dataesr/scientific-paragraphs-categorization huggingface dataset:
Study participants We retrospectively evaluated the data on PRSE treated in the ICU from 1 January 2001 to 31 December 2011. One hundred and thirty French adult ICUs on a list published by the French Language Society of Critical Care Medicine were invited to participate in the study in September 2012. At each participating ICU, one investigator from the medical staff was responsible for collecting the retrospective data. The diagnosis of prolonged PRSE was considered in all patients >18 years old suffering from a generalized convulsive SE, which was considered uncontrolled after general anesthesia (GA) and mechanical ventilation for at least 7 days. Absence of SE control was defined as clinical (rhythmic motor movements) or electrical seizures while under treatment or recurring within 48 h after stopping anesthetic drugs.
Data collection General data included the simplified acute physiological score (SAPS II), the length of ICU stay and common comorbidities often associated with SE. We also recorded the antiepileptic drugs administered from the beginning to the end of the SRSE, the duration of SRSE, the type of neurological monitoring, and the existence of an electrical interruption in the seizure or burst-suppression during the first 7 days. Morbidity and mortality at ICU discharge were also recorded. The degree of disability was estimated with the modified Rankin Scale (mRS) before hospitalization, at ICU discharge, at last news from the patient, and, if available, at one year after ICU discharge  [11]. The functional outcome was dichotomized into good (mRS 0 to 3) and poor (mRS 4 to 6)  [12]. To obtain this information, local investigators had to contact the attending physician, the patient or the patient's family.
Altimetry and large-scale climatic conditions The altimetry data (sea level anomaly) were produced by Ssalto/Duacs and distributed by Aviso, with support from CNES (http://www. aviso. oceanobs. com/duacs/). The sea level anomaly map centred on the 18 January 2011 was plotted using the Panoply software from NASA (http://www. giss. nasa. gov/tools/panoply/). This map was processed by compiling the data collected over a six week period before and after the chosen date (Fig. 1 ). The current sea maps provided by the bulletin of the Japanese coast guard were used to validate the satellite data and display the paths of both the cyclonic gyre and the Kuroshio Stream (http://www1. kaiho. mlit. go. jp/KANKYO/KAIYO/qboc/index_E. html).
Data were collected using the CellQuest software (BD Biosciences ® ) and the analysis and optical resolution of the various groups of heterotrophic prokaryotes were performed a posteriori using the SUMMIT v4. 3 software (Beckman Coulter). For each sample, the run- Figure  2. Vertical profiles of the Brunt-Väisäla buoyancy frequency (N 2 ) calculated from the temperature-salinity measurements. The white circles display the thermocline depth and the black triangles display the depths of 1 % of photosynthetically active radiation (limit of the euphotic zone). time of the flow cytometer was 2 min and the flow rate set to 50 µL min-1 (corresponding to the "Med" flow rate of the flow cytometer). Trucount ™ calibration beads (Becton Dickinson Biosciences) were also added to the samples just prior to analysis as an internal standard to monitor the instrument stability and accurately determine the volume analyzed.
Statistical analysis To analyse the multivariate data set, principal component analyses (PCA) and redundancy analysis (RDA) were performed using the R software (vegan package) and the Biplot macro for Excel ®  (Lipkovich and Smith, 2002). PCA was performed in order to qualitatively identify the relationships between heterotrophic prokaryotes and the environmental variables  (Pearson, 1901). Possible links between each heterotrophic prokaryote subgroup and their environmental variables were quantitatively examined using the RDA. For the RDA, the data set was log10 (x + 1)-transformed to correct for the large differences in scale among the original variables. A Monte Carlo test was used in order to test the significance of the RDA results. Partial RDAs were also carried out to evaluate the effects of each explanatory variable set on the heterotrophic prokaryote composition  (Liu, 1997).
