dataesr/scientific-paragraphs-categorization huggingface dataset:
Altogether, the six taxa of interest accounted for 36. 4% of the DNA-V4 reads, 23. 5% of the cDNA-V4 reads, and 32. 4% of the cDNA-V9 reads. In addition to the taxonomic classification of OTUs in the OTU table, we classified the unclustered 454 and Illumina reads to obtain the raw reads for probe checking (see Results) and to double-check the taxonomic classification. For this second classification, we downloaded GenBank sequences representative of each picoeukaryotic group of interest and used this specific taxon database to retrieve HTS reads by local BLAST (sequence similarity, Ͼ97%).
In some cases (Blanes, Oslo-2010 DCM, Roscoff, and Varna DCM), phototrophic cells were Ͼ6 times more abundant than heterotrophic cells. Counts of phototrophic picoeukaryotes obtained by flow cytometry correlated well with the microscopic counts in the 10 samples analyzed (linear slope, 0. 74; Pearson's r ϭ 0. 9; P Ͻ 0. 001). When the regression line was forced to intercept at 0, the slope was 0. 90. The general eukaryotic probe EUK502 was also used to estimate total picoeukaryotic abundance. Cell counts by TSA-FISH were always lower than the DAPI counts (60% on average) (Fig. 1 ). In fact, the sample with the highest total cell abundance was different if estimated by DAPI (Oslo-2010 DCM) or by TSA-FISH (Oslo-2009 surface). The regression between the two data sets was significant but had a slope very distant from 1 (linear slope, 0.
26; Pearson's r ϭ 0. 74; P Ͻ 0. 05). When the line was forced to intercept at 0, the slope was still very low (0. 43). There was some tendency to this discrepancy, as TSA-FISH seemed to underestimate more severely the total cell counts in samples dominated by very small cells. Clearly, DAPI counts provided a better estimate than TSA-FISH counts of total picoeukaryotic abundance; therefore, DAPI counts were used to calculate the relative cell abundances of each of the 6 specific picoeukaryotic groups. TSA-FISH counts of each group were in the numerator, and total DAPI counts were in the denominator. Abundance of specific picoeukaryotic taxa. We used TSA-FISH to estimate the total abundance of six groups of picoeukaryotes, chosen because they were well represented in the se-quencing data sets of the picoplankton from the studied samples (and poorly represented in the nanoplankton; see Table  S1  in the supplemental material).
This analysis was done with raw reads (extracted from the initial data set by using GenBank sequences of each group as search templates) to take into account all sequence variants. The number of raw reads per group obtained from this way was very similar to the number derived from the OTU table  (Table 2 ). About 1,000 to 3,000 reads were extracted per group (except MALV-II, which had about 30,000 reads). Then, we calculated the percentage of raw reads that had a 100% match with the probes (Table  2 ). The five specific probes validated this way retrieved a very high percentage of reads, more than 95%, in all cases except MALV-II (83%). Therefore, the vast majority of reads from these five groups in our samples had the target region of the probes. The probe targeting Micromonas was not designed at the V4 region of the 18S rDNA, so it could not be directly evaluated with V4 reads from this study.
Therefore, we took the OTUs affiliating with Micromonas (7 OTUs and 11,166 reads), retrieved the closest GenBank complete sequence from these OTUs (nearly identical at the V4 region), and verified the effectiveness of the probe against these 7 GenBank sequences. Only 3 sequences (accounting for 30% of the reads) exhibited a perfect match, whereas the remaining 4 sequences had a mismatch in the first position of the probe. Thus, probe MICRO01 could be improved perhaps by removing the first base, but since this mismatch is located in the first position, it likely does not affect the FISH counts. Comparison of group-specific read abundances and TSA-FISH counts. The relative abundances of 454 V4 reads (from DNA and cDNA templates) and Illumina V9 reads (from cDNA templates) of each group of interest were compared with the relative cell abundance assessed by epifluorescence microscopy (spe-cific TSA-FISH counts relative to total DAPI counts) in 13 samples for the V4 reads, and in 9 samples for the V9 reads (DCM samples from Naples and Oslo were excluded) (Fig.
