dataesr/scientific-paragraphs-categorization huggingface dataset:
Citation categories We compiled and classified the way in which data, citations and sources were included in the IUCNbased assessments First, we analysed whether it was possible to link the detailed information in assessments to citations and sources. Next, the reliability of the cited information was classified through consensus between the two authors (MC and MS) into one of four categories as defined in Todd et al. (  2010 ): (1) There is 'Clear support', when the cited article provides unequivocal support of the assertion via either statements in the text or the data presented. (2) 'Ambiguous', when the material (either text or data) in the cited article has been interpreted one way, but could also be interpreted in other ways, including the opposite. The assertion in the primary article is supported by a portion of the cited article, but that portion runs contrary to the overall thrust of the cited article.
Traceability Although all 66 species from our sample were included in the global and national Red Lists, only 17-63 of these species were included in the European and sub-national lists (table  1 ). The classification criteria were clearly presented in almost all studied lists, the exceptions being the lists for Midi-Pyrénées, Provence-Alpes-Côte-d'Azur and Bretagne. Sources and clear links between data in assessments and sources were simultaneously available for global and European Red Lists but not for national and sub-national lists. Nevertheless, sources (but not links) were given for the Bourgogne, Limousin, Île-de-France, Midi-Pyrénées and Provence-Alpes-Côte-d'Azur sub-national lists (table  2 ). Accessibility and language constrained the literature review. The analysis of the types of information sources was based on 76.
IUCN standards and transparency We found clear differences in the transparency and the traceability of the assessment processes used for Red Lists at different geographic scales. Although all the Lists considered in this study were certified by logos and labels that are directly linked to the IUCN guidelines (or indirectly through the IUCN French committee), national and sub-national lists in France were the product of data and processes that could not be verified and were not presented in a transparent and accessible way. Thus, the national and sub-national Red Lists in France do not fully comply with the standardized processes 'to be applied without deviation or modification, if regional Red List authorities wish to state that their assessment follows the IUCN system'  (IUCN, 2012). Thus, we need additional information to be able to fully understand       (Szabo et al.
, 2012). Nevertheless, the averagely higher threatened statuses of birds on Red Lists at smaller scales might also be linked to the risk of pessimistic assessments at regional level owing to over-narrow scale-dependent geographical focus  (Keller et al. , 2005; IUCN, 2012). As seen above, a risk of subjectivity in the regional adjustment process has already been identified  (Keller and Bollmann, 2004; Rodríguez et al. , 2004; Keller et al. , 2005) , in addition to risks of 'scale-' and 'edge-effect'  (Keller et al. , 2005; Milner-Gulland et al. , 2006; Brito et al. , 2010 ). Thus, these potential risks and the observed not supported data that was included in Red Lists does not rule out the possibility that the higher threatened statuses of Red Lists at smaller scales in France might be due, at least in part, to methodological factors or potential bias.
g. for Alauda arvensis, Aythya ferina, Gallinago gallinago, Limosa limosa, Numenius arquata, Tetrao urogallus). These results underline the fact that numerous assertions that were either ambiguous or not supported by the cited books and grey literature were included in regional assessments. Thus, the studied Red Lists, focused at different geographic scales, exhibit significant heterogeneity in both fundaments and reliability. This highlights the need for additional reviewing processes for sub-global assessments and, in particular, checks of  the accuracy of links between citations and primary sources. Furthermore, the relative lack of data and the difficulties of the publication process may potentially increase the temptation to use grey literature in Red List assessments. Nevertheless, our results reveal that such practices increase the risk of inclusion of ambiguous and not supported data in regional assessments.
Compensating for a lack of data  (Butchart and Bird, 2010 ) by using grey literature may misrepresent the situation of species that would otherwise be regarded as 'data deficient' according to IUCN guidelines (DD conservation status), and thus may reduce the visibility of the ignored information that could justify financial support for additional research and species monitoring. Consequently, conservation decisions may be associated with an 'assessment dilemma': should we report data deficiencies strictly to highlight the need for further research and thus have to confront potential delays in evidence-based management?, or should we use all available information to promote reactive management, albeit at the risk of using not-supported and/or unreliable data in assessments, thereby jeopardizing the credibility of Red Lists and reducing the visibility of needs to improve species monitoring? Further studies directly focused on this dilemma could have constructive implications for the monitoring and consensual conservation of species.
