dataesr/scientific-paragraphs-categorization huggingface dataset:
Excluded names Uvariastrum neglectum  Paiva, Mem. Soc. Brot. 19: 55. 1966   LBV, LISC, M, MO, P, UPS, US, UC, WAG, and Z. Finally, I am grateful to two anonymous reviewers and Sandra Knapp for improving the manuscript thanks to their detailed comments on an earlier version. Access to ArcMAp 10. 0 was provided via the IUCN Palm Specialist Group.
Boutique, Bull. Jard. Bot. État Bruxelles 21: 120. 1951. http://species-id. net/wiki/Uvariastrum_germainii Figure 5 Type. Democratic Republic of Congo. Orientale: Yangambi, 29 Feb 1910, R. G. A. Germain 213 (lectotype, designated here: BR! [BR8824400]; isolectotypes: BR! [BR8824417], FT! [FT001090], K! [K000198809], P! [P00315823, P00315825], US! [accession number US00104141]).
Acknowledgments I am grateful to  Th ierry Deroin  for allowing me access to the archives of  Annick Le Th  omas as well as unpublished drawings at the  Muséum d'Histoire Naturelle in Paris. Marc Sosef ,  Jan Weiringa ,  Th eo Damen  and  Foulkert Aleva  are thanked for their assistance and help during my visit to the WAG herbarium in the framework of this revision. David Harris  is thanked for sharing details of unmounted specimens of Uvariastrum. Th e curators of the following herbaria are thanked for the loan of plant material used in this revision: A, B, BM, BR, C, COI, CGB, EA, F, FHO, G, HBG, IEC, K,.
E. Fries 1260 (lectotype, designated here: UPS! [accession number V-043384]; isotypes: USP! [accession number V-061951]), Z! [Z-000000874]). Type. Based on Uvaria hexaloboides R. E. Fr. Description. Tree up to 15 m high, d. b. h. up to 45 cm; old branches, glabrous, bark brown, striate; young.
Uvariastrum zenkeri Engl. & Diels, Bot. Jahrb. Syst. 39: 473. 1907. http ://species-id. net/wiki/Uvariastrum_zenkeri Figure12Uvariastrum zenkeri Engl. & Diels var. nigritanum Baker f. , Cat. Talbot's Plants 3. 1913. 5. Type. Nigeria. Cross River State: Oban district, recd. at Paris 21 Feb 1912, P. A. Talbot 1341 (lectotype, here designated: K!; isotypes: FHO! [accession number 15560, barcode 3586], P! [P01983332]). Uvariastrum pynaertii De Wild. , Ann. Mus. Congo Belge, Bot. sér. 5, 3[1]: 74. 1909. Type. Democratic Republic of Congo. Equateur: Eala, Mar 1907 L. A. Py- naert 1234 (lectotype designated by Le Th omas (1969) pp. 292, sheet desig- nated here: BR! [BR0000008824288]; isolectotypes: BR! [BR0000008824295, BR0000008824301], S!) syn. nov. NIGERIA. Edo State : Ugwega (Beni), Compt. 86, 16 Jan 1948, Brenan, J.
incisa the richest plant source of the pharmaceutically and nutraceutically valuable AA and a target organism of high biotechnological interest  [3]   [4]. The ability to store AA within reserve lipids, TAGs, was thought to be related to the need to maintain a buffering capacity for the long-chain polyunsaturated FA (LC-PUFA) pool under conditions of temperature change or growth recovery when rapid LC-PUFA incorporation into the cellular membranes is required for adjusting membrane fluidity  [5]   [6]. The conversion of dihomo-c-linolenic acid (DGLA, 20:3 n-6) to AA is mediated by the enzyme D5 desaturase (DES5, GenBank: GU390533). Based on its chlorotic phenotype at 15uC, we have been able to isolate P127, a L. incisa mutant strain in DES5  [7]   [8]. The chemically induced non-sense mutation caused a nucleotide alteration in the DES5 gene, leading to the appearance of stop codon and the complete loss of AA biosynthesis.
