dataesr/scientific-paragraphs-categorization huggingface dataset:
In addition, mitochondrial genomes of Periphylla periphylla and Polypodium hydriforme, were assembled from high throughput transcriptomic and genomic data (SRX956805 and SRX687102, respectively). Inferred amino acid sequences from nine mitochondrial genes (cob, cox1-3, nad1-5) were aligned with MAFFT v7. 215  (Katoh and Standley 2013). Conserved blocks within the alignments were selected with Gblocks 0. 91 b (Talavera and Castresana 2007) using relaxed parameters (parameters 1 and 2 = ½, parameter 3 = 8, parameter 4 = 5, all gap positions in parameter 5). Cleaned alignments were concatenated in a dataset 2,228 positions in length. Bilateria, Cnidaria, Ctenophora, Placozoa, and Porifera were constrained as monophyletic and the best constrained topology was identified using RAxML with the MTREV + GAMMA + F substitution model and 32 initial tree searches.
Acknowledgments We thank  Daniel Sloan ,  Jonathan Wendel ,  Kateryna Makova -our associate editor and two anonymous reviewers for their insightful comments on earlier versions of this article, and  Paul Veach  for his help with illustrations. A large part of the research reviewed here was supported by a grant from the  National Science Foundation  to DVL ( DEB-0829783 ). W. P. was supported in part by the  French National Research Agency (ANR)  grant  Ancestrome  ( ANR-10-BINF-01-01 ).
Specific Liver Side Effects of Psychiatric Treatments Liver specific damage of all medications needs more investigations that can lead to interruption of market authorization. Danan classification of toxicity criteria, including extrinsic criteria, based on anamnesis, and intrinsic criteria, corresponding to literature report and phamarcovigilance descriptions, should be used  (56). Hy's law is a potential method to conduct investigation and, overall, predict mortality  (57). Pharmacovigilance sources are available on the web, for example on the Livertox database (http://livertox. nih. gov/). Moreover, interactions with cytochromes should be known before prescription. Particularly, carbamazepine, metabolized by CYP3A4, or valproate, metabolized by cytochromes and mitochondrial oxydase, is associated with toxicity in case of overdose.
Planned contrasts were then done with post-hoc Tukey t tests  [57]  and LMM-corrected Kenward-Roger (KR) degrees of freedom  [58] : * p < 0. 05, *** p < 0. 001. Data deposited in the Dryad repository: http://dx. doi. org/10. 5061/dryad. 56bb4 [59]. doi:10. 1371/journal. pbio. 1002388. g002.
Statistical Analysis of Glycogen Content and Oocyte Size Data As for the other traits, we modelled the natural logarithm of the ratio of glycogen content of the derived populations (generation 60 P1-4 and U1-4, or generation 30 C1-4) over the ancestral mean value per glass slide. Each regime was separately modelled with LMM, taking maternal hatching treatment as a fixed factor with two levels and random population and individual hermaphrodite as random factors (Fig  6 ). For oocyte and embryo glycogen content data in the predictable populations, LMM residuals deviated from normality, but results are similar when removing two or three "outlier" observations, respectively, to resolve this issue. Ancestral and generation P1-4 populations were also scored for pixel intensity in slides that were not stained with iodine, to confirm that the responses observed are specific to stained samples.
Genotyping Immature L4 hermaphrodites were handpicked from GA250, generation 60 P1-4 and U1-4, and generation 30 and generation 60 C1-4 populations, and their gDNA collected using the prepGEM Insect kit (ZyGEM). Biallelic SNPs were chosen based on the pooled genome sequence of the A6140 population (M. Rockman and H. Teotónio, unpublished data). SNPs were genotyped with the iPlex Sequenom technology  [98]. WS200 genome version was used for the oligonucleotide design and physical coordinates (www. wormbase. org). SNPs in chromosome I and II were genotyped in 48 GA250 individuals and in 16 individuals from each of the evolved populations. Chromosomes III and IV and, separately, V and VI were genotyped with similar sample sizes. For data quality control, SNPs had to be polymorphic in A6140. SNPs for which the assay failed in more than 30% of the samples were eliminated.
