dataesr/scientific-paragraphs-categorization huggingface dataset:
5. 2  71. In this combined alignment, the proportion of fully resolved quartets was 85. 2%, with 9. 4% partly resolved and 5. 5% unresolved. In view of its relatively high phylogenetic content and the use of independently evolving (unlinked) markers, such concatenated nuclear-mitochondrial dataset allows for more robust (co-)phylogenetic hypotheses to be put forward (see also the recommendations by de Vienne et al. 56  ). Bayesian inference of phylogeny (BI) was carried out in MrBayes v. 3  72. Posterior probabilities were calculated over 10 7 generations. Stationarity of the Markov chain was reached, as evidenced by a standard deviation of split frequencies of 0. 008, by a potential scale reduction factor converging to 1 and by the absence of a trend in the plot of log-probabilities as a function of generations.
The Markov chain was sampled with a frequency of 10 2 generations; one-fourth of the samples were discarded as "burn-in". A ML search was carried out in RAxML v. 7. 3. 0  73  , assessing nodal support through 1000 bootstrap samples. The evolutionary model was optimized for each fragment separately, suggesting HKY + Γ for ITS-1, JC for 5. 8S rDNA, TPM1uf + Γ for ITS-2 and GTR + Γ for COI. These models were substituted by GTR + Γ in RAxML and, in the case of ITS-2, also in MrBayes, as this was the implemented model with the best AICc score. In the latter software, all parameter estimates for the various sequence portions were unlinked. To assess the rate of diversification as a function of time, we started from the largest dataset (ITS rDNA) in order to include a maximal sample size. Identical sequences were removed, as well as haplotypes differing less than 0.
Cophylogenetic analyses. A range of methods exists to compare the phylogeny and divergence in host-parasite or other symbiotic systems, inferring the speciation patterns that contributed to the consistencies or inconsistencies in their evolutionary trajectories. Of these, methods reconciling host and parasite tree topologies are often considered to maximize cospeciation events, and to take topological congruence as an evidence for cospeciation, which is not always justified  56. To minimize the risks of such assumptions, host and parasite tree were reconciled in the software package CoRe-Pa v. 0. 5  78  , checking 10 4 cost sets using a simplex method on the quality function. This software carries out an event-based analysis. A major asset is its parameter-adaptive approach that allows for the automated estimation of proportional event costs, thus avoiding a priori cost assignment to the different categories of parasite speciation mechanisms  79, 80.
Root-to-root mapping was enforced and the chronological consistency of events checked. To work with a fully resolved tree that best approaches the "species tree", the ML parasite phylogram reconstructed by RAxML for the combined nuclear-mitochondrial dataset, was included in cophylogenetic analysis. The AFLP tree of Koblmüller et al. 8  was coded with the help of TreeSnatcher 81 to provide a host topology. The selection of optimal trees obviously entails some uncertainty for this topology-based analysis. Therefore, the analysis was repeated with a parasite phylogeny in which all nodes receiving less than 70% of bootstrap support were collapsed. As within-host speciation in terminal taxa can artificially infer cospeciations at the cost of additional duplications  56, 63  , terminal monophyletic clades associated with a single host species were collapsed.
For the same reason, the software was set not to bill an additional duplication for a host-switching event. Host and parasite tree were also reconciled in a heuristic search in TreeMap v. 1. 0a  82. Because this topology-based software is known to maximize the number of cospeciation events, the number of the various speciation mechanisms that TreeMap proposes will not be taken into consideration. The test for the significance of the number of cospeciation events inferred is only considered as a measure of topological congruence rather than of cospeciation  56. This was assessed by randomizing host and parasite topologies (10 4 random trees used) under the proportion-to-distinguishable model. Distance-based cophylogenetic analyses test for correlation between phylogenies without assuming congruence to be produced by cospeciation, and are hence considered less biased than topology-based methods  56.
Distance-based cophylogenetic analysis was carried out in Copycat v. 1. 14  83 making use of AxParafit and AxPcoords 84 using 9999 permutations under default settings. In this analysis, the independence between host and parasite patristic distances is tested. To this end, distance matrices were constructed with the help of T-rex  85. For the hosts, the mitochondrial ND2 and control region data from   24, 25, 40, 44, 86. **Also represented in the tissue collection of the Zoological Institute of the University of Basel. ***Parasite voucher in the RMCA invertebrates collection: MRAC 37791. Koblmüller et al. 8  were used, as these mitochondrial fragments are better suited for distance calculations than AFLP data (long terminal and short internal branches in the AFLP tree). Because of the large number of insertions/deletions in the nuclear fragment which inevitably bias genetic distance estimates over the whole dataset, only all COI mitochondrial fragments, omitting the third codon position, were used to infer parasite patristic distances.
