dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We would like to thank our colleagues from the  BigPicture Group at the Swiss Federal Office for the Environment  for fruitful discussions in the development of the basic ideas of the suggested conceptual framework. We appreciated the valuable feedback from the participants of two workshops at the international conference "Towards the  Best Practice of River Restoration and Maintenance " in September 2016 in Krakow, Poland. The constructive review of early ideas by our colleagues from the Eawag-internal advisory group helped to improve the present framework. We thank  Sandra Schwab  for her help with the figures.
10 11 rengths and limitations of this study ► This study will generate new evidence to strengthen public policy recommendations for vaccination of people with diabetes, especially among adults of working age. ► This is the first rigorous assessment of the effectiveness of influenza vaccination using the French National Health Insurance System database permitting analysis of about 40 000 patients over a 10-year period. ► This study explicitly accounts for healthy vaccine bias that arises in observational studies where those patients who are more likely to be vaccinated are also more likely to prioritise other areas of their health. This bias may result in overestimation of vaccine effectiveness. In our study, we hypothesise that matching cases and controls by their propensity for other preventive behaviours may reduce this bias.
Database The study will be performed by analysing reimbursement data from the French National Health Insurance Fund. Data will be anonymously extracted from the fund's permanent sample of beneficiaries ('Echantillon Généraliste des Bénéficiaires' (EGB)) database. The EGB, created in 2003, is a permanent representative sample of persons affiliated to the French health insurance system, a cohort of beneficiaries for whom information on healthcare use is conserved for 20 years. These data can thus be used to assess longitudinal use patterns for research purposes. It is obtained by a 1/97th national random sampling with stratification for age and sex as described in more detail previously. 23 The identification of persons included in the sample is protected by a two-level cryptographic anonymisation process.
The EGB is obtained from the reimbursement databases of the major public health insurance funds (salaried workers), which record information on the healthcare use of nearly 85% of the general population in France. On 1 January 2016, the EGB database included 675 906 individuals for whom it contains the following information: age, sex, all reimbursements for medical expenses for outpatient care and their 'chronic disease status' with its diagnostic codes according to the 10th revision of the International Classification of Diseases (ICD-10). 'Chronic disease status' is attributed to people with specific and expensive chronic diseases defined by the French health insurance system and makes them eligible for 100% reimbursement of the costs of their treatment as described in more detail previously.
definition of the study cohort This historical cohort of people treated for diabetes will be followed from 12 October 2006 (date that the 2006-2007 campaign vaccination started) through 9 October 2016 (day before the start of the 2016-2017 campaign vaccination). Patients will be included only if they were in the database for at least 3 years before their follow-up begins. People treated for diabetes will be identified according to the following criteria, previously used in epidemiological studies: they are listed in the databases as having received at least three deliveries of oral diabetes drugs or insulin on three distinct dates in the 12 months before inclusion. 25 For patients to whom oral diabetes drugs were dispensed in the year before the start of follow-up (prevalent diabetes at inclusion), the inclusion date will be the study start date.
] [40]  The non-epidemic periods will be those during which there is no recorded circulation of the virus: 15 May to 31 July each year since 1985 ( websenti. u707. jussieu. fr). Moreover, the analyses will be stratified for age: they will be performed separately for patients aged 65 years or older and for those younger than 65 years. SIV is doubly indicated for patients with diabetes aged 65 years or older-for both their age and their chronic condition. Vaccination coverage of people with diabetes younger than 65 years is lower than that of older patients,  20  and clear VE data lack for this younger age group, who account for nearly half the patients with diabetes treated pharmacologically in France. 41.
Diabetes severity The severity of diabetes is simultaneously positively associated with the risk of hospitalisation for infectious causes,  56  including seasonal influenza,  2 57  and with vaccination coverage. 20 It is therefore a confounding factor. Because the EGB databases do not include any individual clinical or laboratory variable to measure diabetes severity directly, it will be approached indirectly by two different variables: ► The intensity of the treatments prescribed: a single oral diabetes medication for mild diabetes, two different such medications for moderate diabetes and more than two different drugs and/or insulin for severe diabetes; ► Time since diagnosis of diabetes is associated with the risks of influenza complications and of immunodeficiency secondary to chronic hyperglycaemia.
