dataesr/scientific-paragraphs-categorization huggingface dataset:
In contrast, we found that two paralogues of PtrWOX13, PtrWOX13a (Potri. 005G101800) and PtrWOX13b (Potri. 005G252800), were up-regulated in OP42 at 24 h after cutting and transfer into hydroponic conditions (Supplementary Dataset S3, sheet 2). PtrWOX13 belongs to an ancient clade of PtrWOX genes (B. Liu et al. , 2014)  and the Arabidopsis AtWOX13 and AtWOX14 are involved in the regulation of primary and lateral root development in Arabidopsis  (Deveaux et al. , 2008). AP2 0 1 2 2 2 1 2 1 ARF 2 3 0 12 5 5 1 0 ARR-B 0 0 0 1 1 0 0 0 B3 0 1 1 4 8 3 6 2 BBR-BPC 0 0 0 1 0 2 0 0 BES1 0 0 3 0 0 0 1 0 bHLH CAMTA 0 0 0 1 0 1 1 0 CO-like 0 1 0 3 2 0 3 0 CPP 0 0 0 0 0 1 0 0 DBB 0 1 1 4 0 1 0 0 Dof 1 3 3 7 1 3 1 0 EIL 1 0 0 0 1 0 1 0 ERF 21 5 42 12 7 14 4 7 FAR1 0 0 0 0 1 0 0 1 G2-like 1 0 2 7 3 5 1 0 GATA 1 1 4 2 3 3 0 1 GeBP 0 0 1 0 0 0 0 0 GRAS 1 1 3 8 3 2 3 1 GRF 0 1 1 5 0 3 0 0 HB-other 0 0 0 2 0 1 0 0 HD-ZIP 2 0 6 6 3 0 3 1 HRT-like 0 0 0 1 0 0 0 0 HSF 1 1 5 2 4 3 1 1 LBD 3 0 11 2 1 3 3 2 LSD 0 0 1 0 0 0 1 1 M-type_MADS 0 0 1 1 0 3 0 1 MIKC_MADS 2 3 0 5 4 3 0 9 2 0 1 0 NF-YB 0 1 0 2 2 2 1 1 NF-YC 0 0 1 0 0 1 0 0 Nin-like 0 0 0 1 2 0 1 0 SBP 0 3 1 7 2 3 0 0 TALE 0 0 1 7 1 1 1 1 RAV 1 0 2 0 0 0 0 0 S1Fa-like 0 0 1 0 0 1 0 0 TCP 1 0 0 3 2 1 0 0 Trihelix 5 0 7 2 5 1 4 0 WOX 0 0 2 0 1 0 0 0 VOZ 0 0 0 0 0 1 0 0 WRKY 13 0 23 3 4 6 3 2 ZF-HD 0 0 2 0 3 1 0 1 YABBY 0 0 0 2 0 0 0 0 Recently  Wei et al.
(2020)  showed that the P. ussuriensis PuHox52 gene, which belongs to the HD-Zip sub-family of TFs, positively controls adventitious rooting in P. ussuriensis. It acts by inducing nine regulatory hubs, including the jasmonic acid (JA) signalling pathway PuMYC2 gene (MH644082; Potri. 002G176900), a TF from the bHLH family, which has been demonstrated to be a positive regulator of AR development in P. ussuriensis. In contrast, in our dataset, we found that P. trichocarpa PtrHox52 (Potri. 014G103000) was down-regulated in the cambium of the easy-to-root genotype OP42 at T 1 , i. e. 24 h after cutting and transfer to hydroponic conditions (Supplementary Dataset 3, sheet 2). PtrHox52 was also up-regulated in the difficult-to-root genotype T89 compared with OP42 at T 1 (Supplementary Dataset S3, sheet 2).