Acknowledgements J. Bamps ,  A. F. Grégoir ,  L. Makasa ,  J. K. Zimba ,  C. Katongo ,  T. Veall ,  O. R. Mangwangwa ,  V. Nshombo Muderhwa ,  T. Mulimbwa  N'sibula,  D. Muzumani Risasi ,  F. Muterezi Bukinga ,  J. Mbirize Ndalozibwa ,  V. Lumami Kapepula , the  Schreyen-Brichard  family,  F. Willems ,  S. Dessein ,  A. Indermaur ,  A. Theis ,  B. Egger  and  W. Salzburger  are thanked for their help in collecting samples,  R. Bills  for permission to inspect Simochromis margaretae specimens for gill parasites,  T. Musschoot  for Fig. 4, M. Parrent  for curatorial services and  A. Konings  and  R. Blažek  for fish pictures. D. T. J. Littlewood ,  E. Verheyen ,  S. B. Janssens ,  M. H. D. Larmuseau ,  F. Van den Broeck ,  N. Van Steenkiste ,  L. Rüber ,  M. Gelnar ,  D. R. Brooks  and  W. A.
Boeger  are gratefully acknowledged for valuable suggestions. This is publication ISE-M 2015-047. M. P. M. V. and M. V. S. were recipients of a PhD fellowship, and T. H. of a post-doctoral fellowship, of the  Research Foundation-Flanders (FWO-Vlaanderen ). Fieldwork was funded by two travel grants from the  Research Foundation-Flanders  (to M. P. M. V. ) and from the  King Leopold III Fund for Nature Conservation and Exploration  (to M. P. M. V. and M. V. S. ), while molecular analysis was funded by the  Joint Experimental Molecular Unit (JEMU)  project  PARATROPH. C. S. was supported by the  Austrian Science Foundation , Grant numbers  I48-B06 ,  P20994-B03  and  P22737-B09. We gratefully acknowledge the support of  KU Leuven -VES/12/005 , of  FWO-Vlaanderen Research Programme G. 0553. 10 , and of the  Czech Science Foundation , Project no.
Here, we exploit these tracers to identify regions and periods in the POLMIP model simulations for which air is strongly influenced by fire emissions. Several aircraft flew missions into the Arctic troposphere during summer 2008 as part of the POLARCAT experiment  (Law et al. , 2014). The POLARCAT-France and GRACE experiments, based in Southwest Greenland, sampled aged fire plumes and anthropogenic air masses transported into the Arctic from Siberia and North America. ARCTAS-B, based in central Canada, sampled fresh and aged fire emissions over Canada and the Arctic. In this analysis, we make use only of data from the ARCTAS-B mission, for which the NASA DC8 aircraft was equipped with an extensive suite of gas phase and aerosol instrumentation, including ozone, CO, speciated oxides of nitrogen (NO y ), volatile organic compounds and peroxides  (Jacob et al.
, 2010). Monks et al. (2015)  present a detailed comparison of the POLMIP model simulations with CO and ozone data from all POLARCAT experiments. During ARCTAS-B, the DC8 aircraft made seven flights, based from Cold Lake, Canada from 29 June to 10 July 2008. The vast majority of observations were made in fresh Saskatchewan fire plumes, although some flights also targeted aged plumes transported to Canada from Siberian and Californian fires. All ARCTAS DC8 data are available in a publicly accessible archive (http://www-air. larc. nasa. gov/ cgi-bin/arcstat-c), and described in  Jacob et al. (2010). 3 Fire emission influence on ozone and NO y enhancement in POLMIP models.
Acknowledgements. S. R. Arnold acknowledges support from the  NCAR   Advanced Study Program  via a  Faculty Fellowship award , and the  NCAR Atmospheric Chemistry Division. S. R. Arnold  and  S. A. Monks  were supported by the  EurEX  project, funded by the  UK Natural Environment Research Council  (ref:  NE/H020241/1 ). L. K. Emmons  and  S. Tilmes  acknowledge the  National Center for Atmospheric Research , which is sponsored by the  US National Science Foundation. Author L. K. Emmons acknowledges support from the  National Aeronautics and Space Administration  under Award No. NNX08AD22G  issued through the  Science Mission Directorate, Tropospheric Composition Program. Authors K. S. Law ,  J. L. Thomas ,  S. Turquety  and  Y. Long  acknowledge support from projects  Agence National de Recherche (ANR)   Climate Impact of Short-lived Climate Forcers and Methane in the Arctic (CLIMSLIP)  Blanc  SIMI 5-6 021 01  and  CLIMSLIP-LEFE (CNRS-INSU).