Our results indicate a good correlation between the two methods, implying that more cells result in more sequences, although they give different quantitative information, i. e. , the relative read abundance cannot be directly related to relative cell abundance. The cD-NA-V4 survey showed the best agreement with TSA-FISH abundance, providing 1:1 relationships in half of the assayed taxa, but the cDNA-V9 was best for other taxa. Thus, the targeted region of the 18S rDNA gene clearly affected the relative abundance of specific taxa. Finally, based on the data mentioned here, we suggest that the sequencing platform used (454 or Illumina) does not produce major biases in diversity. In conclusion, the most quantitative option is to use cDNA templates rather than DNA, while the choice of the targeted region will result in different relative abundances in each particular taxon.
FUNDING INFORMATION This work, including the efforts of Colomban de Vargas, was funded by  BioMarKs  ( 2008-6530 ,  ERA-net Biodiversa ). This work, including the efforts of  Ramon Massana , was funded by  DEVOTES  ( FP7-ENV-2012 ,  308392 ,  European Union ). This work, including the efforts of Irene Forn, was funded by  MICRO-3B  ( FP7-OCEAN-2011 ,  287589 ,  European Union ). This work, including the efforts of  Caterina R. Giner , was funded by  MEFISTO  ( CTM2013-43767-P , MINECO).
This technology, which was developed and used by the oil and gas industry for more than a century (Economides & Nolte 1989), has been adapted to deep geothermal wells during the previous 20 yr to enhance the fracture network, particularly in EGS projects  (Rose et al. 2007; Nami et al. 2008; Portier et al. 2009). The chemical stimulation of well GRT-1 targeted minerals that plugged the fracture zones. The stimulated zones and targeted minerals were identified from the cuttings and the post-drilling well-logging data from well GRT-1. The stimulation was performed using the biodegradable chelating agent GLTA (glutanic acid N, N -diacetic acid) to dissolve carbonates (calcite, dolomite, ankerite) and sulphates (Recalde  Lummer et al. 2014). This environmentally friendly fluid does not dissolve alumino-silicates (clay minerals, quartz), is effective up to 200 • C and penetrates more deeply into the rock mass than conventional stimulation fluids.
No proppant or packer was used during the hydraulic stimulation, and the injectivity index was improved by a factor of 1. 50. After the TCH treatments, the injectivity of well GRT-1 increased fivefold. Only a few significant microseismic events were recorded during the thermal stimulation, approximately a couple of hundred events were detected by the automatic detection system during the hydraulic stimulations based on data from the real-time seismic monitoring network deployed during the stimulation, and none occurred during the chemical simulation. Due to the low wellhead pressure during the stimulation operations, no events were felt by nearby residents  (Maurer et al. 2015).
Well logging and mud logging During all drilling operations, mud-logging data were recorded. Cuttings were collected from the drilling mud every 3 or 4 m of advancement, and their analysis provided a lithostratigraphic survey of the well. It also indicated where the well intersected major fractures based on the presence of secondary quartz and hydrothermal minerals and higher calcite content (Fig. 3 ). Investigation of the rock cuttings was an efficient method for identifying hydrothermally altered zones in the granite  (Dezayes et al. 2014; Meller et al. 2014). To evaluate the geometry of these fractures, an acoustic image log was acquired following the drilling operations in December 2012 (Fig. 2 ). The present study is based on these acoustic image logs, which were produced by Schlumberger and are referred to as Ultrasonic Borehole Images (UBIs).
M E T H O D O L O G Y Data processing of acoustic image logs The acoustic image logs were processed using the software program WellCAD (ALT). First, the amplitude (AW) data and transit times (TT) in the image logs recorded in 2012 were reoriented with respect to magnetic north based on the azimuths acquired by the orientation tool. In 2013, unfortunately, the orientation tool was missing during the acquisition. Thus, the 2013 images were reoriented manually by visually superimposing 2013 images on the 2012 images. The manually reoriented images were rotated clockwise by an angle that varied with depth based on the rotation of the acoustic tool during the up-hole acquisition. The variation in the offset angle is important, and uniform rotation by a fixed angle in a long vertical section is not possible.