Accordingly, we observed that PtrMYC2. 5 (Potri. 003G147300) was upregulated in the cambium of T89 compared with OP42 at T 1. There are six paralogues of MYC2 in Populus. Three of these paralogues -PtrMYC2. 1 (Potri. 003G092200), PtrMYC2. 2 (Potri. 001G142200), and PtrMYC2. 4 (Potri. 001G083500), were up-regulated in both T89 and OP42 at T 1 , but with a higher fold change in T89, while PtrMYC2. 5 (Potri. 003G147300) was exclusively up-regulated in T89 at T 1 , which led to a significant increase in PtrMYC2 expression in T89 compared with OP42 (Supplementary Dataset S3, sheet 2). The potential up-regulation of JA signalling in T89 was corroborated by a higher fold change in the expression of several JA-inducible JA ZIM DOMAIN (JAZ) genes 24 h after cutting in T89, compared with OP42. PtrJAZ6 (Potri.
003G068900), PtrJAZ8 (Potri. 011G083900) and PtrJAZ10 (Potri. 001G062500) were up-regulated in T89 compared with OP42 at T 1 , with a respective log 2 FC of 4. 25, 5. 5, and 4. 7 (Supplementary Dataset S2, sheet 6). These results suggest a negative role of JA signalling on AR development, as described in Arabidopsis  (Gutierrez et al. , 2012; Lakehal et al. , 2020a)  and contradict the positive role of JA on AR development, as described for P. ussuriensis  (Wei et al. , 2020). Several genes from the AUXIN RESPONSE FACTOR (ARF) family have been shown to be involved in AR development in Arabidopsis and Populus  (Gutierrez et al. , 2009 (Gutierrez et al. , , 2012;; Cai et al. , 2019; Lakehal et al. , 2019; Liu et al. , 2020). AtARF6 and AtARF8 are positive regulators of adventitious root initiation (ARI), while AtARF17 negatively regulates adventitious rooting  (Gutierrez et al.
, 2009). In Populus, PeARF8 also positively regulates AR formation  (Cai et al. , 2019)  but PeARF17, in contrast to the Arabidopsis gene, acts as a positive regulator of AR development in the hybrid poplar P. davidiana × P. bolleana  (Liu et al. , 2020). We identified 36 PtrARF genes encoding paralogues of 15 out of the 27 Arabidopsis ARF orthologues. Although some of them were more significantly down-regulated in OP42 than in T89 24 h after cutting, they mostly behaved in a similar manner in both genotypes (Supplementary Fig. S6 ; Supplementary Dataset S3, sheet 6). In particular, expression of PtrARF6. 2 (Potri. 002G055000) and PtrARF6. 3 (Potri. 001G358500) was up-regulated, while PtrARF6. 1(Potri. 005G207700) and PtrARF6. 4 (Potri. 011G091900) were down-regulated in both T89 and OP42 at T 1 compared with T 0 (Supplementary Fig.
S6 ; Supplementary Dataset S3, sheet 6). Similarly, both PtrARF8. 1 (Potri. 004G078200) and PtrARF8. 2 (Potri. 017G141000) were down-regulated at time T 1 compared with T 0 in both T89 and OP42. Interestingly, PtrARF17. 1 (Potri. 002G089900) was significantly less expressed in the cambium of the difficult-toroot T89 than in OP42, at both T 0 and T 1 , which agrees with a potential positive role of PtARF17. 1 in AR development.
PttARF6 and PttARF8 positively control, while PttARF17 negatively controls, adventitious rooting in hybrid aspen To assess the role of PttARF6, PttARF8, and PttARF17 in adventitious rooting in Populus, we produced transgenic plants that either overexpressed these genes or down-regulated their expression. Using the PopGenIE data base (http://popgenie. org) we identified the Populus genes most closely related to the corresponding Arabidopsis genes (Supplementary Fig. S4A ), and checked their expression pattern in the cambium and wood-forming region in the PopGenie database (http:// aspwood. popgenie. org/aspwood-v3. 0/; Sundell et al. , 2017). AspWood provides high resolution in silico transcript expression profiling of the genes expressed over the phloem, cambium, and other xylem development zones in aspen trees.
