assessments and decisions concerning the promotion of researchers. To facilitate this recognition, the COMETS recommends that appropriate indicators be created and that a section on these activities be added in the activity report and the annual activity sheet concerning researchers. " 12 + New criteria for the evaluation of researchers will need to be introduced, and in any event publication in Open Science will need to be taken into account.
The march towards Open Science seems to have an historic inevitability. In addition, stressing the fundamental importance of published works in the way researchers are assessed, the Recommendation suggests revising the system for academic advancement: by rewarding "researchers who participate in a culture of sharing the results of their research, in particular by ensuring open access to their publications"; by "developing, encouraging and using new, alternative models of career assessment". Horizon 2020. In the framework of the Horizon 2020 programme (an EU financial instrument for the development of an Innovation Union, which provides funding for research and innovation for the period 2014-2020), the European Commission has made free access to scientific publications a general principle. The Guidelines on Open Access to Scientific Publications and Research Data were drafted in the framework of this programme and first published on 16 December 2013.
The plant heritage is managed by the Common Service for the Study and Preservation of Heritage Collections. The Herbarium of the University of Toulouse has about 300,000 8  plant sheets distributed in sixty different physical herbaria. The collection consists of mushrooms, lichens, mosses, flowering plants, algae and conifers collected by researchers and students during their research in the south of France and abroad since 1811. In order to unify the methods of documentation among these physicallydistributed herbaria, a centralized database of these specimens, called Flora, is being produced in partnership with the Botanical Conservatory of the Pyrenees. A plant sheet digitization project is currently underway with the University of Montpellier. In this research, it was necessary to compare physical and digital herbaria; because the digital herbarium of the University of Toulouse is not yet available, observations were conducted on other digital herbaria.
Typically specimens would be moved after drying, but some MNHN herbaria were kept in this state. Thus the project of digitization has also been an opportunity to improve the storage conditions of the physical collections. Properly preserved, the plant is secured on board by glue, thread or an overlay, and then annotated. These annotations are made either directly on the board alongside the plant or on labels which are then fixed to the board. The electronic database also refers to related documents, such as registries, collection notebooks or DNA samples. On the digitized specimen, a code appears on the image which is used to identify the physical plant. So we can say that an herbarium is the result of three stages of work. The first stage involves the collection of the plant. A plant is generally chosen for collection because of its peculiarity and its usage by the people who share its environment.
Czech Republic The impact of META-NET and similar initiatives in the Czech Republic is most visible in the area of language resources, where two long-term infrastructural projects have been established recently: the LINDAT repository and the Czech National Corpus project at Charles University in Prague, funded by the Ministry of Education. More than 70 large, specialised resources have been made available in the LINDAT repository, which is also part of CLARIN and serves both the humanities research and LT needs; its metadata structure is compatible with META-SHARE and CLARIN, and it is harvested by both networks. Awareness has been raised, mainly thanks to the White Paper  (Bojar et al. 2012) , at both Czech research grant agencies, even though a specialised LT programme has not been constituted yet on the research side.
Denmark The White Paper  (Pedersen et al. 2012 ) raised the awareness within the society regarding LT and the need for actions to avoid the digital extinction of Danish. The idea of a Danish LT resource collection has matured and is currently a central focus area for the Danish Language Council. Recently funded LT projects include an ERC grant, "Lowlands", which aims to develop robust learning algorithms for LT with a focus on languages and domains for which little linguistically annotated data exists, as well as "Semantic Processing [of Danish] across Domains", funded by the Danish Research Council. Furthermore, a digital humanities infrastructure (including LT elements) is being nationally funded via the DigHumLab project and through CLARIN-ERIC. In 2014, a CLARIN Nordic Network was funded by NORD-FORSK.
