dataesr/scientific-paragraphs-categorization huggingface dataset:
The working groups are by no means separate entities. Work on common or overarching issues is encouraged in several ways: (a) the group membership is not fixed and all IPWG members are encouraged to participate in several working groups bringing their own expertise; (b) initiatives stem from the working groups on important issues such as validation exercises and participation in international and/or national activities. The rapporteur of the IPWG to CGMS works closely with the IPWG co-chairs and working group chairs to formulate the recommendations from the working group sessions into actionable requests to the CGMS satellite operators. CGMS tracks these items and requests updates from the co-chairs on an annual basis. Following the IPWG/IWSSM workshop in Bologna a number of recommendations have been made to CGMS centred upon sustaining the precipitation constellation and the need for the formulation of a coordinated plan towards a sustainable PMW-based constellation  (Huffman, Ferraro, Kidd, Levizzani, & Turk, 2016a) ; accounting for user requirements when specifying instrument temporal/spatial sampling requirements; developing and implementing scattering and emissivity databases; enhancing scientific and operational activities for mixed/solid phase precipitation at mid-high latitudes; and support for training activities (with WMO/CGMS support) on an annual basis.
, 1994; PIP-2: Smith et al. , 1998; PIP-3: Adler, Kidd, Petty, Morrissey, & Goodman, 2001). These studies targeted specific periods and regions comparing both satellite and model-based precipitation products against surface reference datasets from both gauges and radars. These studies typically showed a large variation in the performance of the products, although this range was reduced somewhat when more mature products were considered. The IPWG worldwide validation effort has triggered local studies aimed at characterizing the various precipitation products available at different space and time scales. Kidd et al. (  2012 ) evaluated several high-resolution precipitation products (HRPP) over northwest Europe and found that satellite products generally exhibit a seasonal cycle in correlation, bias ratio, probability of detection, and false alarm ratio, with poorer statistics during the winter and a general underestimation of precipitation in all seasons.
One of the most important ways of conveying results and guidance to the users of satellite-derived precipitation products is the publication of ad hoc studies informing the user on the characteristics of the datasets and reporting the pros and cons together with some guidelines. For example,  Kidd, Levizzani, Turk, and Ferraro (2009)  addressed the needs of the water management community, while  Tapiador et al. (2012)  concentrated on global precipitation estimates trying to organize the many links and feedbacks between precipitation measurement, estimation and modelling to identify areas requiring further attention for product development, and to show the limits within which datasets can be successfully used. A similar strategy was recently followed by  Tapiador et al. (2017)  in indicating paths for the use of global precipitation datasets for climate model validation.
Hossain, Biswas, Ashraf, and Bhatti (2017)  used the Integrated Multi-satellitE Retrievals for GPM (IMERG) precipitation data products for flood and irrigation advisories in the Hindu-Kush region, distributed via mobile phone text messages. The interaction of IPWG members with other communities has also fostered studies for the development of new multidisciplinary approaches towards the retrieval of precipitation from space. Although the individual efforts are the work of specific groups of people, the IPWG provided guidance and a testbed to act as a catalyst for such developments, as well as a forum for disseminating datasets and products worldwide. Two examples are represented by the Multi-Source Weighted-Ensemble Precipitation (MSWEP) dataset  (Beck et al. , 2017) , which merges gauge, satellite and reanalysis data, and the Soil Moisture to Rain (SM2RAIN) bottom-up approach  (Brocca et al.
At the same time, research is necessary for overcoming the current limitations that still prevent a wider use of satellite precipitation datasets in global and regional hydrology (e. g. McCabe et al. , 2017). The IPWG has long since tackled the problem of representativeness and the unconstrained nature of the precipitation retrievals, which suggest a need for combined efforts in remote sensing, modelling and assimilation to improve products  (Michaelides et al. , 2009). A careful characterisation of the different satellite-derived precipitation products is also needed since they have different estimation accuracies depending, among other things, on the physics of the algorithm, the input data, and the differences over sea/land/coast; this is the reason why no unique dataset exists for all applications and why the selection of the most suited precipitation dataset depends on the application itself.
