dataesr/scientific-paragraphs-categorization huggingface dataset:
SAOZ network in Russia An stations. The measurements of total ozone and NO 2 by SAOZ instruments in Russia, providing data all year round, cover a vast polar regions in the Northern Hemisphere. The data of total ozone and NO 2 observations by the SAOZ UV-Vis spectrometers in Russia are submitted and presented at the World SAOZ database in France http: //saoz. obs. uvsq. fr/SAOZ-RT. html and at the NDACC database http://www. ndsc. ncep. noaa. gov/.
Ozonesounding in Siberia At the Yakutsk aerological stations coordinated ozonesonde flights were started in late 1994. At the same time coordinated measurements of vertical ozone distribution were made by European scientists at 30 stations of the Northern Hemisphere in the frame of international program on investigation of mechanisms of ozone layer depletion. Ozonesonde flights were performed in a manner to monitor the changes of ozone concentration in the same air masses. For this purpose the local time and date of ozonesonde launches were determined using the daily forecasts of air mass trajectories. Using the data of balloon ozonesounding at Yakutsk quantitative estimation of ozone depletion in the lower stratosphere were made for spring months of 1995-1997 inside and outside the polar vortex.
campaigns. The wavelength range of the SAOZ instrument is in the Chappuis band of ozone absorption, with a spectral resolution of 1 nm for version V-1024. Measurement accuracy is 6 % for total ozone and 10 % for nitrogen dioxide. Data for the atmospheric content of O 3 and NO 2 measured by SAOZ spectrometers are available at the World SAOZ database, since 1988 from Dumont d'Urville station in the Southern Hemisphere, since 1989 from the Sodankyl ä observatory in Finland, and from additional SAOZ stations in 1990-1991. The first Asiatic SAOZ station started operation in December of 1991 at Zhigansk aerological station, Eastern Siberia. A SAOZ spectrometer has been operating at Salekhard aerological station, Western Siberia since 1998. Discussion Paper | Discussion Paper | Discussion Paper |.
The total ozone was as low as 235 DU at Zhigansk on 23 March 2011 and 242 DU in Salekhard on 31 March 2011. The SAOZ spectrometer observed low total ozone values 250-270 DU in Salekhard during the first week of April 2011 when the polar vortex was still located in this area. The SAOZ instrument at Zhigansk station did not measure low total ozone at this time. The SAOZ low total ozone levels in winter-spring period of 2011 are well documented in Fig. 4 for Salekhard and Zhigansk. The total ozone reduction in the vortex conditions in 2012 was about 14 % ± 4 % or 60 DU and the loss rate 0. 35 % per day between end of December and early February 2012. The SAOZ long-term total ozone and NO 2 dataset at Zhigansk aerological station in 1991-2011 and at Salekhard aerological station in 2001-2011 are presented in Fig.
stratospheric ozone had been observed over the polar latitudes of Western and Eastern Siberia. Such an interannual variability of ozone amount in the lower stratosphere, within the zone of action of the northern circumpolar vortex, is due to the weather conditions of its formation. During the winter-spring season of 2011 the observed ozone decrease exceeded 70 % within the 19-21 km altitude range. During the winter-spring season of 2012 we have seen usual Arctic conditions and no significant ozone loss above Salekhard station. Ozonesonde data from the Salekhard station during the Arctic winter-spring season of 2010/2011 and 2011/2012 are available from the NDACC database. Discussion Paper | Discussion Paper | Discussion Paper | ozone destruction occurs over the Arctic and Antarctic regions in local winter-spring.
tex conditions in March-April 2011 and February 2012 are shown in Fig. 7. The total 150 ozonesondes were launched at Yakutsk aerological station in Eastern Siberia during the winter-spring season of 1994-2006 and 250 ozonesondes, version 2Z-ECC, were used for vertical ozone profile observations at the Salekhard aerological station in Western Siberia, Russia. The data of the Salekhard ozonesonde measurements in 2005-2012 are available from the NDACC database ftp://ftp. cpc. ncep. noaa. gov/ndacc/ station/salekhar/ames/o3sonde/Discussion Paper | Discussion Paper | Discussion Paper |.
