dataesr/scientific-paragraphs-categorization huggingface dataset:
Availability of supporting data The data sets supporting the results of this article are available in the GenBank and TreeBase repositories, under accession numbers AUXH00000000, AUXI00000000, AUXJ00000000, AUXK00000000, AUXL00000000, AUXM 00000000, and AUXN00000000 (genome sequences of S. culicis, C. acanthocephali, H. muscarum, S. oncopelti, A. desouzai, A. deanei, and S. galati, respectively), and S14564, for the sequence alignments and phylogenetic trees (http:// purl. org/phylo/treebase/phylows/study/TB2:S14564).
Introduction RFID provides a way to connect the real world to the virtual world. An RFID tag can link a physical entity like a location, an object, a plant, an animal, or a human being to its avatar which belongs to a global information system. For instance, let's consider the case of an RFID tag attached to a tree. The tree is the physical entity. Its avatar can contain the type of the tree, the size of its trunk, and the list of actions a gardener took on it. When designing an RFID-based application, a system architect must choose between three locations to store the information: a centralized database, a database locally attached to the device hold by each user of the application, or the tag itself. Each location leads to an RFIDbased architectural pattern 1. But how to choose the right architectural pattern? What are the application attributes which must be taken into account in order to make the right choice? The state of the art does not bring satisfactory answers.
Indeed, when an article describes a RFID-based architectural pattern, it does not mention the application attributes which lead to choose this architectural pattern. On the other hand, some books or articles present the qualities of architectural patterns. But they do not take into account specificities of RFID. For instance, EPCglobal provides a standardized answer  [2] : the centralized architectural pattern. A mobile device, NFC-enabled for example, reads an identifier on the RFID tag, then sends a message to a server which associates the identifier to the avatar stored in a central database. Thanks to its simplicity, this architectural pattern is used by several applications. But, it requires a global computer network: Such requirement increases operational costs. Moreover, it does not withstand an important number of simultaneous RFID read operations.
Thus this pattern does not fit all RFID-based applications. [3]  presents the stakes of introducing RFIDs inside an enterprise. But it does not contain any system architecture thoughts. In a survey about RFID in pervasive computing,  [4]  presents several application examples. Depending on the application, avatars are stored either in a central database or in the tags themselves. But the authors do not give any clues on why an application has chosen to store its avatars in a given location. On the other hand,  [1]  lists the attributes which must be accommodated in a system architecture. Above all, there are the functionalities which are required from the system. Then, orthogonal to these functionality attributes, there are quality attributes. The authors distinguish system quality attributes (availability, modifiability, performance, scalability, security, testability, and usability), business qualities (time to market, cost and benefits, and projected lifetime), and qualities about the architecture itself (e.
g. conceptual integrity). But the authors do not focus on RFID specific features. So we have analyzed several existing industrial or experimental RFID-based applications. Moreover, we have developed RFID-based applications. From this experience, we identify the relevant attributes to compare RFID-based architectural patterns. We present them in section 2. With these identified attributes and their different aspects, we analyze four RFIDbased architectural patterns, used by applications to access the avatar of a tagged entity. In the centralized architectural pattern, the mobile device reads an identifier on the RFID tag; then it contacts a server which associates this identifier to the avatar stored in a central database or in a database distributed between several companies  [2]. With the semi-distributed architectural pattern, each mobile device holds a local copy of a central database associating RFID identifiers to avatars  [5].
Centralized architectural pattern This architectural pattern is often used by manufacturing applications. It has been standardized by EPCglobal  [2]. When a reader is near a tag (for instance, the blue mobile in Figure  1 ), it reads the tag's identifier or an identifier stored in the tag's data zone (its Electronic Product Code in the case of EPCglobal). This identifier is represented by the hexagon in Figure  1. Then, the reader asks a server (ONS lookup service in the case of EPCglobal) which machine (EPC Manager in the case of EPCglobal) manages the avatar corresponding to the read identifier. When the server responds, the reader contacts this machine with the identifier of the tag. The machine queries its database and returns the avatar (for instance, the contents of the hexagon in the database in Figure  1 ).