By being aware of this limitation, a more complex approach including the path of the eddy associated with multiple nutrient inputs has www. biogeosciences. net/12/3607/2015/ Biogeosciences, 12, 3607-3621, 2015 been purposed to explain the variability in microorganisms as demonstrated by  Nencioli et al. (2008). This scenario did match well with the Tokyo-Palau data set, where the cold core of the cyclonic eddy moved to the north-west between December and the sampling time of the cruise. The path of the cold core cyclonic eddy could explain the possible decrease in the nutrient uptake from the bottom layer at station 4 and lead to an oligotrophic system dominated by regeneration processes. The high abundance of heterotrophic prokaryotes measured at the edge of the cyclonic eddy could be explained by the high activity in the microbial loop.
Acknowledgements. We thank  Akira Noda , crew members of the research training vessel  Shinyo Maru  of the  Tokyo University of Marine Science and Technology, (TUMSAT)  for their cooperation at sea. We appreciated the English correction of the manuscript made by  Tracy L. Bentley. We thank  Yuta Nakagawa  and  Shinko Kinouchi  for their help during the cruise. We are grateful to the  PRECYM Flow Cytometry Platform of the Mediterranean Institute of Oceanography (MIO)  for the flow cytometry analyses. We also thank the  Société franco-japonaise d'Océanographie  for its support in shipping the samples from Japan to France. Edited by:  G. Herndl.
Firstly, the data were collected manually by very well trained medical staff, then they were entered and checked in a database by the principal investigator and finally validated by 2 senior epidemiological experts. Records are kept in hard and soft copies in 2 places. Air pollution monitoring network provides continuous information on PM 10 , PM 2. 5 and NO 2 whose origins are mainly from traffic, construction activities and dust storm. Relative humidity, temperature, direction and wind speed are also measured by the monitoring network of Beirut city, but, due to lack of data, the daily pollen level was not collected as for the case of several international studies  [21] [22] [23] [24].
Health data collection In international studies, epidemiological health data are based on their availability and are usually compiled from official registers. In France for example, data on mortality are provided by CépiDc (Centre d'épidémiologie sur les causes médicales de décès), and are classified following the International Classification of Disease (ICD 10). In all developed countries, health information system exists and the number of hospital admissions can be extracted anonymously. Nevertheless, in some developing countries official registers managed by public authorities do not exist; consequently, investigators are obliged to get an alternative source of data by collecting information from emergency department registers, insurance database or pharmacies, …etc. In BAPHE, a pilot study of 15 days was conducted in 2 out of the 7 hospitals.
Digestive system diseases Considered as a control However, our study presents some weaknesses. The disadvantage of studies like BAPHE involves in data collection since the health system in Lebanese hospital is not yet computerized. The hard part of the project was to collect the data manually. On another hand, this operation allows an efficient control of data through database checking by 3 different qualified experts. If we consider the fact that time series studies have lack of individual measurements in exposure and outcomes and the possible presence of unmeasured confounders, this could be a weak point for our study. However, in BAPHE as in international studies we worked on the short term effects by using long series of small units (days) to minimize errors  [26, 27]. In that design the population serves as its own control over time and confounders can only be factors varying according to the small time-units from day to day like cigarette smoking or other confounding factors.
Acknowledgments The authors wish to thank the  University of Saint Joseph , the Lebanese non-governmental organization arcenciel and the  CEDRE  project (Ministry of Foreign affairs in France and the  Ministry of Higher Education and Research in France and Lebanon)  for the financial support of this research. We thank  Hotel Dieu   de France Hospital (HDF) ,  University Medical Center Rizk Hospital (UMCRH) ,  Trad Hospital ,  Rosaire Hospital, Libanais Hospital (Geitawi), Makassed Hospital, St Georges University Medical Center , for providing health data. We thank the  Lebanese Air Quality Research Unit (AQRU)  for providing air pollution data.
Methods. Participants responded to open-ended questions on an online survey administered by Lupus UK and Lupus Group Ireland. Qualitative data from 133 participants (77 % of respondents) were analysed. Results. Thematic analysis revealed three overarching themes: invisibility, inadequate care, and validation. Respondents felt that their SLE was invisible to social ties and to medical professionals. In addition, treatment and organisational factors in health care contributed to the sense of inadequate care. Finally, validation was derived from informational and emotional support from both support groups, and from some medical professionals.