BIOINFORMATIC ANALYSES A blast was performed on the Medicago IMGAG Mt3. 5. 1 version using the Arabidopsis ABI5 amino acid sequence (At2g36270. 1) to retrieve homologous genes (score e < 1E-20). An unrooted tree was constructed with the nine identified MtABI5-like sequences and the Arabidopsis ABI5 using the sequence alignment program ClustalW (http://www. ebi. ac. uk/Tools/msa/clustalo/) and presented using Treeview  (Page, 1996). Gene lists were analyzed for enrichment in gene ontology (GO) terms using the Singular Enrichment Analysis (SEA) tool of AgriGO (http://bioinfo. cau. edu. cn/agriGO/) with a Chi-square statistical test method and the Yekutieli multi-test adjustment method  (Du et al. , 2010). For the large dataset of down-regulated transcripts related to DT, Plant Slim GO analysis was used.
Data lists were analyzed using the Arabidopsis TAIR9 background based on homology with the Medicago sequences since the M. truncatula genome background in AgriGO is incomplete. For cis-element enrichment analysis of the DT-UP list, 1. 5 Kb promoter regions upstream of the translational start of the 382 IMGAG Mt3. 5. 1 sequences were retrieved using the Legoo gateway (https://www. legoo. org/). Promoter sequences were analyzed using the PLACE database resource, (http://www. dna. affrc. go. jp/ PLACE/signalup. html). The frequency of a specific motif in the promoters of genes was tested against a background frequency generated using a randomized sample of 1470 Medicago genes. The significance of the enriched cis-elements was calculated using a Chi-square test against the background sample.
DATA SUBMISSION Nimblegen microarray data were deposited on the NCBI GEO database [  (Barrett et al. , 2012) ; accession GSE51830]. Data on the ectopic expression of MtABI3 in hairy roots discussed in this publication have been deposited in NCBI Gene Expression Omnibus  (Edgar et al. , 2002)  and are accessible through GEO Series accession number GSE44291 (http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE44291).
IDENTIFICATION OF THE TRANSCRIPTIONAL DESICCOME USING TWO PHYSIOLOGICAL MODELS OF DESICCATION TOLERANCE To obtain an overview of the genes implicated in DT, we produced two transcriptome data sets using an updated Medicago Nimblegen microarray: one on the acquisition of DT during maturation (GEO database accession GSE49350), and a second one on the re-establishment of DT during PEG incubation. To identify genes that are differentially expressed during the acquisition of DT, transcript levels were compared between 14 days after pollination (DAP), when seeds are still desiccation sensitive, and 32 DAP, when 100% of the seeds have acquired their DT (Figure  1A ). Data analysis identified 3626 and 14601 transcripts that increased or decreased at least two-fold, respectively, between 14 and 32 DAP.
Next, we characterized the transcriptome in relation to the re-establishment of DT. DT is lost following germination after the radicle is protruded, first in the radicles and then in the cotyledons. However, it is possible to re-establish DT in these protruded radicles by an osmotic stress treatment using a PEG solution at -1. 7 MPa  (Buitink et al. , 2003; Faria et al. , 2005). We performed a transcriptome analysis on 2. 7 mm long protruded radicles before and after 72 h of PEG incubation, corresponding to desiccation sensitive and -tolerant tissues, respectively (Figure  1B ). A total of 3598 and 6691 transcripts increased or decreased significantly (ratio log2 > 1 or <-1, P < 0. 01). Both datasets were compared to each other to identify overlapping transcripts (Figure  1C ). This resulted in the identification of 740 transcripts that positively correlate with DT (hereafter referred to as the DT-UP list) and 2829 transcripts that are downregulated when DT is installed (DT-DOWN list) (Figure  1C ) (Supplementary Table  S1 ).