Quantitative real-time PCR (qRT-PCR) qRT-PCR analysis was carried out in optical 96-well plates using the CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA). qRT-PCR primer pairs (Table  1 ) were designed for LiDES5 and the housekeeping gene LiAct (actin) and the reactions were performed using iTaq Universal SYBR Green Supermix (Bio-Rad). PCR cycling conditions consisted of an initial polymerase activation step at 95uC for 30 s followed by 40 cycles at 95uC for 5 s and 60uC for 30 s, and a final melting step at 65-95uC. Results were analyzed using the 2 2DDCt method, a function of the CFX Manager Software v3. 0, using the relative expression value of the housekeeping gene as the calibrator. The experiment was performed twice, with two biological replicates and three technical replicates for each sample.
Results Cloning and analysis of the L. incisa RBCS and DES5 genes The RBCS and DES5 genes, their putative promoters and 39flanking flanking regions were identified in a draft assembly of the L. incisa genome generated in the framework of the EU FP7 GIAVAP project (www. GIAVAP. eu). The sequences were submitted to Genbank, accession numbers KJ633120 and KJ633121 for RBCS and DES5 genes respectively. The RBCS gene contains two introns within the 570 bp coding sequence, while DES5 contains seven introns within the 1356 bp of CDS. Genes and their upstream and downstream sequences were cloned into plasmid vectors.
This research was financially supported by the  European Commission's Seventh Framework Program for Research and Technology Development  ( FP7 ), project  GIAVAP , Grant No. 266401. BZ, OG and YK acknowledge support from the  Kreitman School of Advanced Graduate Studies at Ben-Gurion University. OV acknowledges support from the  French state "Initiative d'Excellence" program  (Grant " DYNAMO ",  ANR-11-LABX-0011-01 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
CACTUS code The Code for Axial and Cross-flow TUrbine Simulation (CACTUS) [Murray and Barone, 2011] is a three-dimensional free vortex code in which the rotor blades are modelled using the lifting line approximation, with each blade discretized into a number of blade elements containing a bound vortex line. The wake is represented using a free vortex lattice; at each time step, each blade element produces a new shed vortex line segment connected to the bound vortex by two trailing vortex line segments. The velocity field induced by the entire vortex system, including bound and wake vortex elements, is calculated using the Biot-Savart law. The bound vortex strengths are calculated by determining the blade element force consistent with the local flow at each element produced by the wake, free-stream velocity, and the bound vorticity.
Aims: A reliable prediction tool is needed to identify acute coronary syndrome (ACS) patients with high mortality risk after their initial hospitalization. Methods: EPICOR (long-tErm follow uP of antithrombotic management patterns In acute CORonary syndrome patients: NCT01171404) is a prospective cohort study of 10,568 consecutive hospital survivors after an ACS event (4943 STsegment elevation myocardial infarction (STEMI) and 5625 non-ST-elevation ACS (NSTE-ACS)). Of these cases, 65. 1% underwent percutaneous coronary intervention (PCI) and 2. 5% coronary artery bypass graft (CABG). Post-discharge mortality was recorded for up to two years. From over 50 potential predictor variables a new risk score for oneyear mortality was developed using forward stepwise Cox regression, and examined for goodness-of-fit, discriminatory power, and external validation.
Methods EPICOR (long-tErm follow uP of antithrombotic management patterns In acute CORonary syndrome patients) is a prospective, international, observational, real-world practice, cohort study (NCT01171404) comprising consecutive patients, hospitalized for ACS within 24 h of symptom onset, who survived to hospital discharge. In total, 10,568 patients with non-fatal ACS who survived until hospital discharge were enrolled between September 2010-March 2011 from 555 hospitals in 20 countries across Europe and Latin America. A detailed account of the methodology of the study is described elsewhere. 8, 9 or external validation of our risk model, we used data from the EPICOR-Asia study  10  (NCT01361386) which enrolled 12,993 patients from eight Asian countries from June 2011-April 2012. This Asian study has followed an almost identical protocol and case record forms as in our EPICOR study.
For each there is specific wording to elicit whether the patient has no, moderate, or severe limitation. For each we have scored 0, 1 or 2 points respectively, and adding up these scores yields a simple overall score ranging from 0 points up to a maximum of 10 points. While there do exist more complex weighted schemes for handling the EQ-5D,  12  we feel that for practical use in our context of user-friendly risk prediction this required the adoption of such simple scoring. The multiple imputations were performed using Stata 12. 0 while all other analyses used SAS version 9. 2.