Recruitment and Participants The final open-ended survey questions (Table  1 ) were administered in an online survey format. These were developed by the authors to address aspects of social support highlighted in the literature as important (i. e. , from the medical profession, and from support groups), but that are not captured by well-used psychometric measures of social support in everyday life. Participants were recruited through a study link distributed by Lupus Group Ireland and Lupus UK. The inclusion criteria were: aged 18 and over with a diagnosis of Lupus; there were no other inclusion/exclusion criteria. Of 172 respondents, 133 (77%) provided qualitative data and were included in the thematic analysis. Over half (54. 13%) reported currently experiencing SLE symptoms, 39. 85% reported being in remission, and the remainder did not specify their current disease status.
Data Analysis Thematic analysis was performed in line with Braun and Clarke's  [13]  guidelines. The nature, meaning, and impact of support for individuals with lupus were concepts that guided the interpretation of the data. Prior to analysis, a theme was said to consist of a recurring aspect throughout the data that represented an important feature of the participants' experiences. The first step in analysis was becoming familiar with the data. Responses were initially reviewed by the first author, and discussed with the second author. Preliminary codes were extracted by the first author; both authors then independently reviewed the transcripts with codes and emergent themes discussed to ensure reliability. Themes were reviewed to identify potential overlap and to ensure all relevant information was included.
, 2014). Ocean and coastal environments are complex adaptive SESs where social relationships of stewardship are diverse and resource use is most often unsustainable  (Cinner et al. , 2009b; Cinner, 2011 Cinner, , 2014;; Kittinger et al. , 2012 Kittinger et al. , , 2013)). In marine environments, successful resource planning, therefore, requires diverse datasets and tools  (Kittinger et al. , 2014). Understanding how such complex adaptive systems are structured, evolve through time, respond to different pressures (e. g. environmental stressors, policy decisions, or management actions), and provide ecosystem services important for human wellbeing is crucial for social-ecological theory to inform marine conservation and management that produces long-term benefits for nature and people. In this paper, we review the challenges of evolving socialecological science towards applied outcomes to support resource management and marine conservation.
Conclusion There have been repeated calls for a transdisciplinary approach to complex linked socio-ecological systems (SESs) that incorporates resilience, complexity science, emergent properties, non-linear dynamics and uncertainty. To achieve this vision, we need to embrace diverse research methodologies that incorporate ecology, sociology, anthropology, political science, economics and other disciplines that are anchored in empirical data. Here, we synthesize conceptual frameworks, applied modeling approaches, as well as case studies to highlight complex SES dynamics that inform environmental policy, conservation and management (Table  1 ). While a number of modeling approaches have been developed, robust social-ecological monitoring and empirical social datasets remain scarce, limiting our ability to fully consider the complex processes, functions and dynamics of SESs.
Acknowledgment Preparation of this paper was carried out with the financial support of the Project INTHENSE funded by the  Fondation de France  and by the  Programme Doctoral International: Mod elisation des Syst emes Complexes (PDIMSC). We are grateful to the organisations that supported participation of the co-authors in the 3rd International Marine Conservation Congress in August 2014 in Glasgow, Scotland. We also thank  Olivia Langmead  and  Ness Smith  for their crucial inputs during the preliminary discussion of this paper.
Discussion ALOMYbase, the first A. myosuroides transcriptomic resource Our main aim was to establish a resource to study transcriptomic patterns in A. myosuroides plants resistant or sensitive to leaf-applied herbicides in the absence of herbicide and at the early stages of response to herbicide, using experimental conditions as similar as possible to realistic field conditions. Herbicide damage to plants starts occurring 3 to 8 h after herbicide application (reviewed in  [10] ). To be efficient, NTSR must be implemented before herbicide damage is irreversible, and must be upheld long enough to allow resistant plants to recover  [10]. Accordingly, RNA-Seq data was obtained from a time course experiment ranging from UT until 73HAT. A commercial iodosulfuron + mesosulfuron formulation that is applied in the field was used together with its recommended adjuvant in our experiments, because NTSR is selected for in the field by recurrent  applications of not only herbicide molecules, but also associated formulations and adjuvants.