Conclusion This study mainly revealed information about monitoring schemes, data collection and availability at different spatial scales in birds from Europe and France in particular. Sub-national to global Red Lists differed in regard to (i) the reported conservations status, (ii) the transparency and traceability of assessments, (iii) the most commonly adduced criteria, (iv) the categories of the sources synthetized during assessments, (v) and the reliability of assertions compared to cited references. Such variability between lists in terms of both data and transparency confirms that the sources used in the global Red List were cited as reliably as usual in ecological sciences  (Todd et al. , 2007 (Todd et al. , , 2010)). However, there were many ambiguous and not supported citations on the European Red List and unverifiable assessments on the national and sub-national lists.
Alignments for each locus were made with the MEGA (Molecular Evolutionary Genetics Analysis) software v. 6. 0. (Tamura et al. 2013) , using the ClustalW algorithm  (Thompson et al. 1994 ) and refined with MUSCLE  (Edgar 2004)  or manually, if necessary, on the same platform. The alignment included our sequences complemented with available sequences of NCBI and NITE Biological Resource Center (NBRC) of species that conformed the different genera of the family Dictyosporiaceae (Table  1 ). This determined the phylogenetic position of the dendryphiella-like isolates in this group of fungi. Phylogenetic reconstructions with ITS and LSU sequences were made using Maximum Likelihood (ML) and Bayesian Inference (BI) approaches under the MEGA software v. 6. 0. (Tamura et al. 2013) and MrBayes v. 3.
For the LSU region, we used the Kimura 2-parameter with Gamma distribution (K80+G) and, for the ITS symmetrical model, we used Gamma distribution (SYM+G). The parameter settings used were two simultaneous runs of 5M generations, four Markov chains, sampled every 1000 generations. The 50% majority-rule consensus tree and posterior probability values (PP) were calculated after discarding the first 25% of the samples. A PP value of ≥0. 95 was considered significant. The DNA sequences and alignments generated in this study were deposited in GenBank (Table  1 ) and in TreeBASE (http://treebase. org), respectively.
Results The BLAST query revealed that LSU sequences of our dendryphiella-like isolates  (FMR 16098, FMR 16234 and FMR 17003)  showed a high percentage of identity (99%) with that of the isolate CBS 139. 95 of Di. asperum and all of them were related to the Dictyosporiaceae. However, they showed a sequence identity of between 96-97% with LSU sequences of Dictyosporium species and other members of this family, including several species of Dendryphiella deposited in the GenBank. The ITS sequences did not match significantly any of those deposited in the NCBI database. We carried out individual and combined analyses with the LSU and ITS loci to assess relationships with members of the Dictyosporiaceae, including reference strains of D. vinosa and D. infuscans sequenced in the present study. Single phylogenies of LSU and ITS loci encompassed 31 and 30 sequences, respectively, representing 12 genera and including Paradendryphiella arenaria and P.
salina (Pleosporaceae) as outgroup (Figs. S1 and S2 in the supplementary material). LSU analysis comprised 630 bp from which 111 bp were variable and 84 bp phylogenetically informative. The ITS comprised 496 bp, 266 bp being variable and 206 bp being phylogenetically informative. The topology of trees for single loci were very similar and the ILD test showed that the LSU and ITS datasets loci were congruent (P = 0. 16) and could be combined. The final combined analysis encompassed 30 sequences and comprised 1126 bp (ITS 496 bp, LSU 630 bp). The ML tree showed that FMR 16098, FMR 16234, FMR 17003 and CBS 139. 95 clustered together in a well-supported undescribed monophyletic lineage representing a new genus in the family (Fig. 1 ). The LSU and ITS sequence comparison of the four isolates revealed them as different taxa.
