dataesr/scientific-paragraphs-categorization huggingface dataset:
62 ***. Based on this finding, we produced a map of user accuracy estimates over the region. We found that the MODIS LCP user accuracy was superior for three farming systems: Agro-Pastoral Millet/Sorghum, Cereal-Root Crop Mixed and Irrigated farming systems. To our knowledge, this is the first attempt to map global land cover uncertainties for a specific class at such a scale. Because of the moderate resolution, the MODIS LCP has an inherent limitation in discriminating low cropping pixels due to the subpixel heterogeneity  [11, 29]. However, it represents a valuable approach for determining cropland areas from a consistent land cover map at a large scale. Overall, mapping crop areas in fragmented landscapes from coarse-resolution data remains a difficult task and a significant challenge. However, initiatives such as the GEO-Global Agricultural Monitoring Project (GEO-GLAM Project) have started to work at improving global agriculture monitoring and crop production estimations  [57].
In addition, the forthcoming Sentinel-2 satellites will routinely deliver high-resolution images (10 m resolution) and are expected to significantly contribute to the current efforts. With their high temporal resolution, agricultural land cover maps and information on agricultural land use practices (crop type, cropping intensities, irrigation, and crop rotation) could be provided regularly. However, for present and future agricultural monitoring, historical datasets will continue to be important for understanding the processes that shaped the agricultural landscapes. Thus, it is necessary to continue developing methods for handling past data.
Acknowledgments This study was funded by  Louise Leroux 's  CIRAD fellowship  and by the  Centre National d'Etudes Spatiales  (Project  CNES-TOSCA "Dynafrique "). The authors thank the MODIS team for sharing the MODIS Land Cover Product and  Elodie Vintrou  and  Kadidiatou Yéro Souley  for providing the crop masks in Mali and Niger, respectively. Finally, the authors thank the  AGRHYMET Center in Niamey  for providing the agricultural statistics in Burkina Faso.
RNA-Seq Analysis Transcriptomic high-throughput sequencing data were analyzed using a bioinformatic pipeline implemented in the MicroScope platform (http://www. genoscope. cns. fr/agc/mi croscope/, last accessed April 12, 2014)  (Vallenet et al. 2013). The current pipeline is a "Master" shell script that launches the various parts of the analysis (i. e. , a collection of Shell/Perl/R scripts) and controls for all tasks having been completed without errors. In a first step, the RNA-seq data quality was assessed by including option-like reads trimming or merging/split paired-end reads. In a second step, reads were mapped onto the D. deserti VCD115 genome sequence (GenBank accession numbers CP001114, CP001115, CP001116, and CP001117 for the chromosome and plasmids P1, P2, and P3, respectively) using the SSAHA2 package  (Ning et al.
2001 ) that combines the SSAHA searching algorithm (sequence information is encoded in a perfect hash function) aiming at identifying regions of high similarity and the crossmatch sequence alignment program  (Ewing et al. 1998) , which aligns these regions using a banded Smith-Waterman-Gotoh algorithm  (Smith and Waterman 1981). An alignment score equal to at least half of the read is required for a hit to be retained. To lower false-positive discovery rate, the SAMtools (v. 0. 1. 8) (Li et al. 2009)  were then used to extract reliable alignments from SAM formatted files. The number of reads matching each genomic object harbored by the reference genome was subsequently computed with the Bioconductor-GenomicFeatures package  (Carlson et al. 2011). If reads matched several genomic objects, the count number was weighted to keep the same total number of reads.
The Bioconductor-DESeq package  (Anders and Huber 2010)  with default parameters was used to analyze raw counts data and test for differential expression between conditions. The complete data set from this study has been deposited in National Center for Biotechnology Information's Gene Expression Omnibus and is accessible through GEO Series accession number GSE56058. TSSs were annotated manually as described  (Kro ¨ger et al. 2012 ), with enrichment de  Groot et al. in the +TEX libraries as the first criterion. In the case of no enrichment, a TSS was assigned if the four libraries agreed on the nucleotide position and if its location was plausible in relation to an adjacent open reading frame (ORF). Rapid amplification of cDNA ends (5 0 -RACE) was performed as described  (Tillett et al. 2000).
