dataesr/scientific-paragraphs-categorization huggingface dataset:
The semantics and its abstractions lend themselves well to being implemented in the proof assistant Coq. This is an important point, as some form of mechanization is required to evaluate the scalability of the method. Scalability is indeed one of the goals for this work. The present paper establishes the principles with which we hope to achieve the generation of an analysis for full JAVASCRIPT based on its Coq formalization. However, this will require some form of machine-assistance in the production of the abstract semantics. The present work provides a first experience of how to proceed. Further work will now have to extract the essence of this process and investigate how to program it in Coq. One this has been achieved, we will be well armed to attack other analyses. One immediate candidate for further work is full information flow analysis, taking indirect flows due to conditionals into account.
Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France. Conclusions: The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages.
Complementing mtDNA datasets with biparentally inherited nuclear DNA (nDNA) marker data is often essential to obtain a more complete picture of lineage history  [11, 21]. Here we undertake a multilocus phylogeographic survey across the region using both mtDNA sequences and genome-wide AFLP loci and an improved geographic sampling in order to document the presence and distribution of major genetic lineages and test the role of the Pyrenees and the Cantabrian Mountains in driving lineage divergence in Z. vivipara. We also use this largescale phylogeographic context to assess patterns of introgression and test hypotheses related to the history of contact zones.
Mitochondrial DNA structure and diversity Sequencing of 200 individuals of Z. vivipara from 48 localities (Table  1 ) revealed 14 cyt-b and 29 ND2 haplotypes, for a total of 33 haplotypes for the concatenated dataset  (1,370 bp). Phylogenetic analysis revealed two major clades corresponding generally to southern France and northern Spain, respectively (Figures  1  & 2A ). The Spanish clade is further divided into three major subclades, including a NW Spain clade (Western Cantabrian Mountains), a north-central Spain clade (Eastern Cantabrian Mountains and Basque Country) and a NE Spain clade (Pyrenees) (Figures  1  & 2A ). Lizards carrying haplotypes from the latter clade were also found on the French slope of the Pyrenees, where they were found sympatrically with the divergent French clade haplotypes (Figures  2A  and 3A ).
The pattern of haplotype frequency and distribution of the The first letter of each haplotype designation corresponds to the ND2 haplotype, and the second one to the cyt-b haplotype. For the GenBank accession associated with each haplotype see Additional file 1: Table  S1. NE Spain (blue) clade reflects higher haplotype diversity on the Spanish side of the Pyrenees than on the French side, where the relative frequency of haplotype "AA" is more pronounced. This pattern, together with the evidence for a recent population expansion in this lineage, suggests that the presence of Spanish haplotypes on the French side is the result of a trans-Pyrenean colonization of the French side. We estimated time since the population expansion from the distribution of pairwise differences among blue-clade haplotypes, which yielded a value of τ = 3.
30 (P < 0. 001), with Φ PT values between the yellow cluster and other eastern clusters ranging from 0. 32 to 0. 41 (Table  5 ). None of the 34 loci showed significant departures from neutrality in the BAYSCAN 2. 0 analysis across all comparisons, although one of them (locus "15c194") was identified as an outlier in the K = 2 comparison, and another one (locus "19c84") in the K = 3 and K = 4 comparisons (Additional file 1: Figure  S2 ). Excluding these two loci from the dataset yielded results for the Structure analysis and the PCoA analysis in GENALEX that were indistinguishable from those using all loci. This is due to the fact that most markers in these comparisons had F ST values above 0. 20 (mean across-loci F ST-K2 = 0. 27, SD = 0. 01; Mean F ST-K3 = 0. 25, SD = 0. 01; Mean F ST-K4 = 0.
Discussion Phylogeography and mtDNA lineage history Our mtDNA dataset revealed four major clades and a remarkable degree of geographic structuring among Zootoca vivipara lineages. The high variation found in the ND2 gene relative to cyt-b, together with a more thorough geographic sampling allowed us to identify several distinct and geographically segregated clades in northern Spain, which help explain their historical interactions with the divergent clade found in southern France and clarify the phylogeographic history of the region. In line with previous phylogeographic studies on the species, our study shows that populations of Z. vivipara at the Ibero-Pyrenean zone do not show an actual "suture zone" between Iberian and northern European lineages  [8, 24] , in sharp contrast to patterns found in other species, like the grasshopper Chorthippus parallelus  [25]  or the warbler Phylloscopus collybita  [26].
AFLP structure: contrasting patterns with mtDNA The pattern of spatial variation in genome-wide AFLP markers revealed both important similarities and differences compared to that of mtDNA sequence. Both datasets revealed the presence of four genetic units that are geographically concordant, yet relative divergence among groups differs in both datasets. AFLP variation forms two main genetic groups that separate NW Spain from the rest, while the two main mtDNA clades separate Spain from France. This difference suggests that at a large geographic scale different neutral and/or selective factors have shaped diversity and structure in both types of markers, yet identifying the specific cause is beyond the scope of our dataset. Potential causes range from neutral factors such as random sorting of loci or chromosomal rearrangements, to the role of natural selection.