PtMYC2. 1 is a negative regulator of adventitious root development in hybrid aspen In Arabidopsis, the AtARF6, AtARF8, and AtARF17 genes have been shown to act upstream of AtMYC2, which is a negative regulator of AR development  (Gutierrez et al. , 2012; Lakehal et al. , 2020a). In our present study, five out of the six PtrMYC2 paralogues are shown to be among the DEGs (Fig. 6A ; Supplementary Dataset S3, sheet 2). They mostly behaved the same way in both T89 and OP42, but the fold change induction was higher for four of them at T 1 in the difficult-to-root genotype T89, and PtMYC2. 5 was significantly up-regulated in T89 compared with OP42 at 24 h after cutting (Fig. 6A ; Supplementary Dataset S3, sheet 2). These results suggest that PtrMYC2 could be a negative regulator of adventitious rooting in hybrid aspen.
Acknowledgements The authors sincerely thank  Dr Marta Derba Maceluch  from the  UPSC Microscopy platform , and  Dr Nicolas Delhomme  and the  UPSC bioinformatic platform  for their support with the data analysis; the personnel from the  UPSC transgenic facility  for the production of the transgenic plants; and  Dr Didier Le Thiec  from  INRAE of Nancy  for the use of the cryostat and his help and useful suggestions.
Funding This research was supported by the  Ministry of Higher Education and Scientific Research in Iraq  (to SA); by grants from the  Knut and Alice Wallenberg Foundation  and the  Swedish Governmental Agency for Innovation Systems (VINNOVA) , by grants from the  Swedish research councils FORMAS, VR, Kempestiftelserna , and the  Carl Tryggers Stiftelse  (to CB). This research was also supported by the  Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems  ( ANR-11-LABX-0002-01 ), the  Region Lorraine  and the  European Regional Development Fund  (to FM and AK).
S. cerevisiae telomere analysis from whole genome sequences We developed Y ea ISTY (Yeast ITS, Telomeres and Y' elements estimator) to estimate TL, ITS content and Y' copy number from yeast whole genome sequencing data (Methods). The performance of Y ea ISTY has been extensively benchmarked against simulated and experimental datasets and its running parameters have been optimized. The Y ea ISTY workflow begins with a screening of Illumina paired-end reads to retain the ones containing telomeric sequences (Fig. 1a  and Supplementary Fig. 1a ). Reads are retained if they contain a stretch of telomeric repeats (either C{1,3}A or TG{1,3}) longer or equal to 40 bp with only one gap of maximum 2 nucleotides allowed. Since telomeric and ITS-derived reads are virtually impossible to distinguish from each other based solely on their sequences, we introduced an additional step consisting in mapping all the reads to a modified reference genome in which all repetitive sequences, including telomeres, ITS and Y' elements, have been masked.
One strain (1. 2. C-ADI) had extremely long telomeres, in accordance with previous reports showing that this strain has atypical TL and massive amplification of ITS and Y' elements  (Bergstrom et al. , 2014). However, TL resulting from Y ea ISTY was underestimated by 4-fold respect to the values of the teloblot. We therefore applied a 4-fold correction factor to the estimations of the S. cerevisiae collection. A detailed description of the implementation of Y ea ISTY's algorithm is presented in supplementary discussion 1, while further benchmarking of Y ea ISTY on additional datasets is presented in supplementary discussions 2 and 3 (Supplementary Fig. 1 2 3 4 and Supplementary Tables  2 3 4 ). Taken together, these results show that Y ea ISTY estimations are reliable and can be used for further analyses.
Discussion By estimating the telomeric DNA length (TL) and ITS content of 918 Saccharomyces cerevisiae isolates collected worldwide and associated with an extensive genomic and phenotyping dataset  (De Chiara, Barré, et al. , 2020; De Chiara, Friedrich, et al. , 2020; Peter et al. , 2018)  we unveiled the 13 species span of telomere length variation. We observed a wide spectrum of normally distributed TLs whose median value is close to what previously measured in the classical S288C laboratory strain. This variation is not explained by ploidy and aneuploidy and instead is associated with several punctuated genetic variants. We analysed the association between TL and the ecological origin of the yeast isolates. Remarkably, we found that TL was shorter in wild strains than in domesticated ones, although the distributions within these two groups are broad.