Examples Aspire RFID is an Open Source middleware which is compliant to the specifications of EPCglobal  [8]. It proposes several examples of industrial applications for tracking goods. Next paragraphs present products or prototypes developed according to centralized architectural pattern, but without being compliant to EPCglobal. PAC-LAN is a game prototype in which players are equipped with NFC mobile phones without any GPS capabilities  [9]. Players must interact with NFC tags which have been disseminated throughout a neighborhood. In a central database, the identifier of each tag is associated to geographical coordinates. When a player reads a tag, her mobile phone uses the UMTS network to contact the server with the tag's identifier. The server queries its database, finds the geographical coordinates, and broadcasts them to all of the players.
An administrative application is provided to reset a game on the server. Such reset has an impact on all of the players' mobile phones. [10]  proposes an application so that visitors of an art exhibition can discover the paintings in another way. NFC tags are dispatched on the back of exposed paintings. Equipped with an NFC-enabled phone, the visitor puts her phone on spots of the paintings which intrigue her. Phone reads the identifier stored in the tag. Then, it contacts an uGASP server  [11] [12]. After consulting an internal database, this server indicates to the mobile phone what must be done: display a text, an image, or play an audio comment. Thus the author of the painting is able to communicate with the visitor. Via Mineralia is a pervasive serious game which goal is to enrich the visit of a Freiberg museum  [13].
Then, via the Internet network to which the computer is connected, this application contacts a Touchatag service called Application Correlation Service (ACS). Touchatag application gives tag's identifier to ACS. Then, ACS queries Touchatag database to find reaction associated to the reading of this tag. It sends back this information to Touchatag application. The touchatag application reacts in the appropriate way. For instance, let's assume that the customer has specified the following action on Touchatag web site: when tag r with identifier i is put on the reader, customer wants her browser to access to Uniform Resource Locator (URL) of a web site w. Then, when customer puts tag r on the reader, Touchatag application contacts ACS with identifier i. ACS replies with URL of w. Then, Touchatag application opens a browser with this URL w.
Analysis Concerning the functional attribute, any transponder which wants to modify the avatar of a tag does so by sending a modification message to the server. Thus the server is always aware of the last update done on any avatar. As a reader always queries the central database to know the avatar of a tag, it is not possible that the read value is stale. Moreover, knowing a tag identifier, a reader is able to query the server to know the avatar associated to this identifier: the reader is able to know the avatar of a remote tag. As a mobile device queries the server to know the avatar of a remote tag, it is sure that the returned value is not stale. Concerning the scalability attribute, the maximum number of tags which can be handled by this architectural pattern is limited by the number of avatars which can be stored in the central database.
Let s be the average size in bytes of an avatar. Let S central be the maximum size in bytes of the database. We neglect the storage of the link between tag identifiers and avatars in the database. Moreover, we neglect the overhead due to the storage of data in the database. Then, the maximum number of tags is bounded by S central /s. About sensitivity to the number of simultaneous reads, this architectural pattern is restrained by its centralized nature. The server holding the ONS lookup service may become a bottleneck. Moreover, the different servers of avatars may not return avatar values fast enough. Of course, it is possible to increase the number of servers. But that makes the hardware architecture more complex and more costly (from an installation and a management point of view). Thus this architectural pattern may not be applicable for some applications.
Concerning the cost attribute, the reader must always be in contact with the server holding the ONS lookup service and the servers of avatars: a global network is required. On the other hand, this architectural pattern only needs to read an identifier on the tag. And this identifier can be stored in ROM as it is never modified: no RAM is required on the tags. When a new tag is introduced in the system, three operations are required: (i) the tag is linked to the physical entity; (ii) the avatar of this entity is initialized in the central database; and (iii) a link between the tag identifier and this avatar is created into the central database. When all of the tags have to be reinitialized, a program is run on the server hosting the central database. It sets each avatar to its new value. This section has analyzed centralized architectural pattern according to the attributes presented in section 2.