Original identification Strain number 1 Country Genbank accession no. 2 ITS LSU Aquaticheirospora lignicola RK-2006a (T) Thailand AY864770 AY736378 Cheirosporium triseriale HMAS 180703 (T) China EU413953 EU413954 Drechslera biseptata Dendryphiella vinosa CBS 117. 14 Scotland LT963770 LT963509 Dendryphiella eucalyptorum CBS 137987 (T) Spain KJ869139 KJ869196 Dendryphiella fasciculata MFLUCC 17-1074 (T) Thailand MF399213 MF399214 Dendryphiella paravinosa Dendryphiella vinosa CBS 118716 New Zealand LT963357 LT963359 Dendryphiella paravinosa Dendryphiella vinosa CBS 121797 Spain LT963354 LT963355 Dendryphiella paravinosa CBS 141286 (T) Italy KX228257 KX228309 Dendryphiella variabilis Dendryphiella vinosa CBS 584. 96 (T) Cuba LT963453 LT963454 Dendryphiella vinosa NBRC 32669 Japan DQ307316 03266901 3 Dendryphiella vinosa - - - EU848590 Dictyocheirospora bannica KH 332 (T) Japan LC014543 AB807513 Dictyocheirospora pseudomusae KH 412 Japan LC014549 AB807516 Dictyocheirospora rotunda MFLUCC 14-0293b (T) Thailand KU179099 KU179100 Dictyosporium bulbosum yone 221 Japan LC014544 AB807511 Dictyosporium elegans NBRC 32502 (T) Japan DQ018087 DQ018100 Dictyosporium strelitziae CBS 123359 (T) South Africa FJ839618 FJ839653 Digitodesmium bambusicola CBS 110279 (T) Philippines DQ018091 DQ018103 Gregarithecium curvisporum KT 922 (T) Japan AB809644 AB807547 Jalapriya inflata NTOU 3855 UK JQ267362 JQ267363 Jalapriya pulchra MFLUCC 15-0348 (T) China KU179108 KU179109 Jalapriya toruloides CBS 209.
Hirayama; KT: K. Tanaka; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Rai, Thailand; NBRC: NITE Biological Resource Centre, Japan; NTOU: Institute of Marine Biology, National Taiwan Ocean University; RK: R. Kodsueb; yone: H. Yonezawa. (T): ex-type strain. 2 Sequences newly generated in this study are indicated in bold. 3 Number of sequence of the NBRC database.
e. within the same scaffold, showing the expected orientation and being separated 500 bp or less). This alignment has a mean coverage per contig of 11. 37 (±5. 77). A second BAM file containing exclusively singleton alignments, average depth of coverage 5. 8 (±18), was also produced. Both files were combined into a single run at SRA (Supplementary Data S4 -https://www. ncbi. nlm. nih. gov/sra/ SRX3427716).
Contracted services involved the construction of a single genomic library, sequencing, delivery of raw data and bioinformatics microsatellite search. The short fragments library was constructed according to BGI's in-house protocols, with random DNA fragmentation and agarose gel purification for genomic fragments with nominal size of 500 bp, followed by adaptor ligation and linear amplification, for the enrichment of fragments with adaptors at both ends. Sequencing was performed over approximately 50% of a single lane from a flow-cell in a HiSeq 2000 equipment (Illumina, San Diego, USA). Sequencing run was January 01, 2014. The library was sequenced targeting an average of 10× coverage depth, for a genome estimated, a priori, to be 1. 5 Gb. The sequencing assay layout was paired-end with reads 90 bases long.
Bioinformatics. Service providers performed a bioinformatics pipeline and produced a first table of microsatellite loci and the raw (filtered) short reads data, but delivered no genomic assembly (as per contract), here called A0 (not available): at BGI, short reads were demultiplexed, trimmed for adaptors and filtered by removing reads with quality rate values of Q ≤ 5 in 50% or more bases, and deleting duplicates. The resulting paired-end data were stored in two parallel FASTQ files and used by BGI for de novo assembly based on de Bruijn graph using SOAPdenovo 2  18  , with k-mer = 47. The resulting assembly (A0) was screened for perfect simple sequence repeats (microsatellite loci), with repeat motifs ranging from di-through hexanucleotides, with a minimum of five repetitions, except for hexanucleotides which had the minimum number of repeats parameter set as four, with the aid of the SSRIT program  19.
Acknowledgements Thanks to  João de Magalhães Lopes, PhD ;  Míriam Aparecida de Castro ,  MSc and everyone at Projeto Peixe-Vivo at CEMIG ;  Juliana Pimenta, BSc  at  Síntese Biotecnologia  and  Vicente Wen, PhD  at  BGI ;  Professors André Luiz Mota, PhD  (PROPE);  Hewerson Zansávio Teixeira, PhD  (DEZOO);  Milene Barbosa Carvalho, MSc (DCOMP) ;  Daniel Cardoso Carvalho, PhD  at  PUC-MG ;  Carolina Ferreira Cardoso, PhD  and  PPGBiotec-UFSJ  for their direct or indirect assistance to this study. We would also like to thank  UFSJ ,  CNPq  and  CAPES. This work was supported by grants  CEMIG-ANEEL (GT345 ) and  FAPEMIG  ( APQ-04569-10 ).