It should be noted that some redundancy exists between the probes. Some of them are recognized by the same gene transcript, which can only be removed when the assembly of the M. truncatula genome is completed. The DT associated transcriptome of Medicago corresponding to a more complete dataset using updated slides, was compared to the recently obtained data set on a similar system of re-establishment of DT in Arabidopsis  (Maia et al. , 2011). Compared to this study, the number of transcripts overlapping between Arabidopsis and Medicago increased from 22 (48 transcripts) to 77% (115) of the total amount of up-regulated genes in Arabidopsis during re-establishment of DT and from 13 (49 transcripts) to 50% (139) for the down-regulated genes. These values reinforce the idea that core mechanisms and key regulators involved in DT are conserved across species, despite the fact that whole seeds were used for Arabidopsis and only radicles for M.
CHARACTERIZATION OF TRANSCRIPTIONAL REGULATORS AND REGULATORY Cis-ELEMENTS IN THE UP-REGULATED DESICCATION-TOLERANCE RELATED TRANSCRIPTOME To gain further insight into the transcriptional machinery regulating DT independently of the developmental context, 48 TF that were manually curated using Ensembl and Plantdtb (http:// planttfdb. cbi. pku. edu. cn) were retrieved from the up-regulated gene list (Table  1 ). AP2/EREBP, bHLH, and bZIP family members were found to be the most abundant TF. Twenty-two percent of these TF correspond to Arabidopsis homologs associated with freezing, cold and drought response and/or mediating an ABA response such as members of the DREB (DRE binding protein) subfamilies (Table  1 , bold characters) as previously described  (Fujita et al. , 2011). Strikingly, 17 TF (35%) with increased transcript levels in relation to DT were homologs of Arabidopsis regulators that are broadly associated with cell fate or cell identity (see italics characters in Table  1 ).
, 2011) , we first determined whether the Medicago gene Medtr7g104480 is homologous to ABI5 or other ABI5-like genes. The Arabidopsis ABI5 amino acid sequence was blasted against the Mt3. 5. 1 Medicago database and nine sequences were retrieved. A phylogenetic tree was constructed including the Arabidopsis ABI5 sequence (Figure  3A ) and confirmed that Medtr7g104480 is indeed the closest homolog to ABI5. The function of MtABI5 in DT was assessed using two independent homozygous Tnt1 insertion mutants (Mtabi5-1 and Mtabi5-2, Figure  3B ) that were obtained from the insertion collection curated by the Samuel Noble Foundation. The Tnt1 insertions were located at 599 and 1034 bp from the start-codon, respectively, before the bZIP domain (Figure  3B ). After the production of freshly harvested seeds, the ABA sensitivity of both Mtabi5 mutants was tested (Figure  3C ).
TRANSCRIPTOME ANALYSIS IDENTIFIES MtABI3-RELATED GENES INVOLVED IN DT A recent characterization of Tnt1 abi3 mutants of Medicago demonstrated that like for Arabidopsis, Medicago abi3 mutant seeds are desiccation sensitive and contain reduced amount of LEA proteins  (Delahaie et al. , 2013). To investigate which genes of the desiccome were regulated directly or acting downstream of MtABI3, we took advantage of recently published transcriptome data of developing desiccation-sensitive Mtabi3 mutant seeds  (Verdier et al. , 2013 , GEO database accession GSE44291). These seeds were analyzed at 32 DAP and compared to wild type seeds of the same age, after DT had been acquired  (Verdier et al. , 2013). In addition, we compared this dataset to that of the transcriptome of Medicago roots ectopically expressing the genomic sequence of MtABI3 (35S::ABI3,  Verdier et al.