Two new funding programmes have been initiated by the German Federal Ministry of Economics and Energy (BMWi) and the German Federal Ministry of Research (BMBF) recently. While Big Data is at the core of both programmes, LT is included with regard to Text Analytics. DFKI is involved in the project Smart Data Web (funded by BMWi) and the Berlin Big Data Center (BBDC, funded by BMBF), among others. Our close collaboration with the German Federal Ministry of Economics and Technology led to  META-FORUM 2013 (Sept. 19/20, 2013 ) being organised at the conference centre of this very ministry.
Greece META-NET reinforced interest in LT in Greece. The White Paper  (Gavrilidou et al. 2012 ) generated sustainable interest not only from the media but also from government representatives at ministerial level. Recently, the White Paper attracted the interest of the Athens Field Office of DG Translation and served as input at the conference "The Future of Language Professions", an event of the EU's Translating Europe initiative. This interest has led to a substantial improvement in the position of LT in the Greek research agenda. A new large-scale collaborative effort has been endorsed by the Ministry of Education, aiming to design a research infrastructure as an open framework for LRs/LTs. The new initiative, "Language and Knowledge Technologies Enabled Content Access and Services Infrastructure", will provide access to Greek language resources, digital content and processing services through a distributed platform, offering to its users (scholars, researchers, industry) services enabling data access, processing and annotation, evaluation as well as application development.
Italy As a result of the White Paper  (Calzolari et al. 2012) , the achievements of META-NET have been presented twice in conferences and debates organised in the Italian Parliament. There is now much more awareness of the need for both research and technology in the LT area. Almost all existing resources for Italian are now available through META-SHARE, which has become the natural repository for the distribution of resources produced in national or European projects. EVENTI (Evaluation of Events and Temporal Information), one of the new tasks organised in the Evalita 2014 Evaluation campaign for Italian, has chosen to distribute training and test data through META-SHARE, which is also gaining more visibility in the private sector. As a significant example, SAVAS, a FP7 SME project, focusing on innovative products and services for multilingual subtitling, has chosen to distribute all datasets through their own META-SHARE node.
The warm reaction of the private sector towards the Spanish resources available through META-SHARE has also been noticeable. The nodes are now supported by the Spanish national projects Speech Tech4All and the IULA-UPF CLARIN Competence Center, co-funded by the EU Regional Structural Funds and the Generalitat de Catalunya. In 2014 and 2015, the Regional Council of Aquitaine, The Ministere de la Culture et de la Communication of France and Linguamondi in Corse, organised several workshops to prepare roadmaps for the development of technologies and resources for Occitan and Corsican respectively. Participants were briefed about what has been done for other languages. Specifically, experts in Basque and Catalan were chosen to present the status of LT/LR in these two languages, including META-NET and the SRA.
A large number of Swedish resources is now available through META-SHARE. META-NET helped to reduce the fragmentation in the Swedish LT community, instilling a sense of common cause at the national level, as evidenced by a number of joint funding proposals and awarded grants. In 2013 the Swedish Research Council approved a proposal coordinated by the University of Gothenburg for Swedish membership in the CLARIN ERIC, where Sweden is now the tenth member as of October 2014. Negotiations are underway towards setting up SWE-CLARIN, a national infrastructure consisting of nine CLARIN centres including universities, a national data archive, and two public offices charged with coordinating the safeguarding of Sweden's linguistic and cultural heritage. Sweden participated in a successful proposal to the Nordic research funding agency NORDFORSK to set up a Nordic  CLARIN network (2014 CLARIN network ( -2017)).
Acknowledgments The first phase of the  META-NET initiative  was co-funded by  FP7  and the  ICT-PSP  programme of the  European Commission  through the contracts  T4ME  (grant agreement no. 249 119 ),  CESAR  (no. 271 022 ),  METANET4U  (no. 270 893 ) and  META-NORD  (no. 270 899 ). CRACKER has received funding from the  EU 's  Horizon 2020 research and innovation programme  (no. 645 357 ).