Semi-distributed architectural pattern In semi-distributed architectural pattern, mobile RFID-enabled devices (PDAs, mobile phones, etc. ) are periodically synchronized with a central database holding all of the avatars (see Figure  2 ). Then, human operators carry the mobile devices near the entities to which the tags are associated. When a device comes close to an entity, the device reads the identifier of the entity's tag. By querying its local copy of the central database, the device is able to find the avatar of this entity. Any modification of an avatar is done on the local copy. It is propagated to the central database at the next synchronization. Next section presents an example of this architectural pattern.
Example The unique example of use of such architectural pattern is Paris trees management application  [5]. Each of the ninety-five thousand trees of Paris avenues is equipped with an RFID tag. Each gardener synchronizes her tablet PC with the central database before a new day of work. During her day of work, whenever a gardener does something to a tree, she identifies the tree thanks to its RFID tag: Her tablet PC modifies the avatar in the local database. Then, in the evening, she synchronizes her tablet PC with the central database. Thus she uploads her database updates and downloads updates from other gardeners. Now, let's analyze the semi-distributed architectural pattern.
Analysis Concerning the functional attribute, the avatar of a read tag may be stale. Suppose users U 1 and U 2 synchronize their mobile device with the central database. Then U 1 modifies avatar of tag r. Thus she modifies her local copy of the database. When U 2 comes to tag r, as her device reads its local copy of the database, the returned value of the avatar is the value before U 1 's modification: the read value is stale. Notice we can limit this issue by assigning sets of entities to each mobile device. For instance, in the case of the Paris trees management application, a supervisor can assign a set of trees to be taken care of during the day, to each of the gardeners. If all of these sets are apart, this issue cannot be observed anymore. About remote tags, by querying its local database, the device is able to read the avatar of a remote tag, even though there is no global network.
But the read value can be stale. It will be again correct only when all of the mobile devices have synchronized themselves with the central database. Concerning the scalability attribute, the maximum number of tags which can be handled by this architectural pattern is limited by the number of avatars which can be stored in the central database and in the local copy of this database. Let S local be the maximum size in bytes of the local database. The maximum number of tags is bounded by min(S central /s,S local /s), which is likely to be S local /s as mobile devices do not have as much memory as servers. Notice that this bound can be increased to S central /s by assigning to each mobile only a subset of the central database. For instance, in the case of Paris trees management application, the mobile device of a gardener could receive only the avatars of the trees she will take care of during the day.
About sensitivity to the number of simultaneous reads, this architectural pattern is not as sensitive as centralized architectural pattern. It does not need to query a server upon each RFID tag read. Nevertheless all of the readers must periodically synchronize themselves with the central database. As the synchronization time is proportional to the number of readers, it may reach unbearable values. This issue can be tackled by limiting the number of avatars copied on the local devices, thus reducing the volume of data transferred between each device and the central database. Concerning the cost attribute, the mobile RFID-enabled devices only need an access to the server hosting the central database during synchronization phase. At that moment, devices are probably near the central database: A Wi-Fi network may be used.
Otherwise it is the local database which is queried. Thus no global communication network is required around the working area. Moreover, as in centralized architectural pattern, there is no need for RAM on the tags. When a new tag is inserted in the system, the procedure to be applied is the same as in the centralized architectural pattern. When all of the tags have to be reinitialized, a program is run on the server hosting the central database. It sets each avatar to its new value. However, the reinitialization of the tags will be effective only when all mobile devices will get synchronized with the central database. This section has analyzed semi-distributed architectural pattern according to the attributes presented in section 2. This architectural pattern does not require any global network and has a medium sensitivity to the number of simultaneous tag reads.