The standard deviation was estimated from the transit time in 2012 and 2013 for different average diameter. We used the casing of well GRT-1 as a fixed reference that did not vary with depth or time. Its internal diameter given by the manufacturer is 22. 05 cm. We then measured this casing diameter using the acoustic tool both in 2012 and 2013. The average diameter estimated from the transit time in 2012 was 22. 17 cm ±0. 011, which indicates a systematic error of +1. 2 mm with respect to the reference value (Table  2 ). Accordingly, all the calculated diameter data obtained in 2012 were then reduced by 1. 2 mm. The average diameter estimated from the transit time in 2013 was 21. 95 cm ± 0. 017, and the acoustic tool measurements obtained in 2013 were reduced accordingly by 1 mm. The source of error between measurements in 2012, 2013 and the given value of the internal diameter is assumed to be governed by the error on the internal diameter given by the constructor.
When the acoustic tools encountered cavities in the borehole wall, the diameters exceeded the acquisition range, and null data were recorded. In these instances, the transit time data appear as saturated zones, that is, white spots, in the images. A 3-D image of the well was constructed by mapping the acoustic image onto the geometry provided by the transit times and using the amplitude data to create the colour palette in the 3-D image (Fig. 4 ). From this 3-D image, cross-sections of the well were prepared. Another technique was developed to assess error bars of the diameter data in the sandstones. A massive zone (one not cut by fractures) was identified between depths of 2208 and 2210. 5 m (Fig. 4 ). The rms of this zone was ±0. 095 cm in 2012 and ±0. 084 cm in 2013 (Table  2 ). Thus, for each cross-section, the thickness of the line in Fig.
Accuracies of the fracture attitudes are important for the comparison of the 2012 and 2013 images. In this study, the primary source of error in the fracture dip direction and dip angle arose from the ability of the interpreter to pick dipping planes consistently. To quantify the accuracy of measurements from the acoustic image log in the openhole section of well GRT-1, a series of tests were performed. These tests involved three acoustic image interpreters who hand-measured strikes and dips independently in the hydrothermally altered granite section. The reproducibility error was ±3. 85 • for the strikes and ±1. 04 • for the dips. The overall error considering the inclinometer accuracy and the reproducibility error may be regarded as very low. The colour scale of the amplitude and transit time data were adjusted visually.
A C K N O W L E D G E M E N T S This work was based on data from the ECOGI EGS project at Rittershoffen, France. A part of the work was performed in the framework of the LabEx G-Eau-Thermie Profonde, which is co-funded by the French government under the program 'Investissements d'Avenir'. The manuscript was prepared as a contribution to the PhD thesis of Jeanne Vidal, co-funded by ADEME (French Agency for Environment and Energy). A part of this work was done in the framework of the H2020 DESTRESS Eu project which has received funding from the European Union Framework Programme for Research and Innovation under grant agreement No. 691728. The authors would like to kindly thank two anonymous reviewers for their contributions and manuscript improvement.
Exploratory phase: survey and database Public users of health information in the European Union were surveyed to see what they already understood about clinical trials, and what they wanted to learn more about. The survey also aimed to identify differences between the perspectives and approaches of the public and those of experts concerning what they need to learn about clinical trials, and to systematically identify open access resources that explain important aspects of clinical trials. The purpose was to inform subsequent resources development and enable new resources to be tailored to the public's self-identified needs. For the survey the ECRAN experts developed a list of the important concepts needed to understand clinical trials. The survey was piloted informally with a few people from the Cochrane Consumer Network, without further validation, because these concepts are wellestablished.