Simulating Supply and Demand HLA haplotype frequencies for simulation were published by the National Marrow Donor Program (NMDP)  [8]. Ancestry representation within the simulated population was adapted from the 2012 U. S. Census Bureau estimates for California  [9]  and from data provided by the California Institute of Regenerative Medicine (S. Talib) (Table  1 ). The haplobank and population included the following broad ancestry categories (in decreasing order of representation): white (non-Hispanic; CAU), Hispanic (HIS), Asian and Pacific Islanders (API), American Indian and Alaska native (NAM), and black or African American (AFA). Haplobanks were assembled by combining the top 20, 40, 60, 80, and 100 HLA-A∼B∼DRB1 haplotypes (haplolines) from each ancestry and filtered for nonredundant haplotypes.
Various Jewish authors of Medieval Europe, from Cordova to Krakow, in texts such as biblical commentaries, letters, or responsa, offered legal advice to fellow Jews on the proper and legal limits to relations with Christians and Muslims. There is thus a rich and varied corpus of texts dealing with the legal status of religious minorities in pre-modern Europe. These texts, in Latin, Arabic, Greek, Hebrew and Aramaic (and also in Medieval Spanish, Portuguese, and other European vernaculars), are dispersed in libraries and archives across Europe. The ERC project RELMIN (www. relmin. eu) has created a database containing many of these texts. The database (http://www. cn-telma. fr/relmin) contains texts in the original languages (principally Latin, Arabic, Greek and Hebrew, but also in the European vernacular languages).
The database is consultable in English and in French: each text is translated and a brief commentary, explaining its historical significance, is included, as are references to the relevant bibliography. These sources are fully searchable, in the various languages used. The use of thematic keywords will allow comparative searches of texts from different religious traditions (e. g. , ablutions or dietary restrictions). The website also allows access to the various seminars and conferences organized by the project (text, audio and video), to the proceedings of the conferences, and to other articles posted by members of the RELMIN research team. This database provides a unique and valuable tool for researchers in the history of minority law and in the history of interreligious relations. It serves as an eloquent testimony to the permanence and ubiquity of interreligious cohabitation in Europe.
Interdisciplinary and cross-cultural research on the status of minorities in pre-modern Europe RELMIN's team and collaborators have embarked on the comparative study of these sources and have explored their implications for research in the history of interreligious relations. The database was put together by a team including myself, 4 doctoral students, 13 post-docs and a number of invited guest scholars. The team of researchers assembled in Nantes is interdisciplinary (including scholars in law, religion, history, Greek, Latin, and Arabic) and international (with members from France, Spain, the UK, Israel, Algeria, Italy, Poland, Turkey, Canada, and the USA). In March 2011, I organized with Maribel Fierro a conference at the Centro Superior de Investigaciones Científicas (CSIC) in Madrid a conference on The Legal Status of Ḏimmī-s in the Islamic West; we subsequently published the acts of this conference as the first volume in our collection Religion and Law in Medieval Christian and Muslim Societies with Brepols publishers.
How do the new involuntary immigrants integrate their new homelands? This of course depends on a wide variety of factors: language, diet, religion, etc. And of course small numbers integrate more readily than large groups, which are more likely to cling to a specific group identity within the larger society. An important element is the attitude of the authorities of the new lands of exile. A Diaspora community, in theory, conserves its distinct identity (linguistic, cultural, religious, etc. ) within a foreign host society. But in fact, of course, the degrees of assimilation and acculturation vary widely, and over time certain diaspora communities blend into the host societies completely. Others keep a distinctive identity while adopting important elements of their host cultures: within the Medieval Jewish diaspora, Iraqi Jews and English Jews resemble in many ways more their respective host cultures than they do each other.