Data availability. The genomic data revealed here are now publicly available from NCBI's Sequence Read Archive (SRA -https://www. ncbi. nlm. nih. gov/sra) database. Short reads (Supplementary Data S1) can be fetched under Accession https://www. ncbi. nlm. nih. gov/sra/SRX3350440. Supplementary Data S4 with the BAM alignments (made using the genomic assembly A1 as reference) can be retrieved from https://www. ncbi. nlm. nih. gov/ sra/SRX3427716. The proposed genome-wide microsatellite panel for B. orbignyanus (Supplementary Table  S2  -https://doi. org/10. 6084/m9. figshare. 5661988) in the ". xlsx" format for Microsoft Excel and the genomic assembly A1 (Supplementary Data S3 -https://doi. org/10. 6084/m9. figshare. 5661802) in ". fsa" (fasta) format are both available from the Figshare data repository.
Mass-spectrometric analysis Resulting peptides were analysed by nano LC-MS/MS. Further details of proteomic experiments, and processing of Data output files, generation of identified protein lists and bioinformatic analyses of positive hits are elaborated under Supplementary methods in the accompanying File S1. Differential analysis of control and positive samples was performed using extracted specific spectral counts (SSC). For potent stringency, SSC of negative control were calculated as the sum of three biological replicates whereas for SSC of individual baits, two biological replicates were summed. To be considered as a pol III TC binding partner, a protein was to be identified with a minimum of 4 summed SSC and only in a bait IP (not in control) or enriched at least 5 times in the sample as compared to the control one.
Northern blotting for tRNA estimations The method used by  Karkusiewicz et al, 2011 (44)  was used for tRNA estimations by Northern blotting. Per lane 10 µg of total RNA was resolved on 15 % Urea-PAGE and transferred from gel to Hybond N+ membrane (GE Healthcare) by electroblotting in 1x TBE, cross-linked by UV radiation (1200 mJ/cm2). The membrane was pre-hybridized in prehyb/hyb buffer (2x SSC, 1X Denhardt's solution, 0. 2%SDS) and hybridized at 37°C in the same solution with oligonucleotide probes (listed in the Table  S2 ) labeled with [γ 32 P]-ATP by T4 polynucleotide kinase (New England Biolabs). The membrane was washed 3 times for 15 min with wash buffer (2X SSC and 0. 2% SDS) at 42°C and exposed to phosphorimaging screen (Fujifilm). Bands were visualized in phosphoimager (BIORAD) and intensities were quantified using Image Gauge software from Fuji.
Genome-wide data analysis The processed tab files containing forward and reverse tag counts, with their respective chromosomal location were used for the analysis of the ChIP-exo data  (45)  on the occupancy of the PAF1C subunits on the tRNA genes were downloaded from GSE83348. The open source "Bio toolbox" from Timothy J. Parnell was used to map binding sites of all the subunits of Paf1 complex around the TSS of the tRNAs genes. The genome-wide occupancy of Rtf1 on the tRNA genes in the yeast genome was analysed also from the published ChIPseq data  (46). The reads uniquely aligned to sacCer3 yeast assembly with mapping quality scores >30 were processed for further analyses. The "bamCompare" function from deepTools package was used for Library size adjustments (SES method) and log 2 ratio of IP vs Input was calculated  (47).
The "plotProfile" and "plotHeatmap" functions of deepTools were used for plotting the average occupancy profiles and heatmaps  (47). All Raw data files for nucleosomal DNA  (48)  from the wild type and paf1∆ cells as treatment group and whole genome fragmented DNA as a control group were downloaded from NCBI GEO under accession no. GSE44879. The two sample analysis was performed on the nucleosomal occupancy data by employing Affymetrix Tiling Analysis Software (TAS) v1. 1. Data were quantile normalized in pairs using only perfect match probes with a bandwidth of 30. Resulting bar files were used for Interval analysis with p-value threshold of 0. 05, minimum run of 50 and maximum gap of 20 probes. Processed MNase-seq data files on histone methylations were downloaded under accession no GSE61888 from NCBI GEO.
Indeed 26% of proteins in both active and repressed states (Fig. 1C  and S2C ) are known to exhibit such a dual localization. They include some of the pol III (Rpc6, Rpc9 and Rpc10) and TFIIIC (Tfc3 and Tfc4) subunits classified as both nuclear and cytoplasmic in the Saccharomyces Genome Database (SGD; http://www. yeastgenome. org/). Cytoplasmic assembly of the multi-subunit pol III  (51, 52)  and an earlier report on human pol III activity even in the cytoplasm (53) support the possibility of cytoplasmic interactome for pol III TC.