The questions used were multiple-choice, free-text and matrix-type. The surveys were distributed through: (a) PatientView, an organisation that holds a database of patient groups, through emails to 20,000 English-speaking patient groups across Europe, and (b) National Health Service Choices, a website funded by the English Department of Health, dedicated to informing the public on health issues. No reminders or follow-up emails were sent to non-responders. Open access resources that explained important aspects of clinical trials were sought through (1) professional contacts (e. g. survey of members of the Network to Support Understanding of Health Research); (2) online searches by ECRAN partner organisations; (3) clinical trials search engines or trial registers; and (4) websites communicating information about clinical trials to patients, the public and/or professionals, developed by governments, institutions, and patient organisations.
Resources focusing on one or more of ECRAN's key messages were collated. These resources were catalogued in an online Koha database, so further data could be collected and the resources reviewed and evaluated. Koha was chosen as it is a highly developed and reliable open source library cataloguing system that has templates for the major categories of resources (e. g. videos), the ability to add or edit templates, a flexible frontend design, Web 2. 0 functionality for rating resources, and the ability to use iFrames to host particular content elsewhere to facilitate dissemination. The Koha database is also searchable in all 23 European languages. It works through a search engine into which people, in order to identify and link to learning resources, can put the terms about which they wish to learn more.
Results Exploratory phase: survey and database A total of 1852 completed survey responses were received. Although the survey was directed at lay people, less than half the respondents were health service users, patients, parents or carers. The other responders were health advocates (e. g. health organisations), medical or allied health professionals, health educators, policymakers or librarians. The overwhelming majority had a college/university-level qualification or higher. Nonetheless, over half of the respondents said their main reason for seeking health information was for personal use. Three quarters of respondents were women. The survey provided a glimpse into the lack of public understanding about how clinical trials are conducted. While most participants (73 % or 1358/1852) understood why clinical trials are necessary, over half (57 % or 1060/1852,) understood 'little or not at all' about the four pre-licensing phases.
Development phase: materials Several materials were developed by the ECRAN project, available at www. ecranproject. eu, including the Koha database. The materials differed according to target users as shown in Table  1. Although we received suggestions for improving translations of materials on our website during the development phase, we did not receive any negative comments about the style or our approach to the topics covered. The animated film  [20]  starts with the story of Scottish naval surgeon, James Lind, and his quest to learn how to treat scurvy by conducting an intervention experiment in 1747, hailed today as one of the earliest clinical trials in the world. The film's modular structure allows either the whole film or its eight different modules to be displayed, covering: a clinical trial, ethics committees; randomisation; double blinding/masking; analysing the data; 'one trial is not enough'; outcomes to be important to patients; and some pitfalls.
Examples of images of the film are in Fig. 3. About clinical trials  [21]  is a section of the website with different documents. These include a 76-page original interactive tutorial, in which the phases of clinical research are described in simple language, with a selfevaluating test. In this section, several glossaries have been assembled using information collected in the database of resources and the analysis of websites. No ECRAN glossary was developed because many good-quality glossaries are already available through academic institutions, scientific societies, patients' organisations, or other European projects. At the voice glossary of the ECRAN website a list of available glossaries with related links is available for each of the six languages of the project. The list includes ten glossaries in English, six in Italian, two in French, seven in German, two in Spanish, and one in Polish selected on the basis of the information collected in the database of resources, an analysis of existing websites, and suggestions from partners.
Dissemination phase Some data on dissemination of the ECRAN project are reported in Table  2. As all the materials developed are available and downloadable by the ECRAN website it is difficult to know the number of people or organisations receiving the materials, as well as the geographic distribution. To celebrate the completion of the project and to facilitate dissemination about it, ECRIN and ECRAN organised a 3-day event in Luxembourg in 2014. Here the audience largely consisted of ECRIN and ECRAN participants. On 20 May 2014 the whole ECRAN project as well as the ECRAN video were presented to an international audience during the ECRIN and ECRAN celebrations of International Clinical Trials Day. The audience consisted of patients' representatives, ECRAN partners, ECRIN researchers, international researchers, and journalists.