Conclusions Our results show that lineages of Z. vivipara in northern Iberia and the Ibero-Pyrenean suture zone show marked levels of differentiation that is congruent with major topographical features in the region. Our data reveal that mountain ranges do not necessarily represent impassable barriers for this species, as demonstrated by a recent high-elevation colonization event across the Pyrenees that has led to secondary contact and partial introgression among divergent lineages. In contrast, we find indirect evidence of contact zones in lowland areas, in the absence of obvious barriers to dispersal. Our results underscore the importance of multilocus datasets in reconstructing the evolutionary history of independent intraspecific lineages  [57] , and understanding the dynamics of introgression upon secondary contact.
For most analysis, the two gene fragments (cyt-b and ND2) were concatenated into a single sequence of 1370 bp. Haplotype and nucleotide diversity indices were calculated in DNASP V5  [62]. We constructed a haplotype network using a maximum parsimony algorithm as implemented in the program TCS 1. 21  [63] , setting minimum branch probability at 95%. We used JMODELTEST  [64]  to determine the model of sequence evolution for each marker (HKY + G for ND2 and HKY + I for Cyt-b) and obtained an optimal partitioning scheme for the dataset (by gene and by codon position) using the sotware package PartitionFinder  [65]. We then constructed a phylogeny of mtDNA haplotypes using Bayesian analysis with MRBAYES 3. 2. 2 (http:// mrbayes. csit. fsu. edu/) [66] , and ran two simultaneous parallel runs of four Markov chains each (3 heated and one cold) for 4 million generations and sampled every 100 generations.
The first 25% of the trees were excluded as burn-in, and a consensus topology was obtained from the remaining 60,002 samples (30,001 per run). We confirmed MCMC chain convergence using TRACER v1. 5  [67] , and output parameters such as an average PSRF value of 1. 00, and an average value of 0. 0035 for the standard deviation of the split frequencies between simultaneous runs. To estimate divergence times among lineages we used a coalescence approach that uses Bayesian inference and MCMC simulations to generate posterior probability values for divergence times as implemented in the program BEAST  [68]. We partitioned our dataset by gene and codon position, and ran the analysis with unlinked substitution and clock models for each partition, yet generated a single tree from both. We conducted preliminary runs using an uncorrelated relaxed lognormal clock to account for rate heterogeneity among lineages, but obtained a value of zero for the ucld.
stdev parameter, indicating that our data are clock-like. We therefore used the strict clock in the final analysis, as well as a coalescent model of diversification, and a UPGMA starting tree. After optimizing the priors with preliminary runs, we conducted two final runs of 20 million generations, sampled every 2000 steps. Chain convergence and burn-in were determined with the program TRACER v1. 5  [67] , and all ESS values in the final runs were above 600. As a prior for the mutation rate we used a value of 0. 0228 subst. /site/Myr (0. 0114 s/s/Myr per lineage) for Cyt b, a rate estimated from a comprehensive phylogenetic study of several squamate groups  [69]  that used as time calibration points the known age of the Canary Islands and the opening of the Strait of Gibraltar 5. 3 Mya, well known geological events that have been associated with speciation events in several reptile and amphibian species  [70, 71].
Selectively amplified fragments were run in an ABI 3730XL genetic analyser with a LIZ500 size standard. Peaks were visualized using GENEMAPPER 3. 7 and scored manually by a single observer (BM). Only unambiguously scorable loci and individuals were included in the analysis and peaks found in less than 2% of individuals were excluded. Methodological error rate was assessed by running a subset of 10 individuals twice from the pre-selective amplification step. The average per-locus genotyping error rate for the AFLP loci selected, measured as recommended by Bonin et al. [79] , was low at 1. 2%. To determine whether AFLP markers were selectively neutral, we conducted an outlier analysis using the program BAYESCAN 2. 0, which uses differences in allele frequencies between populations and a reversiblejump MCMC algorithm to estimate the locus-specific posterior probability for a model including selection vs.
a neutral model  [80]. We used 10,000 iterations, a thinning interval of 100, 40 pilot runs, an additional burnin of 5,000, and a value of 10 for the prior odds for the neutral model  [80]. We estimated allelic frequencies using Zhivotovsky's  [81]  Bayesian method with uniform prior distributions and assuming Hardy-Weinberg genotypic proportions. Genetic diversity (H e ) was based on allele frequencies calculated using the method by Lynch and Milligan  [82]  as implemented in the program AFLP-SURV v. 1. 0  [83]. A matrix of pairwise population F ST values using the F ST analogue Φ PT was calculated with GENALEX 6. 0  [84]. Φ PT is calculated as V AP /(V AP + V WP ) where V AP is the variance among populations and V WP is the variance within populations. Probability values of pairwise Φ PT were based on 10,000 permutations.