After 5 days, the total number of secondary neurospheres was counted in each condition using microscope analysis. The morphology of primary neurospheres was observed with an inverted microscope (Leica DMI6000; Leica Biosystems, Nussloch, Germany, http://www. leicabiosystems. com) equipped with a CoolSNAP-HQ2 camera and analyzed using MetaMorph, version 7. 1. 7. 0, software (Molecular Devices, Sunnyvale, CA, http://www. moleculardevices. com). They were also observed using scanning electron microscopy.
Neurospheres were washed three times with PBS before adding 3 mmol/l 49,6-diamidino-2-phenylindole (DAPI; Sigma-Aldrich) for 5 minutes. After PBS washing, coverslips were mounted with a Pro-Long Gold antifade solution. Finally, neurospheres were observed with an inverted fluorescent microscope (Leica DMI6000; Leica Biosystems) equipped with a CoolSNAP-HQ2 camera and analyzed using MetaMorph, version 7. 1. 7. 0, software (Molecular Devices), or with a confocal microscope (Leica TCS SP8; Leica Biosystems). The morphology of neurospheres was observed by incubating dissociated NSCs on 10 mg/ml of poly-L-lysine (Sigma-Aldrich)coated coverslips in 24-well plates (5 3 10 3 cells per well). The NSCs were treated with 0, 20, or 60 mmol/l biotinylated NFL-TBS. 40-63 peptide for 7 days to obtain neurospheres.
abcam. com) antibodies diluted 1/200, 1/200, 1/50, 1/200, 1/100, and 1/100, respectively, in PBS with 5% bovine serum albumin. After washing three times in PBS, primary antibodies were revealed using Alexa Fluor 568-labeled anti-mouse or anti-rabbit antibodies (Thermo Fisher Scientific Life Sciences) at a 1/200 dilution in PBS containing 5% bovine serum albumin. They were incubated for 90 minutes at room temperature and then washed in PBS. The brain sections were then counterstained with 3 mmol/l DAPI for 5 minutes and rinsed twice with PBS. Finally, the slides were mounted with the ProLong Gold antifade reagent and observed with an inverted fluorescent microscope (Leica DMI6000; Leica Biosystems) equipped with a CoolSNAP-HQ2 camera and analyzed with the MetaMorph, version 7. 1. 7. 0, software (Molecular Devices) or with a confocal microscope (Leica TCS SP8; Leica Biosystems).
ACKNOWLEDGMENTS We acknowledge the assistance of  Rodolphe Perrot  and  Guillaume Mabilleau  from  Service Commun d'Imageries et d'Analyses Microscopiques ,  Catherine Guillet  and  J érôme Cayon  from  Plateforme d'Analyses Cellulaire et Mol éculaire , and the staff from  Service Commun d'Animalerie Hospitalo-Universitaire. This work was supported by  Association Française contre les Myopathies ,  Association pour la Recherche sur le Cancer ,  Ciblage Mol  éculaire et  Th érapeutique, Maturation & Accelerating Translation With Industry, L'Universit é Nantes, Angers ,  Le Mans , and  "R égion des Pays de la Loire " to J. E. C. L. -C. was supported by the  "Minist ère de l'Enseignement Sup érieur et de la Recherche ," by  Association pour la Recherche sur le Cancer , and by the " Soci ét és d'Acc él ération du Transfert de Technologie Ouest Valorisation.
Background: The risk of several types of cancer is increased in type 2 diabetes mellitus. The earliest possible diagnosis of cancerdifficult within regular outpatient diabetes care -is of utmost importance for patients' survival. The aim of this multicenter, retrospective (years 1998-2015), case-control study was to identify risk factors associated with malignancy in subjects with diabetes treated in a typical outpatient setting. Methods: In the databases of 3 diabetic and 1 primary care clinics 203 patients (115 women) with type 2 diabetes mellitus who developed malignancy while treated for diabetes were identified. The control group consisted of 203 strictly age-and gender matched subjects with type 2 diabetes without cancer. Factors associated with diabetes: disease duration, antidiabetic medications use and metabolic control of diabetes were analyzed.