05; ** p < 0. 01; *** p < 0. 001. (B) From (A), the geometric mean fitness is calculated over anoxia-normoxia and normoxiaanoxia absolute fitness separately for each of the four replicate predictable populations, or over all mother-offspring environments for each of eight unpredictable populations, and compared to the absolute fitness of the ancestral population. Error bars show one standard error of the mean among replicate populations. Significance of a Student t test is shown above the bar: * p < 0. 05. Data deposited in the Dryad repository: http://dx. doi. org/10. 5061/dryad. 56bb4 [59]. doi:10. 1371/journal. pbio. 1002388. g004.
The randomizing maternal effect allele (RME; grey line) does not invade the ancestral population (dashed line). (C) As in panel (B), W A-to-N = 0. 335 and W A-to-A = 2. 63, but the probability of environmental transition was 0. 55, as the unpredictable populations experienced during experimental evolution. After 60 generations, the frequency of the RME allele reaches 0. 91. Fifty simulations with the same parameter values show that the RME generally approaches fixation by generation 60 (grey circle; mean and one standard deviation) and, thus, that some variation is maintained in geometric mean fitness (black circle; mean and one standard deviation). Simulation code deposited in the Dryad repository: http://dx. doi. org/10. 5061/dryad. 56bb4 [59]. doi:10. 1371/journal. pbio. 1002388. g007.
Acknowledgments We thank  S. Carvalho ,  I. M. Chelo ,  M. A. Félix ,  H. Gendrot ,  T. Guzella ,  P. Ibañez ,  S. Nunes ,  A. Pino , and  S. Santos  for technical support;  L. Noble  and  M. Rockman  for access to unpublished genome sequence data;  F. Besnard ,  I. M. Chelo ,  M. A. Félix , and  P. C. Phillips  for discussion.
More precisely, we contribute to the literature in four ways. First, we include in the analysis nine diverse Western European Union countries: Belgium, Denmark, France, Germany, Ireland, Italy, Portugal, Spain, and the United Kingdom. The related literature typically investigates the issue for one or more countries, posing a challenge when comparing results across studies that use different methodologies and data sets. By contrast, in this article, consistent farm-level data sets and methodologies are used. Second, we examine 18 years  (1990) (1991) (1992) (1993) (1994) (1995) (1996) (1997) (1998) (1999) (2000) (2001) (2002) (2003) (2004) (2005) (2006) (2007) , a longer period than what has been typically used in the literature on the link between technical efficiency and subsidies in agriculture.
Data Source This article uses farm-level data for farms located in nine Western European countries for the 18-year period from 1990 to 2007. The countries included are Belgium, Denmark, France, Germany, Ireland, Italy, Portugal, Spain, and the United Kingdom. In other words, we focus on all the old member states that have been in the European Union since 1990, except for Greece, which has a limited number of dairy farms in the data set, and for Luxembourg and the Netherlands, for which econometric convergence could not be achieved. The data are extracted from the European Farm Accountancy Data Network (FADN), which provides high quality and consistent data sets from individual country FADNs across the European Union. This database comprises yearly accounting information for commercial farms over a minimum size, rotating over several years, typically five; therefore, the data sets are unbalanced panels.
Empirical Model We estimate a Cobb-Douglas stochastic production frontier, where the single output and the four inputs are expressed in natural logarithms, and accounts for the production environment and technological change. Five variables (z) are incorporated in the inefficiency component of the model based on the existing literature, on what in principle could influence managerial effort  (Martin and Page 1983) , and on data availability. Among these variables we include a subsidy variable, as well as an interaction of the subsidy variable and a decoupling dummy variable equal to one for the period 2005 and after, and zero otherwise (2005 is the year when the CAP 2003 reform was implemented in practice). The subsidy variable includes the following: direct payments linked to cropped area and to the number of livestock, that is, payments provided to farmers for specific crops planted or specific livestock raised; decoupled subsidies consisting of Single Farm Payments; and subsidies provided to farms located in less favored areas.