myosuroides that had been deposited in GenBank/EMBL to the 5 th of June 2015. Our work therefore tremendously increased the sequence data available for A. myosuroides. The contigs in ALOMYbase were assembled for RNA-Seq data obtained from the aerial part of six F2 plants at the vegetative growth stage. Thus, ALOMYbase was not expected to be a comprehensive A. myosuroides transcriptomic resource. Accordingly, the completeness of ALOMYbase as estimated by CEGMA analysis was 61. 3 %. Considering our starting material and CEGMA estimates of completeness for the transcript sets associated to the five grass genomes (79. 8 to 99. 2 %), A. myosuroides transcriptome representation in ALOMYbase was deemed satisfactory for our purpose. As A. myosuroides genetic variability is high  [40] , the two parental plants used to generate the F2 population were most likely genetically different.
Thus, nucleotide variation was certainly present among the F2 plants used for RNA-Seq, which likely introduced some redundancy among the assembled contigs: more than one contig in ALOMYbase may represent a same unigene and/or several contigs may represent different segments of the same unigene. The precise size of A. myosuroides genome is unknown. Estimations based on DNA cell contents give an expected genome size between 1200 and 4330 Mb  [41, 42] , i. e. , a relatively large genome. Large genomes have a low proportion of transcribed sequences encoding proteins (e. g. , 5 to 8 % of the large genomes of fully sequenced legume species genomes  [38] ). From the range of A. myosuroides genome size estimates, ALOMYbase sequence data would represent 1. 6 to 5. 7 % coverage of the A. myosuroides genome.
thaliana genes used as markers for the signature of the response to ALS-inhibiting herbicides were established. ALOMYbase orthologs of A. thaliana marker genes in groups 1a and 1b showed expression patterns remarkably similar to those of their A. thaliana orthologs in both the resistant and the sensitive pools (Additional file 3: Table  S3 ). Similarities in the expression patterns increased with time, with a maximum similarity observed at 73HAT. Our data thus support previous findings that grasses and broadleaved plants share common regulatory mechanisms of gene expression in response to abiotic stresses  [67]. From all the foregoing, it is clear that ALOMYbase quantitative and qualitative data are reliable and relevant to study the response to ALS inhibitors in A. myosuroides. Plants resistant to iodosulfuron + mesosulfuron because of NTSR reacted to the stress exerted by the herbicide application, with a part of their transcriptomic response being similar to that of sensitive plants and consistent with the effects of ALS inhibitors described in the literature.
Candidate NTSR contigs The primary aim of this work was to identify as many as possible of the contigs presents in plants resistant and/ or sensitive to ALS inhibitors before herbicide application and at the early stages of herbicide response, in order to establish a transcriptomic resource as comprehensive as possible to allow subsequent studies of A. myosuroides response and NTSR to ALS inhibitors. For this purpose, and because performing RNA-Seq on 42 RNA samples was not affordable, the 42 individual RNA samples studied were sequenced as pooled samples. Transcriptomic data from each pooled sample reflected the average variation in gene expression induced by biological variation among individuals (using three F2 plants per phenotype and per experimental modality) and by the environment (using two clones per F2 plant and per experimental modality).
The pooled samples used for RNA-Seq did not contain distinct biological replicates, as is generally recommended to identify contigs differentially expressed among experimental modalities (e. g. ,  [21, 25] ). This experimental design was thus not optimal for the purpose of identifying contigs specifically up-regulated in resistant plants that could be candidate NTSR contigs  [10] , especially because we observed that variation in gene expression could be substantial among the individual samples constituting each pooled sample (Additional file 4: Figure  S4 ; Additional file 7: Figure  S7 ). However, A. myosuroides transcriptomic response to ALS inhibitor action obtained from ALOMYbase expression data was fully consistent with the literature. Despite the limitations inherent to our experimental design, this encouraged us to seek potential NTSR determinants using ALOMYbase expression data.