Concerning the cost attribute, in RFID-based DSM architectural pattern, the reader does not need any global network to access to the avatar of the RFID tag. Nevertheless RAM is required on each tag. Its size must be at least the size of the avatar times the number of tags in the environment (so that a tag can hold a local copy of all avatars). This means that the avatar can contain even less information than in the case of distributed architectural pattern. When a new tag is introduced in the system, four operations are required: (i) the tag is linked to the physical entity; (ii) the avatar of this entity is created and initialized in DB init , the database used to (re)initialize the local copy on each mobile (DB init is stored on a dedicated machine which can be one of the mobiles); (iii) a link between the tag identifier and this avatar is created in DB init ; and (iv) all of the elements of the tag's vector clock are initialized to zero.
Initializing the avatar is done in a few milliseconds by an initialization program. For reinitializing tags, synchronizing all of the 8 mobiles with a dedicated machine takes about 1 minute, that is an average of 4 seconds per tag. Notice that synchronization is based on NFC peer-to-peer communication. The project could have saved synchronization time if it has used Bluetooth®, but it would have used more battery. If the project is going to use centralized or semi-centralized architectural pattern, it will use a dedicated machine for hosting the central database. This machine will be equipped with a 500 gigabytes disk (S central =500 GB). In the case of the semi-distributed architectural pattern, the project will use half of the micro-SD memory of each mobile phone to host the local copy of the database (S local =1 GB).
a. Yes Maximum number of tags S central /s S local /s Infinite S tag /(s+L) Sensitivity to number of simultaneous reads High Medium None Medium Network required Yes No No No RAM required on tag No No Yes Yes Cost of introducing a tag (most costly operation) Link tag to Link tag to Link tag to Link tag to physical entity physical entity physical entity physical entity Cost of reinit. Tags (most costly operation) Reinit. Database Sync. Database Go to all tags Sync. database.
2005) , and the second SEEDS (SEEDS II;  Tsumune et al. 2009) , were all performed, adopting the older technique first developed for the IronEx project  (Law et al. 1998). Minor modifications to this strategy were then implemented within the Subarctic Ecosystem Response to Iron Enrichment Study (SERIES) experiment  (Law et al. 2006) , during which the Lagrangian tracer release was coordinated using the Electronic Chart Precise Integrated Navigation System (ECPINS) package. This is a commercial search and rescue computerized package for shipboard navigational aid that displays electronic charts and the ship's position in real time along with sensor data (http:// osigeospatial. com/offshoresystems/pdf/OSI_ECPINS-5000. pdf). To our knowledge, no other papers report detailed descriptions of the techniques and software adopted for Lagrangian tracer release and sampling strategy, although they are a key point for the success of in situ tracer experiments.
Hence, the expanding square spiral route was chosen for the Latex10 cruise. The signal range and communication delay problems of the Argos system described above led us to take into consideration the Iridium transmission system. The Iridium network covers the whole earth thanks to a satellite constellation mainly used for hand-held phone communications. In 2007, at the beginning of our project some manufacturers were beginning to develop Iridium buoys. Indeed, MetOcean provided Iridium Surface Velocity Program (SVP) drifters. Nevertheless, (i) the MetOcean buoys sent data once per hour, (ii) the transmission frequency was not adjustable, (iii) there was no receiver to receive messages directly on board, and (iv) there was no possibility to remotely change the buoy setup. Therefore, we decided to develop our own prototype buoy with an Iridium transmitter/receiver (Fig.
The entire package for MATLAB is distributed in the hope that it will be useful for the oceanographic community and it can be freely downloaded (from http:// mio. pytheas. univ-amu. fr/;doglioli). Future foreseeable developments include the possibility to take more advantage of the bidirectional Iridium communication, by implementing an automatic position query to the reference buoy when the vessel is near turn points. Moreover, as already mentioned in section 2, multibuoy marking of the water mass could also be considered for (i) a more precise positioning of the center of the Lagrangian reference frame and (ii) an estimation of rotation and stirring effects of the investigated water mass.