To assess genetic structure among samples we conducted a principal coordinate analysis (PCoA; Orloci  [85] ) on a genetic distance matrix generated from the binary presence-absence matrix as implemented in GENALEX 6. 0. [84]. We further examined patterns of population structure using the Bayesian assignment probability test in the program STRUCTURE 3. 1  [86]. This program uses a Bayesian approach to generate posterior probabilities of assignment of individuals to each of a given number of groups (K). As recommended for dominant markers, we applied a model of no admixture with correlated allele frequencies  [23] , and used the Locprior setting, which incorporates sampling locality as a prior without affecting the value of the optimal K  [87]. We run five different chains of 1,000,000 steps for each value of K after a burn-in of 100,000 steps.
Acknowledgements Comments by three anonymous referees and the subject editor improved previous versions of the manuscript. We are grateful to  G. Perron  ( Parc National des Pyrénées ) for providing authorizations to collect tissue samples in the Ossau Valley. BM was funded by an  I3P  postdoctoral grant from the  Spanish Research Council (CSIC) , and  PSF  by a grant from the  Spanish Ministry of Education and Science (Programa Ramón y Cajal ,  RYC-2003-006136 ). BH was funded by the  French National Research Center (CNRS). YSG was financially supported by the  European Community 's programme 'Structuring the  European Research Area ' under SYNTHESYS at the  Museo Nacional de Ciencias Naturales (CSIC) , contract number  ES-TAF 5305. The project was financed by two grants from the  Spanish Ministry of Education and Science  ( CGL2005-01187 ,  CGL2008-01522 ) and the  Swiss National Science Foundation  ( PPOOP3_128375 ) to PSF.
C. The Communication module The Communication module implements basic functions to facilitate communications, over TCP or UDP, among WUW instances at different peers. Moreover, an epidemic protocol is provided to disseminate among the peers: user intentions, user public profiles and additional data related to content dissemination, e. g. the number of content items at each peer. The epidemic dissemination of up-to-date information makes it possible for any local user to know what are the recently computed intentions of remote users towards her and what is the state of the diffusion of a given content. The overlay used by the epidemic protocol is different from the content distribution overlay and it is locally maintained at each peer with negligible overhead. The delay between the local generation of an updated descriptor and its fruition by remote peers, modeled by the known properties of the epidemic protocols  [20] , can be modified by tuning the parameters of this module.
D. The P2P Handler module This module is the only part of WUW that is aware of the specific P2P application being used by the local user. The interfaces provided by this module allow other modules to transparently exchange information with a specific distribution protocol. The P2P Handler module contains the logic that defines content items and their parts in a way that is consistent with the P2P application. It comprises all that concerns the specific way WUW get information from and gives information to the rest of the P2P system. This includes the communication with the P2P overlay manager, concerning the global list of peers sharing a given content. For each content being shared and for each neighbor in the overlay, the P2P Handler module retrieves data about any distinct download or upload event from/to a given neighbor, related to a given item.
E. The Core module The main functionalities of WUW are placed in this module, which is the orchestrator of the service. User intentions and feedback measures are computed in a timely way. Every n seconds, a routine is started which performs the following steps: 1) Get updates about the remote users from the Communication module. 2) Get the latest information about the activity of the local P2P application from the P2P Handler module. 3) Get the latest changes in the users preferences from the UI Handler module. 4) Update the local state with the collected information. 5) Compute the feedback measures related to the latest local activity, considering the current intentions for all the neighbors and all the contents. 6) Make the feedback measures available to the local user via the UI Handler module.
7) Compute the intention values to be associated to every neighbor for every content, according to the local strategy. 8) Build a global ranking of all neighbors, considering the associated intentions for all the contents. 9) Create a LBP for each content currently shared by the local user. 10) Send the LBP s to the P2P application, via the P2P Handler module. By repeating this routine periodically, the local user is updated about the impact that her choices have on the local computation. While any QoS-related performance issue is usually reported by the P2P application being used, WUW's feedback measures enable users to evaluate the overall "quality" of their neighbors as determined by user profiles and strategies and the average quality of the WUW service itself.