For example, hydrological model-based evaluation strategies are instrumental in identifying the suitability of the various products for hydrology at the catchment level  (Behrangi et al. , 2011). The increasing number of applications of precipitation products requires that the IPWG supports end users in finding the appropriate datasets and ensuring their correct usage. dom). CGMS has continuously provided support and fruitful interactions and guidance. The IPWG is also indebted to former and present representatives of the WMO Space Programme (Stephan Bojinski, Donald E. Hinsman, Jérôme Lafeuille, Wenjian Zhang) for their continuous support and encouragement. All the colleagues of the satellite precipitation community who have made available to the IPWG their precious time and competence on a totally voluntary basis are also to be gratefully recognised.
The work by FJT was performed at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. VL acknowledges support from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 603608, Global Earth Observation for integrated water resource assessment: eartH2Observe. Levizzani https://orcid. org/0000-0002-7620-5235 C. Kidd https://orcid. org/0000-0001-5906-8446.
ACKNOWLEDGEMENTS The authors wish to recognise the efforts of all past and present co-chairs of the IPWG ( Peter Bauer ,  Tufa Dinku ,  Arnold Gruber ,  Ziad S. Haddad ,  Christian Klepp ,  Paul A. Kucera ,  Bo ̇zena Łapeta, Dong-Bin Shin ) and of the former Rapporteurs to CGMS ( Volker Gärtner  and  James F. W. Pur -.
In the microwave spectrum, spaceborne radar remote sensing, whose continuous observations began with the launch of the ERS (European Remote Sensing) satellite in 1991, showed potential for monitoring surface parameters (e. g. ,soil moisture, vegetation biomass). Because radar data are not sensitive to the atmosphere and cloud cover, they can be expected to provide a more robust estimate of vegetation parameters, including phenology. The same compromise as in the optical domain was sought, which was to monitor seasonal variations at regional scales using scatterometers  [7, 8]  with high temporal frequency (3-4 days) and low spatial resolution (~20 to 50 km), or to focus on local scales using SAR (Synthetic Aperture Radar), which has a spatial resolution of about 10 to 30 m. However, the corresponding temporal revisit time (about one month) hinders its ability to monitor temporal dynamics related to seasonal variations  [8] [9] [10].
The characteristics of both products are summarized in Table 1  [15]. The Fontainebleau Forest is located at the intersection of ascending and descending orbits (relative no. 59 and 110, respectively) whose incidence angles range from 39-40°. Consequently, the temporal profiles shown over the different stands (Section 3. 2) combine measurements acquired during both passes. Both the radar backscattering coefficient σ 0 and the modulus of the interferometric coherence |ρ| were analyzed. After orthorectifying the passes  [16] , σ 0 was extracted from the GRDH products using python scripts  [17]  implemented in QGIS software and based on Orfeo Toolbox Software  [18]. These open-source tools, designed to process multiple Sentinel images automatically, can be used on a common PC (4 GB RAM) (A program to install the customized QGIS software in the Windows or Linux environments is available fromhttp://remotesensing4all.
The characteristics of both products are summarized in Table 1  [15]. The Fontainebleau Forest is located at the intersection of ascending and descending orbits (relative no. 59 and 110, respectively) whose incidence angles range from 39-40 •. Consequently, the temporal profiles shown over the different stands (Section 3. 2) combine measurements acquired during both passes. Both the radar backscattering coefficient σ 0 and the modulus of the interferometric coherence |ρ| were analyzed. After orthorectifying the passes  [16] , σ 0 was extracted from the GRDH products using python scripts  [17]  implemented in QGIS software and based on Orfeo Toolbox Software  [18]. These open-source tools, designed to process multiple Sentinel images automatically, can be used on a common PC (4 GB RAM) (A program to install the customized QGIS software in the Windows or Linux environments is available from http://remotesensing4all.