Over sixty of the texts in the RELMIN database deal with food in one way or another: which foods one can eat or cannot eat, the possibility (or not) of »contamination« of food or drink through contact with an infidel, the legality (or not) of buying food from an infidel or sharing a meal with him. We have seen that the council of Vannes in 465 prohibits Christian clerics from sharing meals with Jews. Food prohibitions -what one can eat, and above all with whom one can eat -have often been used to mark and separate the faithful from outsiders. 35 Rena Lauer shows how Jewish authorities in Crete worried about the effects of Jews using gentile bake-houses; Farid Bouchiba gives examples of how Mālikī jurists tried carefully to determine which meat was licit, depending on who killed the animal in what circumstances.
All PCR reactions included negative control samples for quality assurance. We analyzed each multiplex PCR product on an ABI 3130 capillary array genetic analyzer (Applied Biosystems, Foster City, CA, USA). We determined fragment sizes against a Genescan 600 Liz size standard (Applied Biosystems, Foster City, CA, USA), and allele sizes using the Genemapper ID version 4 software (Applied Biosystems, Foster City, CA, USA). We discarded all samples with unsuccessful amplification after five PCR attempts and two independent DNA extractions. We discarded from further analyses all samples that displayed an incomplete allelic profile (less than four loci), a multiple peak profile for the same locus, or discordant results. A In MA and ML sites 11 and 1 SIV strains were both amplified in pol and env respectively.
We calculated P(ID)HW for each individual (Data not shown). P(ID)HW is the probability that two individuals drawn at random from a population will have the same genotype at multiple loci, assuming that the loci we chose for these analyses are inherited independently (i. e. , that they are unlinked). For parentage analysis, we assumed that we collected and successfully genotyped a quarter of the offspring in every group and a quarter of the candidate parents. The frequency of typing errors and the error rate in likelihood calculations were set at 0. 01. The minimum number of typed loci was set at four out of seven. Allele frequencies, critical to run simulations and to assess confidence of parentage assignment were also calculated. Confidence in assignment of parentage to the most likely candidate parent is evaluated relative to a critical threshold determined in the simulation (LOD score).
For the first PCR round, bovine serum albumin (BSA) was added at the final concentration of 0. 2 µg/mL to improve the success of amplification. All RT-PCR reactions were performed using the Expand Reverse transcriptase, and the Expand long Template PCR kit (Roche Diagnostics, Indianapolis, IN, USA), according to the manufacturer's instructions. After purification with the Geneclean Turbo Kit (Qbiogene, Inc. , Carlsbad, CA, USA), PCR products were sequenced on an automated sequencer (3130xl Genetic Analyser, Applied Biosystems, Foster City, CA, USA). The resulting sequences were aligned with SEQMAN DNASTAR software (Lasergene, DNASTAR, Inc. , Madison, WI, USA).
Acknowledgments: This work was supported in part by the  Centre International de Recherches Médicales de Franceville (CIRMF) , the  Institut de Recherche pour le Développement (IRD)  and by grants from the  National Institute of Health  ( RO1 AI 50529 ), the  Agence Nationale de Recherches sur le SIDA  ( ANRS 12255 ) and the  Agence Nationale de la Recherche  ( ANR JCJC ORIGIN 2012 ). We thank the  Ministry of Water and Forests of Gabon. We thank  Martine Koné  for her collaboration and participation in this study. Vanina Boué  was supported by a  Ph. D grant from  Sidaction. Ahidjo Ayouba ,  Christelle Butel ,  Amandine Esteban ,  Alain-Prince Okouga ,  Alphonse Ngoundouet ,  Paul Ngari. Analyzed the data:  Florian Liégeois ,  Floriane Boucher ,  Vanina Boué ,  Sabrina Locatelli. Contributed reagents/materials/analysis tools:  Florian Liégeois ,  Vanina Boué ,  Sabrina Locatelli.
Wind Measurements We use wind measurements at a height of 10 m above the ground from the NOAA ISD-Lite database  (Smith et al. 2011). This database has long time records, but we only use measurements made between January 1 2010 and December 31 2013 because the accuracy is better over these recent years: the wind speed M is binned with intervals of 1 knot (0. 514 m s - 1  ) 1 instead of 2 knots for previous years, and there are less gaps in the records. The wind direction D is binned with intervals of 10 •. The 10-min averaged wind speeds and directions are recorded every hour. Among all the stations present in the ISD-Lite database, we select stations in France where the accuracy is 1 knot over the four years and where the data availability is greater than 97 % over each one of the four years, with a minimum of 85 % for each month.