A New Mitochondrial Gene Present only in Sterilizing Cytoplasms The above results suggested that the cytoplasm of Kz-9, although non-sterilizing, is closely related to that of Sha. We explored high-throughput sequencing data available for Sha  [28]  (www. 1001genomes. org) for predicted polymorphisms in chloroplast and mitochondrial genes (mainly in exons), and checked them by sequencing the corresponding regions in Sha and Kz-9. We sequenced 11 chloroplast fragments and 24 mitochondrial fragments (,24 kb in total). Among 69 verified polymorphisms (16 in the chloroplast and 53 in mitochondria), only three positions (2 in the chloroplast and 1 in the mitochondria) differed between Sha and Kz-9. The mitochondrial variation destroyed an EcoRI site in the rpl5-cob intergenic region of Sha (see below).
With the atp8 probe, Sha displayed the expected profile, whereas that of Kz-9 was different. The sequence of the rearranged regions in Sha and Kz-9 (EMBL accessions HF543671 & HF543672, respectively) showed that the regions downstream of orf122c and upstream of atp8 were in close vicinity in both accessions. Therefore, all the mitochondrial structural variations detected in DNA hybridization experiments pointed to the same single region (Figure  4A ). The Sha sequence showed the additional presence of 1025 bp from the cob-rpl5 intergenic region (59201-60225) and contained 400bp of unknown origin (no hits in the public nucleotide databases after a Blast search). Interestingly, this unknown fragment contained an ORF potentially encoding a peptide of 117 amino acids, that we named orf117Sha. The predicted ORF117SHA peptide was found 56% identical and 69% similar to the ORF108 peptide of the Moricandia arvensis mitochondria, suspected to induce male sterility in Brassica juncea  [31]  (Figure  4B ).
Plant Material Arabidopsis thaliana accessions used in this study were obtained from the Versailles Arabidopsis Stock Centre (http://www-ijpb. versailles. inra. fr/en/cra/cra_accueil. htm). Monte-Rosso (Mr-0) is misspelled 'Monte-Tosso' in most stock centers. 598 accessions were previously genotyped with 341 nuclear SNP polymorphisms, among which our worldwide panel of 240. The clustering analysis of the whole dataset resulted in an optimal cluster number of K = 4, thus defining four nuclear genetic groups, among which group 1 predominantly contained accessions originating from Central Asia and Russia  [24]. The complete neo-Sha population was kindly provided by Olivier Loudet. It has been partially described in  [32, 50]. Information on this population is available at http://www. inra. fr/vast/collections.
Organelle SNP Analysis We recovered predicted SNPs with a quality score of 20 or more for the Sha chloroplast and mitochondrial genomes on the 1001 genome database (http://1001genomes. org/data/MPI/ MPICao2010/releases/current/strains/Sha/). As some polymorphic positions appeared ambiguous, we also recovered the raw data of the Sha Illumina sequencing  [28]  and aligned them onto the reference sequences for A. thaliana chloroplast (NC_000932) and mitochondrial (NC_001284) genomes using BWA  [54]. Alignments were visualized using IGV (Integrative Genomics Viewer) software (http://www. broadinstitute. org/igv) and the polymorphic positions were checked manually. This survey also detected predicted polymorphisms that had not been previously predicted, such as small (1-4 bp) insertions. Whenever a predicted polymorphism was located in an exon, we developed PCR primers to check it by sequencing (Table  S7 ).
Open reading frames are represented by arrows indicating the direction of translation. Horizontal brackets show parts that were sequenced (EMBL accessions HF543671 & HF543672), the corresponding positions of endpoints in the reference sequence are given in parentheses. B. Peptide alignment between ORF117SHA and ORF108. One-letter-code sequences of ORF117SHA predicted peptide and ORF108 [31]  were aligned with Clustal 2. 0. 3 at phylogeny. fr [56] and the alignment was edited with Jalview [57]. Identical residues are shaded, residues with similar physicochemical properties are boxed [58]. doi:10. 1371/journal. pone. 0062450. g004.