No data describe the proportion of NAIs dispensed for these two indications. The other limitation is related to the lack of specificity of the initial clinical presentation of influenza. Work has shown that primary-care physicians' NAI prescriptions are suboptimal,  73  but no evidence shows that this bias is differential. Antibiotic prescriptions for influenza complications are the second principal component of outpatient care for influenza accessible in the database. Susceptibility to secondary infection of the lungs and bronchi by bacteria, for example, Streptococcus pneumoniae and Haemophilus influenzae, seems to result from increased binding of bacteria to the basal membrane of the respiratory epithelium. This may be the result of direct viral damage. 74 urthermore, the neuraminidase activity of influenzae viruses might thereby decrease the viscosity of the mucus and increase adherence of pneumococci.
75 Finally, the risk of bacterial infections in patients with diabetes in the presence of influenza is aggravated by the immunodeficiency caused by chronic hyperglycaemia. 76 Numerous studies have shown that seasonal influenza epidemics are strongly associated with increased use of antibiotics, especially aminopenicillins and macrolides. 77 Thus, influenza vaccination should result in a reduction in antibiotic use. This variable has already been used as an indirect outcome for assessing SIV effectiveness: in Ontario (Canada): antibiotic prescriptions fell after the introduction of universal free vaccination against influenza. 78 79 rengths and limitations associated with the database This will be the first study of the effectiveness of seasonal influenza vaccine performed in France from a nationwide healthcare-related administrative database.
Nonetheless, these databases do not provide access to laboratory results when laboratory tests are performed, and these tests are not systematically performed. The studies of the VE of SIV with a direct end point measure, such as PCR for influenza from nasopharyngeal swabs, show that indirect outcome measures, such as ILI, can overestimate VE compared with the former (direct outcomes). 80 oreover, it is probable that the quality of coding varies between hospitals. Given that the EGB sample is national and random, these coding variations are probably not differential. This type of bias is likely to induce underestimation of VE, which should be made up for in part by our study's statistical power. contributors LC drafted this study protocol under the direction of PVE and PV. SC contributed to the data management and construction of the statistical model.
In this study, we include for the first time a wide range of Philippine Ixora species in a phylogenetic analysis using sequence data from two chloroplast regions, the rps16 intron and the trnT-F region including the trnT-trnL and trnL-trnF intergenic spacers and the trnL intron, and the 5′ external transcribed spacer (ETS) and internal transcribed spacers (ITS1, ITS2) of the nuclearencoded 35S rDNA cistron. We interpret our results in the light of the hitherto known patterns of faunal and floral migrations and evolution in the Philippines. We address the following questions. (1) Are the Philippine Ixora species monophyletic? (2) Are phylogenies derived from chloroplast and nuclear DNA congruent? (3) Which species or groups of species are the closest relatives of the Philippine Ixora species? (4) Does the phylogenetic pattern of Philippine Ixora have wider implications on the biogeographic history of the Philippines?.
Outgroup sampling and ingroup sequence characteristics One of the non-coding gene regions used here, the nuclear-encoded ITS1, cannot be aligned across all Ixoroideae, and alignment of the most divergent and length-polymorphic plastid region, the trnT-trnL intergenic spacer, is difficult in some parts. Also, the other two nuclear spacers, the ITS2 and the ETS, include sequence portions that will lead to ambiguous alignments when incorporating all Ixoroideae data. Nonetheless, we could infer four guide trees based on the harvested data (ETS, ITS excluding non-alignable regions, rps16 intron, entire trnT-F region), which confirmed that our outgroup selection includes the closest relatives of Ixora with best-possible data coverage on the gene regions used here (see Additional file 1). The 151 new sequences generated in this study were combined with sequences previously generated and used by Mouly et al.