Acknowledgements We thank  David Schneider  for deletion strains of Paf1 subunits,  David Donze  for Tfc1-Flag and  Kevin Struhl  for Tfc6-Flag strains of yeast. Proteomic experiments were partly supported by the  Agence Nationale pour la Recherche  ( ProFi  grant  ANR-10-INBS-08-01 ). DVV,  AS.
Objective: Secreted frizzled related protein 5 (SFRP5) is a novel anti-inflammatory adipokine that is implicated in metabolic and cardiovascular disease (CVD). However, little is known about the relevance of SFRP5 with asymptomatic hypertensive target organ damages (TODs). We aimed to investigate the association between SFRP5 and TOD in a large population. Clinical trial registration: NCT02368938. Methods: A total of 1,745 community-dwelling elderly subjects aged over 65 years from northern Shanghai were recruited in the study. Plasma SFRP5 level was measured by an enzyme-linked immunosorbent assay. Asymptomatic TODs, including left ventricular mass index, peak transmitral pulsed Doppler velocity/early diastolic tissue Doppler velocity, carotid intima-media thickness (CIMT), pulse wave velocity (PWV), estimated glomerular filtration rate, and urinary albumin-creatinine ratio were evaluated.
statistical analysis Quantitative and qualitative parameters are presented as means ± standard deviation (SD) and numbers with the percentage in parentheses. Normal distribution of the data was tested using Kolmogorov-Smirnov test. Comparisons between groups were performed with Wilcoxon test. Correlations between SFRP5 and relative variables were assessed using Spearman correlation analyses. Further, multivariate logistic regressions were conducted to investigate the association of hypertensive TODs with SFRP5 in the entire population, in hypertensives, and in diabetics. Statistical analysis was performed using SAS software, V. 9. 3 (SAS Institute, Cary, NC, USA). P0. 05 was considered statistically significant.
Conclusion Plasma SFRP5 level was inversely correlated with conventional cardiovascular risk factors, and low plasma SFRP5 was also significantly associated with arterial stiffening in the elderly. Clinical Interventions in Aging is an international, peer-reviewed journal focusing on evidence-based reports on the value or lack thereof of treatments intended to prevent or delay the onset of maladaptive correlates of aging in human beings. This journal is indexed on PubMed Central, MedLine, CAS, Scopus and the Elsevier Bibliographic databases. The manuscript management system is completely online and includes a very quick and fair peer-review system, which is all easy to use. Visit http://www. dovepress. com/testimonials. php to read real quotes from published authors. Clinical Interventions in Aging 2018:13.
Acknowledgments We thank all the investigators and subjects who participated in the  Northern Shanghai Study. Hongwei Ji  and  Ximin Fan  provided writing assistance, while  Jing Xiong  and  Jun Zhang  provided technical help. This study was authorized and financially supported by the  Shanghai municipal government  (grant IDs:  2013ZYJB0902 ;  15GWZK1002 ). Dr Yi Zhang  was supported by the  National Nature Science Foundation of China  (grant IDs:  81300239 ;  81670377 ).
Large tropical trees store significant amounts of carbon in woody components and their distribution plays an important role in forest carbon stocks and dynamics. Here, we explore the properties of a new Lidar derived index, large tree canopy area (LCA) defined as the area occupied by canopy above a reference height. We hypothesize that this simple measure of forest structure representing the crown area of large canopy trees could consistently explain the landscape variations of forest volume and aboveground biomass (AGB) across a range of climate and edaphic conditions. To test this hypothesis, we assembled a unique dataset of high-resolution airborne Light Detection and Ranging (Lidar) and ground inventory data in nine undisturbed old growth Neotropical forests. We found that the LCA for trees greater than 27 m (~25-30 m) in height and at least 100 m 2 crown size in a unit area (1 ha), explains more than 75 % of total forest volume variations, irrespective of the forest biogeographic conditions.
, 2015). Moreover, different forests with the same MCH may differ in their stem density, notably of large trees, and in stand mean wood density, two aspects that are important in constructing a robust model to infer AGB from lidar data  (Asner et al. , 2012;  Biogeosciences Discuss. , https://doi. org/10. 5194/bg-2017-547 Manuscript under review for journal Biogeosciences Discussion started: 5 January 2018 c Author(s) 2018. CC BY 4. 0 License. Mascaro et al. , 2011). Ground observations suggest that stem density, basal area, height and crown size of large tropical trees may all be good indicators of forest AGB  (Clark and Clark, 1996; Goodman et al. , 2014). This implies that including information on crown area of individual large trees should improve carbon stock assessments, as confirmed in temperate and boreal regions (eg.