V. PRELIMINARY EXPERIMENTAL RESULTS Our WUW prototype is implemented in Java and requires JVM 1. 7 or higher. The source code is available under GPL license on Github  6. The current implementation features a P2P Handler module that is able to interact with BitTorrent MainLine 3. 1. 9 (in the following: BT). We provide an instrumentation class in MainLine that periodically collects the required information from the working memory of the BT process and sends it to WUW via a local socket. The Communication module hosts the NEWSCAST epidemic protocol  [21]  to maintain the overlay used to disseminate user profiles, intentions and content related information. The UI Handler module is currently a facility to handle the service configuration via XML files. In the following we present experimental results obtained by deploying our WUW prototype on the Grid5000 distributed platform  [22].
ACKNOWLEDGEMENTS This work was partially funded by the  Region Pays de la Loire. We thank our colleagues of the  P2PWeb  project for our useful discussions all along this project. We sincerely thanks  Philippe Lamarre  for his support and very interesting discussions at the beginning of this work. Experiments presented in this paper were carried out using the Grid'5000 experimental testbed, being developed under the  INRIA   ALADDIN development action  with support from  CNRS ,  RENATER  and several Universities as well as other funding bodies (see https://www. grid5000. fr).
Introduction Nowadays, one of the research lines that the multi-agent systems are following is directed toward ensuring that these systems become more open and dinamic. An open MAS  [BAJO, J. et al. 2009 ] should allow for the interaction between heterogeneous agents, which change over time, and architectures and even different languages. Because of their inherent changing nature, we cannot rely on agents' behaviour when it is necessary to establish controls on the basis of norms or social rules. For this reason, and because of the characteristics of open environments, new approaches are needed to support evolutive systems and to facilitate their growth and runtime updates. The dynamics of open environments is one of the reasons that have encouraged the use of Virtual Organizations of Agents (VOs).
This communication is easy to implement and enables agents deployed in different devices to cooperate. These agents can be developed both quickly and in any language using the tools provided by the platform. PANGEA also includes facilities for implementing VOs and suborganizations, following any topology and with the appropiate tools for managing the VO itself. It is important to highlight that PANGEA is not a framework or a simple tool; it is a complete platform for the execution and management of VOs. The remainder of the paper is structured as follows: the next section introduces some existing platforms. Section 3 presents an overview of the main characteristics of the platform and the communication protocol. Section 4 presents the case study and finally, the last section includes the conclusions.
et al. 1999]  and Jadex  [POKAHR, F. et al. 2005]. Jadex is a software framework and a extension of JADE for the creation of goal-oriented agents following the BDI model. One of the more recent platforms is JIAC  [HIRSCH, B. et al. 2009 ] [LUTZENBERGER, M. et al. 2009 ], a service-aware framework. JIAC V is a Java based agent framework with an emphasis on industrial requirements such as software standards, security, management, and scalability. It combines agent technology with a service oriented approach. Together with the framework, a new language called JADL++ was created; this platform stands out because of its service matching capabilities and an excellent usability. Until now, these platforms can create agents (some with different models), follow their life cycle and manage communication and services.
Once the client agent's request has been received, the provider agent extracts the required parameters and establishes contact. Once received, the results are sent to the client agent. Using Web Services also allows the platform to introduce the SOA architecture (Service-oriented Arquitecture) [JOSUTTIS,  N. et al. 2007 ] into MAS systems. SOA is an architectural style for building applications that use services available in a network such as the web. It promotes loose coupling between software components so that they can be reused. Applications in SOA are built based on services. A service is an implementation of a welldefined functionality, and such services can then be consumed by clients in different applications or processes. SOA allows for the reuse of existing services and a level of flexibility that was not possible before in the sense that: • Services are software components with well-defined interfaces that are implementation-independent.
• InterfaceAgent: allows the user to set up a personal profile for the first time, moreover, it stays aware of the configuration changes that can occur during the execution and store them for the next execution. The translation tool emerged as a result of the difficulty encountered by employers in communicating to their hearing impaired employees the actions that they have to do in their jobs. Given the ineffectiveness of avatar translators, the solution chosen was to study the main communication needs and provide some recorded videos with commands and explanations specifically related to the performance of a particular job. These videos are pre-recorded by a sign language interpreter and stored on a Web server where they can be accessed anytime through the request of an issuing agent. The issuing agents, deployed on both Smartphones (Android or iPhone) or computers, will be responsible for playing the video required at that moment.
This agent interprets the message by translating it into Morse code and then uses Bluetooth to send the message content to the the bracelet. The bracelet transmits vibrations to the disabled worker, who is the receiver of the message. Finally, for monitoring purposes all workers are represented by DisabledAgents and are adhered to the suborganization OfficeOrganization when the proximity detection tool detects them in a workplace. In summary, the suborganizations in were developed in this case study within the PANGEA platform. For simplicity, interactions The NormAgent makes it possible to modify the behavior of certain agents by prohibiting or allowing the consumption of certain services or cutting off communication with other agents. Moreover, the ServiceAgent agent is also essential in the development of this integrated system, since it records all the services offered by each agent and the address for the invocation of those services.