[30, 31]  and Tosh et al. [32]  resulting in a total of 264 sequences of 78 Ixora samples, representing approximately 60 Ixora species. Levels of genetic variation between species were generally low for all investigated regions. The total number of parsimony informative characters (PICs) ranged from 40 in rps16 to 122 in ETS for the ingroup; the number of distinct alignment patterns (DAPs) ranged from 209 in rps16 to 450 in trnT-F. In the concatenated cpDNA dataset, 265 characters (10%) were variable, with 360 characters (32. 4%) variable in the nuclear dataset. The characteristics of the individual chloroplast and nuclear regions are listed in Table  1.
Incongruence and congruence between nuclear and plastid genealogies Phylogenetic analyses of individual gene regions generate largely unresolved and poorly supported phylogenetic trees (data not shown). Concatenation of the nuclear data and the plastid gene regions respectively leads to better resolved phylogenetic trees (Fig. 1 ) and limits the number of scenarios of potential phylogenetic relationships between species and clades (Figs. 2  and 3 ). Two large, mutually monophyletic lineages, an Asian-Pacific clade (I) and an Asian-Afro-Neotropical clade (clades II-IV), are inferred based on the nuclear dataset (Figs. 1a  and 2 ). Based on the plastid data, three main clades emerge: a Philippine clade (A), a mixed Asian-Pacific clade (B), and a clade including the African and New World species (clade C; Figs.
Signal ambiguity in nuclear and plastid data sets Detailed inspection of split patterns in the bootstrap samples (Figs. 2  and 3 ; datasets excluding cultivars) demonstrate that the nuclear types are generally more distinct than the plastid types of the same specimens; this is illustrated in the more tree-like general structure of the nuclear-based bootstrap network. Signal ambiguity in the nuclear data relates to the initial radiation within the core group Ixora and the initial diversification of clade III. The plastid signal is not sufficiently clear either to resolve several backbone relationships. Most importantly, the signal from many Philippine taxa of clade B commonly is ambiguous. Other taxa (or pairs of taxa) inflicting topological ambiguity at deeper nodes in the    and 5 ). The outgroup-inferred root suggests an initial split in Ixora between a lineage that today occurs from the Pacific Islands to the Philippines (except for Palawan) with an outlier in Sri Lanka (yellow in Fig.
Relationships of the Philippine Ixora species Well-supported incongruence between the nuclear and the plastid datasets prevents the analysis of a combined dataset (  [40, 41] , and references therein). Therefore, the two different genealogies were explored separately. Our main nuclear clades, the Asian-Pacific clade (I) and the Asian-Afro-Neotropical clade (II-IV), correspond to those of Mouly et al. [31] , who also found an Afro-Neotropical and a Pacific clade. However, while Mouly et al. [31]  inferred a poorly supported monophyletic Asian clade, our greatly increased sampling of Asian, and in particular Philippine taxa, shows that Asian (including Philippine) species occur in both major clades in Ixora. The species from the Philippines are represented in five different lineages, corresponding to three major ribo -/haplotypes in the nuclear and the chloroplast dataset.
Biogeography The signal from nuclear and plastid data is far too complex to allow for application of currently available methods of biogeographic inference. All current methods need a fully-, or at least well-resolved, ultrametric phylogenetic tree as input. Computation of such trees for the nuclear and plastid data, which would provide the necessary discriminating topology to obtain meaningful ancestral area reconstructions, is not feasible based on the available data. Signal strength is a limiting factor in the nuclear, and to aneven greater extent, the plastid, data. Deep incongruences prevent concatenating both data sets. In addition to primary nuclear-plastid incongruence, the genetic complexity in Ixora indicates phases of secondary reticulation (I. brunonis, possibly I. acuticauda) and incomplete lineage sorting (situation in lineages II+IV/B).