It would be useful if the GRACE and EPICOR risk models were directly compared in an independent cohort of ACS patients followed from hospital discharge. There are some limitations inherent to our risk model. Being a study on hospital survivors, blood pressure and heart rate at admission were not recorded in our database and hence could not be included in the model. Certain other variables (e. g. probrain natiuretic peptide, incomplete revascularization) were also not available for inclusion. Even after taking account of our 12 highly predictive risk factors, there persist substantial unexplained geographic differences in post-discharge mortality risk. In Eastern Europe and Latin America one-year mortality is markedly higher than in Western Europe, and further investigation is needed to clarify why this discrepancy exists.
Thus, this does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. Modalities to shape clonal phenotypic variants produced without sex, and consequently without gene mixing by crossing over in meiosis, are still poorly understood. Our assumption is that this scenario appears to limit the role of allele recruitment and chromosome recombination that sexuality renders possible. This phenotypic repertoire in conditions where the genome is apparently unchanged was analyzed to determine whether some variants are correlated with epigenetic marks located on specific sites in the genomic scaffolds. For this purpose, covalent modification by addition of methyl groups on the whole aphid genome was investigated as the epigenetic mark that is the most amenable to analytical procedures.
Orange aphids injected with green aphid extract gave immediately green progenies in cold (black triangles). Green aphids placed at 22uC lost their green pigments after few days and their progenies were immediately orange (open circles). (C) Green aphids were placed at 22uC for 8 generations and for each one, 20 newly orange adults were placed back at 8uC. A preliminary experiment allowed us to determine the time required to get 20 newly green adult aphids from the 20 original orange at the first generation. This time scale was used to count the newly green adult aphids at each generation and data are represented as the ratio newly green adults versus initial orange aphids. Dots are the mean+/2 SEM, n54. doi:10. 1371/journal. pone. 0115022. g001 The total reads of the methylome were matched on the scaffolds.
The reads were contigated and matched against the scaffolds. Out of 2,540 orange contigs and 2,008 green contigs, a reciprocal BLAST between the green and orange samples gave 864 pairs of contigs with high similarity (e-value ,1e-50) and associated to a low number of reads. This category of contigs was used as internal control to calibrate the samples and then the contigs whose number of associated reads displays a large difference between the two variants were considered for further analysis (see Experimental and S1 Procedures for the cut off thresholds). The reliability of the data obtained with the SSH technique followed by pyrosequencing analysis was assessed by quantitative PCR. A subset of genes that were expressed in only one variant was selected arbitrarily and the analysis by qPCR is presented in Fig.
and S1 Procedures. A gene was considered to have a strong variation of expression if 20 or more transcriptome reads are associated with this gene in one sample whereas no transcriptomic read is associated with the other sample. Some coherent trends emerge regarding the biological process: the genes associated to strong decrease of expression in the green are relevant to mRNA catabolic process, DNA-dependent replication, translation process, mRNA splicing and mRNA transport; the genes associated to Fig. 4. Representative scaffolds decorated with the mapping of the exact matches corresponding to the methyl reads and the transcriptomic contigs. The methylome reads were directly mapped to the genome scaffolds of A. pisum strain LSR1 version Acyr_1. 0 with the program Razers  [43]. The contigs were searched for sequence similarity using BLAST  [46].
This suggests also that a massive transposition of mobile elements is not a valid scenario that might explain the green and the orange clonal phenotypes. The green variant is the result of a complex genetic network remodeling, likely associated to site-specific methyl DNA assortment. Epigenetic marks heritable over a limited number of generations might constitute a solid mechanism for adaptation and fitness of aphids in a fluctuating environment. On the other hand, it has been suggested that methylation of cytosine in the gene body might affect the alternative use of promoters and the rate of polymerase that regulates alternative splicing (through recruitment of factors in the polymerase/ spliceosome complex)  [33] [34] [35]. The databases linked to this report will allow addressing these topics.
Specific metabolic pathways highlighted by GO analysis are consistent with environmental adaptability. We hypothesize that epigenetic stable marks might be transmitted through generations in clonality context and that the sexual barrier in fall could preserve those that are advantageous for the wave of clonal individuals the next spring. By this work, tools like the full differential transcriptome and the full methylome databases between environment-selected variants issued from a single founder This table displays significantly enriched GO terms (using a p-value,0. 05) with respect to the ''Molecular Function'' GO category. (A) Molecular function of genes that show at least two-fold increase of expression value in the green compared to the orange sample. (B) Significantly enriched GO terms in the list of over-expressed genes that show a reduction of methylation.