STUDY REGIONS AND DATA Following  Bolch and others (2012)  and  Frey and others (2014)  the HK region is divided into four sub-regions: the Karakoram, and the western, central and eastern Himalaya (Fig. 1 ; cf. Gurung, 1999; Shroder, 2011). Glacier bed topographies are calculated for all glaciers in all four subregions. For each sub-region, a test area is chosen to visualize and discuss the results: 1. For the Karakoram the test region is located between K2 and the Karakoram Pass in the borderland of India, Pakistan and China. This test region, covering a wide elevation range (3500-8000 m a. s. l. ), is dominated by the largest glaciers in the HK region (e. g. Siachen glacier (�72 km long) and Baltoro glacier (�64 km)). These two compound glaciers comprise a large number of tributary glaciers, and both end in large, very thick and flat (partly) debris-covered glacier tongues, flowing southeast (Siachen) and west (Baltoro).
Data from the following sources are used: the International Centre for Integrated Mountain Development (ICIMOD;  Bajracharya and Shrestha, 2011) , the GlobGlacier project  (Frey and others, 2012) , the first Chinese Glacier Inventory  (Shi and others, 2010)  and  Bhambri and others (2013)  (Fig. 1 ). Most outlines are available via the Global Land Ice Measurements from Space (GLIMS) database and are contained in the Randolph Glacier Inventory (RGI version 4. 0;  Pfeffer and others, 2014). In the eastern Himalaya, the quality is in some parts lower than in the remainder of the study area. In a few places the outlines   Frey and others, 2014. ) seem to be misplaced, as they do not fit with the terrain (Fig. 2a ). Glacier polygons smaller than 0. 05 km 2 were removed as they are subject to high uncertainties (i.
e. distinction between temporary snowfields and glacierets is not obvious). This inventory includes >28 000 glaciers, covering an area of �40 800 km 2. The DEM used for the ice thickness estimation for the entire HK region  (Frey and others, 2014)  is from the voidfilled Shuttle Radar Topography Mission (SRTM) version 4 from the Consultative Group on International Agricultural Research (CGIAR;  Farr and others, 2007; Reuter and others, 2007)  acquired using radar interferometry with a spatial resolution of 3 arcsec (�90 m). In mountainous terrain with steep slopes, the SRTM DEM results in numerous data voids (radar shadow and layover effects) which have been filled using different interpolation algorithms, or auxiliary DEMs where available  (Reuter and others, 2007). Especially over the western Himalaya, this void-filled version of the SRTM DEM shows large crater-like depressions.
This bathymetry raster fills the overdeepenings to the brim, which may overestimate potential lake volumes. A bathymetry raster with a reasonable level (10 m lower) was therefore created. This 10 m freeboard represents a mid-range value used in glacier lake hazard assessments in the Himalaya  (Worni and others, 2013). Based on the bathymetry raster and the outlines of the modelled overdeepenings the mean and maximum depths of the potential lakes are calculated using zonal statistics. The maximum length is measured along the longest axis completely contained within the polygon of the overdeepening, and the mean width is obtained by dividing total area by maximum length. While the modelled overdeepenings from model runs with different input data (e. g. DEMs, glacier outlines) differ in shape and size, their locations are consistent and the values for the extracted parameters are comparable  (Linsbauer and others, 2012).
Western Himalaya The erroneous void fillings within the western Himalaya SRTM DEM have an influence on the modelled geometry. As illustrated in Figure  5a , in mountainous terrain with steep slopes and associated data voids, many modelled depressions correspond closely with the filled voids (shadowed areas) in the DEM. Flatter glacier parts with continuous DEM data are not affected by these artefacts. For Chhota Shigri glacier, five GPR profiles are available  (Azam and others, 2012) , allowing us to compare measured and modelled ice thicknesses directly (Fig. 5b ). The measured glacier surface elevations are generally lower than the SRTM DEM at the same locations. Therefore, for the comparison, the glacier surface from the SRTM and the associated modelled bed topography have been shifted to match the elevation of the GPR measurements at the surface.