Acknowledgements ECRAN is a project funded by the  EU   Seventh Framework Programme , grant agreement no. HEALTH-FX-2012-305125. The funder played no role in the project design; in the collection, analysis, and interpretation of data; or in the writing of the report and the decision to submit the article for publication. All researchers were independent from funders. The authors thank a large number of dedicated people working in the different work packages of the  ECRAN  project:  Alicja Szofer-Araya ,  Christine Kubiak  ( Institute National de la Santé et de la Recherche Médicale, France );  Christa Bast  ( University Medical Centre Freiburg, Universitätsklinikum Freiburg, Germany );  Koen Block  and  Nikos Dedes  (European  AIDS Treatment Group, Belgium );  Insa Bruns  ( KKS-Network of the Coordinating Centres for Clinical Trials, University Hospital of Cologne, Germany );  Simona Calmi ,  Giulia Candiani ,  Sergio Cima ,  Davide Coero Borga ,  Paolo Griselli ,  Marco Milano ,  Debora Serra  and  Valentina Vecellio  ( Zadig, Science and Health Communication, Milano, Italy );  Berit Grevstad  ( The Copenhagen Trial Unit, Centre for Clinical Intervention Research, Copenhagen, Denmark );  Gianna Costa ,  Niccolò Pieri ,  Anna Roberto  ( IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Italy ).
A total of 13,289 participants with diabetes who had both patient and nurse forms filled out were included in the database. Not every parameter will reflect this total number owing to the occasional skipping of an item in the survey. However, the large overall numbers help overcome any potential bias that missing data may introduce. Patient demographic data included age, sex, type of diabetes, years with diabetes, years injecting, and devices used. We recognize the importance of economic standing of patients, availability of health care resources, and rural vs urban settings in influencing outcomes. However, it was decided not to pursue such detailed socioeconomic data in an already-lengthy survey with so much intercountry variability. Although we do not have precise data on place of residence, we do know that most centers that performed the survey were in urban areas, especially in countries such as India and China.
There were 3853 Chinese patients in the study, 29% of the total. Of these, 3354 were given a slightly shorter questionnaire (although with identical questions from the full study questionnaire) and 499 were given the complete questionnaire. Health care in China is often delivered in very rapid physician visits; it is not uncommon for a physician to see up to 100 outpatients in a day. In such a fastmoving system, it is difficult to complete a full ITQ survey. For this reason, the shorter questionnaire was used in most patients (n¼3354), with the full questionnaire used in the remaining 499. To prevent undue weighting of the worldwide data by the Chinese data, the results were assessed with and without the additional 3354 patients. Results for nearly all the parameters remained unchanged, hence the extra Chinese patients were included in the overall analysis.
One of us (K. W. S. ) wrote the initial draft of this article, which was then reviewed and revised by the other authors. The content was also presented at the FITTER meeting in Rome, Italy, in 2015, where it was reviewed and commented on by the 183 diabetes experts gathered from 54 countries, which included the 42 countries in the survey. IBM SPSS Statistics for Windows software, Version 19 (IBM Corp) was used to perform the data analysis. Descriptive statistics, frequencies, and rankings were calculated. c 2 Analysis was performed where appropriate for contingency tables. The relationship between needle length and other clinically relevant parameters was assessed in R software using a linear model with log transformation of the needle length as response and was further analyzed using a type 2 analysis of variance (ANOVA) (which is better suited for unbalanced designs).
Conversely, the most clinically relevant variables were also assessed with needle length as a predictor using multivariate models and adjusting whenever possible for other relevant variables. These models were compared using ANOVA and Tukey multiple comparisons for continuous responses and logistic models and adjusted odd ratios for binary categorical variables. The threshold for staying in the model was P<. 05. Two-tailed tests were used in all the analyses. Initially, results from each of the 42 countries were analyzed independently, and only when the distributions of key demographic parameters (age, sex, body mass index [BMI], and duration of diabetes) were found to be comparable were all the data pooled into an overall database. Findings from individual countries will be the subject of additional, secondary analyses and publications.