It characterizes the geometric stability, at a wavelength scale, of the elementary scatterers within a resolution cell. It is low over dense vegetation (in which elementary scatterers, i. e. , leaves and twigs, move with weather events, i. e. , rain and wind) and high over solid bare soils, such as rocky soils. Coherence was estimated from SLC data over a 11 × 3 local neighborhood (i. e. , N = 33 in rel. 1), yielding an approximately square area of ground (~42 × 44 m). A tutorial to calculate the interferometric coherence from IW SLC products with SNAP software is available in  [20].
Landsat-8 Data To analyze the sensitivity of radar data to vegetation phenology, radar temporal profiles were compared to the Normalized Difference Vegetation Index (NDVI) derived from bands 4 and 5 of the Landsat-8 optical Operational Land Imager (OLI) sensor. This sensor has a 180 km-wide swath, covering the globe every 16 days, and the spatial resolution associated with bands 4 and 5 is 30 m. Many studies have demonstrated the sensitivity of NDVI to photosynthetic green materials in the vegetation canopy. Consequently, NDVI is widely used for monitoring vegetation phenology. To correct atmospheric perturbations (which decrease NDVI values recorded from the top of the canopy), a maximum-value filter over a 48-day period (i. e. , three consecutive acquisitions) was used.
Temporal Profile Analysis To further analyze the temporal behavior of Sentinel-1 data over temperate forests, temporal profiles were extracted from March 2015 to December 2017 over different stands. On the whole, two main different classes of temporal signatures could be observed, depending on whether the species were deciduous or coniferous. We show here the temporal behavior observed over one mature stand of deciduous (oaks) and one mature stand of pine trees, which are representative of both classes. Figure  5  shows temporal profiles of σ 0 over the oak stand. Each point corresponds to the mean σ 0 of all pixels (~10,500) in each image of the stand. As previously observed 10], and unlike observations of bare soils over areas with little vegetation  [21] [22] [23] , we did not observe any direct relation between precipitation (or cumulative precipitation, or in situ soil moisture, not shown) and σ 0 profiles.
Conclusions Sentinel-1 data were analyzed for a temperate forest located near Paris, France. Two parameters were analyzed: the backscattering coefficient σ 0 , and the coherence|ρ|. Over the entire Ile de France region, σ 0 appeared stable over urban areas and showed large spatio-temporal variations over agricultural areas. Over the forest,  appeared relatively stable, while  had more pronounced variations. The coherence |ρ| had similar behavior to both VV and VH polarizations, and appeared stable over urban areas and forests but had distinct spatio-temporal variations over agricultural areas. Analysis of temporal signatures over deciduous (oaks) and coniferous (pines) stands showed distinct seasonality (with an annual amplitude of about 3dB) observed for the  / ratio over the oak stand. The similarity between  / and NDVI derived from the Landsat-8 OLI sensor confirms the sensitivity of the C-band to leaves and stems in the upper canopy.
Conclusions Sentinel-1 data were analyzed for a temperate forest located near Paris, France. Two parameters were analyzed: the backscattering coefficient σ 0 , and the coherence|ρ|. Over the entire Ile de France region, σ 0 appeared stable over urban areas and showed large spatio-temporal variations over agricultural areas. Over the forest, σ 0 VV appeared relatively stable, while σ 0 V H had more pronounced variations. The coherence |ρ| had similar behavior to both VV and VH polarizations, and appeared stable over urban areas and forests but had distinct spatio-temporal variations over agricultural areas. Analysis of temporal signatures over deciduous (oaks) and coniferous (pines) stands showed distinct seasonality (with an annual amplitude of about 3dB) observed for the σ 0 VV /σ 0 V H ratio over the oak stand.