Data quality In general we suggest that with higher data quality, particularly surface DEMs, the robustness of the modelled overdeepenings could be enhanced. Frey and Paul (2012)  found that in glacier-covered terrain the SRTM DEM is slightly superior to the first version of the photogrammetric ASTER GDEM. The main problem with the SRTM DEM in our study region is the erroneous void filling in the western Himalaya (Fig. 2a ). As shown in Figure  5a , some modelled overdeepenings correspond closely with the filled voids of the SRTM DEM, and, as a consequence, some of these overdeepenings are very deep. This might partly explain why the overdeepenings in the western (and eastern) Himalaya are generally deeper than in the other regions (Table  2 ). The quality of the glacier outlines used in this study is high for most parts of the HK region.
ACKNOWLEDGEMENTS This study was funded by the  Swiss Agency for Development and Cooperation (SDC) Indian Himalayas Climate Adaptation Programme  (IHCAP: http://ihcap. in/)and the  National Cooperative for the Disposal of Radioactive Waste (Nagra)  in Switzerland within the framework of studies on glacial overdeepenings. We acknowledge the constructive reviews provided by two anonymous reviewers, which resulted in significant improvements to our manuscript, and the work of the Scientific Editor  Surendra Adhikari  and  Chief Editor Graham Cogley.
Introduction Health records from different health systems might provide insights into the care of patients with chronic diseases and the long-term outcomes of these conditions, 1,2 but there have been few comparisons across countries. National hospital data are collected and coded in health systems in many countries and such data (compared with voluntary registries or consented studies) may provide samples that are larger, more nationally representative, and not limited to the study of any one disease, or any one stage of its development. 3 owever, there are important concerns about the quality and validity of such data. In coronary disease, most studies of outcomes following myocardial infarction (MI) have focused on the acute phase post-MI, typically up to 1 year. However, given marked improvements over the past decade in short-term and long-term mortality following MI,  4 -6  there is a growing need to characterize the outcomes experienced by patients in whom follow-up begins after the acute phase.
Health record data sources and study population We analysed anonymized patient data from national ongoing hospital sources that use the International Classification of Diseases (ICD) coding system. In Sweden, we used nationwide (100% population coverage) administrative linked data (not directly used for reimbursement) obtained from mandatory Swedish national registries: the National Inpatient Register, the Swedish Prescribed Drug Register, and the Cause of Death Register. In the USA, we used an administrative claims database (Medicare) obtained from the Centers for Medicare & Medicaid Service's standard analytic files that are publicly available; these contain a nationally representative 5% random sample of all Medicare beneficiaries, based on selecting records with 05, 20, 45, 70, or 95 in positions 8 and 9 of the Social Security Number (SSN) (Centers for Medicaid and Medicare, Standard Analytical Files.
https://www. cms. gov/ research-statistics-data-and-systems/files-for-order/limiteddatasets/ standardanalyticalfiles. html, accessed 17 December 2015). Patients are linked across the enrolment and eligibility file and service claims files using a unique encrypted SSN. Deaths are determined by linkage to the National Death file. In England, a single primary care electronic health record (EHR) covers. 95% of the population and we used a 4% sample available for research. We used the CALIBER research platform of primary care EHRs (Clinical Practice Research Datalink), linked via the unique identifier of the National Health Service number with other record sources [the Myocardial Ischaemia National Audit Project (MINAP), the Hospital Episodes Statistics database, and the nationwide cause-specific mortality database].
The CALIBER data resource has been shown to be representative of the general population,  21 -23  and valid for cardiovascular research. 24 -28 In France, the source data came from the administrative claims insurance database, which covers 95% of the French population. The sample [Echantillon Generaliste des Beneficiaires (EGB)] available for researchers was built by randomly selecting patients from their national id check number (97 random possibilities). This permanent 1/97 sample has been shown to be representative in terms of age, sex, social status, and overall medical expenses. 29 -33 The EGB health insurance claims data are linked to hospital discharge summaries and death registry through the unique healthcare identifier number. Our study population was defined by the presence of three characteristics.
Baseline risk factors and co-morbidities We included demographics (age, sex) and cardiovascular and noncardiovascular co-morbidities (ICD-9 and ICD-10 codes in Supplementary material online, Table  S1 ) appearing as primary or secondary diagnoses in hospital admissions before the study entry date. We considered patients as currently receiving a medication (codes in Supplementary material online, Table  S2 ) if their last active prescription or dispensation ended ,60 days before study entry. No prescription data were available in the Medicare data. We included percutaneous coronary intervention (PCI) and International health record data for evaluating chronic disease outcomes coronary artery bypass graft (CABG) procedures performed on the day of the index MI up to the following 12 months.