, 2013 ; GEO database accession GSE44291). Amongst the 1151 transcripts with significantly decreased levels in the Mtabi3 seeds, 249 were present in DT-UP list (i. e. , 33% of the list, Figure  5 , Supplementary Table  S3 ) and 43 were present in the three data sets. Similarly, out 3745 transcripts that increased significantly in the Mtabi3 seeds, 817 were present in the DT-DOWN list (i. e. , 28%) and 39 were found in common between the three data sets (Figure  5 , Supplementary Table  S3 ). To further validate the MtABI3-mediated expression of DT genes, we verified whether their Arabidopsis homologs were among the list of the experimentally validated targets of the Arabidopsis ABI3 regulon  (Mönke et al. , 2012). For the 43 up-regulated genes present in all three dataset (Figure  5 ), 19 Arabidopsis homologs were identified as part of the regulon of MtABI3.
ANALYSIS OF ABI3-AND ABI5-SPECIFIC DATASETS IN RELATION TO DT Having identified the transcripts that are affected in the Mtabi3and Mtabi5 mutants in relation to DT, we investigated the putative function of the genes that modulated by one or both TFs (Figure  6 ). It should be noted that the change in transcript levels is not necessarily through a direct action of ABI3 and or ABI5, since transcript levels can be modified by downstream targets of these TFs or through other mechanisms than transcriptional activation. However, to facilitate the reading, we refer hereafter to ABI3 or ABI5-related genes. The putative regulation of transcripts by these two TFs is annotated in Table  1  and Supplemental Table  1. A GO-enrichment analysis was performed on these gene lists (Table  3 ). Only a small amount of transcripts are influenced by both TFs, representing 4 and 7% of the DT-UP and DT-DOWN lists, respectively (Figure  6 ).
, 2012). A GO enrichment analysis on the DT-DOWN list revealed that the main biological processes for which transcripts are down-regulated by both TFs are cell cycle, secondary metabolic processes and specific kinase or receptor signaling pathways (Table  4 ). The ABI5-related dataset showed a highly significant overrepresentation of processes related to cell division and actin cytoskeleton organization. This category goes together with the previously mentioned CUC3 TF whose expression is affected by ABI5 and involved in the repression of cell division (Table  1 ). Another biological processes enriched in the ABI5-related probe list is "defense response," including genes involved in flavonoid and phenylpropanoid biosynthesis and programmed cell death. The GO analysis of the overrepresented biological processes of the down-regulated transcripts that are related to ABI3 is complementary to that of the ABI5related list (Table  4 ).
ACKNOWLEDGMENTS Emmanuel Terrasson  and this work were supported by a grant from the  Région Pays-de-la-Loire  ( QUALISEM 2009 ( QUALISEM -2013 )). We acknowledge  Dr. Pascal Gamas  and  Jérôme Gouzy  ( INRA, Toulouse, France ) for sharing the Medicago truncatula genome data. The abi5 mutants of Medicago truncatula used in this research project, which are jointly owned by the  Centre National de la Recherche Scientifique , were obtained from The  Samuel Roberts Noble Foundation, Inc. and were created through research funded, in part, by a grant from the  National Science Foundation  (NSF#  703285 ).
3 5 6 4. 0 6. 54E-03 SGBFGMGMAUX28 TCCACGTGTC 16 4. 2 4 0. 3 1. 40E-10 SURE2STPAT21 AATACTAAT 33 8. 6 5 8 4. 1 2. 64E-04 CACGTGMOTIF CACGTG 127 33. 2 235 16. 7 1. 44E-12 EMBP1TAEM CACGTGGC 36 9. 4 5 4 3. 8 1. 08E-05 IRO2OS CACGTGG 83 21. 7 111 7. 9 1. 72E-14 QARBNEXTA AACGTGT 71 18. 5 1 7 6 1 2. 5 2. 60E-03 UPRMOTIFIIAT CC(N)12CCACG 27 7. 0 4 8 3. 4 1. 70E-03 Promoter enrichment analysis of 382 up-regulated genes from the desiccome (DT-UP list, Figure1) using 1. 5Kb promoter regions upstream of the translational start. DNA motifs were counted using PLACE database resource (http://www. dna. affrc. go. jp/PLACE/signalup. html). #, mumber of cis-elements in the indicated data sets.