Annotation was transferred from strain S26/3  [16]  to the genomes of AB7 and 1B using AnnotateBacteria [https://github. com/sanger-pathogens/Bio-AutomatedAnnotation/blob/master/lib/ Bio/AutomatedAnnotation/CommandLine/AnnotateBacteria. pm], as previously described  [19] , and manually curated using Artemis  [20]. Comparative genome analysis was performed using the Artemis Comparison Tool (ACT)  [21]. The AB7, 1B and 1H genomes were manually curated for the presence of pseudogenes, which were defined as having one or more mutations (frameshift, premature stop codon) that would ablate expression.
Nucleotide sequence accession numbers Genome sequences of AB7, 1B-Cevac and 1H have been deposited in EMBL under accession numbers LN554882, LN589721 and LN554883, respectively. Read data for AB7, 1B-Cevac, 1B-Enzovax, 1H, 6012, 6181, 10DC0084, 11-669_5380/2 and AB15 have been deposited in the European Nucleotide Archive (ENA, http://www. ebi. ac. uk/ena/) under accessions ERS200120, ERS200134, ERS067056, ERS200121, ERS200136, ERS200137, ERS067060, ERS200127 and ERS200131, respectively.
Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages.
important to better understand these interactions, is that it has been demonstrated that Staphylococcus aureus strains devoid of prophages ɸNM1-4 are either incapable of infection or have altered virulence patterns and that phages ɸ80α and ɸJB can mediate transfer of methicillin-resistance encoding plasmids between S. aureus strains  25, 26. Phage therapies have been investigated in mouse models for the treatment of Staphylococcus skin infections with some success  27  , and it is widely thought that this is a potential avenue for the treatment of a variety of bacterial infections. The modular nature of bacteriophage genomes and the limited robustness of existing databases limit the understanding of phage genome architecture and can lead to annotation as "multiple hits" instead of a single species during taxonomic assignment during metagenomic data analysis  20.
Adding new phage genomic information, especially complete phage genomes, to these databases will help with future studies of these skin microbial populations. Most of the published studies have been performed on American, European and Asian skin types  19, 20, 28  , whereas our study represents the first that investigates phages on skin from African inhabitants (participants were predominantly of African and mixed ancestry). Here, we took a semi culture-independent approach to better understand the potential composition of phage communities on skin from six South African male study participants, sampling the scalp, axilla and forearm, which are representative of the three main ecosystems of the skin (sebaceous, moist and dry respectively). We looked at the phage genome architectures of some of the phages that infect bacteria from the skin which may have clinical relevance and how they differ from those currently known.
One ng of uncloned, unamplified viral DNA was used to prepare one NexteraXT library per sample. The resultant libraries were sequenced using the Illumina MiSeq at the University of the Western Cape generating 2 × 300 bp reads per sample. The raw reads were trimmed (bases with a Q-score less than 36 were trimmed from the 3′ end) and demultiplexed at the sequencing facility. Assembly of read data, phage annotation and comparison. Read data was assembled using CLC Genomics Workbench version v7. 5. 1 (Qiagen, http://www. clcbio. com) with the length fraction set at 0. 8 and similarity fraction at 0. 9. Mismatch insertion and deletion costs were left at their default values. The "global alignment" and "update contigs" settings were enabled, while scaffolding was turned off. Word-and bubble size was set to automatic mode as well as paired distance detection.
As we were expecting to recover complete phage genomes due to viral enrichment, only contigs above 2. 5 kb were considered for analysis. The assembled contigs used in the analysis presented here were submitted to the GenBank database under accession numbers MF417837-MF417995. Reads from various metagenome and metavirome studies were mapped to our phage contigs using the built in "map reads to reference" function in CLC Genomics Workbench. The same length and similarity fraction parameters mentioned above were used for read mapping of these datasets to our phage contigs. Non-specific match handling was set to "ignore" and no mask was applied. Mismatch, insertion and deletion costs were left at the default settings. The SRR file names from metavirome and metagenome datasets used for read mapping against the contigs identified here are provided in Table  S3  while the "Earth's virome" contigs are available at http://portal.