Methylome The multiplex barcoded pyrosequencing was performed in a single run, with two samples tagged uniquely by multiplex identifiers (MID). The reads were directly mapped to the genome scaffolds of the A. pisum strain LSR1 version Acyr_1. 0 with the program Razers  [43]. By setting the default mismatch cutoff at 4%, about 95% of reads could be covered  [44]. Dataset were deposited to NIH Short Read Archive under the references SRX719262 for methylated fragment found in the green variant and SRX719263 for methylated fragment found in the pink variant.
Transcriptome The reads for both samples were assembled using the Newbler 2,0 program  [45]  after removal of the adapter sequences. The contigs were then searched for sequence similarity using BLAST  [46]  against the genome scaffolds of A. pisum strain LSR1 version Acyr_1. 0. Contigs could be mapped unambiguously to the genome with default BLAST parameters and e-values #10 250 or better. To standardize the differential expression data between the two variants, we used DNA sequences that escaped the suppression step as internal control of the method (see detailed explanation in S1 Procedures). 864 contigs presenting high similarity (e-value , 1e-50) were filtered and retrieved by a reciprocal BLAST. The low number of similar reads between the two variants for each contig in this category was used to calibrate the size of the samples (see S1 Procedures).
Quantitative RT-PCR RNA extraction was performed on 10 adult aphids using ISOLATE II RNA Mini Kit according to manufacturer's instructions (BIOLINE). cDNA synthesis was done using the Tetro cDNA Synthesis Kit (BIOLINE). cDNA were amplified using SensiFAST SYBR No-ROX Kit (BIOLINE) and analyzed with Opticon Chromo 4 (Bio-Rad). The accumulation of each transcript was measured in three independent biological samples with three technical replicates. Expression of Ef1-1a, RPL7 and GAPDH was used to normalize the transcript level in each sample. Primer sequences are listed in table  S4. Quantification and statistical analysis were calculated using the RqPCR Analysis Package  [47].
From each of these lists, two sub-lists were created: one for the genes that show an increase of methylation and one for the genes that have a decrease of methylation. A Gene Ontology term enrichment analysis has been performed on each of these lists. The Gene Ontology Enrichment Analysis Software Toolkit  [48, 49, 50]  was used to test the GO term enrichment within these given gene lists. Two ratios were compared in order to assess the probability of coherent changes: the ratio between the total number of genes found in the aphid genome by automatic annotation (N) and the number of these genes annotated by a given GO term (m) and, on the other side, the ratio between the number of genes in the list (n) and the number of these genes annotated by the GO term (k). The statistical method used to identify significantly enriched GO terms among the lists of genes is the hypergeometric test  [48, 49, 50].
The authors were supported by  ANR ''Exdisum  '' 2006-2009, grant PEPS  CNRS 2010 and ANR ''Methylclonome '' 2011-2015. The authors are thankful for the support of the  French National Research Agency (ANR)  for PhD students through the '' Investments for the Future ''  LABEX SIGNALIFE  (# ANR-11-LABX-0028-01 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of.
1% Triton X-100 in PBS for 5 min at 4°C. Samples were blocked with 2% fetal bovine serum for 1 h followed by sequential incubation with the respective primary and secondary antibodies for 45 min and 30 min at room temperature, respectively. Finally, cell nuclei were stained with 4=,6-diamidino-2-phenylindole (DAPI) for 1 min at room temperature. Images were obtained using a confocal microscope (Olympus FluoView 1000) during 405-nm, 561nm, and 633-nm laser stimulation using an UOlanSApo 60ϫ/1. 35 oil objective. Colocalization was analyzed using the ImageJ software Intensity correlation analysis plugin (National Institutes of Health). Pearson's coefficients were calculated for every cell individually by manually defining the region of interest. Values Ϫ1 to 0 indicate no colocalization, values around zero represent random distribution (no correlation), and values 0 to 1 indicate colocalization.
ACKNOWLEDGMENTS The p125-Luc plasmid was a kind gift of  Georg Kochs at the Institute for Medical Microbiology and Hygiene, University of Freiburg, Germany , and the mda5 and RIG-I expression plasmids were generously provided by  Manoj Krishnan  at the  Duke-NUS Graduate Medical School. We thank all laboratory members for continuing support and lively discussions. This work was supported by  CIHR  grant  MOP66989 , funding from the  German Ministry of Health , and a  Duke-NUS   Signature Research Program start-up grant  (funded by the  Agency for Science, Technology and Research of Singapore  and the  Ministry of Health of Singapore)  to V. V. M. ,  NIH  grant  R01 AI063476  to R. C. ,  Armand-Frappier Foundation  fellowships to N. S. and C. G. , a postdoctoral fellowship by the  German Research Foundation  (DFG;  GE2325/1-1 ) to I.