Nano-LC-MS/MS Analysis and Proteomic Data Processing Peptide samples were analyzed by nano-LC-MS/MS using an LTQ-Orbitrap XL hybrid mass spectrometer (ThermoFisher) coupled to an UltiMate 3000 LC system (Dionex-LC Packings) in similar conditions as described previously  (Rubiano-Labrador et al. 2014). The recorded MS/MS spectra were processed as described for peptide assignment  (Christie-Oleza et al. 2013). Briefly, peak lists were generated with the Mascot Daemon software (version 2. 3. 2; Matrix Science) using the extract_msn. exe data import filter (Thermo) from the Xcalibur FT package (version 2. 0. 7; Thermo). Data import filter options were set to 400 (minimum mass), 5,000 (maximum mass), 0 (grouping tolerance), 0 (intermediate scans), and 1,000 (threshold). The search was performed using the following criteria: Tryptic peptides with a maximum of two miscleavages, mass tolerances of 5 ppm on the parent ion and 0.
5 Da on the MS/MS, fixed modification for carbamidomethylated cysteine, and variable modification for methionine oxidation. The home-made polypeptide sequence database used here was described previously  (de Groot et al. 2009). This database comprises 65,801 polypeptide sequences, totaling 6,040,642 amino acids, derived from a six-frame translation of the D. deserti genome sequence but restricted to ORFs (defined from STOP to STOP) with at least 33 amino acids. Mascot results were parsed using the IRMa 1. 28. 0 software  (Dupierris et al. 2009 ) with a P-value threshold below 0. 05 for peptide identification.
2009 ). Before the present work was started, 3,459 coding sequences (CDSs) were annotated on the genome, as well as 12 rRNAs and 48 tRNAs. The read coverage for the entire genome can be visualized using the Integrative Genomics Viewer  (Thorvaldsdottir et al. 2013 ) via the MicroScope platform  (Vallenet et al. 2013 ). An example of such displayed read coverage for a 2. 5 kb region is shown in figure  1A , where the data indicate a monocistronic transcript for rpsF and a polycistronic transcript for ssb-rpsR-rplI. An overview of the obtained read numbers mapped to D. deserti's genome is presented in supplementary table  S1 , Supplementary Material online. To compare the relative transcription levels of the four replicons, the mapped read numbers (without reads for rRNA and tRNA genes) were normalized for the size of each replicon.
New Gene Predictions and Proteome Data Correlate with Novel Leaderless mRNAs For many of the deduced translation products of the additional leaderless transcripts, no protein homologs were identified using sequence-or structure-based homology searches. These putative peptides and proteins may be specific for D. deserti, or failure to detect homologs may be related to the small peptide sizes. To see whether the additional leaderless transcripts correspond to CDSs that were missed previously, new gene predictions were obtained and analyzed. In addition, a new proteome analysis after enrichment of small proteins was performed. For the initial D. deserti genome annotation, FrameD and MED were used  (de Groot et al. 2009 ). Here, we applied  The data show the number of mRNAs with the indicated start codon and the number of mRNAs for which the protein product and N-terminal peptide have been detected by proteomics.
AMIGene for identification of potential new CDSs  (Bocs et al. 2003). After analysis of these new predictions, 142 CDSs were added and annotated (including 49 partial genes) (supplementary table S10, Supplementary Material online). Identification of these new genes and reannotation of several start codons also allowed removal of 49 erroneously annotated hypothetical genes (supplementary table S10, Supplementary Material online). It is worth noting that the software did not predict the 14 leader peptide genes proposed to be involved in transcription attenuation and 3 of the 17 conserved genes described in the previous subsection, that is, Deide_15148 (encoding Gly-, Ser-, Arg-, and His-rich protein), Deide_2p00483 (Lys-and Ala-rich), and Deide_11672 (gene fragment). Homology with one or more proteins in databases was detected for 43 of the new CDSs, but a putative function could be assigned to only two (Deide_11194, putative excisionase; Deide_2p02235, putative transposase).
Twenty-seven of the new additional leaderless transcripts appeared to correlate with new predicted genes (supplementary table  S10 , Supplementary Material online). For the new proteome analysis, fractions were proteolyzed with trypsin on one hand, and chymotrypsin on the other, with the intention to increase the global polypeptide sequence coverage. The peptides were analyzed by orbitrap-based tandem mass spectrometry resulting in a data set of 556,375 MS/MS spectra. A total of 233,301 spectra could be assigned to peptide sequences after querying a six-frame translation database, revealing the presence of 21,232 peptide sequences (supplementary table  S11 , Supplementary Material online) and pointing at a total of 1,481 proteins detected with two or more tryptic or chymotryptic peptides (supplementary table  S12 , Supplementary Material online).