We therefore retain 89 stations. At each station we have about 3. 4 × 10 4 measurements so that the extremes should be well described. However, on average, the wind-speed records are correlated over a 10-h time period leaving thus about 3 × 10 3 independent samples. Calm conditions (M = 0) have been removed before all calculations since they are not taken into account in the Weibull distribution nor in the other distributions that we plan to use. The calm conditions represent 5. 2 % of the entire dataset with of course disparities among stations. Most are around 3 % but 14 stations are above 10 %. When wind components are used instead of wind speed, the zonal (west-east) and meridional (south-north) wind components (u and v) are derived from the wind speeds and directions. The wind components are often correlated so we use the procedure described by  Crutcher and Baer (1962)  to reduce component correlation to zero.
The change of variable u → u , v → v , is obtained by a simple rotation of an angle ψ defined by tan(2ψ) = 2 ρ uv σ 2 u -σ 2 v , (2) where ρ uv is the correlation coefficient and σ 2 u and σ 2 v are the component variances. The procedure relies on the property that any Gaussian joint probability distribution is characterized by a covariance matrix, which is positive and definite. Therefore, the matrix is fully characterized by its eigenvalues (which we call σ u and σ v ) and its eigenvectors are orthonormal. In the new base (which has been rotated by an angle ψ calculated over the entire dataset), the matrix is diagonal and has no cross-terms, corresponding to the correlation. We verified at all stations that u and v have no correlation. Considering correlation free components for the wind field allows the manipulation of simpler expressions for the distributions.
Importantly, the number of mapped RNA-seq reads was similar for the Col-0, dcl2/3/4, pol IV and rdr2 RNA-seq datasets (see Table  2 ). Consistent with the genome browser views of Figures 4 and 5, P4R2 RNAs that accumulate in dcl2/3/4 triple mutants show a high degree of correspondence to 24 and 23 nt siRNA sequences, genome-wide. To simplify the discussion we focus solely on 24 nt siRNAs. Ninety-six percent of P4R2 RNAs identified in dcl2/3/4 mutants fully encompass or overlap 24 nt siRNA sequences (Figure  6A ). Among the P4R2 loci we identified are 20 of the 22 loci that Li et al. (Li et al. , 2015)  confirmed by reverse transcription-polymerase chain reaction to be capable of generating Pol IV and RDR2dependent RNAs (Supplementary file 2). We next examined how P4R2 RNAs and their matching siRNAs align with one another.
, who showed that DCL3 preferentially cleaves short synthetic dsRNAs of 30-50 nt, but not longer RNAs  (Nagano et al. , 2014). Our analyses indicate that 24 nt siRNAs are preferentially generated from the 5' or 3' ends of P4R2 RNAs, suggesting that P4R2 duplex RNAs can be diced from either end, also in agreement with Nagano et al. 's studies. Generation of siRNAs from the ends of P4R2 RNAs, rather than from internal sequences, leads to the prediction that each P4R2 RNA sequence has limited capacity to specify multiple alternative siRNAs. Thus, the multitude of unique 24 nt siRNA sequences present in wildtype cells can be expected to be derived from a similarly large number of P4R2 precursors, depending on whether one or both strands of diced duplexes are utilized as siRNAs. Consistent with this prediction, our sequenced datasets included 1,055,471 unique 23 or 24 nt siRNA sequences (in wildtype plants) and 933,453 unique P4R2 RNAs of 26-94 nt (in dcl2/3/4 triple mutants).
RNA size markers were run in lane M. The 51 nt RNA template, 5' end-labeled using T4 polynucleotide kinase, was run as a size marker in the lane at far right. DOI: 10. 7554/eLife. 09591. 016 formal possibility, one might similarly expect to detect RDR2 transcripts in a pol IV mutant. However, our RNA blot results (Figure  2 ) defy these predictions, as do the RNA-seq data for pol IV and rdr2 mutants. Instead, precursors are depleted if either RDR2 or Pol IV is absent. This suggests that Pol IV and RDR2 are each required for the synthesis of both strands of P4R2 RNA duplexes, as was also noted by  Li et al. (Li et al. , 2015) , which fits with the physical association of Pol IV and RDR2 and the hypothesis that the two enzymes function as a complex  (Haag et al. , 2012; Law et al. , 2011). We have shown previously that RDR2 activity detected in vitro using affinity-purified Pol IV-RDR2 complexes from wild-type plants is not apparent using RDR2 affinity purified from a pol IV mutant  (Haag et al.