Methods The study was approved by the institutional Bioethics Committee at the University of Rzeszow and by the all appropriate administrative bodies. The study was carried out in accordance with ethical standards laid down in Polish regulations and in an appropriate version of the Declaration of Helsinki (as revised in Brazil 2013). After Bioethics Committee approval, we performed retrospective analysis of existing individual patients' records in the databases of 3 diabetic and 1 primary care clinics. Inclusion criteria for the 'case' group included: cancer diagnosed after diagnosis of type 2 diabetes, at least one HbA 1c measurement before or at the time of cancer diagnosis, date of diabetes diagnosis, diabetes treatment, BMI and history of comorbidities available. We identified 203 patients (115 women) with T2DM eligible for analysis.
Data analysis covered the period from January 1998 (the first eligible patient with diagnosed cancer) to 30 April 2015. The mean age of diabetic patients at the time of cancer diagnosis was 67. 1 ± 9. 7 years, and 141 persons were aged ≥65 years. The control group consisted of 203 strictly age-and gender matched subjects with T2DM without cancer. Patients were selected from the same databases in the case-control manner, with the 1:1 ratio. For each 'case' patient, an eligible 'control' subject with the same gender, and with the nearest possible date of birth was chosen, and any given pair was recruited always at one center to avoid impact of different treatment algorithms used in different clinics. Individuals who died within the analyzed time period but before the moment of data collection were also included into the analysis if their data were available.
Data for patients with malignancy were taken from the period preceding cancer diagnosis (index time). Data for the 'control' subjects were assessed from the same index time, i. e. , if the 'case' patient had cancer diagnosed in April 2009, the data for his/her comparator were taken from the same period. In both groups metabolic control of diabetes (mean HbA 1c from the preceding up to 3 years before index time, if available), diabetes duration, antidiabetic medications (also from the preceding up to 3 years, and each drug was classified as "used" if it was taken for at least 6 months), mean insulin dose from the preceding 6 months, and duration of insulin treatment up to the moment of cancer diagnosis were analyzed. Also place of residence (rural, small cities or urban), smoking habits (current, former or never smoker), presence of comorbidities (hypertension, hyperlipidemia and cardiovascular disease), BMI and use of aspirin were also included into the analysis.
Cardiovascular disease was confirmed if the patient had a history of non-fatal myocardial infarction, hospitalization for acute coronary syndrome, non-fatal stroke, revascularization or amputation. Statistical analysis of the data was performed using SigmaPlot for Windows version 12. 5 (Systat Software Inc. , San Jose, CA, USA). The analysis was performed in 2 stages. In the first stage comparison of the two groups was made. The continuous data were analyzed using an unpaired two-tailed Student's t-test or by a Mann-Whitney rank sum test where appropriate. The categorical data were compared using χ 2 test. In the second stage patients were divided into subgroups according to BMI (<25. 0, 25. 0-29. 9, 30. 0-34. 9 and ≥35. 0 kg/m 2 ), diabetes duration (<5. 0, 5. 0-9. 9, 10. 0-14. 9 and ≥15.
Importantly, age and gender were not included into risk analysis, because the patients were strictly matched according to them. Data regarding association between HbA 1c level and risk of malignancy are divergent. Some studies showed continuous relationship between increasing HbA 1c level and cancer risk  [23] [24] [25] , others found non-linear association  [26, 27]  (the second one only among women), or elevated risk of malignancy above the specified HbA 1c threshold of 7. 5 % (colorectal cancer)  [28]. In the study by Miao Jonasson et al. no relationship between HbA 1c level and cancer was found  [29]. In the recent meta-analysis significant association between chronic hyperglycemia and elevated risk of several types of malignancies with the exception of prostate cancer was demonstrated  [30].