Cell aggregates were dissociated on a 70 mm filter (Falcon), and placed on ice pending cell sorting as previously described  [27]. Cell sorting was performed on a FACSAria (BD Biosciences, San Jose, CA) fitted with fully sealed sample injection and sort collection chambers operating under negative pressure. After staining with M5/114, DLs were selected by BD FACSDiva software (BD Biosciences). PE-Cy5 and DsRed2 fluorescence was collected through 695/40 and 576/26 band pass filters, respectively. FSC and SSC were displayed on a linear scale and used to discard cell debris  [27]. Live amastigote-hosting DLs were sorted by selecting cells expressing both surface MHC II molecules and DsRed2 fluorescence. Sorting conditions included a sheath pressure of 70 Psi, a flow rate of 7 and the use of a 70 mm nozzle tip.
GeneChip hybridization and data analysis Altogether, 200 ng of total RNA per sample were processed, labelled and hybridized to Affymetrix Mouse Gene ST 1. 0 arrays, following Affymetrix Protocol (http://www. affymetrix. com/ support/downloads/manuals/expression_analysis_technical_manual. pdf). Three Biological replicates per condition were run as described previously  [20]. After hybridization, the arrays were stained and scanned at 532 nm using an Affymetrix GeneChip Scanner 3000 which generated individual CEL files for each array. Gene-level expression values were derived from the CEL file probe-level hybridization intensities using the model-based Robust Multichip Average algorithm (RMA)  [34]. RMA performs normalization, background correction and data summarization. An analysis was performed using the LPE test  [35]  (to identify significant differences in gene expression between parasite-free and parasite-harbouring DLs), and a p-value of p,0.
05 was considered as significant. Estimated false discovery rate (FDR) was calculated using the Benjamini and Hochberg approach  [36]  in order to correct for multiple comparisons. A total of 1,340 probe-sets showing significant differential expression were input into Ingenuity Pathway Analysis software v5. 5. 1 (http://www. ingenuity. com), to perform a biological interaction network analysis. The symbols of the modulated genes are specified in the text (fold change  [FC]  values between brackets), while their full names are given in additional file 1. MIAMEcompliant data are available in the GEO database http://www. ncbi. nlm. nih. gov/geo/ accession GSE.
Finally, samples were mounted on glass slides with Mowiol (Calbiochem, Darmstadt, Germany) containing 5 mg/ml Hoechst 33342 (Molecular Probes): as the latter is incorporated into DNA it stains the nuclei of both the host cells and the amastigotes. Images were acquired on an upright Zeiss Axioplan 2 microscope controlled by Zeiss Axiovision 4. 4 software.
Results and Discussion C57BL/6 and DBA/2 DLs hosting live L. am amastigotes show only minor transcriptional modifications compared to control DLs DLs were derived from GM-CSF-responsive progenitors (otherwise known to be present in the bone marrow cell suspensions prepared from the femurs of C57BL/6 and DBA/2 mouse inbred strains) as previously described for DLs derived from BALB/c mouse bone marrow  [27]. More than 97% of the cells in these cultures expressed CD11c in parallel to CD11a and CD11b (data not shown). Two different cell subsets were defined by flow cytometry (FCM) analysis. The first did not express surface MHC II molecules, and consequently was not considered as bona fide DLs (subset 1, figure  S1A ). The second did express surface MHC II molecules, albeit at various intensities.
Parasitized DLs were detected by the orange fluorescence of intracellular DsRed2 + amastigotes. Figure  4A  shows the outcome of a representative FCM experiment performed on C57BL/6 mice, and Figure  4B  the collective results of 7 independent experiments. Similar results were obtained for DBA/2 DLs (data not shown). White histogram (Figure  4A1 ) represents background mean fluorescence emitted by ctrl DLs (here mean fluorescence intensity (mfi) was 214). This value was increased (Figure  4A3 , mfi = 716, black histogram) in the oleate-free DLs containing DsRed2 + amastigotes fraction. A statistical analysis showed that the quantity of neutral lipids was significantly higher in L. am + than in both L. am 2 DLs from the same culture (Figure  4A3 , grey histogram), and ctrl DLs (Figure  4A1 , white bars) (p,0.