Conclusions We obtained RNA-Seq data from the aerial part of young herbicide-resistant and herbicide-sensitive A. myosuroides plants that provided substantial transcriptome coverage. This data was assembled to generate ALOMYbase, the first A. myosuroides transcriptomic resource. ALOMYbase was used to get insight into the transcriptomic variation occurring in plants resistant or sensitive to iodosulfuron + mesosulfuron following the application of this herbicide. In both resistant and sensitive A. myosuroides plants, the transcriptomic response to iodosulfuron + mesosulfuron mirrored known effects of ALS inhibitors and were consistent with the literature data. Striking similarities with the transcriptomic response of A. thaliana to ALS inhibitors were observed. Specificities in the response to iodosulfuron + mesosulfuron were observed in the resistant and in the sensitive A.
Libraries were subjected to 15 PCR cycles. Fragments were purified on agarose gel to recover fragments with inserts in the range of 160-240 base pairs. All libraries were sequenced in two independent flow cell lanes (technical replicates) on an Illumina HiSeq2000 system. Sequencing was carried out following the manufacturer's instructions for the generation of single-end, 100-base long reads. Sequence data was extracted using the CASAVA 1. 8. 1 pipeline (Illumina). The sequence reads from all 14 libraries were analysed according to Fasteris quality control, using an indexed PhiX reference sequence on each call lane to estimate sequencing error.
As these data were very similar in quantity and quality to Sanger EST data, an iterative pipeline was developed that integrated a "containment clustering"-like program (nrcl-like program) and the cap3 assembler  [75]  that is widely used to assemble Sanger ESTs. Each iteration in the pipeline combined a nrcl run that removed redundancy by including short redundant contigs into longer contigs to a cap3 assembly that merged contigs. At each iteration, less and less stringent parameters were used because each iteration added constraints to the subsequent one. The thresholds used both for nrcl and cap3 were an "Identity percentage" ranging from 92 to 99 %, a length of the overhang of 20 nucleotides, an "High-scoring Segment Pair" (HSP) length of 100 and 75 nucleotides, respectively. The quality of the assembly was manually checked on a set of contigs expected to correspond to single-copy genes.
The assembly parameters were selected so that single consensus sequences were obtained for this set of genes. Putative coding sequences were sought in the assembled contigs using FrameDP trained on A. thaliana, B. distachyon and M. truncatula proteomes  [76]. Putative peptide annotation was performed using an automatic InterproScan analysis  [77]  and included Gene Ontology (GO) terms, Enzyme Commission (EC) codes and Pfam domains. Similarity searches for peptide annotation were also conducted against TAIR10, Brachypodium distachyon proteome, Swiss-Prot and TrEMBL using the BLASTp algorithm with an E-value < 10 -5. Additional Pfam domain assignation was performed using the Pfam-A 27. 0 database and the hmmsearch program  [78].
Comparison with other grass species (Poaceae) The predicted peptide contents of A. myosuroides transcriptomic database (ALOMYbase) was compared to those of the five grass (Poaceae) species for which a full genome sequence is available: the weed Brachypodium distachyon and the crop species Hordeum vulgare (barley), Zea mays (maize), Oryza sativa (rice) and Sorghum bicolor (sorghum). All data were collected from Phytozome v. 9. 0, except H. vulgare data that were collected from the MIPS database (http://mips. helmholtz-muenchen. de/plant/barley). Inter-ProScan annotation was performed anew for the five grass genomes using the same procedure as for ALOMYbase to homogenise functional annotation and more accurately identify peptides assigned the same annotations in all species. Comparison of the Pfam families present in ALOMYbase and in the five grass genomes was performed using OrthoMCL  [79]  with an 80 % match cutoff threshold for ortholog clustering.
A Pfam family was considered present in one species if at least one peptide in this species was assigned to this family. The distribution of the predicted peptides among Pfam families was compared among ALOMYbase and the grass genomes. The completeness of A. myosuroides transcriptome assembly was assessed using CEGMA VM (Core Eukaryotic Genes Mapping Approach) that checks the presence of a core protein set consisting of 248 highly conserved proteins found in a wide range of eukaryotes  [39]  (http://korflab. ucdavis. edu/datasets/cegma). For comparison purpose, CEGMA analysis was also performed on the set of transcripts available for each of the five grass species with a full genome.