Two closely related species are more likely to hybridize and introgress, which will eventually lead to a homogenization of the nucleome but not necessarily of the plastome. Widespread species with species-diagnostic nuclear signatures can carry distinct plastid signatures (e. g. Quercus coccifera and Q. ilex  [54, 56] ). Thus, nuclear data will more likely reflect the (current) systematic affinity of an individual or species, whereas plastid data may reflect the provenance of the (mother) population (e. g. [55, 56]  for oaks, and  [57, 58]  for Nothofagaceae). The simplest explanation for the geographic distribution of nuclear and plastid lineages (Fig. 4 ) is that an originally South Asian-Indomalayan sister lineage (orange) of the exclusively Philippine lineage (red), migrated or expanded into the southern Pacific area, possibly in response to the expansion of earlier diverged other Ixora in that region (green and purple members of the African-Asian clade).
Primers used for the amplification of nuclear  [64] [65] [66] [67]  and chloroplast  [68] [69] [70] [71]  DNA regions are listed in Additional file 4. PCR amplifications were run on a BIOMETRA thermocycler. All amplification products were cleaned using Qia-Quick PCR purification kit (Qiagen, Germany) and sent to LGC Genomics (Germany) for sequencing. Forward and reverse sequences were edited and aligned using CodonCode Aligner version 4. 0. 4 (CodonCode Co. , USA) and the consensus was exported in fasta format. The fasta files were aligned using SeaView version 4. 0  [72]  and the OPAL package  [73]  inside Mesquite  [74]  and the resulting alignment was corrected manually, following the recommendations of Kelchner  [75]. All variable nucleotide positions were verified against the original electropherograms and final sequences uploaded to the European Nucleotide Archive (ENA).
Phylogenetic analyses Separate and combined analyses of the rps16, trnT-F (i. e. trnT-trnL spacer + trnLLF region), ITS and ETS matrices were performed using the Maximum Likelihood (ML) criterion as implemented in RAxML v. 8. 1. 20 [76]  and Bayesian Markov Chain Monte Carlo (MCMC) inference  [77]  as implemented in the program MrBayes version 3. 1  [78]. For ML, we run partitioned and unpartitioned analyses, treating each gene region as one partition. We used the standard command lines which allow for quick, simultaneous optimization of substitution model, topology and branch support via fast, non-parametric bootstrapping (options -f a; -x; -m GTRCAT). The number of necessary bootstrap (BS) replicates were determined by the extended majority rule criterion (-\# autoMRE  [79] ). MrBayes analyses used the same partitioning scheme as RAxML and two parallel runs with each one cold and three heated chains (standard set-up), 10 6 generations, with every 1000 th topology sampled.
Posterior probabilities (PP) are based on the final 5000 saved topologies from both runs. Investigation of differential support for alternative relationships can directly reveal significant incongruence between nuclear and plastid genealogies. Phylogenetic resolution at the intrageneric level is typically low, hence, the lack of (high) support should not be taken as indication for incongruence per se. Instead we regard only conflicting relationships as evidence for highly supported incongruence based on the nuclear vs. plastid data (BS ML > 70, PP > 0. 95; arbitrary thresholds following the common convention in plant phylogenetic literature). Bipartition networks  [80] , a special form of consensus networks  [81]  that use either the bootstrap replicate or Bayesian saved tree sample as input  [82] , visualized the differential support for alternative (competing) relationships (using SplitsTree v.
Acknowledgements The first author thanks  Danilo Tandang  and  Arvin Diesmos  of the  Philippine National Museum  as well as the  Thomasian Angiosperm Phylogeny and Barcoding group  for help and assistance during field collections, and  Angelika Täuber  ( Univ. of Bayreuth ) for guidance during the molecular work. The present work is part of the doctoral dissertation of  C. I. Banag , for which financial assistance was obtained from  Philippine Commission on Higher Education (CHED) ,  Department of Science and Technology (DOST) ,  NAGAO Natural Environment Foundation (NEF) ,  DAAD STIBET Grants for Doctoral Studies , and the  Katholischer Akademischer Ausländer-Dienst  (KAAD). GWG acknowledges funding by the  Austrian Science Fund , project number  M1751-B16 , and the  Public Employment Service (AMS) Austria.