nersc. gov/dna/microbial/prokpubs/EarthVirome_DP/. All contigs recovered after de novo assembly were screened using Virsorter to identify true phage contigs among those generated after assembly using the Viromedb as selection criteria  32. In parallel, contigs were uploaded to MetaVir 2 for analysis  33. For more complete annotation of individual contigs PHAST (database update December 23 rd , 2016), which includes prophage sequences, and MetaVir2 were employed together with manual curation in CLC Genomics Workbench  34, 35. For those contigs not recognized as phage or prophage by VirSorter, manual inspection of contigs searching for the presence of "viral keywords" (terminase, capsid-, head-; tail-, portal-, sheath-, tape measure-, phage replication-protein) was performed to ensure that no genuine phage contigs were missed.
For those contigs where no "viral keyword" genes could be identified, the relation to phage was estimated based on the relation of encoded proteins to known phages using the MetaVir 2 parameters (comparison against RefseqVirus with a threshold of 10 -3 on e-value and 50 on bitscore). All contigs identified as phage or prophage by VirSorter were used in downstream analysis. For taxonomic classification of the phage contigs, MetaVir 2′s annotation was used and Kronatools was used for visualization of taxonomic composition  36. The taxonomic affiliation was used to generate a network for visualization of the presence or absence of related phages in the various samples performed with Cytoscape v3. 4. 0 (http://www. cytoscape. org/). Phage genomes were compared using Easyfig  36. Using the protein sequences identified by MetVir 2 and PHAST as well as the nucleotide sequence of the contig GenBank formatted files are created using Sequin (https://tinyurl.
com/y7g3rd9c) then manually edited in DNA Master (http://cobamide2. bio. pitt. edu/computer. htm) and then used for comparison in Easyfig. Manual pairwise alignments were performed, and the final figures constructed to display the closest relationship between pairs of phage genomes. Cluster analysis was performed with Primer v6, following conversion of phage taxonomic affiliation to presence/absence data  37. Amino acid sequence concatenation was performed using SequenceMatrix v1. 8  38. Sequence alignment for phylogenetic tree construction was performed with the MUSCLE program included with the MEGA 6 software package  39  , and the tree constructed using the neighbour-joining method. Potential CRISPR sequences were identified through BLASTn against the CRISPR database on CRISPR finder using the default BLAST settings (E-value of 0.
Results and Discussion Overall description of the enriched skin metavirome and diversity analysis. The first step in the analysis of this enriched metavirome was the direct observation of phage particles from the enriched culture broth (Fig. 1 ). As expected, the samples were dominated by tailed phages with Sipho-and Myoviruses predominating based on tail morphology. Of the 18 sequenced samples, two datasets were not informative (2S, 3AX, Supplementary Table  S1 ). The total dataset contained 17. 4 million reads, with 964554 reads per sample on average. Of the total read dataset, 8. 3 million reads are represented by the contigs described here. Sample 2 S sequenced poorly, while 3AX consisted mainly of Bacillus pumilus genomic DNA. A total of 1391 contigs were analyzed with VirSorter, resulting in 115 (112 categorized as phages and 3 as prophages) contigs being retained as phages or prophages.
If these pairs are considered to belong to the same genome, this reduces the number of singletons to 56. There is the possibility that due to low similarity to related phages and the inability to join the contigs, more of these associations may have been missed here, making our number of unique phages an upper limit for this dataset. If contigs that cluster together according to the vConTACT analysis are considered to belong to a single phage "species", the diversity of phages shared among individuals and body sites  11  was much lower than the number of unique contigs/phages  42  (Fig. 2A ). This is in agreement with other studies that show high interpersonal and inter site variation in the viral metagenome. However, unlike other studies, our data points out that there is a small group of highly similar, if not identical, phages shared between most individuals and the three body sites analyzed.