GBE for a peptide  (Dinger et al. 2008). As suggested by the read numbers, many potential noncoding RNAs are well expressed in D. deserti (supplementary table S4, Supplementary Material online). For three of the transcripts, homology was found with noncoding RNAs belonging to conserved RNA families present in the Rfam database  (Burge et al. 2013) , that is, signal recognition particle RNA, transfer-messenger RNA and bacterial RNase P class A (supplementary table  S13 , Supplementary Material online). Besides these noncoding RNAs, the long 5 0 -UTR of 13 genes appeared to correspond to cis-regulatory elements (supplementary table S13, Supplementary Material online). These include TPP, FMN, SAM, cyclic di-GMP-I, cyclic di-GMP-II, and cobalamin riboswitches for genes involved in processes such as thiamine biosynthesis and transport, riboflavin biosynthesis, and methionine and vitamin B12 transport.
gobiensis (DGo_CA1576 is also located downstream of uvrC). Alternatively, Deide_11446 may correspond to a novel noncoding RNA (no homology was detected using BLASTN and the Rfam database). A 17-base pair palindromic motif called RDRM (radiation and desiccation response motif) has been found upstream of about 20 radiation-induced genes in D. radiodurans and their homologs in D. geothermalis  (Makarova et al. 2007) , and found to be conserved in D. deserti  (de Groot et al. 2009 ). Here, we analyzed the location of the RDRM with respect to the TSS of the radiation-induced genes (supplementary fig. S9 , Supplementary Material online). There was clearly no conserved distance between the TSS and the RDRM. TSSs were found up to 20 bp upstream, within, or up to 50 bp downstream of the RDRM. These data would be compatible with a potential repressor protein binding to the RDRM and blocking initiation of transcription in standard growth conditions.
deserti. Three other new small proteins, Deide_04426, Deide_12656, and Deide_15253, might have a similar function in the periplasm. They have a signal peptide followed by the mature part of the protein consisting almost entirely of a hydrophilic region of low complexity. Lipoprotein Deide_04426 would be anchored to the periplasmic side of the cytoplasmic membrane. Noteworthy, Deide_12656 and Deide_15253 were detected by tandem mass spectrometry. No homology was found for the deduced peptides from many other new leaderless transcripts in D. deserti. As previous data have established that an AUG or GUG at the 5 0end of RNA is generally sufficient for ribosome binding and translation initiation  (Brock et al. 2008 ), many of these transcripts could also be translated. Interestingly, recent studies have revealed that peptides are abundant components of protein-free cell extracts of D.
RNase E homologs are universally present in cyanobacteria Cyanobacteria is a bacterial phylum that comprises numerous species with great morphological, ecological, and genetic diversity. Although RNase E homologs were found in some cyanobacterial strains  (Shahbabian et al. 2009) , it is still unclear whether the enzyme is universally present in this phylum. Currently, the GenBank database has the entries of the genomic data for as many as 60 cyanobacterial strains, which represent a diverse group of cyanobacteria. We performed a BLAST analysis using the query of Synechocystis PCC6803 RNase E, the first cyanobacterial RNase E protein experimentally investigated  (Kaberdin et al. 1998) , and determined that a single copy of an RNase E homolog exists in each available cyanobacterial genome (data not shown).
5 ). On the membrane with AnaPnp incubation, the interaction levels between AneRneC variants and AnaPnp were estimated by the intensity of the immunoblotting signals. The result obtained showed that the AneRneC variant lacking C4 lost completely the ability to interact with AnaPnp. In contrast, deletion of other subregions in AneRneC did not disrupt the interaction between AnaRneC and AnaPnp, although the absence of C3 and V3 appeared to weaken the interaction slightly. These data indicate that C4 is the key element for AnaPnp recognition by AnaRneC. We further tested whether the motif C4, when fused to other proteins, could confer on the fusion proteins the ability to interact with AnaPnp. The green fluorescent protein GFP was chosen for the test as GFP alone was found unable to interact with AnaPnp in pilot experiments (data not shown).