Availability of data and materials The datasets supporting the conclusions of this article are available in TreeBase (http://purl. org/phylo/treebase/phylows/study/TB2:S20219). An electronic supplementary data archive (ESA) containing all original data files and results, including the NCBI GenBank harvest and all employed matrices in NEXUS format, is available for anonymous download at www. palaeogrimm. org/data/Bng17_ESF. zip (please refer to the accompanying index document, GuideToFiles. txt, for a detailed description). Lists of voucher specimens, ENA (European Nucleotide Archive) accession numbers, and primers used are included in this article as Additional files.
Participants Data collection took place at the Meditation Research Institute (MRI) in Rishikesh, India. Subjects which lived close to the Institute received about 10 US dollars (500 Rupees) as compensation and subjects who traveled longer distances received about 20 US dollars (1000 Rupees) in addition to reimbursement of their travel fees, accommodation and meals. About one third of the subjects (mostly from the ISY group) traveled more than 2000 km to participate in the experiment. Participants all provided written consent to participate in the study. The project was approved by the local MRI Indian ethical committee and the ethical committee of the University of California San Diego (IRB project # 090731). All meditators were chosen for inclusion in the study based on age, gender and years of practice of meditation.
Control subjects were chosen for inclusion in this study based on age and gender and their absence of a meditation practice. We collected data on 20 meditators from the Vipassana tradition, 27 meditators from Himalayan Yoga Tradition, 20 meditators from Isha Shoonya Yoga tradition and 32 controls. All meditators were used to practice meditation with their eyes closed. In the current study, we aimed at analyzing homogeneous groups of subjects and groups were formed by matching subjects based on gender and age. Following this matching procedure we obtained 4 groups of 16 subjects each. Because the Isha shoonya and Vipassana groups did not contain as many subjects as the control and Himalayan yoga groups, the matching process implied leaving out of the present analysis some control and Himalayan yoga participants.
In addition, after the instructed mind-wandering and meditation blocks, participants were presented with a diverse set of auditory and visual tasks-the results of which will not be reported here. Immediately after each session, participants completed a questionnaire to assess the subjective characteristics of their mental state during the session (see below Psychometric data collection) and were allowed to stand up, stretch and walk around. The order of the sessions was counterbalanced between participants to prevent any order effects. The day preceding the study, participants were invited to visit the experimental room to practice the tasks for 10 minutes (5 minutes instructed mind-wandering and 5 minutes meditation). Participants entering the study as meditators were asked to avoid meditating before coming to the laboratory on the day of the experiment.
Data collection We recorded data using an 64 + 8 channels Biosemi Active-Two amplifier system and a 10-20 Headcap standard 64-channel cap from the same company. Using external electrodes, we also recorded right and left mastoid electrodes as well as vertical and horizontal electrooculogram (EOG) by placing two periocular electrodes above and below the left eye and two electrodes at both the left and right outer canthi. The experimental room was soundproof and the floor was electrically shielded and grounded. In order to ensure good quality of EEG signal, participants were asked to wash their hair before attending the recording session and, for non scalp electrodes, their skin was carefully cleaned using an alcohol solution. All electrodes were kept within 50mV offset of the BIOSEMI system metric for measuring impedance.
Data processing and artifact rejection Data processing was done using the EEGLAB open source software version 12  [44]  running on Matlab R2009b (The Matworks, Inc. ) under a Linux operating system (Ubuntu 12. 04). EEG data were first referenced to the right mastoid and down-sampled from 1024 Hz to 256 Hz. We then applied a high-pass filter at 1 Hz using an infinite impulse response (IIR) filter with a transition bandwidth of 0. 3 Hz and an order of 6. We automatically removed portions of the signal presenting non-stereotyped artifacts using the pop_rejcont function of the EEGLAB software  [44]. The data were first segmented in 1-second epochs with 0. 5-second overlap. Segments of 8 contiguous epochs in which the 0-10 Hz frequency band and the 35-128 Hz frequency band had an amplitude higher than 17 and 14 decibels respectively were labelled as artifactual.