, 2017). After applying the pipeline, 93 isolates stood out from the rest because they exhibited extremely high TL. These 93 isolates were sequenced in previous studies. Given that the results were not comparable to the rest of the collection, we excluded these isolates from this study and only considered the remaining 918 strains. We observed an underestimation rate of 4-and 8-fold for TL and ITS content, respectively, as compared to the average values measured by teloblot and the annotation of the 12 genome assemblies. We adjusted this bias by increasing TL and ITS content of 4-and 8-fold, respectively, in the estimations of the 1011 S. cerevisiae collection. Values reported in supplementary table 5 are already adjusted. Estimates from the other datasets used in this study varied around a different average value respect to the one of the 1011 S.
cerevisiae collection, indicating that the underestimation rate differs across datasets and therefore estimates are not directly comparable between datasets, but only within them  (Puddu et al. , 2019; Tattini et al. , 2019). Since we did not perform teloblots of representative strains from all the other datasets, their exact underestimation rates remained unknown and their estimates were not adjusted. The exact reasons of this variation are unknown and might depend on the combination of the sequencing technology, library.
Simulations of sequencing runs from genomes carrying synthetic telomeres To estimate the efficiency of Y ea ISTY, we applied it to artificially constructed datasets, consisting of simulated sequencing runs from genomes carrying synthetic telomeres of known length. We masked the native telomeres of the 12 previously described genome assemblies by using the program maskfasta contained in the suite bedtools (version 2. 17. 0)  (Quinlan & Hall, 2010). Subsequently, we replaced the masked native telomeres with 14 synthetic telomeres of known length, consisting of yeast telomeric TG{1,3} or C{1,3}A repeats. We created 168 (12 x 14) synthetic genomes in each of which single telomeres were all identical to each other. The lengths of the synthetic telomeres had the following values:  18, 49, 77, 99, 135, 174, 208, 296, 360, 416, 504, 553, 602, 651 bp.
Correlation analyses were performed using the function cor. test included in the R software and applying both Pearson's and Spearman's models. P-values were subsequently re-computed using both FDR and Bonferroni correction for multiple hypothesis testing and associations were considered statistically significant if their Spearman-derived FDR-corrected p<0. 05. Y ea ISTY (Yeast ITS, Telomeres and Y' elements estimator) is freely available at: https://github. com/mdangiolo89/Different-telomere-length-patterns-between-domestic-and-wild-S. cerevisiae-isolates.
Acknowledgements and funding We thank the  French National Research Agency (ANR)   LABEX SIGNALIFE ANR-11-LABX-0028-01  and the  Fondation pour la Recherche Médicale  ( FDT201904008453 ) for supporting M. D. PhD  fellowship. This study was supported by  ANR  ( ANR-18-CE12-0004 ,  ANR-20-CE12-0020 ),  Fondation pour la Recherche Médicale  ( EQU202003010413 ),  CEFIPRA ,  Fondation ARC  ( N°P JA32020070002320 ) to G. L. Work in E. G. laboratory is supported by grants from the  Fondation ARC pour la recherche sur le cancer (Labelisation   N° PGA20160203873 ) and the INSERM cross cutting program on aging (AGEMED).
preparation methods and coverage. While relative values can still indicate whether one strain carries longer/shorter telomeres than another one, a comparison with already known TL and ITS is needed to determine the exact underestimation rate of each dataset and obtain absolute TL and ITS Y ea ISTY constitutes a valid tool to estimate TL, ITS content and Y' copy number from whole genome sequencing data and it is freely available through github (https://github. com/mdangiolo89/Different-telomere-length-patterns-between-domestic-and-wild- S. -cerevisiae-isolates). estimates. 16.
EgrIAA20 Transcripts Accumulate Preferentially in Cambium in Eucalyptus We previously identified 26 Aux/IAA genes in the E. grandis genome and numbered them according to their phylogenetic relationship with their Arabidopsis orthologs  [26]. Large scale RT-qPCR expression analyses of these genes across various tissues and organs, including cambium and developing xylem, enabled us to identify 11 members with significantly high expression levels in vascular tissues  [26]. Among these Aux/IAA paralogs, EgrIAA20 presented the highest expression level in vascular tissues, especially in cambium and xylem (Figure  1A ,B), followed by EgrIAA19, EgrIAA31, EgrIAA4, and EgrIAA13. Complementary analyses using the EucGenIE database, an online resource for Eucalyptus genomics and RNAseq transcriptomics, further confirmed the preferential expression of EgrIAA20 in tree trunks (Figure  1C ).