Statistics Data from each of the four countries were analysed independently following a common protocol. We estimated the direct age-and sex-standardized prevalence of co-morbidities in each country using as reference the 2012 World Health Organization world population truncated to ages 65 years and older. For each country and endpoint, we estimated observed (Kaplan -Meier) and predicted risks, adjusted to the average characteristics of the Swedish patients (aged 78 years, with covariate values shown in Supplementary material online, Table  S4 ). We chose Sweden as the reference population because it had the largest sample size. Predicted risks were based on incrementally adjusted Cox models (fitted separately per country): Model 1 included age, sex, and year of index MI; Model 2 included Model 1 covariates plus co-morbidities [history of more than one MI, diabetes, renal disease, heart failure, peripheral arterial disease (PAD), atrial fibrillation, stroke, hospitalized bleeding, chronic obstructive pulmonary disease, and cancer]; Model 3 included Model 2 covariates plus revascularization procedures (CABG or PCI) received in the 12 months following the index MI.
Second, such health record data will inevitably lack relevant data items. For example, MI subtype (STEMI or NSTEMI) was not recorded across all four countries and could not therefore be included in the model adjustments. However, there is strong evidence that, at 1 year following the index MI, STEMI and NSTEMI shared similar mortality, suggesting that MI subclass is unlikely to have influenced our comparisons. 39 Information on younger patients, socioeconomic position, ethnicity, drug use, primary care, and cause-specific death was not simultaneously available in all four countries. It is a challenge to these health systems to improve the coverage, depth, and quality of data as part of efforts to expand international comparisons. We observed an annual risk of death ranging from 6. 5% (England) to 10.
Funding This study was funded by  AstraZeneca , the  Medical Research Council Prognosis Research Strategy (PROGRESS) Partnership  (H. H. , grant  G0902393/99558 ), and by awards to establish the  Farr Institute of Health Informatics Research, London  from the  Medical Research Council, Arthritis Research UK ,  British Heart Foundation ,  Cancer Research UK, Chief Scientist Office, Economic and Social Research Council, Engineering and Physical Sciences Research Council, National Institute for Health Research (UK) ,  National Institute for Social Care and Health Research (UK) , and  Wellcome Trust  (E. R. , D. S. , M. P. -R. , and S. D. ). S. -C. C. was supported by the  Medical Research Population Health Scientist Fellowship (grant   MR/M015084/1 ). T. J. was supported by the  Swedish Heart and Lung Foundation.
This paper will start with a presentation of the legal French framework for research evaluation, concentrating on the individual level; this first part will also summarize the main oppositions to the idea of evaluation, as they are expressed mainly by unions and other researcher associations. In a second move, we will review the main French actors and practices of evaluation, separating the 'traditional' forms of assessment still in use in the CNU, and the recent evolutions caused by the introduction of a dual financing system (through ANR), of an external evaluation of research units by an independent agency (AERES/HCERES) and by the building of a database in the CNRS. In the light of criticisms that can be formulated about all these practices, we will introduce the projects DisValHum and IMPRESHS, dedicated, respectively, to a study of dissemination strategies in the SSH and to case studies of the impact of the research in the SSH.
The Need for Evaluation in the Post-'loi LRU' Period During the last decade, the need for evaluation increased in all higher-education systems. This movement did not spare France, in spite of this country's tendency to stay away from the general trends in culture-related matters 1  and, more specifically, in education issues, as shown, for example, by France's non-participation in the European University Data Collection (EUMIDA) surveys (European Commission 2010). Nevertheless, the claims and methods of the so-called new public management did find a favourable echo in France among some politicians and members of the administrative apparatus. In the meantime, the Shanghai rankings came as a shock to the system, and still create a huge discussion about the low ranking of French universities in the top 50 and top 100 league tables (AEF 2013b, 'Dépêche no.