During the last years, we have developed the  platform for providing a practical support to the so-called Multi-Adjoint Logic Programming approach (MALP in brief), which represents an extremely flexible framework into the Fuzzy Logic Programming arena. Nowadays,  is useful for compiling (to standard Prolog code), executing and debugging (by drawing execution trees) MALP programs, and it is ready for being extended in the near future with powerful transformation and optimization techniques designed in our research group during the recent past. Our last update consists in the integration of a graphical interface for a comfortable interaction with the system which allows, among other capabilities, the use of projects for packing scripts and auxiliary definitions of fuzzy sets/connectives, together with fuzzy programs and their associated lattices modeling truth-degrees beyond the simpler crisp case { ; } true false.
Introduction Logic programming  [1]  has been widely used for problem solving and knowledge representation in the past. Nevertheless, traditional pure logic programming languages (i. e. , Prolog ) do not incorporate techniques or constructs to explicitly deal with uncertainty and approximated reasoning. To overcome this situation, during the last decades several fuzzy logic programming systems have been developed where the classical inference mechanism of SLD-resolution is replaced with a fuzzy variant able to handle partial truth and to reason with uncertainty, thus promoting the development of real-world applications in the fields of artificial/computational intelligence, soft-computing, semantic web, etc. Most of these systems implement the fuzzy resolution principle introduced by Lee in  [2] , such as languages Prolog-Elf  [3] , F-Prolog  [4] , Fril  [5] , (S-)QLP  [6]   [7] , RFuzzy  [8]  and MALP  [9] , being this last approach our target goal.
The "Fuzzy LOgic Programming Environment for Research"  As shown in the web page http://dectau. uclm. es/floper/ designed in our research group for freely accessing  -see also references  [20] -  [25] -during the last years we have been involved in the development of this tool for aliving MALP programs (which can be easily loaded into the system by means of plain-text files with extension ". fpl"). For example, our previous illustrative program included into file "P1. fpl", contains the following rules where, note for instance that the fuzzy connectives for implication, disjunction and conjunction symbols belonging to the product logic are respectively referred as "<prod", "|prod" and "&prod": In order to simplify the task of coding fuzzy logic programs, our tool is able to parse MALP rules with "syntactic sugar" trying to look as conservative extensions of Prolog clauses:  Since the weight of a rule can be omitted if it coincides with the  element of the corresponding lattice then, a rule like "p(X) with 1.
".  We can also include Prolog clauses between "$$" symbols, for instance "$p(X):-!,var(X). $", and moreover, it is possible too to insert pure Prolog code between "{}" symbols into the body of a fuzzy logic MALP rule, as occurs with "p([H|T]) < -{Y is H + 1} q(Y) & p(T). " Once the application is loaded inside any standard Prolog interpreter (like SWI or Sicstus-which is our case, by using v3. 12. 5-), it shows the menu shown in Figure  3. The parser has been implemented by using the classical DCG's ( Definite Clause Grammars) resource of the Prolog language, since it is a convenient notation for expressing grammar rules. Via the "parse" option, it is possible to load a ". fpl" file for which  generates two different Prolog representations of the fuzzy code, as we will describe in sub-Sections 3.
1 and 3. 2. Such code will cohabit with the set of clauses introduced by the user (together the Prolog -based definition of the  associated lattice that we will describe in sub-Section 3. 3) via the "load" option for consulting pure Prolog files (". pl"). The system is equipped too with choices for saving and listing such rules as well as the "clean" option for removing all clauses from the  database. The remaining menus are useful for executing goals and displaying evaluation trees, as well as for managing multi-adjoint lattices, as we are going to explain in what follows helped by the graphical interface recently developed for  and shown in Figure  4 , which allows the comfortable use of "projects" in order to manage files with the following different purposes:  several ". fpl" files can contain the set of MALP rules implementing a single MALP program,  the set of clauses modeling its (unique) associated multi-adjoint lattice must be included into a file with obvious extension ".