The reporter constructs used a synthetic auxin-responsive promoter DR5 followed by the GFP reporter gene. For co-transfection assays, aliquots of protoplasts (0. 5 × 10 6 ) were transformed with 10 µg of the reporter vector, containing the DR5 synthetic promoter fused to the GFP reporter gene, and with either the effector vector of EgrIAA20 under the CaMV 35S promoter or the empty vector as mock treatment. After 16 h incubation, GFP expression was quantified by flow cytometry (FACS calibur II, BD Bioscience), and the data were analyzed using Cell Quest software (BD Biosciences, San Jose, CA, USA). Transfection assays were performed in three independent replicates, and 400-1000 protoplasts were gated for each sample. GFP fluorescence corresponds to the average fluorescence intensity of the protoplasts' population after subtraction of auto-fluorescence determined with non-transformed protoplasts.
Acknowledgments: Thanks to the  Bioinfo Genotoul Platform  (http://bioinfo. genotoul. fr,accessed from September 2011 to April 2021 for access to resources and to the  Genome and transcriptome Platform  (http://get. genotoul. fr/,accessed from September 2012 to April 2019) for advice and technical assistance with high-throughput Biomark Fluidigm qRT-PCR amplifications. Thanks to  Y. Martinez  ( FR3450 ) for assistance with microscopy analysis (Plateforme Imagerie TRI tri. ups-tlse. fr/,accessed from September 2014 to September 2020).
cFigure 1. 1 Figure 1. EgrIAA20 transcript (Eucgr. K00561) shows preferential accumulation in the cambium of Eucalyptus. (A) Ratio of relative mRNA abundance of all Eucalyptus Aux/IAA members in vascular tissues including: juvenile vascular cambium (Cabium-7-year-old tree), mature vascular cambium (Cambium-25-year-old tree), phloem (7-year-old tree), and xylem (7-year-old tree). (B) Real-time PCR expression levels of EgrIAA20 in various Eucalyptus tissues and organs. Each relative mRNA abundance was normalized to a control sample (in vitro Eucalyptus plantlets). Error bars indicate mean expression values ±SE from three independent experiments. (C) Pictographic view of EgrIAA20 expression across a diverse range of RNAseq expression datasets by exImage (https://eucgenie. org/ exImage, accessed on 25 April 2022).
The current occupational exposure limit was set at 15 mg/m 3 [8]. The limit was based on the most sensitive effects in human, i. e. , neurotoxicity and cardiotoxicity  [9]. In addition, epidemiological studies on occupational cohorts exposed to CS 2 also reported effects of concern (i. e. , at low dose) on reproductive function  [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]  or thyroxine (T4) levels  [20] [21] [22] [23]. CS 2 has been identified as a potential ED in different lists, such as the "Database of endocrine disrupting chemicals and their toxicity profiles" list (DEDuCT)  [24]  or "The Endocrine Disruption Exchange" list (TEDX)  [25]. Our goal was to evaluate the ED properties of CS 2 to help decide if extra risk management measures should be put in place to ensure safe use of this chemical.
Information was gathered based on the data available in the REACh registration dossier for CS 2. In addition, a literature search was performed on CS 2 in Pubmed ® using the search term "75-15-0 [CAS] in abstract-title and key words" in papers from 2013 to 2019. A set of inclusion and exclusion criteria was then applied to select the relevant studies (Table  S1  of supplementary material). Previously published international evaluations were also taken into consideration  [9, [27] [28] [29] [30] [31]. A search has also been conducted in the U. S. Environmental Protection Agency's Endocrine Disruptor Screening Program  [32]  to determine the potential for CS 2 to interact with estrogen, androgen or thyroid (E, A or T) bioactivity based on in vitro high-throughput screening assays. In vitro, in vivo animal data, mechanistic data and human data relevant for the assessment of ED properties were evaluated.