The synthetic nonapeptide of C4 was also tested to see if it could act as a competitor to interfere with the formation of the AnaRne-AnaPnp complex using the Far-Western dotblot assay. First, AnaRneC, AnaPnp, and BSA were dotted onto multiple nitrocellulose membranes; then, each membrane was incubated with a fixed concentration of AnaPnp (2 µM) and a varying amount of the synthetic peptide of C4 (0-20 µM). After the incubation, the membranes were immunodetected with the antibody against AnaPnp. The data in Figure  7A  showed that the interaction between AnaRneC and AnaPnp was weakened by the addition of the peptide C4 in a concentration-dependent manner. Nearly 50% of the interaction signal was lost when the C4 peptide concentration was at 4 µM, while almost no interaction signal FIGURE 6.
Subsequently, one of the membranes was incubated with 2 µM AnaPnp and the other one was not. Both membranes were finally subjected to immunodetection with the antibody against AnaPnp (see Materials and Methods for details). The deleted regions in AnaRneC variants are illustrated with boxes with gray stripes. BSA and AnaPnp were used as the negative control and the positive control, respectively. could be observed when the concentration was increased to 20 µM. These data that the synthetic C4 nonapeptide could efficiently compete with AnaRneC for binding to AnaPnp.
Bioinformatic analysis By the time we did the analysis, the data of a total of 60 cyanobacterial genomes were available in the GenBank database. The RNase E homologs encoded by the genomes were identified by BLAST analysis using the query of Synechocystis PCC6803 RNase E. Sequence alignment for cyanobacterial RNase E homologs was performed in the program MEGA5  (Tamura et al. 2011 ) using the program's Conserved PNPase-RNase E complex in cyanobacteria www. rnajournal. org 575 default parameters. The alignment for the noncatalytic domains of cyanobacterial RNase Es produced MEGA was refined manually.
ACKNOWLEDGMENTS We thank  Dr. Ben F. Luisi  at the  University of Cambridge  for helpful guidance in preparing E. coli 9S RNA. We thank  Xiaozhen Huang  for help in the enzymatic assay,  Songbo Li  for construction of some protein expression plasmids, and  Shuang Wan  for help in the bacterial two-hybrid assay and native-PAGE assay. This work was supported by the  National Natural Science Foundation of China  ( 31100038 ,  30970088 ) and the  Fundamental Research Funds for the Central Universities of China  ( 2011PY090 ). Received November 15, 2013; accepted January 23, 2014.
The deletion of rex affects anaerobic fermentative and aerobic respiratory metabolism of B. cereus by decreasing and increasing, respectively, the carbon flux through the NADH-recycling lactate pathway. We compared both the cellular proteome and exoproteome of the wild-type and Drex cells using a high throughput shotgun label-free quantitation approach and identified proteins that are under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXchange with identifier PXD000886. The data suggest that Rex regulates both the cross-talk between metabolic pathways that produce NADH and NADPH and toxinogenesis, especially in oxic conditions.
Proteomic sample preparation and nanoLC-MS/MS analysis of tryptic peptides Three independent biological replicates were harvested for each of the two conditions (aerobiosis and anaerobiosis) and two strains (Drex mutant and its parent strain, ATCC 14579). The extracellular proteins of the 12 cultures were extracted by trichloroacetic acid precipitation  [8]. The cellular proteins from the 12 samples were obtained as previously described  [9]. The 24 resulting samples were subjected to SDS-PAGE, and then identified after trypsin proteolysis by nanoLC-MS/MS tandem mass spectrometry with an LTQ-Orbitrap XL mass spectrometer as previously described  [8, 9]. A total of 131 nanoLC-MS/MS runs were carried out to acquire the whole dataset. The MS/MS spectra were assigned to tryptic peptide sequences with the Mascot Daemon software (version 2.
3. 2; Matrix Science) with mass tolerances of 5 ppm on the parent ion and 0. 5 Da on the MS/ MS, fixed modification for carbamidomethylated cysteine, and variable modification for methionine oxidation. Mascot results were parsed with a p-value threshold below 0. 05 for peptide identification and proteins were validated when at least two peptides were detected. The number of MS/MS spectra per protein recorded by nanoLC-MS/MS was extracted for each sample. In each condition, proteins were further considered for comparison only if peptides were seen in at least two of the three replicates. The resulting datasets were normalized taking into account the total protein concentration of the corresponding pellet and supernatant. Protein concentrations in B. cereus were determined using the Reducing agent Compatible Detergent Compatible (RCDC) protein assay (Bio-Rad) following the supplier's instructions.
MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2. 0. 0. 13  [33]  using a p-value cut-off set at 0. 05. Log 2 (fold-change) were then calculated for comparisons and only the proteins for which the p-value was lower than the 0. 05 cut-off were considered. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://www. proteomexchange. org) via the PRIDE partner repository  [34]  with the dataset identifier PXD000856 and DOI 10. 6019/ PXD000856.
we report mass change in Tables  1  and S2  as (dH /dt) hyps • (A) • ρ, (2) where (dH /dt) hyps is the elevation-band-weighted mean measured dH /dt, A is area of the glacier basin or island, and ρ is our assumed mean density of ice and firn lost by dynamics (900 kg m -3 ). We eliminated the nunatak areas from each of the basins, based on the Antarctic Digital Database mapping of rock outcroppings in the region similar to previous studies (e. g. ,  Gardner et al. , 2013). Our estimate of mass balance for the combined nAP region is -24. 9 ± 7. 8 Gt a -1 , with the great majority of the mass loss occurring at elevations below 1000 m a. s. l. (-21. 9 ± 6. 3 Gt a -1 , or 88 %; Table  1 ). Regionally, the eastern nAP basins dominate the mass loss at -17. 7±3. 7 Gt a -1 , or 72 % of the loss, and of this, -15.
Acknowledgements. The ICESat data for this paper are available at the  NASA Distributed Active Archive Center at NSIDC  ( GLA12 -GLAS/ICESat L2  Antarctic and Greenland Ice Sheet Altimetry Data). The SPOT5 HRS data were provided at no cost by  CNES  through the  SPIRIT  project. The ASTER data were provided at no cost by  NASA/USGS  through the  Global Land Ice Measurements from Space (GLIMS)  project. This work was supported by  NASA  grant  NNX10AR76G  to  T. Scambos  and  W. Abdalati , the  TOSCA and ISIS programs of the French Space Agency (CNES)  to  E. Berthier ,  NASA   Cryospheric Program funds  to  C. Shuman ,  NSF  grant  ANT-0732921  to  T. Scambos , and the  Netherlands Polar Program and European Union Seventh Framework Programme  grant  226375  to  S. Ligtenberg. Edited by:  J.
Datasets This study is based on the combination of two complementary datasets: (i) the Global Inundation Extent Multi-Satellites (GIEMS) that provide the percentage of inundation in a pixel of 773 km 2 of spatial resolution and enable spatio-temporal monitoring of the flood dynamics; and (ii) radar altimetry heights from Envisat that permitted us to establish a network of virtual stations for the monitoring of water stages throughout the basin. The combination of datasets enabled us to compute water level maps from which we estimated surface water storage in the Orinoco Basin. We used ancillary data for validation purposes (in situ gauge records) and for improved understanding of the hydrological cycle in the Orinoco Basin (gridded rainfall and gravimetry from space products and in situ discharge at the mouth of the basin).
(3) Backscatter at 5. 25 GHz from the European Remote Sensing (ERS) satellite scatterometer. ERS observations are averaged over each month and mapped to an equal area grid of 0. 25° resolution at the equator (each pixel equals 773 km2)  [23, 38]. An unsupervised classification of the three sources of satellite data was performed, and the pixels with satellite signatures likely related to inundation were retained. For each inundated pixel, the monthly fractional coverage by open water was obtained using the passive microwave signal and a linear mixture model with end members calibrated with scatterometer observations to account for the effects of vegetation cover  [23, 24]. As the microwave measurements are also sensitive to snow cover, snow and ice masks were used to filter the results and to avoid any confusion with snow-covered pixels  [41].
Because the ERS scatterometer encountered serious technical problems after 2000, the processing scheme had to be adapted to extend the dataset via use of monthly mean climatology from ERS and NDVI from AVHRR observations  [24, 26]. Fifteen years of global monthly water surface extent for the period 1993-2007 have been generated  [26]. Maximum error on the inundation estimate is less than 10% for some scales of wetlands  [24]. The dataset has been extensively evaluated at the global scale and for a wide range of environments (e. g. ,  [24, 26, 42] ).