75 μg (CCG)8×-Cy3 DNA oligonucleotide probe (Sigma-Aldrich). The coverslips or slides were washed twice in 2× SCC/50% formamide and twice in 2× SCC. Following FISH, the coverslips or slides were washed twice successively in 2× SCC/50% formamide, in 23 SCC, and in PBS. The coverslips or slides were incubated 2 hr with primary antibody against Drosha (1:100 dilution, AB12286; Abcam) or DGCR8 (1:100 dilution, HPA019965; Sigma-Aldrich). Slides or coverslips were washed twice with PBS before incubation with a goat anti-rabbit secondary antibody conjugated with Alexa Fluor 488 (1:500 dilution; Thermo Fisher Scientific) for 60 min, incubated for 10 min in 2× SCC/DAPI (1:10,000 dilution), and rinsed twice in 2 × SSC before mounting in Pro-Long media (Molecular Probes). Slides were examined using a fluorescence microscope (Leica), and identical exposure or microscope setting was used for control or FXTAS brain section analyses.
Acknowledgments We thank  Tom Cooper  ( Baylor College of Medicine, Houston ) and  Joelle Marie  ( CNRS, Gif-sur-Yvette, France ) for the gift of the CUG-expressing plasmids,  Karen Usdin  ( NIH, Bethesda, MD, USA ) for the gift of the CGG 65xexpressing plasmid,  Narry Kim  ( University of Seoul, Seoul, Korea ) for the gift of the Flag-DROSHA and Flag-DGCR8 WT or mutant plasmids,  Peng Jin  ( Emory School of Medicine, Atlanta ), who provided the FXTAS model flies,  Scott Pletcher  ( University of Michigan, Ann Arbor, MI, USA ), who provided the Geneswitch flies, and  Claudio Sette  ( University of Tor Vergata, Roma ) for the gift of the GFP-SAM68 construct. This work was supported by  ANR GENOPAT  grant  P007942  (to N. C. -B. ),  AFM and Jérôme Lejeune funding  (to N. C. -B. ),  Collège de France  (to C.
The ESA processor had to perform the operational near real time analysis of the observations and its products needed to be available for data assimilation. Therefore, it has been designed for fast, continuous and automated analysis of observations made in quite different atmospheric conditions and for a minimum use of external constraints in order to avoid biases in the products. The dense vertical sampling of the measurements adopted in the second phase of the MIPAS mission resulted in sampling intervals finer than the instantaneous field of view of the instrument. Together with the choice of a retrieval grid aligned with the vertical sampling of the measurements, this made ill-conditioned the retrieval problem of the MI-PAS operational processor. This problem has been handled with minimal changes to the original retrieval approach but with significant improvements nonetheless.
With these changes, which provide, for the operational data products, an optimized compromise between spectral and spatial resolutions (optimized resolution, OR), MIPAS restarted operations on 9 January 2005 with a duty cycle shorter than 40 %. Since then, due to the recovering performance of the drive unit, the duty cycle was progressively increased until 1 December 2007 when a 100 % duty cycle was again attained. MIPAS was successfully operated with this full duty cycle until 8 April 2012, when an Envisat anomaly occurred resulting into the loss of communication between ground and satellite and the end of MIPAS observations  (ESA, 2012a). MIPAS was one of the first Envisat instruments to be fully operational after the launch, providing very high quality Level 1 and Level 2 products. The ESA operational near real time analysis provided from the very beginning vertical profiles of temperature and of volume mixing ratio (VMR) of H 2 O, O 3 , HNO 3 , CH 4 , N 2 O and NO 2 from pole to pole, approximately following the orbital track.