The quality of the experimental animal studies was assessed and was rated using Klimisch scores: score 1 (reliable without limitations), 2 (reliable with limitations), 3 (unreliable) or 4 (not assignable)  [33]. Human data were also assessed, including a risk of bias analysis. Relevant parameters and tests for the identification of the substance as ED were identified based on the OECD test guideline 150  [34]  and the review published by  Manibusan and Touart (2017)   [35]. A detailed description of all the studies considered and their quality assessment is available in the conclusion document written by ANSES (  [36] , in press). A total of 69 animal studies and 43 human epidemiological studies were considered and assessed for their reliability when evaluating the toxicological profile of the substance.
These features allow for a broad and holistic review of the mechanistic evidence  [26]. Information was gathered based on the data available in the REACh registration dossier for CS2. In addition, a literature search was performed on CS2 in Pubmed ® using the search term "75-15-0 [CAS] in abstract-title and key words" in papers from 2013 to 2019. A set of inclusion and exclusion criteria was then applied to select the relevant studies (Table  S1  of supplementary material). Previously published international evaluations were also taken into consideration  [9, [27] [28] [29] [30] [31]. A search has also been conducted in the U. S. Environmental Protection Agency's Endocrine Disruptor Screening Program  [32]  to determine the potential for CS2 to interact with estrogen, androgen or thyroid (E, A or T) bioactivity based on in vitro high-throughput screening assays.
In vitro, in vivo animal data, mechanistic data and human data relevant for the assessment of ED properties were evaluated. The quality of the experimental animal studies was assessed and was rated using Klimisch scores: score 1 (reliable without limitations), 2 (reliable with limitations), 3 (unreliable) or 4 (not assignable)  [33]. Human data were also assessed, including a risk of bias analysis. Relevant parameters and tests for the identification of the substance as ED were identified based on the OECD test guideline 150  [34]  and the review published by  Manibusan and Touart (2017)   [35]. A detailed description of all the studies considered and their quality assessment is available in the conclusion document written by ANSES (  [36] , in press). A total of 69 animal studies and 43 human epidemiological studies were considered and assessed for their reliability when evaluating the toxicological profile of the substance.
From this selection, 29 animal studies and 23 human epidemiological studies were considered key in the assessment of the ED properties of the substance. Figure  1  presents the information flow diagram used for data search. The references, the reliability assessment and the type of studies used in this evaluation are available in Tables  S2  and S3  of the supplementary material. The relevant parameters have been grouped, as recommended in the guidance, into four categories: parameters measured in silico/in vitro, parameters measured in vivo that provide information on potential alteration of the endocrine function (referred as endocrine activity), parameters measured in vivo that provide information on adversity and indicative of estrogen, androgen, thyroid or steroidogenesis MoA (referred as EATSmediated), parameters measured in vivo that are sensitive to, but not diagnostic on their own of EATS.
Acknowledgments: We would like to thank the  ANSES team  for their scientific contribution to the evaluation of CS 2 under REACH, including  Johanna Berneron  and  Juliette Deweirdt , the  ANSES  expert group on REACH, including  Paule Vasseur , and the  ANSES Working group  on endocrine disruption. In addition, we would like to thank  ECHA  for its in-depth review of the conclusion document on carbon disulfide in the context of REACh regulation.
Analysing temporal patterns in plant communities is extremely important to quantify the extent and the consequences of ecological changes, especially considering the current biodiversity crisis. Long-term data collected through the regular sampling of permanent plots represent the most accurate resource to study ecological succession, analyse the stability of a community over time and understand the mechanisms driving vegetation change. We hereby present the LOng-Term Vegetation Sampling (LOTVS) initiative, a global collection of vegetation time-series derived from the regular monitoring of plant species in permanent plots. With 79 data sets from five continents and 7,789 vegetation time-series monitored for at least 6 years and mostly on an annual basis, LOTVS possibly represents the largest collection of temporally finegrained vegetation time-series derived from permanent plots and made accessible to the research community.